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Merge branch 'master' into restart-consistency 

# Conflicts:
#	doc/src/fix_halt.rst
This commit is contained in:
Axel Kohlmeyer 2020-03-18 20:30:00 -04:00
parent cf48a0f01d d1388b4ea8
commit 3e36acc533
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
1215 changed files with 7690 additions and 15148 deletions
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16
cmake/CMakeLists.txt
View File

@ -255,8 +255,9 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(LAPACK)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
if(CMAKE_GENERATOR STREQUAL "Ninja")
status(FATAL_ERROR "Cannot build internal linear algebra library with Ninja build tool due to lack for Fortran support")
include(CheckGeneratorSupport)
if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
endif()
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
@ -587,14 +588,14 @@ if(BUILD_TOOLS)
add_executable(binary2txt ${LAMMPS_TOOLS_DIR}/binary2txt.cpp)
install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
# ninja-build currently does not support fortran. thus we skip building this tool
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(STATUS "Skipping building 'chain.x' with Ninja build tool due to lack of Fortran support")
else()
include(CheckGeneratorSupport)
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
else()
message(WARNING "CMake build doesn't support fortran, skipping building 'chain.x'")
endif()
enable_language(C)
@ -686,6 +687,7 @@ feature_summary(DESCRIPTION "The following tools and libraries have been found a
message(STATUS "<<< Build configuration >>>
Build type ${CMAKE_BUILD_TYPE}
Install path ${CMAKE_INSTALL_PREFIX}
Generator ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}
Compilers and Flags:
C++ Compiler ${CMAKE_CXX_COMPILER}
Type ${CMAKE_CXX_COMPILER_ID}
@ -718,7 +720,7 @@ else()
endif()
message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
if(BUILD_MPI)
message(STATUS "Using MPI with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
message(STATUS "Using MPI with headers in ${MPI_CXX_INCLUDE_PATH} and these libraries: ${MPI_CXX_LIBRARIES};${MPI_Fortran_LIBRARIES}")
endif()
if(PKG_GPU)
message(STATUS "GPU API: ${GPU_API}")

21
cmake/Modules/CheckGeneratorSupport.cmake Normal file
View File

@ -0,0 +1,21 @@
# ninja-build<1.10 does not support fortran.
if(CMAKE_GENERATOR STREQUAL "Ninja")
set(CMAKE_GENERATOR_SUPPORT_FORTRAN FALSE)
execute_process(COMMAND "${CMAKE_MAKE_PROGRAM}" --version
OUTPUT_VARIABLE NINJA_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE
RESULT_VARIABLE _Ninja_version_result
)
if(_Ninja_version_result)
message(WARNING "Unable to determine ninja version: ${_Ninja_version_result}, assuming fortran isn't supported")
elseif(NINJA_VERSION VERSION_LESS "1.10")
message(WARNING "Ninja build tool too old, to compile Fortran code, please install ninja-1.10 or newer")
else()
set(CMAKE_GENERATOR_SUPPORT_FORTRAN TRUE)
endif()
else()
set(CMAKE_GENERATOR_SUPPORT_FORTRAN TRUE)
if(NOT CMAKE_GENERATOR STREQUAL "Unix Makefiles")
message(WARNING "Assuming fortran is supported for ${CMAKE_GENERATOR}")
endif()
endif()

14
cmake/Modules/Packages/KIM.cmake
View File

@ -34,26 +34,22 @@ if(PKG_KIM)
endif()
option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
if(DOWNLOAD_KIM)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
endif()
message(STATUS "KIM-API download requested - we will build our own")
include(CheckLanguage)
include(ExternalProject)
enable_language(C)
check_language(Fortran)
if(NOT CMAKE_Fortran_COMPILER)
message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
endif()
enable_language(Fortran)
ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
BINARY_DIR build
CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
BUILD_BYPRODUCTS <INSTALL_DIR>/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}
)
ExternalProject_get_property(kim_build INSTALL_DIR)
set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)

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

@ -8,9 +8,6 @@ if(PKG_LATTE)
endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
endif()
message(STATUS "LATTE download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
@ -21,6 +18,8 @@ if(PKG_LATTE)
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
BUILD_BYPRODUCTS <INSTALL_DIR>/${CMAKE_INSTALL_LIBDIR}/liblatte.a
)
ExternalProject_get_property(latte_build INSTALL_DIR)
set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)

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

@ -8,9 +8,6 @@ if(PKG_MSCG)
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
endif()
include(ExternalProject)
if(NOT LAPACK_FOUND)
set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
@ -19,8 +16,16 @@ if(PKG_MSCG)
URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
URL_MD5 8c45e269ee13f60b303edd7823866a91
SOURCE_SUBDIR src/CMake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
BUILD_COMMAND make mscg INSTALL_COMMAND ""
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
BUILD_COMMAND ${CMAKE_COMMAND} --build . --target mscg
INSTALL_COMMAND ""
BUILD_BYPRODUCTS <BINARY_DIR>/libmscg.a
)
ExternalProject_get_property(mscg_build BINARY_DIR)
set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)

17
cmake/Modules/Packages/USER-COLVARS.cmake
View File

@ -5,22 +5,7 @@ if(PKG_USER-COLVARS)
file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
# Build Lepton by default
set(COLVARS_LEPTON_DEFAULT ON)
# but not if C++11 is disabled per user request
if(DEFINED DISABLE_CXX11_REQUIREMENT)
if(DISABLE_CXX11_REQUIREMENT)
set(COLVARS_LEPTON_DEFAULT OFF)
endif()
endif()
option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})
# Verify that the user's choice is consistent
if(DEFINED DISABLE_CXX11_REQUIREMENT)
if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
endif()
endif()
option(COLVARS_LEPTON "Build and link the Lepton library" ON)
if(COLVARS_LEPTON)
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)

2
cmake/Modules/Packages/USER-NETCDF.cmake
View File

@ -1,6 +1,6 @@
if(PKG_USER-NETCDF)
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
find_package(NetCDF)
if(NETCDF_FOUND)
find_package(PNetCDF)

11
cmake/Modules/Packages/USER-PLUMED.cmake
View File

@ -29,9 +29,6 @@ if(PKG_USER-PLUMED)
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool")
endif()
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
@ -47,6 +44,13 @@ if(PKG_USER-PLUMED)
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
message(STATUS "PLUMED download requested - we will build our own")
if(PLUMED_MODE STREQUAL "STATIC")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
elseif(PLUMED_MODE STREQUAL "SHARED")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
endif()
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
@ -59,6 +63,7 @@ if(PKG_USER-PLUMED)
${PLUMED_CONFIG_OMP}
CXX=${PLUMED_CONFIG_CXX}
CC=${PLUMED_CONFIG_CC}
BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
set(PLUMED_INSTALL_DIR ${INSTALL_DIR})

20
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -4,6 +4,7 @@ if(PKG_USER-SCAFACOS)
find_package(GSL REQUIRED)
find_package(PkgConfig QUIET)
find_package(MPI REQUIRED)
set(DOWNLOAD_SCAFACOS_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(SCAFACOS QUIET scafacos)
@ -13,9 +14,6 @@ if(PKG_USER-SCAFACOS)
endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
endif()
message(STATUS "ScaFaCoS download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(scafacos_build
@ -29,6 +27,22 @@ if(PKG_USER-SCAFACOS)
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
F77=
BUILD_BYPRODUCTS
<INSTALL_DIR>/lib/libfcs.a
<INSTALL_DIR>/lib/libfcs_direct.a
<INSTALL_DIR>/lib/libfcs_ewald.a
<INSTALL_DIR>/lib/libfcs_fmm.a
<INSTALL_DIR>/lib/libfcs_p2nfft.a
<INSTALL_DIR>/lib/libfcs_p3m.a
<INSTALL_DIR>/lib/libfcs_near.a
<INSTALL_DIR>/lib/libfcs_gridsort.a
<INSTALL_DIR>/lib/libfcs_resort.a
<INSTALL_DIR>/lib/libfcs_redist.a
<INSTALL_DIR>/lib/libfcs_common.a
<INSTALL_DIR>/lib/libfcs_pnfft.a
<INSTALL_DIR>/lib/libfcs_pfft.a
<INSTALL_DIR>/lib/libfcs_fftw3_mpi.a
<INSTALL_DIR>/lib/libfcs_fftw3.a
)
ExternalProject_get_property(scafacos_build INSTALL_DIR)
set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})

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

@ -7,9 +7,6 @@ if(PKG_VORONOI)
endif()
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
if(DOWNLOAD_VORO)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
endif()
message(STATUS "Voro++ download requested - we will build our own")
include(ExternalProject)
@ -29,6 +26,7 @@ if(PKG_VORONOI)
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
)
ExternalProject_get_property(voro_build SOURCE_DIR)
set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)

8
cmake/README.md
View File

@ -217,7 +217,7 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
</tr>
<tr>
<td><code>CMAKE_VERBOSE_MAKEFILE</code></td>
<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achieved by adding `VERBOSE=1` to the `make` call.</td>
<td>
<dl>
<dt><code>off</code> (default)</dt>
@ -576,7 +576,7 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
Several fixes and a pair style that have Monte Carlo (MC) or MC-like
attributes. These include fixes for creating, breaking, and swapping bonds,
for performing atomic swaps, and performing grand-canonical MC (GCMC) in
conjuction with dynamics.
conjunction with dynamics.
</td>
<td>
<dl>
@ -1383,8 +1383,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
Some potentials that are also implemented in the Yet Another Force Field (YAFF) code.
The expressions and their use are discussed in the following papers:
<ul>
<li><a href="http://dx.doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
<li><a href="http://dx.doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
<li><a href="https://doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
<li><a href="https://doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
</ul>
</td>
<td>

6
cmake/presets/all_off.cmake
View File

@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

6
cmake/presets/all_on.cmake
View File

@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

14
cmake/presets/most.cmake
View File

@ -2,13 +2,13 @@
# external libraries. Compared to all_on.cmake some more unusual packages
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
USER-DRUDE USER-FEP USER-MEAMC USER-MESO
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
USER-SPH USER-SMD USER-UEF USER-YAFF)
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

2
doc/Makefile
View File

@ -78,7 +78,7 @@ html: $(ANCHORCHECK) $(MATHJAX)
@cp -r src/PDF html/PDF
@cp -r src/USER html/USER
@mkdir -p html/JPG
@cp `grep -A2 '\.\. image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
@cp `grep -A2 '\.\. .*image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
@rm -rf html/PDF/.[sg]*
@rm -rf html/USER/.[sg]*
@rm -rf html/USER/*/.[sg]*

2
doc/msi2lmp.1
View File

@ -31,7 +31,7 @@ of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
in the current working directory.
.B msi2lmp
will then read and process those files according to its remaining settings.
All other settins are optional and have defaults as listed.
All other settings are optional and have defaults as listed.
.TP
\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
The \-c or \-class option selects the force field class, i.e which pair

2
doc/src/2001/README.html
View File

@ -10,7 +10,7 @@ LAMMPS</H2>
LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
<P>
This is the documentation for the LAMMPS 2001 version, written in F90,
which has been superceded by more current versions. See the <A
which has been superseded by more current versions. See the <A
HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
Site</A> for more information.
<P>

2
doc/src/2001/basics.html
View File

@ -47,7 +47,7 @@ directories: </P>
<P>
The src directory contains the F90 and C source files for LAMMPS as
well as several sample Makefiles for different machines. To make LAMMPS
for a specfic machine, you simply type</P>
for a specific machine, you simply type</P>
<P>
make machine</P>
<P>

6
doc/src/2001/input_commands.html
View File

@ -1079,7 +1079,7 @@ for style aveforce, average force on the group of fixed atoms is computed,
to new total value -> has effect of applying same force to entire group
of atoms
thermostatting constraints (rescale, hoover/drag, langevin) cannot be used in
conjuction with global &quot;temp control&quot;, since they conflict and will
conjunction with global &quot;temp control&quot;, since they conflict and will
cause atom velocities to be reset twice
thermostatting constraints (rescale, hoover/drag, langevin) cannot be used
when performing a minimization
@ -1089,7 +1089,7 @@ meaning of rescale and Langevin thermostatting coefficients is same as in
&quot;temp control&quot; command
for rescale style, it can be used as a coarse temperature rescaler,
for example &quot;rescale 200.0 300.0 100 10.0 1.0&quot; will ramp the temperature
up during the simulation, resetting it to the target temperatue as needed
up during the simulation, resetting it to the target temperature as needed
for rescale style, it can be used to create an instantaneous
drag force that slowly rescales the temperature without oscillation,
for example &quot;rescale 300.0 300.0 1 0.0 0.0001&quot; will force (or keep)
@ -1952,7 +1952,7 @@ for rescale style, the amount of rescaling is contfolled by the fractional
to halfway between the current and target temperature
for rescale style, it can be used as a coarse temperature rescaler,
for example "rescale 200.0 300.0 100 10.0 1.0" will ramp the temperature
up during the simulation, resetting it to the target temperatue as needed
up during the simulation, resetting it to the target temperature as needed
for rescale style, it can be used to create an instantaneous
drag force that slowly rescales the temperature without oscillation,
for example "rescale 300.0 300.0 1 0.0 0.0001" will force (or keep)

2
doc/src/99/README.html
View File

@ -10,7 +10,7 @@ LAMMPS</H2>
LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
<P>
This is the documentation for the LAMMPS 99 version, written in F77,
which has been superceded by more current versions. See the <A
which has been superseded by more current versions. See the <A
HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
Site</A> for more information.
<P>

2
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View File

@ -45,7 +45,7 @@ directories: </P>
<P>
The src directory contains the F77 and C source files for LAMMPS as
well as several sample Makefiles for different machines. To make LAMMPS
for a specfic machine, you simply type</P>
for a specific machine, you simply type</P>
<P>
make machine</P>
<P>

4
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View File

@ -430,7 +430,7 @@ accuracy criterion effectively determines how many k-space vectors are used
for PPPM, accuracy criterion determines mesh spacing (see &quot;particle mesh&quot;
command)
for PPPM, must be running on power-of-2 number of processors for FFTs
must use periodic boundary conditions in conjuction with Ewald and PPPM
must use periodic boundary conditions in conjunction with Ewald and PPPM
cannot use any styles other than none with nonbond style = lj/shift or
nonbond style = soft
Coulomb style = smooth should be used with nonbond style = lj/switch,
@ -772,7 +772,7 @@ for style aveforce, average force on the group of fixed atoms is computed,
to new total value -&gt; has effect of applying same force to entire group
of atoms
thermostatting constraints (rescale, langevin, nose/hoover) cannot be used in
conjuction with global &quot;temp control&quot;, since they conflict and will
conjunction with global &quot;temp control&quot;, since they conflict and will
cause atom velocities to be reset twice
if multiple Langevin constraints are specified the Marsaglia RNG will
only use the last RNG seed specified for initialization

1
doc/src/Build.rst
View File

@ -8,7 +8,6 @@ for use with GNU make or gmake, or a build environment generated by CMake
alternative you can download a package with pre-built executables
as described on the :doc:`Install <Install>` doc page.
.. toctree::
:maxdepth: 1

128
doc/src/Build_basics.rst
View File

@ -10,10 +10,8 @@ CMake and make:
* :ref:`Build the LAMMPS documentation <doc>`
* :ref:`Install LAMMPS after a build <install>`
----------
.. _serial:
Serial vs parallel build
@ -42,14 +40,14 @@ is below.
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
The executable created by CMake (after running make) is named *lmp* unless
the LAMMPS\_MACHINE option is set. When setting `LAMMPS_MACHINE=name`
the executable will be named *lmp\_name*\. Using `BUILD\_MPI=no` will
The executable created by CMake (after running make) is named ``lmp`` unless
the LAMMPS_MACHINE option is set. When setting ``LAMMPS_MACHINE=name``
the executable will be called ``lmp_name``. Using ``BUILD_MPI=no`` will
enforce building a serial executable using the MPI STUBS library.
**Traditional make**\ :
The build with traditional makefiles has to be done inside the source folder `src`.
The build with traditional makefiles has to be done inside the source folder ``src``.
.. code-block:: bash
@ -57,19 +55,18 @@ The build with traditional makefiles has to be done inside the source folder `sr
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
Any "make machine" command will look up the make settings from a file
Makefile.machine, create a folder Obj\_machine with all objects and
generated files and an executable called *lmp\_machine*\ . The standard
parallel build with `make mpi` assumes a standard MPI installation with
Makefile.machine, create a folder Obj_machine with all objects and
generated files and an executable called ``lmp_machine``\ . The standard
parallel build with ``make mpi`` assumes a standard MPI installation with
MPI compiler wrappers where all necessary compiler and linker flags to
get access and link with the suitable MPI headers and libraries are set
by the wrapper programs. For other cases or the serial build, you have
to adjust the make file variables MPI\_INC, MPI\_PATH, MPI\_LIB as well
as CC and LINK. To enable OpenMP threading usually a compiler specific
flag needs to be added to the compile and link commands. For the GNU
compilers, this is *-fopenmp*\ , which can be added to the CC and LINK
makefile variables.
to adjust the make file variables ``MPI_INC``, ``MPI_PATH``, ``MPI_LIB``
as well as ``CC`` and ``LINK``\ . To enable OpenMP threading usually
a compiler specific flag needs to be added to the compile and link
commands. For the GNU compilers, this is ``-fopenmp``\ , which can be
added to the ``CC`` and ``LINK`` makefile variables.
For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
@ -82,8 +79,8 @@ For the serial build the following make variables are set (see src/MAKE/Makefile
MPI_LIB = -lmpi_stubs
You also need to build the STUBS library for your platform before making
LAMMPS itself. A "make serial" build does this for you automatically,
otherwise, type "make mpi-stubs" from the src directory, or "make" from
LAMMPS itself. A ``make serial`` build does this for you automatically,
otherwise, type ``make mpi-stubs`` from the src directory, or ``make`` from
the src/STUBS dir. If the build fails, you will need to edit the
STUBS/Makefile for your platform. The stubs library does not provide
MPI/IO functions required by some LAMMPS packages, e.g. MPIIO or USER-LB,
@ -91,8 +88,8 @@ and thus is not compatible with those packages.
.. note::
The file STUBS/mpi.c provides a CPU timer function called
MPI\_Wtime() that calls gettimeofday() . If your operating system
The file ``src/STUBS/mpi.c`` provides a CPU timer function called
MPI_Wtime() that calls gettimeofday() . If your operating system
does not support gettimeofday() , you will need to insert code to
call another timer. Note that the ANSI-standard function clock()
rolls over after an hour or so, and is therefore insufficient for
@ -129,35 +126,33 @@ to: e.g. LATTE and USER-COLVARS. See the :doc:`Packages details
<Packages_details>` doc page for more info on these packages and the doc
pages for their respective commands for OpenMP threading info.
For CMake, if you use BUILD\_OMP=yes, you can use these packages and
turn on their native OpenMP support and turn on their native OpenMP
support at run time, by setting the OMP\_NUM\_THREADS environment
For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
and turn on their native OpenMP support and turn on their native OpenMP
support at run time, by setting the ``OMP_NUM_THREADS`` environment
variable before you launch LAMMPS.
For building via conventional make, the CCFLAGS and LINKFLAGS
For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS``
variables in Makefile.machine need to include the compiler flag that
enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel
compilers it is -qopenmp. If you are using a different compiler,
enables OpenMP. For GNU compilers it is ``-fopenmp``\ . For (recent) Intel
compilers it is ``-qopenmp``\ . If you are using a different compiler,
please refer to its documentation.
.. _default-none-issues:
**OpenMP Compiler compatibility info**\ :
Some compilers do not fully support the 'default(none)' directive
Some compilers do not fully support the ``default(none)`` directive
and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
semantics, which are incompatible with the OpenMP 3.1 directives used
semantics, which are incompatible with the OpenMP 3.1 semantics used
in LAMMPS (for maximal compatibility with compiler versions in use).
In those case, all 'default(none)' directives (which aid in detecting
incorrect and unwanted sharing) can be replaced with 'default(shared)'
while dropping all 'shared()' directives. The script
'src/USER-OMP/hack\_openmp\_for\_pgi\_gcc9.sh' can be used to automate
In those case, all ``default(none)`` directives (which aid in detecting
incorrect and unwanted sharing) can be replaced with ``default(shared)``
while dropping all ``shared()`` directives. The script
'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
this conversion.
----------
.. _compile:
Choice of compiler and compile/link options
@ -188,11 +183,11 @@ optimization flags appropriate to that compiler and any
build.
You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
in C or Fortran are built with a compiler consistent with the one used
for all the C++ files:
settings. Likewise you can specify the corresponding ``CMAKE_*_FLAGS``
variables if you want to experiment with alternate optimization flags.
You should specify all 3 compilers, so that the small number of LAMMPS
source files written in C or Fortran are built with a compiler consistent
with the one used for all the C++ files:
.. code-block:: bash
@ -204,7 +199,6 @@ for all the C++ files:
-D CMAKE_C_FLAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler
A few example command lines are:
.. code-block:: bash
@ -306,33 +300,32 @@ are set, defaults are applied.
-D LAMMPS_LIB_SUFFIX=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
Setting BUILD\_EXE=no will not produce an executable. Setting
BUILD\_LIB=yes will produce a static library named *liblammps.a*\ .
Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a
shared library named *liblammps.so* instead. If LAMMPS\_LIB\_SUFFIX is
set to *name* in addition, the name of the generated libraries will be
changed to either *liblammps\_name.a* or *liblammps\_name.so*\ ,
respectively.
Setting ``BUILD_EXE=no`` will not produce an executable. Setting
``BUILD_LIB=yes`` will produce a static library named ``liblammps.a``\ .
Setting both ``BUILD_LIB=yes`` and ``BUILD_SHARED_LIBS=yes`` will produce a
shared library named ``liblammps.so`` instead. If ``LAMMPS_LIB_SUFFIX=name``
is set in addition, the name of the generated libraries will be changed to
either ``liblammps_name.a`` or ``liblammps_name.so``\ , respectively.
**Traditional make**\ :
With the traditional makefile based build process, the choice of
the generated executable or library depends on the "mode" setting.
Several options are available and "mode=exe" is the default.
Several options are available and ``mode=exe`` is the default.
.. code-block:: bash
make machine # build LAMMPS executable lmp_machine
mkae mode=exe machine # same as "make machine"
make mode=exe machine # same as "make machine"
make mode=lib machine # build LAMMPS static lib liblammps_machine.a
make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so
make mode=shexe machine # same as "mode=exe" but uses objects from "mode=shlib"
The two "exe" builds will generate and executable *lmp\_machine*\ ,
while the two library builds will create a file *liblammps\_machine.a*
or *liblammps\_machine.so*\ . They will also create generic soft links,
named *liblammps.a* and *liblammps.so*\ , which point to the specific
*liblammps\_machine.a/so* files.
The two "exe" builds will generate and executable ``lmp_machine``\ ,
while the two library builds will create a file ``liblammps_machine.a``
or ``liblammps_machine.so``\ . They will also create generic soft links,
named ``liblammps.a`` and ``liblammps.so``\ , which point to the specific
``liblammps_machine.a/so`` files.
**CMake and make info**\ :
@ -341,13 +334,12 @@ the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
the lib/packages directory, since they are always built in a shared
library compatible way using the -fPIC switch. However, if a library
library compatible way using the ``-fPIC`` switch. However, if a library
like MPI or FFTW does not exist as a shared library, the shared library
build may generate an error. This means you will need to install a
shared library version of the auxiliary library. The build instructions
for the library should tell you how to do this.
As an example, here is how to build and install the `MPICH library
<mpich_>`_, a popular open-source version of MPI, as a shared library
in the default /usr/local/lib location:
@ -360,10 +352,10 @@ in the default /usr/local/lib location:
make
make install
You may need to use "sudo make install" in place of the last line if you
do not have write privileges for /usr/local/lib. The end result should
be the file /usr/local/lib/libmpich.so. On many Linux installations the
folder "${HOME}/.local" is an alternative to using /usr/local and does
You may need to use ``sudo make install`` in place of the last line if you
do not have write privileges for ``/usr/local/lib``. The end result should
be the file ``/usr/local/lib/libmpich.so``. On many Linux installations the
folder ``${HOME}/.local`` is an alternative to using ``/usr/local`` and does
not require superuser or sudo access. In that case the configuration
step becomes:
@ -377,7 +369,6 @@ recommended to ensure the integrity of the system software installation.
----------
.. _doc:
Build the LAMMPS documentation
@ -412,7 +403,6 @@ LAMMPS source distribution.
make package_check # check for complete and consistent package lists
make spelling # spell-check the manual
Thus "make html" will create a "doc/html" directory with the HTML format
manual pages so that you can browse them with a web browser locally on
your system.
@ -421,8 +411,7 @@ your system.
You can also download a tarball of the documentation for the
current LAMMPS version (HTML and PDF files), from the website
`download page <http://lammps.sandia.gov/download.html>`_.
`download page <https://lammps.sandia.gov/download.html>`_.
**CMake build option**\ :
@ -430,16 +419,14 @@ It is also possible to create the HTML version of the manual within
the :doc:`CMake build directory <Build_cmake>`. The reason for this
option is to include the installation of the HTML manual pages into
the "install" step when installing LAMMPS after the CMake build via
"make install".
``make install``.
.. code-block:: bash
-D BUILD_DOC=value # yes or no (default)
----------
.. _tools:
Build LAMMPS tools
@ -450,7 +437,6 @@ using CMake or Make.
**CMake build3**\ :
.. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default)
@ -460,7 +446,6 @@ The generated binaries will also become part of the LAMMPS installation
**Traditional make**\ :
.. code-block:: bash
cd lammps/tools
@ -470,10 +455,8 @@ The generated binaries will also become part of the LAMMPS installation
make micelle2d # build only micelle2d tool
make thermo_extract # build only thermo_extract tool
----------
.. _install:
Install LAMMPS after a build
@ -487,7 +470,6 @@ you want to copy files to is protected.
**CMake build**\ :
.. code-block:: bash
cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
@ -496,6 +478,6 @@ you want to copy files to is protected.
**Traditional make**\ :
There is no "install" option in the src/Makefile for LAMMPS. If you
wish to do this you will need to first build LAMMPS, then manually
There is no "install" option in the ``src/Makefile`` for LAMMPS. If
you wish to do this you will need to first build LAMMPS, then manually
copy the desired LAMMPS files to the appropriate system directories.

