tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'develop' of github.com:lammps/lammps into comm-brick-direct

Browse Source
This commit is contained in:
Stan Moore
2024-08-30 09:01:52 -06:00
parent 43b3bf5bd5 05e836f50e
commit 7d5bddf95e
964 changed files with 135001 additions and 17435 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
.github/CODEOWNERS vendored
View File

@ -50,6 +50,7 @@ src/PTM/* @pmla
src/QMMM/* @akohlmey
src/REACTION/* @jrgissing
src/REAXFF/* @hasanmetin @stanmoore1
src/RHEO/* @jtclemm
src/SCAFACOS/* @rhalver
src/SNAP/* @athomps
src/SPIN/* @julient31
@ -65,6 +66,9 @@ src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/MANYBODY/pair_nb3b_screened.* @flodesani
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMMAND/geturl.* @akohlmey
src/EXTRA-COMMAND/group_ndx.* @akohlmey
src/EXTRA-COMMAND/ndx_group.* @akohlmey
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
@ -95,9 +99,10 @@ src/fix.* @sjplimp
src/force.* @sjplimp
src/group.* @sjplimp
src/improper.* @sjplimp
src/info.* @akohlmey
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/library.* @sjplimp
src/library.* @sjplimp @akohlmey
src/main.cpp @sjplimp
src/min_*.* @sjplimp
src/memory.* @sjplimp
@ -105,12 +110,12 @@ src/modify.* @sjplimp @stanmoore1
src/molecule.* @sjplimp
src/my_page.h @sjplimp
src/my_pool_chunk.h @sjplimp
src/npair*.* @sjplimp
src/ntopo*.* @sjplimp
src/nstencil*.* @sjplimp
src/neighbor.* @sjplimp
src/nbin*.* @sjplimp
src/neigh_*.* @sjplimp
src/npair*.* @sjplimp @jtclemm
src/ntopo*.* @sjplimp @jtclemm
src/nstencil*.* @sjplimp @jtclemm
src/neighbor.* @sjplimp @jtclemm
src/nbin*.* @sjplimp @jtclemm
src/neigh_*.* @sjplimp @jtclemm
src/output.* @sjplimp
src/pair.* @sjplimp
src/rcb.* @sjplimp

39
cmake/CMakeLists.txt
View File

@ -12,6 +12,11 @@ endif()
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about requiring execute permission for find_program
# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
@ -164,6 +169,22 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# warn about potentially problematic GCC compiler versions
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
"with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
endif()
endif()
if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
"with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
endif()
endif()
endif()
# export all symbols when building a .dll file on windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@ -198,7 +219,6 @@ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
option(BUILD_SHARED_LIBS "Build shared library" OFF)
option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
# Support using clang-tidy for C++ files with selected options
@ -306,6 +326,7 @@ set(STANDARD_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK
@ -410,6 +431,7 @@ pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
pkg_depends(MESONT MOLECULE)
pkg_depends(RHEO BPM)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -493,6 +515,14 @@ if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_T
endif()
endif()
find_package(CURL QUIET COMPONENTS HTTP HTTPS)
option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
if(WITH_CURL)
find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
target_link_libraries(lammps PRIVATE CURL::libcurl)
endif()
# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
set(JPEG_NAMES libjpeg libjpeg-62)
find_package(JPEG QUIET)
@ -550,7 +580,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -870,7 +900,7 @@ endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
find_package(ClangFormat 8.0)
find_package(ClangFormat 11.0)
if(ClangFormat_FOUND)
add_custom_target(format-src
@ -1047,9 +1077,6 @@ endif()
if(BUILD_TOOLS)
message(STATUS "<<< Building Tools >>>")
endif()
if(BUILD_LAMMPS_SHELL)
message(STATUS "<<< Building LAMMPS Shell >>>")
endif()
if(BUILD_LAMMPS_GUI)
message(STATUS "<<< Building LAMMPS GUI >>>")
if(LAMMPS_GUI_USE_PLUGIN)

3
cmake/Modules/FindClangFormat.cmake
View File

@ -1,5 +1,8 @@
# Find clang-format
find_program(ClangFormat_EXECUTABLE NAMES clang-format
clang-format-20.0
clang-format-19.0
clang-format-18.0
clang-format-17.0
clang-format-16.0
clang-format-15.0

8
cmake/Modules/LAMMPSUtils.cmake
View File

@ -32,7 +32,13 @@ function(check_omp_h_include)
set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
check_include_file_cxx(omp.h _have_omp_h)
# there are all kinds of problems with finding omp.h
# for Clang and derived compilers so we pretend it is there.
if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
set(_have_omp_h TRUE)
else()
check_include_file_cxx(omp.h _have_omp_h)
endif()
else()
set(_have_omp_h FALSE)
endif()

6
cmake/Modules/Packages/COLVARS.cmake
View File

@ -24,6 +24,12 @@ target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
target_link_libraries(lammps PRIVATE colvars)
if(BUILD_OMP)
# Enable OpenMP for Colvars as well
target_compile_options(colvars PRIVATE ${OpenMP_CXX_FLAGS})
target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
endif()
if(COLVARS_DEBUG)
# Need to export the define publicly to be valid in interface code
target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)

8
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,5 +1,11 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
# PACE library support for ML-PACE package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)

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

@ -1,5 +1,10 @@
# Plumed2 support for PLUMED package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
@ -81,6 +86,9 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
DEPENDS plumed_build
COMMENT "Copying Plumed files"
)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
endif()
else()
@ -155,6 +163,9 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
@ -169,7 +180,9 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
endif()
endif()
endif()
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

2
cmake/Modules/Packages/RHEO.cmake Normal file
View File

@ -0,0 +1,2 @@
find_package(GSL 2.6 REQUIRED)
target_link_libraries(lammps PRIVATE GSL::gsl)

31
cmake/Modules/Tools.cmake
View File

@ -37,37 +37,6 @@ if(BUILD_TOOLS)
add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
endif()
find_package(PkgConfig QUIET)
if(BUILD_LAMMPS_SHELL)
if(NOT PkgConfig_FOUND)
message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
endif()
find_package(PkgConfig REQUIRED)
pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
# include resource compiler to embed icons into the executable on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
enable_language(RC)
set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
endif()
add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
# workaround for broken readline pkg-config file on FreeBSD
if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
target_include_directories(lammps-shell PRIVATE /usr/local/include)
endif()
if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
endif()
install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
endif()
if(BUILD_LAMMPS_GUI)
get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)

BIN
cmake/packaging/LAMMPS_DMG_Background.xcf Normal file
View File

Binary file not shown.

5
cmake/packaging/build_linux_tgz.sh
View File

@ -2,9 +2,10 @@
APP_NAME=lammps-gui
DESTDIR=${PWD}/../LAMMPS_GUI
VERSION="$1"
echo "Delete old files, if they exist"
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64.tar.gz
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
@ -71,7 +72,7 @@ do \
done
pushd ..
tar -czvvf LAMMPS_GUI-Linux-amd64.tar.gz LAMMPS_GUI
tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
popd
echo "Cleanup dir"

9
cmake/packaging/build_macos_dmg.sh
View File

@ -1,9 +1,10 @@
#!/bin/bash
APP_NAME=lammps-gui
VERSION="$1"
echo "Delete old files, if they exist"
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch.dmg
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch*.dmg
echo "Create initial dmg file with macdeployqt"
macdeployqt lammps-gui.app -dmg
@ -96,12 +97,12 @@ sync
echo "Unmount modified disk image and convert to compressed read-only image"
hdiutil detach "${DEVICE}"
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch.dmg"
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg"
echo "Attach icon to .dmg file"
echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch.dmg
SetFile -a C LAMMPS_GUI-macOS-multiarch.dmg
Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
SetFile -a C LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
rm icon.rsrc
echo "Delete temporary disk images"

5
cmake/packaging/build_windows_cross_zip.sh
View File

@ -3,9 +3,10 @@
APP_NAME=lammps-gui
DESTDIR=${PWD}/LAMMPS_GUI
SYSROOT="$1"
VERSION="$2"
echo "Delete old files, if they exist"
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64*.zip
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
@ -60,5 +61,5 @@ cat > ${DESTDIR}/bin/qt.conf <<EOF
[Paths]
Plugins = ../qt5plugins
EOF
zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI
zip -9rvD LAMMPS-Win10-amd64-${VERSION}.zip LAMMPS_GUI

1
cmake/presets/all_off.cmake
View File

@ -82,6 +82,7 @@ set(ALL_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK

1
cmake/presets/all_on.cmake
View File

@ -84,6 +84,7 @@ set(ALL_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK

4
cmake/presets/clang.cmake
View File

@ -1,10 +1,10 @@
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
find_program(CLANG_FORTRAN NAMES flang-new flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
if (_tmp_fc STREQUAL "flang")
if ((_tmp_fc STREQUAL "flang") OR (_tmp_fc STREQUAL "flang-new"))
set(FC_STD_VERSION "-std=f2018")
set(BUILD_MPI OFF)
else()

18
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "27 June 2024" "2024-06-27"
.TH LAMMPS "1" "29 August 2024" "2024-08-29"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 27 June 2024
\- Molecular Dynamics Simulator. Version 29 August 2024
.SH SYNOPSIS
.B lmp
@ -226,6 +226,20 @@ arguments of the "dump" command. See the
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-r2info <restart file> <keyword> ...\fR or
\fB\-restart2info <restart file> <keyword> ...\fR
Write information about the <restart file> previously written by
.B LAMMPS
to the screen and immediately exit. Following <restart file>
argument, additional keywords for the
.B LAMMPS
"info" command may be added to increase the amount of information
written. By default "system" "group" "fix" "compute" are already
set. See the
.B LAMMPS
manual for details on the "info" command.
.TP
.TP
\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
Specify a file for
.B LAMMPS

458
doc/src/Bibliography.rst
View File

@ -1,6 +1,12 @@
Bibliography
************
**(Abascal1)**
Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
**(Abascal2)**
Abascal, J Chem Phys, 123, 234505 (2005)
**(Ackland)**
Ackland, Jones, Phys Rev B, 73, 054104 (2006).
@ -22,21 +28,24 @@ Bibliography
**(Agnolin and Roux 2007)**
Agnolin, I. & Roux, J-N. (2007). Internal states of model isotropic granular packings. I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
**(Ahrens-Iwers2022)**
Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).
**(Ahrens-Iwers)**
Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
**(Aktulga)**
Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).
**(Albe)**
J.\ Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
**(Albe)**
**(Albe1)**
K.\ Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
**(Allen)**
Allen and Germano, Mol Phys 104, 3225-3235 (2006).
**(Allen)**
Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
**(AllenTildesley)**
Allen and Tildesley, Computer Simulation of Liquids, Oxford University Press (1987)
@ -49,6 +58,9 @@ Bibliography
**(Anderson)**
Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006).
**(Appshaw)**
Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022).
**(Avendano)**
C.\ Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).
@ -58,7 +70,7 @@ Bibliography
**(Babadi)**
Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
**(Babadi)**
**(Babadi2)**
Babadi and Ejtehadi, EPL, 77 (2007) 23002.
**(Baczewski)**
@ -73,23 +85,23 @@ Bibliography
**(Ballenegger)**
Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009).
**(Banna)**
Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).
**(Barrat)**
Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).
**(Barrett)**
Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
**(Barros)**
Barros, Sinkovits, Luijten, J. Chem. Phys, 140, 064903 (2014)
**(Bartok)**
Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
**(Bartok2010)**
Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
**(Bartok_2010)**
AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010).
**(Bartok2013)**
Bartok, Kondor, Csanyi, Phys Rev B, 87, 184115 (2013).
**(Bartok_PhD)**
A Bartok-Partay, PhD Thesis, University of Cambridge, (2010).
@ -97,36 +109,51 @@ Bibliography
**(Baskes)**
Baskes, Phys Rev B, 46, 2727-2742 (1992).
**(Baskes2)**
Baskes, Phys Rev B, 75, 094113 (2007).
**(Beck)**
Beck, Molecular Physics, 14, 311 (1968).
**(Becton)**
Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019).
**(Behler and Parrinello 2007)**
Behler, J.; Parrinello, M. Phys. Rev. Lett. 2007, 98 (14), 146401.
**(Bennet)**
Bennet, J Comput Phys, 22, 245 (1976)
**(Berardi)**
Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
**(Berendsen)**
Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
**(Berendsen)**
Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).
**(Berendsen2)**
Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
**(Bessarab)**
Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015).
**(Beutler)**
Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994).
**(Bialke)**
J.\ Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
**(Bird)**
G.\ A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994).
**(Bitzek)**
Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006).
**(Bolintineanu1)**
Bolintineanu, Lechman, Plimpton, Grest, Phys Rev E, 86, 066703 (2012).
**(Bolintineanu2)**
Bolintineanu, Grest, Lechman, Pierce, Plimpton, Schunk, Comp Particle Mechanics, 1, 321-356 (2014).
**(Bomont)**
Bomont, Bretonnet, J. Chem. Phys. 124, 054504 (2006).
**(Bond)**
Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).
@ -134,7 +161,7 @@ Bibliography
Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
**(BoreschKarplus)**
Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
Boresch and Karplus, J Phys Chem A, 103, 103 (1999).
**(Botu1)**
V.\ Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
@ -169,8 +196,11 @@ Bibliography
**(Buck)**
Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006).
**(Bulacu)**
Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
**(Bussi)**
G.\ Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
**(Bussi1)**
Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
@ -178,20 +208,20 @@ Bibliography
**(Bussi2)**
Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
**(COMB)**
**(COMB_1)**
J.\ Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
**(COMB_2)**
T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
**(COMB3)**
T.\ Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013).
**(COMB_1)**
J.\ Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
**(Calhoun)**
A.\ Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).
**(Campana)**
C.\ Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
C.\ Campana and M. H. Muser, Phys. Rev. B [74], 075420 (2006).
**(Cao1)**
J.\ Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
@ -215,6 +245,9 @@ Bibliography
Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
**(Ceriotti)**
M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
**(Ceriotti1)**
Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, 1170-80 (2010)
**(Ceriotti2)**
@ -232,6 +265,18 @@ Bibliography
**(Clarke)**
Clarke and Smith, J Chem Phys, 84, 2290 (1986).
**(Clavier)**
G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
**(Clemmer)**
Clemmer and Robbins, Phys. Rev. Lett. (2022).
**(Clemmer1)**
Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).
**(Clemmer2)**
Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
**(Coleman)**
Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).
@ -244,8 +289,17 @@ Bibliography
**(Cornell)**
Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
**(Cundall, 1987)**
Cundall, P. A. Distinct Element Models of Rock and Soil
**(Curk1)**
T. Curk, J. Yuan, and E. Luijten, JCP 156 (2022).
**(Curk2)**
T. Curk and E. Luijten, PRL 126 (2021)
**(Cusentino)**
Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020)
**(Daivis and Todd)**
Daivis and Todd, J Chem Phys, 124, 194103 (2006).
@ -268,6 +322,15 @@ Bibliography
**(Daw2)**
M.\ S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).
**(de Buyl)**
de Buyl, Colberg and Hofling, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
**(Deissenbeck)**
Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
**(de Koning)**
de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
**(DeVane)**
Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
@ -277,12 +340,24 @@ Bibliography
**(Destree)**
M.\ Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, J Chem Phys, 112, 9632 (2000).
**(Dickel)**
Dickel, Francis, and Barrett, Computational Materials Science 171 (2020): 109157.
**(Dietz)**
Dietz and Hoy, J. Chem Phys, 156, 014103 (2022).
**(Dobson)**
Dobson, J Chem Phys, 141, 184103 (2014).
**(Drautz)**
Drautz, Phys Rev B, 99, 014104 (2019).
**(Duffy)**
D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, 016207-016218 (2007).
**(Dufils)**
Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019).
**(Dullweber)**
Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997).
@ -295,6 +370,9 @@ Bibliography
**(Dunweg)**
Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
**(EcheverriRestrepo)**
Echeverri Restrepo, Andric, Comput Mater Sci, 218, 111978 (2023).
**(EDIP)**
J F Justo et al, Phys Rev B 58, 2539 (1998).
@ -304,12 +382,21 @@ Bibliography
**(Elliott)**
Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
**(Ellis)**
Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021)
**(Emmrich)**
Emmrich, Weckner, Commun. Math. Sci., 5, 851-864 (2007),
**(Elstner)**
M.\ Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998).
**(Erdmann)**
U.\ Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, Eur. Phys. J. B 15, 105-113, 2000.
**(Eshelby)**
J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
**(Espanol and Revenga)**
Espanol, Revenga, Physical Review E, 67, 026705 (2003).
@ -328,9 +415,18 @@ Bibliography
**(Faken)**
Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
**(Falk)**
Falk and Langer PRE, 57, 7192 (1998).
**(Fath)**
Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
**(Feng1)**
Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C. 127(18), 8704-8713 (2023).
**(Feng2)**
Z. Feng, ..., and W. Ouyang, Langmuir 39(50), 18198-18207 (2023).
**(Fennell)**
C.\ J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006).
@ -367,18 +463,36 @@ Bibliography
**(Frenkel)**
Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
**(GLE4MD)**
`https://gle4md.org/ <https://gle4md.org/>`_
**(Fu)**
Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017).
**(Gao)**
Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
**(Gingrich)**
Gingrich, `MSc thesis` <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).
**(Gissinger2017)**
Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
**(Gissinger2020)**
Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
**(Gissinger)**
Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
Jacob R. Gissinger, Scott R. Zavada, Joseph G. Smith, Josh Kemppainen, Ivan Gallegos, Gregory M. Odegard, Emilie J. Siochi, and Kristopher E. Wise, Carbon, 202, 336-347 (2023).
**(Gissinger2024)**
J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
**(Gloor)**
Gloor, J Chem Phys, 123, 134703 (2005)
**(Glosli)**
Glosli, unpublished, 2005. Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference Series, 46, 254 (2006).
**(Goff)**
Goff, Zhang, Negre, Rohskopf, Niklasson, Journal of Chemical Theory and Computation 19, no. 13 (2023).
**(Goldman1)**
Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)
@ -412,6 +526,9 @@ Bibliography
**(Guo)**
Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
**(Gupta)**
Gupta ,Phys Rev. B, 23, 6265-6270 (1981).
**(Hardy)**
David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006).
@ -433,6 +550,9 @@ Bibliography
**(Henrich)**
O.\ Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
**(Herman)**
M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
**(Hess)**
Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
@ -454,24 +574,42 @@ Bibliography
**(Hoover)**
Hoover, Phys Rev A, 31, 1695 (1985).
**(Huang)**
Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013).
**(Huang2014)**
X. Huang, "Exploring critical-state behavior using DEM", Doctoral dissertation, Imperial College. (2014). https://doi.org/10.25560/25316
**(Hu)**
Hu, and Adams J. Comp. Physics, 213, 844-861 (2006).
**(Hu)**
Hu, J. Chem. Theory Comput. 10, 5254 (2014).
**(Hummer)**
Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)
**(Hunt)**
Hunt, Mol Simul, 42, 347 (2016).
**(Ikeshoji)**
Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
**(Ikeshoji2)**
Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
**(Ilie)**
Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
**(In 't Veld)**
In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
**(IPI)**
`https://ipi-code.org/ <https://ipi-code.org/>`
**(IPI-CPC)**
Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
**(Ikeshoji)**
Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
**(In 't Veld)**
In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
**(Isele-Holder)**
Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).
@ -490,6 +628,9 @@ Bibliography
**(Izvekov)**
Izvekov, Voth, J Chem Phys 123, 134105 (2005).
**(Jadhao)**
Jadhao, Solis, Olvera de la Cruz, J Chem Phys, 138, 054119 (2013)
**(Janssens)**
Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature Materials, 5, 124-127 (2006).
@ -502,6 +643,15 @@ Bibliography
**(Jiang)**
Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011).
**(Jiang1)**
Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011).
**(Jiang2)**
J.-W. Jiang, Nanotechnology 26, 315706 (2015).
**(Jiang3)**
J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).
**(Johnson et al, 1971)**
Johnson, K. L., Kendall, K., & Roberts, A. D. (1971). Surface energy and the contact of elastic solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
@ -571,21 +721,24 @@ Bibliography
**(Lamoureux)**
Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).
**(Larentzos)**
J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
**(Landsgesell)**
J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, Macromolecules 53, 3007-3020 (2020).
**(Larentzos1)**
J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using Shardlow-Like Splitting
J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, Comput. Phys. Commun., 185, 1987-1998 (2014).
**(Larentzos2)**
J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014).
**(Larsen)**
Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
**(Lebedeva et al.)**
**(Lebedeva1)**
I.\ V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
**(Lebedeva2)**
I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
**(Lechman)**
Lechman, et al, in preparation (2010).
@ -595,6 +748,9 @@ Bibliography
**(Lee2)**
Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001).
**(Lee2020)**
C.W. Lee, et al. (2020) Physical Review B, 102(2), 024107.
**(Lenart)**
Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007).
@ -619,8 +775,11 @@ Bibliography
**(Li2015_JCP)**
Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI:10.1063/1.4923254.
**(Liang)**
Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012)
**(Lisal)**
M.\ Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",
M.\ Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011).
**(Liu1)**
L.\ Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011).
@ -637,6 +796,15 @@ Bibliography
**(Luding, 2008)**
Luding, S. (2008). Cohesive, frictional powders: contact models for tension. Granular matter, 10(4), 235.
**(Lysogorskiy)**
Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
**(Lysogorskiy21)**
Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
**(Lysogorskiy23)**
Lysogorskiy, Bochkarev, Mrovec, Drautz, Phys Rev Mater, 7, 043801 (2023) / arXiv:2212.08716 (2022).
**(Maaravi)**
T.\ Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
@ -655,12 +823,18 @@ Bibliography
**(Maginn)**
Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007).
**(Mahoney)**
Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
**(Malolepsza)**
Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), 13379-13384 (2015).
**(Mandadapu)**
Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
**(Mandelli_1)**
D. Mandelli, W. Ouyang, M. Urbakh, and O. Hod, ACS Nano 13(7), 7603-7609 (2019).
**(Maras)**
Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016).
@ -676,6 +850,9 @@ Bibliography
**(Martyna1994)**
Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
**(Martyna2)**
G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
**(Mason)**
J.\ K. Mason, Acta Cryst A65, 259 (2009).
@ -715,6 +892,9 @@ Bibliography
**(Mie)**
G.\ Mie, Ann Phys, 316, 657 (1903).
**(Milano)**
G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).
**(Miller1)**
T.\ F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
@ -745,12 +925,18 @@ Bibliography
**(Mitchell2011a)**
Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011).
**(Miyazaki)**
Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).
**(Mniszewski)**
S.\ M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015).
**(Monaghan)**
Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983).
**(Monti)**
Monti, Clemmer, Srivastava, Silbert, Grest, and Lechman, Phys. Rev. E, (2022).
**(Moore)**
Moore, J Chem Phys, 144, 104501 (2016).
@ -770,7 +956,7 @@ Bibliography
Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
**(Moustafa)**
Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
**(Muller-Plathe1)**
Muller-Plathe, J Chem Phys, 106, 6082 (1997).
@ -790,9 +976,6 @@ Bibliography
**(Neelov)**
Neelov, Holm, J Chem Phys 132, 234103 (2010)
**(Negre2016)**
C.\ F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016).
**(Nelson)**
Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
@ -802,12 +985,24 @@ Bibliography
**(Neyts)**
E.\ C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013).
**(Nguyen2023)**
Nguyen, Physical Review B, 107(14), 144103, (2023).
**(Nguyen2024)**
Nguyen, Journal of Computational Physics, 113102, (2024).
**(Nguyen and Rohskopf)**
Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
**(Nguyen and Sema)**
Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
**(NguyenTD)**
Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Comput Phys Commun 241, 80-19 (2019)
**(Nicholson and Rutledge)**
Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016).
**(Nicklas)**
The spline-based MEAM+SW format was first devised and used to develop potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
**(Niklasson2002)**
A.\ M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
@ -820,6 +1015,9 @@ Bibliography
**(Niklasson2017)**
A.\ M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
**(Nitol)**
Nitol, Dickel, and Barrett, Computational Materials Science 188 (2021): 110207.
**(Noid)**
Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008).
@ -841,6 +1039,9 @@ Bibliography
**(O'Connor)**
O'Connor et al., J. Chem. Phys. 142, 024903 (2015).
**(O'Hearn)**
O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020).
**(Okabe)**
T.\ Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).
@ -850,6 +1051,8 @@ Bibliography
**(Omelyan)**
Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001).
**(OPLS-AA96)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).
**(Oppelstrup)**
Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published.
@ -871,14 +1074,17 @@ Bibliography
**(Ouyang2)**
W.\ Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
**(PASS)**
PASS webpage: https://www.sdu.dk/en/DPASS
**(Ouyang_1)**
W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
**(PLUMED)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Ouyang6)**
W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).
**(Pavlov)**
D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
**(Ouyang7)**
W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
**(Palkar)**
Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022
**(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
@ -889,21 +1095,33 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Parks)**
Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
**(Parrinello1981)**
**(Parrinello)**
Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
**(PASS)**
PASS webpage: https://www.sdu.dk/en/DPASS
**(Paula Leite2016)**
Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016).
**(Paula Leite2017)**
Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96, 32115 (2017).
**(Pavlov1)**
D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
**(Pavlov2)**
Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)
**(Pearlman)**
Pearlman, J Chem Phys, 98, 1487 (1994)
**(Pedersen)**
Pedersen, J. Chem. Phys., 139, 104102 (2013).
**(Pedone)**
A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006)
**(Peng)**
Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 (1996).
@ -925,6 +1143,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Pettifor_3)**
D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002).
**(PFC)**
PFC Particle Flow Code 6.0 Documentation. Itasca Consulting Group.
**(Phillips)**
C.\ L. Phillips, J. A. Anderson, S. C. Glotzer, Comput Phys Comm, 230, 7191-7201 (2011).
@ -934,9 +1155,21 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Pisarev)**
V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014).
**(Plimpton)**
Plimpton and Knight, JPDC, 147, 184-195 (2021).
**(PLUMED)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Pollock)**
Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
**(Ponder)**
Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
**(Popov1)**
A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
**(Price1)**
Price and Brooks, J Chem Phys, 121, 10096 (2004).
@ -976,6 +1209,12 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Rick)**
S.\ W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141 (1994).
**(Rick2)**
S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
**(Roberts)**
R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning. `<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
**(Rohart)**
Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).
@ -1012,9 +1251,18 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Sadigh)**
B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
**(Sadigh1)**
B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012)
**(Sadigh2)**
B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012)
**(Safran)**
Safran, Statistical Thermodynamics of Surfaces, Interfaces, And Membranes, Westview Press, ISBN: 978-0813340791 (2003).
**(Salanne)**
Salanne, Rotenberg, Jahn, Vuilleumier, Simon, Christian and Madden, Theor Chem Acc, 131, 1143 (2012).
**(Salerno)**
Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).
@ -1024,9 +1272,18 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Sanyal2)**
Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
**(Scalfi)**
Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
**(Schelling)**
Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
**(Scherer1)**
C. Scherer and D. Andrienko, Phys. Chem. Chem. Phys. 20, 22387-22394 (2018).
**(Scherer2)**
C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020).
**(Schlitter1)**
Schlitter, Swegat, Mulders, "Distance-type reaction coordinates for modelling activated processes", J Molecular Modeling, 7, 171-177 (2001).
@ -1045,21 +1302,36 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Schroeder)**
Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010).
**(Seleson 2010)**
Seleson, Parks, Int J Mult Comp Eng 9(6), pp. 689-706, 2011.
**(Semaev)**
Semaev, Cryptography and Lattices, 181 (2001).
**(Seo)**
Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
**(Sheppard)**
Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008). See ref 1 in this paper for original reference to Qmin in Jonsson, Mills, Jacobsen.
**(Shi)**
Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
**(Shinoda)**
Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
**(Shinoda)**
Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
**(Shire)**
Shire, Hanley and Stratford, Comp. Part. Mech., (2020).
**(Sides)**
Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, 199-208 (2004).
**(Siepmann)**
Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
**(Silbert)**
Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001).
@ -1069,12 +1341,21 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Silling 2000)**
Silling, J Mech Phys Solids, 48, 175-209 (2000).
**(Silling 2005)**
Silling Askari, Computer and Structures, 83, 1526-1535 (2005).
**(Silling 2007)**
Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
**(Singh)**
Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
**(Singraber, Behler and Dellago 2019)**
Singraber, A.; Behler, J.; Dellago, C. J., Chem. Theory Comput. 2019, 15 (3), 1827-1840
**(Singraber et al 2019)**
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C., J. Chem. Theory Comput. 2019, 15 (5), 3075-3092.
**(Sirk1)**
Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012.
@ -1087,6 +1368,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Snodin)**
B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
**(Son)**
Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).
**(Srivastava)**
Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).
@ -1096,6 +1380,12 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Steinhardt)**
P.\ Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
**(Steward)**
Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013).
**(Stewart2018)**
J.A. Stewart, et al. (2018) Journal of Applied Physics, 123(16), 165902.
**(Stiles)**
Stiles , Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982).
@ -1153,12 +1443,21 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Tainter 2015)**
Tainter, Shi, and Skinner, 11, 2268 (2015)
**(Tang and Toennies)**
J Chem Phys, 80, 3726 (1984).
**(Tee)**
Tee and Searles, J. Chem. Phys. 156, 184101 (2022).
**(Templeton2010)**
Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
**(Templeton2011)**
Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
**(tenWolde)**
P.\ R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
**(Tersoff_1)**
J.\ Tersoff, Phys Rev B, 37, 6991 (1988).
@ -1201,6 +1500,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Tranchida)**
Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018).
**(Tribello)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Tsuji et al, 1992)**
Tsuji, Y., Tanaka, T., & Ishida, T. (1992). Lagrangian numerical simulation of plug flow of cohesionless particles in a horizontal pipe. Powder technology, 71(3),
@ -1219,6 +1521,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Tuckerman4)**
Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997).
**(Tyagi)**
Tyagi, Suzen, Sega, Barbosa, Kantorovich, Holm, J Chem Phys, 132, 154112 (2010)
**(Ulomek)**
Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007
@ -1228,6 +1533,15 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Valone)**
Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
**(vanWijk)**
M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)
**(Van Workum)**
K. Van Workum et al., J. Chem. Phys. 125 144506 (2006)
**(Vargas and McCarthy 2001)**
Vargas, W.L. and McCarthy, J.J. (2001).
**(Varshalovich)**
Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987).
@ -1240,6 +1554,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Veld)**
In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
**(Verstraelen)**
Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013).
**(Volkov1)**
Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
@ -1264,6 +1581,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Wang et al, 2015)**
Wang, Y., Alonso-Marroquin, F., & Guo, W. W. (2015). Rolling and sliding in 3-D discrete element models. Particuology, 23, 49-55.
**(Wang2020)**
X. Wang, S. Ramirez-Hinestrosa, J. Dobnikar, and D. Frenkel, Phys. Chem. Chem. Phys. 22, 10624 (2020).
**(Wang1)**
J.\ Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011).
@ -1303,6 +1623,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Wicaksono2)**
Wicaksono, figshare, https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).
**(Winkler)**
Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).
**(Wirnsberger)**
Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015).
@ -1315,9 +1638,27 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Wood)**
Wood and Thompson, J Chem Phys, 148, 241721, (2018)
**(Xie23)**
Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7
**(Yade-DEM)**
V. Smilauer et al. (2021), Yade Documentation 3rd ed.
**(Yanxon2020)**
Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020).
**(Yeh)**
Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
**(Yuan2010a)**
Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010).
**(Yuan2010b)**
Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010).
**(Zagaceta2020)**
Zagaceta, Yanxon, Zhu, J Appl Phys, 128, 045113 (2020).
**(ZBL)**
J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press.
@ -1387,17 +1728,6 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Zimmerman2010)**
Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
**(de Buyl)**
de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
**(de Koning)**
de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
**(electronic stopping)**
Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29
**(tenWolde)**
P.\ R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
**(vanWijk)**
M.\ M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)

