Provided by: lammps_20220106.git7586adbb6a+ds1-2build1_amd64 bug

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'.