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lammps.1
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lammps.1
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.TH LAMMPS "1" "2 June 2022" "2022-6-2"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 2 June 2022
.SH SYNOPSIS
.B lmp
\-in <input file> [OPTIONS] ...
or
mpirun \-np 2
.B lmp
\-in <input file> [OPTIONS] ...
or
.B lmp
\-r2data file.restart file.data
or
.B lmp
\-h
.SH DESCRIPTION
.B LAMMPS
is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator.
.B 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.
.SH EXECUTABLE NAME
The
.B LAMMPS
executable can have different names depending on how it was configured,
compiled and installed. It will be either
.B lmp
or
.B lmp_<machine name>.
The <machine name> suffix corresponds to the (machine specific) makefile
used to compile
.B LAMMPS
when using the conventional build process. When building
.B LAMMPS
using
.B CMake
this <machine name> parameter can be chosen arbitrarily at configuration
time, but more common is to just use
.B lmp
without a suffix. In this man page we will use
.B lmp
to represent any of those names.
.SH OPTIONS
.TP
\fB\-h\fR or \fB\-help\fR
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.
.TP
\fB\-e\fR or \fB\-echo\fR
Set the style of command echoing. The style can be
.B none
or
.B screen
or
.B log
or
.B 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
.B log.
.TP
\fB\-i <input file>\fR or \fB\-in <input file>\fR
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.
.TP
\fB\-k on/off [keyword value]\fR or \fB\-kokkos on/off [keyword value]\fR
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 \fBon\fR 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
.TP
\fB\-l <log file>\fR or \fB\-log <log file>\fR
Specify a log file for LAMMPS to write status information to.
The default value is "log.lammps". If the file name "none" is used,
\fBLAMMPS\fR 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).
.TP
\fB\-m <number>\fR or \fB\-mpicolor <number>\fR
If used, this must be the first command-line argument after the
.B LAMMPS
executable name. It is only used when
.B LAMMPS
is launched by an mpirun command which also launches one or more
other executable(s) at the same time.
.B 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
.B LAMMPS
to perform client/server messaging with another application.
.B LAMMPS
can act as either a client or server (or both).
.TP
\fB\-mdi '<mdi_flags>'\fR
This flag is only recognized and used when
.B 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
.B 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
.TP
\fB\-c\fR or \fB\-cite <style or filename>\fR
Select how and where to output a reminder about citing contributions
to the
.B 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
.B LAMMPS
.
.TP
\fB\-nc\fR or \fB\-nocite\fR
Disable writing the "log.cite" file which is normally written to
list references for specific cite-able features used during a
.B LAMMPS
run.
.TP
\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
Invoke the \fBpackage\R command 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
.B 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.
.TP
\fB\-p\fR or \fB\-partition\fR
Invoke
.B LAMMPS
in multi-partition mode. Without this,
.B 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.
.TP
\fB\-pl <basename>\fR or \fB\-plog <basename>\fR
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.
.TP
\fB\-ps <basename>\fR or \fB\-pscreen <basename>\fR
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.
.TP
\fB\-r2data <restart file> [remap] <data file>\fR or
\fB\-restart2data <restart file> [remap] <data file>\fR
Convert <restart file> previously written by
.B 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
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-r2dump <restart file> [remap] <dump file>\fR or
\fB\-restart2dump <restart file> [remap] <dump file>\fR
Convert <restart file> previously written by
.B 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
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
Specify a file for
.B 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).
.TP
\fB\-sf <suffix>\fR or \fB\-suffix <suffix>\fR
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.
.TP
\fB\-sr\fR or \fB\-skiprun\fR
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
.B 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.
.SH 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
.B before
the simulation box is defined and others can only be issued
.B after.
Many input script errors are detected by
.B 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
.B LAMMPS
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2022 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'.