94
doc/src/Build_basics.rst
View File

@ -37,8 +37,9 @@ standard. A more detailed discussion of that is below.
.. code-block:: bash
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no
-D BUILD_OMP=value # yes or no, default is yes if a compatible compiler is detected
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI
-D BUILD_OMP=value # yes or no, default is yes if a compatible
# compiler is detected
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
@ -54,9 +55,9 @@ standard. A more detailed discussion of that is below.
.. code-block:: bash
make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
Any ``make machine`` command will look up the make settings from a
file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
@ -74,15 +75,15 @@ standard. A more detailed discussion of that is below.
this is ``-fopenmp``\ , which can be added to the ``CC`` and
``LINK`` makefile variables.
For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
For the serial build the following make variables are set (see ``src/MAKE/Makefile.serial``):
.. code-block:: make
CC = g++
LINK = g++
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs
CC = g++
LINK = g++
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs
You also need to build the STUBS library for your platform before
making LAMMPS itself. A ``make serial`` build does this for you
@ -231,24 +232,32 @@ LAMMPS.
.. code-block:: bash
# Building with GNU Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
# Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ \
-DCMAKE_Fortran_COMPILER=gfortran ../cmake
# Building with Intel Classic Compilers:
cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc \
-DCMAKE_Fortran_COMPILER=ifort ../cmake
# Building with Intel oneAPI Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx \
-DCMAKE_Fortran_COMPILER=ifx ../cmake
# Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
-DCMAKE_Fortran_COMPILER=flang ../cmake
# Building with PGI/Nvidia Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran
cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ \
-DCMAKE_Fortran_COMPILER=pgfortran ../cmake
# Building with the NVHPC Compilers:
cmake -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ \
-DCMAKE_Fortran_COMPILER=nvfortran ../cmake
For compiling with the Clang/LLVM compilers a CMake preset is
provided that can be loaded with
`-C ../cmake/presets/clang.cmake`. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the compiler
toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
``-C ../cmake/presets/clang.cmake``. Similarly,
``-C ../cmake/presets/intel.cmake`` should switch the compiler
toolchain to the legacy Intel compilers, ``-C ../cmake/presets/oneapi.cmake``
will switch to the LLVM based oneAPI Intel compilers,
and `-C ../cmake/presets/pgi.cmake`
will switch the compiler to the PGI compilers.
``-C ../cmake/presets/pgi.cmake`` will switch the compiler to the PGI compilers,
and ``-C ../cmake/presets/nvhpc.cmake`` will switch to the NVHPC compilers.
Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts.
@ -259,7 +268,7 @@ LAMMPS.
When the cmake command completes, it prints a summary to the
screen which compilers it is using and what flags and settings
will be used for the compilation. Note that if the top-level
compiler is mpicxx, it is simply a wrapper on a real compiler.
compiler is ``mpicxx``, it is simply a wrapper on a real compiler.
The underlying compiler info is what CMake will try to
determine and report. You should check to confirm you are
using the compiler and optimization flags you want.
@ -278,19 +287,19 @@ LAMMPS.
.. code-block:: make
CC = mpicxx
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O
CC = mpicxx
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O
Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
.. code-block:: make
CC = g++
CCFLAGS = -g -O3
LINK = g++
LINKFLAGS = -g -O
CC = g++
CCFLAGS = -g -O3
LINK = g++
LINKFLAGS = -g -O
.. note::
@ -316,10 +325,10 @@ LAMMPS.
there may be specific compiler or linker flags that are either
required or recommended to enable required features and to
achieve optimal performance. You need to include these in the
CCFLAGS and LINKFLAGS settings above. For details, see the
``CCFLAGS`` and ``LINKFLAGS`` settings above. For details, see the
documentation for the individual packages listed on the
:doc:`Speed_packages` page. Or examine these files in the
src/MAKE/OPTIONS directory. They correspond to each of the 5
``src/MAKE/OPTIONS`` directory. They correspond to each of the 5
accelerator packages and their hardware variants:
.. code-block:: bash
@ -388,7 +397,8 @@ running LAMMPS from Python via its library interface.
make machine # build LAMMPS executable lmp_machine
make mode=static machine # same as "make machine"
make mode=shared machine # build LAMMPS shared lib liblammps_machine.so instead
make mode=shared machine # build LAMMPS shared lib liblammps_machine.so
# instead
The "static" build will generate a static library called
``liblammps_machine.a`` and an executable named ``lmp_machine``\ ,
@ -450,7 +460,7 @@ installation.
Including or removing debug support
-----------------------------------
By default the compilation settings will include the *-g* flag which
By default the compilation settings will include the ``-g`` flag which
instructs the compiler to include debug information (e.g. which line of
source code a particular instruction correspond to). This can be
extremely useful in case LAMMPS crashes and can help to provide crucial
@ -463,7 +473,7 @@ If this is a concern, you can change the compilation settings or remove
the debug information from the LAMMPS executable:
- **Traditional make**: edit your ``Makefile.<machine>`` to remove the
*-g* flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
``-g`` flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
- **CMake**: use ``-D CMAKE_BUILD_TYPE=Release`` or explicitly reset
the applicable compiler flags (best done using the text mode or
graphical user interface).
@ -488,9 +498,10 @@ using CMake or Make.
.. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
-D BUILD_LAMMPS_SHELL=value # yes or no (default). Build lammps-shell
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build lammps-gui
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt,
# chain.x, micelle2d.x, msi2lmp, phana,
# stl_bin2txt
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build LAMMPS-GUI
The generated binaries will also become part of the LAMMPS installation
(see below).
@ -505,8 +516,9 @@ using CMake or Make.
make chain # build only chain tool
make micelle2d # build only micelle2d tool
cd lammps/tools/lammps-shell
make # build LAMMPS shell
.. note::
Building the LAMMPS-GUI *requires* building LAMMPS with CMake.
----------

12
doc/src/Build_cmake.rst
View File

@ -131,20 +131,20 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
configuration step. The cache file contains all current CMake settings.
To modify settings, enable or disable features, you need to set
*variables* with either the *-D* command line flag (``-D
*variables* with either the ``-D`` command line flag (``-D
VARIABLE1_NAME=value``) or change them in the text mode of the graphical
user interface. The *-D* flag can be used several times in one command.
user interface. The ``-D`` flag can be used several times in one command.
For your convenience, we provide :ref:`CMake presets <cmake_presets>`
that combine multiple settings to enable optional LAMMPS packages or use
a different compiler tool chain. Those are loaded with the *-C* flag
a different compiler tool chain. Those are loaded with the ``-C`` flag
(``-C ../cmake/presets/basic.cmake``). This step would only be needed
once, as the settings from the preset files are stored in the
``CMakeCache.txt`` file. It is also possible to customize the build
by adding one or more *-D* flags to the CMake command line.
by adding one or more ``-D`` flags to the CMake command line.
Generating files for alternate build tools (e.g. Ninja) and project files
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
command line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``.
@ -171,7 +171,7 @@ files. E.g. with:
In that case the resulting binaries are not in the build folder directly
but in subdirectories corresponding to the build type (i.e. Release in
the example from above). Similarly, for running unit tests the
configuration is selected with the *-C* flag:
configuration is selected with the ``-C`` flag:
.. code-block:: bash

107
doc/src/Build_development.rst
View File

@ -153,7 +153,12 @@ development headers to compile (if those are not found locally a recent
version of that library will be downloaded and compiled along with
LAMMPS and the test programs) and will download and compile a specific
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
test framework that is used to implement the tests.
test framework that is used to implement the tests. Those unit tests
may be combined with memory access and leak checking with valgrind
(see below for how to enable it). In that case, running so-called
death tests will create a lot of false positives and thus they can be
disabled by configuring compilation with the additional setting
``-D SKIP_DEATH_TESTS=on``.
.. admonition:: Software version and LAMMPS configuration requirements
:class: note
@ -176,24 +181,24 @@ The output of this command will be looking something like this:
$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: RunLammps
1/563 Test #1: RunLammps .......................................... Passed 0.28 sec
1/563 Test #1: RunLammps .................................. Passed 0.28 sec
Start 2: HelpMessage
2/563 Test #2: HelpMessage ........................................ Passed 0.06 sec
2/563 Test #2: HelpMessage ................................ Passed 0.06 sec
Start 3: InvalidFlag
3/563 Test #3: InvalidFlag ........................................ Passed 0.06 sec
3/563 Test #3: InvalidFlag ................................ Passed 0.06 sec
Start 4: Tokenizer
4/563 Test #4: Tokenizer .......................................... Passed 0.05 sec
4/563 Test #4: Tokenizer .................................. Passed 0.05 sec
Start 5: MemPool
5/563 Test #5: MemPool ............................................ Passed 0.05 sec
5/563 Test #5: MemPool .................................... Passed 0.05 sec
Start 6: ArgUtils
6/563 Test #6: ArgUtils ........................................... Passed 0.05 sec
6/563 Test #6: ArgUtils ................................... Passed 0.05 sec
[...]
Start 561: ImproperStyle:zero
561/563 Test #561: ImproperStyle:zero ................................. Passed 0.07 sec
561/563 Test #561: ImproperStyle:zero ......................... Passed 0.07 sec
Start 562: TestMliapPyUnified
562/563 Test #562: TestMliapPyUnified ................................. Passed 0.16 sec
562/563 Test #562: TestMliapPyUnified ......................... Passed 0.16 sec
Start 563: TestPairList
563/563 Test #563: TestPairList ....................................... Passed 0.06 sec
563/563 Test #563: TestPairList ............................... Passed 0.06 sec
100% tests passed, 0 tests failed out of 563
@ -208,24 +213,25 @@ The output of this command will be looking something like this:
The ``ctest`` command has many options, the most important ones are:
.. list-table::
:widths: 20 80
* - Option
- Function
* - -V
* - ``-V``
- verbose output: display output of individual test runs
* - -j <num>
* - ``-j <num>``
- parallel run: run <num> tests in parallel
* - -R <regex>
* - ``-R <regex>``
- run subset of tests matching the regular expression <regex>
* - -E <regex>
* - ``-E <regex>``
- exclude subset of tests matching the regular expression <regex>
* - -L <regex>
* - ``-L <regex>``
- run subset of tests with a label matching the regular expression <regex>
* - -LE <regex>
* - ``-LE <regex>``
- exclude subset of tests with a label matching the regular expression <regex>
* - -N
* - ``-N``
- dry-run: display list of tests without running them
* - -T memcheck
* - ``-T memcheck``
- run tests with valgrind memory checker (if available)
In its full implementation, the unit test framework will consist of multiple
@ -331,16 +337,17 @@ paths in the individual source files.
The force style test programs have a common set of options:
.. list-table::
:widths: 25 75
* - Option
- Function
* - -g <newfile>
* - ``-g <newfile>``
- regenerate reference data in new YAML file
* - -u
* - ``-u``
- update reference data in the original YAML file
* - -s
* - ``-s``
- print error statistics for each group of comparisons
* - -v
* - ``-v``
- verbose output: also print the executed LAMMPS commands
The ``ctest`` tool has no mechanism to directly pass flags to the individual
@ -354,10 +361,10 @@ set in an environment variable ``TEST_ARGS``. Example:
To add a test for a style that is not yet covered, it is usually best
to copy a YAML file for a similar style to a new file, edit the details
of the style (how to call it, how to set its coefficients) and then
run test command with either the *-g* and the replace the initial
test file with the regenerated one or the *-u* option. The *-u* option
run test command with either the ``-g`` and the replace the initial
test file with the regenerated one or the ``-u`` option. The ``-u`` option
will destroy the original file, if the generation run does not complete,
so using *-g* is recommended unless the YAML file is fully tested
so using ``-g`` is recommended unless the YAML file is fully tested
and working.
Some of the force style tests are rather slow to run and some are very
@ -507,27 +514,51 @@ After post-processing with ``gen_coverage_html`` the results are in
a folder ``coverage_html`` and can be viewed with a web browser.
The images below illustrate how the data is presented.
.. list-table::
.. only:: not latex
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
.. list-table::
Top of the overview page
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
- .. figure:: JPG/coverage-overview-manybody.png
:scale: 25%
Top of the overview page
Styles with good coverage
- .. figure:: JPG/coverage-overview-manybody.png
:scale: 25%
- .. figure:: JPG/coverage-file-top.png
:scale: 25%
Styles with good coverage
Top of individual source page
- .. figure:: JPG/coverage-file-top.png
:scale: 25%
- .. figure:: JPG/coverage-file-branches.png
:scale: 25%
Top of individual source page
Source page with branches
- .. figure:: JPG/coverage-file-branches.png
:scale: 25%
Source page with branches
.. only:: latex
.. figure:: JPG/coverage-overview-top.png
:width: 60%
Top of the overview page
.. figure:: JPG/coverage-overview-manybody.png
:width: 60%
Styles with good coverage
.. figure:: JPG/coverage-file-top.png
:width: 60%
Top of individual source page
.. figure:: JPG/coverage-file-branches.png
:width: 60%
Source page with branches
Coding style utilities
----------------------

