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Merge branch 'master' of github.com:Pakketeretet2/lammps

Browse Source
This commit is contained in:
Stefan Paquay
2018-10-28 16:09:25 -04:00
parent 6618ca2270 dd9166f896
commit 681be091c8
529 changed files with 37134 additions and 3262 deletions
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68
.github/CODEOWNERS vendored
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@ -17,6 +17,7 @@ src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MESSAGE/* @sjplimp
src/SPIN/* @julient31
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
@ -29,19 +30,86 @@ src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
src/USER-SCAFACOS/* @rhalver
src/USER-TALLY/* @akohlmey
src/USER-UEF/* @danicholson
src/USER-VTK/* @rbberger
# individual files in packages
src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/USER-MISC/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
src/USER-MISC/compute_stress_mop*.* @RomainVermorel
# core LAMMPS classes
src/lammps.* @sjplimp
src/pointers.h @sjplimp
src/atom.* @sjplimp
src/atom_vec.* @sjplimp
src/angle.* @sjplimp
src/bond.* @sjplimp
src/comm*.* @sjplimp
src/compute.* @sjplimp
src/dihedral.* @sjplimp
src/domain.* @sjplimp
src/dump*.* @sjplimp
src/error.* @sjplimp
src/finish.* @sjplimp
src/fix.* @sjplimp
src/force.* @sjplimp
src/group.* @sjplimp
src/improper.* @sjplimp
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/library.* @sjplimp
src/main.cpp @sjplimp
src/memory.* @sjplimp
src/modify.* @sjplimp
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/output.* @sjplimp
src/pair.* @sjplimp
src/rcb.* @sjplimp
src/random_*.* @sjplimp
src/region*.* @sjplimp
src/rcb.* @sjplimp
src/read*.* @sjplimp
src/rerun.* @sjplimp
src/run.* @sjplimp
src/respa.* @sjplimp
src/set.* @sjplimp
src/special.* @sjplimp
src/suffix.h @sjplimp
src/thermo.* @sjplimp
src/universe.* @sjplimp
src/update.* @sjplimp
src/variable.* @sjplimp
src/verlet.* @sjplimp
src/velocity.* @sjplimp
src/write_data.* @sjplimp
src/write_restart.* @sjplimp
# overrides for specific files
src/dump_movie.* @akohlmey
src/exceptions.h @rbberger
src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
# tools
tools/msi2lmp/* @akohlmey

58
cmake/CMakeLists.txt
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@ -13,7 +13,7 @@ get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUT
# To avoid conflicts with the conventional Makefile build system, we build everything here
file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
@ -69,6 +69,8 @@ get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
include(PreventInSourceBuilds)
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
#release comes with -O3 by default
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
@ -164,12 +166,13 @@ set(LAMMPS_DEPS)
set(LAMMPS_API_DEFINES)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS
USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
@ -348,7 +351,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
set(LAPACK_LIBRARIES linalg)
else()
@ -550,8 +553,9 @@ if(PKG_USER-SMD)
set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
list(APPEND LAMMPS_DEPS Eigen3_build)
else()
find_package(Eigen3)
if(NOT Eigen3_FOUND)
find_package(Eigen3 NO_MODULE)
mark_as_advanced(Eigen3_DIR)
if(NOT EIGEN3_FOUND)
message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
endif()
endif()
@ -603,8 +607,9 @@ endif()
if(PKG_MESSAGE)
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
if(BUILD_SHARED_LIBS)
add_library(cslib SHARED ${cslib_SOURCES})
@ -720,8 +725,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
foreach(PKG ${DEFAULT_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -739,8 +744,8 @@ endforeach()
foreach(PKG ${ACCEL_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -754,8 +759,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
@ -830,6 +837,7 @@ if(PKG_USER-OMP)
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
@ -838,7 +846,7 @@ if(PKG_USER-OMP)
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h")
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
@ -1038,7 +1046,7 @@ if(PKG_GPU)
set(GPU_PREC_SETTING "SINGLE_SINGLE")
endif()
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
@ -1051,15 +1059,15 @@ if(PKG_GPU)
set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(CUDPP_OPT)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
@ -1108,7 +1116,7 @@ if(PKG_GPU)
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
foreach(GPU_KERNEL ${GPU_LIB_CU})
@ -1235,7 +1243,7 @@ if(BUILD_DOC)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt)
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})

23
cmake/Modules/PreventInSourceBuilds.cmake Normal file
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@ -0,0 +1,23 @@
# - Prevent in-source builds.
# https://stackoverflow.com/questions/1208681/with-cmake-how-would-you-disable-in-source-builds/
function(prevent_in_source_builds)
# make sure the user doesn't play dirty with symlinks
get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH)
get_filename_component(srcdir2 "${CMAKE_SOURCE_DIR}/.." REALPATH)
get_filename_component(srcdir3 "${CMAKE_SOURCE_DIR}/../src" REALPATH)
get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
# disallow in-source builds
if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}")
message(FATAL_ERROR "\
CMake must not to be run in the source directory. \
Rather create a dedicated build directory and run CMake there. \
To clean up after this aborted in-place compilation:
rm -r CMakeCache.txt CMakeFiles
")
endif()
endfunction()
prevent_in_source_builds()

10
cmake/Modules/StyleHeaderUtils.cmake
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@ -85,19 +85,23 @@ function(RegisterNPairStyle path)
AddStyleHeader(${path} NPAIR)
endfunction(RegisterNPairStyle)
function(RegisterFixStyle path)
AddStyleHeader(${path} FIX)
endfunction(RegisterFixStyle)
function(RegisterStyles search_path)
FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force
FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid
FindStyleHeaders(${search_path} BODY_CLASS body_ BODY ) # body ) # atom_vec_body
FindStyleHeaders(${search_path} BOND_CLASS bond_ BOND ) # bond ) # force
FindStyleHeaders(${search_path} COMMAND_CLASS "" COMMAND ) # command ) # input
FindStyleHeaders(${search_path} COMMAND_CLASS "[^.]" COMMAND ) # command ) # input
FindStyleHeaders(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify
FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
FindStyleHeaders(${search_path} INTEGRATE_CLASS "" INTEGRATE ) # integrate ) # update
FindStyleHeaders(${search_path} KSPACE_CLASS "" KSPACE ) # kspace ) # force
FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
FindStyleHeaders(${search_path} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update
FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor
FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor

21
doc/Makefile
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@ -38,7 +38,7 @@ OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML doc pages in html dir"
@echo " pdf create Manual.pdf and Developer.pdf in this dir"
@echo " pdf create Developer.pdf and Manual.pdf in this dir"
@echo " old create old-style HTML doc pages in old dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@ -95,9 +95,10 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
@echo "Spell check finished."
epub: $(OBJECTS)
@mkdir -p epub
@mkdir -p epub/JPG
@rm -f LAMMPS.epub
@cp src/JPG/lammps-logo.png epub/
@cp src/JPG/*.* epub/JPG
@(\
. $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\
@ -116,17 +117,17 @@ mobi: epub
pdf: utils/txt2html/txt2html.exe
@(\
set -e; \
cd src; \
../utils/txt2html/txt2html.exe -b *.txt; \
htmldoc --batch lammps.book; \
for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
do grep -q $$s lammps.book || \
echo doc file $$s missing in src/lammps.book; done; \
rm *.html; \
cd Developer; \
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
cd ..; \
../utils/txt2html/txt2html.exe -b *.txt; \
htmldoc --batch lammps.book; \
for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
do grep -q ^$$s lammps.book || \
echo WARNING: doc file $$s missing in src/lammps.book; done; \
rm *.html; \
)
old: utils/txt2html/txt2html.exe

4
doc/src/Build_basics.txt
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@ -292,6 +292,10 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
you can browse them locally on your system. Type "make" from the
lammps/doc dir to see other options.
NOTE: You can also download a tarball of the documention for the
current LAMMPS version (HTML and PDF files), from the website
"download page"_http://lammps.sandia.gov/download.html.
:line
Install LAMMPS after a build :h4,link(install)

8
doc/src/Build_extras.txt
View File

@ -563,9 +563,9 @@ file.
VORONOI package :h4,link(voronoi)
To build with this package, you must download and build the "Voro++
library"_voro_home.
library"_voro-home.
:link(voro_home,http://math.lbl.gov/voro++)
:link(voro-home,http://math.lbl.gov/voro++)
[CMake build]:
@ -932,9 +932,9 @@ successfully build on your system.
USER-SCAFACOS package :h4,link(user-scafacos)
To build with this package, you must download and build the "ScaFaCoS
Coulomb solver library"_scafacos_home
Coulomb solver library"_scafacos-home
:link(scafacos_home,http://www.scafacos.de)
:link(scafacos-home,http://www.scafacos.de)
[CMake build]:

4
doc/src/Build_package.txt
View File

@ -42,7 +42,7 @@ packages:
"KOKKOS"_Build_extras.html#kokkos,
"LATTE"_Build_extras.html#latte,
"MEAM"_Build_extras.html#meam,
"MESSAGE"_#Build_extras.html#message,
"MESSAGE"_Build_extras.html#message,
"MSCG"_Build_extras.html#mscg,
"OPT"_Build_extras.html#opt,
"POEMS"_Build_extras.html#poems,
@ -59,7 +59,7 @@ packages:
"USER-OMP"_Build_extras.html#user-omp,
"USER-QMMM"_Build_extras.html#user-qmmm,
"USER-QUIP"_Build_extras.html#user-quip,
"USER-SCAFACOS"_#Build_extras.html#user-scafacos,
"USER-SCAFACOS"_Build_extras.html#user-scafacos,
"USER-SMD"_Build_extras.html#user-smd,
"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)

13
doc/src/Commands_bond.txt
View File

@ -34,7 +34,7 @@ OPT.
"fene (iko)"_bond_fene.html,
"fene/expand (o)"_bond_fene_expand.html,
"gromos (o)"_bond_gromos.html,
"harmonic (ko)"_bond_harmonic.html,
"harmonic (iko)"_bond_harmonic.html,
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
"morse (o)"_bond_morse.html,
@ -57,9 +57,11 @@ OPT.
"zero"_angle_zero.html,
"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
"charmm (ko)"_angle_charmm.html,
"charmm (iko)"_angle_charmm.html,
"class2 (ko)"_angle_class2.html,
"class2/p6"_angle_class2.html,
"cosine (o)"_angle_cosine.html,
"cosine/buck6d"_angle_cosine_buck6d.html,
"cosine/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html,
"cosine/shift (o)"_angle_cosine_shift.html,
@ -70,7 +72,7 @@ OPT.
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"quartic (o)"_angle_quartic.html,
"sdk"_angle_sdk.html,
"sdk (o)"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
:line
@ -97,7 +99,7 @@ OPT.
"nharmonic (o)"_dihedral_nharmonic.html,
"opls (iko)"_dihedral_opls.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
"spherical"_dihedral_spherical.html,
"table (o)"_dihedral_table.html,
"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
@ -112,7 +114,7 @@ OPT.
"none"_improper_none.html,
"zero"_improper_zero.html,
"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
"class2 (ko)"_improper_class2.html,
"cossq (o)"_improper_cossq.html,
@ -120,5 +122,6 @@ OPT.
"distance"_improper_distance.html,
"fourier (o)"_improper_fourier.html,
"harmonic (iko)"_improper_harmonic.html,
"inversion/harmonic"_improper_inversion_harmonic.html,
"ring (o)"_improper_ring.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

10
doc/src/Commands_compute.txt
View File

@ -25,6 +25,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"ackland/atom"_compute_ackland_atom.html,
"adf"_compute_adf.html,
"aggregate/atom"_compute_cluster_atom.html,
"angle"_compute_angle.html,
"angle/local"_compute_angle_local.html,
@ -35,6 +36,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"chunk/atom"_compute_chunk_atom.html,
"chunk/spread/atom"_compute_chunk_spread_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"cnp/atom"_compute_cnp_atom.html,
@ -91,12 +93,15 @@ KOKKOS, o = USER-OMP, t = OPT.
"pe/tally"_compute_tally.html,
"plasticity/atom"_compute_plasticity_atom.html,
"pressure"_compute_pressure.html,
"pressure/cylinder"_compute_pressure_cylinder.html,
"pressure/uef"_compute_pressure_uef.html,
"property/atom"_compute_property_atom.html,
"property/chunk"_compute_property_chunk.html,
"property/local"_compute_property_local.html,
"ptm/atom"_compute_ptm_atom.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/chunk"_compute_reduce_chunk.html,
"reduce/region"_compute_reduce.html,
"rigid/local"_compute_rigid_local.html,
"saed"_compute_saed.html,
@ -115,7 +120,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
@ -126,6 +131,8 @@ KOKKOS, o = USER-OMP, t = OPT.
"snav/atom"_compute_sna_atom.html,
"spin"_compute_spin.html,
"stress/atom"_compute_stress_atom.html,
"stress/mop"_compute_stress_mop.html,
"stress/mop/profile"_compute_stress_mop.html,
"stress/tally"_compute_tally.html,
"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
"temp (k)"_compute_temp.html,
@ -133,6 +140,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"temp/body"_compute_temp_body.html,
"temp/chunk"_compute_temp_chunk.html,
"temp/com"_compute_temp_com.html,
"temp/cs"_compute_temp_cs.html,
"temp/deform"_compute_temp_deform.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/drude"_compute_temp_drude.html,

36
doc/src/Commands_fix.txt
View File

@ -40,11 +40,13 @@ OPT.
"ave/time"_fix_ave_time.html,
"aveforce"_fix_aveforce.html,
"balance"_fix_balance.html,
"bocs"_fix_bocs.html,
"bond/break"_fix_bond_break.html,
"bond/create"_fix_bond_create.html,
"bond/react"_fix_bond_react.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"client/md"_fix_client_md.html,
"cmap"_fix_cmap.html,
"colvars"_fix_colvars.html,
"controller"_fix_controller.html,
@ -54,7 +56,7 @@ OPT.
"drag"_fix_drag.html,
"drude"_fix_drude.html,
"drude/transform/direct"_fix_drude_transform.html,
"drude/transform/reverse"_fix_drude_transform.html,
"drude/transform/inverse"_fix_drude_transform.html,
"dt/reset"_fix_dt_reset.html,
"edpd/source"_fix_dpd_source.html,
"efield"_fix_efield.html,
@ -65,13 +67,14 @@ OPT.
"eos/table/rx (k)"_fix_eos_table_rx.html,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"ffl"_fix_ffl.html,
"filter/corotate"_fix_filter_corotate.html,
"flow/gauss"_fix_flow_gauss.html,
"freeze"_fix_freeze.html,
"freeze (k)"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gld"_fix_gld.html,
"gle"_fix_gle.html,
"gravity (o)"_fix_gravity.html,
"gravity (ko)"_fix_gravity.html,
"grem"_fix_grem.html,
"halt"_fix_halt.html,
"heat"_fix_heat.html,
@ -104,17 +107,18 @@ OPT.
"nph/asphere (o)"_fix_nph_asphere.html,
"nph/body"_fix_nph_body.html,
"nph/eff"_fix_nh_eff.html,
"nph/sphere (o)"_fix_nph_sphere.html,
"nph/sphere (ko)"_fix_nph_sphere.html,
"nphug (o)"_fix_nphug.html,
"npt (kio)"_fix_nh.html,
"npt (iko)"_fix_nh.html,
"npt/asphere (o)"_fix_npt_asphere.html,
"npt/body"_fix_npt_body.html,
"npt/eff"_fix_nh_eff.html,
"npt/sphere (o)"_fix_npt_sphere.html,
"npt/uef"_fix_nh_uef.html,
"nve (kio)"_fix_nve.html,
"nve (iko)"_fix_nve.html,
"nve/asphere (i)"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
"nve/awpmd"_fix_nve_awpmd.html,
"nve/body"_fix_nve_body.html,
"nve/dot"_fix_nve_dot.html,
"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
@ -169,26 +173,26 @@ OPT.
"rhok"_fix_rhok.html,
"rigid (o)"_fix_rigid.html,
"rigid/nph (o)"_fix_rigid.html,
"rigid/nph/small"_fix_rigid.html,
"rigid/npt (o)"_fix_rigid.html,
"rigid/npt/small"_fix_rigid.html,
"rigid/nve (o)"_fix_rigid.html,
"rigid/nve/small"_fix_rigid.html,
"rigid/nvt (o)"_fix_rigid.html,
"rigid/nvt/small"_fix_rigid.html,
"rigid/small (o)"_fix_rigid.html,
"rigid/small/nph"_fix_rigid.html,
"rigid/small/npt"_fix_rigid.html,
"rigid/small/nve"_fix_rigid.html,
"rigid/small/nvt"_fix_rigid.html,
"rx (k)"_fix_rx.html,
"saed/vtk"_fix_saed_vtk.html,
"setforce (k)"_fix_setforce.html,
"shake"_fix_shake.html,
"shardlow (k)"_fix_shardlow.html,
"smd"_fix_smd.html,
"smd/adjust/dt"_fix_smd_adjust_dt.html,
"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
"smd/adjust_dt"_fix_smd_adjust_dt.html,
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
"smd/setvel"_fix_smd_setvel.html,
"smd/wall/surface"_fix_smd_wall_surface.html,
"smd/wall_surface"_fix_smd_wall_surface.html,
"spring"_fix_spring.html,
"spring/chunk"_fix_spring_chunk.html,
"spring/rg"_fix_spring_rg.html,
@ -216,7 +220,7 @@ OPT.
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/ees"_fix_wall_ees.html,
"wall/gran"_fix_wall_gran.html,
"wall/gran (o)"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,