62
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@ -9,17 +9,14 @@ Richard Berger (Temple U) has also written a `more comprehensive guide <https://
for how to use CMake to build LAMMPS. If you are new to CMake it is a
good place to start.
----------
Building LAMMPS with CMake is a two-step process. First you use CMake
to create a build environment in a new directory. On Linux systems,
this will be based on makefiles for use with make. Then you use the
make command to build LAMMPS, which uses the created
this will be by default based on Unix-style makefiles for use with make.
Then you use the *make* command to build LAMMPS, which uses the created
Makefile(s). Example:
.. code-block:: bash
cd lammps # change to the LAMMPS distribution directory
@ -31,8 +28,8 @@ The cmake command will detect available features, enable selected
packages and options, and will generate the build environment. By default
this build environment will be created for "Unix Makefiles" on most
platforms and particularly on Linux. However, alternate build tools
(e.g. Ninja) and support files for Integrated Development Environments
(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
(e.g. Ninja) and project files for Integrated Development Environments
(IDEs) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
selected via the "-G" command line flag. For the rest of the documentation
we will assume that the build environment is generated for makefiles
and thus the make command will be used to compile and link LAMMPS as
@ -51,7 +48,6 @@ even more.
After compilation, you may optionally install the LAMMPS executable into
your system with:
.. code-block:: bash
make install # optional, copy LAMMPS executable & library elsewhere
@ -59,18 +55,17 @@ your system with:
This will install the lammps executable and library (if requested), some
tools (if configured) and additional files like library API headers,
manpages, potential and force field files. The location of the installation
tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults
tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults
to ${HOME}/.local
----------
There are 3 variants of CMake: a command-line version (cmake), a text mode
UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use
any of them interchangeably to configure and create the LAMMPS build
environment. On Linux all the versions produce a Makefile as their
output. See more details on each below.
There are 3 variants of the CMake command itself: a command-line version
(*cmake* or *cmake3*), a text mode UI version (*ccmake* or *ccmake3*),
and a graphical GUI version (*cmake-gui*). You can use any of them
interchangeably to configure and create the LAMMPS build environment.
On Linux all the versions produce a Makefile as their output by default.
See more details on each below.
You can specify a variety of options with any of the 3 versions, which
affect how the build is performed and what is included in the LAMMPS
@ -88,12 +83,13 @@ this directory or sub-directories within it that CMake creates.
.. note::
To perform a CMake build, no packages can be installed or a
build been previously attempted in the LAMMPS src directory by using
"make" commands to :doc:`perform a conventional LAMMPS build <Build_make>`. CMake detects if this is the case and
generates an error, telling you to type "make no-all purge" in the src
directory to un-install all packages. The purge removes all the \*.h
files auto-generated by make.
To perform a CMake build, no packages can be installed or a build
been previously attempted in the LAMMPS src directory by using "make"
commands to :doc:`perform a conventional LAMMPS build <Build_make>`.
CMake detects if this is the case and generates an error, telling you
to type "make no-all purge" in the src directory to un-install all
packages. The purge removes all the \*.h files auto-generated by
make.
You must have CMake version 3.10 or later on your system to build
LAMMPS. Installation instructions for CMake are below.
@ -106,30 +102,28 @@ ccmake or cmake-gui) again from the same build directory and alter
various options; see details below. Or you can remove the entire build
folder, recreate the directory and start over.
----------
**Command-line version of CMake**\ :
.. code-block:: bash
cmake [options ...] /path/to/lammps/cmake # build from any dir
cmake [options ...] ../cmake # build from lammps/build
cmake3 [options ...] ../cmake # build from lammps/build
The cmake command takes one required argument, which is the LAMMPS
cmake directory which contains the CMakeLists.txt file.
The argument can be preceeded or followed by various CMake
The argument can be prefixed or followed by various CMake
command-line options. Several useful ones are:
.. code-block:: bash
-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
-D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
-G output # style of output CMake generates
-G output # style of output CMake generates (e.g. "Unix Makefiles" or "Ninja")
-D CMAKE_MAKE_PROGRAM=builder # name of the builder executable (e.g. set to "gmake" instead of "make")
-DVARIABLE=value # setting for a LAMMPS feature to enable
-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir
-C path/to/preset/file # load some CMake settings before configuring
@ -137,7 +131,7 @@ command-line options. Several useful ones are:
All the LAMMPS-specific -D variables that a LAMMPS build supports are
described on the pages linked to from the :doc:`Build <Build>` doc page.
All of these variable names are upper-case and their values are
lower-case, e.g. -D LAMMPS\_SIZES=smallbig. For boolean values, any of
lower-case, e.g. -D LAMMPS_SIZES=smallbig. For boolean values, any of
these forms can be used: yes/no, on/off, 1/0.
On Unix/Linux machines, CMake generates a Makefile by default to
@ -168,13 +162,10 @@ In these cases it is usually better to first remove all the
files/directories in the build directory, or start with a fresh build
directory.
----------
**Curses version (terminal-style menu) of CMake**\ :
.. code-block:: bash
ccmake ../cmake
@ -186,13 +177,10 @@ required to edit some of the entries of CMake configuration variables
in between. Please see the `ccmake manual <https://cmake.org/cmake/help/latest/manual/ccmake.1.html>`_ for
more information.
----------
**GUI version of CMake**\ :
.. code-block:: bash
cmake-gui ../cmake
@ -205,15 +193,12 @@ edit some of the entries of CMake configuration variables in between.
Please see the `cmake-gui manual <https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html>`_
for more information.
----------
**Installing CMake**
Check if your machine already has CMake installed:
.. code-block:: bash
which cmake # do you have it?
@ -223,7 +208,6 @@ Check if your machine already has CMake installed:
On clusters or supercomputers which use environment modules to manage
software packages, do this:
.. code-block:: bash
module list # is a module for cmake already loaded?

16
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@ -4,10 +4,8 @@ Development build options (CMake only)
The CMake build of LAMMPS has a few extra options which are useful during
development, testing or debugging.
----------
.. _compilation:
Verify compilation flags
@ -17,22 +15,18 @@ Sometimes it is necessary to verify the complete sequence of compilation flags
generated by the CMake build. To enable a more verbose output during
compilation you can use the following option.
.. code-block:: bash
-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes
Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
.. code-block:: bash
make VERBOSE=1
----------
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support
@ -47,17 +41,14 @@ The following settings allow you enable these features if your compiler supports
it. Please note that they come with a performance hit. However, they are
usually faster than using tools like Valgrind.
.. code-block:: bash
-D ENABLE_SANITIZE_ADDRESS=value # enable Address Sanitizer, value = no (default) or yes
-D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behaviour Sanitizer, value = no (default) or yes
-D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behavior Sanitizer, value = no (default) or yes
-D ENABLE_SANITIZE_THREAD=value # enable Thread Sanitizer, value = no (default) or yes
----------
.. _testing:
Code Coverage and Testing
@ -71,7 +62,6 @@ developers can run the tests directly on their workstation.
this is incomplete and only represents a small subset of tests that we run
.. code-block:: bash
-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
@ -80,7 +70,6 @@ developers can run the tests directly on their workstation.
If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
.. code-block:: bash
make test
@ -92,14 +81,12 @@ faster.
You can also collect code coverage metrics while running the tests by enabling
coverage support during building.
.. code-block:: bash
-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes
This will also add the following targets to generate coverage reports after running the LAMMPS executable:
.. code-block:: bash
make test # run tests first!
@ -108,7 +95,6 @@ This will also add the following targets to generate coverage reports after runn
These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
.. code-block:: bash
pip install git+https://github.com/gcovr/gcovr.git

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18
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@ -11,7 +11,7 @@ The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in one of
these 2 files:
.. parsed-literal::
.. code-block:: bash
liblammps.so # shared library
liblammps.a # static library
@ -25,13 +25,12 @@ these 2 files:
then its mpi.h file needs to be included. While it is technically
possible to use a full MPI library in the calling code and link to
a serial LAMMPS library compiled with MPI STUBS, it is recommended
to use the *same* MPI library for both, and then use MPI\_Comm\_split()
to use the *same* MPI library for both, and then use MPI_Comm_split()
in the calling code to pass a suitable communicator with a subset
of MPI ranks to the function creating the LAMMPS instance.
----------
**Link with LAMMPS as a static library**\ :
The calling application can link to LAMMPS as a static library with
@ -44,7 +43,7 @@ executable code from the library is copied into the calling executable.
*CMake build*\ :
This assumes that LAMMPS has been configured with "-D BUILD_LIB=yes"
and installed with "make install" and the PKG\_CONFIG\_PATH environment
and installed with "make install" and the PKG_CONFIG_PATH environment
variable updated to include the *liblammps.pc* file installed into the
configured destination folder, if needed. The commands to compile and
link the coupled executable are then:
@ -54,7 +53,6 @@ link the coupled executable are then:
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
*Traditional make*\ :
This assumes that LAMMPS has been compiled in the folder
@ -169,7 +167,7 @@ traditional make build using "make mode=shlib serial" becomes:
However, now the `liblammps.so` file is required at runtime and needs
to be in a folder, where the shared linker program of the operating
system can find it. This would be either a folder like "/usr/local/lib64"
or "${HOME}/.local/lib64" or a folder pointed to by the LD\_LIBRARY\_PATH
or "${HOME}/.local/lib64" or a folder pointed to by the LD_LIBRARY_PATH
environment variable. You can type
.. code-block:: bash
@ -179,7 +177,7 @@ environment variable. You can type
to see what directories are in that list.
Or you can add the LAMMPS src directory (or the directory you performed
a CMake style build in) to your LD\_LIBRARY\_PATH, so that the current
a CMake style build in) to your LD_LIBRARY_PATH, so that the current
version of the shared library is always available to programs that use it.
For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you
@ -193,7 +191,6 @@ would add something like this to your ~/.profile file:
For the csh or tcsh shells, you would equivalently add something like this
to your ~/.cshrc file:
.. code-block:: csh
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src
@ -212,7 +209,6 @@ You can verify whether all required shared libraries are found with the
libc.so.6 => /lib64/libc.so.6 (0x00007fc91b65b000)
/lib64/ld-linux-x86-64.so.2 (0x00007fc91c094000)
If a required library is missing, you would get a 'not found' entry:
.. code-block:: bash
@ -226,16 +222,14 @@ If a required library is missing, you would get a 'not found' entry:
libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
/lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
----------
**Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program. When used from a
C++ program, most of the symbols and functions in LAMMPS are wrapped
in a LAMMPS\_NS namespace; you can safely use any of its classes and
in a LAMMPS_NS namespace; you can safely use any of its classes and
methods from within the calling code, as needed, and you will not incur
conflicts with functions and variables in your code that share the name.
This, however, does not extend to all additional libraries bundled with

6
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@ -31,7 +31,7 @@ machines, especially workstations, desktops, and laptops, so we suggest
you try it first when building LAMMPS in those cases.
The commands below perform a default LAMMPS build, producing the LAMMPS
executable lmp\_serial and lmp\_mpi in lammps/src:
executable lmp_serial and lmp_mpi in lammps/src:
.. code-block:: bash
@ -73,8 +73,7 @@ in the LAMMPS distribution. Typing "make machine" uses
use Makefile.serial and Makefile.mpi, respectively. Other makefiles
are in these directories:
.. parsed-literal::
.. code-block:: bash
OPTIONS # Makefiles which enable specific options
MACHINES # Makefiles for specific machines
@ -93,7 +92,6 @@ customized machine Makefile are contributed by users. Since both
compilers, OS configurations, and LAMMPS itself keep changing, their
settings may become outdated:
.. code-block:: bash
make mac # build serial LAMMPS on a Mac

29
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@ -47,15 +47,13 @@ versus make.
**CMake build**\ :
.. code-block:: bash
.. code-block:: csh
-D PKG_NAME=value # yes or no (default)
Examples:
.. code-block:: bash
.. code-block:: csh
-D PKG_MANYBODY=yes
-D PKG_USER-INTEL=yes
@ -76,7 +74,6 @@ once with CMake.
**Traditional make**\ :
.. code-block:: bash
cd lammps/src
@ -87,7 +84,6 @@ once with CMake.
Examples:
.. code-block:: bash
make no-rigid
@ -132,10 +128,8 @@ src directory.
That is no longer the case, so that CMake will build as-is without the
need to un-install those packages.
----------
**CMake shortcuts for installing many packages**\ :
Instead of specifying all the CMake options via the command-line,
@ -169,7 +163,6 @@ one of them as a starting point and customize it to your needs.
**Example:**
.. code-block:: bash
# build LAMMPS with most commonly used packages, but then remove
@ -186,15 +179,13 @@ one of them as a starting point and customize it to your needs.
# but leaving all other settings untouched. You can run:
cmake -C ../cmake/presets/no_all.cmake .
----------
**Make shortcuts for installing many packages**\ :
The following commands are useful for managing package source files
and their installation when building LAMMPS via traditional make.
Just type "make" in lammps/src to see a one-line summary.
Just type ``make`` in lammps/src to see a one-line summary.
These commands install/un-install sets of packages:
@ -211,8 +202,8 @@ These commands install/un-install sets of packages:
make yes-ext # install packages that require external libraries
make no-ext # uninstall packages that require external libraries
which install/un-install various sets of packages. Typing "make
package" will list all the these commands.
which install/un-install various sets of packages. Typing ``make
package`` will list all the these commands.
.. note::
@ -229,23 +220,23 @@ need to use these commands unless you are editing LAMMPS files or are
:doc:`installing a patch <Install_patch>` downloaded from the LAMMPS web
site.
Type "make package-status" or "make ps" to show which packages are
Type ``make package-status`` or ``make ps`` to show which packages are
currently installed. For those that are installed, it will list any
files that are different in the src directory and package
sub-directory.
Type "make package-installed" or "make pi" to show which packages are
Type ``make package-installed`` or ``make pi`` to show which packages are
currently installed, without listing the status of packages that are
not installed.
Type "make package-update" or "make pu" to overwrite src files with
Type ``make package-update`` or ``make pu`` to overwrite src files with
files from the package sub-directories if the package is installed.
It should be used after a :doc:`patch has been applied <Install_patch>`,
since patches only update the files in the package sub-directory, but
not the src files.
Type "make package-overwrite" to overwrite files in the package
Type ``make package-overwrite`` to overwrite files in the package
sub-directories with src files.
Type "make package-diff" to list all differences between pairs of
Type ``make package-diff`` to list all differences between pairs of
files in both the source directory and the package directory.