562
doc/src/Build_extras.rst
View File

@ -14,7 +14,7 @@ in addition to
cmake -D PKG_NAME=yes
- .. code-block:: console
- .. code-block:: bash
make yes-name
@ -59,6 +59,7 @@ This is the list of packages that may require additional steps.
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`RHEO <rheo>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`VORONOI <voronoi>`
* :ref:`VTK <vtk>`
@ -72,7 +73,7 @@ COMPRESS package
To build with this package you must have the `zlib compression library
<https://zlib.net>`_ available on your system to build dump styles with
a '/gz' suffix. There are also styles using the
a ``/gz`` suffix. There are also styles using the
`Zstandard <https://facebook.github.io/zstd/>`_ library which have a
'/zstd' suffix. The zstd library version must be at least 1.4. Older
versions use an incompatible API and thus LAMMPS will fail to compile.
@ -94,7 +95,7 @@ versions use an incompatible API and thus LAMMPS will fail to compile.
<https://www.freedesktop.org/wiki/Software/pkg-config/>`_ tool to
identify the necessary flags to compile with this library, so the
corresponding ``libzstandard.pc`` file must be in a folder where
pkg-config can find it, which may require adding it to the
``pkg-config`` can find it, which may require adding it to the
``PKG_CONFIG_PATH`` environment variable.
.. tab:: Traditional make
@ -126,46 +127,53 @@ CMake build
# value = double or mixed (default) or single
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX (see below, default is sm_50)
-D GPU_DEBUG=value # enable debug code in the GPU package library, mostly useful for developers
-D GPU_DEBUG=value # enable debug code in the GPU package library,
# mostly useful for developers
# value = yes or no (default)
-D HIP_PATH=value # value = path to HIP installation. Must be set if GPU_API=HIP
-D HIP_PATH=value # value = path to HIP installation. Must be set if
# GPU_API=HIP
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
# default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for
# HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no
-D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs)
# enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
-D CUDPP_OPT=value # use GPU binning with CUDA (should be off for modern GPUs)
# enables CUDA Performance Primitives, must be "no" for
# CUDA_MPS_SUPPORT=yes
# value = yes or no (default)
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active
# nvidia-cuda-mps daemon
# value = yes or no (default)
-D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU architectures
-D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU
# architectures
# value = yes (default) or no
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library,
# no local OpenCL headers/libs needed
# value = yes (default) or no
:code:`GPU_ARCH` settings for different GPU hardware is as follows:
``GPU_ARCH`` settings for different GPU hardware is as follows:
* sm_30 for Kepler (supported since CUDA 5 and until CUDA 10.x)
* sm_35 or sm_37 for Kepler (supported since CUDA 5 and until CUDA 11.x)
* sm_50 or sm_52 for Maxwell (supported since CUDA 6)
* sm_60 or sm_61 for Pascal (supported since CUDA 8)
* sm_70 for Volta (supported since CUDA 9)
* sm_75 for Turing (supported since CUDA 10)
* sm_80 or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
* sm_89 for Lovelace (supported since CUDA 11.8)
* sm_90 for Hopper (supported since CUDA 12.0)
* ``sm_30`` for Kepler (supported since CUDA 5 and until CUDA 10.x)
* ``sm_35`` or ``sm_37`` for Kepler (supported since CUDA 5 and until CUDA 11.x)
* ``sm_50`` or ``sm_52`` for Maxwell (supported since CUDA 6)
* ``sm_60`` or ``sm_61`` for Pascal (supported since CUDA 8)
* ``sm_70`` for Volta (supported since CUDA 9)
* ``sm_75`` for Turing (supported since CUDA 10)
* ``sm_80`` or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
* ``sm_89`` for Lovelace (supported since CUDA 11.8)
* ``sm_90`` for Hopper (supported since CUDA 12.0)
A more detailed list can be found, for example,
at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
CMake can detect which version of the CUDA toolkit is used and thus will
try to include support for **all** major GPU architectures supported by
this toolkit. Thus the GPU_ARCH setting is merely an optimization, to
this toolkit. Thus the ``GPU_ARCH`` setting is merely an optimization, to
have code for the preferred GPU architecture directly included rather
than having to wait for the JIT compiler of the CUDA driver to translate
it. This behavior can be turned off (e.g. to speed up compilation) by
setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
setting ``CUDA_ENABLE_MULTIARCH`` to ``no``.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
CUDA toolkit is required and a GPU architecture of Kepler or later,
@ -184,21 +192,21 @@ build, and link with a static OpenCL ICD loader library and standard
OpenCL headers. This way no local OpenCL development headers or library
needs to be present and only OpenCL compatible drivers need to be
installed to use OpenCL. If this is not desired, you can set
:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
``USE_STATIC_OPENCL_LOADER`` to ``no``.
The GPU library has some multi-thread support using OpenMP. If LAMMPS
is built with ``-D BUILD_OMP=on`` this will also be enabled.
If you are compiling with HIP, note that before running CMake you will
have to set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are
necessary for :code:`hipcc` and the linker to work correctly.
``HCC_AMDGPU_TARGET`` (for ROCm <= 4.0) or ``CUDA_PATH`` are
necessary for ``hipcc`` and the linker to work correctly.
.. versionadded:: 3Aug2022
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this
option in preparations to run on Aurora system at Argonne.
@ -256,28 +264,35 @@ script with the specified args:
.. code-block:: bash
make lib-gpu # print help message
make lib-gpu args="-b" # build GPU library with default Makefile.linux
make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
# print help message
make lib-gpu
# build GPU library with default Makefile.linux
make lib-gpu args="-b"
# create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-m xk7 -p single -o xk7.single"
# build GPU library with mixed precision and P100 using other settings in Makefile.mpi
make lib-gpu args="-m mpi -a sm_60 -p mixed -b"
Note that this procedure starts with a Makefile.machine in lib/gpu, as
specified by the "-m" switch. For your convenience, machine makefiles
specified by the ``-m`` switch. For your convenience, machine makefiles
for "mpi" and "serial" are provided, which have the same settings as
the corresponding machine makefiles in the main LAMMPS source
folder. In addition you can alter 4 important settings in the
Makefile.machine you start from via the corresponding -c, -a, -p, -e
Makefile.machine you start from via the corresponding ``-c``, ``-a``, ``-p``, ``-e``
switches (as in the examples above), and also save a copy of the new
Makefile if desired:
* ``CUDA_HOME`` = where NVIDIA CUDA software is installed on your system
* ``CUDA_ARCH`` = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
* ``CUDA_ARCH`` = ``sm_XX``, what GPU hardware you have, same as CMake ``GPU_ARCH`` above
* ``CUDA_PRECISION`` = precision (double, mixed, single)
* ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps
* ``EXTRAMAKE`` = which ``Makefile.lammps.*`` file to copy to Makefile.lammps
The file Makefile.cuda is set up to include support for multiple
The file ``Makefile.cuda`` is set up to include support for multiple
GPU architectures as supported by the CUDA toolkit in use. This is done
through using the "--gencode " flag, which can be used multiple times and
through using the ``--gencode`` flag, which can be used multiple times and
thus support all GPU architectures supported by your CUDA compiler.
To enable GPU binning via CUDA performance primitives set the Makefile variable
@ -348,12 +363,16 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes
-D KIM_EXTRA_UNITTESTS=value # enables extra unit tests, value = no (default) or yes
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build
# value = no (default) or yes
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off
# value = off (default) or on
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer
# value = no (default) or yes
-D KIM_EXTRA_UNITTESTS=value # enables extra unit tests
# value = no (default) or yes
If ``DOWNLOAD_KIM`` is set to *yes* (or *on*), the KIM API library
If ``DOWNLOAD_KIM`` is set to ``yes`` (or ``on``), the KIM API library
will be downloaded and built inside the CMake build directory. If
the KIM library is already installed on your system (in a location
where CMake cannot find it), you may need to set the
@ -361,7 +380,7 @@ minutes to hours) to build. Of course you only need to do that once.)
found, or run the command ``source kim-api-activate``.
Extra unit tests can only be available if they are explicitly requested
(``KIM_EXTRA_UNITTESTS`` is set to *yes* (or *on*)) and the prerequisites
(``KIM_EXTRA_UNITTESTS`` is set to ``yes`` (or ``on``)) and the prerequisites
are met. See :ref:`KIM Extra unit tests <kim_extra_unittests>` for
more details on this.
@ -375,15 +394,28 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash
make lib-kim # print help message
make lib-kim args="-b " # (re-)install KIM API lib with only example models
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
# print help message
make lib-kim
When using the "-b " option, the KIM library is built using its native
# (re-)install KIM API lib with only example models
make lib-kim args="-b"
# ditto plus one model
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"
# install KIM API lib with all models
make lib-kim args="-b -a everything"
# add one model or model driver
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"
# use an existing KIM API installation at the provided location
make lib-kim args="-p <prefix>"
# ditto but add one model or driver
make lib-kim args="-p <prefix> -a EAM_Dynamo_Ackland_W__MO_141627196590_002"
When using the ``-b`` option, the KIM library is built using its native
cmake build system. The ``lib/kim/Install.py`` script supports a
``CMAKE`` environment variable if the cmake executable is named other
than ``cmake`` on your system. Additional environment variables may be
@ -393,7 +425,9 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash
CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b " # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
# (re-)install KIM API lib using cmake3 and gnu v11 compilers
# with only example models
CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b"
Settings for debugging OpenKIM web queries discussed below need to
be applied by adding them to the ``LMP_INC`` variable through
@ -433,7 +467,7 @@ KIM Extra unit tests (CMake only)
During development, testing, or debugging, if
:doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also
enable extra tests on :doc:`KIM commands <kim_commands>` by setting the
``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*).
``KIM_EXTRA_UNITTESTS`` to ``yes`` (or ``on``).
Enabling the extra unit tests have some requirements,
@ -448,10 +482,12 @@ Enabling the extra unit tests have some requirements,
*conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in
Conda. More detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
* It is also necessary to install
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
* It is also necessary to install the following KIM models:
* ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``
* ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``
* ``LennardJones612_UniversalShifted__MO_959249795837_003``
See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see
@ -638,6 +674,9 @@ They must be specified in uppercase.
* - AMD_GFX1100
- GPU
- AMD GPU RX7900XTX
* - AMD_GFX1103
- GPU
- AMD Phoenix APU with Radeon 740M/760M/780M/880M/890M
* - INTEL_GEN
- GPU
- SPIR64-based devices, e.g. Intel GPUs, using JIT
@ -725,7 +764,8 @@ This list was last updated for version 4.3.0 of the Kokkos library.
mkdir build-kokkos-cuda
cd build-kokkos-cuda
cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake -C ../cmake/presets/basic.cmake \
-C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake --build .
.. tab:: Basic traditional make settings:
@ -753,9 +793,10 @@ This list was last updated for version 4.3.0 of the Kokkos library.
.. code-block:: make
KOKKOS_DEVICES = Cuda
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is hosting the GPU
KOKKOS_CUDA_OPTIONS = "enable_lambda"
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is
# hosting the GPU
# GPUARCH = GPU from list above
KOKKOS_CUDA_OPTIONS = "enable_lambda"
FFT_INC = -DFFT_CUFFT # enable use of cuFFT (optional)
FFT_LIB = -lcufft # link to cuFFT library
@ -783,10 +824,11 @@ This list was last updated for version 4.3.0 of the Kokkos library.
.. code-block:: make
KOKKOS_DEVICES = HIP
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is hosting the GPU
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is
# hosting the GPU
# GPUARCH = GPU from list above
FFT_INC = -DFFT_HIPFFT # enable use of hipFFT (optional)
FFT_LIB = -lhipfft # link to hipFFT library
FFT_INC = -DFFT_HIPFFT # enable use of hipFFT (optional)
FFT_LIB = -lhipfft # link to hipFFT library
Advanced KOKKOS compilation settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -870,11 +912,16 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
.. code-block:: bash
make lib-lepton # print help message
make lib-lepton args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-lepton args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
# print help message
make lib-lepton
The "machine" argument of the "-m" flag is used to find a
# build with GNU g++ compiler (settings as with "make serial")
make lib-lepton args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-lepton args="-m mpi"
The "machine" argument of the ``-m`` flag is used to find a
Makefile.machine to use as build recipe.
The build should produce a ``build`` folder and the library ``lib/lepton/liblmplepton.a``
@ -896,7 +943,8 @@ Eigen3 is a template library, so you do not need to build it.
.. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location)
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a
# custom location)
If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
downloaded and inside the CMake build directory. If the Eigen3
@ -914,9 +962,14 @@ Eigen3 is a template library, so you do not need to build it.
.. code-block:: bash
make lib-machdyn # print help message
make lib-machdyn args="-b" # download to lib/machdyn/eigen3
make lib-machdyn args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
# print help message
make lib-machdyn
# download to lib/machdyn/eigen3
make lib-machdyn args="-b"
# use existing Eigen installation in /usr/include/eigen3
make lib-machdyn args="-p /usr/include/eigen3"
Note that a symbolic (soft) link named ``includelink`` is created
in ``lib/machdyn`` to point to the Eigen dir. When LAMMPS builds it
@ -990,7 +1043,7 @@ OPT package
The compiler flag ``-restrict`` must be used to build LAMMPS with
the OPT package when using Intel compilers. It should be added to
the :code:`CCFLAGS` line of your ``Makefile.machine``. See
the ``CCFLAGS`` line of your ``Makefile.machine``. See
``src/MAKE/OPTIONS/Makefile.opt`` for an example.
----------
@ -1017,10 +1070,17 @@ POEMS package
.. code-block:: bash
make lib-poems # print help message
make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-poems args="-m icc" # build with Intel icc compiler
# print help message
make lib-poems
# build with GNU g++ compiler (settings as with "make serial")
make lib-poems args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-poems args="-m mpi"
# build with Intel Classic compiler
make lib-poems args="-m icc"
The build should produce two files: ``lib/poems/libpoems.a`` and
``lib/poems/Makefile.lammps``. The latter is copied from an
@ -1084,9 +1144,12 @@ binary package provided by your operating system.
.. code-block:: bash
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location)
-D DOWNLOAD_VORO=value # download Voro++ for build
# value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file
# (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory
# (only needed if at custom location)
If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded
and built inside the CMake build directory. If the Voro++ library
@ -1106,12 +1169,19 @@ binary package provided by your operating system.
.. code-block:: bash
make lib-voronoi # print help message
make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
# print help message
make lib-voronoi
Note that 2 symbolic (soft) links, ``includelink`` and
# download and build the default version in lib/voronoi/voro++-<version>
make lib-voronoi args="-b"
# use existing Voro++ installation in $HOME/voro++
make lib-voronoi args="-p $HOME/voro++"
# download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
make lib-voronoi args="-b -v voro++0.4.6"
Note that two symbolic (soft) links, ``includelink`` and
``liblink``, are created in lib/voronoi to point to the Voro++
source dir. When LAMMPS builds in ``src`` it will use these
links. You should not need to edit the
@ -1185,10 +1255,17 @@ The ATC package requires the MANYBODY package also be installed.
.. code-block:: bash
make lib-atc # print help message
make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-atc args="-m icc" # build with Intel icc compiler
# print help message
make lib-atc
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-atc args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-atc args="-m mpi"
# build with Intel Classic compiler
make lib-atc args="-m icc"
The build should produce two files: ``lib/atc/libatc.a`` and
``lib/atc/Makefile.lammps``. The latter is copied from an
@ -1207,10 +1284,17 @@ The ATC package requires the MANYBODY package also be installed.
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU Fortran compiler
# print help message
make lib-linalg
# build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU Fortran compiler
make lib-linalg args="-m g++"
----------
@ -1236,10 +1320,17 @@ AWPMD package
.. code-block:: bash
make lib-awpmd # print help message
make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-awpmd args="-m icc" # build with Intel icc compiler
# print help message
make lib-awpmd
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-awpmd args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-awpmd args="-m mpi"
# build with Intel Classic compiler
make lib-awpmd args="-m icc"
The build should produce two files: ``lib/awpmd/libawpmd.a`` and
``lib/awpmd/Makefile.lammps``. The latter is copied from an
@ -1258,10 +1349,17 @@ AWPMD package
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
# print help message
make lib-linalg
# build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
----------
@ -1294,10 +1392,17 @@ module included in the LAMMPS source distribution.
.. code-block:: bash
make lib-colvars # print help message
make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
# print help message
make lib-colvars
# build with GNU g++ compiler (settings as with "make serial")
make lib-colvars args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-colvars args="-m mpi"
# build with GNU g++ compiler and colvars debugging enabled
make lib-colvars args="-m g++-debug"
The "machine" argument of the "-m" flag is used to find a
``Makefile.machine`` file to use as build recipe. If such recipe does
@ -1316,8 +1421,11 @@ module included in the LAMMPS source distribution.
.. code-block:: bash
COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
# Build with debug code (much slower)
COLVARS_DEBUG=yes make lib-colvars args="-m machine"
# Build without Lepton (included otherwise)
COLVARS_LEPTON=no make lib-colvars args="-m machine"
The build should produce two files: the library
``lib/colvars/libcolvars.a`` and the specification file
@ -1364,9 +1472,14 @@ This package depends on the KSPACE package.
.. code-block:: bash
make lib-electrode # print help message
make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
# print help message
make lib-electrode
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-electrode args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-electrode args="-m mpi"
Note that the ``Makefile.lammps`` file has settings for the BLAS
@ -1377,10 +1490,17 @@ This package depends on the KSPACE package.
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
# print help message
make lib-linalg
# build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE``
@ -1397,6 +1517,11 @@ in lib/pace or somewhere else, which must be done before building
LAMMPS with this package. The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
Instead of including the ML-PACE package directly into LAMMPS, it
is also possible to skip this step and build the ML-PACE package as
a plugin using the CMake script files in the ``examples/PACKAGE/pace/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build
@ -1420,8 +1545,11 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. code-block:: bash
make lib-pace # print help message
make lib-pace args="-b" # download and build the default version in lib/pace
# print help message
make lib-pace
# download and build the default version in lib/pace
make lib-pace args="-b"
You should not need to edit the ``lib/pace/Makefile.lammps`` file.
@ -1448,10 +1576,17 @@ ML-POD package
.. code-block:: bash
make lib-mlpod # print help message
make lib-mlpod args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-mlpod args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-mlpod args="-m mpi -e linalg" # same as above but use the bundled linalg lib
# print help message
make lib-mlpod
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-mlpod args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-mlpod args="-m mpi"
# same as above but use the bundled linalg lib
make lib-mlpod args="-m mpi -e linalg"
Note that the ``Makefile.lammps`` file has settings to use the BLAS
and LAPACK linear algebra libraries. These can either exist on
@ -1461,10 +1596,17 @@ ML-POD package
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
# print help message
make lib-linalg
# build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
The package itself is activated with ``make yes-ML-POD``.
@ -1487,10 +1629,13 @@ within CMake will download the non-commercial use version.
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
-D DOWNLOAD_QUIP=value # download QUIP library for build
# value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a
# (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library
# instead of LAPACK
# value = no (default) or yes
CMake will try to download and build the QUIP library from GitHub,
if it is not found on the local machine. This requires to have git
@ -1561,29 +1706,38 @@ try a different one, switch to a different build system, consider a
global PLUMED installation or consider downloading PLUMED during the
LAMMPS build.
Instead of including the PLUMED package directly into LAMMPS, it
is also possible to skip this step and build the PLUMED package as
a plugin using the CMake script files in the ``examples/PACKAGE/plumed/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build
When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
command you must ensure that GSL is installed in locations that
are specified in your environment. There are then two additional
variables that control the manner in which PLUMED is obtained and
linked into LAMMPS.
command you must ensure that `the GNU Scientific Library (GSL)
<https://www.gnu.org/software/gsl/>` is installed in locations
that are accessible in your environment. There are then two
additional variables that control the manner in which PLUMED is
obtained and linked into LAMMPS.
.. code-block:: bash
-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime
-D DOWNLOAD_PLUMED=value # download PLUMED for build
# value = no (default) or yes
-D PLUMED_MODE=value # Linkage mode for PLUMED
# value = static (default), shared,
# or runtime
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
If ``DOWNLOAD_PLUMED`` is set to ``yes``, the PLUMED library will be
downloaded (the version of PLUMED that will be downloaded is
hard-coded to a vetted version of PLUMED, usually a recent stable
release version) and built inside the CMake build directory. If
``DOWNLOAD_PLUMED`` is set to "no" (the default), CMake will try
to detect and link to an installed version of PLUMED. For this to
work, the PLUMED library has to be installed into a location where
the ``pkg-config`` tool can find it or the PKG_CONFIG_PATH
the ``pkg-config`` tool can find it or the ``PKG_CONFIG_PATH``
environment variable has to be set up accordingly. PLUMED should
be installed in such a location if you compile it using the
default make; make install commands.
@ -1612,14 +1766,21 @@ LAMMPS build.
.. code-block:: bash
make lib-plumed # print help message
make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
# /usr/local and use shared linkage mode
# print help message
make lib-plumed
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``
are created in lib/plumed that point to the location of the PLUMED
# download and build PLUMED in lib/plumed/plumed2
make lib-plumed args="-b"
# use existing PLUMED installation in $HOME/.local
make lib-plumed args="-p $HOME/.local"
# use existing PLUMED installation in /usr/local and
# use shared linkage mode
make lib-plumed args="-p /usr/local -m shared"
Note that two symbolic (soft) links, ``includelink`` and ``liblink``
are created in ``lib/plumed`` that point to the location of the PLUMED
build to use. A new file ``lib/plumed/Makefile.lammps`` is also
created with settings suitable for LAMMPS to compile and link
PLUMED using the desired linkage mode. After this step is
@ -1634,17 +1795,17 @@ LAMMPS build.
Once this compilation completes you should be able to run LAMMPS
in the usual way. For shared linkage mode, libplumed.so must be
found by the LAMMPS executable, which on many operating systems
means, you have to set the LD_LIBRARY_PATH environment variable
means, you have to set the ``LD_LIBRARY_PATH`` environment variable
accordingly.
Support for the different linkage modes in LAMMPS varies for
different operating systems, using the static linkage is expected
to be the most portable, and thus set to be the default.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings **and** do a re-install if
the PLUMED package with "make yes-plumed" to update the
required makefile settings with the changes in the lib/plumed
If you want to change the linkage mode, you have to re-run ``make
lib-plumed`` with the desired settings **and** do a re-install if
the PLUMED package with ``make yes-plumed`` to update the
required makefile settings with the changes in the ``lib/plumed``
folder.
----------
@ -1718,8 +1879,10 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
.. code-block:: bash
-D DOWNLOAD_N2P2=value # download n2p2 for build, value = no (default) or yes
-D N2P2_DIR=path # n2p2 base directory (only needed if a custom location)
-D DOWNLOAD_N2P2=value # download n2p2 for build
# value = no (default) or yes
-D N2P2_DIR=path # n2p2 base directory
# (only needed if a custom location)
If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
built inside the CMake build directory. If the *n2p2* library is already
@ -1736,12 +1899,19 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
.. code-block:: bash
make lib-hdnnp # print help message
make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-...
make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
# print help message
make lib-hdnnp
Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
# download and build in lib/hdnnp/n2p2-...
make lib-hdnnp args="-b"
# download and build specific version
make lib-hdnnp args="-b -v 2.1.4"
# use the existing n2p2 installation in /usr/local/n2p2
make lib-hdnnp args="-p /usr/local/n2p2"
Note that three symbolic (soft) links, ``includelink``, ``liblink`` and
``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
respectively. When LAMMPS is built in ``src`` it will use these links.
@ -1788,19 +1958,19 @@ code when using features from the INTEL package.
.. code-block:: make
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
For KNLs:
.. code-block:: make
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
In Long-range thread mode (LRT) a modified verlet style is used, that
operates the Kspace calculation in a separate thread concurrently to
@ -1829,7 +1999,8 @@ MDI package
.. code-block:: bash
-D DOWNLOAD_MDI=value # download MDI Library for build, value = no (default) or yes
-D DOWNLOAD_MDI=value # download MDI Library for build
# value = no (default) or yes
.. tab:: Traditional make
@ -1858,7 +2029,8 @@ MOLFILE package
.. code-block:: bash
-D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile plugin headers are installed
-D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile
# plugin headers are installed
-D PKG_MOLFILE=yes
Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
@ -2017,10 +2189,17 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
.. code-block:: bash
make lib-qmmm # print help message
make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
# print help message
make lib-qmmm
# build with GNU Fortran compiler (settings as in "make serial")
make lib-qmmm args="-m serial"
# build with default MPI compiler (settings as in "make mpi")
make lib-qmmm args="-m mpi"
# build with GNU Fortran compiler
make lib-qmmm args="-m gfortran"
The build should produce two files: ``lib/qmmm/libqmmm.a`` and
``lib/qmmm/Makefile.lammps``. The latter is copied from an
@ -2033,10 +2212,40 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
You can then install QMMM package and build LAMMPS in the usual
manner. After completing the LAMMPS build and compiling Quantum
ESPRESSO with external library support (via "make couple"), go
ESPRESSO with external library support (via ``make couple``), go
back to the ``lib/qmmm`` folder and follow the instructions in the
README file to build the combined LAMMPS/QE QM/MM executable
(pwqmmm.x) in the lib/qmmm folder.
(``pwqmmm.x``) in the ``lib/qmmm`` folder.
----------
.. _rheo:
RHEO package
------------
To build with this package you must have the `GNU Scientific Library
(GSL) <https://www.gnu.org/software/gsl/>` installed in locations that
are accessible in your environment. The GSL library should be at least
version 2.7.
.. tabs::
.. tab:: CMake build
If CMake cannot find the GSL library or include files, you can set:
.. code-block:: bash
-D GSL_ROOT_DIR=path # path to root of GSL installation
.. tab:: Traditional make
LAMMPS will try to auto-detect the GSL compiler and linker flags
from the corresponding ``pkg-config`` file (``gsl.pc``), otherwise
you can edit the file ``lib/rheo/Makefile.lammps``
to specify the paths and library names where indicated by comments.
This must be done **before** the package is installed.
----------
@ -2076,11 +2285,16 @@ To build with this package, you must download and build the
.. code-block:: bash
make lib-scafacos # print help message
make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
# print help message
make lib-scafacos
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
# download and build in lib/scafacos/scafacos-<version>
make lib-scafacos args="-b"
# use existing ScaFaCoS installation in $HOME/scafacos
make lib-scafacos args="-p $HOME/scafacos
Note that two symbolic (soft) links, ``includelink`` and ``liblink``, are
created in ``lib/scafacos`` to point to the ScaFaCoS src dir. When LAMMPS
builds in src it will use these links. You should not need to edit
the ``lib/scafacos/Makefile.lammps`` file.

