Provided by: lammps_20220106.git7586adbb6a+ds1-2_amd64 
NAME
LAMMPS - Molecular Dynamics Simulator.
SYNOPSIS
lmp -in <input file> [OPTIONS] ...
or
mpirun -np 2 lmp -in <input file> [OPTIONS] ...
or
lmp -r2data file.restart file.data
or
lmp -h
DESCRIPTION
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials
(bio-molecules, polymers) and solid-state materials (metals, semiconductors) and coarse-
grained or mesoscopic systems. It can be used to model atoms or, more generically, as a
parallel particle simulator at the atomic, meso, or continuum scale.
See https://www.lammps.org/ for more information and documentation.
EXECUTABLE NAME
The LAMMPS executable can have different names depending on how it was configured,
compiled and installed. It will be either lmp or lmp_<machine name>. The <machine name>
suffix corresponds to the (machine specific) makefile used to compile LAMMPS when using
the conventional build process. When building LAMMPS using CMake this <machine name>
parameter can be chosen arbitrarily at configuration time, but more common is to just use
lmp without a suffix. In this man page we will use lmp to represent any of those names.
OPTIONS
-h or -help
Print a brief help summary and a list of settings and options compiled into this
executable. It also explicitly lists all LAMMPS styles (atom_style, fix, compute,
pair_style, bond_style, etc) available in the specific executable. This can tell
you if the command you want to use was included via the appropriate package at
compile time. LAMMPS will print the info and immediately exit if this switch is
used.
-e or -echo
Set the style of command echoing. The style can be none or screen or log or both.
Depending on the style, each command read from the input script will be echoed to
the screen and/or logfile. This can be useful to figure out which line of your
script is causing an input error. The default value is log.
-i <input file> or -in <input file>
Specify a file to use as an input script. If it is not specified, LAMMPS reads its
script from standard input. This is a required switch when running LAMMPS in multi-
partition mode.
-k on/off [keyword value] or -kokkos on/off [keyword value]
Enable or disable general KOKKOS support, as provided by the KOKKOS package. Even
if LAMMPS is built with this package, this switch must be set to on to enable
running with KOKKOS-enabled styles. More details on this switch and its optional
keyword value pairs are discussed at: https://docs.lammps.org/Run_options.html
-l <log file> or -log <log file>
Specify a log file for LAMMPS to write status information to. The default value is
"log.lammps". If the file name "none" is used, LAMMPS will not write a log file. In
multi-partition mode only some high-level all-partition information is written to
the "<log file>" file, the remainder is written in a per-partition file "<log
file>.N" with "N" being the respective partition number, unless overridden by the
-plog flag (see below).
-m <number> or -mpicolor <number>
If used, this must be the first command-line argument after the LAMMPS executable
name. It is only used when LAMMPS is launched by an mpirun command which also
launches one or more other executable(s) at the same time. LAMMPS and the other
executable(s) perform an MPI_Comm_split(), each with their own different colors, to
split the MPI_COMM_WORLD communicator for each executable to the subset of
processors they are supposed to be actually running on. Currently, this is only
used in LAMMPS to perform client/server messaging with another application. LAMMPS
can act as either a client or server (or both).
-mdi '<mdi_flags>'
This flag is only recognized and used when LAMMPS has support for the MolSSI Driver
Interface (MDI) included as part of the MDI package. This flag is specific to the
MDI library and controls how LAMMPS interacts with MDI. There are usually multiple
flags that have to follow it and those have to be placed in quotation marks. For
more information about how to launch LAMMPS in MDI client/server mode please refer
to the MDI How-to at https://docs.lammps.org/Howto_mdi.html
-c or -cite <style or filename>
Select how and where to output a reminder about citing contributions to the LAMMPS
code that were used during the run. Available keywords for styles are "both",
"none", "screen", or "log". Any other keyword will be considered a file name to
write the detailed citation info to instead of logfile or screen. Default is the
"log" style where there is a short summary in the screen output and detailed
citations in BibTeX format in the logfile. The option "both" selects the detailed
output for both, "none", the short output for both, and "screen" will write the
detailed info to the screen and the short version to the log file. If a dedicated
citation info file is requested, the screen and log file output will be in the
short format (same as with "none").
See https://docs.lammps.org/Intro_citing.html for more details on how to correctly
reference and cite LAMMPS
-nc or -nocite
Disable writing the "log.cite" file which is normally written to list references
for specific cite-able features used during a LAMMPS run.
-pk <style> [options] or -package <style> [options]
Invoke the packagecommand with <style> and optional arguments. The syntax is the
same as if the command appeared in an input script. For example "-pk gpu 2" is the
same as "package gpu 2" in the input script. The possible styles and options are
discussed in the LAMMPS manual for the "package" command. This switch can be used
multiple times, e.g. to set options for the INTEL and OPENMP packages when used
together. Along with the "-sf" or "-suffix" switch, this is a convenient mechanism
for invoking accelerator packages and their options without having to edit an input
script.