61
doc/src/Commands_pair.txt
View File

@ -26,13 +26,13 @@ OPT.
"none"_pair_none.html,
"zero"_pair_zero.html,
"hybrid"_pair_hybrid.html,
"hybrid (k)"_pair_hybrid.html,
"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
"adp (o)"_pair_adp.html,
"agni (o)"_pair_agni.html,
"airebo (oi)"_pair_airebo.html,
"airebo/morse (oi)"_pair_airebo.html,
"airebo (io)"_pair_airebo.html,
"airebo/morse (io)"_pair_airebo.html,
"atm"_pair_atm.html,
"awpmd/cut"_pair_awpmd.html,
"beck (go)"_pair_beck.html,
@ -42,21 +42,23 @@ OPT.
"bop"_pair_bop.html,
"born (go)"_pair_born.html,
"born/coul/dsf"_pair_born.html,
"born/coul/dsf/cs"_pair_born.html,
"born/coul/dsf/cs"_pair_cs.html,
"born/coul/long (go)"_pair_born.html,
"born/coul/long/cs"_pair_born.html,
"born/coul/long/cs (g)"_pair_cs.html,
"born/coul/msm (o)"_pair_born.html,
"born/coul/wolf (go)"_pair_born.html,
"born/coul/wolf/cs"_pair_born.html,
"born/coul/wolf/cs (g)"_pair_cs.html,
"brownian (o)"_pair_brownian.html,
"brownian/poly (o)"_pair_brownian.html,
"buck (giko)"_pair_buck.html,
"buck/coul/cut (giko)"_pair_buck.html,
"buck/coul/long (giko)"_pair_buck.html,
"buck/coul/long/cs"_pair_buck.html,
"buck/coul/long/cs"_pair_cs.html,
"buck/coul/msm (o)"_pair_buck.html,
"buck/long/coul/long (o)"_pair_buck_long.html,
"buck/mdf"_pair_mdf.html,
"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
"colloid (go)"_pair_colloid.html,
"comb (o)"_pair_comb.html,
"comb3"_pair_comb.html,
@ -66,13 +68,13 @@ OPT.
"coul/diel (o)"_pair_coul_diel.html,
"coul/dsf (gko)"_pair_coul.html,
"coul/long (gko)"_pair_coul.html,
"coul/long/cs"_pair_coul.html,
"coul/long/cs (g)"_pair_cs.html,
"coul/long/soft (o)"_pair_lj_soft.html,
"coul/msm"_pair_coul.html,
"coul/msm (o)"_pair_coul.html,
"coul/shield"_pair_coul_shield.html,
"coul/streitz"_pair_coul.html,
"coul/wolf (ko)"_pair_coul.html,
"coul/wolf/cs"_pair_coul.html,
"coul/wolf/cs"_pair_cs.html,
"dpd (gio)"_pair_dpd.html,
"dpd/fdt"_pair_dpd_fdt.html,
"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
@ -81,6 +83,7 @@ OPT.
"eam (gikot)"_pair_eam.html,
"eam/alloy (gikot)"_pair_eam.html,
"eam/cd (o)"_pair_eam.html,
"eam/cd/old (o)"_pair_eam.html,
"eam/fs (gikot)"_pair_eam.html,
"edip (o)"_pair_edip.html,
"edip/multi"_pair_edip.html,
@ -90,11 +93,11 @@ OPT.
"exp6/rx (k)"_pair_exp6_rx.html,
"extep"_pair_extep.html,
"gauss (go)"_pair_gauss.html,
"gauss/cut"_pair_gauss.html,
"gauss/cut (o)"_pair_gauss.html,
"gayberne (gio)"_pair_gayberne.html,
"gran/hertz/history (o)"_pair_gran.html,
"gran/hooke (o)"_pair_gran.html,
"gran/hooke/history (o)"_pair_gran.html,
"gran/hooke/history (ko)"_pair_gran.html,
"gw"_pair_gw.html,
"gw/zbl"_pair_gw.html,
"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
@ -109,9 +112,9 @@ OPT.
"list"_pair_list.html,
"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
"lj/charmm/coul/long (giko)"_pair_charmm.html,
"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
"lj/charmm/coul/msm"_pair_charmm.html,
"lj/charmm/coul/long (gikot)"_pair_charmm.html,
"lj/charmm/coul/long/soft (o)"_pair_lj_soft.html,
"lj/charmm/coul/msm (o)"_pair_charmm.html,
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
"lj/charmmfsw/coul/long"_pair_charmm.html,
"lj/class2 (gko)"_pair_class2.html,
@ -124,12 +127,12 @@ OPT.
"lj/cut/coul/debye (gko)"_pair_lj.html,
"lj/cut/coul/dsf (gko)"_pair_lj.html,
"lj/cut/coul/long (gikot)"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_cs.html,
"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
"lj/cut/coul/msm (go)"_pair_lj.html,
"lj/cut/coul/wolf (o)"_pair_lj.html,
"lj/cut/dipole/cut (go)"_pair_dipole.html,
"lj/cut/dipole/long"_pair_dipole.html,
"lj/cut/dipole/long (g)"_pair_dipole.html,
"lj/cut/dipole/sf (go)"_pair_dipole.html,
"lj/cut/soft (o)"_pair_lj_soft.html,
"lj/cut/thole/long (o)"_pair_thole.html,
@ -137,15 +140,17 @@ OPT.
"lj/cut/tip4p/long (ot)"_pair_lj.html,
"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
"lj/expand (gko)"_pair_lj_expand.html,
"lj/expand/coul/long (g)"_pair_lj_expand.html,
"lj/gromacs (gko)"_pair_gromacs.html,
"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
"lj/long/coul/long (io)"_pair_lj_long.html,
"lj/long/coul/long (iot)"_pair_lj_long.html,
"lj/long/dipole/long"_pair_dipole.html,
"lj/long/tip4p/long"_pair_lj_long.html,
"lj/long/tip4p/long (o)"_pair_lj_long.html,
"lj/mdf"_pair_mdf.html,
"lj/sdk (gko)"_pair_sdk.html,
"lj/sdk/coul/long (go)"_pair_sdk.html,
"lj/sdk/coul/msm (o)"_pair_sdk.html,
"lj/sf/dipole/sf (go)"_pair_dipole.html,
"lj/smooth (o)"_pair_lj_smooth.html,
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
"lj96/cut (go)"_pair_lj96.html,
@ -160,14 +165,14 @@ OPT.
"meam/spline (o)"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"mgpt"_pair_mgpt.html,
"mie/cut (o)"_pair_mie.html,
"mie/cut (g)"_pair_mie.html,
"momb"_pair_momb.html,
"morse (gkot)"_pair_morse.html,
"morse/smooth/linear"_pair_morse.html,
"morse/smooth/linear (o)"_pair_morse.html,
"morse/soft"_pair_morse.html,
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
"nb3b/harmonic"_pair_nb3b_harmonic.html,
"nm/cut (o)"_pair_nm.html,
"nm/cut/coul/cut (o)"_pair_nm.html,
"nm/cut/coul/long (o)"_pair_nm.html,
@ -179,7 +184,9 @@ OPT.
"oxdna2/coaxstk"_pair_oxdna2.html,
"oxdna2/dh"_pair_oxdna2.html,
"oxdna2/excv"_pair_oxdna2.html,
"oxdna2/hbond"_pair_oxdna2.html,
"oxdna2/stk"_pair_oxdna2.html,
"oxdna2/xstk"_pair_oxdna2.html,
"peri/eps"_pair_peri.html,
"peri/lps (o)"_pair_peri.html,
"peri/pmb (o)"_pair_peri.html,
@ -189,11 +196,11 @@ OPT.
"quip"_pair_quip.html,
"reax"_pair_reax.html,
"reax/c (ko)"_pair_reaxc.html,
"rebo (oi)"_pair_airebo.html,
"rebo (io)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
"smd/hertz"_pair_smd_hertz.html,
"smd/tlsph"_pair_smd_tlsph.html,
"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
"smd/tri_surface"_pair_smd_triangulated_surface.html,
"smd/ulsph"_pair_smd_ulsph.html,
"smtbq"_pair_smtbq.html,
"snap (k)"_pair_snap.html,
@ -225,8 +232,8 @@ OPT.
"tip4p/long/soft (o)"_pair_lj_soft.html,
"tri/lj"_pair_tri_lj.html,
"ufm (got)"_pair_ufm.html,
"vashishta (ko)"_pair_vashishta.html,
"vashishta (gko)"_pair_vashishta.html,
"vashishta/table (o)"_pair_vashishta.html,
"yukawa (gok)"_pair_yukawa.html,
"yukawa (gko)"_pair_yukawa.html,
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)

36
doc/src/Developer/developer.tex
View File

@ -22,10 +22,10 @@ users.
LAMMPS source files are in two directories of the distribution
tarball. The src directory has the majority of them, all of which are
C++ files (*.cpp and *.h). Many of these files are in the src
directory itself. There are also dozens of "packages", which can be
directory itself. There are also dozens of ``packages'', which can be
included or excluded when LAMMPS is built. See the
doc/Section\_build.html section of the manual for more information
about packages, or type "make" from within the src directory, which
about packages, or type ``make'' from within the src directory, which
lists package-related commands, such as ``make package-status''. The
source files for each package are in an all-uppercase sub-directory of
src, like src/MOLECULE or src/USER-CUDA. If the package is currently
@ -38,17 +38,17 @@ The lib directory also contains source code for external libraries,
used by a few of the packages. Each sub-directory, like meam or gpu,
contains the source files, some of which are in different languages
such as Fortran. The files are compiled into libraries from within
each sub-directory, e.g. performing a "make" in the lib/meam directory
each sub-directory, e.g. performing a ``make'' in the lib/meam directory
creates a libmeam.a file. These libraries are linked to during a
LAMMPS build, if the corresponding package is installed.
LAMMPS C++ source files almost always come in pairs, such as run.cpp
and run.h. The pair of files defines a C++ class, the Run class in
this case, which contains the code invoked by the "run" command in a
this case, which contains the code invoked by the ``run'' command in a
LAMMPS input script. As this example illustrates, source file and
class names often have a one-to-one correspondence with a command used
in a LAMMPS input script. Some source files and classes do not have a
corresponding input script command, e.g. force.cpp and the Force
corresponding input script command, e.g. ``force.cpp'' and the Force
class. They are discussed in the next section.
\pagebreak
@ -57,12 +57,12 @@ class. They are discussed in the next section.
Though LAMMPS has a lot of source files and classes, its class
hierarchy is quite simple, as outlined in Fig \ref{fig:classes}. Each
boxed name refers to a class and has a pair of associated source files
in lammps/src, e.g. memory.cpp and memory.h. More details on the
in lammps/src, e.g. ``memory.cpp'' and ``memory.h''. More details on the
class and its methods and data structures can be found by examining
its *.h file.
LAMMPS (lammps.cpp/h) is the top-level class for the entire code. It
holds an "instance" of LAMMPS and can be instantiated one or more
holds an ``instance'' of LAMMPS and can be instantiated one or more
times by a calling code. For example, the file src/main.cpp simply
instantiates one instance of LAMMPS and passes it the input script.
@ -81,7 +81,7 @@ enabled by a bit of cleverness in the Pointers class (see
src/pointers.h) which every class inherits from.
There are a handful of virtual parent classes in LAMMPS that define
what LAMMPS calls "styles". They are shaded red in Fig
what LAMMPS calls ``styles''. They are shaded red in Fig
\ref{fig:classes}. Each of these are parents of a number of child
classes that implement the interface defined by the parent class. For
example, the fix style has around 100 child classes. They are the
@ -89,17 +89,17 @@ possible fixes that can be specified by the fix command in an input
script, e.g. fix nve, fix shake, fix ave/time, etc. The corresponding
classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime,
etc. The source files for these classes are easy to identify in the
src directory, since they begin with the word "fix", e,g,
src directory, since they begin with the word ``fix'', e,g,
fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc.
The one exception is child class files for the "command" style. These
The one exception is child class files for the ``command'' style. These
implement specific commands in the input script that can be invoked
before/after/between runs or which launch a simulation. Examples are
the create\_box, minimize, run, and velocity commands which encode the
CreateBox, Minimize, Run, and Velocity classes. The corresponding
files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp.
The list of command style files can be found by typing "grep
COMMAND\_CLASS *.h" from within the src directory, since that word in
The list of command style files can be found by typing ``grep
COMMAND\_CLASS *.h'' from within the src directory, since that word in
the header file identifies the class as an input script command.
Similar words can be grepped to list files for the other LAMMPS
styles. E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS,
@ -471,13 +471,13 @@ FixStyle(your/fix/name,FixMine)
\end{verbatim}
\end{center}
Where "your/fix/name" is a name of your fix in the script and FixMine
Where ``your/fix/name'' is a name of your fix in the script and FixMine
is the name of the class. This code allows LAMMPS to find your fix
when it parses input script. In addition, your fix header must be
included in the file "style\_fix.h". In case if you use LAMMPS make,
included in the file ``style\_fix.h''. In case if you use LAMMPS make,
this file is generated automatically - all files starting with prefix
fix\_ are included, so call your header the same way. Otherwise, don't
forget to add your include into "style\_fix.h".
forget to add your include into ``style\_fix.h''.
Let's write a simple fix which will print average velocity at the end
of each timestep. First of all, implement a constructor:
@ -567,11 +567,11 @@ void FixPrintVel::end_of_step()
\end{center}
In the code above, we use MathExtra routines defined in
"math\_extra.h". There are bunch of math functions to work with
``math\_extra.h''. There are bunch of math functions to work with
arrays of doubles as with math vectors.
In this code we use an instance of Atom class. This object is stored
in the Pointers class (see "pointers.h"). This object contains all
in the Pointers class (see ``pointers.h''). This object contains all
global information about the simulation system. Data from Pointers
class available to all classes inherited from it using protected
inheritance. Hence when you write you own class, which is going to use
@ -689,7 +689,7 @@ int FixSavePos::unpack_exchange(int nlocal, double *buf)
Now, a little bit about memory allocation. We used Memory class which
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.
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

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@ -0,0 +1,21 @@
\documentclass[12pt,article]{article}
\usepackage{indentfirst}
\usepackage{amsmath}
\newcommand{\set}[1]{\ensuremath{\mathbf{#1}}}
\newcommand{\mean}[1]{\ensuremath{\overline{#1}}}
\newcommand{\norm}[1]{\ensuremath{\left|\left|{#1}\right|\right|}}
\begin{document}
\begin{equation*}
\text{RMSD}(\set{u}, \set{v}) = \min_{s, \set{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
\norm{
s[\vec{u_i} - \mean{\set{u}}]
-
\set{Q} \vec{v_i}
}^2}
\end{equation*}
\end{document}

62
doc/src/Errors_messages.txt
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@ -1092,11 +1092,6 @@ correct. :dd
The specified file cannot be opened. Check that the path and name are
correct. :dd
{Cannot open fix ave/spatial file %s} :dt
The specified file cannot be opened. Check that the path and name are
correct. :dd
{Cannot open fix ave/time file %s} :dt
The specified file cannot be opened. Check that the path and name are
@ -1677,10 +1672,6 @@ provided by an atom map. An atom map does not exist (by default) for
non-molecular problems. Using the atom_modify map command will force
an atom map to be created. :dd
{Cannot use fix ave/spatial z for 2 dimensional model} :dt
Self-explanatory. :dd
{Cannot use fix bond/break with non-molecular systems} :dt
Only systems with bonds that can be changed can be used. Atom_style
@ -2425,10 +2416,6 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Compute ID for fix ave/spatial does not exist} :dt
Self-explanatory. :dd
{Compute ID for fix ave/time does not exist} :dt
Self-explanatory. :dd
@ -4074,10 +4061,6 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Fix ID for fix ave/spatial does not exist} :dt
Self-explanatory. :dd
{Fix ID for fix ave/time does not exist} :dt
Self-explanatory. :dd
@ -4379,51 +4362,6 @@ same style. :dd
Self-explanatory. :dd
{Fix ave/spatial compute does not calculate a per-atom array} :dt
Self-explanatory. :dd
{Fix ave/spatial compute does not calculate a per-atom vector} :dt
A compute used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/spatial compute does not calculate per-atom values} :dt
A compute used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/spatial compute vector is accessed out-of-range} :dt
The index for the vector is out of bounds. :dd
{Fix ave/spatial fix does not calculate a per-atom array} :dt
Self-explanatory. :dd
{Fix ave/spatial fix does not calculate a per-atom vector} :dt
A fix used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/spatial fix does not calculate per-atom values} :dt
A fix used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/spatial fix vector is accessed out-of-range} :dt
The index for the vector is out of bounds. :dd
{Fix ave/spatial for triclinic boxes requires units reduced} :dt
Self-explanatory. :dd
{Fix ave/spatial settings invalid with changing box size} :dt
If the box size changes, only the units reduced option can be
used. :dd
{Fix ave/spatial variable is not atom-style variable} :dt
A variable used by fix ave/spatial must generate per-atom values. :dd
{Fix ave/time cannot set output array intensive/extensive from these inputs} :dt
One of more of the vector inputs has individual elements which are

18
doc/src/Errors_warnings.txt
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@ -291,24 +291,6 @@ This may cause accuracy problems. :dd
This may cause accuracy problems. :dd
{Fix thermal/conductivity comes before fix ave/spatial} :dt
The order of these 2 fixes in your input script is such that fix
thermal/conductivity comes first. If you are using fix ave/spatial to
measure the temperature profile induced by fix viscosity, then this
may cause a glitch in the profile since you are averaging immediately
after swaps have occurred. Flipping the order of the 2 fixes
typically helps. :dd
{Fix viscosity comes before fix ave/spatial} :dt
The order of these 2 fixes in your input script is such that
fix viscosity comes first. If you are using fix ave/spatial
to measure the velocity profile induced by fix viscosity, then
this may cause a glitch in the profile since you are averaging
immediately after swaps have occurred. Flipping the order
of the 2 fixes typically helps. :dd
{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt
This is current restriction with Kokkos. :dd

45
doc/src/Howto_chunk.txt
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@ -22,7 +22,7 @@ commands, to calculate various properties of a system:
"fix ave/chunk"_fix_ave_chunk.html
any of the "compute */chunk"_compute.html commands :ul
Here, each of the 3 kinds of chunk-related commands is briefly
Here, each of the 4 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
@ -83,8 +83,9 @@ chunk.
Compute */chunk commands: :h4
Currently the following computes operate on chunks of atoms to produce
per-chunk values.
The following computes operate on chunks of atoms to produce per-chunk
values. Any compute whose style name ends in "/chunk" is in this
category:
"compute com/chunk"_compute_com_chunk.html
"compute gyration/chunk"_compute_gyration_chunk.html
@ -111,8 +112,8 @@ of a center of mass, which requires summing mass*position over the
atoms and then dividing by summed mass.
All of these computes produce a global vector or global array as
output, wih one or more values per chunk. They can be used
in various ways:
output, wih one or more values per chunk. The output can be used in
various ways:
As input to the "fix ave/time"_fix_ave_time.html command, which can
write the values to a file and optionally time average them. :ulb,l
@ -122,9 +123,27 @@ histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates. :l
As input to special functions of "equal-style
variables"_variable.html, like sum() and max(). E.g. to find the
largest cluster or fastest diffusing molecule. :l
:ule
variables"_variable.html, like sum() and max() and ave(). E.g. to
find the largest cluster or fastest diffusing molecule or average
radius-of-gyration of a set of molecules (chunks). :l,ule
Other chunk commands: :h4
"compute chunk/spread/atom"_compute_chunk_spread_atom.html
"compute reduce/chunk"_compute_reduce_chunk.html :ul
The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
spreads per-chunk values to each atom in the chunk, producing per-atom
values as its output. This can be useful for outputting per-chunk
values to a per-atom "dump file"_dump.html. Or for using an atom's
associated chunk value in an "atom-style variable"_variable.html.
The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
peratom value across the atoms in each chunk to produce a value per
chunk. When used with the "compute
chunk/spread/atom"_compute_chunk_spread_atom.html command it can
create peratom values that induce a new set of chunks with a second
"compute chunk/atom"_compute_chunk_atom.html command.
Example calculations with chunks :h4
@ -164,3 +183,13 @@ compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
(6) An example of using a per-chunk value to apply per-atom forces to
compress individual polymer chains (molecules) in a mixture, is
explained on the "compute
chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
(7) An example of using one set of per-chunk values for molecule
chunks, to create a 2nd set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the "compute
chunk/reduce"_compute_reduce_chunk.html command doc page.