78
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@ -14,10 +14,8 @@ explain how to do this for building both with CMake and make.
* :ref:`Workaround for long long integers <longlong>`
* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
----------
.. _cxx11:
C++11 standard compliance
@ -35,7 +33,6 @@ flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
----------
.. _fft:
FFT library
@ -49,7 +46,6 @@ LAMMPS can use them if they are available on your system.
**CMake variables**\ :
.. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
@ -69,7 +65,6 @@ OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is
used. If CMake cannot detect the FFT library, you can set these variables
to assist:
.. code-block:: bash
-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files
@ -81,7 +76,6 @@ to assist:
**Makefile.machine settings**\ :
.. code-block:: make
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
@ -91,8 +85,7 @@ to assist:
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT\_PACK\_ARRAY if not specified
# default is FFT_PACK_ARRAY if not specified
.. code-block:: make
@ -102,14 +95,14 @@ to assist:
FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler, serial interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier, serial interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compiler, serial interface
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core # MKL with GNU compiler, threaded interface
FFT_LIB = -lmkl_rt # MKL with automatic runtime selection of interface libs
As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
the compiler can find the FFT header and library files in its default search path.
You must specify FFT\_LIB with the appropriate FFT libraries to include in the link.
You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.
**CMake and make info**\ :
@ -133,14 +126,15 @@ platform and can be faster than the KISS FFT library. You can
download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ./configure; make;
make install. The install command typically requires root privileges
Building FFTW for your box should be as simple as ``./configure; make;
make install``\ . The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type "./configure --help" to see
the "--prefix" option of configure. Type ``./configure --help`` to see
various options.
The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see FFT\_LIB setting above).
can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
above).
Performing 3d FFTs in parallel can be time consuming due to data
access and required communication. This cost can be reduced by
@ -149,16 +143,15 @@ precision means the real and imaginary parts of a complex datum are
4-byte floats. Double precision means they are 8-byte doubles. Note
that Fourier transform and related PPPM operations are somewhat less
sensitive to floating point truncation errors and thus the resulting
error is less than the difference in precision. Using the -DFFT\_SINGLE
error is less than the difference in precision. Using the ``-DFFT_SINGLE``
setting trades off a little accuracy for reduced memory use and
parallel communication costs for transposing 3d FFT data.
When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW
When using ``-DFFT_SINGLE`` with FFTW3 you may need to build the FFTW
library a second time with support for single-precision.
For FFTW3, do the following, which should produce the additional
library libfftw3f.a or libfftw3f.so.
library ``libfftw3f.a`` or ``libfftw3f.so``\ .
.. code-block:: bash
@ -167,15 +160,13 @@ library libfftw3f.a or libfftw3f.so.
Performing 3d FFTs requires communication to transpose the 3d FFT
grid. The data packing/unpacking for this can be done in one of 3
modes (ARRAY, POINTER, MEMCPY) as set by the FFT\_PACK syntax above.
modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is
ARRAY mode.
----------
.. _size:
Size of LAMMPS data types
@ -187,19 +178,18 @@ adequate.
**CMake variable**\ :
.. code-block:: bash
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
# default is LAMMPS\_SMALLBIG if not specified
The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
**CMake and make info**\ :
The default "smallbig" setting allows for simulations with:
@ -247,12 +237,10 @@ than crashing randomly or corrupting data.
Also note that the GPU package requires its lib/gpu library to be
compiled with the same size setting, or the link will fail. A CMake
build does this automatically. When building with make, the setting
in whichever lib/gpu/Makefile is used must be the same as above.
in whichever ``lib/gpu/Makefile`` is used must be the same as above.
----------
.. _graphics:
Output of JPG, PNG, and movie files
@ -265,7 +253,6 @@ following settings:
**CMake variables**\ :
.. code-block:: bash
-D WITH_JPEG=value # yes or no
@ -279,7 +266,6 @@ Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executable files, you can set these
variables:
.. code-block:: bash
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
@ -292,7 +278,6 @@ variables:
**Makefile.machine settings**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_JPEG
@ -303,15 +288,16 @@ variables:
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz # library names
As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
find the graphics header and library files. You must specify JPG\_LIB
As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
if make can find the graphics header and library files. You must
specify ``JPG_LIB``
with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime,
that is a directory in your PATH environment variable.
**CMake and make info**\ :
Using ffmpeg to output movie files requires that your machine
Using ``ffmpeg`` to output movie files requires that your machine
supports the "popen" function in the standard runtime library.
.. note::
@ -321,10 +307,8 @@ supports the "popen" function in the standard runtime library.
communication library and lead to simulations using ffmpeg to hang or
crash.
----------
.. _gzip:
Read or write compressed files
@ -336,7 +320,6 @@ gzip compression by several LAMMPS commands, including
**CMake variables**\ :
.. code-block:: bash
-D WITH_GZIP=value # yes or no
@ -345,7 +328,6 @@ gzip compression by several LAMMPS commands, including
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_GZIP
@ -365,16 +347,14 @@ found by LAMMPS during a run.
I/O is also available using a compression library instead, which is
what the :ref:`COMPRESS package <PKG-COMPRESS>` enables.
----------
.. _align:
Memory allocation alignment
---------------------------------------
This setting enables the use of the posix\_memalign() call instead of
This setting enables the use of the posix_memalign() call instead of
malloc() when LAMMPS allocates large chunks or memory. This can make
vector instructions on CPUs more efficient, if dynamically allocated
memory is aligned on larger-than-default byte boundaries.
@ -385,33 +365,29 @@ aligned on 64-byte boundaries.
**CMake variable**\ :
.. code-block:: bash
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
Use a LAMMPS\_MEMALIGN value of 0 to disable using posix\_memalign()
Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using posix_memalign()
and revert to using the malloc() C-library function instead. When
compiling LAMMPS for Windows systems, malloc() will always be used
and this setting ignored.
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
Do not set -DLAMMPS\_MEMALIGN, if you want to have memory allocated
with the malloc() function call instead. -DLAMMPS\_MEMALIGN **cannot**
Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory allocated
with the malloc() function call instead. ``-DLAMMPS_MEMALIGN`` **cannot**
be used on Windows, as it does use different function calls for
allocating aligned memory, that are not compatible with how LAMMPS
manages its dynamical memory.
----------
.. _longlong:
Workaround for long long integers
@ -424,22 +400,18 @@ those systems:
**CMake variable**\ :
.. code-block:: bash
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
----------
.. _exceptions:
Exception handling when using LAMMPS as a library
@ -453,14 +425,12 @@ e.g. to Python. Of course the calling code has to be set up to
**CMake variable**\ :
.. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS

6
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@ -6,10 +6,8 @@ Notes for building LAMMPS on Windows
* :ref:`Using GNU GCC ported to Windows <gnu>`
* :ref:`Using a cross-compiler <cross>`
----------
.. _generic:
General remarks
@ -57,8 +55,8 @@ and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. Using CMake for this mode of compilation
is untested and not likely to work.
When compiling for Windows do **not** set the -DLAMMPS\_MEMALIGN define
in the LMP\_INC makefile variable and add -lwsock32 -lpsapi to the linker
When compiling for Windows do **not** set the -DLAMMPS_MEMALIGN define
in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
flags in LIB makefile variable. Try adding -static-libgcc or -static or
both to the linker flags when your resulting LAMMPS Windows executable
complains about missing .dll files. The CMake configuration should set

1
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@ -4,7 +4,6 @@ Commands
These pages describe how a LAMMPS input script is formatted and the
commands in it are used to define a LAMMPS simulation.
.. toctree::
:maxdepth: 1

1
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@ -99,7 +99,6 @@ have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
.. table_from_list::
:columns: 4

4
doc/src/Commands_input.rst
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@ -16,7 +16,6 @@ simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
.. code-block:: LAMMPS
timestep 0.5
@ -25,7 +24,6 @@ Thus this sequence of commands:
does something different than this sequence:
.. code-block:: LAMMPS
run 100
@ -48,7 +46,7 @@ is to have the desired effect. For example, the
:doc:`read_data <read_data>` command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the :doc:`processors <processors>` and
:doc:`boundary <boundary>` commands need to be used before read\_data to
:doc:`boundary <boundary>` commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or

3
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@ -86,7 +86,6 @@ LAMMPS:
This can be useful for formatting print output to a desired precision:
.. code-block:: LAMMPS
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
@ -102,7 +101,7 @@ LAMMPS:
print "B2 = ${b$a}"
Nor can you specify an expression like "$($x-1.0)" for an immediate
variable, but you could use $(v\_x-1.0), since the latter is valid
variable, but you could use $(v_x-1.0), since the latter is valid
syntax for an :doc:`equal-style variable <variable>`.
See the :doc:`variable <variable>` command for more details of how

1
doc/src/Errors.rst
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@ -7,7 +7,6 @@ and warnings doc pages give complete lists of all the messages the
code may generate (except those generated by USER packages), with
additional details for many of them.
.. toctree::
:maxdepth: 1

6
doc/src/Errors_bugs.rst
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@ -4,7 +4,7 @@ Reporting bugs
If you are confident that you have found a bug in LAMMPS, please follow the steps outlined below:
* Check the `New features and bug fixes
<http://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
<https://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
<lws_>`_ to see if the bug has already been addressed in a patch.
* Check that your issue can be reproduced with the latest development
version of LAMMPS.
@ -14,7 +14,7 @@ If you are confident that you have found a bug in LAMMPS, please follow the step
if your issue has already been reported and if it is still open.
* Check the `GitHub Pull Requests page <https://github.com/lammps/pulls>`_
if there is already a fix for your bug pending.
* Check the `mailing list archives <http://lammps.sandia.gov/mail.html>`_
* Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_
to see if the issue has been discussed before.
If none of these steps yields any useful information, please file
@ -41,5 +41,5 @@ is overlooked and then forgotten. Issues on GitHub have to be explicitly
closed, so that will *guarantee* that at least one LAMMPS developer will
have looked at it.
.. _lws: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov
.. _gip: https://github.com/lammps/issues

10
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@ -39,7 +39,7 @@ figure out your physics or numerical mistakes, like choosing too big a
timestep, specifying erroneous force field coefficients, or putting 2
atoms on top of each other! If you run into errors that LAMMPS
doesn't catch that you think it should flag, please send an email to
the `developers <http://lammps.sandia.gov/authors.html>`_.
the `developers <https://lammps.sandia.gov/authors.html>`_.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by
@ -63,25 +63,23 @@ is an integer or floating-point number, respectively, and reject the
input with an error message (for instance, when an integer is required,
but a floating-point number 1.0 is provided):
.. parsed-literal::
ERROR: Expected integer parameter instead of '1.0' in input script or data file
Some commands allow for using variable references in place of numeric
constants so that the value can be evaluated and may change over the
course of a run. This is typically done with the syntax *v\_name* for a
course of a run. This is typically done with the syntax *v_name* for a
parameter, where name is the name of the variable. On the other hand,
immediate variable expansion with the syntax $\ *name* is performed while
immediate variable expansion with the syntax ${name} is performed while
reading the input and before parsing commands,
.. note::
Using a variable reference (i.e. *v\_name*) is only allowed if
Using a variable reference (i.e. *v_name*) is only allowed if
the documentation of the corresponding command explicitly says it is.
Otherwise, you will receive an error message of this kind:
.. parsed-literal::
ERROR: Expected floating point parameter instead of 'v_name' in input script or data file

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@ -7,7 +7,6 @@ documentation for the offending command may help. Warning messages
also list the source file and line number where the warning was
generated. For example, a message like this:
.. parsed-literal::
WARNING: Bond atom missing in box size check (domain.cpp:187)
@ -21,12 +20,8 @@ code or contact the author of the package.
Doc page with :doc:`ERROR messages <Errors_messages>`
----------
*Adjusting Coulombic cutoff for MSM, new cutoff = %g*
The adjust/cutoff command is turned on and the Coulombic cutoff has been
adjusted to match the user-specified accuracy.
@ -42,7 +37,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Angles are defined but no angle style is set*
The topology contains angles, but there are no angle forces computed
since there was no angle\_style command.
since there was no angle_style command.
*Atom style in data file differs from currently defined atom style*
Self-explanatory.
@ -67,7 +62,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Bonds are defined but no bond style is set*
The topology contains bonds, but there are no bond forces computed
since there was no bond\_style command.
since there was no bond_style command.
*Bond/angle/dihedral extent > half of periodic box length*
This is a restriction because LAMMPS can be confused about which image
@ -88,8 +83,8 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
Self-explanatory.
*Calling write\_dump before a full system init.*
The write\_dump command is used before the system has been fully
*Calling write_dump before a full system init.*
The write_dump command is used before the system has been fully
initialized as part of a 'run' or 'minimize' command. Not all dump
styles and features are fully supported at this point and thus the
command may fail or produce incomplete or incorrect output. Insert
@ -136,11 +131,11 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
degrees-of-freedom for the atoms in those partial rigid bodies will
not be accounted for.
*Create\_bonds max distance > minimum neighbor cutoff*
*Create_bonds max distance > minimum neighbor cutoff*
This means atom pairs for some atom types may not be in the neighbor
list and thus no bond can be created between them.
*Delete\_atoms cutoff > minimum neighbor cutoff*
*Delete_atoms cutoff > minimum neighbor cutoff*
This means atom pairs for some atom types may not be in the neighbor
list and thus an atom in that pair cannot be deleted.
@ -163,7 +158,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Dihedrals are defined but no dihedral style is set*
The topology contains dihedrals, but there are no dihedral forces computed
since there was no dihedral\_style command.
since there was no dihedral_style command.
*Dump dcd/xtc timestamp may be wrong with fix dt/reset*
If the fix changes the timestep, the dump dcd file will not
@ -177,7 +172,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Estimated error in splitting of dispersion coeffs is %g*
Error is greater than 0.0001 percent.
*Ewald/disp Newton solver failed, using old method to estimate g\_ewald*
*Ewald/disp Newton solver failed, using old method to estimate g_ewald*
Self-explanatory. Choosing a different cutoff value may help.
*FENE bond too long*
@ -217,8 +212,8 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
This is probably an error, since you should not delete only one atom
of a molecule.
*Fix gcmc using full\_energy option*
Fix gcmc has automatically turned on the full\_energy option since it
*Fix gcmc using full_energy option*
Fix gcmc has automatically turned on the full_energy option since it
is required for systems like the one specified by the user. User input
included one or more of the following: kspace, triclinic, a hybrid
pair style, an eam pair style, or no "single" function for the pair
@ -273,19 +268,19 @@ This will most likely cause errors in kinetic fluctuations.
*Fixes cannot send data in Kokkos communication, switching to classic communication*
This is current restriction with Kokkos.
*For better accuracy use 'pair\_modify table 0'*
*For better accuracy use 'pair_modify table 0'*
The user-specified force accuracy cannot be achieved unless the table
feature is disabled by using 'pair\_modify table 0'.
feature is disabled by using 'pair_modify table 0'.
*Geometric mixing assumed for 1/r\^6 coefficients*
Self-explanatory.
*Group for fix\_modify temp != fix group*
The fix\_modify command is specifying a temperature computation that
*Group for fix_modify temp != fix group*
The fix_modify command is specifying a temperature computation that
computes a temperature on a different group of atoms than the fix
itself operates on. This is probably not what you want to do.
*H matrix size has been exceeded: m\_fill=%d H.m=%d\n*
*H matrix size has been exceeded: m_fill=%d H.m=%d\n*
This is the size of the matrix.
*Ignoring unknown or incorrect info command flag*
@ -307,7 +302,7 @@ This will most likely cause errors in kinetic fluctuations.
*Impropers are defined but no improper style is set*
The topology contains impropers, but there are no improper forces computed
since there was no improper\_style command.
since there was no improper_style command.
*Inconsistent image flags*
The image flags for a pair on bonded atoms appear to be inconsistent.
@ -342,22 +337,22 @@ This will most likely cause errors in kinetic fluctuations.
*KIM Model does not provide 'particleVirial'; virial per atom will be zero*
Self-explanatory.
*Kspace\_modify slab param < 2.0 may cause unphysical behavior*
The kspace\_modify slab parameter should be larger to insure periodic
*Kspace_modify slab param < 2.0 may cause unphysical behavior*
The kspace_modify slab parameter should be larger to insure periodic
grids padded with empty space do not overlap.
*Less insertions than requested*
The fix pour command was unsuccessful at finding open space
for as many particles as it tried to insert.
*Library error in lammps\_gather\_atoms*
*Library error in lammps_gather_atoms*
This library function cannot be used if atom IDs are not defined
or are not consecutively numbered.
*Library error in lammps\_scatter\_atoms*
*Library error in lammps_scatter_atoms*
This library function cannot be used if atom IDs are not defined or
are not consecutively numbered, or if no atom map is defined. See the
atom\_modify command for details about atom maps.
atom_modify command for details about atom maps.
*Likewise 1-2 special neighbor interactions != 1.0*
The topology contains bonds, but there is no bond style defined
@ -380,15 +375,15 @@ This will most likely cause errors in kinetic fluctuations.
pairs in the neighbor list in expectation of interactions for
those pairs being computed from the dihedral style.
*Lost atoms via change\_box: original %ld current %ld*
*Lost atoms via change_box: original %ld current %ld*
The command options you have used caused atoms to be lost.
*Lost atoms via displace\_atoms: original %ld current %ld*
*Lost atoms via displace_atoms: original %ld current %ld*
The command options you have used caused atoms to be lost.
*Lost atoms: original %ld current %ld*
Lost atoms are checked for each time thermo output is done. See the
thermo\_modify lost command for options. Lost atoms usually indicate
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
box, or moved further than one processor's sub-domain away before
reneighboring.
@ -411,8 +406,8 @@ This will most likely cause errors in kinetic fluctuations.
This means the bonded atoms will not be excluded in pair-wise
interactions.
*Molecule template for create\_atoms has multiple molecules*
The create\_atoms command will only create molecules of a single type,
*Molecule template for create_atoms has multiple molecules*
The create_atoms command will only create molecules of a single type,
i.e. the first molecule in the template.
*Molecule template for fix gcmc has multiple molecules*
@ -477,21 +472,21 @@ This will most likely cause errors in kinetic fluctuations.
*Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
This is because excluding specific pair interactions also excludes
them from long-range interactions which may not be the desired effect.
The special\_bonds command handles this consistently by insuring
The special_bonds command handles this consistently by insuring
excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
consistently by both the short-range pair style and the long-range
solver. This is not done for exclusions of charged atom pairs via the
neigh\_modify exclude command.
neigh_modify exclude command.
*New thermo\_style command, previous thermo\_modify settings will be lost*
If a thermo\_style command is used after a thermo\_modify command, the
settings changed by the thermo\_modify command will be reset to their
default values. This is because the thermo\_modify command acts on
the currently defined thermo style, and a thermo\_style command creates
*New thermo_style command, previous thermo_modify settings will be lost*
If a thermo_style command is used after a thermo_modify command, the
settings changed by the thermo_modify command will be reset to their
default values. This is because the thermo_modify command acts on
the currently defined thermo style, and a thermo_style command creates
a new style.
*No Kspace calculation with verlet/split*
The 2nd partition performs a kspace calculation so the kspace\_style
The 2nd partition performs a kspace calculation so the kspace_style
command must be used.
*No automatic unit conversion to XTC file format conventions possible for units lj*
@ -515,7 +510,7 @@ This will most likely cause errors in kinetic fluctuations.
of two and the number of grid points in one or more directions have been
adjusted to meet this requirement.
*OMP\_NUM\_THREADS environment is not set.*
*OMP_NUM_THREADS environment is not set.*
This environment variable must be set appropriately to use the
USER-OMP package.
@ -549,10 +544,10 @@ This will most likely cause errors in kinetic fluctuations.
*Pair dpd needs newton pair on for momentum conservation*
Self-explanatory.
*Pair dsmc: num\_of\_collisions > number\_of\_A*
*Pair dsmc: num_of_collisions > number_of_A*
Collision model in DSMC is breaking down.
*Pair dsmc: num\_of\_collisions > number\_of\_B*
*Pair dsmc: num_of_collisions > number_of_B*
Collision model in DSMC is breaking down.
*Pair style in data file differs from currently defined pair style*
@ -577,15 +572,15 @@ This will most likely cause errors in kinetic fluctuations.
sub-domain before reneighboring is triggered.
*Reducing PPPM order b/c stencil extends beyond nearest neighbor processor*
This may lead to a larger grid than desired. See the kspace\_modify overlap
This may lead to a larger grid than desired. See the kspace_modify overlap
command to prevent changing of the PPPM order.
*Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor*
This may lead to a larger grid than desired. See the kspace\_modify overlap
This may lead to a larger grid than desired. See the kspace_modify overlap
command to prevent changing of the PPPM order.
*Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor*
This may lead to a larger grid than desired. See the kspace\_modify overlap
This may lead to a larger grid than desired. See the kspace_modify overlap
command to prevent changing of the PPPM order.
*Replacing a fix, but new group != old group*
@ -598,19 +593,19 @@ This will most likely cause errors in kinetic fluctuations.
dimension to be replicated; this may cause unwanted behavior.
*Resetting reneighboring criteria during PRD*
A PRD simulation requires that neigh\_modify settings be delay = 0,
A PRD simulation requires that neigh_modify settings be delay = 0,
every = 1, check = yes. Since these settings were not in place,
LAMMPS changed them and will restore them to their original values
after the PRD simulation.
*Resetting reneighboring criteria during TAD*
A TAD simulation requires that neigh\_modify settings be delay = 0,
A TAD simulation requires that neigh_modify settings be delay = 0,
every = 1, check = yes. Since these settings were not in place,
LAMMPS changed them and will restore them to their original values
after the PRD simulation.
*Resetting reneighboring criteria during minimization*
Minimization requires that neigh\_modify settings be delay = 0, every =
Minimization requires that neigh_modify settings be delay = 0, every =
1, check = yes. Since these settings were not in place, LAMMPS
changed them and will restore them to their original values after the
minimization.
@ -714,7 +709,7 @@ This will most likely cause errors in kinetic fluctuations.
which does operate on group all, so this may be inconsistent.
*Temperature for thermo pressure is not for group all*
User-assigned temperature to thermo via the thermo\_modify command does
User-assigned temperature to thermo via the thermo_modify command does
not compute temperature for all atoms. Since thermo computes a global
pressure, the kinetic energy contribution from the temperature is
assumed to also be for all atoms. Thus the pressure printed by thermo
@ -746,12 +741,12 @@ This will most likely cause errors in kinetic fluctuations.
LAMMPS simulation may be inefficient as a result.
*Use special bonds = 0,1,1 with bond style fene*
Most FENE models need this setting for the special\_bonds command.
Most FENE models need this setting for the special_bonds command.
*Use special bonds = 0,1,1 with bond style fene/expand*
Most FENE models need this setting for the special\_bonds command.
Most FENE models need this setting for the special_bonds command.
*Using a many-body potential with bonds/angles/dihedrals and special\_bond exclusions*
*Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions*
This is likely not what you want to do. The exclusion settings will
eliminate neighbors in the neighbor list, which the many-body potential
needs to calculated its terms correctly.
@ -780,13 +775,13 @@ This will most likely cause errors in kinetic fluctuations.
*Using largest cutoff for lj/long/coul/long*
Self-explanatory.
*Using largest cutoff for pair\_style lj/long/tip4p/long*
*Using largest cutoff for pair_style lj/long/tip4p/long*
Self-explanatory.
*Using package gpu without any pair style defined*
Self-explanatory.
*Using pair potential shift with pair\_modify compute no*
*Using pair potential shift with pair_modify compute no*
The shift effects will thus not be computed.
*Using pair tail corrections with nonperiodic system*
@ -794,8 +789,8 @@ This will most likely cause errors in kinetic fluctuations.
computed by integrating the density of a periodic system out to
infinity.
*Using pair tail corrections with pair\_modify compute no*
*Using pair tail corrections with pair_modify compute no*
The tail corrections will thus not be computed.
*pair style reax is now deprecated and will soon be retired. Users should switch to pair\_style reax/c*
*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c*
Self-explanatory.

