1LAMMPS(1) General Commands Manual LAMMPS(1)
2
6 LAMMPS - Molecular Dynamics Simulator. Version 2 August 2023
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10 lmp -in <input file> [OPTIONS] ...
11 or
13 mpirun -np 2 lmp -in <input file> [OPTIONS] ...
15 or
17 lmp -r2data file.restart file.data
19 or
21 lmp -h
23
26 LAMMPS is a classical molecular dynamics code, and an acronym for
27 Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
28 potentials for soft materials (bio-molecules, polymers) and solid-state
29 materials (metals, semiconductors) and coarse-grained or mesoscopic
30 systems. It can be used to model atoms or, more generically, as a par‐
31 allel particle simulator at the atomic, meso, or continuum scale.
32 See https://www.lammps.org/ for more information and documentation.
34
37 The LAMMPS executable can have different names depending on how it was
38 configured, compiled and installed. It will be either lmp or lmp_<ma‐
39 chine name>. The <machine name> suffix corresponds to the (machine
40 specific) makefile used to compile LAMMPS when using the conventional
41 build process. When building LAMMPS using CMake this <machine name> pa‐
42 rameter can be chosen arbitrarily at configuration time, but more com‐
43 mon is to just use lmp without a suffix. In this man page we will use
44 lmp to represent any of those names.
45
48 -h or -help
49 Print a brief help summary and a list of settings and options
50 compiled into this executable. It also explicitly lists all
51 LAMMPS styles (atom_style, fix, compute, pair_style, bond_style,
52 etc) available in the specific executable. This can tell you if
53 the command you want to use was included via the appropriate
54 package at compile time. LAMMPS will print the info and immedi‐
55 ately exit if this switch is used.
56 -e or -echo
58 Set the style of command echoing. The style can be none or
59 screen or log or both. Depending on the style, each command
60 read from the input script will be echoed to the screen and/or
61 logfile. This can be useful to figure out which line of your
62 script is causing an input error. The default value is log.
63 -i <input file> or -in <input file>
65 Specify a file to use as an input script. If it is not speci‐
66 fied, LAMMPS reads its script from standard input. This is a re‐
67 quired switch when running LAMMPS in multi-partition mode.
68 -k on/off [keyword value] or -kokkos on/off [keyword value]
70 Enable or disable general KOKKOS support, as provided by the
71 KOKKOS package. Even if LAMMPS is built with this package, this
72 switch must be set to on to enable running with KOKKOS-enabled
73 styles. More details on this switch and its optional keyword
74 value pairs are discussed at: https://docs.lammps.org/Run_op‐
75 tions.html
76 -l <log file> or -log <log file>
78 Specify a log file for LAMMPS to write status information to.
79 The default value is "log.lammps". If the file name "none" is
80 used, LAMMPS will not write a log file. In multi-partition mode
81 only some high-level all-partition information is written to the
82 "<log file>" file, the remainder is written in a per-partition
83 file "<log file>.N" with "N" being the respective partition num‐
84 ber, unless overridden by the -plog flag (see below).
85 -m <number> or -mpicolor <number>
87 If used, this must be the first command-line argument after the
88 LAMMPS executable name. It is only used when LAMMPS is launched
89 by an mpirun command which also launches one or more other exe‐
90 cutable(s) at the same time. LAMMPS and the other executable(s)
91 perform an MPI_Comm_split(), each with their own different col‐
92 ors, to split the MPI_COMM_WORLD communicator for each exe‐
93 cutable to the subset of processors they are supposed to be ac‐
94 tually running on. Currently, this is only used in LAMMPS to
95 perform client/server messaging with another application.