6
doc/src/Howto_client_server.txt
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@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
Using LAMMPS in client/server mode
Using LAMMPS in client/server mode :h3
Client/server coupling of two codes is where one code is the "client"
and sends request messages to a "server" code. The server responds to
@ -61,7 +61,7 @@ client or server.
"message"_message.html
"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
"server md"_server_md.html = LAMMPS is a server for computing MD forces
"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy
"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul
The server doc files give details of the message protocols
for data that is exchanged bewteen the client and server.
@ -119,7 +119,7 @@ For message exchange in {mpi/one} mode:
Launch both codes in a single mpirun command:
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server :pre
The two -np values determine how many procs the client and the server
run on.

11
doc/src/Howto_nemd.txt
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@ -24,6 +24,11 @@ by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/chunk"_fix_ave_chunk.html command.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
@ -46,3 +51,9 @@ An alternative method for calculating viscosities is provided via the
NEMD simulations can also be used to measure transport properties of a fluid
through a pore or channel. Simulations of steady-state flow can be performed
using the "fix flow/gauss"_fix_flow_gauss.html command.
:line
:link(Daivis-nemd)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

11
doc/src/Howto_thermostat.txt
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@ -43,6 +43,11 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of "fix
langevin"_fix_langevin.html.
@ -87,3 +92,9 @@ specify them explicitly via the "thermo_style
custom"_thermo_style.html command. Or you can use the
"thermo_modify"_thermo_modify.html command to re-define what
temperature compute is used for default thermodynamic output.
:line
:link(Daivis-thermostat)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

11
doc/src/Howto_viscosity.txt
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@ -37,6 +37,11 @@ used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
command, which determines grad(Vstream) in the equation above.
@ -131,3 +136,9 @@ mean-square-displacement formulation for self-diffusivity. The
time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.
:line
:link(Daivis-viscosity)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

109
doc/src/Install_linux.txt
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@ -9,39 +9,16 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Download an executable for Linux :h3
Binaries are available for many different versions of Linux:
Binaries are available for different versions of Linux:
"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm
"Pre-built Ubuntu Linux executables"_#ubuntu
"Pre-built Fedora Linux executables"_#fedora
"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
"Pre-built OpenSuse Linux executables"_#opensuse
"Pre-built Gentoo Linux executable"_#gentoo :all(b)
:line
Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE :h4,link(rpm)
Pre-built LAMMPS executables for various Linux distributions
can be downloaded as binary RPM files from this site:
"http://rpm.lammps.org"_http://rpm.lammps.org
There are multiple package variants supporting serial, parallel and
Python wrapper versions. The LAMMPS binaries contain all optional
packages included in the source distribution except: GPU, KIM, REAX,
and USER-INTEL.
Installation instructions for the various versions are here:
"http://rpm.lammps.org/install.html"_http://rpm.lammps.org/install.html
The instructions show how to enable the repository in the respective
system's package management system. Installing and updating are then
straightforward and automatic.
Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
up this RPM capability.
:line
Pre-built Ubuntu Linux executables :h4,link(ubuntu)
A pre-built LAMMPS executable suitable for running on the latest
@ -60,10 +37,10 @@ To install LAMMPS do the following once:
sudo apt-get install lammps-daily :pre
This downloads an executable named "lammps-daily" to your box, which
This downloads an executable named "lmp_daily" to your box, which
can then be used in the usual way to run input scripts:
lammps-daily < in.lj :pre
lmp_daily -in in.lj :pre
To update LAMMPS to the most current version, do the following:
@ -99,6 +76,80 @@ Ubuntu package capability.
:line
Pre-built Fedora Linux executables :h4,link(fedora)
Pre-built LAMMPS packages for stable releases are available
in the Fedora Linux distribution as of version 28. The packages
can be installed via the dnf package manager. There are 3 basic
varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
lammps-openmpi = OpenMPI MPI library) and for each support for
linking to the C library interface (lammps-devel, lammps-mpich-devel,
lammps-openmpi-devel), the header for compiling programs using
the C library interface (lammps-headers), and the LAMMPS python
module for Python 3. All packages can be installed at the same
time and the name of the LAMMPS executable is {lmp} in all 3 cases.
By default, {lmp} will refer to the serial executable, unless
one of the MPI environment modules is loaded
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
Then the corresponding parallel LAMMPS executable is used.
The same mechanism applies when loading the LAMMPS python module.
To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
dnf install lammps-openmpi
module load mpi/openmpi-x86_64
mpirun -np 2 lmp -in in.lj :pre
The "dnf install" command is needed only once. In case of a new LAMMPS
stable release, "dnf update" will automatically update to the newer
version as soon at the RPM files are built and uploaded to the download
mirrors. The "module load" command is needed once per (shell) session
or shell terminal instance, unless it is automatically loaded from the
shell profile.
Please use "lmp -help" to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
:line
Pre-built EPEL Linux executable :h4,link(epel)
Pre-built LAMMPS packages for stable releases are available
in the "Extra Packages for Enterprise Linux (EPEL) repository"_https://fedoraproject.org/wiki/EPEL
for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
and compatible Linux distributions. Names of packages, executable,
and content are the same as described above for Fedora Linux.
But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
in Fedora 28.
Please use "lmp -help" to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
:line
Pre-built OpenSuse Linux executable :h4,link(opensuse)
A pre-built LAMMPS package for stable releases is available
in OpenSuse as of Leap 15.0. You can install the package with:
zypper install lammps :pre
This includes support for OpenMPI. The name of the LAMMPS executable
is {lmp}. Thus to run an input in parallel on 2 CPUs you would do:
mpirun -np 2 lmp -in in.lj :pre
Please use "lmp -help" to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
:line
Pre-built Gentoo Linux executable :h4,link(gentoo)
LAMMPS is part of Gentoo's main package tree and can be installed by

3
doc/src/Install_mac.txt
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@ -49,7 +49,8 @@ Lennard-Jones benchmark file:
% brew test lammps -v :pre
If you have problems with the installation you can post issues to
"this link"_https://github.com/Homebrew/homebrew-science/issues.
"this link"_homebrew.
Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
up the Homebrew capability.
:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)

6
doc/src/Install_tarball.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
Download source as a tarball :h3
Download source and documentation as a tarball :h3
You can download a current LAMMPS tarball from the "download page"_download
of the "LAMMPS website"_lws.
@ -22,6 +22,10 @@ few times per year, and undergo more testing before release. Patch
releases occur a couple times per month. The new contents in all
releases are listed on the "bug and feature page"_bug of the website.
Both tarballs include LAMMPS documentation (HTML and PDF files)
corresponding to that version. The download page also has an option
to download the current-version LAMMPS documentation by itself.
Older versions of LAMMPS can also be downloaded from "this
page"_older.

4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="31 Aug 2018 version">
<META NAME="docnumber" CONTENT="24 Oct 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
31 Aug 2018 version :c,h2
24 Oct 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html

45
doc/src/Packages_details.txt
View File

@ -46,6 +46,7 @@ as contained in the file name.
"MANYBODY"_#PKG-MANYBODY,
"MC"_#PKG-MC,
"MEAM"_#PKG-MEAM,
"MESSAGE"_#PKG-MESSAGE,
"MISC"_#PKG-MISC,
"MOLECULE"_#PKG-MOLECULE,
"MPIIO"_#PKG-MPIIO,
@ -88,11 +89,12 @@ as contained in the file name.
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
"USER-PHONON"_#PKG-USER-PHONON,
"USER-PTM"_#PKG-USER-PTM,
"USER-QMMM"_#PKG-USER-QMMM,
"USER-QTB"_#PKG-USER-QTB,
"USER-QUIP"_#PKG-USER-QUIP,
"USER-REAXC"_#PKG-USER-REAXC,
"USER-SCAFACOS"_#USER-SCAFACOS,
"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
"USER-SMD"_#PKG-USER-SMD,
"USER-SMTBQ"_#PKG-USER-SMTBQ,
"USER-SPH"_#PKG-USER-SPH,
@ -460,10 +462,10 @@ dynamics can be run with LAMMPS using density-functional tight-binding
quantum forces calculated by LATTE.
More information on LATTE can be found at this web site:
"https://github.com/lanl/LATTE"_latte_home. A brief technical
"https://github.com/lanl/LATTE"_latte-home. A brief technical
description is given with the "fix latte"_fix_latte.html command.
:link(latte_home,https://github.com/lanl/LATTE)
:link(latte-home,https://github.com/lanl/LATTE)
[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE
itself is developed at Los Alamos National Laboratory by Marc
@ -666,9 +668,9 @@ MSCG package :link(PKG-mscg),h4
A "fix mscg"_fix_mscg.html command which can parameterize a
Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
library"_mscg_home.
library"_mscg-home.
:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
:link(mscg-home,https://github.com/uchicago-voth/MSCG-release)
To use this package you must have the MS-CG library available on your
system.
@ -1006,11 +1008,11 @@ VORONOI package :link(PKG-VORONOI),h4
[Contents:]
A compute command which calculates the Voronoi tesselation of a
collection of atoms by wrapping the "Voro++ library"_voro_home. This
collection of atoms by wrapping the "Voro++ library"_voro-home. This
can be used to calculate the local volume or each atoms or its near
neighbors.
:link(voro_home,http://math.lbl.gov/voro++)
:link(voro-home,http://math.lbl.gov/voro++)
To use this package you must have the Voro++ library available on your
system.
@ -1518,7 +1520,7 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
[Contents:]
A pair style for the modified embedded atom (MEAM) potential
translated from the Fortran version in the "MEAM"_MEAM package
translated from the Fortran version in the "MEAM"_#PKG-MEAM package
to plain C++. In contrast to the MEAM package, no library
needs to be compiled and the pair style can be instantiated
multiple times.
@ -1599,7 +1601,7 @@ USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]
A "dump molfile"_dump_molfile.html command which uses molfile plugins
that are bundled with the "VMD"_vmd_home
that are bundled with the "VMD"_vmd-home
molecular visualization and analysis program, to enable LAMMPS to dump
snapshots in formats compatible with various molecular simulation
tools.
@ -1651,11 +1653,11 @@ Note that NetCDF files can be directly visualized with the following
tools:
"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
"VMD"_vmd_home
"VMD"_vmd-home
"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
:link(ovito,http://www.ovito.org)
:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/)
:link(vmd-home,https://www.ks.uiuc.edu/Research/vmd/)
:link(atomeye,http://www.libatoms.org)
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
@ -1743,6 +1745,25 @@ examples/USER/phonon :ul
:line
USER-PTM package :link(PKG-USER-PTM),h4
[Contents:]
A "compute ptm/atom"_compute_ptm_atom.html command that calculates
local structure characterization using the Polyhedral Template
Matching methodology.
[Author:] Peter Mahler Larsen (MIT).
[Supporting info:]
src/USER-PTM: filenames not starting with ptm_ -> commands
src/USER-PTM: filenames starting with ptm_ -> supporting code
src/USER-PTM/LICENSE
"compute ptm/atom"_compute_ptm_atom.html :ul
:line
USER-QMMM package :link(PKG-USER-QMMM),h4
[Contents:]
@ -1860,7 +1881,7 @@ examples/reax :ul
:line
USER-SCAFACOS package :link(USER-SCAFACOS),h4
USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
[Contents:]

2
doc/src/Packages_user.txt
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@ -62,6 +62,7 @@ Package, Description, Doc page, Example, Library
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
@ -73,3 +74,4 @@ Package, Description, Doc page, Example, Library
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)

104
doc/src/Run_options.txt
View File

@ -24,8 +24,9 @@ letter abbreviation can be used:
"-p or -partition"_#partition
"-pl or -plog"_#plog
"-ps or -pscreen"_#pscreen
"-r or -restart"_#restart
"-ro or -reorder"_#reorder
"-r2data or -restart2data"_#restart2data
"-r2dump or -restart2dump"_#restart2dump
"-sc or -screen"_#screen
"-sf or -suffix"_#suffix
"-v or -var"_#var :ul
@ -176,7 +177,7 @@ Option -plog will override the name of the partition log files file.N.
:line
[-mpicolor] color :link(mpi)
[-mpicolor] color :link(mpicolor)
If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when LAMMPS is launched by an mpirun
@ -280,34 +281,6 @@ specified by the -screen command-line option.
:line
[-restart restartfile {remap} datafile keyword value ...] :link(restart)
Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
read_restart restartfile {remap}
write_data datafile keyword value ... :pre
Note that the specified restartfile and datafile can have wild-card
characters ("*",%") as described by the
"read_restart"_read_restart.html and "write_data"_write_data.html
commands. But a filename such as file.* will need to be enclosed in
quotes to avoid shell expansion of the "*" character.
Note that following restartfile, the optional flag {remap} can be
used. This has the same effect as adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is only useful if the reading of the restart file triggers
an error that atoms have been lost. In that case, use of the remap
flag should allow the data file to still be produced.
Also note that following datafile, the same optional keyword/value
pairs can be listed as used by the "write_data"_write_data.html
command.
:line
[-reorder] :link(reorder)
This option has 2 forms:
@ -381,6 +354,77 @@ the LAMMPS simulation domain.
:line
[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data)
Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
read_restart restartfile (remap)
write_data datafile keyword value ... :pre
Note that the specified restartfile and/or datafile can have the
wild-card character "*". The restartfile can also have the wild-card
character "%". The meaning of these characters is explained on the
"read_restart"_read_restart.html and "write_data"_write_data.html doc
pages. The use of "%" means that a parallel restart file can be read.
Note that a filename such as file.* will need to be enclosed in quotes
to avoid shell expansion of the "*" character.
Note that following restartfile, the optional word "remap" can be
used. This has the effect of adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is useful if reading the restart file triggers an error
that atoms have been lost. In that case, use of the remap flag should
allow the data file to still be produced.
The syntax following restartfile (or remap), namely
datafile keyword value ... :pre
is identical to the arguments of the "write_data"_write_data.html
command. See its doc page for details. This includes its
optional keyword/value settings.
:line
[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
Convert the restart file into a dump file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
read_restart restartfile (remap)
write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre
Note that the specified restartfile and dumpfile can have wild-card
characters ("*","%") as explained on the
"read_restart"_read_restart.html and "write_dump"_write_dump.html doc
pages. The use of "%" means that a parallel restart file and/or
parallel dump file can be read and/or written. Note that a filename
such as file.* will need to be enclosed in quotes to avoid shell
expansion of the "*" character.
Note that following restartfile, the optional word "remap" can be
used. This has the effect as adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is useful if reading the restart file triggers an error
that atoms have been lost. In that case, use of the remap flag should
allow the dump file to still be produced.
The syntax following restartfile (or remap), namely
group-ID dumpstyle dumpfile arg1 arg2 ... :pre
is identical to the arguments of the "write_dump"_write_dump.html
command. See its doc page for details. This includes what per-atom
fields are written to the dump file and optional dump_modify settings,
including ones that affect how parallel dump files are written, e.g.
the {nfile} and {fileper} keywords. See the
"dump_modify"_dump_modify.html doc page for details.
:line
[-screen file] :link(screen)
Specify a file for LAMMPS to write its screen information to. In

2
doc/src/Speed_intel.txt
View File

@ -499,7 +499,7 @@ MPI task.
When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles
that require skip lists for neighbor builds cannot be offloaded.
Using "hybrid/overlay"_pair_hybrid.html is allowed. Only one intel
accelerated style may be used with hybrid styles.
accelerated style may be used with hybrid styles when offloading.
"Special_bonds"_special_bonds.html exclusion lists are not currently
supported with offload, however, the same effect can often be
accomplished by setting cutoffs for excluded atom types to 0. None of

21
doc/src/Speed_kokkos.txt
View File

@ -106,6 +106,11 @@ modification to the input script is needed. Alternatively, one can run
with the KOKKOS package by editing the input script as described
below.
NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e.
Makefile.kokkos_mpi_only) will give better performance than the OpenMP
backend (i.e. Makefile.kokkos_omp) because some of the overhead to make
the code thread-safe is removed.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. However, when running on CPUs, it
@ -122,6 +127,22 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c
If the "newton"_newton.html command is used in the input
script, it can also override the Newton flag defaults.
For half neighbor lists and OpenMP, the KOKKOS package uses data
duplication (i.e. thread-private arrays) by default to avoid
thread-level write conflicts in the force arrays (and other data
structures as necessary). Data duplication is typically fastest for
small numbers of threads (i.e. 8 or less) but does increase memory
footprint and is not scalable to large numbers of threads. An
alternative to data duplication is to use thread-level atomics, which
don't require duplication. The use of atomics can be forced by compiling
with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all
Kokkos-enabled pair_styles support data duplication. Alternatively, full
neighbor lists avoid the need for duplication or atomics but require
more compute operations per atom. When using the Kokkos Serial backend
or the OpenMP backend with a single thread, no duplication or atomics are
used. For CUDA and half neighbor lists, the KOKKOS package always uses
atomics.
[Core and Thread Affinity:]
When using multi-threading, it is important for performance to bind

2
doc/src/angle_class2.txt
View File

@ -7,8 +7,8 @@
:line
angle_style class2 command :h3
angle_style class2/omp command :h3
angle_style class2/kk command :h3
angle_style class2/omp command :h3
angle_style class2/p6 command :h3
[Syntax:]

8
doc/src/angle_cosine_buck6d.txt
View File

@ -38,10 +38,10 @@ Theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
Additional to the cosine term the {cosine/buck6d} angle style computes
the short range (vdW) interaction belonging to the
"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of
the angle. For this reason this angle style only works in combination
Additional to the cosine term the {cosine/buck6d} angle style computes
the short range (vdW) interaction belonging to the
"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the
angle. For this reason this angle style only works in combination
with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs
the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
0.0 to prevent double counting.