10
doc/src/Build_link.rst
View File

@ -37,7 +37,7 @@ executable code from the library is copied into the calling executable.
.. tab:: CMake build
This assumes that LAMMPS has been configured without setting a
``LAMMPS_MACHINE`` name, installed with "make install", and the
``LAMMPS_MACHINE`` name, installed with ``make install``, and the
``PKG_CONFIG_PATH`` environment variable has been updated to
include the ``liblammps.pc`` file installed into the configured
destination folder. The commands to compile and link a coupled
@ -59,10 +59,10 @@ executable code from the library is copied into the calling executable.
mpicc -c -O -I${HOME}/lammps/src caller.c
mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
The *-I* argument is the path to the location of the ``library.h``
The ``-I`` argument is the path to the location of the ``library.h``
header file containing the interface to the LAMMPS C-style library
interface. The *-L* argument is the path to where the
``liblammps_mpi.a`` file is located. The *-llammps_mpi* argument
interface. The ``-L`` argument is the path to where the
``liblammps_mpi.a`` file is located. The ``-llammps_mpi`` argument
is shorthand for telling the compiler to link the file
``liblammps_mpi.a``. If LAMMPS has been built as a shared
library, then the linker will use ``liblammps_mpi.so`` instead.
@ -142,7 +142,7 @@ When linking to LAMMPS built as a shared library, the situation becomes
much simpler, as all dependent libraries and objects are either included
in the shared library or registered as a dependent library in the shared
library file. Thus, those libraries need not be specified when linking
the calling executable. Only the *-I* flags are needed. So the example
the calling executable. Only the ``-I`` flags are needed. So the example
case from above of the serial version static LAMMPS library with the
POEMS package installed becomes:

2
doc/src/Build_make.rst
View File

@ -25,7 +25,7 @@ additional tools to be available and functioning.
require adding flags like ``-std=c++11`` to enable the C++11 mode.
* A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
* A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* Python (optional, required for ``make lib-<pkg>`` in the src
* Python (optional, required for ``make lib-<pkg>`` in the ``src``
folder). Python scripts are currently tested with python 2.7 and
3.6 to 3.11. The procedure for :doc:`building the documentation
<Build_manual>` *requires* Python 3.5 or later.

59
doc/src/Build_package.rst
View File

@ -62,6 +62,7 @@ packages:
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`RHEO <rheo>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`VORONOI <voronoi>`
* :ref:`VTK <vtk>`
@ -99,10 +100,10 @@ versus make.
.. code-block:: bash
cd lammps/src
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # uninstall a package with name
make mpi # build LAMMPS with whatever packages are now installed
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # uninstall a package with name
make mpi # build LAMMPS with whatever packages are now installed
Examples:
@ -171,18 +172,41 @@ make a copy of one of them and modify it to suit your needs.
.. code-block:: bash
cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake # change settings to use the GNU compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake # change settings to use the PGI compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross-compilers
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS
# enable just a few core packages
cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake
# enable most packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake
# enable packages which download sources or potential files
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake
# disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake
# change settings to use the Clang compilers by default
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake
# change settings to use the GNU compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake
# change settings to use the Intel compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake
# change settings to use the PGI compilers by default
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake
# enable all packages
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake
# disable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake
# compile with MinGW cross-compilers
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake
# compile serial multi-arch binaries on macOS
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake
Presets that have names starting with "windows" are specifically for
compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@ -208,7 +232,8 @@ Example
# GPU package and configure it for using CUDA. You can run.
mkdir build
cd build
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
-D PKG_GPU=on -D GPU_API=cuda ../cmake
# to add another package, say BODY to the previous configuration you can run:
cmake -D PKG_BODY=on .

201
doc/src/Build_settings.rst
View File

@ -1,3 +1,7 @@
.. raw:: latex
\clearpage
Optional build settings
=======================
@ -8,7 +12,8 @@ explains how to do this for building both with CMake and make.
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
* `Size of LAMMPS integer types and size limits`_
* `Read or write compressed files`_
* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
* `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
* `Support for downloading files`_
* `Memory allocation alignment`_
* `Workaround for long long integers`_
* `Exception handling when using LAMMPS as a library`_ to capture errors
@ -19,7 +24,7 @@ explains how to do this for building both with CMake and make.
.. _cxx11:
C++11 standard compliance
------------------------------------------
-------------------------
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
LAMMPS version 3 March 2020 is the last version compatible with the previous
@ -31,12 +36,16 @@ flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
CCFLAGS = -g -O3 -std=c++11
Individual packages may require compliance with a later C++ standard
like C++14 or C++17. These requirements will be documented with the
:doc:`individual packages <Packages_details>`.
----------
.. _fft:
FFT library
---------------------
-----------
When the KSPACE package is included in a LAMMPS build, the
:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
@ -58,8 +67,10 @@ libraries and better pipelining for packing and communication.
.. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found,
# else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT,
# default is KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
-D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
@ -67,11 +78,11 @@ libraries and better pipelining for packing and communication.
.. note::
When the Kokkos variant of a package is compiled and selected at run time,
the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
the FFT library selected by the ``FFT_KOKKOS`` variable applies. Otherwise,
the FFT library selected by the FFT variable applies.
The same FFT settings apply to both. FFT_KOKKOS must be compatible with the
The same FFT settings apply to both. ``FFT_KOKKOS`` must be compatible with the
Kokkos back end - for example, when using the CUDA back end of Kokkos,
you must use either CUFFT or KISS.
you must use either ``CUFFT`` or ``KISS``.
Usually these settings are all that is needed. If FFTW3 is
selected, then CMake will try to detect, if threaded FFTW
@ -89,7 +100,8 @@ libraries and better pipelining for packing and communication.
-D MKL_INCLUDE_DIR=path # ditto for Intel MKL library
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARY=path # path to MKL libraries
-D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock heFFTe back end
-D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock
# heFFTe back end
-D Heffte_ROOT=path # path to an existing heFFTe installation
.. note::
@ -108,30 +120,50 @@ libraries and better pipelining for packing and communication.
.. code-block:: make
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified
FFT_INC = -DFFT_KOKKOS_CUFFT # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS}
# default is KISS if not specified
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT_PACK_ARRAY if not specified
FFT_INC = -DFFT_<NAME> # where <NAME> is KISS (default), FFTW3,
# FFTW (same as FFTW3), or MKL
FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
# FFTW (same as FFTW3), MKL, CUFFT, or HIPFFT
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT_PACK_ARRAY if not specified
.. code-block:: make
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lhipfft # hipFFT either precision
FFT_LIB = -lcufft # cuFFT either precision
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler, serial interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compiler, serial interface
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core # MKL with GNU compiler, threaded interface
FFT_LIB = -lmkl_rt # MKL with automatic runtime selection of interface libs
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
# hipFFT either precision
FFT_LIB = -lhipfft
# cuFFT either precision
FFT_LIB = -lcufft
# FFTW3 double precision
FFT_LIB = -lfftw3
# FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3_omp
# FFTW3 single precision
FFT_LIB = -lfftw3 -lfftw3f
# serial MKL with Intel compiler
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
# serial MKL with GNU compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
# threaded MKL with Intel compiler
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
# threaded MKL with GNU compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core
# MKL with automatic runtime selection of interface libs
FFT_LIB = -lmkl_rt
As with CMake, you do not need to set paths in ``FFT_INC`` or
``FFT_PATH``, if the compiler can find the FFT header and library
@ -147,11 +179,11 @@ libraries and better pipelining for packing and communication.
FFT_PATH =
FFT_LIB = $(heffte_link) $(heffte_libs)
The heFFTe install path will contain `HeffteMakefile.in`.
which will define the `heffte_` include variables needed to link to heFFTe from
The heFFTe install path will contain ``HeffteMakefile.in``.
which will define the ``heffte_`` include variables needed to link to heFFTe from
an external project using traditional make.
The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW`
selects the desired heFFTe back end, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
The ``-DFFT_HEFFTE`` is required to switch to using heFFTe, while the optional ``-DFFT_HEFFTE_FFTW``
selects the desired heFFTe back end, e.g., ``-DFFT_HEFFTE_FFTW`` or ``-DFFT_HEFFTE_MKL``,
omitting the variable will default to the `stock` back end.
The heFFTe `stock` back end is intended to be used for testing and debugging,
but is not performance optimized for large scale production runs.
@ -179,7 +211,7 @@ it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
Building FFTW for your box should be as simple as ``./configure; make;
make install``. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type ``./configure --help`` to see
the ``--prefix`` option of configure. Type ``./configure --help`` to see
various options.
The Intel MKL math library is part of the Intel compiler suite. It
@ -215,7 +247,7 @@ produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
Performing 3d FFTs requires communication to transpose the 3d FFT
grid. The data packing/unpacking for this can be done in one of 3
modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
modes (ARRAY, POINTER, MEMCPY) as set by the ``FFT_PACK`` syntax above.
Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is
ARRAY mode.
@ -232,6 +264,10 @@ and those variables will be passed into the heFFTe build.
----------
.. raw:: latex
\clearpage
.. _size:
Size of LAMMPS integer types and size limits
@ -272,7 +308,7 @@ LAMMPS system size restrictions
.. list-table::
:header-rows: 1
:widths: auto
:widths: 18 27 28 27
:align: center
* -
@ -341,8 +377,8 @@ in whichever ``lib/gpu/Makefile`` is used must be the same as above.
.. _graphics:
Output of JPG, PNG, and movie files
--------------------------------------------------
Output of JPEG, PNG, and movie files
------------------------------------
The :doc:`dump image <dump_image>` command has options to output JPEG or
PNG image files. Likewise, the :doc:`dump movie <dump_image>` command
@ -355,12 +391,13 @@ requires the following settings:
.. code-block:: bash
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB files, else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG development files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB development files,
# else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
Usually these settings are all that is needed. If CMake cannot
find the graphics header, library, executable files, you can set
@ -382,8 +419,10 @@ requires the following settings:
LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings>
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h headers
# if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so)
# files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz # library names
As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
@ -414,8 +453,8 @@ Read or write compressed files
If this option is enabled, large files can be read or written with
compression by ``gzip`` or similar tools by several LAMMPS commands,
including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
:doc:`dump <dump>`. Supported compression tools are currently
``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
:doc:`dump <dump>`. Supported compression tools and algorithms are currently
``gzip``, ``bzip2``, ``zstd``, ``xz``, ``lz4``, and ``lzma`` (via xz).
.. tabs::
@ -423,8 +462,8 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
.. code-block:: bash
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find the gzip program, else no
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find the gzip program
.. tab:: Traditional make
@ -446,18 +485,64 @@ during a run.
available using a compression library instead, which is what the
:ref:`COMPRESS package <PKG-COMPRESS>` enables.
--------------------------------------------------
.. _libcurl:
Support for downloading files
-----------------------------
.. versionadded:: 29Aug2024
The :doc:`geturl command <geturl>` command uses the `the libcurl library
<https://curl.se/libcurl/>`_ to download files. This requires that
LAMMPS is compiled accordingly which needs the following settings:
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D WITH_CURL=value # yes or no
# default = yes if CMake finds CURL development files, else no
Usually these settings are all that is needed. If CMake cannot
find the graphics header, library, executable files, you can set
these variables:
.. code-block:: bash
-D CURL_INCLUDE_DIR=path # path to folder which contains curl.h header file
-D CURL_LIBRARY=path # path to libcurls.a (.so) file
.. tab:: Traditional make
.. code-block:: make
LMP_INC = -DLAMMPS_CURL <other LMP_INC settings>
CURL_INC = -I/usr/local/include # path to curl folder with curl.h
CURL_PATH = -L/usr/lib # paths to libcurl.a(.so) if make cannot find it
CURL_LIB = -lcurl # library names
As with CMake, you do not need to set ``CURL_INC`` or ``CURL_PATH``,
if make can find the libcurl header and library files in their
default system locations. You must specify ``CURL_LIB`` with a
paths or linker flags to link to libcurl.
----------
.. _align:
Memory allocation alignment
---------------------------------------
---------------------------
This setting enables the use of the "posix_memalign()" call instead of
"malloc()" when LAMMPS allocates large chunks of memory. Vector
This setting enables the use of the ``posix_memalign()`` call instead of
``malloc()`` when LAMMPS allocates large chunks of memory. Vector
instructions on CPUs may become more efficient, if dynamically allocated
memory is aligned on larger-than-default byte boundaries. On most
current operating systems, the "malloc()" implementation returns
current operating systems, the ``malloc()`` implementation returns
pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being aligned
on 64-byte boundaries.
@ -471,9 +556,9 @@ on 64-byte boundaries.
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
"posix_memalign()" and revert to using the "malloc()" C-library
``posix_memalign()`` and revert to using the ``malloc()`` C-library
function instead. When compiling LAMMPS for Windows systems,
"malloc()" will always be used and this setting is ignored.
``malloc()`` will always be used and this setting is ignored.
.. tab:: Traditional make
@ -482,7 +567,7 @@ on 64-byte boundaries.
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
allocated with the "malloc()" function call
allocated with the ``malloc()`` function call
instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
Windows different function calls with different semantics for
allocating aligned memory, that are not compatible with how LAMMPS

39
doc/src/Commands_all.rst
View File

@ -1,26 +1,30 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 5
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. raw:: latex
\clearpage
General commands
================
An alphabetic list of general LAMMPS commands. Note that style
commands with many variants, can be more easily accessed via the small
table above.
An alphabetic list of general LAMMPS commands.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
@ -54,6 +58,7 @@ table above.
* :doc:`echo <echo>`
* :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
* :doc:`geturl <geturl>`
* :doc:`group <group>`
* :doc:`if <if>`
* :doc:`improper_coeff <improper_coeff>`
@ -121,7 +126,7 @@ commands have accelerated versions. This is indicated by an
additional letter in parenthesis: k = KOKKOS.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`dynamical_matrix (k) <dynamical_matrix>`
* :doc:`group2ndx <group2ndx>`