96 LAMMPS can act as either a client or server (or both).
97 -mdi '<mdi_flags>'
99 This flag is only recognized and used when LAMMPS has support
100 for the MolSSI Driver Interface (MDI) included as part of the
101 MDI package. This flag is specific to the MDI library and con‐
102 trols how LAMMPS interacts with MDI. There are usually multiple
103 flags that have to follow it and those have to be placed in quo‐
104 tation marks. For more information about how to launch LAMMPS
105 in MDI client/server mode please refer to the MDI How-to at
106 https://docs.lammps.org/Howto_mdi.html
107 -c or -cite <style or filename>
109 Select how and where to output a reminder about citing contribu‐
110 tions to the LAMMPS code that were used during the run. Avail‐
111 able keywords for styles are "both", "none", "screen", or "log".
112 Any other keyword will be considered a file name to write the
113 detailed citation info to instead of logfile or screen. Default
114 is the "log" style where there is a short summary in the screen
115 output and detailed citations in BibTeX format in the logfile.
116 The option "both" selects the detailed output for both, "none",
117 the short output for both, and "screen" will write the detailed
118 info to the screen and the short version to the log file. If a
119 dedicated citation info file is requested, the screen and log
120 file output will be in the short format (same as with "none").
121 See https://docs.lammps.org/Intro_citing.html for more details
123 on how to correctly reference and cite LAMMPS
124 -nc or -nocite
126 Disable writing the "log.cite" file which is normally written to
127 list references for specific cite-able features used during a
128 LAMMPS run.
129 -pk <style> [options] or -package <style> [options]
131 Invoke the package command with <style> and optional arguments.
132 The syntax is the same as if the command appeared in an input
133 script. For example "-pk gpu 2" is the same as "package gpu 2"
134 in the input script. The possible styles and options are dis‐
135 cussed in the LAMMPS manual for the "package" command. This
136 switch can be used multiple times, e.g. to set options for the
137 INTEL and OPENMP packages when used together. Along with the
138 "-sf" or "-suffix" switch, this is a convenient mechanism for
139 invoking accelerator packages and their options without having
140 to edit an input script.
141 -p or -partition
143 Invoke LAMMPS in multi-partition mode. Without this, LAMMPS uses
144 all P processors allocated via MPI to run a single simulation.
145 If this switch is used, the P processors are split into separate
146 partitions and each partition runs its own simulation. The argu‐
147 ments to the switch specify the number of processors in each
148 partition. Arguments of the form "MxN" mean M partitions, each
149 with N processors. Arguments of the form "N" mean a single par‐
150 tition with N processors. The sum of processors in all parti‐
151 tions must be equal P. Thus the command “-partition 8x2 4 5” has
152 10 partitions and runs on a total of 25 processors. Running
153 with multiple partitions is required for multi-replica simula‐
154 tions, where each replica runs on on one or more few processors.
155 -pl <basename> or -plog <basename>
157 Specify the base name for the per-partition log files in multi-
158 partition runs, where partition N writes log information to
159 <basename>.N. If basename is set to "none", then no per-parti‐
160 tion log files are created. This overrides the name specified
161 in the -log command-line option.
162 -ps <basename> or -pscreen <basename>
164 Specify the base name for the per-partition screen files in
165 multi-partition runs, where partition N writes screen output to
166 <basename>.N. If basename is set to "none", then no per-parti‐
167 tion screen files are created. The default value is "screen" or
168 whatever is set by the -screen flag.
169 -r2data <restart file> [remap] <data file> or
171 -restart2data <restart file> [remap] <data file> Convert
172 <restart file> previously written by LAMMPS into a data file and
173 immediately exit. This option has replaced the external
174 restart2data executable. Following <restart file> argument, the
175 optional word "remap" may be used. This has the same effect like
176 adding it to a "read_restart" command. The syntax following the
177 <data file> name is identical to the arguments of the
178 "write_data" command. See the LAMMPS manual for details on ei‐
179 ther of the two commands.
180 -r2dump <restart file> [remap] <dump file> or
182 -restart2dump <restart file> [remap] <dump file> Convert
183 <restart file> previously written by LAMMPS into a dump file and
184 immediately exit. Following <restart file> argument, the op‐
185 tional word "remap" may be used. This has the same effect like
186 adding it to a "read_restart" command. The syntax following the
187 <dump file> name is identical to the arguments of the "dump"
188 command. See the LAMMPS manual for details on either of the two
189 commands.