25
doc/src/angle_sdk.txt
View File

@ -7,6 +7,7 @@
:line
angle_style sdk command :h3
angle_style sdk/omp command :h3
[Syntax:]
@ -43,6 +44,30 @@ internally; hence the units of K are in energy/radian^2.
The also required {lj/sdk} parameters will be extracted automatically
from the pair_style.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the

31
doc/src/angle_style.txt
View File

@ -62,18 +62,27 @@ which are included in the LAMMPS distribution. The full list of all
angle styles are is on the "Commands bond"_Commands_bond.html#angle
doc page.
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style zero"_angle_zero.html - topology but no interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
"none"_angle_none.html - turn off angle interactions
"zero"_angle_zero.html - topology but no interactions
"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
"angle_style charmm"_angle_charmm.html - CHARMM angle
"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_cosine.html - cosine angle potential
"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_harmonic.html - harmonic angle
"angle_style table"_angle_table.html - tabulated by angle :ul
"charmm"_angle_charmm.html - CHARMM angle
"class2"_angle_class2.html - COMPASS (class 2) angle
"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order
"cosine"_angle_cosine.html - angle with cosine term
"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms
"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines
"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
"dipole"_angle_dipole.html - angle that controls orientation of a point dipole
"fourier"_angle_fourier.html - angle with multiple cosine terms
"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
"harmonic"_angle_harmonic.html - harmonic angle
"quartic"_angle_quartic.html - angle with cubic and quartic terms
"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
"table"_angle_table.html - tabulated by angle :ul
:line

1
doc/src/balance.txt
View File

@ -516,3 +516,4 @@ appear in {dimstr} for the {shift} style.
"fix balance"_fix_balance.html
[Default:] none
:link(pizza,http://pizza.sandia.gov)

63
doc/src/bond_oxdna.txt
View File

@ -28,34 +28,44 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
:c,image(Eqs/bond_oxdna_fene.jpg)
to define a modified finite extensible nonlinear elastic (FENE) potential
"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
in the oxDNA force field for coarse-grained modelling of DNA.
to define a modified finite extensible nonlinear elastic (FENE)
potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the
phosphate backbone in the oxDNA force field for coarse-grained
modelling of DNA.
The following coefficients must be defined for the bond type via the
"bond_coeff"_bond_coeff.html command as given in the above example, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
"bond_coeff"_bond_coeff.html command as given in the above example, or
in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
epsilon (energy)
Delta (distance)
r0 (distance) :ul
NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles
for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
style {oxdna2/dh} have to be defined.
The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
NOTE: The oxDNA bond style has to be used together with the
corresponding oxDNA pair styles for excluded volume interaction
{oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and
coaxial stacking interaction {oxdna/coaxstk} as well as
hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2
"(Snodin)"_#oxdna2 bond style the analogous pair styles and an
additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
The coefficients in the above example have to be kept fixed and cannot
be changed without reparametrizing the entire model.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
Example input and data files for DNA duplexes can be found in
examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python
setup tool which creates single straight or helical DNA strands, DNA
duplexes or arrays of DNA duplexes can be found in
examples/USER/cgdna/util/.
Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in
any publication that uses this implementation. The article contains
more information on the model, the structure of the input file, the
setup tool and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found
"here"_PDF/USER-CGDNA.pdf.
:line
@ -65,20 +75,25 @@ This bond style can only be used if LAMMPS was built with the
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
"Build package"_Build_package.html doc page for more info.
[Related commands:]
"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
"pair_style oxdna/excv"_pair_oxdna.html, "pair_style
oxdna2/excv"_pair_oxdna2.html, "fix
nve/dotc/langevin"_fix_nve_dotc_langevin.html,
"bond_coeff"_bond_coeff.html
[Default:] none
:line
:link(Henrich2)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
J. Chem. Phys. 134, 085101 (2011).
:link(oxdna2)
[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
J. Chem. Phys. 142, 234901 (2015).

27
doc/src/bond_style.txt
View File

@ -69,18 +69,23 @@ Note that there are also additional bond styles submitted by users
which are included in the LAMMPS distribution. The full list of all
bond styles is on the "Commands bond"_Commands_bond.html doc page.
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style zero"_bond_zero.html - topology but no interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"none"_bond_none.html - turn off bonded interactions
"zero"_bond_zero.html - topology but no interactions
"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"bond_style class2"_bond_class2.html - COMPASS (class 2) bond
"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_harmonic.html - harmonic bond
"bond_style morse"_bond_morse.html - Morse bond
"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_quartic.html - breakable quartic bond
"bond_style table"_bond_table.html - tabulated by bond length :ul
"class2"_bond_class2.html - COMPASS (class 2) bond
"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"gromos"_bond_gromos.html - GROMOS force field bond
"harmonic"_bond_harmonic.html - harmonic bond
"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
"morse"_bond_morse.html - Morse bond
"nonlinear"_bond_nonlinear.html - nonlinear bond
"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
"quartic"_bond_quartic.html - breakable quartic bond
"table"_bond_table.html - tabulated by bond length :ul
:line

2
doc/src/commands_list.txt
View File

@ -89,6 +89,8 @@ Commands :h1
run
run_style
server
server_mc
server_md
set
shell
special_bonds

68
doc/src/compute.txt
View File

@ -175,40 +175,63 @@ The individual style names on the "Commands
compute"_Commands_compute.html doc page are followed by one or more of
(g,i,k,o,t) to indicate which accelerated styles exist.
"ackland/atom"_compute_ackland_atom.html -
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
"angle"_compute_angle.html -
"angle/local"_compute_angle_local.html -
"angle/local"_compute_bond_local.html - theta and energy of each angle
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
"basal/atom"_compute_basal_atom.html -
"body/local"_compute_body_local.html - attributes of body sub-particles
"bond"_compute_bond.html - values computed by a bond style
"bond/local"_compute_bond_local.html - distance and energy of each bond
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
"cnp/atom"_compute_cnp_atom.html -
"com"_compute_com.html - center-of-mass of group of atoms
"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
"contact/atom"_compute_contact_atom.html - contact count for each spherical particle
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
"dihedral"_compute_dihedral.html -
"dihedral/local"_compute_dihedral_local.html - angle of each dihedral
"dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
"dipole/chunk"_compute_dipole_chunk.html -
"displace/atom"_compute_displace_atom.html - displacement of each atom
"dpd"_compute_dpd.html -
"dpd/atom"_compute_dpd_atom.html -
"edpd/temp/atom"_compute_edpd_temp_atom.html -
"entropy/atom"_compute_entropy_atom.html -
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
"event/displace"_compute_event_displace.html - detect event on atom displacement
"fep"_compute_fep.html -
"force/tally"_compute_tally.html -
"fragment/atom"_compute_cluster_atom.html - fragment ID for each atom
"global/atom"_compute_global_atom.html -
"group/group"_compute_group_group.html - energy/force between two groups of atoms
"gyration"_compute_gyration.html - radius of gyration of group of atoms
"gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
"heat/flux/tally"_compute_tally.html -
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
"improper"_compute_improper.html -
"improper/local"_compute_improper_local.html - angle of each improper
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
"ke"_compute_ke.html - translational kinetic energy
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"ke/atom/eff"_compute_ke_atom_eff.html -
"ke/eff"_compute_ke_eff.html -
"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
"meso/e/atom"_compute_meso_e_atom.html -
"meso/rho/atom"_compute_meso_rho_atom.html -
"meso/t/atom"_compute_meso_t_atom.html -
"msd"_compute_msd.html - mean-squared displacement of group of atoms
"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
"msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
@ -218,36 +241,77 @@ compute"_Commands_compute.html doc page are followed by one or more of
"pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction
"pe"_compute_pe.html - potential energy
"pe/atom"_compute_pe_atom.html - potential energy for each atom
"pe/mol/tally"_compute_tally.html -
"pe/tally"_compute_tally.html -
"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
"pressure"_compute_pressure.html - total pressure and pressure tensor
"pressure/cylinder"_compute_pressure_cylinder.html -
"pressure/uef"_compute_pressure_uef.html -
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
"ptm/atom"_compute_ptm_atom.html -
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
"saed"_compute_saed.html -
"slice"_compute_slice.html - extract values from global vector or array
"smd/contact/radius"_compute_smd_contact_radius.html -
"smd/damage"_compute_smd_damage.html -
"smd/hourglass/error"_compute_smd_hourglass_error.html -
"smd/internal/energy"_compute_smd_internal_energy.html -
"smd/plastic/strain"_compute_smd_plastic_strain.html -
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
"smd/rho"_compute_smd_rho.html -
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
"smd/vol"_compute_smd_vol.html -
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
"spin"_compute_spin.html -
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"stress/mop"_compute_stress_mop.html -
"stress/mop/profile"_compute_stress_mop.html -
"stress/tally"_compute_tally.html -
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
"temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
"temp/body"_compute_temp_body.html - temperature of body particles
"temp/chunk"_compute_temp_chunk.html - temperature of each chunk
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
"temp/cs"_compute_temp_cs.html -
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
"temp/deform/eff"_compute_temp_deform_eff.html -
"temp/drude"_compute_temp_drude.html -
"temp/eff"_compute_temp_eff.html -
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"temp/region/eff"_compute_temp_region_eff.html -
"temp/rotate"_compute_temp_rotate.html -
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
"temp/uef"_compute_temp_uef.html -
"ti"_compute_ti.html - thermodynamic integration free energy values
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
"vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
"xrd"_compute_xrd.html - :ul
[Restrictions:] none

213
doc/src/compute_adf.txt Normal file
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@ -0,0 +1,213 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute adf command :h3
[Syntax:]
compute ID group-ID adf Nbin itype1 jtype1 ktype1 Rjinner1 Rjouter1 Rkinner1 Rkouter1 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
adf = style name of this compute command :l
Nbin = number of ADF bins :l
itypeN = central atom type for Nth ADF histogram (see asterisk form below) :l
jtypeN = J atom type for Nth ADF histogram (see asterisk form below) :l
ktypeN = K atom type for Nth ADF histogram (see asterisk form below) :l
RjinnerN = inner radius of J atom shell for Nth ADF histogram (distance units) :l
RjouterN = outer radius of J atom shell for Nth ADF histogram (distance units) :l
RkinnerN = inner radius of K atom shell for Nth ADF histogram (distance units) :l
RkouterN = outer radius of K atom shell for Nth ADF histogram (distance units) :l
zero or one keyword/value pairs may be appended :l
keyword = {ordinate} :l
{ordinate} value = {degree} or {radian} or {cosine}
Choose the ordinate parameter for the histogram :pre
:ule
[Examples:]
compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 &
1 1 2 0.0 1.2 0.0 1.5 &
1 2 2 0.0 1.5 0.0 1.5 &
2 1 1 0.0 1.2 0.0 1.2 &
2 1 2 0.0 1.5 2.0 3.5 &
2 2 2 2.0 3.5 2.0 3.5
compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5
compute 1 fluid adf 32 :pre
[Description:]
Define a computation that calculates one or more angular distribution functions
(ADF) for a group of particles. Each ADF is calculated in histogram form
by measuring the angle formed by a central atom and two neighbor atoms and
binning these angles into {Nbin} bins.
Only neighbors for which {Rinner} < {R} < {Router} are counted, where
{Rinner} and {Router} are specified separately for the first and second
neighbor atom in each requested ADF.
NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the "special_bonds"_special_bonds.html
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses a neighbor list, it also means
those pairs will not be included in the ADF. This does not apply when
using long-range coulomb interactions ({coul/long}, {coul/msm},
{coul/wolf} or similar. One way to get around this would be to set
special_bond scaling factors to very tiny numbers that are not exactly
zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
use the "rerun"_rerun.html command to compute the ADF for snapshots in
the dump file. The rerun script can use a
"special_bonds"_special_bonds.html command that includes all pairs in
the neighbor list.
NOTE: If you request any outer cutoff {Router} > force cutoff, or if no
pair style is defined, e.g. the "rerun"_rerun.html command is being used to
post-process a dump file of snapshots you must insure ghost atom information
out to the largest value of {Router} + {skin} is communicated, via the
"comm_modify cutoff"_comm_modify.html command, else the ADF computation
cannot be performed, and LAMMPS will give an error message. The {skin} value
is what is specified with the "neighbor"_neighbor.html command.
The {itypeN},{jtypeN},{ktypeN} settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 1st example
above. Or a wild-card asterisk can be used to specify a range of atom
types as in the 2nd example above.
This takes the form "*" or "*n" or "n*" or "m*n". If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
If {itypeN}, {jtypeN}, and {ktypeN} are single values, as in the 1st example
above, this means that the ADF is computed where atoms of type {itypeN}
are the central atom, and neighbor atoms of type {jtypeN} and {ktypeN}
are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN}
represent a range of values via
the wild-card asterisk, as in the 2nd example above, this means that the
ADF is computed where atoms of any of the range of types represented
by {itypeN} are the central atom, and the angle is formed by two neighbors,
one neighbor in the range of types represented by {jtypeN} and another neighbor
in the range of types represented by {ktypeN}.
If no {itypeN}, {jtypeN}, {ktypeN} settings are specified, then
LAMMPS will generate a single ADF for all atoms in the group.
The inner cutoff is set to zero and the outer cutoff is set
to the force cutoff. If no pair_style is specified, there is no
force cutoff and LAMMPS will give an error message. Note that
in most cases, generating an ADF for all atoms is not a good thing.
Such an ADF is both uninformative and
extremely expensive to compute. For example, with liquid water
with a 10 A force cutoff, there are 80,000 angles per atom.
In addition, most of the interesting angular structure occurs for
neighbors that are the closest to the central atom, involving
just a few dozen angles.
Angles for each ADF are generated by double-looping over the list of
neighbors of each central atom I,
just as they would be in the force calculation for
a threebody potential such as "Stillinger-Weber"_pair_sw.html.
The angle formed by central atom I and neighbor atoms J and K is included in an
ADF if the following criteria are met:
atoms I,J,K are all in the specified compute group
the distance between atoms I,J is between Rjinner and Rjouter
the distance between atoms I,K is between Rkinner and Rkouter
the type of the I atom matches itypeN (one or a range of types)
atoms I,J,K are distinct
the type of the J atom matches jtypeN (one or a range of types)
the type of the K atom matches ktypeN (one or a range of types) :ul
Each unique angle satisfying the above criteria is counted only once, regardless
of whether either or both of the neighbor atoms making up the
angle appear in both the J and K lists.
It is OK if a particular angle is included in more than
one individual histogram, due to the way the {itypeN}, {jtypeN}, {ktypeN}
arguments are specified.
The first ADF value for a bin is calculated from the histogram count by
dividing by the total number of triples satisfying the criteria,
so that the integral of the ADF w.r.t. angle is 1, i.e. the ADF
is a probability density function.
The second ADF value is reported as a cumulative sum of
all bins up to the current bins, averaged
over atoms of type {itypeN}. It represents the
number of angles per central atom with angle less
than or equal to the angle of the current bin,
analogous to the coordination
number radial distribution function.
The {ordinate} optional keyword determines
whether the bins are of uniform angular size from zero
to 180 ({degree}), zero to Pi ({radian}), or the
cosine of the angle uniform in the range \[-1,1\] ({cosine}).
{cosine} has the advantage of eliminating the {acos()} function
call, which speeds up the compute by 2-3x, and it is also preferred
on physical grounds, because the for uniformly distributed particles
in 3D, the angular probability density w.r.t dtheta is
sin(theta)/2, while for d(cos(theta)), it is 1/2,
Regardless of which ordinate is chosen, the first column of ADF
values is normalized w.r.t. the range of that ordinate, so that
the integral is 1.
The simplest way to output the results of the compute adf calculation
to a file is to use the "fix ave/time"_fix_ave_time.html command, for
example:
compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5
fix 1 all ave/time 100 1 100 c_myADF\[*\] file tmp.adf mode vector :pre
[Output info:]
This compute calculates a global array with the number of rows =
{Nbins}, and the number of columns = 1 + 2*Ntriples, where Ntriples is the
number of I,J,K triples specified. The first column has the bin
coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has
the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN})
interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The array values calculated by this compute are all "intensive".
The first column of array values is the angle-related ordinate, either
the angle in degrees or radians, or the cosine of the angle. Each
subsequent pair of columns gives the first and second kinds of ADF
for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values
in the first ADF column are normalized numbers >= 0.0,
whose integral w.r.t. the ordinate is 1,
i.e. the first ADF is a normalized probability distribution.
The values in the second ADF column are also numbers >= 0.0.
They are the cumulative density distribution of angles per atom.
By definition, this ADF is monotonically increasing from zero to
a maximum value equal to the average total number of
angles per atom satisfying the ADF criteria.
[Restrictions:]
The ADF is not computed for neighbors outside the force cutoff,
since processors (in parallel) don't know about atom coordinates for
atoms further away than that distance. If you want an ADF for larger
distances, you can use the "rerun"_rerun.html command to post-process
a dump file and set the cutoff for the potential to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you aren't running dynamics and thus are not changing
your model.
[Related commands:]
"compute rdf"_compute_rdf.html, "fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html
[Default:]
The keyword default is ordinate = degree.

66
doc/src/compute_angle_local.txt
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@ -10,20 +10,27 @@ compute angle/local command :h3
[Syntax:]
compute ID group-ID angle/local value1 value2 ... :pre
compute ID group-ID angle/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
angle/local = style name of this compute command :l
one or more values may be appended :l
value = {theta} or {eng} :l
value = {theta} or {eng} or {v_name} :l
{theta} = tabulate angles
{eng} = tabulate angle energies :pre
{eng} = tabulate angle energies
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = theta name
theta = only currently allowed arg
name = name of variable to set with theta :pre
:ule
[Examples:]
compute 1 all angle/local theta
compute 1 all angle/local eng theta :pre
compute 1 all angle/local eng theta
compute 1 all angle/local theta v_cos set theta t :pre
[Description:]
@ -36,6 +43,47 @@ The value {theta} is the angle for the 3 atoms in the interaction.
The value {eng} is the interaction energy for the angle.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the angle theta. The {name}
specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the angle theta. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with theta.
Note that the value of theta for each angle which stored in the
internal variable is in radians, not degrees.
As an example, these commands can be added to the bench/in.rhodo
script to compute the cosine and cosine^2 of every angle in the system
and output the statistics in various ways:
variable t internal 0.0
variable cos equal cos(v_t)
variable cossq equal cos(v_t)*cos(v_t) :pre
compute 1 all property/local aatom1 aatom2 aatom3 atype
compute 2 all angle/local eng theta v_cos v_cossq set theta t
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the energy, angle,
cosine(angle), cosine^2(angle) for every angle in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the cosine(angle) values and write them to a
file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their angles. An angle will only
be included if all 3 atoms in the angle are in the specified compute
@ -65,12 +113,12 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_2\[1\
[Output info:]
This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of angles. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
number of values. The length of the vector or number of rows in the
array is the number of angles. If a single value is specified, a
local vector is produced. If two or more values are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See the "Howto
values. The vector or array can be accessed by any command that uses
local values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.

69
doc/src/compute_bond_local.txt
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@ -10,12 +10,12 @@ compute bond/local command :h3
[Syntax:]
compute ID group-ID bond/local value1 value2 ... :pre
compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
bond/local = style name of this compute command :l
one or more values may be appended :l
value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} :l
value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
{dist} = bond distance
{engpot} = bond potential energy
{force} = bond force :pre
@ -23,13 +23,22 @@ value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {
{engrot} = bond kinetic energy of rotation
{engtrans} = bond kinetic energy of translation
{omega} = magnitude of bond angular velocity
{velvib} = vibrational velocity along the bond length :pre
{velvib} = vibrational velocity along the bond length
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = dist name
dist = only currently allowed arg
name = name of variable to set with distance (dist) :pre
:ule
:ule
[Examples:]
compute 1 all bond/local engpot
compute 1 all bond/local dist engpot force :pre
compute 1 all angle/local dist v_distsq set dist d :pre
[Description:]
@ -38,6 +47,10 @@ interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system, modified by the
group parameter as explained below.
All these properties are computed for the pair of atoms in a bond,
whether the 2 atoms represent a simple diatomic molecule, or are part
of some larger molecule.
The value {dist} is the current length of the bond.
The value {engpot} is the potential energy for the bond,
@ -79,9 +92,41 @@ two atoms in the bond towards each other. A negative value means the
2 atoms are moving toward each other; a positive value means they are
moving apart.
Note that all these properties are computed for the pair of atoms in a
bond, whether the 2 atoms represent a simple diatomic molecule, or are
part of some larger molecule.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the bond distance. The {name}
specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the bond distance. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with theta.
As an example, these commands can be added to the bench/in.rhodo
script to compute the distance^2 of every bond in the system and
output the statistics in various ways:
variable d internal 0.0
variable dsq equal v_d*v_d :pre
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local engpot dist v_dsq set dist d
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the energy, distance,
distance^2 for every bond in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the distance^2 values and write them to a file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
@ -111,12 +156,12 @@ dump 1 all local 1000 tmp.dump index c_1\[*\] c_2\[*\] :pre
[Output info:]
This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of bonds. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See the "Howto
number of values. The length of the vector or number of rows in the
array is the number of bonds. If a single value is specified, a local
vector is produced. If two or more values are specified, a local
array is produced where the number of columns = the number of values.
The vector or array can be accessed by any command that uses local
values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.