26
doc/src/Examples.rst
View File

@ -18,7 +18,7 @@ files and image files.
If you uncomment the :doc:`dump <dump>` command in the input script, a
text dump file will be produced, which can be animated by various
`visualization programs <http://lammps.sandia.gov/viz.html>`_.
`visualization programs <https://lammps.sandia.gov/viz.html>`_.
If you uncomment the :doc:`dump image <dump>` command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
@ -38,10 +38,8 @@ particular quantity.
Lists of both kinds of directories are given below.
----------
Lowercase directories
---------------------
@ -134,7 +132,7 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| reax | RDX and TATB models using the ReaxFF |
+-------------+------------------------------------------------------------------+
| rerun | use of rerun and read\_dump commands |
| rerun | use of rerun and read_dump commands |
+-------------+------------------------------------------------------------------+
| rigid | rigid bodies modeled as independent or coupled |
+-------------+------------------------------------------------------------------+
@ -157,8 +155,7 @@ Lowercase directories
Here is how you can run and visualize one of the sample problems:
.. parsed-literal::
.. code-block:: bash
cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
@ -167,28 +164,25 @@ Here is how you can run and visualize one of the sample problems:
Running the simulation produces the files *dump.indent* and
*log.lammps*\ . You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the
`Visualization <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
web site.
If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
script a series of JPG images will be produced by the run (assuming
you built LAMMPS with JPG support; see the
:doc:`Build\_settings <Build_settings>` doc page for details). These can
:doc:`Build_settings <Build_settings>` doc page for details). These can
be viewed individually or turned into a movie or animated by tools
like ImageMagick or QuickTime or various Windows-based tools. See the
:doc:`dump image <dump_image>` doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
.. code-block:: bash
.. parsed-literal::
% convert -loop 1 \*.jpg foo.gif
% convert -loop 1 *.jpg foo.gif
----------
Uppercase directories
---------------------
@ -201,7 +195,7 @@ Uppercase directories
+------------+--------------------------------------------------------------------------------------------------+
| ELASTIC | compute elastic constants at zero temperature |
+------------+--------------------------------------------------------------------------------------------------+
| ELASTIC\_T | compute elastic constants at finite temperature |
| ELASTIC_T | compute elastic constants at finite temperature |
+------------+--------------------------------------------------------------------------------------------------+
| HEAT | compute thermal conductivity for LJ and water via fix ehex |
+------------+--------------------------------------------------------------------------------------------------+
@ -225,8 +219,8 @@ The USER directory has a large number of sub-directories which
correspond by name to a USER package. They contain scripts that
illustrate how to use the command(s) provided in that package. Many
of the sub-directories have their own README files which give further
instructions. See the :doc:`Packages\_details <Packages_details>` doc
instructions. See the :doc:`Packages_details <Packages_details>` doc
page for more info on specific USER packages.
.. _openkim: https://openkim.org
.. _lws: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov

8
doc/src/Howto.rst
View File

@ -3,7 +3,7 @@ Howto discussions
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
`glossary <http://lammps.sandia.gov>`_ website page also lists MD
`glossary <https://lammps.sandia.gov>`_ website page also lists MD
terminology with links to corresponding LAMMPS manual pages. The
example input scripts included in the examples directory of the LAMMPS
distribution and highlighted on the :doc:`Examples <Examples>` doc page
@ -12,7 +12,6 @@ also show how to setup and run various kinds of simulations.
Tutorials howto
===============
.. toctree::
:name: tutorials
:maxdepth: 1
@ -24,7 +23,6 @@ Tutorials howto
General howto
=============
.. toctree::
:name: general_howto
:maxdepth: 1
@ -40,7 +38,6 @@ General howto
Settings howto
==============
.. toctree::
:name: settings_howto
:maxdepth: 1
@ -56,7 +53,6 @@ Settings howto
Analysis howto
==============
.. toctree::
:name: analysis_howto
:maxdepth: 1
@ -72,7 +68,6 @@ Analysis howto
Force fields howto
==================
.. toctree::
:name: force_howto
:maxdepth: 1
@ -85,7 +80,6 @@ Force fields howto
Packages howto
==============
.. toctree::
:name: packages_howto
:maxdepth: 1

5
doc/src/Howto_2d.rst
View File

@ -8,17 +8,16 @@ command. This is the default.
If using the :doc:`create box <create_box>` command to define a
simulation box, set the z dimensions narrow, but finite, so that the
create\_atoms command will tile the 3d simulation box with a single z
create_atoms command will tile the 3d simulation box with a single z
plane of atoms - e.g.
.. code-block:: LAMMPS
:doc:`create box <create_box>` 1 -10 10 -10 10 -0.25 0.25
If using the :doc:`read data <read_data>` command to read in a file of
atom coordinates, set the "zlo zhi" values to be finite but narrow,
similar to the create\_box command settings just described. For each
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.

40
doc/src/Howto_bash.rst
View File

@ -3,10 +3,8 @@ Using LAMMPS with Bash on Windows
**written by Richard Berger**
----------
Starting with Windows 10 you can install Linux tools directly in Windows. This
allows you to compile LAMMPS following the same procedure as on a real Ubuntu
Linux installation. Software can be easily installed using the package manager
@ -82,10 +80,8 @@ Congratulations, you have installed **Bash on Ubuntu on Windows**\ .
.. image:: JPG/bow_tutorial_10.png
----------
Compiling LAMMPS in Bash on Windows
-----------------------------------
@ -97,7 +93,6 @@ Installing prerequisite packages
First upgrade all existing packages using
.. code-block:: bash
sudo apt update
@ -106,7 +101,6 @@ First upgrade all existing packages using
Next install the following packages, which include compilers and libraries
needed for various LAMMPS features:
.. code-block:: bash
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
@ -126,17 +120,15 @@ Obtain a copy of the LAMMPS code and go into it using "cd"
Option 1: Downloading LAMMPS tarball using wget
"""""""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz
tar xvzf lammps-stable.tar.gz
cd lammps-31Mar17
Option 2: Obtaining LAMMPS code from GitHub
"""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
git clone https://github.com/lammps/lammps.git
@ -150,39 +142,33 @@ At this point you can compile LAMMPS like on Ubuntu Linux.
Compiling serial version
""""""""""""""""""""""""
.. code-block:: bash
cd src/
make -j 4 serial
This will create an executable called lmp\_serial in the src/ directory
This will create an executable called lmp_serial in the src/ directory
Compiling MPI version
"""""""""""""""""""""
.. code-block:: bash
cd src/
make -j 4 mpi
This will create an executable called lmp\_mpi in the src/ directory
This will create an executable called lmp_mpi in the src/ directory
----------
Finally, please note the absolute path of your src folder. You can get this using
.. code-block:: bash
pwd
or
.. code-block:: bash
echo $PWD
@ -190,43 +176,37 @@ or
To run any examples you need the location of the executable. For now, let us
save this location in a temporary variable
.. code-block:: bash
LAMMPS_DIR=$PWD
----------
Running an example script
^^^^^^^^^^^^^^^^^^^^^^^^^
Once compiled you can execute some of the LAMMPS examples. Switch into the
examples/melt folder
.. code-block:: bash
cd ../examples/melt
The full path of the serial executable is $LAMMPS\_DIR/lmp\_serial, while the mpi
version is $LAMMPS\_DIR/lmp\_mpi. You can run the melt example with either
The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi
version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either
version as follows:
.. code-block:: bash
$LAMMPS_DIR/lmp_serial -in in.melt
or
.. code-block:: bash
mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt
Note the use of our variable $LAMMPS\_DIR, which expands into the full path of
Note the use of our variable $LAMMPS_DIR, which expands into the full path of
the LAMMPS src folder we saved earlier.
Adding your executable directory to your PATH
@ -235,21 +215,18 @@ Adding your executable directory to your PATH
You can avoid having to type the full path of your LAMMPS binary by adding its
parent folder to the PATH environment variable as follows:
.. code-block:: bash
export PATH=$LAMMPS_DIR:$PATH
Input scripts can then be run like this:
.. code-block:: bash
lmp_serial -in in.melt
or
.. code-block:: bash
mpirun -np 4 lmp_mpi -in in.melt
@ -258,15 +235,13 @@ However, this PATH variable will not persist if you close your bash window.
To persist this setting edit the $HOME/.bashrc file using your favorite editor
and add this line
.. code-block:: bash
export PATH=/full/path/to/your/lammps/src:$PATH
**Example:**
For an executable lmp\_serial with a full path
For an executable lmp_serial with a full path
.. code-block:: bash
@ -274,7 +249,6 @@ For an executable lmp\_serial with a full path
the PATH variable should be
.. code-block:: bash
export PATH=/home/richard/lammps/src:$PATH

14
doc/src/Howto_bioFF.rst
View File

@ -20,12 +20,8 @@ force field.
.. _charmm: http://www.scripps.edu/brooks
.. _amber: http://amber.scripps.edu
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
command's documentation for the formula it computes.
@ -114,33 +110,23 @@ documentation for the formula it computes.
* :doc:`special_bonds <special_bonds>` dreiding
----------
.. _howto-MacKerell:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
.. _howto-Cornell:
**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
.. _howto-Sun:
**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
.. _howto-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

40
doc/src/Howto_body.rst
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@ -33,10 +33,8 @@ style are described below.
More styles may be added in the future. See the :doc:`Modify body <Modify_body>` doc page for details on how to add a new body
style to the code.
----------
**When to use body particles:**
You should not use body particles to model a rigid body made of
@ -104,10 +102,8 @@ particles of different styles
The pair styles defined for use with specific body styles are listed
in the sections below.
----------
**Specifics of body style nparticle:**
The *nparticle* body style represents body particles as a rigid body
@ -116,10 +112,9 @@ vanilla, prototypical example of a body particle, although as
mentioned above, the :doc:`fix rigid <fix_rigid>` command already
duplicates its functionality.
The atom\_style body command for this body style takes two additional
The atom_style body command for this body style takes two additional
arguments:
.. parsed-literal::
atom_style body nparticle Nmin Nmax
@ -133,7 +128,6 @@ When the :doc:`read_data <read_data>` command reads a data file for this
body style, the following information must be provided for each entry
in the *Bodies* section of the data file:
.. parsed-literal::
atom-ID 1 M
@ -170,7 +164,6 @@ For output purposes via the :doc:`compute body/local <compute_body_local>` and :
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:
.. parsed-literal::
1 = x position of sub-particle
@ -188,26 +181,23 @@ collection of spheres, one for each sub-particle. The size of each
sphere is determined by the *bflag1* parameter for the *body* keyword.
The *bflag2* argument is ignored.
----------
**Specifics of body style rounded/polygon:**
The *rounded/polygon* body style represents body particles as a 2d
polygon with a variable number of N vertices. This style can only be
used for 2d models; see the :doc:`boundary <boundary>` command. See the
"pair\_style body/rounded/polygon" doc page for a diagram of two
"pair_style body/rounded/polygon" doc page for a diagram of two
squares with rounded circles at the vertices. Special cases for N = 1
(circle) and N = 2 (rod with rounded ends) can also be specified.
One use of this body style is for 2d discrete element models, as
described in :ref:`Fraige <body-Fraige>`.
Similar to body style *nparticle*\ , the atom\_style body command for
Similar to body style *nparticle*\ , the atom_style body command for
this body style takes two additional arguments:
.. parsed-literal::
atom_style body rounded/polygon Nmin Nmax
@ -221,7 +211,6 @@ When the :doc:`read_data <read_data>` command reads a data file for this
body style, the following information must be provided for each entry
in the *Bodies* section of the data file:
.. parsed-literal::
atom-ID 1 M
@ -262,7 +251,6 @@ orientation of the square is aligned with the xy coordinate axes which
is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
1 1 4 0 0 0. Note that only Izz matters in 2D simulations.
.. parsed-literal::
3 1 27
@ -281,7 +269,6 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends
by circles of diameter 0.5, is specified as follows:
.. parsed-literal::
1 1 13
@ -293,7 +280,6 @@ by circles of diameter 0.5, is specified as follows:
A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
.. parsed-literal::
1 1 10
@ -308,16 +294,14 @@ interactions. The :doc:`fix wall/body/polygon <fix_wall_body_polygon>`
command can be used with this body style to compute the interaction of
body particles with a wall.
----------
**Specifics of body style rounded/polyhedron:**
The *rounded/polyhedron* body style represents body particles as a 3d
polyhedron with a variable number of N vertices, E edges and F faces.
This style can only be used for 3d models; see the
:doc:`boundary <boundary>` command. See the "pair\_style
:doc:`boundary <boundary>` command. See the "pair_style
body/rounded/polygon" doc page for a diagram of a two 2d squares with
rounded circles at the vertices. A 3d cube with rounded spheres at
the 8 vertices and 12 rounded edges would be similar. Special cases
@ -327,10 +311,9 @@ specified.
This body style is for 3d discrete element models, as described in
:ref:`Wang <body-Wang>`.
Similar to body style *rounded/polygon*\ , the atom\_style body command
Similar to body style *rounded/polygon*\ , the atom_style body command
for this body style takes two additional arguments:
.. parsed-literal::
atom_style body rounded/polyhedron Nmin Nmax
@ -344,7 +327,6 @@ When the :doc:`read_data <read_data>` command reads a data file for this
body style, the following information must be provided for each entry
in the *Bodies* section of the data file:
.. parsed-literal::
atom-ID 3 M
@ -401,7 +383,6 @@ The orientation of the cube is aligned with the xyz coordinate axes
which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz
iyz = 0.667 0.667 0.667 0 0 0.
.. parsed-literal::
1 3 79
@ -438,7 +419,6 @@ iyz = 0.667 0.667 0.667 0 0 0.
A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends
by circles of diameter 0.5, is specified as follows:
.. parsed-literal::
1 1 13
@ -450,7 +430,6 @@ by circles of diameter 0.5, is specified as follows:
A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
.. parsed-literal::
1 1 10
@ -465,15 +444,12 @@ be used with this body style to compute body/body interactions. The
used with this body style to compute the interaction of body particles
with a wall.
----------
For output purposes via the :doc:`compute body/local <compute_body_local>` and :doc:`dump local <dump>`
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:
.. parsed-literal::
1 = x position of vertex
@ -495,20 +471,14 @@ tangent to the spheres). The drawn diameter of each line segment is
determined by the *bflag1* parameter for the *body* keyword. The
*bflag2* argument is ignored.
----------
.. _body-Fraige:
**(Fraige)** F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
Particuology, 6, 455 (2008).
.. _body-Wang:
**(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
Matter, 13, 1 (2011).

7
doc/src/Howto_chunk.rst
View File

@ -110,7 +110,7 @@ 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. The output can be used in
output, with one or more values per chunk. The output can be used in
various ways:
* As input to the :doc:`fix ave/time <fix_ave_time>` command, which can
@ -150,7 +150,6 @@ properties:
(1) Average velocity in each of 1000 2d spatial bins:
.. code-block:: LAMMPS
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
@ -159,7 +158,6 @@ properties:
(2) Temperature in each spatial bin, after subtracting a flow
velocity:
.. code-block:: LAMMPS
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
@ -168,7 +166,6 @@ velocity:
(3) Center of mass of each molecule:
.. code-block:: LAMMPS
compute cc1 all chunk/atom molecule
@ -177,7 +174,6 @@ velocity:
(4) Total force on each molecule and ave/max across all molecules:
.. code-block:: LAMMPS
compute cc1 all chunk/atom molecule
@ -189,7 +185,6 @@ velocity:
(5) Histogram of cluster sizes:
.. code-block:: LAMMPS
compute cluster all cluster/atom 1.0

16
doc/src/Howto_client_server.rst
View File

@ -62,7 +62,7 @@ below. The MESSAGE package also wraps a client/server library called
CSlib which enables two codes to exchange messages in different ways,
either via files, sockets, or MPI. The CSlib is provided with LAMMPS
in the lib/message dir. The CSlib has its own
`website <http://cslib.sandia.gov>`_ with documentation and test
`website <https://cslib.sandia.gov>`_ with documentation and test
programs.
.. note::
@ -93,22 +93,22 @@ client or server code:
* examples/message
* examples/COUPLE/README
* examples/COUPLE/lammps\_mc
* examples/COUPLE/lammps\_nwchem
* examples/COUPLE/lammps\_vasp
* examples/COUPLE/lammps_mc
* examples/COUPLE/lammps_nwchem
* examples/COUPLE/lammps_vasp
The examples/message directory couples a client instance of LAMMPS to a
server instance of LAMMPS.
The files in the *lammps\_mc* folder show how to couple LAMMPS as
The files in the *lammps_mc* folder show how to couple LAMMPS as
a server to a simple Monte Carlo client code as the driver.
The files in the *lammps\_nwchem* folder show how to couple LAMMPS
The files in the *lammps_nwchem* folder show how to couple LAMMPS
as a client code running MD timestepping to NWChem acting as a
server providing quantum DFT forces, through a Python wrapper script
on NWChem.
The files in the *lammps\_vasp* folder show how to couple LAMMPS as
The files in the *lammps_vasp* folder show how to couple LAMMPS as
a client code running MD timestepping to VASP acting as a server
providing quantum DFT forces, through a Python wrapper script on VASP.
@ -134,7 +134,6 @@ together to exchange MPI messages between them.
For message exchange in *file*\ , *zmq*\ , or *mpi/two* modes:
.. code-block:: bash
% mpirun -np 1 lmp_mpi -log log.client < in.client &
@ -150,7 +149,6 @@ For message exchange in *mpi/one* mode:
Launch both codes in a single mpirun command:
.. code-block:: bash
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

14
doc/src/Howto_coreshell.rst
View File

@ -24,7 +24,6 @@ shell of a core/shell pair should be bonded to each other with a
harmonic bond that provides the spring force. For example, a data file
for NaCl, as found in examples/coreshell, has this format:
.. parsed-literal::
432 atoms # core and shell atoms
@ -87,7 +86,6 @@ Ewald solvers can be used.
For the NaCL example problem, these pair style and bond style settings
are used:
.. code-block:: LAMMPS
pair_style born/coul/long/cs 20.0 20.0
@ -131,7 +129,6 @@ this temperature be output for the overall system.
For the NaCl example, this can be done as follows:
.. code-block:: LAMMPS
group cores type 1 2
@ -150,7 +147,6 @@ the default :doc:`temperature <compute_temp>` and specifying it as a
second argument in :doc:`fix modify <fix_modify>` and
:doc:`thermo_modify <thermo_modify>` resulting in:
.. code-block:: LAMMPS
(...)
@ -174,7 +170,6 @@ the pairs. This can be done by using the *bias* keyword of the
:doc:`velocity create <velocity>` command and assigning the :doc:`compute temp/cs <compute_temp_cs>` command to the *temp* keyword of the
:doc:`velocity <velocity>` command, e.g.
.. code-block:: LAMMPS
velocity all create 1427 134 bias yes temp CSequ
@ -211,7 +206,6 @@ pairs as chunks.
For example if core/shell pairs are the only molecules:
.. code-block:: LAMMPS
read_data NaCl_CS_x0.1_prop.data
@ -222,7 +216,6 @@ For example if core/shell pairs are the only molecules:
For example if core/shell pairs and other molecules are present:
.. code-block:: LAMMPS
fix csinfo all property/atom i_CSID # property/atom command
@ -232,7 +225,6 @@ For example if core/shell pairs and other molecules are present:
The additional section in the date file would be formatted like this:
.. parsed-literal::
CS-Info # header of additional section
@ -247,20 +239,14 @@ The additional section in the date file would be formatted like this:
8 4
(...)
----------
.. _MitchellFincham:
**(Mitchell and Fincham)** Mitchell, Fincham, J Phys Condensed Matter,
5, 1031-1038 (1993).
.. _MitchellFincham2:
**(Fincham)** Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
6, 393-404 (1994).

21
doc/src/Howto_couple.rst
View File

@ -12,10 +12,8 @@ LAMMPS can be coupled to other codes in at least 4 ways. Each has
advantages and disadvantages, which you will have to think about in the
context of your application.
----------
(1) Define a new :doc:`fix <fix>` command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
@ -27,12 +25,8 @@ LAMMPS.
.. _poems: http://www.rpi.edu/~anderk5/lab
----------
(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
@ -53,10 +47,8 @@ command writes and reads.
See the :doc:`Modify command <Modify_command>` doc page for info on how
to add a new command to LAMMPS.
----------
(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
@ -72,21 +64,16 @@ examples/COUPLE/README for more details:
library
* plugin: simple driver program in C which invokes LAMMPS as a plugin
from a shared library.
* lammps\_quest: coupling of LAMMPS and `Quest <quest_>`_, to run classical
* lammps_quest: coupling of LAMMPS and `Quest <quest_>`_, to run classical
MD with quantum forces calculated by a density functional code
* lammps\_spparks: coupling of LAMMPS and `SPPARKS <spparks_>`_, to couple
* lammps_spparks: coupling of LAMMPS and `SPPARKS <spparks_>`_, to couple
a kinetic Monte Carlo model for grain growth using MD to calculate
strain induced across grain boundaries
.. _quest: http://dft.sandia.gov/Quest
.. _spparks: http://www.sandia.gov/~sjplimp/spparks.html
The :doc:`Build basics <Build_basics>` doc page describes how to build
LAMMPS as a library. Once this is done, you can interface with LAMMPS
either via C++, C, Fortran, or Python (or any other language that
@ -102,7 +89,7 @@ The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See the :doc:`Howto library <Howto_library>` doc page for a
description of the interface and how to extend it for your needs.
Note that the lammps\_open() function that creates an instance of
Note that the lammps_open() function that creates an instance of
LAMMPS takes an MPI communicator as an argument. This means that
instance of LAMMPS will run on the set of processors in the
communicator. Thus the calling code can run LAMMPS on all or a subset
@ -113,10 +100,8 @@ LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
----------
(4) Couple LAMMPS with another code in a client/server mode. This is
described on the :doc:`Howto client/server <Howto_client_server>` doc
page.