190 -sc <file name> or -screen <file name>
192 Specify a file for LAMMPS to write its screen information to. By
193 default, this will be the standard output. If <file name> is
194 "none", (most) screen output will be suppressed. In multi-par‐
195 tition mode only some high-level all-partition information is
196 written to the screen or "<file name>" file, the remainder is
197 written in a per-partition file "screen.N" or "<file name>.N"
198 with "N" being the respective partition number, and unless over‐
199 ridden by the -pscreen flag (see above).
200 -sf <suffix> or -suffix <suffix>
202 Use variants of various styles in the input, if they exist. This
203 is achieved by transparently trying to convert a style named
204 <my/style> into <my/style/suffix> if that latter style exists,
205 but otherwise fall back to the former. The most useful suffixes
206 are "gpu", "intel", "kk", "omp", "opt", or "hybrid". These re‐
207 fer to styles from optional packages that LAMMPS can be built
208 with. The hybrid suffix is special, as it enables, having two
209 suffixes tried (e.g. first "intel" and then "omp") and thus re‐
210 quires two arguments. Along with the "-package" command-line
211 switch, this is a convenient mechanism for invoking styles from
212 accelerator packages and setting their options without having to
213 edit an input script.
214 -sr or -skiprun
216 Insert the command "timer timeout 0 every 1" at the beginning of
217 an input file or after a "clear" command. This has the effect
218 that the entire LAMMPS input script is processed without execut‐
219 ing actual "run" or "minimize" or similar commands (their main
220 loops are skipped). This can be helpful and convenient to test
221 input scripts of long running calculations for correctness to
222 avoid having them crash after a long time due to a typo or syn‐
223 tax error in the middle or at the end.
224 See https://docs.lammps.org/Run_options.html for additional de‐
226 tails and discussions on command-line options.
227
230 LAMMPS executes by reading commands from a input script (text file),
231 one line at a time. When the input script ends, LAMMPS exits. Each
232 command causes LAMMPS to take some action. It may set or change an in‐
233 ternal, read and parse a file, or run a simulation. Most commands have
234 default settings, which means you only need to use the command if you
235 wish to change the default.
236 The ordering of commands in an input script is usually not very impor‐
238 tant unless a command like "run" is encountered, which starts some cal‐
239 culation using the current internal state. Also, if a "pair_style" or
240 "bond_style" other similar style command is issued that has a different
241 name from what was previously active, it will replace the previous
242 style and wipe out all corresponding "pair_coeff" or "bond_coeff" or
243 equivalent settings. Some commands are only valid when they follow
244 other commands. For example you cannot set the temperature of a group
245 of atoms until atoms have been defined and a group command is used to
246 define which atoms belong to the group of a given name. Sometimes com‐
247 mand B will use values that can be set by command A. This means command
248 A must precede command B in the input to have the desired effect. Some
249 commands must be issued before the simulation box is defined and others
250 can only be issued after. Many input script errors are detected by
251 LAMMPS and an ERROR or WARNING message is printed. The documentation
252 for each command lists restrictions on how the command can be used, and
253 the chapter on errors in the LAMMPS manual gives some additional infor‐
254 mation about error messages, if possible.
255
258 © 2003--2022 Sandia Corporation
259 This package is free software; you can redistribute it and/or modify it
261 under the terms of the GNU General Public License version 2 as pub‐
262 lished by the Free Software Foundation.
263 This package is distributed in the hope that it will be useful, but
265 WITHOUT ANY WARRANTY; without even the implied warranty of MER‐
266 CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
267 Public License for more details.
268 On Debian systems, the complete text of the GNU General Public License
270 can be found in `/usr/share/common-licenses/GPL-2'.
2712023-08-2 2 August 2023 LAMMPS(1)