11
doc/src/compute_chunk_atom.txt
View File

@ -14,7 +14,7 @@ compute ID group-ID chunk/atom style args keyword values ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
chunk/atom = style name of this compute command :l
style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or {compute/fix/variable}
style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name
{bin/1d} args = dim origin delta
dim = {x} or {y} or {z}
origin = {lower} or {center} or {upper} or coordinate value (distance units)
@ -40,7 +40,7 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule}
ncbin = # of concentric circle bins between rmin and rmax
{type} args = none
{molecule} args = none
{compute/fix/variable} = c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name with no args
c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name args = none
c_ID = per-atom vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
@ -85,7 +85,8 @@ compute 1 all chunk/atom bin/1d z lower 0.02 units reduced
compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5
compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes
compute 1 all chunk/atom bin/sphere 5 5 5 2.0 5.0 5 discard yes
compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes :pre
compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes
compute 1 all chunk/atom c_cluster :pre
[Description:]
@ -386,8 +387,8 @@ described below, which resets {Nchunk}. The {limit} keyword is then
applied to the new {Nchunk} value, exactly as described in the
preceding paragraph. Note that in this case, all atoms will end up
with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or
compute/fix/variable value) may have been > {Nc}, because of the
compression operation.
compute/fix/variable) may have been > {Nc}, because of the compression
operation.
If {compress yes} is set, and the {compress} keyword comes after the
{limit} keyword, then the {limit} value of {Nc} is applied first to

174
doc/src/compute_chunk_spread_atom.txt Normal file
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@ -0,0 +1,174 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute chunk/spread/atom command :h3
[Syntax:]
compute ID group-ID chunk/spread/atom chunkID input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
chunk/spread/atom = style name of this compute command :l
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
one or more inputs can be listed :l
input = c_ID, c_ID\[N\], f_ID, f_ID\[N\] :l
c_ID = global vector calculated by a compute with ID
c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global vector calculated by a fix with ID
f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) :pre
:ule
[Examples:]
compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
[Description:]
Define a calculation that "spreads" one or more per-chunk values to
each atom in the chunk. This can be useful for creating a "dump
file"_dump.html where each atom lists info about the chunk it is in,
e.g. for post-processing purposes. It can also be used in "atom-style
variables"_variable.html that need info about the chunk each atom is
in. Examples are given below.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
For inputs that are computes, they must be a compute that calculates
per-chunk values. These are computes whose style names end in
"/chunk".
For inputs that are fixes, they should be a a fix that calculates
per-chunk values. For example, "fix ave/chunk"_fix_ave_chunk.html or
"fix ave/time"_fix_ave_time.html (assuming it is time-averaging
per-chunk data).
For each atom, this compute accesses its chunk ID from the specified
{chunkID} compute, then accesses the per-chunk value in each input.
Those values are copied to this compute to become the output for that
atom.
The values generated by this compute will be 0.0 for atoms not in the
specified compute group {group-ID}. They will also be 0.0 if the atom
is not in a chunk, as assigned by the {chunkID} compute. They will
also be 0.0 if the current chunk ID for the atom is out-of-bounds with
respect to the number of chunks stored by a particular input compute
or fix.
NOTE: LAMMPS does not check that a compute or fix which calculates
per-chunk values uses the same definition of chunks as this compute.
It's up to you to be consistent. Likewise, for a fix input, LAMMPS
does not check that it is per-chunk data. It only checks that the fix
produces a global vector or array.
:line
Each listed input is operated on independently.
If a bracketed index I is used, it can be specified using a wildcard
asterisk with the index to effectively specify multiple values. This
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
columns in the array, then an asterisk with no numeric values means
all indices from 1 to N. A leading asterisk means all indices from 1
to n (inclusive). A trailing asterisk means all indices from n to N
(inclusive). A middle asterisk means all indices from m to n
(inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 compute chunk/spread/atom
commands are equivalent, since the "compute
com/chunk"_compute_com_chunk.html command creates a per-atom array
with 3 columns:
compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com\[*\]
compute 10 all chunk/spread/atom mychunk c_com\[1\] c_com\[2\] c_com\[3\] :pre
:line
Here is an example of writing a dump file the with the center-of-mass
(COM) for the chunk each atom is in. The commands below can be added
to the bench/in.chain script.
compute cmol all chunk/atom molecule
compute com all com/chunk cmol
compute comchunk all chunk/spread/atom cmol c_com[*]
dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*]
dump_modify 1 sort id :pre
The same per-chunk data for each atom could be used to define per-atom
forces for the "fix addforce"_fix_addforce.html command. In this
example the forces act to pull atoms of an extended polymer chain
towards its COM in an attractive manner.
compute prop all property/atom xu yu zu
variable k equal 0.1
variable fx atom v_k*(c_comchunk\[1\]-c_prop\[1\])
variable fy atom v_k*(c_comchunk\[2\]-c_prop\[2\])
variable fz atom v_k*(c_comchunk\[3\]-c_prop\[3\])
fix 3 all addforce v_fx v_fy v_fz :pre
Note that "compute property/atom"_compute_property_atom.html is used
to generate unwrapped coordinates for use in the per-atom force
calculation, so that the effect of periodic boundaries is accounted
for properly.
Over time this applied force could shrink each polymer chain's radius
of gyration in a polymer mixture simulation. Here is output from the
bench/in.chain script. Thermo output is shown for 1000 steps, where
the last column is the average radius of gyration over all 320 chains
in the 32000 atom system:
compute gyr all gyration/chunk cmol
variable ave equal ave(c_gyr)
thermo_style custom step etotal press v_ave :pre
0 22.394765 4.6721833 5.128278
100 22.445002 4.8166709 5.0348372
200 22.500128 4.8790392 4.9364875
300 22.534686 4.9183766 4.8590693
400 22.557196 4.9492211 4.7937849
500 22.571017 4.9161853 4.7412008
600 22.573944 5.0229708 4.6931243
700 22.581804 5.0541301 4.6440647
800 22.584683 4.9691734 4.6000016
900 22.59128 5.0247538 4.5611513
1000 22.586832 4.94697 4.5238362 :pre
:line
[Output info:]
This compute calculates a per-atom vector or array, which can be
accessed by any command that uses per-atom values from a compute as
input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The output is a per-atom vector if a single input value is specified,
otherwise a per-atom array is output. The number of columns in the
array is the number of inputs provided. The per-atom values for the
vector or each column of the array will be in whatever
"units"_units.html the corresponding input value is in.
The vector or array values are "intensive".
[Restrictions:] none
[Related commands:]
"compute chunk/atom"_compute_chunk_atom.html, "fix
ave/chunk"_fix_ave_chunk.html, "compute
reduce/chunk"_compute_reduce_chunk.html
[Default:] none

64
doc/src/compute_dihedral_local.txt
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@ -10,18 +10,25 @@ compute dihedral/local command :h3
[Syntax:]
compute ID group-ID dihedral/local value1 value2 ... :pre
compute ID group-ID dihedral/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
dihedral/local = style name of this compute command :l
one or more values may be appended :l
value = {phi} :l
{phi} = tabulate dihedral angles :pre
value = {phi} or {v_name} :l
{phi} = tabulate dihedral angles
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = phi name
phi = only currently allowed arg
name = name of variable to set with phi :pre
:ule
[Examples:]
compute 1 all dihedral/local phi :pre
compute 1 all dihedral/local phi v_cos set phi p :pre
[Description:]
@ -33,6 +40,47 @@ by the group parameter as explained below.
The value {phi} is the dihedral angle, as defined in the diagram on
the "dihedral_style"_dihedral_style.html doc page.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the dihedral angle phi. The
{name} specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the angle phi. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with phi.
Note that the value of phi for each angle which stored in the internal
variable is in radians, not degrees.
As an example, these commands can be added to the bench/in.rhodo
script to compute the cosine and cosine^2 of every dihedral angle in
the system and output the statistics in various ways:
variable p internal 0.0
variable cos equal cos(v_p)
variable cossq equal cos(v_p)*cos(v_p) :pre
compute 1 all property/local datom1 datom2 datom3 datom4 dtype
compute 2 all dihedral/local phi v_cos v_cossq set phi p
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the angle,
cosine(angle), cosine^2(angle) for every dihedral in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the cosine(angle) values and write them to a
file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their dihedrals. A dihedral will
only be included if all 4 atoms in the dihedral are in the specified
@ -57,12 +105,12 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\
[Output info:]
This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of dihedrals. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
number of values. The length of the vector or number of rows in the
array is the number of dihedrals. If a single value is specified, a
local vector is produced. If two or more values are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See the "Howto
values. The vector or array can be accessed by any command that uses
local values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.

4
doc/src/compute_msd_chunk.txt
View File

@ -90,12 +90,12 @@ This is so that the fix this compute creates to store per-chunk
quantities will also have the same ID, and thus be initialized
correctly with chunk reference positions from the restart file.
The simplest way to output the results of the compute com/msd
The simplest way to output the results of the compute msd/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 all chunk/atom molecule
compute myChunk all com/msd cc1
compute myChunk all msd/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
[Output info:]

25
doc/src/compute_pair.txt
View File

@ -10,17 +10,20 @@ compute pair command :h3
[Syntax:]
compute ID group-ID pair pstyle evalue :pre
compute ID group-ID pair pstyle \[nstyle\] \[evalue\] :pre
ID, group-ID are documented in "compute"_compute.html command
pair = style name of this compute command
pstyle = style name of a pair style that calculates additional values
evalue = {epair} or {evdwl} or {ecoul} or blank (optional setting) :ul
ID, group-ID are documented in "compute"_compute.html command :ulb,l
pair = style name of this compute command :l
pstyle = style name of a pair style that calculates additional values :l
nsub = {n}-instance of a substyle, if a pair style is used multiple times in a hybrid style :l
{evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l
:ule
[Examples:]
compute 1 all pair gauss
compute 1 all pair lj/cut/coul/cut ecoul
compute 1 all pair tersoff 2 epair
compute 1 all pair reax :pre
[Description:]
@ -33,15 +36,19 @@ NOTE: The group specified for this command is [ignored].
The specified {pstyle} must be a pair style used in your simulation
either by itself or as a sub-style in a "pair_style hybrid or
hybrid/overlay"_pair_hybrid.html command.
hybrid/overlay"_pair_hybrid.html command. If the sub-style is
used more than once, an additional number {nsub} has to be specified
in order to choose which instance of the sub-style will be used by
the compute. Not specifying the number in this case will cause the
compute to fail.
The {evalue} setting is optional; it may be left off the command. All
The {evalue} setting is optional. All
pair styles tally a potential energy {epair} which may be broken into
two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {ecoul}.
If the pair style calculates Coulombic interactions, their energy will
be tallied in {ecoul}. Everything else (whether it is a Lennard-Jones
style van der Waals interaction or not) is tallied in {evdwl}. If
{evalue} is specified as {epair} or left out, then {epair} is stored
{evalue} is blank or specified as {epair}, then {epair} is stored
as a global scalar by this compute. This is useful when using
"pair_style hybrid"_pair_hybrid.html if you want to know the portion
of the total energy contributed by one sub-style. If {evalue} is
@ -82,4 +89,4 @@ the doc page for the pair style for details.
[Default:]
The default for {evalue} is {epair}.
The keyword defaults are {evalue} = {epair}, nsub = 0.

81
doc/src/compute_pressure_cylinder.txt Normal file
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@ -0,0 +1,81 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute pressure/cylinder command :h3
[Syntax:]
compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width :pre
ID, group-ID are documented in "compute"_compute.html command
pressure/cylinder = style name of this compute command
zlo = minimum z-boundary for cylinder
zhi = maximum z-boundary for cylinder
Rmax = maximum radius to perform calculation to
bin_width = width of radial bins to use for calculation :ul
[Examples:]
compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 :pre
[Description:]
Define a computation that calculates the pressure tensor of a system in
cylindrical coordinates, as discussed in "(Addington)"_#Addington1.
This is useful for systems with a single axis of rotational symmetry,
such as cylindrical micelles or carbon nanotubes. The compute splits the
system into radial, cylindrical-shell-type bins of width bin_width,
centered at x=0,y=0, and calculates the radial (P_rhorho), azimuthal
(P_phiphi), and axial (P_zz) components of the configurational pressure
tensor. The local density is also calculated for each bin, so that the
true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf. The
output is a global array with 5 columns; one each for bin radius, local
number density, P_rhorho, P_phiphi, and P_zz. The number of rows is
governed by the values of Rmax and bin_width. Pressure tensor values are
output in pressure units.
[Output info:]
This compute calculates a global array with 5 columns and Rmax/bin_width
rows. The output columns are: R (distance units), number density (inverse
volume units), configurational radial pressure (pressure units),
configurational azimuthal pressure (pressure units), and configurational
axial pressure (pressure units).
The values calculated by this compute are
"intensive". The pressure values will be in pressure
"units"_units.html. The number density values will be in
inverse volume "units"_units.html.
[Restrictions:]
This compute currently calculates the pressure tensor contributions
for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
and in the presence of bonded interactions, the result will be incorrect
due to exclusions for special bonds) and requires pair-wise force
calculations not available for most manybody pair styles. K-space
calculations are also excluded. Note that this pressure compute outputs
the configurational terms only; the kinetic contribution is not included
and may be calculated from the number density output by P_kin=density*k*T.
This compute is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"compute temp"_compute_temp.html, "compute
stress/atom"_compute_stress_atom.html,
"thermo_style"_thermo_style.html,
[Default:] none
:line
:link(Addington1)
[(Addington)] Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).

121
doc/src/compute_ptm_atom.txt Normal file
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@ -0,0 +1,121 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute ptm/atom command :h3
[Syntax:]
compute ID group-ID ptm/atom structures threshold :pre
ID, group-ID are documented in "compute"_compute.html command
ptm/atom = style name of this compute command
structures = structure types to search for
threshold = lattice distortion threshold (RMSD) :ul
[Examples:]
compute 1 all ptm/atom default 0.1
compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
compute 1 all ptm/atom all 0 :pre
[Description:]
Define a computation that determines the local lattice structure
around an atom using the PTM (Polyhedral Template Matching) method.
The PTM method is described in "(Larsen)"_#Larsen.
Currently, there are seven lattice structures PTM recognizes:
fcc = 1
hcp = 2
bcc = 3
ico (icosahedral) = 4
sc (simple cubic) = 5
dcub (diamond cubic) = 6
dhex (diamond hexagonal) = 7
other = 8 :ul
The value of the PTM structure will be 0 for atoms not in the specified
compute group. The choice of structures to search for can be specified using the "structures"
argument, which is a hyphen-separated list of structure keywords.
Two convenient pre-set options are provided:
default: fcc-hcp-bcc-ico
all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul
The 'default' setting detects the same structures as the Common Neighbor Analysis method.
The 'all' setting searches for all structure types. A small performance penalty is
incurred for the diamond structures, so it is not recommended to use this option if
it is known that the simulation does not contain diamond structures.
PTM identifies structures using two steps. First, a graph isomorphism test is used
to identify potential structure matches. Next, the deviation is computed between the
local structure (in the simulation) and a template of the ideal lattice structure.
The deviation is calculated as:
:c,image(Eqs/ptm_rmsd.jpg)
Here, u and v contain the coordinates of the local and ideal structures respectively,
s is a scale factor, and Q is a rotation. The best match is identified by the
lowest RMSD value, using the optimal scaling, rotation, and correspondence between the
points.
The 'threshold' keyword sets an upper limit on the maximum permitted deviation before
a local structure is identified as disordered. Typical values are in the range 0.1-0.15,
but larger values may be desirable at higher temperatures.
A value of 0 is equivalent to infinity and can be used if no threshold is desired.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (e.g. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a
{ptm/atom} style.
[Output info:]
This compute calculates a per-atom arry, which can be accessed by
any command that uses per-atom values from a compute as input. See
the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
Results are stored in the per-atom array in the following order:
type
rmsd
interatomic distance
qw
qx
qy
qw :ul
The type is a number from 0 to 8. The rmsd is a positive real number.
The interatomic distance is computed from the scale factor in the RMSD equation.
The (qw,qx,qy,qz) parameters represent the orientation of the local structure
in quaternion form. The reference coordinates for each template (from which the
orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory.
[Restrictions:]
This fix is part of the USER-PTM package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"compute centro/atom"_compute_centro_atom.html
"compute cna/atom"_compute_cna_atom.html
[Default:] none
:line
:link(Larsen)
[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).