22
doc/src/Howto_dispersion.rst
View File

@ -29,7 +29,7 @@ that provide fast and accurate simulations, there are two approaches,
which both have their up- and downsides.
The first approach is to set desired real-space an kspace accuracies
via the *kspace\_modify force/disp/real* and *kspace\_modify
via the *kspace_modify force/disp/real* and *kspace_modify
force/disp/kspace* commands. Note that the accuracies have to be
specified in force units and are thus dependent on the chosen unit
settings. For real units, 0.0001 and 0.002 seem to provide reasonable
@ -37,14 +37,14 @@ accurate and efficient computations for the real-space and kspace
accuracies. 0.002 and 0.05 work well for most systems using lj
units. PPPM parameters will be generated based on the desired
accuracies. The upside of this approach is that it usually provides a
good set of parameters and will work for both the *kspace\_modify diff
ad* and *kspace\_modify diff ik* options. The downside of the method
good set of parameters and will work for both the *kspace_modify diff
ad* and *kspace_modify diff ik* options. The downside of the method
is that setting the PPPM parameters will take some time during the
initialization of the simulation.
The second approach is to set the parameters for the pppm/disp
explicitly using the *kspace\_modify mesh/disp*, *kspace\_modify
order/disp*, and *kspace\_modify gewald/disp* commands. This approach
explicitly using the *kspace_modify mesh/disp*, *kspace_modify
order/disp*, and *kspace_modify gewald/disp* commands. This approach
requires a more experienced user who understands well the impact of
the choice of parameters on the simulation accuracy and
performance. This approach provides a fast initialization of the
@ -60,12 +60,12 @@ To avoid inaccurate or inefficient simulations, the pppm/disp stops
simulations with an error message if no action is taken to control the
PPPM parameters. If the automatic parameter generation is desired and
real-space and kspace accuracies are desired to be equal, this error
message can be suppressed using the *kspace\_modify disp/auto yes*
message can be suppressed using the *kspace_modify disp/auto yes*
command.
A reasonable approach that combines the upsides of both methods is to
make the first run using the *kspace\_modify force/disp/real* and
*kspace\_modify force/disp/kspace* commands, write down the PPPM
make the first run using the *kspace_modify force/disp/real* and
*kspace_modify force/disp/kspace* commands, write down the PPPM
parameters from the output, and specify these parameters using the
second approach in subsequent runs (which have the same composition,
force field, and approximately the same volume).
@ -82,8 +82,8 @@ The second is that the mixing rule of the pair style has an impact on
the computation time when using the pppm/disp. Fastest computations
are achieved when using the geometric mixing rule. Using the
arithmetic mixing rule substantially increases the computational cost.
The computational overhead can be reduced using the *kspace\_modify
mix/disp geom* and *kspace\_modify splittol* commands. The first
The computational overhead can be reduced using the *kspace_modify
mix/disp geom* and *kspace_modify splittol* commands. The first
command simply enforces geometric mixing of the dispersion
coefficients in kspace computations. This introduces some error in
the computations but will also significantly speed-up the
@ -94,7 +94,7 @@ command, but will usually also not provide an equally good increase of
efficiency.
Finally, pppm/disp can also be used when no mixing rules apply.
This can be achieved using the *kspace\_modify mix/disp none* command.
This can be achieved using the *kspace_modify mix/disp none* command.
Note that the code does not check automatically whether any mixing
rule is fulfilled. If mixing rules do not apply, the user will have
to specify this command explicitly.

6
doc/src/Howto_drude.rst
View File

@ -48,7 +48,7 @@ for a Langevin thermostat, or :doc:`fix drude/transform/\* <fix_drude_transform>
thermostat. The former requires use of the command :doc:`comm_modify vel yes <comm_modify>`. The latter requires two separate integration
fixes like *nvt* or *npt*\ . The correct temperatures of the reduced
degrees of freedom can be calculated using the :doc:`compute temp/drude <compute_temp_drude>`. This requires also to use the
command *comm\_modify vel yes*.
command *comm_modify vel yes*.
Short-range damping of the induced dipole interactions can be achieved
using Thole functions through the :doc:`pair style thole <pair_thole>` in :doc:`pair_style hybrid/overlay <pair_hybrid>`
@ -56,12 +56,8 @@ with a Coulomb pair style. It may be useful to use *coul/long/cs* or
similar from the CORESHELL package if the core and Drude particle come
too close, which can cause numerical issues.
----------
.. _howto-Lamoureux:
**(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

98
doc/src/Howto_drude2.rst
View File

@ -30,7 +30,6 @@ zero. The (half-)stiffness of the :doc:`harmonic bond <bond_harmonic>`
:math:`K_D = k_D/2` and the Drude charge :math:`q_D` are related to the atom
polarizability :math:`\alpha` by
.. math::
K_D = \frac 1 2\, \frac {q_D^2} \alpha
@ -46,7 +45,6 @@ fields:
* Alternately :ref:`Schroeder and Steinhauser <Schroeder>` suggest adopting a global charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K.
* In both these force fields hydrogen atoms are treated as non-polarizable.
The motion of of the Drude particles can be calculated by minimizing
the energy of the induced dipoles at each timestep, by an iterative,
self-consistent procedure. The Drude particles can be massless and
@ -78,15 +76,14 @@ important features:
**Preparation of the data file**
The data file is similar to a standard LAMMPS data file for
*atom\_style full*. The DPs and the *harmonic bonds* connecting them
*atom_style full*. The DPs and the *harmonic bonds* connecting them
to their DC should appear in the data file as normal atoms and bonds.
You can use the *polarizer* tool (Python script distributed with the
USER-DRUDE package) to convert a non-polarizable data file (here
*data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ )
.. parsed-literal::
.. code-block:: bash
polarizer -q -f phenol.dff data.102494.lmp data-p.lmp
@ -96,7 +93,6 @@ from *phenol.dff*\ , as well as the DC-DP bond constants. The file
*phenol.dff* contains the polarizabilities of the atom types
and the mass of the Drude particles, for instance:
.. parsed-literal::
# units: kJ/mol, A, deg
@ -113,7 +109,6 @@ have to be specified as comments at the end of lines of the *Masses*
section. You probably need to edit it to add these names. It should
look like
.. parsed-literal::
Masses
@ -124,10 +119,8 @@ look like
4 1.008 # HA
5 1.008 # HO
----------
**Basic input file**
The atom style should be set to (or derive from) *full*\ , so that you
@ -138,7 +131,6 @@ script (the use of these lines will be explained below). In order for
LAMMPS to recognize that you are using Drude oscillators, you should
use the fix *drude*\ . The command is
.. code-block:: LAMMPS
fix DRUDE all drude C C C N N D D D
@ -159,7 +151,6 @@ command. With our phenol, there is 1 more special neighbor for which
space is required. Otherwise LAMMPS crashes and gives the required
value.
.. code-block:: LAMMPS
read_data data-p.lmp extra/special/per/atom 1
@ -168,30 +159,27 @@ Let us assume we want to run a simple NVT simulation at 300 K. Note
that Drude oscillators need to be thermalized at a low temperature in
order to approximate a self-consistent field (SCF), therefore it is not
possible to simulate an NVE ensemble with this package. Since dipoles
are approximated by a charged DC-DP pair, the *pair\_style* must
are approximated by a charged DC-DP pair, the *pair_style* must
include Coulomb interactions, for instance *lj/cut/coul/long* with
*kspace\_style pppm*. For example, with a cutoff of 10. and a precision
*kspace_style pppm*. For example, with a cutoff of 10. and a precision
1.e-4:
.. code-block:: LAMMPS
pair_style lj/cut/coul/long 10.0
kspace_style pppm 1.0e-4
As compared to the non-polarizable input file, *pair\_coeff* lines need
As compared to the non-polarizable input file, *pair_coeff* lines need
to be added for the DPs. Since the DPs have no Lennard-Jones
interactions, their :math:`\epsilon` is 0. so the only *pair\_coeff* line
interactions, their :math:`\epsilon` is 0. so the only *pair_coeff* line
that needs to be added is
.. code-block:: LAMMPS
pair_coeff * 6* 0.0 0.0 # All-DPs
Now for the thermalization, the simplest choice is to use the :doc:`fix langevin/drude <fix_langevin_drude>`.
.. code-block:: LAMMPS
fix LANG all langevin/drude 300. 100 12435 1. 20 13977
@ -205,7 +193,6 @@ atoms need to be in this fix's group. LAMMPS will thermostat the DPs
together with their DC. For this, ghost atoms need to know their
velocities. Thus you need to add the following command:
.. code-block:: LAMMPS
comm_modify vel yes
@ -217,7 +204,6 @@ can add the *zero yes* option at the end of the fix line.
If the fix *shake* is used to constrain the C-H bonds, it should be
invoked after the fix *langevin/drude* for more accuracy.
.. code-block:: LAMMPS
fix SHAKE ATOMS shake 0.0001 20 0 t 4 5
@ -231,16 +217,14 @@ Since the fix *langevin/drude* does not perform time integration (just
modification of forces but no position/velocity updates), the fix
*nve* should be used in conjunction.
.. code-block:: LAMMPS
fix NVE all nve
Finally, do not forget to update the atom type elements if you use
them in a *dump\_modify ... element ...* command, by adding the element
them in a *dump_modify ... element ...* command, by adding the element
type of the DPs. Here for instance
.. code-block:: LAMMPS
dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz
@ -248,30 +232,26 @@ type of the DPs. Here for instance
The input file should now be ready for use!
You will notice that the global temperature *thermo\_temp* computed by
You will notice that the global temperature *thermo_temp* computed by
LAMMPS is not 300. K as wanted. This is because LAMMPS treats DPs as
standard atoms in his default compute. If you want to output the
temperatures of the DC-DP pair centers of mass and of the DPs relative
to their DCs, you should use the :doc:`compute temp\_drude <compute_temp_drude>`
to their DCs, you should use the :doc:`compute temp_drude <compute_temp_drude>`
.. code-block:: LAMMPS
compute TDRUDE all temp/drude
And then output the correct temperatures of the Drude oscillators
using *thermo\_style custom* with respectively *c\_TDRUDE[1]* and
*c\_TDRUDE[2]*. These should be close to 300.0 and 1.0 on average.
using *thermo_style custom* with respectively *c_TDRUDE[1]* and
*c_TDRUDE[2]*. These should be close to 300.0 and 1.0 on average.
.. code-block:: LAMMPS
thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2]
----------
**Thole screening**
Dipolar interactions represented by point charges on springs may not
@ -283,29 +263,27 @@ between nearby dipoles on the same molecule may be exaggerated. Often,
special bond relations prevent bonded neighboring atoms to see the
charge of each other's DP, so that the problem does not always appear.
It is possible to use screened dipole-dipole interactions by using the
:doc:`*pair\_style thole* <pair_thole>`. This is implemented as a
correction to the Coulomb pair\_styles, which dampens at short distance
:doc:`*pair_style thole* <pair_thole>`. This is implemented as a
correction to the Coulomb pair_styles, which dampens at short distance
the interactions between the charges representing the induced dipoles.
It is to be used as *hybrid/overlay* with any standard *coul* pair
style. In our example, we would use
.. code-block:: LAMMPS
pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0
This tells LAMMPS that we are using two pair\_styles. The first one is
This tells LAMMPS that we are using two pair_styles. The first one is
as above (\ *lj/cut/coul/long 10.0*\ ). The second one is a *thole*
pair\_style with default screening factor 2.6 (:ref:`Noskov <Noskov2>`) and
pair_style with default screening factor 2.6 (:ref:`Noskov <Noskov2>`) and
cutoff 10.0.
Since *hybrid/overlay* does not support mixing rules, the interaction
coefficients of all the pairs of atom types with i < j should be
explicitly defined. The output of the *polarizer* script can be used
to complete the *pair\_coeff* section of the input file. In our
to complete the *pair_coeff* section of the input file. In our
example, this will look like:
.. code-block:: LAMMPS
pair_coeff 1 1 lj/cut/coul/long 0.0700 3.550
@ -346,31 +324,27 @@ For the *thole* pair style the coefficients are
#. the atom polarizability in units of cubic length
#. the screening factor of the Thole function (optional, default value
specified by the pair\_style command)
#. the cutoff (optional, default value defined by the pair\_style command)
specified by the pair_style command)
#. the cutoff (optional, default value defined by the pair_style command)
The special neighbors have charge-charge and charge-dipole
interactions screened by the *coul* factors of the *special\_bonds*
interactions screened by the *coul* factors of the *special_bonds*
command (0.0, 0.0, and 0.5 in the example above). Without using the
pair\_style *thole*\ , dipole-dipole interactions are screened by the
same factor. By using the pair\_style *thole*\ , dipole-dipole
pair_style *thole*\ , dipole-dipole interactions are screened by the
same factor. By using the pair_style *thole*\ , dipole-dipole
interactions are screened by Thole's function, whatever their special
relationship (except within each DC-DP pair of course). Consider for
example 1-2 neighbors: using the pair\_style *thole*\ , their dipoles
example 1-2 neighbors: using the pair_style *thole*\ , their dipoles
will see each other (despite the *coul* factor being 0.) and the
interactions between these dipoles will be damped by Thole's function.
----------
**Thermostats and barostats**
Using a Nose-Hoover barostat with the *langevin/drude* thermostat is
straightforward using fix *nph* instead of *nve*\ . For example:
.. code-block:: LAMMPS
fix NPH all nph iso 1. 1. 500
@ -385,7 +359,6 @@ with respect to their DC. The *fix drude/transform/inverse* performs
the reverse transformation. For a NVT simulation, with the DCs and
atoms at 300 K and the DPs at 1 K relative to their DC one would use
.. code-block:: LAMMPS
fix DIRECT all drude/transform/direct
@ -395,7 +368,6 @@ atoms at 300 K and the DPs at 1 K relative to their DC one would use
For our phenol example, the groups would be defined as
.. code-block:: LAMMPS
group ATOMS type 1 2 3 4 5 # DCs and non-polarizable atoms
@ -403,13 +375,12 @@ For our phenol example, the groups would be defined as
group DRUDES type 6 7 8 # DPs
Note that with the fixes *drude/transform*\ , it is not required to
specify *comm\_modify vel yes* because the fixes do it anyway (several
specify *comm_modify vel yes* because the fixes do it anyway (several
times and for the forces also). To avoid the flying ice cube artifact
:ref:`(Lamoureux) <Lamoureux2>`, where the atoms progressively freeze and the
center of mass of the whole system drifts faster and faster, the *fix
momentum* can be used. For instance:
.. code-block:: LAMMPS
fix MOMENTUM all momentum 100 linear 1 1 1
@ -421,10 +392,9 @@ DPs should be *nvt* (or vice versa). Second, the *fix npt* computes a
global pressure and thus a global temperature whatever the fix group.
We do want the pressure to correspond to the whole system, but we want
the temperature to correspond to the fix group only. We must then use
the *fix\_modify* command for this. In the end, the block of
the *fix_modify* command for this. In the end, the block of
instructions for thermostatting and barostatting will look like
.. code-block:: LAMMPS
compute TATOMS ATOMS temp
@ -434,10 +404,8 @@ instructions for thermostatting and barostatting will look like
fix NVT DRUDES nvt temp 1. 1. 20
fix INVERSE all drude/transform/inverse
----------
**Rigid bodies**
You may want to simulate molecules as rigid bodies (but polarizable).
@ -448,7 +416,6 @@ review the different thermostats and ensemble combinations.
NVT ensemble using Langevin thermostat:
.. code-block:: LAMMPS
comm_modify vel yes
@ -458,7 +425,6 @@ NVT ensemble using Langevin thermostat:
NVT ensemble using Nose-Hoover thermostat:
.. code-block:: LAMMPS
fix DIRECT all drude/transform/direct
@ -468,7 +434,6 @@ NVT ensemble using Nose-Hoover thermostat:
NPT ensemble with Langevin thermostat:
.. code-block:: LAMMPS
comm_modify vel yes
@ -478,7 +443,6 @@ NPT ensemble with Langevin thermostat:
NPT ensemble using Nose-Hoover thermostat:
.. code-block:: LAMMPS
compute TATOM ATOMS temp
@ -488,45 +452,31 @@ NPT ensemble using Nose-Hoover thermostat:
fix NVT DRUDES nvt temp 1. 1. 20
fix INVERSE all drude/transform/inverse
----------
.. _Lamoureux2:
**(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)
.. _Schroeder:
**(Schroeder)** Schroeder and Steinhauser, J Chem Phys, 133,
154511 (2010).
.. _Jiang2:
**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
J Phys Chem Lett, 2, 87-92 (2011).
.. _Thole2:
**(Thole)** Chem Phys, 59, 341 (1981).
.. _Noskov2:
**(Noskov)** Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).
.. _SWM4-NDP:
**(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
Let, 418, 245-249 (2006)

18
doc/src/Howto_elastic.rst
View File

@ -4,14 +4,14 @@ Calculate elastic constants
Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation.
In tensor notation, this is expressed as s\_ij = C\_ijkl \* e\_kl, where
the repeated indices imply summation. s\_ij are the elements of the
symmetric stress tensor. e\_kl are the elements of the symmetric strain
tensor. C\_ijkl are the elements of the fourth rank tensor of elastic
In tensor notation, this is expressed as s_ij = C_ijkl \* e_kl, where
the repeated indices imply summation. s_ij are the elements of the
symmetric stress tensor. e_kl are the elements of the symmetric strain
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has 3\^4=81 elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where C\_ij
is now the derivative of s\_i w.r.t. e\_j. Because s\_i is itself a
derivative w.r.t. e\_i, it follows that C\_ij is also symmetric, with at
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
most 7\*6/2 = 21 distinct elements.
At zero temperature, it is easy to estimate these derivatives by
@ -33,12 +33,8 @@ tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`
----------
.. _Shinoda1:
**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

35
doc/src/Howto_github.rst
View File

@ -22,10 +22,8 @@ and will reduce the time until the integration is complete. For more
information on the requirements to have your code included into LAMMPS
please see the :doc:`Modify contribute <Modify_contribute>` doc page.
----------
**Making an account**
First of all, you need a GitHub account. This is fairly simple, just
@ -34,10 +32,8 @@ the "Sign up for GitHub" button. Once your account is created, you
can sign in by clicking the button in the top left and filling in your
username or e-mail address and password.
----------
**Forking the repository**
To get changes into LAMMPS, you need to first fork the `lammps/lammps`
@ -63,10 +59,8 @@ At the same time, you can set things up, so you can include changes from
upstream into your repository and thus keep it in sync with the ongoing
LAMMPS development.
----------
**Adding changes to your own fork**
Additions to the upstream version of LAMMPS are handled using *feature
@ -81,14 +75,12 @@ explained in more detail here: `feature branch workflow <https://www.atlassian.c
First of all, create a clone of your version on github on your local
machine via HTTPS:
.. code-block:: bash
$ git clone https://github.com/<your user name>/lammps.git <some name>
or, if you have set up your GitHub account for using SSH keys, via SSH:
.. code-block:: bash
$ git clone git@github.com:<your user name>/lammps.git
@ -108,7 +100,6 @@ test them without interfering with the repository on GitHub.
To pull changes from upstream into this copy, you can go to the directory
and use git pull:
.. code-block:: bash
$ cd mylammps
@ -117,7 +108,6 @@ and use git pull:
You can also add this URL as a remote:
.. code-block:: bash
$ git remote add lammps_upstream https://www.github.com/lammps/lammps
@ -127,7 +117,6 @@ branch for the feature you want to work on. This tutorial contains the
workflow that updated this tutorial, and hence we will call the branch
"github-tutorial-update":
.. code-block:: bash
$ git checkout -b github-tutorial-update master
@ -140,7 +129,6 @@ unrelated feature, you should switch branches!
After everything is done, add the files to the branch and commit them:
.. code-block:: bash
$ git add doc/src/Howto_github.txt
@ -165,14 +153,12 @@ After everything is done, add the files to the branch and commit them:
After adding all files, the change set can be committed with some
useful message that explains the change.
.. code-block:: bash
$ git commit -m 'Finally updated the github tutorial'
After the commit, the changes can be pushed to the same branch on GitHub:
.. code-block:: bash
$ git push
@ -181,7 +167,6 @@ Git will ask you for your user name and password on GitHub if you have
not configured anything. If your local branch is not present on GitHub yet,
it will ask you to add it by running
.. code-block:: bash
$ git push --set-upstream origin github-tutorial-update
@ -192,22 +177,18 @@ password, the feature branch should be added to your fork on GitHub.
If you want to make really sure you push to the right repository
(which is good practice), you can provide it explicitly:
.. code-block:: bash
$ git push origin
or using an explicit URL:
.. code-block:: bash
$ git push git@github.com:Pakketeretet2/lammps.git
----------
**Filing a pull request**
Up to this point in the tutorial, all changes were to *your* clones of
@ -255,10 +236,8 @@ Now just write some nice comments and click on "Create pull request".
.. image:: JPG/tutorial_create_new_pull_request2.png
:align: center
----------
**After filing a pull request**
.. note::
@ -308,10 +287,10 @@ After each push, the automated checks are run again.
LAMMPS developers may add labels to your pull request to assign it to
categories (mostly for bookkeeping purposes), but a few of them are
important: needs\_work, work\_in\_progress, test-for-regression, and
important: needs_work, work_in_progress, test-for-regression, and
full-regression-test. The first two indicate, that your pull request
is not considered to be complete. With "needs\_work" the burden is on
exclusively on you; while "work\_in\_progress" can also mean, that a
is not considered to be complete. With "needs_work" the burden is on
exclusively on you; while "work_in_progress" can also mean, that a
LAMMPS developer may want to add changes. Please watch the comments
to the pull requests. The two "test" labels are used to trigger
extended tests before the code is merged. This is sometimes done by
@ -408,7 +387,6 @@ Because the changes are OK with us, we are going to merge by clicking on
Now, since in the meantime our local text for the tutorial also changed,
we need to pull Axel's change back into our branch, and merge them:
.. code-block:: bash
$ git add Howto_github.txt
@ -425,7 +403,6 @@ With Axel's changes merged in and some final text updates, our feature
branch is now perfect as far as we are concerned, so we are going to
commit and push again:
.. code-block:: bash
$ git add Howto_github.txt
@ -438,10 +415,8 @@ This merge also shows up on the lammps GitHub page:
.. image:: JPG/tutorial_reverse_pull_request7.png
:align: center
----------
**After a merge**
When everything is fine, the feature branch is merged into the master branch:
@ -456,7 +431,6 @@ It is in principle safe to delete them from your own fork. This helps
keep it a bit more tidy. Note that you first have to switch to another
branch!
.. code-block:: bash
$ git checkout master
@ -472,7 +446,6 @@ first delete and then pull, everything should still be fine.
Finally, if you delete the branch locally, you might want to push this
to your remote(s) as well:
.. code-block:: bash
$ git push origin :github-tutorial-update
@ -485,7 +458,7 @@ should be submitted, there is now also an "unstable" and a "stable"
branch; these have the same content as "master", but are only updated
after a patch release or stable release was made.
Furthermore, the naming of the patches now follow the pattern
"patch\_<Day><Month><Year>" to simplify comparisons between releases.
"patch_<Day><Month><Year>" to simplify comparisons between releases.
Finally, all patches and submissions are subject to automatic testing
and code checks to make sure they at the very least compile.

