forked from lijiext/lammps
265 lines
11 KiB
Groff
265 lines
11 KiB
Groff
.TH LAMMPS "19 September 2019" "2019-09-19"
|
|
.SH NAME
|
|
.B LAMMPS
|
|
\- Molecular Dynamics Simulator.
|
|
|
|
.SH SYNOPSIS
|
|
.B lmp
|
|
\-in <input file> [OPTIONS] ...
|
|
|
|
or
|
|
|
|
mpirun \-np 2
|
|
.B lmp
|
|
<input file> [OPTIONS] ...
|
|
|
|
or
|
|
|
|
.B lmp
|
|
\-r2data file.restart file.data
|
|
|
|
.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://lammps.sandia.gov/ 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 manpage 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://lammps.sandia.gov/doc/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\-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 USER-INTEL and USER-OMP 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.
|
|
|
|
See https://lammps.sandia.gov/doc/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--2019 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'.
|