forked from lijiext/lammps
270 lines
11 KiB
Groff
270 lines
11 KiB
Groff
.TH LAMMPS "15 April 2020" "2020-04-15"
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.SH NAME
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.B LAMMPS
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\- Molecular Dynamics Simulator.
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.SH SYNOPSIS
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.B lmp
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\-in <input file> [OPTIONS] ...
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or
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mpirun \-np 2
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.B lmp
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\-in <input file> [OPTIONS] ...
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or
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.B lmp
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\-r2data file.restart file.data
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or
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.B lmp
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\-h
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.SH DESCRIPTION
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.B LAMMPS
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is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
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\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator.
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.B LAMMPS
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has potentials for soft
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materials (bio-molecules, polymers) and solid-state materials (metals,
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semiconductors) and coarse-grained or mesoscopic systems. It can be used to
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model atoms or, more generically, as a parallel particle simulator at the
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atomic, meso, or continuum scale.
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See https://lammps.sandia.gov/ for more information and documentation.
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.SH EXECUTABLE NAME
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The
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.B LAMMPS
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executable can have different names depending on how it was configured,
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compiled and installed. It will be either
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.B lmp
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or
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.B lmp_<machine name>.
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The <machine name> suffix corresponds to the (machine specific) makefile
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used to compile
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.B LAMMPS
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when using the conventional build process. When building
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.B LAMMPS
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using
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.B CMake
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this <machine name> parameter can be chosen arbitrarily at configuration
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time, but more common is to just use
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.B lmp
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without a suffix. In this manpage we will use
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.B lmp
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to represent any of those names.
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.SH OPTIONS
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.TP
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\fB\-h\fR or \fB\-help\fR
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Print a brief help summary and a list of settings and options compiled
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into this executable. It also explicitly lists all LAMMPS styles
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(atom_style, fix, compute, pair_style, bond_style, etc) available in
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the specific executable. This can tell you if the command you want to
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use was included via the appropriate package at compile time.
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LAMMPS will print the info and immediately exit if this switch is used.
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.TP
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\fB\-e\fR or \fB\-echo\fR
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Set the style of command echoing. The style can be
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.B none
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or
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.B screen
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or
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.B log
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or
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.B both.
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Depending on the style, each command read from the input script will
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be echoed to the screen and/or logfile. This can be useful to figure
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out which line of your script is causing an input error.
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The default value is
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.B log.
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.TP
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\fB\-i <input file>\fR or \fB\-in <input file>\fR
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Specify a file to use as an input script. If it is not specified,
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LAMMPS reads its script from standard input. This is a required
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switch when running LAMMPS in multi-partition mode.
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.TP
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\fB\-k on/off [keyword value]\fR or \fB\-kokkos on/off [keyword value]\fR
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Enable or disable general KOKKOS support, as provided by the KOKKOS
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package. Even if LAMMPS is built with this package, this switch must
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be set to \fBon\fR to enable running with KOKKOS-enabled styles. More
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details on this switch and its optional keyword value pairs are discussed
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at: https://lammps.sandia.gov/doc/Run_options.html
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.TP
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\fB\-l <log file>\fR or \fB\-log <log file>\fR
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Specify a log file for LAMMPS to write status information to.
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The default value is "log.lammps". If the file name "none" is used,
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\fBLAMMPS\fR will not write a log file. In multi-partition mode only
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some high-level all-partition information is written to the "<log file>"
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file, the remainder is written in a per-partition file "<log file>.N"
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with "N" being the respective partition number, unless overridden
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by the \-plog flag (see below).
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.TP
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\fB\-m <number>\fR or \fB\-mpicolor <number>\fR
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If used, this must be the first command-line argument after the
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.B LAMMPS
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executable name. It is only used when
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.B LAMMPS
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is launched by an mpirun command which also launches one or more
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other executable(s) at the same time.
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.B LAMMPS
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and the other executable(s) perform an MPI_Comm_split(), each with
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their own different colors, to split the MPI_COMM_WORLD communicator
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for each executable to the subset of processors they are supposed to
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be actually running on. Currently, this is only used in
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.B LAMMPS
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to perform client/server messaging with another application.
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.B LAMMPS
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can act as either a client or server (or both).
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.TP
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\fB\-nc\fR or \fB\-nocite\fR
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Disable writing the "log.cite" file which is normally written to
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list references for specific cite-able features used during a
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.B LAMMPS
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run.
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.TP
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\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
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Invoke the \fBpackage\R command with <style> and optional arguments.
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The syntax is the same as if the command appeared in an input script.
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For example "-pk gpu 2" is the same as "package gpu 2" in the input
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script. The possible styles and options are discussed in the
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.B LAMMPS
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manual for the "package" command. This switch can be used multiple
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times, e.g. to set options for the USER-INTEL and USER-OMP packages
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when used together. Along with the "-sf" or "-suffix" switch, this
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is a convenient mechanism for invoking accelerator packages and their
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options without having to edit an input script.
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.TP
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\fB\-p\fR or \fB\-partition\fR
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Invoke
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.B LAMMPS
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in multi-partition mode. Without this,
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.B LAMMPS
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uses all P processors allocated via MPI to run a single simulation.