2
doc/src/Howto_granular.rst
View File

@ -22,7 +22,7 @@ Use one of these 3 pair potentials, which compute forces and torques
between interacting pairs of particles:
* :doc:`pair_style <pair_style>` gran/history
* :doc:`pair_style <pair_style>` gran/no\_history
* :doc:`pair_style <pair_style>` gran/no_history
* :doc:`pair_style <pair_style>` gran/hertzian
These commands implement fix options specific to granular systems:

8
doc/src/Howto_kappa.rst
View File

@ -56,26 +56,20 @@ two preceding non-equilibrium methods, where energy flows continuously
between hot and cold regions of the simulation box.
The :doc:`compute heat/flux <compute_heat_flux>` command can calculate
the needed heat flux and describes how to implement the Green\_Kubo
the needed heat flux and describes how to implement the Green_Kubo
formalism using additional LAMMPS commands, such as the :doc:`fix ave/correlate <fix_ave_correlate>` command to calculate the needed
auto-correlation. See the doc page for the :doc:`compute heat/flux <compute_heat_flux>` command for an example input script
that calculates the thermal conductivity of solid Ar via the GK
formalism.
----------
.. _howto-Ikeshoji:
**(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).
.. _howto-Wirnsberger:
**(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
(2015).

73
doc/src/Howto_library.rst
View File

@ -12,7 +12,7 @@ functions therein have a C-style argument list, but contain C++ code
you could write yourself in a C++ application that was invoking LAMMPS
directly. The C++ code in the functions illustrates how to invoke
internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS\_NS) if you use them from another C++
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.
The examples/COUPLE and python/examples directories have example C++
@ -34,7 +34,7 @@ interface LAMMPS to Fortran libraries, or the code uses static variables
Another major issue to deal with is to correctly handle MPI. Creating
a LAMMPS instance requires passing an MPI communicator, or it assumes
the MPI\_COMM\_WORLD communicator, which spans all MPI processor ranks.
the MPI_COMM_WORLD communicator, which spans all MPI processor ranks.
When creating multiple LAMMPS object instances from different threads,
this communicator has to be different for each thread or else collisions
can happen, or it has to be guaranteed, that only one thread at a time
@ -58,7 +58,6 @@ details.
The added functions can access or change any internal LAMMPS data you
wish.
.. code-block:: c
void lammps_open(int, char **, MPI_Comm, void **)
@ -71,11 +70,11 @@ details.
void lammps_commands_string(void *, char *)
void lammps_free(void *)
The lammps\_open() function is used to initialize LAMMPS, passing in a
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were :doc:`command-line arguments <Run_options>` when LAMMPS is run in stand-alone mode
from the command line, and a MPI communicator for LAMMPS to run under.
It returns a ptr to the LAMMPS object that is created, and which is
used in subsequent library calls. The lammps\_open() function can be
used in subsequent library calls. The lammps_open() function can be
called multiple times, to create multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This
@ -87,14 +86,14 @@ half to the other code and run both codes simultaneously before
syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
The lammps\_open\_no\_mpi() function is similar except that no MPI
communicator is passed from the caller. Instead, MPI\_COMM\_WORLD is
The lammps_open_no_mpi() function is similar except that no MPI
communicator is passed from the caller. Instead, MPI_COMM_WORLD is
used to instantiate LAMMPS, and MPI is initialized if necessary.
The lammps\_close() function is used to shut down an instance of LAMMPS
The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.
The lammps\_version() function can be used to determined the specific
The lammps_version() function can be used to determined the specific
version of the underlying LAMMPS code. This is particularly useful
when loading LAMMPS as a shared library via dlopen(). The code using
the library interface can than use this information to adapt to
@ -102,8 +101,8 @@ changes to the LAMMPS command syntax between versions. The returned
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
20150902) that grows with every new LAMMPS version.
The lammps\_file(), lammps\_command(), lammps\_commands\_list(), and
lammps\_commands\_string() functions are used to pass one or more
The lammps_file(), lammps_command(), lammps_commands_list(), and
lammps_commands_string() functions are used to pass one or more
commands to LAMMPS to execute, the same as if they were coming from an
input script.
@ -114,19 +113,19 @@ can interleave the command function calls with operations it performs,
calls to extract information from or set information within LAMMPS, or
calls to another code's library.
The lammps\_file() function passes the filename of an input script.
The lammps\_command() function passes a single command as a string.
The lammps\_commands\_list() function passes multiple commands in a
char\*\* list. In both lammps\_command() and lammps\_commands\_list(),
The lammps_file() function passes the filename of an input script.
The lammps_command() function passes a single command as a string.
The lammps_commands_list() function passes multiple commands in a
char\*\* list. In both lammps_command() and lammps_commands_list(),
individual commands may or may not have a trailing newline. The
lammps\_commands\_string() function passes multiple commands
lammps_commands_string() function passes multiple commands
concatenated into one long string, separated by newline characters.
In both lammps\_commands\_list() and lammps\_commands\_string(), a single
In both lammps_commands_list() and lammps_commands_string(), a single
command can be spread across multiple lines, if the last printable
character of all but the last line is "&", the same as if the lines
appeared in an input script.
The lammps\_free() function is a clean-up function to free memory that
The lammps_free() function is a clean-up function to free memory that
the library allocated previously via other function calls. See
comments in src/library.cpp file for which other functions need this
clean-up.
@ -136,7 +135,6 @@ information from LAMMPS and setting value within LAMMPS. Again, see
the documentation in the src/library.cpp file for details, including
which quantities can be queried by name:
.. code-block:: c
int lammps_extract_setting(void *, char *)
@ -148,22 +146,21 @@ which quantities can be queried by name:
void *lammps_extract_fix(void *, char *, int, int, int, int)
void *lammps_extract_variable(void *, char *, char *)
The extract\_setting() function returns info on the size
The extract_setting() function returns info on the size
of data types (e.g. 32-bit or 64-bit atom IDs) used
by the LAMMPS executable (a compile-time choice).
The other extract functions return a pointer to various global or
per-atom quantities stored in LAMMPS or to values calculated by a
compute, fix, or variable. The pointer returned by the
extract\_global() function can be used as a permanent reference to a
value which may change. For the extract\_atom() method, see the
extract_global() function can be used as a permanent reference to a
value which may change. For the extract_atom() method, see the
extract() method in the src/atom.cpp file for a list of valid per-atom
properties. New names could easily be added if the property you want
is not listed. For the other extract functions, the underlying
storage may be reallocated as LAMMPS runs, so you need to re-call the
function to assure a current pointer or returned value(s).
.. code-block:: c
double lammps_get_thermo(void *, char *)
@ -172,22 +169,21 @@ function to assure a current pointer or returned value(s).
int lammps_set_variable(void *, char *, char *)
void lammps_reset_box(void *, double *, double *, double, double, double)
The lammps\_get\_thermo() function returns the current value of a thermo
The lammps_get_thermo() function returns the current value of a thermo
keyword as a double precision value.
The lammps\_get\_natoms() function returns the total number of atoms in
The lammps_get_natoms() function returns the total number of atoms in
the system and can be used by the caller to allocate memory for the
lammps\_gather\_atoms() and lammps\_scatter\_atoms() functions.
lammps_gather_atoms() and lammps_scatter_atoms() functions.
The lammps\_set\_variable() function can set an existing string-style
The lammps_set_variable() function can set an existing string-style
variable to a new string value, so that subsequent LAMMPS commands can
access the variable.
The lammps\_reset\_box() function resets the size and shape of the
The lammps_reset_box() function resets the size and shape of the
simulation box, e.g. as part of restoring a previously extracted and
saved state of a simulation.
.. code-block:: c
void lammps_gather_atoms(void *, char *, int, int, void *)
@ -206,17 +202,17 @@ owned by different processors.
.. warning::
These functions are not compatible with the
-DLAMMPS\_BIGBIG setting when compiling LAMMPS. Dummy functions
-DLAMMPS_BIGBIG setting when compiling LAMMPS. Dummy functions
that result in an error message and abort will be substituted
instead of resulting in random crashes and memory corruption.
The lammps\_gather\_atoms() function does this for all N atoms in the
The lammps_gather_atoms() function does this for all N atoms in the
system, ordered by atom ID, from 1 to N. The
lammps\_gather\_atoms\_concat() function does it for all N atoms, but
lammps_gather_atoms_concat() function does it for all N atoms, but
simply concatenates the subset of atoms owned by each processor. The
resulting vector is not ordered by atom ID. Atom IDs can be requested
by the same function if the caller needs to know the ordering. The
lammps\_gather\_subset() function allows the caller to request values
lammps_gather_subset() function allows the caller to request values
for only a subset of atoms (identified by ID).
For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
If the count is specified as 1, they are returned
@ -224,24 +220,23 @@ in a packed format with all three image flags stored in a single integer.
If the count is specified as 3, the values are unpacked into xyz flags
by the library before returning them.
The lammps\_scatter\_atoms() function takes a list of values for all N
The lammps_scatter_atoms() function takes a list of values for all N
atoms in the system, ordered by atom ID, from 1 to N, and assigns
those values to each atom in the system. The
lammps\_scatter\_atoms\_subset() function takes a subset of IDs as an
lammps_scatter_atoms_subset() function takes a subset of IDs as an
argument and only scatters those values to the owning atoms.
.. code-block:: c
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
imageint *, int)
The lammps\_create\_atoms() function takes a list of N atoms as input
The lammps_create_atoms() function takes a list of N atoms as input
with atom types and coords (required), an optionally atom IDs and
velocities and image flags. It uses the coords of each atom to assign
it as a new atom to the processor that owns it. This function is
useful to add atoms to a simulation or (in tandem with
lammps\_reset\_box()) to restore a previously extracted and saved state
lammps_reset_box()) to restore a previously extracted and saved state
of a simulation. Additional properties for the new atoms can then be
assigned via the lammps\_scatter\_atoms() or lammps\_extract\_atom()
assigned via the lammps_scatter_atoms() or lammps_extract_atom()
functions.

10
doc/src/Howto_manifold.rst
View File

@ -19,17 +19,17 @@ to the relevant fixes.
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| cylinder | R | x\^2 + y\^2 - R\^2 = 0 | Cylinder along z-axis, axis going through (0,0,0) |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| cylinder\_dent | R l a | x\^2 + y\^2 - r(z)\^2 = 0, r(x) = R if \| z \| > l, r(z) = R - a\*(1 + cos(z/l))/2 otherwise | A cylinder with a dent around z = 0 |
| cylinder_dent | R l a | x\^2 + y\^2 - r(z)\^2 = 0, r(x) = R if \| z \| > l, r(z) = R - a\*(1 + cos(z/l))/2 otherwise | A cylinder with a dent around z = 0 |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| dumbbell | a A B c | -( x\^2 + y\^2 ) + (a\^2 - z\^2/c\^2) \* ( 1 + (A\*sin(B\*z\^2))\^4) = 0 | A dumbbell |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| ellipsoid | a b c | (x/a)\^2 + (y/b)\^2 + (z/c)\^2 = 0 | An ellipsoid |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| gaussian\_bump | A l rc1 rc2 | if( x < rc1) -z + A \* exp( -x\^2 / (2 l\^2) ); else if( x < rc2 ) -z + a + b\*x + c\*x\^2 + d\*x\^3; else z | A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. |
| gaussian_bump | A l rc1 rc2 | if( x < rc1) -z + A \* exp( -x\^2 / (2 l\^2) ); else if( x < rc2 ) -z + a + b\*x + c\*x\^2 + d\*x\^3; else z | A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| plane | a b c x0 y0 z0 | a\*(x-x0) + b\*(y-y0) + c\*(z-z0) = 0 | A plane with normal (a,b,c) going through point (x0,y0,z0) |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| plane\_wiggle | a w | z - a\*sin(w\*x) = 0 | A plane with a sinusoidal modulation on z along x. |
| plane_wiggle | a w | z - a\*sin(w\*x) = 0 | A plane with a sinusoidal modulation on z along x. |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| sphere | R | x\^2 + y\^2 + z\^2 - R\^2 = 0 | A sphere of radius R |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
@ -37,7 +37,7 @@ to the relevant fixes.
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| spine | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | An approximation to a dendritic spine |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| spine\_two | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendritic spine |
| spine_two | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendritic spine |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| thylakoid | wB LB lB | Various, see :ref:`(Paquay) <Paquay1>` | A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
@ -46,7 +46,5 @@ to the relevant fixes.
.. _Paquay1:
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.

4
doc/src/Howto_multiple.rst
View File

@ -8,7 +8,6 @@ If "multiple simulations" means continue a previous simulation for
more timesteps, then you simply use the :doc:`run <run>` command
multiple times. For example, this script
.. code-block:: LAMMPS
units lj
@ -27,7 +26,6 @@ If you wish to run totally different simulations, one after the other,
the :doc:`clear <clear>` command can be used in between them to
re-initialize LAMMPS. For example, this script
.. code-block:: LAMMPS
units lj
@ -48,7 +46,6 @@ For large numbers of independent simulations, you can use
multiple times with different settings. For example, this
script, named in.polymer
.. code-block:: LAMMPS
variable d index run1 run2 run3 run4 run5 run6 run7 run8
@ -65,7 +62,6 @@ file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
.. code-block:: LAMMPS
variable a loop 8

4
doc/src/Howto_nemd.rst
View File

@ -43,13 +43,9 @@ 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 :doc:`fix flow/gauss <fix_flow_gauss>` command.
----------
.. _Daivis-nemd:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

13
doc/src/Howto_output.rst
View File

@ -12,7 +12,6 @@ There are four basic kinds of LAMMPS output:
screen.
* :doc:`Restart files <restart>`.
A simulation prints one set of thermodynamic output and (optionally)
restart files. It can generate any number of dump files and fix
output files, depending on what :doc:`dump <dump>` and :doc:`fix <fix>`
@ -69,11 +68,11 @@ notation, where ID in this case is the ID of a compute. The leading
"c\_" would be replaced by "f\_" for a fix, or "v\_" for a variable:
+-------------+--------------------------------------------+
| c\_ID | entire scalar, vector, or array |
| c_ID | entire scalar, vector, or array |
+-------------+--------------------------------------------+
| c\_ID[I] | one element of vector, one column of array |
| c_ID[I] | one element of vector, one column of array |
+-------------+--------------------------------------------+
| c\_ID[I][J] | one element of array |
| c_ID[I][J] | one element of array |
+-------------+--------------------------------------------+
In other words, using one bracket reduces the dimension of the data
@ -93,7 +92,7 @@ The frequency and format of thermodynamic output is set by the
:doc:`thermo_style <thermo_style>` command also specifies what values
are calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three additional kinds of keywords can
also be specified (c\_ID, f\_ID, v\_name), where a :doc:`compute <compute>`
also be specified (c_ID, f_ID, v_name), where a :doc:`compute <compute>`
or :doc:`fix <fix>` or :doc:`variable <variable>` provides the value to be
output. In each case, the compute, fix, or variable must generate
global values for input to the :doc:`thermo_style custom <dump>`
@ -122,7 +121,7 @@ pre-defined formats (dump atom, dump xtc, etc).
There is also a :doc:`dump custom <dump>` format where the user
specifies what values are output with each atom. Pre-defined atom
attributes can be specified (id, x, fx, etc). Three additional kinds
of keywords can also be specified (c\_ID, f\_ID, v\_name), where a
of keywords can also be specified (c_ID, f_ID, v_name), where a
:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable <variable>`
provides the values to be output. In each case, the compute, fix, or
variable must generate per-atom values for input to the :doc:`dump custom <dump>` command.
@ -130,7 +129,7 @@ variable must generate per-atom values for input to the :doc:`dump custom <dump>
There is also a :doc:`dump local <dump>` format where the user specifies
what local values to output. A pre-defined index keyword can be
specified to enumerate the local values. Two additional kinds of
keywords can also be specified (c\_ID, f\_ID), where a
keywords can also be specified (c_ID, f_ID), where a
:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable <variable>`
provides the values to be output. In each case, the compute or fix
must generate local values for input to the :doc:`dump local <dump>`

33
doc/src/Howto_pylammps.rst
View File

@ -56,7 +56,6 @@ output support enabled.
Step 1a: For the CMake based build system, the steps are:
.. code-block:: bash
mkdir $LAMMPS_DIR/build-shared
@ -68,7 +67,6 @@ Step 1a: For the CMake based build system, the steps are:
Step 1b: For the legacy, make based build system, the steps are:
.. code-block:: bash
cd $LAMMPS_DIR/src
@ -85,7 +83,6 @@ Step 2: Installing the LAMMPS Python package
PyLammps is part of the lammps Python package. To install it simply install
that package into your current Python installation with:
.. code-block:: bash
make install-python
@ -110,7 +107,6 @@ Benefits of using a virtualenv
**Prerequisite (e.g. on Ubuntu)**
.. code-block:: bash
apt-get install python-virtualenv
@ -118,7 +114,6 @@ Benefits of using a virtualenv
Creating a virtualenv with lammps installed
"""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
# create virtualenv named 'testing'
@ -132,7 +127,6 @@ When using CMake and the shared library has already been build, you
need to re-run CMake to update the location of the python executable
to the location in the virtual environment with:
.. code-block:: bash
cmake . -DPYTHON_EXECUTABLE=$(which python)
@ -154,7 +148,6 @@ Creating a new instance of PyLammps
To create a PyLammps object you need to first import the class from the lammps
module. By using the default constructor, a new *lammps* instance is created.
.. code-block:: Python
from lammps import PyLammps
@ -162,7 +155,6 @@ module. By using the default constructor, a new *lammps* instance is created.
You can also initialize PyLammps on top of this existing *lammps* object:
.. code-block:: Python
from lammps import lammps, PyLammps
@ -177,7 +169,6 @@ the command method of the lammps object instance.
For instance, let's take the following LAMMPS command:
.. code-block:: LAMMPS
region box block 0 10 0 5 -0.5 0.5
@ -185,7 +176,6 @@ For instance, let's take the following LAMMPS command:
In the original interface this command can be executed with the following
Python code if *L* was a lammps instance:
.. code-block:: Python
L.command("region box block 0 10 0 5 -0.5 0.5")
@ -193,7 +183,6 @@ Python code if *L* was a lammps instance:
With the PyLammps interface, any command can be split up into arbitrary parts
separated by white-space, passed as individual arguments to a region method.
.. code-block:: Python
L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
@ -206,7 +195,6 @@ The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the original interface parameterization needed to be done
manually by creating formatted strings.
.. code-block:: Python
L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
@ -214,7 +202,6 @@ manually by creating formatted strings.
In contrast, methods of PyLammps accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: Python
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
@ -225,8 +212,6 @@ System state
In addition to dispatching commands directly through the PyLammps object, it
also provides several properties which allow you to query the system state.
L.system
Is a dictionary describing the system such as the bounding box or number of atoms
@ -260,8 +245,6 @@ L.dump
L.groups
List of groups present in the current system
Working with LAMMPS variables
-----------------------------
@ -269,7 +252,6 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: Python
L.variable("a index 2")
@ -279,7 +261,6 @@ A dictionary of all variables is returned by L.variables
you can access an individual variable by retrieving a variable object from the
L.variables dictionary by name
.. code-block:: Python
a = L.variables['a']
@ -287,7 +268,6 @@ L.variables dictionary by name
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: Python
print(a.value)
@ -300,7 +280,6 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The
passed string parameter can be any expression containing global thermo values,
variables, compute or fix data.
.. code-block:: Python
result = L.eval("ke") # kinetic energy
@ -315,7 +294,6 @@ All atoms in the current simulation can be accessed by using the L.atoms list.
Each element of this list is an object which exposes its properties (id, type,
position, velocity, force, etc.).
.. code-block:: Python
# access first atom
@ -329,7 +307,6 @@ position, velocity, force, etc.).
Some properties can also be used to set:
.. code-block:: Python
# set position in 2D simulation
@ -347,7 +324,6 @@ after a run via the L.runs list. This list contains a growing list of run data.
The first element is the output of the first run, the second element that of
the second run.
.. code-block:: Python
L.run(1000)
@ -359,7 +335,6 @@ the second run.
Each run contains a dictionary of all trajectories. Each trajectory is
accessible through its thermo name:
.. code-block:: Python
L.runs[0].thermo.Step # list of time steps in first run
@ -367,7 +342,6 @@ accessible through its thermo name:
Together with matplotlib plotting data out of LAMMPS becomes simple:
.. code-block:: Python
import matplotlib.plot as plt
@ -406,7 +380,6 @@ tutorials and showcasing your latest research.
To launch an instance of Jupyter simply run the following command inside your
Python environment (this assumes you followed the Quick Start instructions):
.. code-block:: bash
jupyter notebook
@ -429,7 +402,6 @@ Four atoms are placed in the simulation and the dihedral potential is applied on
them using a datafile. Then one of the atoms is rotated along the central axis by
setting its position from Python, which changes the dihedral angle.
.. code-block:: Python
phi = [d \* math.pi / 180 for d in range(360)]
@ -463,7 +435,6 @@ Initially, a 2D system is created in a state with minimal energy.
It is then disordered by moving each atom by a random delta.
.. code-block:: Python
random.seed(27848)
@ -483,7 +454,6 @@ It is then disordered by moving each atom by a random delta.
Finally, the Monte Carlo algorithm is implemented in Python. It continuously
moves random atoms by a random delta and only accepts certain moves.
.. code-block:: Python
estart = L.eval("pe")
@ -536,7 +506,6 @@ Using PyLammps and mpi4py (Experimental)
PyLammps can be run in parallel using mpi4py. This python package can be installed using
.. code-block:: bash
pip install mpi4py
@ -544,7 +513,6 @@ PyLammps can be run in parallel using mpi4py. This python package can be install
The following is a short example which reads in an existing LAMMPS input file and
executes it in parallel. You can find in.melt in the examples/melt folder.
.. code-block:: Python
from mpi4py import MPI
@ -561,7 +529,6 @@ executes it in parallel. You can find in.melt in the examples/melt folder.
To run this script (melt.py) in parallel using 4 MPI processes we invoke the
following mpirun command:
.. code-block:: bash
mpirun -np 4 python melt.py

1
doc/src/Howto_replica.rst
View File

@ -37,7 +37,6 @@ replica. The processors assigned to each replica are determined at
run-time by using the :doc:`-partition command-line switch <Run_options>` to launch LAMMPS on multiple partitions,
which in this context are the same as replicas. E.g. these commands:
.. code-block:: bash
mpirun -np 16 lmp_linux -partition 8x2 -in in.temper

10
doc/src/Howto_restart.rst
View File

@ -21,7 +21,6 @@ Look at the *in.chain* input script provided in the *bench* directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line
.. code-block:: LAMMPS
restart 50 tmp.restart
@ -32,7 +31,6 @@ and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
last 50 timesteps:
.. code-block:: LAMMPS
read_restart tmp.restart.50
@ -48,8 +46,8 @@ last 50 timesteps:
run 50
Note that the following commands do not need to be repeated because
their settings are included in the restart file: *units, atom\_style,
special\_bonds, pair\_style, bond\_style*. However these commands do
their settings are included in the restart file: *units, atom_style,
special_bonds, pair_style, bond_style*. However these commands do
need to be used, since their settings are not in the restart file:
*neighbor, fix, timestep*\ .
@ -62,14 +60,12 @@ uses random numbers in a way that does not allow for perfect restarts.
As an alternate approach, the restart file could be converted to a data
file as follows:
.. code-block:: LAMMPS
lmp_g++ -r tmp.restart.50 tmp.restart.data
Then, this script could be used to re-run the last 50 steps:
.. code-block:: LAMMPS
units lj
@ -93,7 +89,7 @@ Then, this script could be used to re-run the last 50 steps:
run 50
Note that nearly all the settings specified in the original *in.chain*
script must be repeated, except the *pair\_coeff* and *bond\_coeff*
script must be repeated, except the *pair_coeff* and *bond_coeff*
commands since the new data file lists the force field coefficients.
Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell
LAMMPS the current timestep. This value is stored in restart files,

22
doc/src/Howto_spc.rst
View File

@ -15,18 +15,18 @@ atoms and the water molecule to run a rigid SPC model.
| H mass = 1.008
| O charge = -0.820
| H charge = 0.410
| LJ epsilon of OO = 0.1553
| LJ sigma of OO = 3.166
| LJ epsilon, sigma of OH, HH = 0.0
| r0 of OH bond = 1.0
| theta of HOH angle = 109.47
| LJ :math:`\epsilon` of OO = 0.1553
| LJ :math:`\sigma` of OO = 3.166
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
| :math:`r_0` of OH bond = 1.0
| :math:`\theta` of HOH angle = 109.47\ :math:`^{\circ}`
|
Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulombic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.
Angstrom cutoff for both LJ and Coulomb terms. It can also be used
with long-range electrostatic solvers (e.g. Ewald or PPPM in LAMMPS)
without changing any of the parameters above, although it becomes
a different model in that mode of usage.
The SPC/E (extended) water model is the same, except
the partial charge assignments change:
@ -40,13 +40,9 @@ the SPC and SPC/E models.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
----------
.. _howto-Berendsen:
**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).

