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LAMMPS(1) General Commands Manual LAMMPS(1) NAME LAMMPS - Molecular Dynamics Simulator. Version 19 November 2024 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 par- allel 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_<ma- chine 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> pa- rameter can be chosen arbitrarily at configuration time, but more com- mon 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 immedi- ately 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 speci- fied, LAMMPS reads its script from standard input. This is a re- quired 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_op- tions.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 num- ber, 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 exe- cutable(s) at the same time. LAMMPS and the other executable(s) perform an MPI_Comm_split(), each with their own different col- ors, to split the MPI_COMM_WORLD communicator for each exe- cutable to the subset of processors they are supposed to be ac- tually 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 con- trols how LAMMPS interacts with MDI. There are usually multiple flags that have to follow it and those have to be placed in quo- tation 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 contribu- tions to the LAMMPS code that were used during the run. Avail- able 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 package 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 dis- cussed 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 argu- ments 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 par- tition with N processors. The sum of processors in all parti- tions 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 simula- tions, 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-parti- tion 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-parti- tion 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 ei- ther 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 op- tional 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. -r2info <restart file> <keyword> ... or -restart2info <restart file> <keyword> ... Write information about the <restart file> previously written by LAMMPS to the screen and immediately exit. Following <restart file> argument, additional keywords for the LAMMPS "info" command may be added to increase the amount of information written. By default "sys- tem" "group" "fix" "compute" are already set. See the LAMMPS manual for details on the "info" command. -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-par- tition 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 over- ridden 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 re- fer 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 re- quires 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 execut- ing 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 syn- tax error in the middle or at the end. See https://docs.lammps.org/Run_options.html for additional de- tails 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 in- ternal, 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 impor- tant unless a command like "run" is encountered, which starts some cal- culation 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 com- mand 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 infor- mation about error messages, if possible. COPYRIGHT 2003--2024 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 pub- lished 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 MER- CHANTABILITY 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'. 2024-11-19 19 November 2024 LAMMPS(1)
NAME | SYNOPSIS | DESCRIPTION | EXECUTABLE NAME | OPTIONS | LAMMPS BASICS | COPYRIGHT
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