55
doc/src/Commands_bond.rst
View File

@ -1,21 +1,7 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _bond:
Bond_style potentials
=====================
Bond styles
===========
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -23,7 +9,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
@ -33,6 +19,8 @@ OPT.
*
*
*
*
*
* :doc:`bpm/rotational <bond_bpm_rotational>`
* :doc:`bpm/spring <bond_bpm_spring>`
* :doc:`class2 (ko) <bond_class2>`
@ -54,13 +42,14 @@ OPT.
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`rheo/shell <bond_rheo_shell>`
* :doc:`special <bond_special>`
* :doc:`table (o) <bond_table>`
.. _angle:
Angle_style potentials
======================
Angle styles
============
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -68,11 +57,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <angle_none>`
* :doc:`zero <angle_zero>`
* :doc:`hybrid <angle_hybrid>`
* :doc:`hybrid (k) <angle_hybrid>`
*
*
*
*
*
@ -100,13 +91,13 @@ OPT.
* :doc:`mesocnt <angle_mesocnt>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`spica (o) <angle_spica>`
* :doc:`spica (ko) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:
Dihedral_style potentials
=========================
Dihedral styles
===============
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -114,11 +105,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <dihedral_none>`
* :doc:`zero <dihedral_zero>`
* :doc:`hybrid <dihedral_hybrid>`
* :doc:`hybrid (k) <dihedral_hybrid>`
*
*
*
*
*
@ -143,8 +136,8 @@ OPT.
.. _improper:
Improper_style potentials
=========================
Improper styles
===============
All LAMMPS :doc:`improper_style <improper_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -152,11 +145,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <improper_none>`
* :doc:`zero <improper_zero>`
* :doc:`hybrid <improper_hybrid>`
* :doc:`hybrid (k) <improper_hybrid>`
*
*
*
*
*

40
doc/src/Commands_category.rst
View File

@ -1,3 +1,7 @@
.. raw:: latex
\clearpage
Commands by category
====================
@ -6,8 +10,8 @@ This page lists most of the LAMMPS commands, grouped by category. The
alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically.
Initialization:
------------------------------
Initialization
--------------
.. table_from_list::
:columns: 5
@ -18,8 +22,8 @@ Initialization:
* :doc:`suffix <suffix>`
* :doc:`units <units>`
Setup simulation box:
------------------------------
Setup simulation box
--------------------
.. table_from_list::
:columns: 4
@ -31,8 +35,8 @@ Setup simulation box:
* :doc:`lattice <lattice>`
* :doc:`region <region>`
Setup atoms:
------------------------------
Setup atoms
-----------
.. table_from_list::
:columns: 4
@ -55,8 +59,8 @@ Setup atoms:
* :doc:`set <set>`
* :doc:`velocity <velocity>`
Force fields:
------------------------------
Force fields
------------
.. table_from_list::
:columns: 4
@ -79,8 +83,8 @@ Force fields:
* :doc:`pair_write <pair_write>`
* :doc:`special_bonds <special_bonds>`
Settings:
------------------------------
Settings
--------
.. table_from_list::
:columns: 4
@ -98,8 +102,8 @@ Settings:
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
Operations within timestepping (fixes) and diagnostics (computes):
------------------------------------------------------------------------------------------
Operations within timestepping (fixes) and diagnostics (computes)
-----------------------------------------------------------------
.. table_from_list::
:columns: 4
@ -111,8 +115,8 @@ Operations within timestepping (fixes) and diagnostics (computes):
* :doc:`uncompute <uncompute>`
* :doc:`unfix <unfix>`
Output:
------------------------------
Output
------
.. table_from_list::
:columns: 4
@ -131,8 +135,8 @@ Output:
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`
Actions:
------------------------------
Actions
-------
.. table_from_list::
:columns: 6
@ -146,8 +150,8 @@ Actions:
* :doc:`tad <tad>`
* :doc:`temper <temper>`
Input script control:
------------------------------
Input script control
--------------------
.. table_from_list::
:columns: 7

21
doc/src/Commands_compute.rst
View File

@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Compute commands
================
Compute styles
==============
An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
Some styles have accelerated versions. This is indicated by
@ -21,7 +7,7 @@ additional letters in parenthesis: g = GPU, i = INTEL, k =
KOKKOS, o = OPENMP, t = OPT.
.. table_from_list::
:columns: 5
:columns: 4
* :doc:`ackland/atom <compute_ackland_atom>`
* :doc:`adf <compute_adf>`
@ -126,6 +112,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`reduce <compute_reduce>`
* :doc:`reduce/chunk <compute_reduce_chunk>`
* :doc:`reduce/region <compute_reduce>`
* :doc:`rheo/property/atom <compute_rheo_property_atom>`
* :doc:`rigid/local <compute_rigid_local>`
* :doc:`saed <compute_saed>`
* :doc:`slcsa/atom <compute_slcsa_atom>`

20
doc/src/Commands_dump.rst
View File

@ -1,24 +1,10 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Dump commands
=============
Dump styles
===========
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`

26
doc/src/Commands_fix.rst
View File

@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============
Fix styles
==========
An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -21,13 +7,14 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 5
:columns: 4
* :doc:`accelerate/cos <fix_accelerate_cos>`
* :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`add/heat <fix_add_heat>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`alchemy <fix_alchemy>`
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
@ -204,6 +191,11 @@ OPT.
* :doc:`reaxff/species (k) <fix_reaxff_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rheo <fix_rheo>`
* :doc:`rheo/oxidation <fix_rheo_oxidation>`
* :doc:`rheo/pressure <fix_rheo_pressure>`
* :doc:`rheo/thermal <fix_rheo_thermal>`
* :doc:`rheo/viscosity <fix_rheo_viscosity>`
* :doc:`rhok <fix_rhok>`
* :doc:`rigid (o) <fix_rigid>`
* :doc:`rigid/meso <fix_rigid_meso>`

16
doc/src/Commands_input.rst
View File

@ -10,14 +10,14 @@ for any commands that may be processed later. Commands may set an
internal variable, read in a file, or run a simulation. These actions
can be grouped into three categories:
a) commands that change a global setting (examples: timestep, newton,
echo, log, thermo, restart),
a) commands that change a global setting (examples: :doc:`timestep <timestep>`, :doc:`newton <newton>`,
:doc:`echo <echo>`, :doc:`log <log>`, :doc:`thermo <thermo>`, :doc:`restart <restart>`),
b) commands that add, modify, remove, or replace "styles" that are
executed during a "run" (examples: pair_style, fix, compute, dump,
thermo_style, pair_modify), and
executed during a "run" (examples: :doc:`pair_style <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, :doc:`dump <dump>`,
:doc:`thermo_style <thermo_style>`, :doc:`pair_modify <pair_modify>`), and
c) commands that execute a "run" or perform some other computation or
operation (examples: print, run, minimize, temper, write_dump, rerun,
read_data, read_restart)
operation (examples: :doc:`print <print>`, :doc:`run <run>`, :doc:`minimize <minimize>`, :doc:`temper <temper>`, :doc:`write_dump <write_dump>`, :doc:`rerun <rerun>`,
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`)
Commands in category a) have default settings, which means you only
need to use the command if you wish to change the defaults.
@ -61,7 +61,7 @@ between commands in the c) category. The following rules apply:
<read_data>` command initializes the system by setting up the
simulation box and assigning atoms to processors. If default values
are not desired, the :doc:`processors <processors>` and
:doc:`boundary <boundary>` commands need to be used before read_data
:doc:`boundary <boundary>` commands need to be used before ``read_data``
to tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
@ -70,6 +70,6 @@ more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
You can use the :ref:`-skiprun <skiprun>` command line flag
to have LAMMPS skip the execution of any "run", "minimize", or similar
to have LAMMPS skip the execution of any ``run``, ``minimize``, or similar
commands to check the entire input for correct syntax to avoid crashes
on typos or syntax errors in long runs.

20
doc/src/Commands_kspace.rst
View File

@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
KSpace solvers
==============
KSpace styles
=============
All LAMMPS :doc:`kspace_style <kspace_style>` solvers. Some styles have
accelerated versions. This is indicated by additional letters in
@ -21,7 +7,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`ewald (o) <kspace_style>`
* :doc:`ewald/disp <kspace_style>`

28
doc/src/Commands_pair.rst
View File

@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================
Pair styles
===========
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -21,7 +7,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 3
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
@ -35,10 +21,6 @@ OPT.
*
*
*
*
*
*
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@ -195,7 +177,7 @@ OPT.
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/long (gko) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
@ -264,6 +246,8 @@ OPT.
* :doc:`rebo (io) <pair_airebo>`
* :doc:`rebomos (o) <pair_rebomos>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`rheo <pair_rheo>`
* :doc:`rheo/solid <pair_rheo_solid>`
* :doc:`saip/metal (t) <pair_saip_metal>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`smatb <pair_smatb>`

12
doc/src/Commands_parse.rst
View File

@ -42,8 +42,8 @@ LAMMPS:
If the $ is followed by text in curly brackets '{}', then the
variable name is the text inside the curly brackets. If no curly
brackets follow the $, then the variable name is the single character
immediately following the $. Thus ${myTemp} and $x refer to variables
named "myTemp" and "x", while "$xx" will be interpreted as a variable
immediately following the $. Thus ``${myTemp}`` and ``$x`` refer to variables
named "myTemp" and "x", while ``$xx`` will be interpreted as a variable
named "x" followed by an "x" character.
How the variable is converted to a text string depends on what style
@ -79,10 +79,10 @@ LAMMPS:
Additionally, the entire "immediate" variable expression may be
followed by a colon, followed by a C-style format string,
e.g. ":%f" or ":%.10g". The format string must be appropriate for
e.g. ``:%f`` or ``:%.10g``. The format string must be appropriate for
a double-precision floating-point value. The format string is used
to output the result of the variable expression evaluation. If a
format string is not specified, a high-precision "%.20g" is used as
format string is not specified, a high-precision ``%.20g`` is used as
the default format.
This can be useful for formatting print output to a desired precision:
@ -101,8 +101,8 @@ LAMMPS:
variable b2 equal 4
print "B2 = ${b$a}"
Nor can you specify an expression like "$($x-1.0)" for an immediate
variable, but you could use $(v_x-1.0), since the latter is valid
Nor can you specify an expression like ``$($x-1.0)`` for an immediate
variable, but you could use ``$(v_x-1.0)``, since the latter is valid
syntax for an :doc:`equal-style variable <variable>`.
See the :doc:`variable <variable>` command for more details of how

29
doc/src/Commands_removed.rst
View File

@ -8,6 +8,18 @@ stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
restart2data tool
-----------------
.. versionchanged:: 23Nov2013
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
@ -151,17 +163,16 @@ and allow running LAMMPS with GPU acceleration.
i-PI tool
---------
.. versionchanged:: 27June2024
.. versionchanged:: 27Jun2024
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPI via pip are provided.
restart2data tool
-----------------
LAMMPS shell
------------
.. versionchanged:: 29Aug2024
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`

8
doc/src/Commands_structure.rst
View File

@ -8,10 +8,10 @@ page.
A LAMMPS input script typically has 4 parts:
1. :ref:`Initialization <init>`
2. :ref:`System definition <system>`
3. :ref:`Simulation settings <settings>`
4. :ref:`Run a simulation <run>`
#. :ref:`Initialization <init>`
#. :ref:`System definition <system>`
#. :ref:`Simulation settings <settings>`
#. :ref:`Run a simulation <run>`
The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4

12
doc/src/Developer_atom.rst
View File

@ -2,7 +2,7 @@ Accessing per-atom data
-----------------------
This page discusses how per-atom data is managed in LAMMPS, how it can
be accessed, what communication patters apply, and some of the utility
be accessed, what communication patterns apply, and some of the utility
functions that exist for a variety of purposes.
@ -14,11 +14,11 @@ As described on the :doc:`parallel partitioning algorithms
simulation domain, either in a *brick* or *tiled* manner. Each MPI
process *owns* exactly one subdomain and the atoms within it. To compute
forces for tuples of atoms that are spread across sub-domain boundaries,
also a "halo" of *ghost* atoms are maintained within a the communication
also a "halo" of *ghost* atoms are maintained within the communication
cutoff distance of its subdomain.
The total number of atoms is stored in `Atom::natoms` (within any
typical class this can be referred to at `atom->natoms`. The number of
typical class this can be referred to at `atom->natoms`). The number of
*owned* (or "local" atoms) are stored in `Atom::nlocal`; the number of
*ghost* atoms is stored in `Atom::nghost`. The sum of `Atom::nlocal`
over all MPI processes should be `Atom::natoms`. This is by default
@ -27,8 +27,8 @@ LAMMPS stops with a "lost atoms" error. For convenience also the
property `Atom::nmax` is available, this is the maximum of
`Atom::nlocal + Atom::nghost` across all MPI processes.
Per-atom properties are either managed by the atom style, or individual
classes. or as custom arrays by the individual classes. If only access
Per-atom properties are either managed by the atom style, individual
classes, or as custom arrays by the individual classes. If only access
to *owned* atoms is needed, they are usually allocated to be of size
`Atom::nlocal`, otherwise of size `Atom::nmax`. Please note that not all
per-atom properties are available or updated on *ghost* atoms. For
@ -61,7 +61,7 @@ can be found via the `Atom::sametag` array. It points to the next atom
index with the same tag or -1 if there are no more atoms with the same
tag. The list will be exhaustive when starting with an index of an
*owned* atom, since the atom IDs are unique, so there can only be one
such atom. Example code to count atoms with same atom ID in subdomain:
such atom. Example code to count atoms with same atom ID in a subdomain:
.. code-block:: c++

9
doc/src/Developer_code_design.rst
View File

@ -69,7 +69,7 @@ The basic LAMMPS class hierarchy which is created by the LAMMPS class
constructor is shown in :ref:`class-topology`. When input commands
are processed, additional class instances are created, or deleted, or
replaced. Likewise, specific member functions of specific classes are
called to trigger actions such creating atoms, computing forces,
called to trigger actions such as creating atoms, computing forces,
computing properties, time-propagating the system, or writing output.
Compositing and Inheritance
@ -110,9 +110,10 @@ As mentioned above, there can be multiple instances of classes derived
from the ``Fix`` or ``Compute`` base classes. They represent a
different facet of LAMMPS' flexibility, as they provide methods which
can be called at different points within a timestep, as explained in
`Developer_flow`. This allows the input script to tailor how a specific
simulation is run, what diagnostic computations are performed, and how
the output of those computations is further processed or output.
the :doc:`How a timestep works <Developer_flow>` doc page. This allows
the input script to tailor how a specific simulation is run, what
diagnostic computations are performed, and how the output of those
computations is further processed or output.
Additional code sharing is possible by creating derived classes from the
derived classes (e.g., to implement an accelerated version of a pair

2
doc/src/Developer_flow.rst
View File

@ -128,7 +128,7 @@ reflect particles off box boundaries in the :doc:`FixWallReflect class
The ``decide()`` method in the Neighbor class determines whether
neighbor lists need to be rebuilt on the current timestep (conditions
can be changed using the :doc:`neigh_modify every/delay/check
<neigh_modify>` command. If not, coordinates of ghost atoms are
<neigh_modify>` command). If not, coordinates of ghost atoms are
acquired by each processor via the ``forward_comm()`` method of the Comm
class. If neighbor lists need to be built, several operations within
the inner if clause of the pseudocode are first invoked. The

2
doc/src/Developer_grid.rst
View File

@ -433,7 +433,7 @@ from owned to ghost cells, or ghost to owned cells, respectively, as
described above. The *caller* argument should be one of these values
-- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
depending on the style of the caller class. The *ptr* argument is the
"this" pointer to the caller class. These 2 arguments are used to
"this" pointer to the caller class. These two arguments are used to
call back to pack()/unpack() functions in the caller class, as
explained below.

33
doc/src/Developer_notes.rst
View File

@ -20,7 +20,7 @@ Available topics are:
Reading and parsing of text and text files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
It is frequently required for a class in LAMMPS to read in additional
Classes in LAMMPS frequently need to read in additional
data from a file, e.g. potential parameters from a potential file for
manybody potentials. LAMMPS provides several custom classes and
convenience functions to simplify the process. They offer the
@ -128,9 +128,8 @@ that determines the kind of neighbor list requested. The default value
used here asks for a perpetual "half" neighbor list.
Non-default values of the second argument need to be used to adjust a
neighbor list request to the specific needs of a style an additional
request flag is needed. The :doc:`tersoff <pair_tersoff>` pair style,
for example, needs a "full" neighbor list:
neighbor list request to the specific needs of a style. The :doc:`tersoff
<pair_tersoff>` pair style, for example, needs a "full" neighbor list:
.. code-block:: c++
@ -141,8 +140,8 @@ for example, needs a "full" neighbor list:
}
When a pair style supports r-RESPA time integration with different cutoff regions,
the request flag may depend on the corresponding r-RESPA settings. Here an example
from pair style lj/cut:
the request flag may depend on the corresponding r-RESPA settings. Here is an
example from pair style lj/cut:
.. code-block:: c++
@ -160,7 +159,7 @@ from pair style lj/cut:
}
Granular pair styles need neighbor lists based on particle sizes and not cutoff
and also may require to have the list of previous neighbors available ("history").
and also may need to store data across timesteps ("history").
For example with:
.. code-block:: c++
@ -169,7 +168,7 @@ For example with:
else neighbor->add_request(this, NeighConst::REQ_SIZE);
In case a class would need to make multiple neighbor list requests with different
settings each request can set an id which is then used in the corresponding
settings, each request can set an id which is then used in the corresponding
``init_list()`` function to assign it to the suitable pointer variable. This is
done for example by the :doc:`pair style meam <pair_meam>`:
@ -279,8 +278,8 @@ And here is how the code operates:
* The :doc:`thermo_style custom <thermo_style>` command defines
*ecouple* and *econserve* keywords.
* These keywords sum the energy contributions from all the
*ecouple_flag* = 1 fixes by invoking the energy_couple() method in
the Modify class, which calls the compute_scalar() method of each
*ecouple_flag* = 1 fixes by invoking the *energy_couple()* method in
the Modify class, which calls the *compute_scalar()* method of each
fix in the list.
------------------
@ -320,19 +319,19 @@ The fix must also do the following:
The ev_init() and ev_tally() methods also account for global and
peratom virial contributions. Thus you do not need to invoke the
v_init() and v_tally() methods, if the fix also calculates peratom
v_init() and v_tally() methods if the fix also calculates peratom
energies.
The fix must also specify whether (by default) to include or exclude
these contributions to the global/peratom energy/virial of the system.
For the fix to include the contributions, set either of both of these
For the fix to include the contributions, set either or both of these
variables in the constructor:
* *thermo_energy* = 1, for global and peratom energy
* *thermo_virial* = 1, for global and peratom virial
Note that these variables are zeroed in fix.cpp. Thus if you don't
set the variables, the contributions will be excluded (by default)
set the variables, the contributions will be excluded (by default).
However, the user has ultimate control over whether to include or
exclude the contributions of the fix via the :doc:`fix modify
@ -406,9 +405,11 @@ processor owns, within the global grid:
.. parsed-literal::
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in = 3d decomposition brick
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft = FFT decomposition brick
nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out = 3d decomposition brick + ghost cells
nFOO_in = 3d decomposition brick
nFOO_fft = FFT decomposition brick
nFOO_out = 3d decomposition brick + ghost cells
where ``FOO`` corresponds to ``xlo, xhi, ylo, yhi, zlo,`` or ``zhi``.
The ``in`` and ``fft`` indices are from 0 to N-1 inclusive in each
dimension, where N is the grid size.

5
doc/src/Developer_par_comm.rst
View File

@ -4,8 +4,7 @@ Communication
Following the selected partitioning scheme, all per-atom data is
distributed across the MPI processes, which allows LAMMPS to handle very
large systems provided it uses a correspondingly large number of MPI
processes. Since The per-atom data (atom IDs, positions, velocities,
types, etc.) To be able to compute the short-range interactions, MPI
processes. To be able to compute the short-range interactions, MPI
processes need not only access to the data of atoms they "own" but also
information about atoms from neighboring subdomains, in LAMMPS referred
to as "ghost" atoms. These are copies of atoms storing required
@ -37,7 +36,7 @@ be larger than half the simulation domain.
Efficient communication patterns are needed to update the "ghost" atom
data, since that needs to be done at every MD time step or minimization
step. The diagrams of the `ghost-atom-comm` figure illustrate how ghost
step. The diagrams of the :ref:`ghost-atom-comm` figure illustrate how ghost
atom communication is performed in two stages for a 2d simulation (three
in 3d) for both a regular and irregular partitioning of the simulation
box. For the regular case (left) atoms are exchanged first in the

4
doc/src/Developer_par_long.rst
View File

@ -93,7 +93,7 @@ processors, since each tile in the initial tiling overlaps with a
handful of tiles in the final tiling.
The transformations could also be done using collective communication
across all $P$ processors with a single call to ``MPI_Alltoall()``, but
across all :math:`P` processors with a single call to ``MPI_Alltoall()``, but
this is typically much slower. However, for the specialized brick and
pencil tiling illustrated in :ref:`fft-parallel` figure, collective
communication across the entire MPI communicator is not required. In
@ -138,7 +138,7 @@ grid/particle operations that LAMMPS supports:
:math:`O(P^{\frac{1}{2}})`.
- For efficiency in performing 1d FFTs, the grid transpose
operations illustrated in Figure \ref{fig:fft} also involve
operations illustrated in Figure :ref:`fft-parallel` also involve
reordering the 3d data so that a different dimension is contiguous
in memory. This reordering can be done during the packing or
unpacking of buffers for MPI communication.