3
doc/src/Howto_spherical.rst
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@ -38,7 +38,6 @@ The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command
like
.. code-block:: LAMMPS
atom_style hybrid sphere dipole
@ -116,7 +115,7 @@ such interactions. These are the various :doc:`pair styles <pair_style>` that g
* :doc:`pair_style gran/history <pair_gran>`
* :doc:`pair_style gran/hertzian <pair_gran>`
* :doc:`pair_style gran/no\_history <pair_gran>`
* :doc:`pair_style gran/no_history <pair_gran>`
* :doc:`pair_style dipole/cut <pair_dipole>`
* :doc:`pair_style gayberne <pair_gayberne>`
* :doc:`pair_style resquared <pair_resquared>`

4
doc/src/Howto_spins.rst
View File

@ -56,13 +56,9 @@ the magnetic energy. The second command is :doc:`compute property/atom <compute_
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
----------
.. _Tranchida:
**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, 372, 406-425, (2018).

4
doc/src/Howto_thermostat.rst
View File

@ -82,13 +82,9 @@ specify them explicitly via the :doc:`thermo_style custom <thermo_style>` comman
:doc:`thermo_modify <thermo_modify>` command to re-define what
temperature compute is used for default thermodynamic output.
----------
.. _Daivis-thermostat:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

36
doc/src/Howto_tip3p.rst
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@ -20,19 +20,19 @@ set to 0.0, it corresponds to the original 1983 TIP3P model
| H mass = 1.008
| O charge = -0.834
| H charge = 0.417
| LJ epsilon of OO = 0.1521
| LJ sigma of OO = 3.1507
| LJ epsilon of HH = 0.0460
| LJ sigma of HH = 0.4000
| LJ epsilon of OH = 0.0836
| LJ sigma of OH = 1.7753
| LJ :math:`\epsilon` of OO = 0.1521
| LJ :math:`\sigma` of OO = 3.1507
| LJ :math:`\epsilon` of HH = 0.0460
| LJ :math:`\sigma` of HH = 0.4000
| LJ :math:`\epsilon` of OH = 0.0836
| LJ :math:`\sigma` of OH = 1.7753
| K of OH bond = 450
| r0 of OH bond = 0.9572
| :math:`r_0` of OH bond = 0.9572
| K of HOH angle = 55
| theta of HOH angle = 104.52
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
These are the parameters to use for TIP3P with a long-range Coulombic
These are the parameters to use for TIP3P with a long-range Coulomb
solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) <Price1>` for
details:
@ -40,37 +40,29 @@ details:
| H mass = 1.008
| O charge = -0.830
| H charge = 0.415
| LJ epsilon of OO = 0.102
| LJ sigma of OO = 3.188
| LJ epsilon, sigma of OH, HH = 0.0
| LJ :math:`\epsilon` of OO = 0.102
| LJ :math:`\sigma` of OO = 3.188
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
| K of OH bond = 450
| r0 of OH bond = 0.9572
| :math:`r_0` of OH bond = 0.9572
| K of HOH angle = 55
| theta of HOH angle = 104.52
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
----------
.. _howto-tip3p:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
.. _Jorgensen1:
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
.. _Price1:
**(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004).

56
doc/src/Howto_tip4p.rst
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@ -11,7 +11,7 @@ angle style of *harmonic* or *charmm* should also be used.
A TIP4P model is run with LAMMPS using either this command
for a cutoff model:
:doc:`pair_style lj/cut/tip4p/cut <pair_lj>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj>`
or these two commands for a long-range model:
@ -31,45 +31,45 @@ coefficients.
| H mass = 1.008
| O charge = -1.040
| H charge = 0.520
| r0 of OH bond = 0.9572
| theta of HOH angle = 104.52
| :math:`r_0` of OH bond = 0.9572
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
| OM distance = 0.15
| LJ epsilon of O-O = 0.1550
| LJ sigma of O-O = 3.1536
| LJ epsilon, sigma of OH, HH = 0.0
| Coulombic cutoff = 8.5
| LJ :math:`\epsilon` of O-O = 0.1550
| LJ :math:`\sigma` of O-O = 3.1536
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
| Coulomb cutoff = 8.5
|
For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
http://dx.doi.org/10.1063/1.1931662) these values can be used:
https://doi.org/10.1063/1.1931662) these values can be used:
| O mass = 15.9994
| H mass = 1.008
| O charge = -1.1794
| H charge = 0.5897
| r0 of OH bond = 0.9572
| theta of HOH angle = 104.52
| :math:`r_0` of OH bond = 0.9572
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
| OM distance = 0.1577
| LJ epsilon of O-O = 0.21084
| LJ sigma of O-O = 3.1668
| LJ epsilon, sigma of OH, HH = 0.0
| Coulombic cutoff = 8.5
| LJ :math:`\epsilon` of O-O = 0.21084
| LJ :math:`\sigma` of O-O = 3.1668
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
| Coulomb cutoff = 8.5
|
For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
http://dx.doi.org/10.1063/1.2121687), these values can be used:
https://doi.org/10.1063/1.2121687), these values can be used:
| O mass = 15.9994
| H mass = 1.008
| O charge = -1.1128
| H charge = 0.5564
| r0 of OH bond = 0.9572
| theta of HOH angle = 104.52
| :math:`r_0` of OH bond = 0.9572
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
| OM distance = 0.1546
| LJ epsilon of O-O = 0.1852
| LJ sigma of O-O = 3.1589
| LJ epsilon, sigma of OH, HH = 0.0
| Coulombic cutoff = 8.5
| LJ :math:`\epsilon` of O-O = 0.1852
| LJ :math:`\sigma` of O-O = 3.1589
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
| Coulomb cutoff = 8.5
|
These are the parameters to use for TIP4P with a long-range Coulombic
@ -79,12 +79,12 @@ solver (e.g. Ewald or PPPM in LAMMPS):
| H mass = 1.008
| O charge = -1.0484
| H charge = 0.5242
| r0 of OH bond = 0.9572
| theta of HOH angle = 104.52
| :math:`r_0` of OH bond = 0.9572
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
| OM distance = 0.1250
| LJ epsilon of O-O = 0.16275
| LJ sigma of O-O = 3.16435
| LJ epsilon, sigma of OH, HH = 0.0
| LJ :math:`\epsilon` of O-O = 0.16275
| LJ :math:`\sigma` of O-O = 3.16435
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
Note that the when using the TIP4P pair style, the neighbor list
@ -99,13 +99,9 @@ and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
----------
.. _Jorgensen5:
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).

4
doc/src/Howto_triclinic.rst
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@ -200,7 +200,6 @@ an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:
.. parsed-literal::
ITEM: BOX BOUNDS xy xz yz
@ -212,7 +211,6 @@ This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
.. parsed-literal::
xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
@ -223,7 +221,7 @@ calculated from the 9 triclinic box parameters
zhi_bound = zhi
These formulas can be inverted if you need to convert the bounding box
back into the triclinic box parameters, e.g. xlo = xlo\_bound -
back into the triclinic box parameters, e.g. xlo = xlo_bound -
MIN(0.0,xy,xz,xy+xz).
One use of triclinic simulation boxes is to model solid-state crystals

5
doc/src/Howto_viscosity.rst
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@ -62,7 +62,6 @@ simulation box.
Here is an example input script that calculates the viscosity of
liquid Ar via the GK formalism:
.. code-block:: LAMMPS
# Sample LAMMPS input script for viscosity of liquid Ar
@ -131,13 +130,9 @@ time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.
----------
.. _Daivis-viscosity:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

10
doc/src/Howto_viz.rst
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@ -25,12 +25,8 @@ RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.
.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
.. _pizza: https://pizza.sandia.gov
.. _ensight: https://daac.hpc.mil/software/EnSight/
.. _ensight: http://www.ensight.com
.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
.. _atomeye: http://li.mit.edu/Archive/Graphics/A/

1
doc/src/Install.rst
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@ -8,7 +8,6 @@ have more flexibility as to what features to include or exclude in the
build. If you plan to :doc:`modify or extend LAMMPS <Modify>`, then you
need the source code.
.. toctree::
:maxdepth: 1

6
doc/src/Install_git.rst
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@ -16,8 +16,7 @@ commands explained below to communicate with the git servers on
GitHub. For people still using subversion (svn), GitHub also
provides `limited support for subversion clients <svn_>`_.
.. warning::
.. note::
As of October 2016, the official home of public LAMMPS development is
on GitHub. The previously advertised LAMMPS git repositories on
@ -35,7 +34,6 @@ You can follow LAMMPS development on 3 different git branches:
To access the git repositories on your box, use the clone command to
create a local copy of the LAMMPS repository with a command like:
.. code-block:: bash
$ git clone -b unstable https://github.com/lammps/lammps.git mylammps
@ -57,7 +55,6 @@ LAMMPS, as listed on :doc:`this page <Errors_bugs>`, you can stay
up-to-date by typing the following git commands from within the
"mylammps" directory:
.. code-block:: bash
$ git checkout unstable # not needed if you always stay in this branch
@ -92,7 +89,6 @@ Once you have updated your local files with a "git pull" (or "git
checkout"), you still need to re-build LAMMPS if any source files have
changed. To do this, you should cd to the src directory and type:
.. code-block:: bash
$ make purge # remove any deprecated src files

10
doc/src/Install_linux.rst
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@ -38,7 +38,7 @@ To install LAMMPS do the following once:
$ sudo apt-get install lammps-daily
This downloads an executable named "lmp\_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:
.. code-block:: bash
@ -103,10 +103,10 @@ 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* and *lmp\_openmpi*
or *lmp\_mpich* respectively. By default, *lmp* will refer to the
time and the name of the LAMMPS executable is *lmp* and *lmp_openmpi*
or *lmp_mpich* respectively. 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").
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
Then the corresponding parallel LAMMPS executable can be used.
The same mechanism applies when loading the LAMMPS python module.
@ -206,7 +206,6 @@ Gentoo Linux executable
LAMMPS is part of Gentoo's main package tree and can be installed by
typing:
.. code-block:: bash
% emerge --ask lammps
@ -216,7 +215,6 @@ built on the your machine.
Certain LAMMPS packages can be enable via USE flags, type
.. code-block:: bash
% equery uses lammps

6
doc/src/Install_mac.rst
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@ -10,18 +10,16 @@ GPU, KOKKOS, LATTE, MSCG, MESSAGE, MPIIO POEMS VORONOI.
After installing Homebrew, you can install LAMMPS on your system with
the following commands:
.. code-block:: bash
% brew install lammps
This will install the executables "lammps\_serial" and "lammps\_mpi", as well as
This will install the executables "lammps_serial" and "lammps_mpi", as well as
the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
Once LAMMPS is installed, you can test the installation with the
Lennard-Jones benchmark file:
.. code-block:: bash
% brew test lammps -v
@ -31,7 +29,6 @@ results in Homebrew also installing the `kim-api` binaries when LAMMPS is
installed. In order to use potentials from `openkim.org <openkim_>`_, you can
install the `openkim-models` package
.. code-block:: bash
% brew install openkim-models
@ -44,5 +41,4 @@ If you have problems with the installation you can post issues to
Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
up the Homebrew capability.
.. _openkim: https://openkim.org

2
doc/src/Install_patch.rst
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@ -8,7 +8,7 @@ how to stay current are on the
If you prefer to download a tarball, as described on the :doc:`Install git <Install_tarball>` doc page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
a patch file is posted on the `bug and feature page <http://lammps.sandia.gov/bug.html>`_ of the LAMMPS website, along
a patch file is posted on the `bug and feature page <https://lammps.sandia.gov/bug.html>`_ of the LAMMPS website, along
with a list of changed files and details about what is in the new patch
release. This page explains how to apply the patch file to your local
LAMMPS directory.

13
doc/src/Install_tarball.rst
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@ -4,10 +4,10 @@ Download source and documentation as a tarball
You can download a current LAMMPS tarball from the `download page <download_>`_
of the `LAMMPS website <lws_>`_.
.. _download: http://lammps.sandia.gov/download.html
.. _bug: http://lammps.sandia.gov/bug.html
.. _older: http://lammps.sandia.gov/tars
.. _lws: http://lammps.sandia.gov
.. _download: https://lammps.sandia.gov/download.html
.. _bug: https://lammps.sandia.gov/bug.html
.. _older: https://lammps.sandia.gov/tars
.. _lws: https://lammps.sandia.gov
You have two choices of tarballs, either the most recent stable
release or the most current patch release. Stable releases occur a
@ -26,7 +26,7 @@ command:
.. code-block:: bash
$ tar -xzvf lammps\*.tar.gz
$ tar -xzvf lammps*.tar.gz
This will create a LAMMPS directory with the version date
in its name, e.g. lammps-23Jun18.
@ -40,7 +40,7 @@ a lammps-master dir:
.. code-block:: bash
$ unzip lammps\*.zip
$ unzip lammps*.zip
This version is the most up-to-date LAMMPS development version. It
will have the date of the most recent patch release (see the file
@ -52,7 +52,6 @@ the next patch release tarball.
----------
If you download a current LAMMPS tarball, one way to stay current as
new patch tarballs are released, is to download a patch file which you
can apply to your local directory to update it for each new patch

6
doc/src/Install_windows.rst
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@ -4,7 +4,9 @@ Download an executable for Windows
Pre-compiled Windows installers which install LAMMPS executables on a
Windows system can be downloaded from this site:
`http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_
.. parsed-literal::
`http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_
Note that each installer package has a date in its name, which
corresponds to the LAMMPS version of the same date. Installers for
@ -26,7 +28,7 @@ When you download the installer package, you run it on your Windows
machine. It will then prompt you with a dialog, where you can choose
the installation directory, unpack and copy several executables,
potential files, documentation pdfs, selected example files, etc. It
will then update a few system settings (e.g. PATH, LAMMPS\_POTENTIALS)
will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS)
and add an entry into the Start Menu (with references to the
documentation, LAMMPS homepage and more). From that menu, there is
also a link to an uninstaller that removes the files and undoes the

1
doc/src/Intro.rst
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@ -3,7 +3,6 @@ Introduction
These pages provide a brief introduction to LAMMPS.
.. toctree::
:maxdepth: 1

13
doc/src/Intro_authors.rst
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@ -11,25 +11,20 @@ University:
* Richard Berger, richard.berger at temple.edu
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _lws: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
and Ray Shan, now at Materials Design.
----------
The `Authors page <http://lammps.sandia.gov/authors.html>`_ of the
The `Authors page <https://lammps.sandia.gov/authors.html>`_ of the
`LAMMPS website <lws_>`_ has a comprehensive list of all the individuals
who have contributed code for a new feature or command or tool to
LAMMPS.
----------
The following folks deserve special recognition. Many of the packages
they have written are unique for an MD code and LAMMPS would not be as
general-purpose as it is without their expertise and efforts.
@ -49,11 +44,9 @@ general-purpose as it is without their expertise and efforts.
* Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD
* Greg Wagner (Northwestern U), MEAM package for MEAM potential
----------
As discussed on the `History page <http://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
As discussed on the `History page <https://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:

8
doc/src/Intro_features.rst
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@ -16,10 +16,8 @@ classes of functionality:
10. :ref:`Pre- and post-processing <prepost>`
11. :ref:`Specialized features (beyond MD itself) <special>`
----------
.. _general:
General features
@ -189,14 +187,10 @@ Pre- and post-processing
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in `Python <python_>`_ and is available for download from `the Pizza.py WWW site <pizza_>`_.
.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
.. _pizza: https://pizza.sandia.gov
.. _python: http://www.python.org
.. _special:
Specialized features

4
doc/src/Intro_nonfeatures.rst
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@ -66,7 +66,7 @@ Here are suggestions on how to perform these tasks:
on-the-fly via its :doc:`dump image <dump_image>` command and pass
them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
movies from them. For high-quality, interactive visualization there are
many excellent and free tools available. See the `Other Codes page <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS website for
many excellent and free tools available. See the `Other Codes page <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS website for
visualization packages that can use LAMMPS output data.
* **Plotting:** See the next bullet about Pizza.py as well as the
:doc:`Python <Python_head>` doc page for examples of plotting LAMMPS
@ -75,7 +75,7 @@ Here are suggestions on how to perform these tasks:
it easier to analyze and plot. See the :doc:`Tools <Tools>` doc page
for more discussion of the various tools.
* **Pizza.py:** Our group has also written a separate toolkit called
`Pizza.py <http://pizza.sandia.gov>`_ which can do certain kinds of
`Pizza.py <https://pizza.sandia.gov>`_ which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in `Python <http://www.python.org>`_

6
doc/src/Intro_opensource.rst
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@ -15,16 +15,10 @@ distribution.
.. _gnu: http://www.gnu.org/copyleft/gpl.html
.. _gnuorg: http://www.gnu.org
.. _opensource: http://www.opensource.org
Here is a summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they

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

42
doc/src/Intro_website.rst
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@ -5,32 +5,32 @@ The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some of the other pages in
this Intr are included in this list.
.. _lws: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov
* `Brief intro and recently added significant features <lws_>`_
* `List of features <http://lammps.sandia.gov/features.html>`_
* `List of non-features <http://lammps.sandia.gov/non_features.html>`_
* `Recent bug fixes and new features <http://lammps.sandia.gov/bug.html>`_
* `List of features <https://lammps.sandia.gov/features.html>`_
* `List of non-features <https://lammps.sandia.gov/non_features.html>`_
* `Recent bug fixes and new features <https://lammps.sandia.gov/bug.html>`_
* `Download info <http://lammps.sandia.gov/download.html>`_
* `Download info <https://lammps.sandia.gov/download.html>`_
* `GitHub site <https://github.com/lammps/lammps>`_
* `SourceForge site <https://sourceforge.net/projects/lammps>`_
* `LAMMPS open-source license <http://lammps.sandia.gov/open_source.html>`_
* `LAMMPS open-source license <https://lammps.sandia.gov/open_source.html>`_
* `Glossary of MD terms relevant to LAMMPS <http://lammps.sandia.gov/glossary.html>`_
* `LAMMPS highlights with images <http://lammps.sandia.gov/pictures.html>`_
* `LAMMPS highlights with movies <http://lammps.sandia.gov/movies.html>`_
* `Mail list <http://lammps.sandia.gov/mail.html>`_
* `Workshops <http://lammps.sandia.gov/workshops.html>`_
* `Tutorials <http://lammps.sandia.gov/tutorials.html>`_
* `Developer guide <http://lammps.sandia.gov/Developer.pdf>`_
* `Glossary of MD terms relevant to LAMMPS <https://lammps.sandia.gov/glossary.html>`_
* `LAMMPS highlights with images <https://lammps.sandia.gov/pictures.html>`_
* `LAMMPS highlights with movies <https://lammps.sandia.gov/movies.html>`_
* `Mail list <https://lammps.sandia.gov/mail.html>`_
* `Workshops <https://lammps.sandia.gov/workshops.html>`_
* `Tutorials <https://lammps.sandia.gov/tutorials.html>`_
* `Developer guide <https://lammps.sandia.gov/Developer.pdf>`_
* `Pre- and post-processing tools for LAMMPS <http://lammps.sandia.gov/prepost.html>`_
* `Other software usable with LAMMPS <http://lammps.sandia.gov/offsite.html>`_
* `Viz tools usable with LAMMPS <http://lammps.sandia.gov/viz.html>`_
* `Pre- and post-processing tools for LAMMPS <https://lammps.sandia.gov/prepost.html>`_
* `Other software usable with LAMMPS <https://lammps.sandia.gov/offsite.html>`_
* `Viz tools usable with LAMMPS <https://lammps.sandia.gov/viz.html>`_
* `Benchmark performance <http://lammps.sandia.gov/bench.html>`_
* `Publications that have cited LAMMPS <http://lammps.sandia.gov/papers.html>`_
* `Authors of LAMMPS <http://lammps.sandia.gov/authors.html>`_
* `History of LAMMPS development <http://lammps.sandia.gov/history.html>`_
* `Funding for LAMMPS <http://lammps.sandia.gov/funding.html>`_
* `Benchmark performance <https://lammps.sandia.gov/bench.html>`_
* `Publications that have cited LAMMPS <https://lammps.sandia.gov/papers.html>`_
* `Authors of LAMMPS <https://lammps.sandia.gov/authors.html>`_
* `History of LAMMPS development <https://lammps.sandia.gov/history.html>`_
* `Funding for LAMMPS <https://lammps.sandia.gov/funding.html>`_