-p or -partition
Invoke LAMMPS in multi-partition mode. Without this, LAMMPS uses all P processors
allocated via MPI to run a single simulation. If this switch is used, the P
processors are split into separate partitions and each partition runs its own
simulation. The arguments to the switch specify the number of processors in each
partition. Arguments of the form "MxN" mean M partitions, each with N processors.
Arguments of the form "N" mean a single partition with N processors. The sum of
processors in all partitions must be equal P. Thus the command “-partition 8x2 4 5”
has 10 partitions and runs on a total of 25 processors. Running with multiple
partitions is required for multi-replica simulations, where each replica runs on on
one or more few processors.
-pl <basename> or -plog <basename>
Specify the base name for the per-partition log files in multi-partition runs,
where partition N writes log information to <basename>.N. If basename is set to
"none", then no per-partition log files are created. This overrides the name
specified in the -log command-line option.
-ps <basename> or -pscreen <basename>
Specify the base name for the per-partition screen files in multi-partition runs,
where partition N writes screen output to <basename>.N. If basename is set to
"none", then no per-partition screen files are created. The default value is
"screen" or whatever is set by the -screen flag.
-r2data <restart file> [remap] <data file> or
-restart2data <restart file> [remap] <data file> Convert <restart file> previously
written by LAMMPS into a data file and immediately exit. This option has replaced
the external restart2data executable. Following <restart file> argument, the
optional word "remap" may be used. This has the same effect like adding it to a
"read_restart" command. The syntax following the <data file> name is identical to
the arguments of the "write_data" command. See the LAMMPS manual for details on
either of the two commands.
-r2dump <restart file> [remap] <dump file> or
-restart2dump <restart file> [remap] <dump file> Convert <restart file> previously
written by LAMMPS into a dump file and immediately exit. Following <restart file>
argument, the optional word "remap" may be used. This has the same effect like
adding it to a "read_restart" command. The syntax following the <dump file> name
is identical to the arguments of the "dump" command. See the LAMMPS manual for
details on either of the two commands.
-sc <file name> or -screen <file name>
Specify a file for LAMMPS to write its screen information to. By default, this will
be the standard output. If <file name> is "none", (most) screen output will be
suppressed. In multi-partition mode only some high-level all-partition information
is written to the screen or "<file name>" file, the remainder is written in a per-
partition file "screen.N" or "<file name>.N" with "N" being the respective
partition number, and unless overridden by the -pscreen flag (see above).
-sf <suffix> or -suffix <suffix>
Use variants of various styles in the input, if they exist. This is achieved by
transparently trying to convert a style named <my/style> into <my/style/suffix> if
that latter style exists, but otherwise fall back to the former. The most useful
suffixes are "gpu", "intel", "kk", "omp", "opt", or "hybrid". These refer to
styles from optional packages that LAMMPS can be built with. The hybrid suffix is
special, as it enables, having two suffixes tried (e.g. first "intel" and then
"omp") and thus requires two arguments. Along with the "-package" command-line
switch, this is a convenient mechanism for invoking styles from accelerator
packages and setting their options without having to edit an input script.
-sr or -skiprun
Insert the command "timer timeout 0 every 1" at the beginning of an input file or
after a "clear" command. This has the effect that the entire LAMMPS input script
is processed without executing actual "run" or "minimize" or similar commands
(their main loops are skipped). This can be helpful and convenient to test input
scripts of long running calculations for correctness to avoid having them crash
after a long time due to a typo or syntax error in the middle or at the end.
See https://docs.lammps.org/Run_options.html for additional details and discussions
on command-line options.
LAMMPS BASICS
LAMMPS executes by reading commands from a input script (text file), one line at a time.
When the input script ends, LAMMPS exits. Each command causes LAMMPS to take some action.
It may set or change an internal, read and parse a file, or run a simulation. Most
commands have default settings, which means you only need to use the command if you wish
to change the default.
The ordering of commands in an input script is usually not very important unless a command
like "run" is encountered, which starts some calculation using the current internal state.
Also, if a "pair_style" or "bond_style" other similar style command is issued that has a
different name from what was previously active, it will replace the previous style and
wipe out all corresponding "pair_coeff" or "bond_coeff" or equivalent settings. Some
commands are only valid when they follow other commands. For example you cannot set the
temperature of a group of atoms until atoms have been defined and a group command is used
to define which atoms belong to the group of a given name. Sometimes command B will use
values that can be set by command A. This means command A must precede command B in the
input to have the desired effect. Some commands must be issued before the simulation box
is defined and others can only be issued after. Many input script errors are detected by
LAMMPS and an ERROR or WARNING message is printed. The documentation for each command
lists restrictions on how the command can be used, and the chapter on errors in the LAMMPS
manual gives some additional information about error messages, if possible.
COPYRIGHT
© 2003--2021 Sandia Corporation
This package is free software; you can redistribute it and/or modify it under the terms of
the GNU General Public License version 2 as published by the Free Software Foundation.
This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
On Debian systems, the complete text of the GNU General Public License can be found in
`/usr/share/common-licenses/GPL-2'.