2
doc/src/Developer_par_neigh.rst
View File

@ -149,7 +149,7 @@ supports:
- Dependent on the "pair" setting of the :doc:`newton <newton>` command,
the "half" neighbor lists may contain **all** pairs of atoms where
atom *j* is a ghost atom (i.e. when the newton pair setting is *off*)
atom *j* is a ghost atom (i.e. when the newton pair setting is *off*).
For the newton pair *on* setting the atom *j* is only added to the
list if its *z* coordinate is larger, or if equal the *y* coordinate
is larger, and that is equal, too, the *x* coordinate is larger. For

6
doc/src/Developer_par_openmp.rst
View File

@ -1,13 +1,13 @@
OpenMP Parallelism
^^^^^^^^^^^^^^^^^^
The styles in the INTEL, KOKKOS, and OPENMP package offer to use OpenMP
The styles in the INTEL, KOKKOS, and OPENMP packages offer to use OpenMP
thread parallelism to predominantly distribute loops over local data
and thus follow an orthogonal parallelization strategy to the
decomposition into spatial domains used by the :doc:`MPI partitioning
<Developer_par_part>`. For clarity, this section discusses only the
implementation in the OPENMP package, as it is the simplest. The INTEL
and KOKKOS package offer additional options and are more complex since
and KOKKOS packages offer additional options and are more complex since
they support more features and different hardware like co-processors
or GPUs.
@ -16,7 +16,7 @@ keep the changes to the source code small, so that it would be easier to
maintain the code and keep it in sync with the non-threaded standard
implementation. This is achieved by a) making the OPENMP version a
derived class from the regular version (e.g. ``PairLJCutOMP`` from
``PairLJCut``) and overriding only methods that are multi-threaded or
``PairLJCut``) and only overriding methods that are multi-threaded or
need to be modified to support multi-threading (similar to what was done
in the OPT package), b) keeping the structure in the modified code very
similar so that side-by-side comparisons are still useful, and c)

8
doc/src/Developer_plugins.rst
View File

@ -53,7 +53,7 @@ Members of ``lammpsplugin_t``
.. list-table::
:header-rows: 1
:widths: auto
:widths: 15 85
* - Member
- Description
@ -135,7 +135,7 @@ unique inside the entire LAMMPS executable.
Fix style example
^^^^^^^^^^^^^^^^^
If the factory function would be for a fix or compute, which take three
If the factory function is for a fix or compute, which take three
arguments (a pointer to the LAMMPS class, the number of arguments and the
list of argument strings), then the pointer type is ``lammpsplugin_factory2``
and it must be assigned to the *creator.v2* member of the plugin struct.
@ -271,7 +271,7 @@ Plugins need to be compiled with the same compilers and libraries
as the LAMMPS executable and library. Otherwise the plugin will likely
not load due to mismatches in the function signatures (LAMMPS is C++ so
scope, type, and number of arguments are encoded into the symbol names
and thus differences in them will lead to failed plugin load commands.
and thus differences in them will lead to failed plugin load commands).
Compilation of the plugin can be managed via both, CMake or traditional
GNU makefiles. Some examples that can be used as a template are in the
``examples/plugins`` folder. The CMake script code has some small
@ -283,7 +283,7 @@ in the ``examples/kim/plugin`` folder. No changes to the sources of the
KIM package themselves are needed; only the plugin interface and loader
code needs to be added. This example only supports building with CMake,
but is probably a more typical example. To compile you need to run CMake
with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
with ``-DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>``. Other
configuration setting are identical to those for compiling LAMMPS.
A second example for a plugin from a package is in the

31
doc/src/Developer_unittest.rst
View File

@ -44,7 +44,7 @@ available:
.. list-table::
:header-rows: 1
:widths: auto
:widths: 32 18 50
:align: left
* - File name:
@ -227,12 +227,12 @@ Tests for the C-style library interface
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tests for validating the LAMMPS C-style library interface are in the
``unittest/c-library`` folder. They are implemented in either way used
for utility functions and for LAMMPS commands, but use the functions
``unittest/c-library`` folder. They are implemented either to be used
for utility functions or for LAMMPS commands, but use the functions
implemented in the ``src/library.cpp`` file as much as possible. There
may be some overlap with other tests, but only in as much as is required
to test the C-style library API. The tests are distributed over
multiple test programs which tries to match the grouping of the
multiple test programs which try to match the grouping of the
functions in the source code and :ref:`in the manual <lammps_c_api>`.
This group of tests also includes tests invoking LAMMPS in parallel
@ -258,7 +258,7 @@ Tests for the Python module and package
The ``unittest/python`` folder contains primarily tests for classes and
functions in the LAMMPS python module but also for commands in the
PYTHON package. These tests are only enabled, if the necessary
PYTHON package. These tests are only enabled if the necessary
prerequisites are detected or enabled during configuration and
compilation of LAMMPS (shared library build enabled, Python interpreter
found, Python development files found).
@ -272,7 +272,7 @@ Tests for the Fortran interface
Tests for using the Fortran module are in the ``unittest/fortran``
folder. Since they are also using the GoogleTest library, they require
to also implement test wrappers in C++ that will call fortran functions
implementing test wrappers in C++ that will call fortran functions
which provide a C function interface through ISO_C_BINDINGS that will in
turn call the functions in the LAMMPS Fortran module.
@ -293,7 +293,7 @@ The ``unittest/formats`` folder contains test programs for reading and
writing files like data files, restart files, potential files or dump files.
This covers simple things like the file i/o convenience functions in the
``utils::`` namespace to complex tests of atom styles where creating and
deleting of atoms with different properties is tested in different ways
deleting atoms with different properties is tested in different ways
and through script commands or reading and writing of data or restart files.
Tests for styles computing or modifying forces
@ -411,7 +411,7 @@ With this scheme a large fraction of the code of any tested pair style
will be executed and consistent results are required for different
settings and between different accelerated pair style variants and the
base class, as well as for computing individual pairs through the
``Pair::single()`` where supported.
``Pair::single()`` method where supported.
The ``test_pair_style`` tester is used with 4 categories of test inputs:
@ -443,7 +443,7 @@ file for a style that is similar to one to be tested. The file name should
follow the naming conventions described above and after copying the file,
the first step is to replace the style names where needed. The coefficient
values do not have to be meaningful, just in a reasonable range for the
given system. It does not matter if some forces are large, for as long as
given system. It does not matter if some forces are large, as long as
they do not diverge.
The template input files define a large number of index variables at the top
@ -535,7 +535,7 @@ The are by default no unit tests for newly added features (e.g. pair, fix,
or compute styles) unless your pull request also includes tests for the
added features. If you are modifying some features, you may see failures
for existing tests, if your modifications have some unexpected side effects
or your changes render the existing text invalid. If you are adding an
or your changes render the existing test invalid. If you are adding an
accelerated version of an existing style, then only tests for INTEL,
KOKKOS (with OpenMP only), OPENMP, and OPT will be run automatically.
Tests for the GPU package are time consuming and thus are only run
@ -543,7 +543,7 @@ Tests for the GPU package are time consuming and thus are only run
to the pull request. After the test has started, it is often best to
remove the label since every PR activity will re-trigger the test (that
is a limitation of triggering a test with a label). Support for unit
tests with using KOKKOS with GPU acceleration is currently not supported.
tests when using KOKKOS with GPU acceleration is currently not supported.
When you see a failed build on GitHub, click on ``Details`` to be taken
to the corresponding LAMMPS Jenkins CI web page. Click on the "Exit"
@ -589,11 +589,10 @@ While the epsilon (relative precision) for a single, `IEEE 754 compliant
point operation is at about 2.2e-16, the achievable precision for the
tests is lower due to most numbers being sums over intermediate results
and the non-associativity of floating point math leading to larger
errors. In some cases specific properties of the tested style. As a
rule of thumb, the test epsilon can often be in the range 5.0e-14 to
1.0e-13. But for "noisy" force kernels, e.g. those a larger amount of
arithmetic operations involving `exp()`, `log()` or `sin()` functions,
and also due to the effect of compiler optimization or differences
errors. As a rule of thumb, the test epsilon can often be in the range
5.0e-14 to 1.0e-13. But for "noisy" force kernels, e.g. those a larger
amount of arithmetic operations involving `exp()`, `log()` or `sin()`
functions, and also due to the effect of compiler optimization or differences
between compilers or platforms, epsilon may need to be further relaxed,
sometimes epsilon can be relaxed to 1.0e-12. If interpolation or lookup
tables are used, epsilon may need to be set to 1.0e-10 or even higher.

41
doc/src/Developer_updating.rst
View File

@ -52,10 +52,9 @@ Rename of pack/unpack_comm() to pack/unpack_forward_comm()
.. versionchanged:: 8Aug2014
In this change set the functions to pack data into communication buffers
and to unpack data from communication buffers for :doc:`forward
communications <Developer_comm_ops>` were renamed from ``pack_comm()``
and ``unpack_comm()`` to ``pack_forward_comm()`` and
In this change set, the functions to pack/unpack data into communication buffers
for :doc:`forward communications <Developer_comm_ops>` were renamed from
``pack_comm()`` and ``unpack_comm()`` to ``pack_forward_comm()`` and
``unpack_forward_comm()``, respectively. Also the meaning of the return
value of these functions was changed: rather than returning the number
of items per atom stored in the buffer, now the total number of items
@ -109,7 +108,7 @@ Use ev_init() to initialize variables derived from eflag and vflag
There are several variables that need to be initialized based on
the values of the "eflag" and "vflag" variables and since sometimes
there are new bits added and new variables need to be set to 1 or 0.
To make this consistent, across all styles, there is now an inline
To make this consistent across all styles, there is now an inline
function ``ev_init(eflag, vflag)`` that makes those settings
consistently and calls either ``ev_setup()`` or ``ev_unset()``.
Example from a pair style:
@ -211,14 +210,14 @@ The :cpp:func:`utils::open_potential()
calls to ``force->open_potential()`` and should be used to replace
``fopen()`` for opening potential files for reading. The custom
function does three additional steps compared to ``fopen()``: 1) it will
try to parse the ``UNITS:`` and ``DATE:`` metadata will stop with an
try to parse the ``UNITS:`` and ``DATE:`` metadata and will stop with an
error on a units mismatch and will print the date info, if present, in
the log file; 2) for pair styles that support it, it will set up
possible automatic unit conversions based on the embedded unit
information and LAMMPS' current units setting; 3) it will not only try
to open a potential file at the given path, but will also search in the
folders listed in the ``LAMMPS_POTENTIALS`` environment variable. This
allows to keep potential files in a common location instead of having to
allows potential files to reside in a common location instead of having to
copy them around for simulations.
Old:
@ -246,36 +245,38 @@ to use scoped enumerators instead.
.. list-table::
:header-rows: 1
:widths: auto
:widths: 23 10 23 10 23 10
* - Symbolic Constant
- Value
- Symbolic Constant
- Value
- Symbolic Constant
- Value
* - Atom::GROW
- 0
- Atom::ATOMIC
- 0
- Atom::MAP_NONE
- 0
* - Atom::RESTART
- 1
- Atom::MOLECULAR
- 1
- Atom::MAP_ARRAY
- 1
* - Atom::BORDER
- 2
- Atom::TEMPLATE
- 2
- Atom::MAP_HASH
- 2
* - Atom::ATOMIC
* - AtomVec::PER_ATOM
- 0
- Atom::MAP_YES
- 3
* - Atom::MOLECULAR
- 1
- AtomVec::PER_ATOM
- 0
* - Atom::TEMPLATE
- 2
- AtomVec::PER_TYPE
- 1
- Atom::MAP_YES
- 3
Old:
@ -306,7 +307,7 @@ Simplify customized error messages
Aided by features of the bundled {fmt} library, error messages now
can have a variable number of arguments and the string will be interpreted
as a {fmt} style format string so that custom error messages can be
as a {fmt} style format string so that error messages can be
easily customized without having to use temporary buffers and ``sprintf()``.
Example:
@ -332,7 +333,7 @@ Use of "override" instead of "virtual"
.. versionchanged:: 17Feb2022
Since LAMMPS requires C++11 we switched to use the "override" keyword
Since LAMMPS requires C++11, we switched to use the "override" keyword
instead of "virtual" to indicate polymorphism in derived classes. This
allows the C++ compiler to better detect inconsistencies when an
override is intended or not. Please note that "override" has to be
@ -370,7 +371,7 @@ Simplified function names for forward and reverse communication
.. versionchanged:: 24Mar2022
Rather then using the function name to distinguish between the different
Rather than using the function name to distinguish between the different
forward and reverse communication functions for styles, LAMMPS now uses
the type of the "this" pointer argument.

2
doc/src/Developer_utils.rst
View File

@ -622,7 +622,7 @@ classes:
of a dense, symmetric, real matrix.
#. The "PEigenDense" class only calculates the principal eigenvalue
(ie. the largest or smallest eigenvalue), and its corresponding
(i.e. the largest or smallest eigenvalue), and its corresponding
eigenvector. However it is much more efficient than "Jacobi" when
applied to large matrices (larger than 13x13). PEigenDense also can
understand complex-valued Hermitian matrices.

19
doc/src/Developer_write_fix.rst
View File

@ -74,8 +74,7 @@ The next method we need to implement is ``setmask()``:
Here the we specify which methods of the fix should be called during
:doc:`execution of a timestep <Developer_flow>`. The constant
``END_OF_STEP`` corresponds to the ``end_of_step()`` method. The most
important available methods that are called during a timestep.
``END_OF_STEP`` corresponds to the ``end_of_step()`` method.
.. code-block:: c++
@ -127,7 +126,7 @@ there is no need to inherit from it directly.
The code above computes average velocity for all particles in the
simulation. Yet you have one unused parameter in fix call from the
script: ``group_name``. This parameter specifies the group of atoms
used in the fix. So we should compute average for all particles in the
used in the fix. So we should compute the average for all particles in the
simulation only if ``group_name == "all"``, but it can be any group.
The group membership information of an atom is contained in the *mask*
property of an atom and the bit corresponding to a given group is
@ -142,7 +141,7 @@ stored in the groupbit variable which is defined in Fix base class:
}
Class Atom encapsulates atoms positions, velocities, forces, etc. Users
can access them using particle index. Note, that particle indexes are
can access them using the particle index. Note, that particle indexes are
usually changed every few timesteps because of neighbor list rebuilds
and spatial sorting (to improve cache efficiency).
@ -154,8 +153,8 @@ this situation there are several methods which should be implemented:
- ``double memory_usage()``: return how much memory the fix uses (optional)
- ``void grow_arrays(int)``: do reallocation of the per-particle arrays in your fix
- ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
information to j-th. Used when atom sorting is performed. if delflag is set
and atom j owns a body, move the body information to atom i.
information to j-th particle position. Used when atom sorting is performed.
if delflag is set and atom j owns a body, move the body information to atom i.
- ``void set_arrays(int i)``: sets i-th particle related information to zero
Note, that if your class implements these methods, it must add calls of
@ -230,11 +229,11 @@ is just a bunch of template functions for allocating 1D and 2D
arrays. So you need to add include ``memory.h`` to have access to them.
Finally, if you need to write/read some global information used in
your fix to the restart file, you might do it by setting flag
``restart_global = 1`` in the constructor and implementing methods void
``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
your fix to the restart file, you might do it by setting the flag
``restart_global = 1`` in the constructor and implementing methods
``void write_restart(FILE *fp)`` and ``void restart(char *buf)``.
If, in addition, you want to write the per-atom property to restart
files additional settings and functions are needed:
files then these additional settings and functions are needed:
- a fix flag indicating this needs to be set ``restart_peratom = 1;``
- ``atom->add_callback()`` and ``atom->delete_callback()`` must be called

33
doc/src/Developer_write_pair.rst
View File

@ -371,9 +371,9 @@ but moving this to a separate function allows users to change global
settings like the default cutoff without having to reissue all
pair_coeff commands or re-read the ``Pair Coeffs`` sections from the
data file. In the ``settings()`` function, also the arrays for storing
parameters, to define cutoffs, track with pairs of parameters have been
explicitly set are allocated and, if needed, initialized. In this case,
the memory allocation and initialization is moved to a function
parameters, to define cutoffs, track which pairs of parameters have been
explicitly set and allocated and, if needed, initialized. In this case,
the memory allocation and initialization are moved to a function
``allocate()``.
.. code-block:: c++
@ -588,17 +588,20 @@ loop atoms are also initialized.
jnum = numneigh[i];
The inner loop (index *j*) processes the neighbor lists. The neighbor
list code encodes in the upper 2 bits whether a pair is a regular pair
of neighbor (= 0) or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3)
:doc:`"special" neighbor <special_bonds>`. The ``sbmask()`` inline
function extracts those bits and converts them into a number. This
number is used to look up the corresponding scaling factor for the
non-bonded interaction from the ``force->special_lj`` array and stores
it in the `factor_lj` variable. Due to the additional bits, the value
of *j* would be out of range when accessing data from per-atom arrays,
so we apply the NEIGHMASK constant with a bit-wise and operation to mask
them out. This step *must* be done, even if a pair style does not use
special bond scaling of forces and energies to avoid segmentation faults.
list code encodes extra information using the upper 3 bits. The 2
highest bits encode whether a pair is a regular pair of neighbor (= 0)
or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3) :doc:`"special" neighbor
<special_bonds>`. The next highest bit encodes whether the pair stores
data in a ``fix neigh/history`` instance (an undocumented internal fix
style). The ``sbmask()`` inline function extracts those bits and
converts them into a number. This number is used to look up the
corresponding scaling factor for the non-bonded interaction from the
``force->special_lj`` array and stores it in the `factor_lj` variable.
Due to the additional bits, the value of *j* would be out of range when
accessing data from per-atom arrays, so we apply the NEIGHMASK constant
with a bit-wise and operation to mask them out. This step *must* be
done, even if a pair style does not use special bond scaling of forces
and energies to avoid segmentation faults.
With the corrected *j* index, it is now possible to compute the distance
of the pair. For efficiency reasons, the square root is only taken
@ -891,7 +894,7 @@ through *multiple* :doc:`pair_coeff commands <pair_coeff>`. Pair styles
that require a single "pair_coeff \* \*" command line are not compatible
with reading their parameters from data files. For pair styles like
*born/gauss* that do support writing to data files, the potential
parameters will be read from the data file, if present and
parameters will be read from the data file, if present, and
:doc:`pair_coeff commands <pair_coeff>` may not be needed.
The member variable ``writedata`` should be set to 1 in the constructor,

3
doc/src/Errors_common.rst
View File

@ -39,7 +39,8 @@ 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://www.lammps.org/authors.html>`_.
the `developers <https://www.lammps.org/authors.html>`_ or create an new
topic on the dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by

22
doc/src/Errors_messages.rst
View File

@ -96,13 +96,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
are too far apart to make a valid angle.
*Angle atoms %d %d %d missing on proc %d at step %ld*
One or more of 3 atoms needed to compute a particular angle are
One or more of three atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
*Angle atoms missing on proc %d at step %ld*
One or more of 3 atoms needed to compute a particular angle are
One or more of three atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
@ -1932,7 +1932,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Self-explanatory.
*Compute chunk/atom fix array is accessed out-of-range*
the index for the array is out of bounds.
The index for the array is out of bounds.
*Compute chunk/atom fix does not calculate a per-atom array*
Self-explanatory.
@ -6073,9 +6073,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*New atom IDs exceed maximum allowed ID*
See the setting for tagint in the src/lmptype.h file.
*New bond exceeded bonds per atom in create_bonds*
See the read_data command for info on using the "extra/bond/per/atom"
keyword to allow for additional bonds to be formed
*New bond exceeded bonds per atom in create\_bonds*
See the read_data command for info on using the "extra/bond/per/atom"
keyword to allow for additional bonds to be formed
*New bond exceeded bonds per atom in fix bond/create*
See the read_data command for info on using the "extra/bond/per/atom"
@ -7310,12 +7310,12 @@ keyword to allow for additional bonds to be formed
atom has moved too far.
*Restrain atoms %d %d %d missing on proc %d at step %ld*
The 3 atoms in a restrain angle specified by the fix restrain
The three atoms in a restrain angle specified by the fix restrain
command are not all accessible to a processor. This probably means an
atom has moved too far.
*Restrain atoms %d %d missing on proc %d at step %ld*
The 2 atoms in a restrain bond specified by the fix restrain
The two atoms in a restrain bond specified by the fix restrain
command are not all accessible to a processor. This probably means an
atom has moved too far.
@ -7406,7 +7406,7 @@ keyword to allow for additional bonds to be formed
*Shake angles have different bond types*
All 3-atom angle-constrained SHAKE clusters specified by the fix shake
command that are the same angle type, must also have the same bond
types for the 2 bonds in the angle.
types for the two bonds in the angle.
*Shake atoms %d %d %d %d missing on proc %d at step %ld*
The 4 atoms in a single shake cluster specified by the fix shake
@ -7414,12 +7414,12 @@ keyword to allow for additional bonds to be formed
an atom has moved too far.
*Shake atoms %d %d %d missing on proc %d at step %ld*
The 3 atoms in a single shake cluster specified by the fix shake
The three atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
*Shake atoms %d %d missing on proc %d at step %ld*
The 2 atoms in a single shake cluster specified by the fix shake
The two atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.