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If this switch is used, the P processors are split into separate
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partitions and each partition runs its own simulation. The arguments
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to the switch specify the number of processors in each partition.
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Arguments of the form "MxN" mean M partitions, each with N processors.
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Arguments of the form "N" mean a single partition with N processors.
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The sum of processors in all partitions must be equal P. Thus the
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command “-partition 8x2 4 5” has 10 partitions and runs on a total
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of 25 processors. Running with multiple partitions is required for
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multi-replica simulations, where each replica runs on on one or more
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few processors.
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.TP
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\fB\-pl <basename>\fR or \fB\-plog <basename>\fR
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Specify the base name for the per-partition log files in multi-partition
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runs, where partition N writes log information to <basename>.N.
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If basename is set to "none", then no per-partition log files are created.
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This overrides the name specified in the \-log command-line option.
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.TP
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\fB\-ps <basename>\fR or \fB\-pscreen <basename>\fR
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Specify the base name for the per-partition screen files in multi-partition
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runs, where partition N writes screen output to <basename>.N.
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If basename is set to "none", then no per-partition screen files are created.
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The default value is "screen" or whatever is set by the \-screen flag.
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.TP
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\fB\-r2data <restart file> [remap] <data file>\fR or
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\fB\-restart2data <restart file> [remap] <data file>\fR
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Convert <restart file> previously written by
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.B LAMMPS
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into a data file and immediately exit. This option has replaced the
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external restart2data executable. Following <restart file>
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argument, the optional word "remap" may be used. This has the
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same effect like adding it to a "read_restart" command.
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The syntax following the <data file> name is identical to the
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arguments of the "write_data" command. See the
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.B LAMMPS
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manual for details on either of the two commands.
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.TP
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\fB\-r2dump <restart file> [remap] <dump file>\fR or
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\fB\-restart2dump <restart file> [remap] <dump file>\fR
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Convert <restart file> previously written by
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.B LAMMPS
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into a dump file and immediately exit. Following <restart file>
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argument, the optional word "remap" may be used. This has the
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same effect like adding it to a "read_restart" command.
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The syntax following the <dump file> name is identical to the
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arguments of the "dump" command. See the
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.B LAMMPS
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manual for details on either of the two commands.
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.TP
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\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
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Specify a file for
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.B LAMMPS
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to write its screen information to. By default, this will be
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the standard output. If <file name> is "none", (most) screen
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output will be suppressed. In multi-partition mode only
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some high-level all-partition information is written to the
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screen or "<file name>" file, the remainder is written in a
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per-partition file "screen.N" or "<file name>.N"
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with "N" being the respective partition number, and unless
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overridden by the \-pscreen flag (see above).
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.TP
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\fB\-sf <suffix>\fR or \fB\-suffix <suffix>\fR
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Use variants of various styles in the input, if they exist. This is
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achieved by transparently trying to convert a style named <my/style>
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into <my/style/suffix> if that latter style exists, but otherwise
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fall back to the former. The most useful suffixes are "gpu",
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"intel", "kk", "omp", "opt", or "hybrid". These refer to styles from
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optional packages that LAMMPS can be built with. The hybrid suffix is
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special, as it enables, having two suffixes tried (e.g. first "intel"
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and then "omp") and thus requires two arguments. Along with the
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"-package" command-line switch, this is a convenient mechanism for
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invoking styles from accelerator packages and setting their options
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without having to edit an input script.
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See https://lammps.sandia.gov/doc/Run_options.html for additional
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details and discussions on command-line options.
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.SH LAMMPS BASICS
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LAMMPS executes by reading commands from a input script (text file),
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one line at a time. When the input script ends, LAMMPS exits. Each
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command causes LAMMPS to take some action. It may set or change an
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internal, read and parse a file, or run a simulation. Most commands
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have default settings, which means you only need to use the command
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if you wish to change the default.
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The ordering of commands in an input script is usually not very important
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unless a command like "run" is encountered, which starts some calculation
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using the current internal state. Also, if a "pair_style" or "bond_style"
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other similar style command is issued that has a different name from what
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was previously active, it will replace the previous style and wipe out
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all corresponding "pair_coeff" or "bond_coeff" or equivalent settings.
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Some commands are only valid when they follow other commands. For
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example you cannot set the temperature of a group of atoms until atoms
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have been defined and a group command is used to define which atoms
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belong to the group of a given name. Sometimes command B will use values
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that can be set by command A. This means command A must precede command
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B in the input to have the desired effect. Some commands must be issued
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.B before
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the simulation box is defined and others can only be issued
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.B after.
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Many input script errors are detected by
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.B LAMMPS
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and an ERROR or WARNING message is printed. The documentation for
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each command lists restrictions on how the command can be used, and
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the chapter on errors in the
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.B LAMMPS
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manual gives some additional information about error messages, if possible.
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.SH COPYRIGHT
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© 2003--2020 Sandia Corporation
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This package is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License version 2 as
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published by the Free Software Foundation.
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This package is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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On Debian systems, the complete text of the GNU General
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Public License can be found in `/usr/share/common-licenses/GPL-2'.
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