3
doc/src/compute_rdf.txt
View File

@ -191,7 +191,8 @@ via "compute_modify dynamic yes"_compute_modify.html
[Related commands:]
"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html
"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html,
"compute adf"_compute_adf.html
[Default:]

6
doc/src/compute_reduce.txt
View File

@ -97,9 +97,9 @@ equivalent, since the "compute stress/atom"_compute_stress_atom.html
command creates a per-atom array with 6 columns:
compute myPress all stress/atom NULL
compute 2 all reduce min myPress\[*\]
compute 2 all reduce min myPress\[1\] myPress\[2\] myPress\[3\] &
myPress\[4\] myPress\[5\] myPress\[6\] :pre
compute 2 all reduce min c_myPress\[*\]
compute 2 all reduce min c_myPress\[1\] c_myPress\[2\] c_myPress\[3\] &
c_myPress\[4\] c_myPress\[5\] c_myPress\[6\] :pre
:line

177
doc/src/compute_reduce_chunk.txt Normal file
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@ -0,0 +1,177 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute reduce/chunk command :h3
[Syntax:]
compute ID group-ID reduce/chunk chunkID mode input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
reduce/chunk = style name of this compute command :l
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
mode = {sum} or {min} or {max} :l
one or more inputs can be listed :l
input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_ID :l
c_ID = per-atom vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom vector calculated by a fix with ID
f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name :pre
:ule
[Examples:]
compute 1 all reduce/chunk/atom mychunk min c_cluster :pre
[Description:]
Define a calculation that reduces one or more per-atom vectors into
per-chunk values. This can be useful for diagnostic output. Or when
used in conjunction with the "compute
chunk/spread/atom"_compute_chunk_spread_atom.html command it can be
used ot create per-atom values that induce a new set of chunks with a
second "compute chunk/atom"_compute_chunk_atom.html command. An
example is given below.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
For each atom, this compute accesses its chunk ID from the specified
{chunkID} compute. The per-atom value from an input contributes
to a per-chunk value corresponding the the chunk ID.
The reduction operation is specified by the {mode} setting and is
performed over all the per-atom values from the atoms in each chunk.
The {sum} option adds the pre-atom values to a per-chunk total. The
{min} or {max} options find the minimum or maximum value of the
per-atom values for each chunk.
Note that only atoms in the specified group contribute to the
reduction operation. If the {chunkID} compute returns a 0 for the
chunk ID of an atom (i.e. the atom is not in a chunk defined by the
"compute chunk/atom"_compute_chunk_atom.html command), that atom will
also not contribute to the reduction operation. An input that is a
compute or fix may define its own group which affects the quantities
it returns. For example, a compute with return a zero value for atoms
that are not in the group specified for that compute.
Each listed input is operated on independently. Each input can be the
result of a "compute"_compute.html or "fix"_fix.html or the evaluation
of an atom-style "variable"_variable.html.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "*" or "*n" or "n*" or
"m*n". If N = the size of the vector (for {mode} = scalar) or the
number of columns in the array (for {mode} = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 compute reduce/chunk
commands are equivalent, since the "compute
property/chunk"_compute_property_chunk.html command creates a per-atom
array with 3 columns:
compute prop all property/atom vx vy vz
compute 10 all reduce/chunk mychunk max c_prop\[*\]
compute 10 all reduce/chunk mychunk max c_prop\[1\] c_prop\[2\] c_prop\[3\] :pre
:line
Here is an example of using this compute, in conjunction with the
compute chunk/spread/atom command to identify self-assembled micelles.
The commands below can be added to the examples/in.micelle script.
Imagine a collection of polymer chains or small molecules with
hydrophobic end groups. All the hydrophobic (HP) atoms are assigned
to a group called "phobic".
These commands will assign a unique cluster ID to all HP atoms within
a specified distance of each other. A cluster will contain all HP
atoms in a single molecule, but also the HP atoms in nearby molecules,
e.g. molecules that have clumped to form a micelle due to the
attraction induced by the hydrophobicity. The output of the
chunk/reduce command will be a cluster ID per chunk (molecule).
Molecules with the same cluster ID are in the same micelle.
group phobic type 4 # specific to in.micelle model
compute cluster phobic cluster/atom 2.0
compute cmol all chunk/atom molecule
compute reduce phobic reduce/chunk cmol min c_cluster :pre
This per-chunk info could be output in at least two ways:
fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector :pre
compute spread all chunk/spread/atom cmol c_reduce
dump 1 all custom 1000 tmp.dump id type mol x y z c_cluster c_spread
dump_modify 1 sort id :pre
In the first case, each snapshot in the tmp.phobic file will contain
one line per molecule. Molecules with the same value are in the same
micelle. In the second case each dump snapshot contains all atoms,
each with a final field with the cluster ID of the micelle that the HP
atoms of that atom's molecule belong to.
The result from compute chunk/spread/atom can be used to define a new
set of chunks, where all the atoms in all the molecules in the same
micelle are assigned to the same chunk, i.e. one chunk per micelle.
compute micelle all chunk/atom c_spread compress yes :pre
Further analysis on a per-micelle basis can now be performed using any
of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html
doc page. E.g. count the number of atoms in each micelle, calculate
its center or mass, shape (moments of intertia), radius of gyration,
etc.
compute prop all property/chunk micelle count
fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector :pre
Each snapshot in the tmp.micelle file will have one line per micelle
with its count of atoms, plus a first line for a chunk with all the
solvent atoms. By the time 50000 steps have elapsed there are a
handful of large micelles.
:line
[Output info:]
This compute calculates a global vector if a single input value is
specified, otherwise a global array is output. The number of columns
in the array is the number of inputs provided. The length of the
vector or the number of vector elements or array rows = the number of
chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The vector or array can
be accessed by any command that uses global values from a compute as
input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The per-atom values for the vector or each column of the array will be
in whatever "units"_units.html the corresponding input value is in.
The vector or array values are "intensive".
[Restrictions:] none
[Related commands:]
"compute chunk/atom"_compute_chunk_atom.html, "compute
reduce"_compute_reduce.html, "compute
chunk/spread/atom"_compute_chunk_spread_atom.html
[Default:] none

6
doc/src/compute_smd_triangle_mesh_vertices.txt → doc/src/compute_smd_triangle_vertices.txt
View File

@ -6,14 +6,14 @@
:line
compute smd/triangle/mesh/vertices :h3
compute smd/triangle/vertices command :h3
[Syntax:]
compute ID group-ID smd/triangle/mesh/vertices :pre
compute ID group-ID smd/triangle/vertices :pre
ID, group-ID are documented in "compute"_compute.html command
smd/triangle/mesh/vertices = style name of this compute command :ul
smd/triangle/vertices = style name of this compute command :ul
[Examples:]

13
doc/src/compute_spin.txt
View File

@ -10,14 +10,14 @@ compute spin command :h3
[Syntax:]
compute ID group-ID compute/spin :pre
compute ID group-ID spin :pre
ID, group-ID are documented in "compute"_compute.html command
compute/spin = style name of this compute command :ul
spin = style name of this compute command :ul
[Examples:]
compute out_mag all compute/spin :pre
compute out_mag all spin :pre
[Description:]
@ -26,7 +26,8 @@ of atoms having spins.
This compute calculates 6 magnetic quantities.
The three first quantities are the x,y and z coordinates of the total magnetization.
The three first quantities are the x,y and z coordinates of the total
magnetization.
The fourth quantity is the norm of the total magnetization.
@ -39,7 +40,7 @@ The simplest way to output the results of the compute spin calculation
is to define some of the quantities as variables, and to use the thermo and
thermo_style commands, for example:
compute out_mag all compute/spin :pre
compute out_mag all spin :pre
variable mag_z equal c_out_mag\[3\]
variable mag_norm equal c_out_mag\[4\]
@ -53,7 +54,6 @@ the total magnetization, and the magnetic temperature. Three variables are
assigned to those quantities. The thermo and thermo_style commands print them
every 10 timesteps.
[Output info:]
The array values are "intensive". The array values will be in
@ -68,7 +68,6 @@ has to be "spin" for this compute to be valid.
[Related commands:] none
[Default:] none
:line

111
doc/src/compute_stress_mop.txt Normal file
View File

@ -0,0 +1,111 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute stress/mop command :h3
compute stress/mop/profile command :h3
[Syntax:]
compute ID group-ID style dir args keywords ... :pre
ID, group-ID are documented in "compute"_compute.html command
style = {stress/mop} or {stress/mop/profile}
dir = {x} or {y} or {z} is the direction normal to the plane
args = argument specific to the compute style
keywords = {kin} or {conf} or {total} (one of more can be specified) :ul
{stress/mop} args = pos
pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
{stress/mop/profile} args = origin delta
origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
delta = value (distance units) is the distance between planes :pre
compute 1 all stress/mop x lower total
compute 1 liquid stress/mop z 0.0 kin conf
fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
compute 1 all stress/mop/profile x lower 0.1 total
compute 1 liquid stress/mop/profile z 0.0 0.25 kin conf
fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
[Description:]
Compute {stress/mop} and compute {stress/mop/profile} define computations that
calculate components of the local stress tensor using the method of
planes "(Todd)"_#mop-todd. Specifically in compute {stress/mop} calculates 3
components are computed in directions {dir},{x}; {dir},{y}; and
{dir},{z}; where {dir} is the direction normal to the plane, while
in compute {stress/mop/profile} the profile of the stress is computed.
Contrary to methods based on histograms of atomic stress (i.e. using
"compute stress/atom"_compute_stress_atom.html), the method of planes is
compatible with mechanical balance in heterogeneous systems and at
interfaces "(Todd)"_#mop-todd.
The stress tensor is the sum of a kinetic term and a configurational
term, which are given respectively by Eq. (21) and Eq. (16) in
"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that
atoms have crossed the plane if their positions at times t-dt and t are
one on either side of the plane, and uses the velocity at time t-dt/2
given by the velocity-Verlet algorithm.
Between one and three keywords can be used to indicate which
contributions to the stress must be computed: kinetic stress (kin),
configurational stress (conf), and/or total stress (total).
NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
NOTE 2: The local stress does not include any Lennard-Jones tail
corrections to the pressure added by the "pair_modify tail
yes"_pair_modify.html command, since those are contributions to the global system pressure.
[Output info:]
Compute {stress/mop} calculates a global vector (indices starting at 1), with 3
values for each declared keyword (in the order the keywords have been
declared). For each keyword, the stress tensor components are ordered as
follows: stress_dir,x, stress_dir,y, and stress_dir,z.
Compute {stress/mop/profile} instead calculates a global array, with 1 column
giving the position of the planes where the stress tensor was computed,
and with 3 columns of values for each declared keyword (in the order the
keywords have been declared). For each keyword, the profiles of stress
tensor components are ordered as follows: stress_dir,x; stress_dir,y;
and stress_dir,z.
The values are in pressure "units"_units.html.
The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder.
[Restrictions:]
These styles are part of the USER-MISC package. They are only enabled if
LAMMPS is built with that package. See the "Build package"_Build_package.html
doc page on for more info.
The method is only implemented for 3d orthogonal simulation boxes whose
size does not change in time, and axis-aligned planes.
The method only works with two-body pair interactions, because it
requires the class method pair->single() to be implemented. In
particular, it does not work with more than two-body pair interactions,
intra-molecular interactions, and long range (kspace) interactions.
[Related commands:]
"compute stress/atom"_compute_stress_atom.html
[Default:] none
:line
:link(mop-todd)
[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
Phys. Rev. E 52, 1627 (1995).

8
doc/src/computes.txt
View File

@ -6,6 +6,7 @@ Computes :h1
:maxdepth: 1
compute_ackland_atom
compute_adf
compute_angle
compute_angle_local
compute_angmom_chunk
@ -15,6 +16,7 @@ Computes :h1
compute_bond_local
compute_centro_atom
compute_chunk_atom
compute_chunk_spread_atom
compute_cluster_atom
compute_cna_atom
compute_cnp_atom
@ -66,12 +68,15 @@ Computes :h1
compute_pe_atom
compute_plasticity_atom
compute_pressure
compute_pressure_cylinder
compute_pressure_uef
compute_property_atom
compute_property_chunk
compute_property_local
compute_ptm_atom
compute_rdf
compute_reduce
compute_reduce_chunk
compute_rigid_local
compute_saed
compute_slice
@ -89,7 +94,7 @@ Computes :h1
compute_smd_tlsph_strain
compute_smd_tlsph_strain_rate
compute_smd_tlsph_stress
compute_smd_triangle_mesh_vertices
compute_smd_triangle_vertices
compute_smd_ulsph_num_neighs
compute_smd_ulsph_strain
compute_smd_ulsph_strain_rate
@ -98,6 +103,7 @@ Computes :h1
compute_sna_atom
compute_spin
compute_stress_atom
compute_stress_mop
compute_tally
compute_tdpd_cc_atom
compute_temp

2
doc/src/dihedral_nharmonic.txt
View File

@ -16,7 +16,7 @@ dihedral_style nharmonic :pre
[Examples:]
dihedral_style nharmonic
dihedral_coeff 3 10.0 20.0 30.0 :pre
dihedral_coeff * 3 10.0 20.0 30.0 :pre
[Description:]

26
doc/src/dihedral_style.txt
View File

@ -85,16 +85,24 @@ which are included in the LAMMPS distribution. The full list of all
dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
doc page.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style zero"_dihedral_zero.html - topology but no interactions
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"none"_dihedral_none.html - turn off dihedral interactions
"zero"_dihedral_zero.html - topology but no interactions
"hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
"charmm"_dihedral_charmm.html - CHARMM dihedral
"charmmfsw"_dihedral_charmm.html - CHARMM dihedral with force switching
"class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"cosine/shift/exp"_dihedral_cosine_shift_exp.html - dihedral with exponential in spring constant
"fourier"_dihedral_fourier.html - dihedral with multiple cosine terms
"harmonic"_dihedral_harmonic.html - harmonic dihedral
"helix"_dihedral_helix.html - helix dihedral
"multi/harmonic"_dihedral_multi_harmonic.html - dihedral with 5 harmonic terms
"nharmonic"_dihedral_nharmonic.html - same as multi-harmonic with N terms
"opls"_dihedral_opls.html - OPLS dihedral
"quadratic"_dihedral_quadratic.html - dihedral with quadratic term in angle
"spherical"_dihedral_spherical.html - dihedral which includes angle terms to avoid singularities
"table"_dihedral_table.html - tabulated dihedral
"table/cut"_dihedral_table_cut.html - tabulated dihedral with analytic cutoff :ul
:line

6
doc/src/dump_h5md.txt
View File

@ -50,7 +50,7 @@ dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" :pre
[Description:]
Dump a snapshot of atom coordinates every N timesteps in the
"HDF5"_HDF5_ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc.
"HDF5"_HDF5-ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc.
HDF5 files are binary, portable and self-describing. This dump style
will write only one file, on the root node.
@ -102,11 +102,11 @@ enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info. It also requires
(i) building the ch5md library provided with LAMMPS (See the "Build
package"_Build_package.html doc page for more info.) and (ii) having
the "HDF5"_HDF5_ws library installed (C bindings are sufficient) on
the "HDF5"_HDF5-ws library installed (C bindings are sufficient) on
your system. The library ch5md is compiled with the h5cc wrapper
provided by the HDF5 library.
:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
:link(HDF5-ws,http://www.hdfgroup.org/HDF5/)
:line

7
doc/src/dump_image.txt
View File

@ -384,12 +384,7 @@ change this via the "dump_modify"_dump_modify.html command.
:line
The {fix} keyword can be used with a "fix"_fix.html that produces
objects to be drawn. An example is the "fix
surface/global"_fix_surface_global.html command which can draw lines
or triangles for 2d/3d simulations.
NOTE: Aug 2016 - The fix surface/global command is not yet added to
LAMMPS.
objects to be drawn.
The {fflag1} and {fflag2} settings are numerical values which are
passed to the fix to affect how the drawing of its objects is done.

168
doc/src/fix.txt
View File

@ -167,136 +167,211 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"adapt"_fix_adapt.html - change a simulation parameter over time
"adapt/fep"_fix_adapt_fep.html -
"addforce"_fix_addforce.html - add a force to each atom
"addtorque"_fix_addtorque.html -
"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
"atc"_fix_atc.html -
"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
"aveforce"_fix_aveforce.html - add an averaged force to each atom
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
"ave/correlate/long"_fix_ave_correlate_long.html -
"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
"ave/histo/weight"_fix_ave_histo.html -
"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
"aveforce"_fix_aveforce.html - add an averaged force to each atom
"balance"_fix_balance.html - perform dynamic load-balancing
"bocs"_fix_bocs.html -
"bond/break"_fix_bond_break.html - break bonds on the fly
"bond/create"_fix_bond_create.html - create bonds on the fly
"bond/react"_fix_bond_react.html -
"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
"box/relax"_fix_box_relax.html - relax box size during energy minimization
"client/md"_fix_client_md.html -
"cmap"_fix_cmap.html -
"colvars"_fix_colvars.html -
"controller"_fix_controller.html -
"deform"_fix_deform.html - change the simulation box size/shape
"deposit"_fix_deposit.html - add new atoms above a surface
"dpd/energy"_fix_dpd_energy.html -
"drag"_fix_drag.html - drag atoms towards a defined coordinate
"drude"_fix_drude.html -
"drude/transform/direct"_fix_drude_transform.html -
"drude/transform/inverse"_fix_drude_transform.html -
"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
"edpd/source"_fix_dpd_source.html -
"efield"_fix_efield.html - impose electric field on system
"ehex"_fix_ehex.html - ehanced heat exchange algorithm
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
"eos/cv"_fix_eos_cv.html -
"eos/table"_fix_eos_table.html -
"eos/table/rx"_fix_eos_table_rx.html -
"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
"external"_fix_external.html - callback to an external driver program
"ffl"_fix_ffl.html -
"filter/corotate"_fix_filter_corotate.html -
"flow/gauss"_fix_flow_gauss.html -
"freeze"_fix_freeze.html - freeze atoms in a granular simulation
"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
"gld"_fix_gcmc.html - generalized Langevin dynamics integrator
"gld"_fix_gld.html -
"gle"_fix_gle.html -
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"grem"_fix_grem.html -
"halt"_fix_halt.html - terminate a dynamics run or minimization
"heat"_fix_heat.html - add/subtract momentum-conserving heat
"imd"_fix_imd.html -
"indent"_fix_indent.html - impose force due to an indenter
"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
"ipi"_fix_ipi.html -
"langevin"_fix_langevin.html - Langevin temperature control
"langevin/drude"_fix_langevin_drude.html -
"langevin/eff"_fix_langevin_eff.html -
"langevin/spin"_fix_langevin_spin.html -
"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
"lb/fluid"_fix_lb_fluid.html -
"lb/momentum"_fix_lb_momentum.html -
"lb/pc"_fix_lb_pc.html -
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
"lb/viscous"_fix_lb_viscous.html -
"lineforce"_fix_lineforce.html - constrain atoms to move in a line
"manifoldforce"_fix_manifoldforce.html -
"meso"_fix_meso.html -
"meso/stationary"_fix_meso_stationary.html -
"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
"move"_fix_move.html - move atoms in a prescribed fashion
"mscg"_fix_mscg.html -
"msst"_fix_msst.html - multi-scale shock technique (MSST) integration
"mvv/dpd"_fix_mvv_dpd.html -
"mvv/edpd"_fix_mvv_dpd.html -
"mvv/tdpd"_fix_mvv_dpd.html -
"neb"_fix_neb.html - nudged elastic band (NEB) spring forces
"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
"nph/body"_fix_nph_body.html -
"nph/body"_fix_nve_body.html - NPH for body particles
"nph/eff"_fix_nh_eff.html -
"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
"npt/body"_fix_npt_body.html -
"npt/body"_fix_nve_body.html - NPT for body particles
"npt/eff"_fix_nh_eff.html -
"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
"npt/uef"_fix_nh_uef.html -
"nve"_fix_nve.html - constant NVE time integration
"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces"
"nve/awpmd"_fix_nve_awpmd.html -
"nve/body"_fix_nve_body.html - NVE for body particles
"nve/dot"_fix_nve_dot.html -
"nve/dotc/langevin"_fix_nve_dotc_langevin.html -
"nve/eff"_fix_nve_eff.html -
"nve/limit"_fix_nve_limit.html - NVE with limited step length
"nve/line"_fix_nve_line.html - NVE for line segments
"nve/manifold/rattle"_fix_nve_manifold_rattle.html -
"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
"nve/spin"_fix_nve_spin.html -
"nve/tri"_fix_nve_tri.html - NVE for triangles
"nvk"_fix_nvk.html -
"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
"nvt/body"_fix_nve_body.html - NVT for body particles
"nvt/body"_fix_nvt_body.html -
"nvt/eff"_fix_nh_eff.html -
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
"nvt/sllod/eff"_fix_nvt_sllod_eff.html -
"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
"nvt/uef"_fix_nh_uef.html -
"oneway"_fix_oneway.html - constrain particles on move in one direction
"orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
"orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
"phonon"_fix_phonon.html -
"pimd"_fix_pimd.html -
"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
"poems"_fix_poems.html - constrain clusters of atoms to move \
as coupled rigid bodies
"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
"pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain
"press/berendsen"_fix_press_berendsen.html - pressure control by \
Berendsen barostat
"precession/spin"_fix_precession_spin.html -
"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
"print"_fix_print.html - print text and variables during a simulation
"property/atom"_fix_property_atom.html - add customized per-atom values
"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential \
"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method \
"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer \
"qeq/point"_fix_qeq.html - charge equilibration via point method \
"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method \
"qeq/slater"_fix_qeq.html - charge equilibration via Slater method \
"python/invoke"_fix_python_invoke.html -
"python/move"_fix_python_move.html -
"qbmsst"_fix_qbmsst.html -
"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
"qeq/point"_fix_qeq.html - charge equilibration via point method
"qeq/reax"_fix_qeq_reax.html -
"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
"qeq/slater"_fix_qeq.html - charge equilibration via Slater method
"qmmm"_fix_qmmm.html -
"qtb"_fix_qtb.html -
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
"recenter"_fix_recenter.html - constrain the center-of-mass position \
of a group of atoms
"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
"reax/c/bonds"_fix_reax_bonds.html -
"reax/c/species"_fix_reaxc_species.html -
"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
"rigid"_fix_rigid.html - constrain one or more clusters of atoms to \
move as a rigid body with NVE integration
"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to \
move as a rigid body with NPH integration
"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to \
move as a rigid body with NPT integration
"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to \
move as a rigid body with alternate NVE integration
"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to \
move as a rigid body with NVT integration
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with NVE integration
"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with NPH integration
"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with NPT integration
"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with alternate NVE integration
"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with NVT integration
"rhok"_fix_rhok.html -
"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
"rigid/nph/small"_fix_rigid.html -
"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
"rigid/npt/small"_fix_rigid.html -
"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/nve/small"_fix_rigid.html -
"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
"rigid/nvt/small"_fix_rigid.html -
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
"rx"_fix_rx.html -
"saed/vtk"_fix_saed_vtk.html -
"setforce"_fix_setforce.html - set the force on each atom
"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
"shardlow"_fix_shardlow.html -
"smd"_fix_smd.html -
"smd/adjust_dt"_fix_smd_adjust_dt.html -
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html -
"smd/setvel"_fix_smd_setvel.html -
"smd/wall_surface"_fix_smd_wall_surface.html -
"spring"_fix_spring.html - apply harmonic spring force to group of atoms
"spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms
"spring/rg"_fix_spring_rg.html - spring on radius of gyration of \
group of atoms
"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms
"spring/self"_fix_spring_self.html - spring from each atom to its origin
"srd"_fix_srd.html - stochastic rotation dynamics (SRD)
"store/force"_fix_store_force.html - store force on each atom
"store/state"_fix_store_state.html - store attributes for each atom
"temp/berendsen"_fix_temp_berendsen.html - temperature control by \
Berendsen thermostat
"tdpd/source"_fix_dpd_source.html -
"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat
"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
"temp/rescale"_fix_temp_rescale.html - temperature control by \
velocity rescaling
"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
"temp/rescale/eff"_fix_temp_rescale_eff.html -
"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for \
thermal conductivity calculation
"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
"ti/spring"_fix_ti_spring.html -
"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
"ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
"ttm/mod"_fix_ttm.html -
"tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
"vector"_fix_vector.html - accumulate a global vector every N timesteps
"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for \
viscosity calculation
"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
"viscous"_fix_viscous.html - viscous damping for granular simulations
"wall/body/polygon"_fix_wall_body_polygon.html -
"wall/body/polyhedron"_fix_wall_body_polyhedron.html -
"wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
"wall/ees"_fix_wall_ees.html -
"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
"wall/gran/region"_fix_wall_gran_region.html -
"wall/harmonic"_fix_wall.html - harmonic spring wall
"wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
"wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
@ -304,6 +379,7 @@ accelerated styles exist.
"wall/piston"_fix_wall_piston.html - moving reflective piston wall
"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
"wall/region"_fix_wall_region.html - use region surface as wall
"wall/region/ees"_fix_wall_ees.html -
"wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
[Restrictions:]