6
doc/src/Errors_warnings.rst
View File

@ -23,7 +23,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
adjusted to match the user-specified accuracy.
*Angle atoms missing at step %ld*
One or more of 3 atoms needed to compute a particular angle are
One or more of three atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
@ -233,7 +233,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
style.
*Fix langevin gjf using random gaussians is not implemented with kokkos*
This will most likely cause errors in kinetic fluctuations.
This will most likely cause errors in kinetic fluctuations.
*Fix property/atom mol or charge w/out ghost communication*
A model typically needs these properties defined for ghost atoms.
@ -324,7 +324,7 @@ This will most likely cause errors in kinetic fluctuations.
Specifically they are further apart than half a periodic box length.
Or they are more than a box length apart in a non-periodic dimension.
This is usually due to the initial data file not having correct image
flags for the 2 atoms in a bond that straddles a periodic boundary.
flags for the two atoms in a bond that straddles a periodic boundary.
They should be different by 1 in that case. This is a warning because
inconsistent image flags will not cause problems for dynamics or most
LAMMPS simulations. However they can cause problems when such atoms

2
doc/src/Examples.rst
View File

@ -134,6 +134,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| rerun | use of rerun and read_dump commands |
+-------------+------------------------------------------------------------------+
| rheo | RHEO simulations of fluid flows and phase transitions |
+-------------+------------------------------------------------------------------+
| rigid | rigid bodies modeled as independent or coupled |
+-------------+------------------------------------------------------------------+
| shear | sideways shear applied to 2d solid, with and without a void |

6
doc/src/Fortran.rst
View File

@ -1077,7 +1077,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. list-table::
:header-rows: 1
:widths: auto
:widths: 21 20 40 19
* - Style
- Type
@ -1167,7 +1167,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. list-table::
:header-rows: 1
:widths: auto
:widths: 20 19 11 11 21 18
* - Style
- Type
@ -2327,7 +2327,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
retrieved via :f:func:`get_last_error_message`. This allows to
restart a calculation or delete and recreate the LAMMPS instance when
a C++ exception occurs. One application of using exceptions this way
is the :ref:`lammps_shell`.
is the :ref:`lammps_gui`.
:to: :cpp:func:`lammps_config_has_exceptions`
:r has_exceptions:

1
doc/src/Howto.rst
View File

@ -89,6 +89,7 @@ Packages howto
Howto_drude2
Howto_peri
Howto_manifold
Howto_rheo
Howto_spins
Tutorials howto

4
doc/src/Howto_bioFF.rst
View File

@ -43,7 +43,7 @@ have potential energy function of the form
}} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)}
The terms are computed by bond styles (relationship between 2 atoms),
The terms are computed by bond styles (relationship between two atoms),
angle styles (between 3 atoms) , dihedral/improper styles (between 4
atoms), pair styles (non-covalently bonded pair interactions) and
special bonds. The CMAP term (see :doc:`fix cmap <fix_cmap>` command for
@ -73,7 +73,7 @@ with additional switching or shifting functions that ramp the energy
and/or force smoothly to zero between an inner :math:`(a)` and outer
:math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or
*charmmfsh*\ ) in their name compute the LJ and Coulombic interactions
with an energy switching function (esw) S(r) which ramps the energy
with an energy switching function (esw) :math:`S(r)` which ramps the energy
smoothly to zero between the inner and outer cutoff. This can cause
irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which

2
doc/src/Howto_bpm.rst
View File

@ -17,6 +17,8 @@ producing fracture. The examples/bpm directory has sample input scripts
for simulations of the fragmentation of an impacted plate and the
pouring of extended, elastic bodies. See :ref:`(Clemmer) <howto-Clemmer>`
for more general information on the approach and the LAMMPS implementation.
Example movies illustrating some of these capabilities are found at
https://www.lammps.org/movies.html#bpmpackage.
----------

2
doc/src/Howto_cmake.rst
View File

@ -339,8 +339,6 @@ Some common LAMMPS specific variables
- build LAMMPS with OpenMP support (default: ``on`` if compiler supports OpenMP fully, else ``off``)
* - ``BUILD_TOOLS``
- compile some additional executables from the ``tools`` folder (default: ``off``)
* - ``BUILD_LAMMPS_SHELL``
- compile the LAMMPS shell from the ``tools/lammps-shell`` folder (default: ``off``)
* - ``BUILD_DOC``
- include building the HTML format documentation for packaging/installing (default: ``off``)
* - ``CMAKE_TUNE_FLAGS``

2
doc/src/Howto_coreshell.rst
View File

@ -178,7 +178,7 @@ the pairs. This can be done by using the *bias* keyword of the
To maintain the correct polarizability of the core/shell pairs, the
kinetic energy of the internal motion shall remain nearly constant.
Therefore the choice of spring force and mass ratio need to ensure
much faster relative motion of the 2 atoms within the core/shell pair
much faster relative motion of the two atoms within the core/shell pair
than their center-of-mass velocity. This allows the shells to
effectively react instantaneously to the electrostatic environment and
limits energy transfer to or from the core/shell oscillators.

2
doc/src/Howto_couple.rst
View File

@ -36,7 +36,7 @@ the context of your application.
steps, invoke the command, etc.
In this scenario, the other code can be called as a library, as in
1., or it could be a stand-alone code, invoked by a system() call
1., or it could be a stand-alone code, invoked by a ``system()`` call
made by the command (assuming your parallel machine allows one or
more processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS through files that the

8
doc/src/Howto_diffusion.rst
View File

@ -1,8 +1,8 @@
Calculate diffusion coefficients
================================
The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
The diffusion coefficient :math:`D` of a material can be measured in at least
2 ways using various options in LAMMPS. See the ``examples/DIFFUSE``
directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model.
@ -12,7 +12,7 @@ of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the
:doc:`fix vector <fix_vector>` command, and a line fit to the vector to
compute its slope via the :doc:`variable slope <variable>` function, and
thus extract D.
thus extract :math:`D`.
The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the :doc:`compute vacf <compute_vacf>`
@ -20,4 +20,4 @@ command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the :doc:`fix vector <fix_vector>` command,
and time integrated via the :doc:`variable trap <variable>` function,
and thus extract D.
and thus extract :math:`D`.

30
doc/src/Howto_elastic.rst
View File

@ -4,21 +4,27 @@ Calculate elastic constants
Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation.
In tensor notation, this is expressed as s_ij = C_ijkl \* e_kl, where
the repeated indices imply summation. s_ij are the elements of the
symmetric stress tensor. e_kl are the elements of the symmetric strain
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has 3\^4=81 elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
most 7\*6/2 = 21 distinct elements.
In tensor notation, this is expressed as
.. math::
s_{ij} = C_{ijkl} e_{kl}
where
the repeated indices imply summation. :math:`s_{ij}` are the elements of the
symmetric stress tensor. :math:`e_{kl}` are the elements of the symmetric strain
tensor. :math:`C_{ijkl}` are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has :math:`3^4=81` elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where :math:`C_{ij}`
is now the derivative of :math:`s_i` w.r.t. :math:`e_j`. Because :math:`s_i` is itself a
derivative w.r.t. :math:`e_i`, it follows that :math:`C_{ij}` is also symmetric, with at
most :math:`\frac{7 \times 6}{2}` = 21 distinct elements.
At zero temperature, it is easy to estimate these derivatives by
deforming the simulation box in one of the six directions using the
:doc:`change_box <change_box>` command and measuring the change in the
stress tensor. A general-purpose script that does this is given in the
examples/ELASTIC directory described on the :doc:`Examples <Examples>`
``examples/ELASTIC`` directory described on the :doc:`Examples <Examples>`
doc page.
Calculating elastic constants at finite temperature is more
@ -33,7 +39,7 @@ the :doc:`compute born/matrix <compute_born_matrix>` command,
which works for any bonded or non-bonded potential in LAMMPS.
The most expensive part of the calculation is the sampling of
the stress fluctuations. Several examples of this method are
provided in the examples/ELASTIC_T/BORN_MATRIX directory
provided in the ``examples/ELASTIC_T/BORN_MATRIX`` directory
described on the :doc:`Examples <Examples>` doc page.
A second way is to measure
@ -43,7 +49,7 @@ the systematic and statistical errors in this method, the magnitude of
the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress
tensor. An example of this method is provided in the
examples/ELASTIC_T/DEFORMATION directory
``examples/ELASTIC_T/DEFORMATION`` directory
described on the :doc:`Examples <Examples>` doc page.
Another approach is to sample the triclinic cell fluctuations

16
doc/src/Howto_kappa.rst
View File

@ -1,20 +1,22 @@
Calculate thermal conductivity
==============================
The thermal conductivity kappa of a material can be measured in at
least 4 ways using various options in LAMMPS. See the examples/KAPPA
The thermal conductivity :math:`\kappa` of a material can be measured in at
least 4 ways using various options in LAMMPS. See the ``examples/KAPPA``
directory for scripts that implement the 4 methods discussed here for
a simple Lennard-Jones fluid model. Also, see the :doc:`Howto viscosity <Howto_viscosity>` page for an analogous discussion
for viscosity.
The thermal conductivity tensor kappa is a measure of the propensity
The thermal conductivity tensor :math:`\mathbf{\kappa}` is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given
by Fourier's law
J = -kappa grad(T)
.. math::
where J is the heat flux in units of energy per area per time and
grad(T) is the spatial gradient of temperature. The thermal
J = -\kappa \cdot \text{grad}(T)
where :math:`J` is the heat flux in units of energy per area per time and
:math:`\text{grad}(T)` is the spatial gradient of temperature. The thermal
conductivity thus has units of energy per distance per time per degree
K and is often approximated as an isotropic quantity, i.e. as a
scalar.
@ -49,7 +51,7 @@ details.
The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the heat flux
to kappa. The heat flux can be calculated from the fluctuations of
to :math:`\kappa`. The heat flux can be calculated from the fluctuations of
per-atom potential and kinetic energies and per-atom stress tensor in
a steady-state equilibrated simulation. This is in contrast to the
two preceding non-equilibrium methods, where energy flows continuously

854
doc/src/Howto_lammps_gui.rst
View File

File diff suppressed because it is too large Load Diff

3
doc/src/Howto_moltemplate.rst
View File

@ -367,5 +367,4 @@ And execute the simulation with the following:
.. _OPLSAA96:
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc,
118(45), 11225-11236 (1996).
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).

10
doc/src/Howto_multiple.rst
View File

@ -44,7 +44,7 @@ For large numbers of independent simulations, you can use
:doc:`variables <variable>` and the :doc:`next <next>` and
:doc:`jump <jump>` commands to loop over the same input script
multiple times with different settings. For example, this
script, named in.polymer
script, named ``in.polymer``
.. code-block:: LAMMPS
@ -57,7 +57,7 @@ script, named in.polymer
next d
jump in.polymer
would run 8 simulations in different directories, using a data.polymer
would run 8 simulations in different directories, using a ``data.polymer``
file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
@ -83,10 +83,10 @@ partition of processors. LAMMPS can be run on multiple partitions via
the :doc:`-partition command-line switch <Run_options>`.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
scripts could be used if the ``index`` and ``loop`` variables were
replaced with *universe*\ -style variables, as described in the
:doc:`variable <variable>` command. Also, the "next t" and "next a"
commands would need to be replaced with a single "next a t" command.
:doc:`variable <variable>` command. Also, the :lammps:`next t` and :lammps:`next a`
commands would need to be replaced with a single :lammps:`next a t` command.
With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each

56
doc/src/Howto_pylammps.rst
View File

@ -6,19 +6,22 @@ PyLammps Tutorial
Overview
--------
``PyLammps`` is a Python wrapper class for LAMMPS which can be created
on its own or use an existing lammps Python object. It creates a simpler,
:py:class:`PyLammps <lammps.PyLammps>` is a Python wrapper class for
LAMMPS which can be created on its own or use an existing
:py:class:`lammps Python <lammps.lammps>` object. It creates a simpler,
more "pythonic" interface to common LAMMPS functionality, in contrast to
the ``lammps`` wrapper for the C-style LAMMPS library interface which
is written using `Python ctypes <ctypes_>`_. The ``lammps`` wrapper
is discussed on the :doc:`Python_head` doc page.
the :py:class:`lammps <lammps.lammps>` wrapper for the LAMMPS :ref:`C
language library interface API <lammps_c_api>` which is written using
`Python ctypes <ctypes_>`_. The :py:class:`lammps <lammps.lammps>`
wrapper is discussed on the :doc:`Python_head` doc page.
Unlike the flat ``ctypes`` interface, PyLammps exposes a discoverable
API. It no longer requires knowledge of the underlying C++ code
implementation. Finally, the ``IPyLammps`` wrapper builds on top of
``PyLammps`` and adds some additional features for
`IPython integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_,
e.g. for embedded visualization output from :doc:`dump style image <dump_image>`.
Unlike the flat `ctypes <ctypes_>`_ interface, PyLammps exposes a
discoverable API. It no longer requires knowledge of the underlying C++
code implementation. Finally, the :py:class:`IPyLammps
<lammps.IPyLammps>` wrapper builds on top of :py:class:`PyLammps
<lammps.PyLammps>` and adds some additional features for `IPython
integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_, e.g. for
embedded visualization output from :doc:`dump style image <dump_image>`.
.. _ctypes: https://docs.python.org/3/library/ctypes.html
.. _ipython: https://ipython.org/
@ -30,19 +33,22 @@ Comparison of lammps and PyLammps interfaces
lammps.lammps
"""""""""""""
* uses ``ctypes``
* direct memory access to native C++ data
* uses `ctypes <ctypes_>`_
* direct memory access to native C++ data with optional support for NumPy arrays
* provides functions to send and receive data to LAMMPS
* interface modeled after the LAMMPS :ref:`C language library interface API <lammps_c_api>`
* requires knowledge of how LAMMPS internally works (C pointers, etc)
* full support for running Python with MPI using `mpi4py <https://mpi4py.readthedocs.io>`_
lammps.PyLammps
"""""""""""""""
* higher-level abstraction built on top of original ctypes interface
* higher-level abstraction built on *top* of original :py:class:`ctypes based interface <lammps.lammps>`
* manipulation of Python objects
* communication with LAMMPS is hidden from API user
* shorter, more concise Python
* better IPython integration, designed for quick prototyping
* designed for serial execution
Quick Start
-----------
@ -506,14 +512,26 @@ inside of the IPython notebook.
Using PyLammps and mpi4py (Experimental)
----------------------------------------
PyLammps can be run in parallel using mpi4py. This python package can be installed using
PyLammps can be run in parallel using `mpi4py
<https://mpi4py.readthedocs.io>`_. This python package can be installed
using
.. code-block:: bash
pip install mpi4py
The following is a short example which reads in an existing LAMMPS input file and
executes it in parallel. You can find in.melt in the examples/melt folder.
.. warning::
Usually, any :py:class:`PyLammps <lammps.PyLammps>` command must be
executed by *all* MPI processes. However, evaluations and querying
the system state is only available on MPI rank 0. Using these
functions from other MPI ranks will raise an exception.
The following is a short example which reads in an existing LAMMPS input
file and executes it in parallel. You can find in.melt in the
examples/melt folder. Please take note that the
:py:meth:`PyLammps.eval() <lammps.PyLammps.eval>` is called only from
MPI rank 0.
.. code-block:: python
@ -535,10 +553,6 @@ following mpirun command:
mpirun -np 4 python melt.py
.. warning::
Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0.
Feedback and Contributing
-------------------------

18
doc/src/Howto_restart.rst
View File

@ -26,8 +26,8 @@ scripts are based on. If that script had the line
restart 50 tmp.restart
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
added to it, it would produce two binary restart files (``tmp.restart.50``
and ``tmp.restart.100``) as it ran.
This script could be used to read the first restart file and re-run the
last 50 timesteps:
@ -47,21 +47,21 @@ last 50 timesteps:
run 50
Note that the following commands do not need to be repeated because
their settings are included in the restart file: *units, atom_style,
special_bonds, pair_style, bond_style*. However, these commands do
their settings are included in the restart file: :lammps:`units`, :lammps:`atom_style`,
:lammps:`special_bonds`, :lammps:`pair_style`, :lammps:`bond_style`. However, these commands do
need to be used, since their settings are not in the restart file:
*neighbor, fix, timestep*\ .
:lammps:`neighbor`, :lammps:`fix`, :lammps:`timestep`.
If you actually use this script to perform a restarted run, you will
notice that the thermodynamic data match at step 50 (if you also put a
"thermo 50" command in the original script), but do not match at step
:lammps:`thermo 50` command in the original script), but do not match at step
100. This is because the :doc:`fix langevin <fix_langevin>` command
uses random numbers in a way that does not allow for perfect restarts.
As an alternate approach, the restart file could be converted to a data
file as follows:
.. code-block:: LAMMPS
.. code-block:: bash
lmp_g++ -r tmp.restart.50 tmp.restart.data
@ -89,8 +89,8 @@ Then, this script could be used to re-run the last 50 steps:
reset_timestep 50
run 50
Note that nearly all the settings specified in the original *in.chain*
script must be repeated, except the *pair_coeff* and *bond_coeff*
Note that nearly all the settings specified in the original ``in.chain``
script must be repeated, except the :lammps:`pair_coeff` and :lammps:`bond_coeff`
commands, since the new data file lists the force field coefficients.
Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell
LAMMPS the current timestep. This value is stored in restart files, but

112
doc/src/Howto_rheo.rst Normal file
View File

@ -0,0 +1,112 @@
Reproducing hydrodynamics and elastic objects (RHEO)
====================================================
The RHEO package is a hybrid implementation of smoothed particle
hydrodynamics (SPH) for fluid flow, which can couple to the :doc:`BPM package
<Howto_bpm>` to model solid elements. RHEO combines these methods to enable
mesh-free modeling of multi-phase material systems. Its SPH solver supports
many advanced options including reproducing kernels, particle shifting, free
surface identification, and solid surface reconstruction. To model fluid-solid
systems, the status of particles can dynamically change between a fluid and
solid state, e.g. during melting/solidification, which determines how they
interact and their physical behavior. The package is designed with modularity
in mind, so one can easily turn various features on/off, adjust physical
details of the system, or develop new capabilities. For instance, the numerics
associated with calculating gradients, reproducing kernels, etc. are separated
into distinct classes to simplify the development of new integration schemes
which can call these calculations. Additional numerical details can be found in
:ref:`(Clemmer) <howto_rheo_clemmer>`. Example movies illustrating some of these
capabilities are found at https://www.lammps.org/movies.html#rheopackage.
Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
<PKG-SPH>` package is likely better suited for your application. It has fewer advanced
features and therefore benefits from improved performance. The :ref:`MACHDYN
<PKG-MACHDYN>` package for solids may also be relevant for fluid-solid problems.
----------
At the core of the package is :doc:`fix rheo <fix_rheo>` which integrates
particle trajectories and controls many optional features (e.g. the use
of reproducing kernels). In conjunction to fix rheo, one must specify an
instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
of state and viscosity model, respectively. Optionally, one can model
a heat equation with :doc:`fix rheo/thermal <fix_rheo_thermal>`, which also
allows the user to specify equations for a particle's thermal conductivity,
specific heat, latent heat, and melting temperature. The ordering of these
fixes in an an input script matters. Fix rheo must be defined prior to all
other RHEO fixes.
Typically, RHEO requires atom style rheo. In addition to typical atom
properties like positions and forces, particles store a local density,
viscosity, pressure, and status. If thermal evolution is modeled, one must
use atom style rheo/thermal which also includes a local energy, temperature, and
conductivity. Note that the temperature is always derived from the energy.
This implies the *temperature* attribute of :doc:`the set command <set>` does not
affect particles. Instead, one should use the *sph/e* attribute.
The status variable uses bit-masking to track various properties of a particle
such as its current state of matter (fluid or solid) and its location relative
to a surface. Some of these properties (and others) can be accessed using
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status*
attribute in :doc:`the set command <set>` only allows control over the first bit
which sets the state of matter, 0 is fluid and 1 is solid.
Fluid interactions, including pressure forces, viscous forces, and heat exchange,
are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
pair rheo ignores the :doc:`special bond <special_bonds>` settings. Instead,
it determines whether to calculate forces based on the status of particles: e.g.,
hydrodynamic forces are only calculated if a fluid particle is involved.
----------
To model elastic objects, there are currently two mechanisms in RHEO, one designed
for bulk solid bodies and the other for thin shells. Both mechanisms rely on
introducing bonded forces between particles and therefore require a hybrid of atom
style bond and rheo (or rheo/thermal).
To create an elastic solid body, one has to (a) change the status of constituent
particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
pair rheo/solid considers a particles fluid/solid phase to determine whether to
apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
settings such that contact forces do not have to be calculated between two bonded
solid particles in the same elastic body.
In systems with thermal evolution, fix rheo/thermal can optionally set a
melting/solidification temperature allowing particles to dynamically swap their
state between fluid and solid when the temperature exceeds or drops below the
critical temperature, respectively. Using the *react* option, one can specify a maximum
bond length and a bond type. Then, when solidifying, particles will search their
local neighbors and automatically create bonds with any neighboring solid particles
in range. For BPM bond styles, bonds will then use the immediate position of the two
particles to calculate a reference state. When melting, particles will delete any
bonds of the specified type when reverting to a fluid state. Special bonds are updated
as bonds are created/broken.
The other option for elastic objects is an elastic shell that is nominally much
thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
on the surface of a fluid. Currently, this is implemented using
:doc:`fix rheo/oxidation <fix_rheo_oxidation>` and bond style
:doc:`rheo/shell <bond_rheo_shell>`. Essentially, fix rheo/oxidation creates candidate
bonds of a specified type between surface fluid particles within a specified distance.
a newly created rheo/shell bond will then start a timer. While the timer is counting
down, the bond will delete itself if particles move too far apart or move away from the
surface. However, if the timer reaches a user-defined threshold, then the bond will
activate and apply additional forces to the fluid particles. Bond style rheo/shell
then operates very similarly to a BPM bond style, storing a reference length and
breaking if stretched too far. Unlike the above method, this option does not remove
the underlying fluid interactions (although particle shifting is turned off) and does
not modify special bond settings of particles.
While these two options are not expected to be appropriate for every system,
either framework can be modified to create more suitable models (e.g. by changing the
criteria for creating/deleting a bond or altering force calculations).
----------
.. _howto_rheo_clemmer:
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

6
doc/src/Howto_spc.rst
View File

@ -2,7 +2,7 @@ SPC water model
===============
The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
charges and Lennard-Jones parameters assigned to each of the three atoms.
In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
*harmonic* and an angle style of *harmonic* or *charmm* should also be
@ -33,7 +33,7 @@ the partial charge assignments change:
| O charge = -0.8476
| H charge = 0.4238
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
See the :ref:`(Berendsen2) <howto-Berendsen>` reference for more details on both
the SPC and SPC/E models.
Below is the code for a LAMMPS input file and a molecule file
@ -149,4 +149,4 @@ Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wik
.. _howto-Berendsen:
**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
**(Berendsen2)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).