4
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@ -18,7 +18,7 @@ LAMMPS is an open-source code, distributed freely under the terms of
the GNU Public License (GPL).
The `LAMMPS website <lws_>`_ has a variety of information about the code.
It includes links to an on-line version of this manual, a `mailing list <http://lammps.sandia.gov/mail.html>`_ where users can post
It includes links to an on-line version of this manual, a `mailing list <https://lammps.sandia.gov/mail.html>`_ where users can post
questions, and a `GitHub site <https://github.com/lammps/lammps>`_ where
all LAMMPS development is coordinated.
@ -35,7 +35,7 @@ a brief description of the basic code structure of LAMMPS.
Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for
every LAMMPS command.
.. _lws: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov
.. toctree::
:maxdepth: 2

16
doc/src/Manual_build.rst
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@ -5,8 +5,7 @@ Depending on how you obtained LAMMPS, the doc directory has up
to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
plus 2 e-book format files:
.. parsed-literal::
.. code-block:: bash
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
@ -29,8 +28,8 @@ and PDF files are not included. Instead you need to create them, in one
of two ways:
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type "make fetch". This should download a html\_www
directory and Manual\_www.pdf/Developer\_www.pdf files. Note that if
site. Just type "make fetch". This should download a html_www
directory and Manual_www.pdf/Developer_www.pdf files. Note that if
new LAMMPS features have been added more recently than the date of
your LAMMPS version, the fetched documentation will include those
changes (but your source code will not, unless you update your local
@ -49,11 +48,9 @@ b. You can build the HTML or PDF files yourself, by typing "make html"
----------
The generation of all documentation is managed by the Makefile in
the doc directory.
.. code-block:: bash
Documentation Build Options:
@ -74,7 +71,6 @@ the doc directory.
----------
Installing prerequisites for HTML build
=======================================
@ -84,7 +80,6 @@ have to be installed. Here are instructions for common setups:
Ubuntu
------
.. code-block:: bash
sudo apt-get install python-virtualenv
@ -92,7 +87,6 @@ Ubuntu
Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
------------------------------------------------------------------------------------
.. code-block:: bash
sudo yum install python3-virtualenv
@ -100,7 +94,6 @@ Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version
Fedora (since version 22)
-------------------------
.. code-block:: bash
sudo dnf install python3-virtualenv
@ -121,17 +114,14 @@ virtualenv
Once Python 3 is installed, open a Terminal and type
.. code-block:: bash
pip3 install virtualenv
This will install virtualenv from the Python Package Index.
----------
Installing prerequisites for epub build
=======================================

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

1
doc/src/Modify.rst
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@ -10,7 +10,6 @@ If you add a new feature to LAMMPS and think it will be of interest to
general users, we encourage you to submit it for inclusion in LAMMPS
as a pull request on our `GitHub site <https://github.com/lammps/lammps>`_, after reading the :doc:`Modify contribute <Modify_contribute>` doc page.
.. toctree::
:maxdepth: 1

76
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@ -8,78 +8,78 @@ style can be created if one of the existing atom styles does not
define all the attributes you need to store and communicate with
atoms.
Atom\_vec\_atomic.cpp is a simple example of an atom style.
Atom_vec_atomic.cpp is a simple example of an atom style.
Here is a brief description of methods you define in your new derived
class. See atom\_vec.h for details.
class. See atom_vec.h for details.
+-------------------------+--------------------------------------------------------------------------------+
| init | one time setup (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| grow | re-allocate atom arrays to longer lengths (required) |
+-------------------------+--------------------------------------------------------------------------------+
| grow\_reset | make array pointers in Atom and AtomVec classes consistent (required) |
| grow_reset | make array pointers in Atom and AtomVec classes consistent (required) |
+-------------------------+--------------------------------------------------------------------------------+
| copy | copy info for one atom to another atom's array locations (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_comm | store an atom's info in a buffer communicated every timestep (required) |
| pack_comm | store an atom's info in a buffer communicated every timestep (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_comm\_vel | add velocity info to communication buffer (required) |
| pack_comm_vel | add velocity info to communication buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_comm\_hybrid | store extra info unique to this atom style (optional) |
| pack_comm_hybrid | store extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_comm | retrieve an atom's info from the buffer (required) |
| unpack_comm | retrieve an atom's info from the buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_comm\_vel | also retrieve velocity info (required) |
| unpack_comm_vel | also retrieve velocity info (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_comm\_hybrid | retrieve extra info unique to this atom style (optional) |
| unpack_comm_hybrid | retrieve extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_reverse | store an atom's info in a buffer communicating partial forces (required) |
| pack_reverse | store an atom's info in a buffer communicating partial forces (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_reverse\_hybrid | store extra info unique to this atom style (optional) |
| pack_reverse_hybrid | store extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_reverse | retrieve an atom's info from the buffer (required) |
| unpack_reverse | retrieve an atom's info from the buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_reverse\_hybrid | retrieve extra info unique to this atom style (optional) |
| unpack_reverse_hybrid | retrieve extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_border | store an atom's info in a buffer communicated on neighbor re-builds (required) |
| pack_border | store an atom's info in a buffer communicated on neighbor re-builds (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_border\_vel | add velocity info to buffer (required) |
| pack_border_vel | add velocity info to buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_border\_hybrid | store extra info unique to this atom style (optional) |
| pack_border_hybrid | store extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_border | retrieve an atom's info from the buffer (required) |
| unpack_border | retrieve an atom's info from the buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_border\_vel | also retrieve velocity info (required) |
| unpack_border_vel | also retrieve velocity info (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_border\_hybrid | retrieve extra info unique to this atom style (optional) |
| unpack_border_hybrid | retrieve extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_exchange | store all an atom's info to migrate to another processor (required) |
| pack_exchange | store all an atom's info to migrate to another processor (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_exchange | retrieve an atom's info from the buffer (required) |
| unpack_exchange | retrieve an atom's info from the buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| size\_restart | number of restart quantities associated with proc's atoms (required) |
| size_restart | number of restart quantities associated with proc's atoms (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack\_restart | pack atom quantities into a buffer (required) |
| pack_restart | pack atom quantities into a buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack\_restart | unpack atom quantities from a buffer (required) |
| unpack_restart | unpack atom quantities from a buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| create\_atom | create an individual atom of this style (required) |
| create_atom | create an individual atom of this style (required) |
+-------------------------+--------------------------------------------------------------------------------+
| data\_atom | parse an atom line from the data file (required) |
| data_atom | parse an atom line from the data file (required) |
+-------------------------+--------------------------------------------------------------------------------+
| data\_atom\_hybrid | parse additional atom info unique to this atom style (optional) |
| data_atom_hybrid | parse additional atom info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| data\_vel | parse one line of velocity information from data file (optional) |
| data_vel | parse one line of velocity information from data file (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| data\_vel\_hybrid | parse additional velocity data unique to this atom style (optional) |
| data_vel_hybrid | parse additional velocity data unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| memory\_usage | tally memory allocated by atom arrays (required) |
| memory_usage | tally memory allocated by atom arrays (required) |
+-------------------------+--------------------------------------------------------------------------------+
The constructor of the derived class sets values for several variables
that you must set when defining a new atom style, which are documented
in atom\_vec.h. New atom arrays are defined in atom.cpp. Search for
in atom_vec.h. New atom arrays are defined in atom.cpp. Search for
the word "customize" and you will find locations you will need to
modify.
@ -95,13 +95,12 @@ modify.
New :doc:`pair styles <pair_style>`, :doc:`fixes <fix>`, or
:doc:`computes <compute>` can be added to LAMMPS, as discussed below.
The code for these classes can use the per-atom properties defined by
fix property/atom. The Atom class has a find\_custom() method that is
fix property/atom. The Atom class has a find_custom() method that is
useful in this context:
.. code-block:: c++
.. parsed-literal::
int index = atom->find_custom(char \*name, int &flag);
int index = atom->find_custom(char *name, int &flag);
The "name" of a custom attribute, as specified in the :doc:`fix property/atom <fix_property_atom>` command, is checked to verify
that it exists and its index is returned. The method also sets flag =
@ -109,11 +108,10 @@ that it exists and its index is returned. The method also sets flag =
The vector of values associated with the attribute can then be
accessed using the returned index as
.. code-block:: c++
.. parsed-literal::
int \*ivector = atom->ivector[index];
double \*dvector = atom->dvector[index];
int *ivector = atom->ivector[index];
double *dvector = atom->dvector[index];
Ivector or dvector are vectors of length Nlocal = # of owned atoms,
which store the attributes of individual atoms.

12
doc/src/Modify_body.rst
View File

@ -10,14 +10,14 @@ See the :doc:`Howto body <Howto_body>` doc page for an overview of using
body particles and the various body styles LAMMPS supports. New
styles can be created to add new kinds of body particles to LAMMPS.
Body\_nparticle.cpp is an example of a body particle that is treated as
Body_nparticle.cpp is an example of a body particle that is treated as
a rigid body containing N sub-particles.
Here is a brief description of methods you define in your new derived
class. See body.h for details.
+----------------------+-----------------------------------------------------------+
| data\_body | process a line from the Bodies section of a data file |
| data_body | process a line from the Bodies section of a data file |
+----------------------+-----------------------------------------------------------+
| noutrow | number of sub-particles output is generated for |
+----------------------+-----------------------------------------------------------+
@ -25,11 +25,11 @@ class. See body.h for details.
+----------------------+-----------------------------------------------------------+
| output | output values for the Mth sub-particle |
+----------------------+-----------------------------------------------------------+
| pack\_comm\_body | body attributes to communicate every timestep |
| pack_comm_body | body attributes to communicate every timestep |
+----------------------+-----------------------------------------------------------+
| unpack\_comm\_body | unpacking of those attributes |
| unpack_comm_body | unpacking of those attributes |
+----------------------+-----------------------------------------------------------+
| pack\_border\_body | body attributes to communicate when reneighboring is done |
| pack_border_body | body attributes to communicate when reneighboring is done |
+----------------------+-----------------------------------------------------------+
| unpack\_border\_body | unpacking of those attributes |
| unpack_border_body | unpacking of those attributes |
+----------------------+-----------------------------------------------------------+

14
doc/src/Modify_bond.rst
View File

@ -5,7 +5,7 @@ Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
add new potentials to LAMMPS.
Bond\_harmonic.cpp is the simplest example of a bond style. Ditto for
Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
the harmonic forms of the angle, dihedral, and improper style
commands.
@ -14,9 +14,9 @@ new derived class. See bond.h, angle.h, dihedral.h, and improper.h
for details and specific additional methods.
+-----------------------+---------------------------------------------------------------------------+
| init | check if all coefficients are set, calls *init\_style* (optional) |
| init | check if all coefficients are set, calls *init_style* (optional) |
+-----------------------+---------------------------------------------------------------------------+
| init\_style | check if style specific conditions are met (optional) |
| init_style | check if style specific conditions are met (optional) |
+-----------------------+---------------------------------------------------------------------------+
| compute | compute the molecular interactions (required) |
+-----------------------+---------------------------------------------------------------------------+
@ -24,13 +24,13 @@ for details and specific additional methods.
+-----------------------+---------------------------------------------------------------------------+
| coeff | set coefficients for one type (required) |
+-----------------------+---------------------------------------------------------------------------+
| equilibrium\_distance | length of bond, used by SHAKE (required, bond only) |
| equilibrium_distance | length of bond, used by SHAKE (required, bond only) |
+-----------------------+---------------------------------------------------------------------------+
| equilibrium\_angle | opening of angle, used by SHAKE (required, angle only) |
| equilibrium_angle | opening of angle, used by SHAKE (required, angle only) |
+-----------------------+---------------------------------------------------------------------------+
| write & read\_restart | writes/reads coeffs to restart files (required) |
| write & read_restart | writes/reads coeffs to restart files (required) |
+-----------------------+---------------------------------------------------------------------------+
| single | force and energy of a single bond or angle (required, bond or angle only) |
+-----------------------+---------------------------------------------------------------------------+
| memory\_usage | tally memory allocated by the style (optional) |
| memory_usage | tally memory allocated by the style (optional) |
+-----------------------+---------------------------------------------------------------------------+

4
doc/src/Modify_command.rst
View File

@ -2,8 +2,8 @@ Input script command style
==========================
New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create\_atoms,
read\_data, velocity, and run commands are all implemented in this
classes that have a "command" method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
fashion. When such a command is encountered in the LAMMPS input
script, LAMMPS simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments

42
doc/src/Modify_compute.rst
View File

@ -7,8 +7,8 @@ quantities like kinetic energy and the centro-symmetry parameter
are derived from the Compute class. New styles can be created
to add new calculations to LAMMPS.
Compute\_temp.cpp is a simple example of computing a scalar
temperature. Compute\_ke\_atom.cpp is a simple example of computing
Compute_temp.cpp is a simple example of computing a scalar
temperature. Compute_ke_atom.cpp is a simple example of computing
per-atom kinetic energy.
Here is a brief description of methods you define in your new derived
@ -17,41 +17,41 @@ class. See compute.h for details.
+-----------------------+------------------------------------------------------------------+
| init | perform one time setup (required) |
+-----------------------+------------------------------------------------------------------+
| init\_list | neighbor list setup, if needed (optional) |
| init_list | neighbor list setup, if needed (optional) |
+-----------------------+------------------------------------------------------------------+
| compute\_scalar | compute a scalar quantity (optional) |
| compute_scalar | compute a scalar quantity (optional) |
+-----------------------+------------------------------------------------------------------+
| compute\_vector | compute a vector of quantities (optional) |
| compute_vector | compute a vector of quantities (optional) |
+-----------------------+------------------------------------------------------------------+
| compute\_peratom | compute one or more quantities per atom (optional) |
| compute_peratom | compute one or more quantities per atom (optional) |
+-----------------------+------------------------------------------------------------------+
| compute\_local | compute one or more quantities per processor (optional) |
| compute_local | compute one or more quantities per processor (optional) |
+-----------------------+------------------------------------------------------------------+
| pack\_comm | pack a buffer with items to communicate (optional) |
| pack_comm | pack a buffer with items to communicate (optional) |
+-----------------------+------------------------------------------------------------------+
| unpack\_comm | unpack the buffer (optional) |
| unpack_comm | unpack the buffer (optional) |
+-----------------------+------------------------------------------------------------------+
| pack\_reverse | pack a buffer with items to reverse communicate (optional) |
| pack_reverse | pack a buffer with items to reverse communicate (optional) |
+-----------------------+------------------------------------------------------------------+
| unpack\_reverse | unpack the buffer (optional) |
| unpack_reverse | unpack the buffer (optional) |
+-----------------------+------------------------------------------------------------------+
| remove\_bias | remove velocity bias from one atom (optional) |
| remove_bias | remove velocity bias from one atom (optional) |
+-----------------------+------------------------------------------------------------------+
| remove\_bias\_all | remove velocity bias from all atoms in group (optional) |
| remove_bias_all | remove velocity bias from all atoms in group (optional) |
+-----------------------+------------------------------------------------------------------+
| restore\_bias | restore velocity bias for one atom after remove\_bias (optional) |
| restore_bias | restore velocity bias for one atom after remove_bias (optional) |
+-----------------------+------------------------------------------------------------------+
| restore\_bias\_all | same as before, but for all atoms in group (optional) |
| restore_bias_all | same as before, but for all atoms in group (optional) |
+-----------------------+------------------------------------------------------------------+
| pair\_tally\_callback | callback function for *tally*\ -style computes (optional). |
| pair_tally_callback | callback function for *tally*\ -style computes (optional). |
+-----------------------+------------------------------------------------------------------+
| memory\_usage | tally memory usage (optional) |
| memory_usage | tally memory usage (optional) |
+-----------------------+------------------------------------------------------------------+
Tally-style computes are a special case, as their computation is done
in two stages: the callback function is registered with the pair style
and then called from the Pair::ev\_tally() function, which is called for
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute\_scalar or
compute\_vector or compute\_peratom methods. The USER-TALLY package
provides *examples*\ \_compute\_tally.html for utilizing this mechanism.
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The USER-TALLY package
provides *examples*\ _compute_tally.html for utilizing this mechanism.

25
doc/src/Modify_contribute.rst
View File

@ -2,7 +2,7 @@ Submitting new features for inclusion in LAMMPS
===============================================
We encourage users to submit new features or modifications for LAMMPS
to `the core developers <http://lammps.sandia.gov/authors.html>`_ so they
to `the core developers <https://lammps.sandia.gov/authors.html>`_ so they
can be added to the LAMMPS distribution. The preferred way to manage
and coordinate this is as of Fall 2016 via the LAMMPS project on
`GitHub <https://github.com/lammps/lammps>`_. An alternative is to
@ -44,12 +44,12 @@ are listed and described on the :doc:`Packages details <Packages_details>` doc p
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
used as a license for the rest of LAMMPS. See the `Open source <http://lammps.sandia.gov/open_source.html>`_ page on the LAMMPS
used as a license for the rest of LAMMPS. See the `Open source <https://lammps.sandia.gov/open_source.html>`_ page on the LAMMPS
website for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the `Authors page <http://lammps.sandia.gov/authors.html>`_
code and on the `Authors page <https://lammps.sandia.gov/authors.html>`_
of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
@ -63,13 +63,13 @@ unusual event).
If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <http://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
`developers <http://lammps.sandia.gov/authors.html>`_ with info about
`developers <https://lammps.sandia.gov/authors.html>`_ with info about
your package and we will post it there.
.. _lws: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
@ -78,7 +78,7 @@ LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you should `communicate with the
developers <http://lammps.sandia.gov/authors.html>`_, since we may or
developers <https://lammps.sandia.gov/authors.html>`_, since we may or
may not want to include those changes for some reason. An example of a
trivial change is making a parent-class method "virtual" when you derive
a new child class from it.
@ -90,8 +90,8 @@ packages in the src directory for examples. If you are uncertain, please ask.
* All source files you provide must compile with the most current
version of LAMMPS with multiple configurations. In particular you
need to test compiling LAMMPS from scratch with -DLAMMPS\_BIGBIG
set in addition to the default -DLAMMPS\_SMALLBIG setting. Your code
need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG
set in addition to the default -DLAMMPS_SMALLBIG setting. Your code
will need to work correctly in serial and in parallel using MPI.
* For consistency with the rest of LAMMPS and especially, if you want
@ -106,7 +106,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
(<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
<stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
used where possible or needed to avoid including headers.
All added code should be placed into the LAMMPS\_NS namespace or a
All added code should be placed into the LAMMPS_NS namespace or a
sub-namespace; global or static variables should be avoided, as they
conflict with the modular nature of LAMMPS and the C++ class structure.
Header files must **not** import namespaces with *using*\ .
@ -164,7 +164,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
mathematical expression or figures (see doc/JPG for examples).
Additional PDF files with further details (see doc/PDF for examples)
may also be included. The doc page should also include literature
citations as appropriate; see the bottom of doc/fix\_nh.rst for
citations as appropriate; see the bottom of doc/fix_nh.rst for
examples and the earlier part of the same file for how to format the
cite itself. Citation labels must be unique across all .rst files.
The "Restrictions" section of the doc page should indicate if your
@ -191,7 +191,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
* If there is a paper of yours describing your feature (either the
algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the \*.cpp
source file. See src/USER-EFF/atom\_vec\_electron.cpp for an example.
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and a
single line of code that references the variable is added to the
constructor of the class. Whenever a user invokes your feature from
@ -203,7 +203,6 @@ packages in the src directory for examples. If you are uncertain, please ask.
usage. That kind of citation should just be in the doc page you
provide.
Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the
easier you make it for people to get started, e.g. by providing example

8
doc/src/Modify_dump.rst
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@ -4,21 +4,21 @@ Dump styles
Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
class can be added, but it is typically simpler to modify the
DumpCustom class contained in the dump\_custom.cpp file.
DumpCustom class contained in the dump_custom.cpp file.
Dump\_atom.cpp is a simple example of a derived dump class.
Dump_atom.cpp is a simple example of a derived dump class.
Here is a brief description of methods you define in your new derived
class. See dump.h for details.
+---------------+---------------------------------------------------+
| write\_header | write the header section of a snapshot of atoms |
| write_header | write the header section of a snapshot of atoms |
+---------------+---------------------------------------------------+
| count | count the number of lines a processor will output |
+---------------+---------------------------------------------------+
| pack | pack a proc's output data into a buffer |
+---------------+---------------------------------------------------+
| write\_data | write a proc's data to a file |
| write_data | write a proc's data to a file |
+---------------+---------------------------------------------------+
See the :doc:`dump <dump>` command and its *custom* style for a list of

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