1
doc/src/fix_balance.txt
View File

@ -376,3 +376,4 @@ appear in {dimstr} for the {shift} style.
"group"_group.html, "processors"_processors.html, "balance"_balance.html
[Default:] none
:link(pizza,http://pizza.sandia.gov)

4
doc/src/fix_box_relax.txt
View File

@ -221,8 +221,8 @@ This equation only applies when the box dimensions are equal to those
of the reference dimensions. If this is not the case, then the
converged stress tensor will not equal that specified by the user. We
can resolve this problem by periodically resetting the reference
dimensions. The keyword {nreset_ref} controls how often this is done.
If this keyword is not used, or is given a value of zero, then the
dimensions. The keyword {nreset} controls how often this is done. If
this keyword is not used, or is given a value of zero, then the
reference dimensions are set to those of the initial simulation domain
and are never changed. A value of {nstep} means that every {nstep}
minimization steps, the reference dimensions are set to those of the

2
doc/src/fix_client_md.txt
View File

@ -50,7 +50,7 @@ md"_server_md.html doc page.
Note that when using LAMMPS as an MD client, your LAMMPS input script
should not normally contain force field commands, like a
"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or
"pair_style"_pair_style.html, "bond_style"_bond_style.html, or
"kspace_style"_kspace_style.html commmand. However it is possible for
a server code to only compute a portion of the full force-field, while
LAMMPS computes the remaining part. Your LAMMPS script can also

124
doc/src/fix_ffl.txt Normal file
View File

@ -0,0 +1,124 @@
<script type="text/javascript"
src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
</script>
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix ffl command :h3
[Syntax:]
fix ID id-group ffl tau Tstart Tstop seed \[flip-type\] :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
ffl = style name of this fix command :l
tau = thermostat parameter (positive real) :l
Tstart, Tstop = temperature ramp during the run :l
seed = random number seed to use for generating noise (positive integer) :l
one more value may be appended :l
flip-type = determines the flipping type, can be chosen between rescale - no_flip - hard - soft, if no flip type is given, rescale will be chosen by default :pre
:ule
[Examples:]
fix 3 boundary ffl 10 300 300 31415
fix 1 all ffl 100 500 500 9265 soft :pre
[Description:]
Apply a Fast-Forward Langevin Equation (FFL) thermostat as described
in "(Hijazi)"_#Hijazi. Contrary to
"fix langevin"_fix_langevin.html, this fix performs both
thermostatting and evolution of the Hamiltonian equations of motion, so it
should not be used together with "fix nve"_fix_nve.html -- at least not
on the same atom groups.
The time-evolution of a single particle undergoing Langevin dynamics is described
by the equations
\begin\{equation\} \frac \{dq\}\{dt\} = \frac\{p\}\{m\}, \end\{equation\}
\begin\{equation\} \frac \{dp\}\{dt\} = -\gamma p + W + F, \end\{equation\}
where \(F\) is the physical force, \(\gamma\) is the friction coefficient, and \(W\) is a
Gaussian random force.
The friction coefficient is the inverse of the thermostat parameter : \(\gamma = 1/\tau\), with \(\tau\) the thermostat parameter {tau}.
The thermostat parameter is given in the time units, \(\gamma\) is in inverse time units.
Equilibrium sampling a temperature T is obtained by specifying the
target value as the {Tstart} and {Tstop} arguments, so that the internal
constants depending on the temperature are computed automatically.
The random number {seed} must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
The flipping type {flip-type} can be chosen between 4 types described in
"(Hijazi)"_#Hijazi. The flipping operation occurs during the thermostatting
step and it flips the momenta of the atoms. If no_flip is chosen, no flip
will be executed and the integration will be the same as a standard
Langevin thermostat "(Bussi)"_#Bussi3. The other flipping types are : rescale - hard - soft.
[Restart, fix_modify, output, run start/stop, minimize info:]
The instantaneous values of the extended variables are written to
"binary restart files"_restart.html. Because the state of the random
number generator is not saved in restart files, this means you cannot
do "exact" restarts with this fix, where the simulation continues on
the same as if no restart had taken place. However, in a statistical
sense, a restarted simulation should produce the same behavior.
Note however that you should use a different seed each time you
restart, otherwise the same sequence of random numbers will be used
each time, which might lead to stochastic synchronization and
subtle artefacts in the sampling.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Howto_output.html. The scalar is the cumulative
energy change due to this fix. The scalar value calculated by this
fix is "extensive".
[Restrictions:]
In order to perform constant-pressure simulations please use
"fix press/berendsen"_fix_press_berendsen.html, rather than
"fix npt"_fix_nh.html, to avoid duplicate integration of the
equations of motion.
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style
dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html, "fix gle"_fix_gle.html
:line
:link(Hijazi)
[(Hijazi)] M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018)
:link(Bussi3)
[(Bussi)] G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)

1
doc/src/fix_freeze.txt
View File

@ -7,6 +7,7 @@
:line
fix freeze command :h3
fix freeze/kk command :h3
[Syntax:]

1
doc/src/fix_gravity.txt
View File

@ -8,6 +8,7 @@
fix gravity command :h3
fix gravity/omp command :h3
fix gravity/kk command :h3
[Syntax:]

3
doc/src/fix_halt.txt
View File

@ -135,8 +135,7 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output commands"_Howto_output.html.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
the "run"_run.html command.
[Restrictions:] none

2
doc/src/fix_msst.txt
View File

@ -6,7 +6,7 @@
:line
fix msst command :h3
fix msst command :h3
[Syntax:]

4
doc/src/fix_neb.txt
View File

@ -35,7 +35,7 @@ keyword = {parallel} or {perp} or {end} :l
fix 1 active neb 10.0
fix 2 all neb 1.0 perp 1.0 end last
fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre
fix 1 all neb 1.0 parallel ideal end last/efirst 1 :pre
[Description:]
@ -212,7 +212,7 @@ page for more info.
[Default:]
The option defaults are nudge = neigh, perp = 0.0, ends is not
The option defaults are parallel = neigh, perp = 0.0, ends is not
specified (no inter-replica force on the end replicas).
:line

56
doc/src/fix_nve_awpmd.txt Normal file
View File

@ -0,0 +1,56 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix nve/awpmd command :h3
[Syntax:]
fix ID group-ID nve/awpmd :pre
ID, group-ID are documented in "fix"_fix.html command
nve/awpmd = style name of this fix command :ul
[Examples:]
fix 1 all nve/awpmd :pre
[Description:]
Perform constant NVE integration to update position and velocity for
nuclei and electrons in the group for the "Antisymmetrized Wave Packet
Molecular Dynamics"_pair_awpmd.html model. V is volume; E is energy.
This creates a system trajectory consistent with the microcanonical
ensemble.
The operation of this fix is exactly like that described by the "fix
nve"_fix_nve.html command, except that the width and width-velocity of
the electron wavefunctions are also updated.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output commands"_Howto_output.html.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-AWPMD package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"fix nve"_fix_nve.html
[Default:] none

1
doc/src/fix_nve_sphere.txt
View File

@ -8,6 +8,7 @@
fix nve/sphere command :h3
fix nve/sphere/omp command :h3
fix nve/sphere/kk command :h3
[Syntax:]

9
doc/src/fix_nvt_sllod.txt
View File

@ -63,6 +63,11 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain
thermostat in a velocity Verlet formulation, closely following the
implementation used for the "fix nvt"_fix_nh.html command.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
Additional parameters affecting the thermostat are specified by
keywords and values documented with the "fix nvt"_fix_nh.html
command. See, for example, discussion of the {temp} and {drag}
@ -177,3 +182,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1.
:link(Daivis)
[(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006).
:link(Daivis-sllod)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

2
doc/src/fix_poems.txt
View File

@ -6,7 +6,7 @@
:line
fix poems :h3
fix poems command :h3
Syntax:

24
doc/src/fix_property_atom.txt
View File

@ -7,6 +7,7 @@
:line
fix property/atom command :h3
fix property/atom/kk command :h3
[Syntax:]
@ -201,6 +202,7 @@ added classes.
:line
:link(isotopes)
Example for using per-atom masses with TIP4P water to
study isotope effects. When setting up simulations with the "TIP4P
pair styles"_Howto_tip4p.html for water, you have to provide exactly
@ -238,6 +240,28 @@ set group hwat mass 2.0141018 :pre
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the per-atom values it stores to "binary restart

6
doc/src/fix_shake.txt
View File

@ -214,8 +214,10 @@ which can lead to poor energy conservation. You can test for this in
your system by running a constant NVE simulation with a particular set
of SHAKE parameters and monitoring the energy versus time.
SHAKE or RATTLE should not be used to constrain an angle at 180 degrees
(e.g. linear CO2 molecule). This causes numeric difficulties.
SHAKE or RATTLE should not be used to constrain an angle at 180
degrees (e.g. linear CO2 molecule). This causes numeric difficulties.
You can use "fix rigid or fix rigid/small"_fix_rigid.html instead to
make a linear molecule rigid.
[Related commands:] none

2
doc/src/fix_smd_move_triangulated_surface.txt
View File

@ -73,7 +73,7 @@ package"_Build_package.html doc page for more info.
[Related commands:]
"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html,
"smd/wall_surface"_fix_smd_wall_surface.html
[Default:] none

2
doc/src/fix_smd_wall_surface.txt
View File

@ -64,7 +64,7 @@ multiple objects in one file.
[Related commands:]
"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html,
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
"smd/tri_surface"_pair_smd_triangulated_surface.html

19
doc/src/fix_surface_global.txt
View File

@ -1,19 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix wall/surface/global command :h3
[Description:]
This feature is not yet implemented.
[Related commands:]
"dump image"_dump_image.html

23
doc/src/fix_wall_gran.txt
View File

@ -7,6 +7,7 @@
:line
fix wall/gran command :h3
fix wall/gran/omp command :h3
[Syntax:]
@ -136,6 +137,28 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
{vshear} < 0. In this case, {vshear} is the tangential velocity of
the wall at whatever {radius} has been defined.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the shear friction state of atoms interacting with the

4
doc/src/fixes.txt
View File

@ -26,6 +26,7 @@ Fixes :h1
fix_bond_swap
fix_bond_react
fix_box_relax
fix_client_md
fix_cmap
fix_colvars
fix_controller
@ -45,6 +46,7 @@ Fixes :h1
fix_eos_table_rx
fix_evaporate
fix_external
fix_ffl
fix_filter_corotate
fix_flow_gauss
fix_freeze
@ -91,6 +93,7 @@ Fixes :h1
fix_nve
fix_nve_asphere
fix_nve_asphere_noforce
fix_nve_awpmd
fix_nve_body
fix_nve_dot
fix_nve_dotc_langevin
@ -153,7 +156,6 @@ Fixes :h1
fix_srd
fix_store_force
fix_store_state
fix_surface_global
fix_temp_berendsen
fix_temp_csvr
fix_temp_rescale

19
doc/src/improper_style.txt
View File

@ -64,14 +64,19 @@ which are included in the LAMMPS distribution. The full list of all
improper styles is on the "Commands bond"_Commands_bond.html#improper
doc page.
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style zero"_improper_zero.html - topology but no interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"none"_improper_none.html - turn off improper interactions
"zero"_improper_zero.html - topology but no interactions
"hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
"improper_style cvff"_improper_cvff.html - CVFF improper
"improper_style harmonic"_improper_harmonic.html - harmonic improper
"improper_style umbrella"_improper_umbrella.html - DREIDING improper :ul
"class2"_improper_class2.html - COMPASS (class 2) improper
"cossq"_improper_cossq.html - improper with a cosine squared term
"cvff"_improper_cvff.html - CVFF improper
"distance"_improper_distance.html - improper based on distance between atom planes
"fourier"_improper_fourier.html - improper with multiple cosine terms
"harmonic"_improper_harmonic.html - harmonic improper
"inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition
"ring"_improper_ring.html - improper which prevents planar conformations
"umbrella"_improper_umbrella.html - DREIDING improper :ul
:line

2
doc/src/kspace_modify.txt
View File

@ -133,7 +133,7 @@ the code will stop with an error message. When this option is set to
For a typical application, using the automatic parameter generation
will provide simulations that are either inaccurate or slow. Using this
option is thus not recommended. For guidelines on how to obtain good
parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
parameters, see the "How-To"_Howto_dispersion.html discussion.
:line

4
doc/src/kspace_style.txt
View File

@ -383,8 +383,8 @@ dimensions. The only exception is if the slab option is set with
must be periodic and the z dimension must be non-periodic.
The scafacos KSpace style will only be enabled if LAMMPS is built with
the USER-SCAFACOS package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
the USER-SCAFACOS package. See the "Build package"_Build_package.html
doc page for more info.
The use of ScaFaCos in LAMMPS does not yet support molecular charged
systems where the short-range Coulombic interactions between atoms in

12
doc/src/lammps.book
View File

@ -67,6 +67,7 @@ Howto_multiple.html
Howto_replica.html
Howto_library.html
Howto_couple.html
Howto_client_server.html
Howto_output.html
Howto_chunk.html
Howto_2d.html
@ -265,6 +266,7 @@ fix_eos_table.html
fix_eos_table_rx.html
fix_evaporate.html
fix_external.html
fix_ffl.html
fix_filter_corotate.html
fix_flow_gauss.html
fix_freeze.html
@ -310,6 +312,7 @@ fix_npt_sphere.html
fix_nve.html
fix_nve_asphere.html
fix_nve_asphere_noforce.html
fix_nve_awpmd.html
fix_nve_body.html
fix_nve_dot.html
fix_nve_dotc_langevin.html
@ -373,7 +376,6 @@ fix_spring_self.html
fix_srd.html
fix_store_force.html
fix_store_state.html
fix_surface_global.html
fix_temp_berendsen.html
fix_temp_csvr.html
fix_temp_rescale.html
@ -402,6 +404,7 @@ lammps_commands_compute.html
compute.html
compute_modify.html
compute_ackland_atom.html
compute_adf.html
compute_angle.html
compute_angle_local.html
compute_angmom_chunk.html
@ -411,6 +414,7 @@ compute_bond.html
compute_bond_local.html
compute_centro_atom.html
compute_chunk_atom.html
compute_chunk_spread_atom.html
compute_cluster_atom.html
compute_cna_atom.html
compute_cnp_atom.html
@ -462,12 +466,15 @@ compute_pe.html
compute_pe_atom.html
compute_plasticity_atom.html
compute_pressure.html
compute_pressure_cylinder.html
compute_pressure_uef.html
compute_property_atom.html
compute_property_chunk.html
compute_property_local.html
compute_ptm_atom.html
compute_rdf.html
compute_reduce.html
compute_reduce_chunk.html
compute_rigid_local.html
compute_saed.html
compute_slice.html
@ -485,7 +492,7 @@ compute_smd_tlsph_shape.html
compute_smd_tlsph_strain.html
compute_smd_tlsph_strain_rate.html
compute_smd_tlsph_stress.html
compute_smd_triangle_mesh_vertices.html
compute_smd_triangle_vertices.html
compute_smd_ulsph_num_neighs.html
compute_smd_ulsph_strain.html
compute_smd_ulsph_strain_rate.html
@ -494,6 +501,7 @@ compute_smd_vol.html
compute_sna_atom.html
compute_spin.html
compute_stress_atom.html
compute_stress_mop.html
compute_tally.html
compute_tdpd_cc_atom.html
compute_temp.html

4
doc/src/message.txt
View File

@ -137,8 +137,8 @@ If LAMMPS is the server code, it will begin receiving messages when
the "server"_server.html command is invoked.
A fix client command will terminate its messaging with the server when
LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The
server command will terminate its messaging with the client when the
LAMMPS ends, or the fix is deleted via the "unfix"_unfix.html command.
The server command will terminate its messaging with the client when the
client signals it. Then the remainder of the LAMMPS input script will
be processed.