10
doc/src/Howto_structured_data.rst
View File

@ -341,7 +341,12 @@ data files and obtain a list of dictionaries.
.. code-block::
[{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003}, {'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798}, {'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103}, {'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545}, {'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694}, {'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}]
[{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003},
{'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798},
{'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103},
{'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545},
{'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694},
{'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}]
Line Delimited JSON (LD-JSON)
-----------------------------
@ -352,7 +357,8 @@ Each line represents one JSON object.
.. code-block:: LAMMPS
fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" title "" file output.json screen no
fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" &
title "" file output.json screen no
.. code-block:: json
:caption: output.json

6
doc/src/Howto_tip3p.rst
View File

@ -3,7 +3,7 @@ TIP3P water model
The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
<howto-tip3p>` specifies a 3-site rigid water molecule with charges and
Lennard-Jones parameters assigned to each of the 3 atoms.
Lennard-Jones parameters assigned to each of the three atoms.
A suitable pair style with cutoff Coulomb would be:
@ -32,9 +32,9 @@ optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS)
model (without fix shake) is desired, for rigid bonds/angles they are
ignored.
.. list-table::
.. list-table::
:header-rows: 1
:widths: auto
:widths: 38 22 20 20
* - Parameter
- TIP3P-CHARMM

6
doc/src/Howto_tip4p.rst
View File

@ -25,7 +25,7 @@ There are two ways to implement TIP4P water in LAMMPS:
This can be done with the following pair styles for Coulomb with a cutoff:
* :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
* :doc:`pair_style tip4p/cut <pair_coul>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
or these commands for a long-range Coulomb treatment:
@ -70,9 +70,9 @@ parameters adjusted for use with a long-range Coulombic solver
OM distance is specified in the :doc:`pair_style <pair_style>` command,
not as part of the pair coefficients.
.. list-table::
.. list-table::
:header-rows: 1
:widths: auto
:widths: 36 19 13 15 17
* - Parameter
- TIP4P (original)

4
doc/src/Howto_tip5p.rst
View File

@ -32,9 +32,9 @@ The table below lists the force field parameters (in real :doc:`units
<Mahoney>` and the TIP5P-E model :ref:`(Rick) <Rick>` for use with a
long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
.. list-table::
.. list-table::
:header-rows: 1
:widths: auto
:widths: 50 25 25
* - Parameter
- TIP5P

24
doc/src/Howto_viscosity.rst
View File

@ -1,22 +1,24 @@
Calculate viscosity
===================
The shear viscosity eta of a fluid can be measured in at least 6 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
The shear viscosity :math:`\eta` of a fluid can be measured in at least 6 ways
using various options in LAMMPS. See the ``examples/VISCOSITY`` directory
for scripts that implement the 5 methods discussed here for a simple
Lennard-Jones fluid model and 1 method for SPC/E water model.
Also, see the :doc:`page on calculating thermal conductivity <Howto_kappa>`
for an analogous discussion for thermal conductivity.
Eta is a measure of the propensity of a fluid to transmit momentum in
:math:`\eta` is a measure of the propensity of a fluid to transmit momentum in
a direction perpendicular to the direction of velocity or momentum
flow. Alternatively it is the resistance the fluid has to being
sheared. It is given by
J = -eta grad(Vstream)
.. math::
where J is the momentum flux in units of momentum per area per time.
and grad(Vstream) is the spatial gradient of the velocity of the fluid
J = -\eta \cdot \text{grad}(V_{\text{stream}})
where :math:`J` is the momentum flux in units of momentum per area per time.
and :math:`\text{grad}(V_{\text{stream}})` is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time.
@ -38,11 +40,11 @@ velocity to prevent the fluid from heating up.
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the :doc:`fix ave/chunk <fix_ave_chunk>`
command, which determines grad(Vstream) in the equation above.
E.g. the derivative in the y-direction of the Vx component of fluid
motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of
command, which determines :math:`\text{grad}(V_{\text{stream}})` in the equation above.
E.g. the derivative in the y-direction of the :math:`V_x` component of fluid
motion or :math:`\text{grad}(V_{\text{stream}}) = \frac{\text{d} V_x}{\text{d} y}`. The :math:`P_{xy}` off-diagonal component of
the pressure or stress tensor, as calculated by the :doc:`compute pressure <compute_pressure>` command, can also be monitored, which
is the J term in the equation above. See the :doc:`Howto nemd <Howto_nemd>` page for details on NEMD simulations.
is the :math:`J` term in the equation above. See the :doc:`Howto nemd <Howto_nemd>` page for details on NEMD simulations.
The third method is to perform a reverse non-equilibrium MD simulation
using the :doc:`fix viscosity <fix_viscosity>` command which implements
@ -55,7 +57,7 @@ See the :doc:`fix viscosity <fix_viscosity>` command for details.
The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the
stress/pressure tensor to eta. This can be done in a fully
stress/pressure tensor to :math:`\eta`. This can be done in a fully
equilibrated simulation which is in contrast to the two preceding
non-equilibrium methods, where momentum flows continuously through the
simulation box.

10
doc/src/Howto_viz.rst
View File

@ -6,7 +6,7 @@ analyzed in a variety of ways.
LAMMPS snapshots are created by the :doc:`dump <dump>` command, which
can create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized by
text file (see :lammps:`dump atom` or :lammps:`dump custom`) which can be visualized by
`several visualization tools <https://www.lammps.org/viz.html>`_ for MD
simulation trajectories. `OVITO <https://www.ovito.org>`_ and `VMD
<https://www.ks.uiuc.edu/Research/vmd>`_ seem to be the most popular
@ -14,7 +14,13 @@ choices among them.
The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>`
styles can output internally rendered images or convert them to a movie
during the MD run.
during the MD run. It is also possible to create visualizations from
LAMMPS inputs or restart file with the :doc:`LAMMPS-GUI
<Howto_lammps_gui>`, which uses the :doc:`dump image <dump_image>`
command internally. The ``Snapshot Image Viewer`` can be used to
adjust the visualization of the system interactively and then export
the corresponding LAMMPS commands to the clipboard to be inserted
into input files.
Programs included with LAMMPS as auxiliary tools can convert
between LAMMPS format files and other formats. See the :doc:`Tools

58
doc/src/Install.rst
View File

@ -35,35 +35,35 @@ you **must** build LAMMPS from the source code.
These are the files and subdirectories in the LAMMPS distribution:
+------------+---------------------------------------------+
| README | Short description of the LAMMPS package |
+------------+---------------------------------------------+
| LICENSE | GNU General Public License (GPL) |
+------------+---------------------------------------------+
| SECURITY.md| Security policy for the LAMMPS package |
+------------+---------------------------------------------+
| bench | benchmark inputs |
+------------+---------------------------------------------+
| cmake | CMake build files |
+------------+---------------------------------------------+
| doc | documentation and tools to build the manual |
+------------+---------------------------------------------+
| examples | example input files |
+------------+---------------------------------------------+
| fortran | Fortran module for LAMMPS library interface |
+------------+---------------------------------------------+
| lib | additional provided or external libraries |
+------------+---------------------------------------------+
| potentials | selected interatomic potential files |
+------------+---------------------------------------------+
| python | Python module for LAMMPS library interface |
+------------+---------------------------------------------+
| src | LAMMPS source files |
+------------+---------------------------------------------+
| tools | pre- and post-processing tools |
+------------+---------------------------------------------+
| unittest | source code and inputs for testing LAMMPS |
+------------+---------------------------------------------+
+-----------------+---------------------------------------------+
| ``README`` | Short description of the LAMMPS package |
+-----------------+---------------------------------------------+
| ``LICENSE`` | GNU General Public License (GPL) |
+-----------------+---------------------------------------------+
| ``SECURITY.md`` | Security policy for the LAMMPS package |
+-----------------+---------------------------------------------+
| ``bench`` | benchmark inputs |
+-----------------+---------------------------------------------+
| ``cmake`` | CMake build files |
+-----------------+---------------------------------------------+
| ``doc`` | documentation and tools to build the manual |
+-----------------+---------------------------------------------+
| ``examples`` | example input files |
+-----------------+---------------------------------------------+
| ``fortran`` | Fortran module for LAMMPS library interface |
+-----------------+---------------------------------------------+
| ``lib`` | additional provided or external libraries |
+-----------------+---------------------------------------------+
| ``potentials`` | selected interatomic potential files |
+-----------------+---------------------------------------------+
| ``python`` | Python module for LAMMPS library interface |
+-----------------+---------------------------------------------+
| ``src`` | LAMMPS source files |
+-----------------+---------------------------------------------+
| ``tools`` | pre- and post-processing tools |
+-----------------+---------------------------------------------+
| ``unittest`` | source code and inputs for testing LAMMPS |
+-----------------+---------------------------------------------+
You will have all of these if you downloaded the LAMMPS source code.
You will have only some of them if you downloaded executables, as

4
doc/src/Install_git.rst
View File

@ -60,7 +60,7 @@ between them at any time using "git checkout <branch name>".)
files (mostly by accident). If you do not need access to the entire
commit history (most people don't), you can speed up the "cloning"
process and reduce local disk space requirements by using the
*--depth* git command line flag. That will create a "shallow clone"
``--depth`` git command line flag. That will create a "shallow clone"
of the repository, which contains only a subset of the git history.
Using a depth of 1000 is usually sufficient to include the head
commits of the *develop*, the *release*, and the *maintenance*
@ -122,7 +122,7 @@ changed. How to do this depends on the build system you are using.
.. code-block:: bash
cmake . --build
cmake --build .
CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files

10
doc/src/Install_linux.rst
View File

@ -35,11 +35,11 @@ packages listed below), they do not depend on any installed software and
thus should run on *any* 64-bit x86 machine with *any* Linux version.
These executable include most of the available packages and multi-thread
parallelization (via INTEL, KOKKOS, or OPENMP package). They are **not**
compatible with MPI. Several of the LAMMPS tools executables (e.g. ``msi2lmp``)
and the ``lammps-shell`` program are included as well. Because of the
static linkage, there is no ``liblammps.so`` library file and thus also the
LAMMPS python module, which depends on it, is not included.
parallelization (via INTEL, KOKKOS, or OPENMP package). They are
**not** compatible with MPI. Several of the LAMMPS tools executables
(e.g. ``msi2lmp``) are included as well. Because of the static linkage,
there is no ``liblammps.so`` library file and thus also the LAMMPS
python module, which depends on it, is not included.
The compressed tar archives available for download have names following
the pattern ``lammps-linux-x86_64-<version>.tar.gz`` and will all unpack

2
doc/src/Install_tarball.rst
View File

@ -31,7 +31,7 @@ command:
tar -xzvf lammps*.tar.gz
This will create a LAMMPS directory with the version date in its name,
e.g. lammps-28Mar23.
e.g. ``lammps-28Mar23``.
----------

2
doc/src/Install_windows.rst
View File

@ -34,7 +34,7 @@ When you download the installer package, you run it on your Windows
machine. It will then prompt you with a dialog, where you can choose
the installation directory, unpack and copy several executables,
potential files, documentation PDFs, selected example files, etc. It
will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS)
will then update a few system settings (e.g. ``PATH``, ``LAMMPS_POTENTIALS``)
and add an entry into the Start Menu (with references to the
documentation, LAMMPS homepage and more). From that menu, there is
also a link to an uninstaller that removes the files and undoes the

85
doc/src/Intro_authors.rst
View File

@ -1,19 +1,88 @@
Authors of LAMMPS
-----------------
The primary LAMMPS developers are at Sandia National Labs and Temple
University:
The current core LAMMPS developers are listed here (grouped by seniority
and sorted alphabetically by last name). You can email an individual
developer with code related questions for their area of expertise, or
send an email to all of them at this address: "developers at
lammps.org". General questions about LAMMPS should be posted in the
`LAMMPS forum on MatSci <https://matsci.org/lammps/>`_.
* `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
* Aidan Thompson, athomps at sandia.gov
* Stan Moore, stamoor at sandia.gov
* `Axel Kohlmeyer <https://sites.google.com/site/akohlmey/>`_, akohlmey at gmail.com
* Richard Berger, richard.berger at outlook.com
.. raw:: latex
\small
.. list-table::
:widths: 17 15 25 43
:header-rows: 1
* - Name
- Affiliation
- Email
- Areas of expertise
* - `Axel Kohlmeyer <ak_>`_
- Temple U
- akohlmey at gmail.com
- OpenMP, library interfaces, LAMMPS-GUI, GitHub, MatSci forum, code maintenance, testing, releases
* - `Steve Plimpton <sjp_>`_
- SNL (retired)
- sjplimp at gmail.com
- MD kernels, parallel algorithms & scalability, code structure and design
* - `Aidan Thompson <at_>`_
- SNL
- athomps at sandia.gov
- manybody potentials, machine learned potentials, materials science, statistical mechanics
* -
-
-
-
* - `Richard Berger <rb_>`_
- LANL
- richard.berger at outlook.com
- Python, HPC, DevOps
* - `Germain Clavier <gc_>`_
- U Caen
- germain.clavier at unicaen.fr
- organic molecules, polymers, mechanical properties, surfaces, integrators, coarse-graining
* - Joel Clemmer
- SNL
- jtclemm at sandia.gov
- granular systems fluid/solid mechanics
* - `Jacob R. Gissinger <jg_>`_
- Stevens Institute of Technology
- jgissing at stevens.edu
- reactive molecular dynamics, macro-molecular systems, type labels
* - James Goff
- SNL
- jmgoff at sandia.gov
- machine learned potentials, QEq solvers, Python
* - Megan McCarthy
- SNL
- megmcca at sandia.gov
- alloys, micro-structure, machine learned potentials
* - Stan Moore
- SNL
- stamoor at sandia.gov
- Kokkos, KSpace solvers, ReaxFF
* - `Trung Nguyen <tn_>`_
- U Chicago
- ndactrung at gmail.com
- soft matter, GPU package
.. _rb: https://rbberger.github.io/
.. _gc: https://enthalpiste.fr/
.. _jg: https://www.nanocipher.org/
.. _ak: https://sites.google.com/site/akohlmey/
.. _tn: https://sites.google.com/site/ndtrung8/
.. _at: https://www2.sandia.gov/~athomps/
.. _sjp: https://sjplimp.github.io
.. _lws: https://www.lammps.org
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
.. raw:: latex
\normalsize
Past developers include Paul Crozier and Mark Stevens, both at SNL,
and Ray Shan, now at Materials Design.
----------

39
doc/src/Intro_nonfeatures.rst
View File

@ -25,9 +25,13 @@ Here are suggestions on how to perform these tasks:
wraps the library interface is provided. Thus, GUI interfaces can be
written in Python or C/C++ that run LAMMPS and visualize or plot its
output. Examples of this are provided in the python directory and
described on the :doc:`Python <Python_head>` doc page. As of version
2 August 2023 :ref:`a GUI tool <lammps_gui>` is included in LAMMPS.
Also, there are several external wrappers or GUI front ends.
described on the :doc:`Python <Python_head>` doc page.
Since version 2 August 2023 :ref:`a LAMMPS-GUI tool <lammps_gui>` is
included in LAMMPS. Also, there are several external wrappers or GUI
front ends that are mentioned on the `Pre-/post-processing tools page
<https://www.lammps.org/prepost.html>`_ of the LAMMPS homepage.
* **Builder:** Several pre-processing tools are packaged with LAMMPS.
Some of them convert input files in formats produced by other MD codes
such as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of
@ -35,12 +39,13 @@ Here are suggestions on how to perform these tasks:
such as linear bead-spring polymer chains. The moltemplate program is
a true molecular builder that will generate complex molecular models.
See the :doc:`Tools <Tools>` page for details on tools packaged with
LAMMPS. The `Pre-/post-processing page
LAMMPS. The `Pre-/post-processing tools page
<https://www.lammps.org/prepost.html>`_ of the LAMMPS homepage
describes a variety of third party tools for this task. Furthermore,
some internal LAMMPS commands allow reconstructing, or selectively adding
topology information, as well as provide the option to insert molecule
templates instead of atoms for building bulk molecular systems.
* **Force-field assignment:** The conversion tools described in the previous
bullet for CHARMM, AMBER, and Insight will also assign force field
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
@ -49,6 +54,7 @@ Here are suggestions on how to perform these tasks:
`InterMol <https://github.com/shirtsgroup/InterMol>`_ are particularly
powerful and flexible in converting force field and topology data
between various MD simulation programs.
* **Simulation analysis:** If you want to perform analysis on-the-fly as
your simulation runs, see the :doc:`compute <compute>` and :doc:`fix
<fix>` doc pages, which list commands that can be used in a LAMMPS
@ -66,19 +72,38 @@ Here are suggestions on how to perform these tasks:
extract and massage data in dump files to make it easier to import
into other programs. See the :doc:`Tools <Tools>` page for details on
these various options.
The `Pre-/post-processing page <https://www.lammps.org/prepost.html>`_
on the LAMMPS homepage lists some external packages for analysis of MD
simulation data, including data produced by LAMMPS.
* **Visualization:** LAMMPS can produce NETPBM, JPG, or PNG format
snapshot images on-the-fly via its :doc:`dump image <dump_image>`
command and pass them to an external program, `FFmpeg <https://ffmpeg.org/>`_,
to generate movies from them. For high-quality, interactive visualization,
there are many excellent and free tools available. See the `Visualization Tools
command and pass them to an external program, `FFmpeg
<https://ffmpeg.org/>`_, to generate movies from them. The
:ref:`LAMMPS-GUI tool <lammps_gui>` has an *Snapshot Image Viewer*
which uses :doc:`dump image <dump_image>` and allows to modify the
visualization settings interactively. It also has a *Slide Show*
feature where images created by :doc:`dump image <dump_image>` are
collected during a simulation and can be animated interactively or
exported to a movie with FFmpeg.
For high-quality, interactive visualization, there are many excellent
and free tools available. See 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
:doc:`Python <Python_head>` page for examples of plotting LAMMPS
output. Scripts provided with the *python* tool in the ``tools``
directory will extract and process data in log and dump files to make
it easier to analyze and plot. See the :doc:`Tools <Tools>` doc page
for more discussion of the various tools.
The :ref:`LAMMPS-GUI tool <lammps_gui>` has an *Chart Viewer* where
:doc:`thermodynamic data <thermo_style>` computed by LAMMPS is
collected during the simulation and plotted immediately.
* **Pizza.py:** Our group has also written a separate toolkit called
`Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS

18
doc/src/Intro_opensource.rst
View File

@ -34,18 +34,20 @@ choose, including for commercial purposes.
(2) If you **distribute** a modified version of LAMMPS, it must remain
open-source, meaning you are required to distribute **all** of it under
the terms of the GPL. You should clearly annotate such a modified code
as a derivative version of LAMMPS.
the terms of the GPLv2. You should **clearly** annotate such a modified
code as a derivative version of LAMMPS. This is best done by changing
the name (example: LIGGGHTS is such a modified and extended version of
LAMMPS).
(3) If you release any code that includes or uses LAMMPS source code,
then it must also be open-sourced, meaning you distribute it under
the terms of the GPL. You may write code that interfaces LAMMPS to
a differently licensed library. In that case the code that provides
the interface must be licensed GPL, but not necessarily that library
then it must also be open-sourced, meaning you distribute it under the
terms of the GPLv2. You may write code that interfaces LAMMPS to a
differently licensed library. In that case the code that provides the
interface must be licensed GPLv2, but not necessarily that library
unless you are distributing binaries that require the library to run.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
(4) If you give LAMMPS files to someone else, the GPLv2 LICENSE file and
source file headers (including the copyright and GPLv2 notices) should
remain part of the code.

BIN
doc/src/JPG/lammps-gui-chart.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 105 KiB

After

Width:  |  Height:  |  Size: 106 KiB

BIN
doc/src/JPG/lammps-gui-dark.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 78 KiB

BIN
doc/src/JPG/lammps-gui-find.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 113 KiB

BIN
doc/src/JPG/lammps-gui-funnel.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 325 KiB

BIN
doc/src/JPG/lammps-gui-image.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 123 KiB

After

Width:  |  Height:  |  Size: 86 KiB

BIN
doc/src/JPG/lammps-gui-log.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 95 KiB

After

Width:  |  Height:  |  Size: 103 KiB

BIN
doc/src/JPG/lammps-gui-main.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 90 KiB

After

Width:  |  Height:  |  Size: 77 KiB

BIN
doc/src/JPG/lammps-gui-popup-help.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 130 KiB

After

Width:  |  Height:  |  Size: 103 KiB

BIN
doc/src/JPG/lammps-gui-popup-view.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 96 KiB

BIN
doc/src/JPG/lammps-gui-prefs-accel.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 37 KiB

After

Width:  |  Height:  |  Size: 32 KiB

BIN
doc/src/JPG/lammps-gui-prefs-editor.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 44 KiB

After

Width:  |  Height:  |  Size: 39 KiB

BIN
doc/src/JPG/lammps-gui-prefs-general.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 81 KiB

After

Width:  |  Height:  |  Size: 59 KiB

Some files were not shown because too many files have changed in this diff Show More