13
doc/src/minimize.txt
View File

@ -216,10 +216,10 @@ The "fix box/relax"_fix_box_relax.html command can be used to apply an
external pressure to the simulation box and allow it to shrink/expand
during the minimization.
Only a few other fixes (typically those that apply force constraints)
are invoked during minimization. See the doc pages for individual
"fix"_fix.html commands to see which ones are relevant. Current
examples of fixes that can be used include:
Only a few other fixes (typically those that add forces) are invoked
during minimization. See the doc pages for individual "fix"_fix.html
commands to see which ones are relevant. Current examples of fixes
that can be used include:
"fix addforce"_fix_addforce.html
"fix addtorque"_fix_addtorque.html
@ -242,6 +242,11 @@ you MUST enable the "fix_modify"_fix_modify.html {energy} option for
that fix. The doc pages for individual "fix"_fix.html commands
specify if this should be done.
NOTE: The minimizers in LAMMPS do not allow for bonds (or angles, etc)
to be held fixed while atom coordinates are being relaxed, e.g. via
"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. See more
info in the Restrictions section below.
:line
[Restrictions:]

2
doc/src/pair_body_nparticle.txt
View File

@ -6,7 +6,7 @@
:line
pair_style body command :h3
pair_style body/nparticle command :h3
[Syntax:]

27
doc/src/pair_born.txt
View File

@ -11,39 +11,34 @@ pair_style born command :h3
pair_style born/omp command :h3
pair_style born/gpu command :h3
pair_style born/coul/long command :h3
pair_style born/coul/long/cs command :h3
pair_style born/coul/long/cs/gpu command :h3
pair_style born/coul/long/gpu command :h3
pair_style born/coul/long/omp command :h3
pair_style born/coul/msm command :h3
pair_style born/coul/msm/omp command :h3
pair_style born/coul/wolf command :h3
pair_style born/coul/wolf/cs command :h3
pair_style born/coul/wolf/cs/gpu command :h3
pair_style born/coul/wolf/gpu command :h3
pair_style born/coul/wolf/omp command :h3
pair_style born/coul/dsf command :h3
pair_style born/coul/dsf/cs command :h3
[Syntax:]
pair_style style args :pre
style = {born} or {born/coul/long} or {born/coul/long/cs} or {born/coul/msm} or {born/coul/wolf}
style = {born} or {born/coul/long} or {born/coul/msm} or {born/coul/wolf}
args = list of arguments for a particular style :ul
{born} args = cutoff
cutoff = global cutoff for non-Coulombic interactions (distance units)
{born/coul/long} or {born/coul/long/cs} args = cutoff (cutoff2)
{born/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{born/coul/msm} args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{born/coul/wolf} or {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
{born/coul/wolf} args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{born/coul/dsf} or {born/coul/dsf/cs} args = alpha cutoff (cutoff2)
{born/coul/dsf} args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (distance units) :pre
@ -55,9 +50,7 @@ pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/long 10.0
pair_style born/coul/long/cs 10.0
pair_style born/coul/long 10.0 8.0
pair_style born/coul/long/cs 10.0 8.0
pair_style born/coul/long 10.0 8.
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
@ -68,7 +61,6 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/wolf 0.25 10.0
pair_style born/coul/wolf 0.25 10.0 9.0
pair_style born/coul/wolf/cs 0.25 10.0 9.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
@ -107,13 +99,6 @@ Wolf potential in the "coul/wolf"_pair_coul.html pair style.
The {born/coul/dsf} style computes the Coulomb contribution with the
damped shifted force model as in the "coul/dsf"_pair_coul.html style.
Style {born/coul/long/cs} is identical to {born/coul/long} except that
a term is added for the "core/shell model"_Howto_coreshell.html to
allow charges on core and shell particles to be separated by r = 0.0.
The same correction is introduced for the {born/coul/dsf/cs} style
which is identical to {born/coul/dsf}. And likewise for
{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
Note that these potentials are related to the "Buckingham
potential"_pair_buck.html.
@ -174,7 +159,7 @@ for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.
The {born/coul/long} pair style supports the
"pair_modify"_pair_modify.html table option ti tabulate the
"pair_modify"_pair_modify.html table option to tabulate the
short-range portion of the long-range Coulombic interaction.
These styles support the pair_modify tail option for adding long-range

14
doc/src/pair_buck.txt
View File

@ -17,7 +17,6 @@ pair_style buck/coul/cut/intel command :h3
pair_style buck/coul/cut/kk command :h3
pair_style buck/coul/cut/omp command :h3
pair_style buck/coul/long command :h3
pair_style buck/coul/long/cs command :h3
pair_style buck/coul/long/gpu command :h3
pair_style buck/coul/long/intel command :h3
pair_style buck/coul/long/kk command :h3
@ -29,14 +28,14 @@ pair_style buck/coul/msm/omp command :h3
pair_style style args :pre
style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/long/cs} or {buck/coul/msm}
style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm}
args = list of arguments for a particular style :ul
{buck} args = cutoff
cutoff = global cutoff for Buckingham interactions (distance units)
{buck/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/long} or {buck/coul/long/cs} args = cutoff (cutoff2)
{buck/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/msm} args = cutoff (cutoff2)
@ -56,9 +55,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre
pair_style buck/coul/long 10.0
pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long 10.0 8.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
@ -92,10 +89,6 @@ A,C and Coulombic terms. If two cutoffs are specified, the first is
used as the cutoff for the A,C terms, and the second is the cutoff for
the Coulombic term.
Style {buck/coul/long/cs} is identical to {buck/coul/long} except that
a term is added for the "core/shell model"_Howto_coreshell.html to
allow charges on core and shell particles to be separated by r = 0.0.
Note that these potentials are related to the "Born-Mayer-Huggins
potential"_pair_born.html.
@ -184,8 +177,7 @@ respa"_run_style.html command. They do not support the {inner},
[Restrictions:]
The {buck/coul/long} style is part of the KSPACE package. The
{buck/coul/long/cs} style is part of the CORESHELL package. They are
The {buck/coul/long} style is part of the KSPACE package. They are
only enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.

4
doc/src/pair_buck6d_coul_gauss.txt
View File

@ -6,8 +6,8 @@
:line
pair_style buck6d/coul/gauss/dsf :h3
pair_style buck6d/coul/gauss/long :h3
pair_style buck6d/coul/gauss/dsf command :h3
pair_style buck6d/coul/gauss/long command :h3
[Syntax:]

3
doc/src/pair_charmm.txt
View File

@ -8,12 +8,15 @@
pair_style lj/charmm/coul/charmm command :h3
pair_style lj/charmm/coul/charmm/intel command :h3
pair_style lj/charmm/coul/charmm/kk command :h3
pair_style lj/charmm/coul/charmm/omp command :h3
pair_style lj/charmm/coul/charmm/implicit command :h3
pair_style lj/charmm/coul/charmm/implicit/kk command :h3
pair_style lj/charmm/coul/charmm/implicit/omp command :h3
pair_style lj/charmm/coul/long command :h3
pair_style lj/charmm/coul/long/gpu command :h3
pair_style lj/charmm/coul/long/intel command :h3
pair_style lj/charmm/coul/long/kk command :h3
pair_style lj/charmm/coul/long/opt command :h3
pair_style lj/charmm/coul/long/omp command :h3
pair_style lj/charmm/coul/msm command :h3

19
doc/src/pair_coul.txt
View File

@ -19,8 +19,6 @@ pair_style coul/dsf/gpu command :h3
pair_style coul/dsf/kk command :h3
pair_style coul/dsf/omp command :h3
pair_style coul/long command :h3
pair_style coul/long/cs command :h3
pair_style coul/long/cs/gpu command :h3
pair_style coul/long/omp command :h3
pair_style coul/long/gpu command :h3
pair_style coul/long/kk command :h3
@ -30,7 +28,6 @@ pair_style coul/streitz command :h3
pair_style coul/wolf command :h3
pair_style coul/wolf/kk command :h3
pair_style coul/wolf/omp command :h3
pair_style coul/wolf/cs command :h3
pair_style tip4p/cut command :h3
pair_style tip4p/long command :h3
pair_style tip4p/cut/omp command :h3
@ -42,10 +39,8 @@ pair_style coul/cut cutoff
pair_style coul/debye kappa cutoff
pair_style coul/dsf alpha cutoff
pair_style coul/long cutoff
pair_style coul/long/cs cutoff
pair_style coul/long/gpu cutoff
pair_style coul/wolf alpha cutoff
pair_style coul/wolf/cs alpha cutoff
pair_style coul/streitz cutoff keyword alpha
pair_style tip4p/cut otype htype btype atype qdist cutoff
pair_style tip4p/long otype htype btype atype qdist cutoff :pre
@ -68,14 +63,12 @@ pair_style coul/dsf 0.05 10.0
pair_coeff * * :pre
pair_style coul/long 10.0
pair_style coul/long/cs 10.0
pair_coeff * * :pre
pair_style coul/msm 10.0
pair_coeff * * :pre
pair_style coul/wolf 0.2 9.0
pair_style coul/wolf/cs 0.2 9.0
pair_coeff * * :pre
pair_style coul/streitz 12.0 ewald
@ -204,12 +197,6 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {coul/long/cs} is identical to {coul/long} except that a term is
added for the "core/shell model"_Howto_coreshell.html to allow charges
on core and shell particles to be separated by r = 0.0. The same
correction is introduced for the {coul/wolf/cs} style which is
identical to {coul/wolf}.
Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces
a massless site located a short distance away from the oxygen atom
@ -317,9 +304,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
KSPACE package. The {coul/long/cs} style is part of the CORESHELL
package. They are only enabled if LAMMPS was built with that package.
See the "Build package"_Build_package.html doc page for more info.
KSPACE package. They are only enabled if LAMMPS was built with that
package. See the "Build package"_Build_package.html doc page for more
info.
[Related commands:]

9
doc/src/pair_coul_shield.txt
View File

@ -38,7 +38,8 @@ charge and molecule ID information is included.
Where Tap(r_ij) is the taper function which provides a continuous cutoff
(up to third derivative) for inter-atomic separations larger than r_c
"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1.
Here {lambda} is the shielding parameter that
eliminates the short-range singularity of the classical mono-polar
electrostatic interaction expression "(Maaravi)"_#Maaravi1.
@ -82,5 +83,11 @@ package"_Build_package.html doc page for more info.
:line
:link(Leven3)
[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
:link(Leven4)
[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
:link(Maaravi1)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

136
doc/src/pair_cs.txt
View File

@ -6,49 +6,74 @@
:line
pair_style born/coul/long/cs command :h3
pair_style buck/coul/long/cs command :h3
pair_style born/coul/dsf/cs command :h3
pair_style born/coul/long/cs command :h3
pair_style born/coul/long/cs/gpu command :h3
pair_style born/coul/wolf/cs command :h3
pair_style born/coul/wolf/cs/gpu command :h3
pair_style buck/coul/long/cs command :h3
pair_style coul/long/cs command :h3
pair_style coul/long/cs/gpu command :h3
pair_style coul/wolf/cs command :h3
pair_style lj/cut/coul/long/cs command :h3
[Syntax:]
pair_style style args :pre
style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs}
style = {born/coul/dsf/cs} or {born/coul/long/cs} or {born/coul/wolf/cs} or {buck/coul/long/cs} or {coul/long/cs} or {coul/wolf/cs} or {lj/cut/coul/long/cs}
args = list of arguments for a particular style :ul
{born/coul/long/cs} args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/long/cs} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{born/coul/dsf/cs} args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (distance units) :pre
cutoff2 = global cutoff for Coulombic (distance units)
{born/coul/long/cs} args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{born/coul/wolf/cs} args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/long/cs} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{coul/long} args = cutoff
cutoff = global cutoff for Coulombic (distance units)
{coul/wolf} args = alpha cutoff
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for Coulombic (distance units)
{lj/cut/coul/long/cs} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
pair_style born/coul/dsf/cs 0.1 10.0 12.0
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
pair_style born/coul/long/cs 10.0 8.0
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/wolf/cs 0.25 10.0 12.0
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
pair_style born/coul/dsf/cs 0.1 10.0 12.0
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
pair_style coul/long/cs 10.0
pair_coeff * * :pre
pair_style born/coul/wolf/cs 0.25 10.0 12.0
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
pair_style coul/wolf/cs 0.2 9.0
pair_coeff * * :pre
pair_style lj/cut/coul/long/cs 10.0
pair_style lj/cut/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
[Description:]
@ -57,16 +82,28 @@ core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See
the "Howto coreshell"_Howto_coreshell.html doc page for an overview of
the model as implemented in LAMMPS.
The styles with a {coul/long} term are identical to the "pair_style
born/coul/long"_pair_born.html and "pair_style
buck/coul/long"_pair_buck.html styles, except they correctly treat the
special case where the distance between two charged core and shell
atoms in the same core/shell pair approach r = 0.0. This needs
special treatment when a long-range solver for Coulombic interactions
is also used, i.e. via the "kspace_style"_kspace_style.html command.
All the styles are identical to the corresponding pair style without
the "/cs" in the name:
More specifically, the short-range Coulomb interaction between a core
and its shell should be turned off using the
"pair_style born/coul/dsf"_pair_born.html
"pair_style born/coul/long"_pair_born.html
"pair_style born/coul/wolf"_pair_born.html
"pair_style buck/coul/long"_pair_buck.html
"pair_style coul/long"_pair_coul.html
"pair_style coul/wolf"_pair_coul.html
"pair_style lj/cut/coul/long"_pair_lj.html :ul
except that they correctly treat the special case where the distance
between two charged core and shell atoms in the same core/shell pair
approach r = 0.0.
Styles with a "/long" in the name are used with a long-range solver
for Coulombic interactions via the "kspace_style"_kspace_style.html
command. They require special treatment of the short-range Coulombic
interactions within the cor/shell model.
Specifically, the short-range Coulomb interaction between a core and
its shell should be turned off using the
"special_bonds"_special_bonds.html command by setting the 1-2 weight
to 0.0, which works because the core and shell atoms are bonded to
each other. This induces a long-range correction approximation which
@ -81,21 +118,42 @@ where C is an energy-conversion constant, Qi and Qj are the charges on
the core and shell, epsilon is the dielectric constant and r_min is the
minimal distance.
The pair style {born/coul/dsf/cs} is identical to the
"pair_style born/coul/dsf"_pair_born.html style, which uses
the damped shifted force model as in "coul/dsf"_pair_coul.html
to compute the Coulomb contribution. This approach does not require
a long-range solver, thus the only correction is the addition of a
minimal distance to avoid the possible r = 0.0 case for a
core/shell pair.
For styles that are not used with a long-range solver, i.e. those with
"/dsf" or "/wolf" in the name, the only correction is the addition of
a minimal distance to avoid the possible r = 0.0 case for a core/shell
pair.
The pair style {born/coul/wolf/cs} is identical to the
"pair_style born/coul/wolf"_pair_born.html style, which uses
the Wolf summation as in "coul/wolf"_pair_coul.html to compute
the Coulomb contribution. This approach does not require
a long-range solver, thus the only correction is the addition of a
minimal distance to avoid the possible r = 0.0 case for a
core/shell pair.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
See the corresponding doc pages for pair styles without the "cs"
suffix to see how mixing, shifting, tabulation, tail correction,
restarting, and rRESPA are handled by theses pair styles.
:line
[Restrictions:]

1
doc/src/pair_dipole.txt
View File

@ -13,6 +13,7 @@ pair_style lj/sf/dipole/sf command :h3
pair_style lj/sf/dipole/sf/gpu command :h3
pair_style lj/sf/dipole/sf/omp command :h3
pair_style lj/cut/dipole/long command :h3
pair_style lj/cut/dipole/long/gpu command :h3
pair_style lj/long/dipole/long command :h3
[Syntax:]

10
doc/src/pair_eam.txt
View File

@ -20,6 +20,8 @@ pair_style eam/alloy/omp command :h3
pair_style eam/alloy/opt command :h3
pair_style eam/cd command :h3
pair_style eam/cd/omp command :h3
pair_style eam/cd/old command :h3
pair_style eam/cd/old/omp command :h3
pair_style eam/fs command :h3
pair_style eam/fs/gpu command :h3
pair_style eam/fs/intel command :h3
@ -31,7 +33,7 @@ pair_style eam/fs/opt command :h3
pair_style style :pre
style = {eam} or {eam/alloy} or {eam/cd} or {eam/fs} :ul
style = {eam} or {eam/alloy} or {eam/cd} or {eam/cd/old} or {eam/fs} :ul
[Examples:]
@ -268,7 +270,8 @@ Style {eam/cd} is similar to the {eam/alloy} style, except that it
computes alloy pairwise interactions using the concentration-dependent
embedded-atom method (CD-EAM). This model can reproduce the enthalpy
of mixing of alloys over the full composition range, as described in
"(Stukowski)"_#Stukowski.
"(Stukowski)"_#Stukowski. Style {eam/cd/old} is an older, slightly
different and slower two-site formulation of the model "(Caro)"_#Caro.
The pair_coeff command is specified the same as for the {eam/alloy}
style. However the DYNAMO {setfl} file must has two
@ -442,3 +445,6 @@ Daw, Baskes, Phys Rev B, 29, 6443 (1984).
:link(Stukowski)
[(Stukowski)] Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
Materials Science & Engineering, 7, 075005 (2009).
:link(Caro)
[(Caro)] A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)

1
doc/src/pair_edip.txt
View File

@ -7,6 +7,7 @@
:line
pair_style edip command :h3
pair_style edip/omp command :h3
pair_style edip/multi command :h3
[Syntax:]

3
doc/src/pair_gran.txt
View File

@ -7,9 +7,10 @@
:line
pair_style gran/hooke command :h3
pair_style gran/omp command :h3
pair_style gran/hooke/omp command :h3
pair_style gran/hooke/history command :h3
pair_style gran/hooke/history/omp command :h3
pair_style gran/hooke/history/kk command :h3
pair_style gran/hertz/history command :h3
pair_style gran/hertz/history/omp command :h3

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