Merge branch 'master' into report-uninstalled-pkg-style
# Conflicts: # cmake/CMakeLists.txt
This commit is contained in:
Axel Kohlmeyer
259
doc/lammps.1
259
doc/lammps.1
@ -1,40 +1,259 @@
|
||||
.TH LAMMPS "2018-08-22"
|
||||
.TH LAMMPS "11 April 2019" "2019-04-11"
|
||||
.SH NAME
|
||||
.B LAMMPS
|
||||
\- Molecular Dynamics Simulator.
|
||||
|
||||
.SH SYNOPSIS
|
||||
.B lmp
|
||||
-in in.file
|
||||
.B lmp
|
||||
\-in <input file> [OPTIONS] ...
|
||||
|
||||
or
|
||||
|
||||
mpirun \-np 2
|
||||
.B lmp
|
||||
-in in.file
|
||||
mpirun \-np 2
|
||||
.B lmp
|
||||
<input file> [OPTIONS] ...
|
||||
|
||||
or
|
||||
|
||||
.B lmp
|
||||
\-r2data file.restart file.data
|
||||
|
||||
.SH DESCRIPTION
|
||||
.B LAMMPS
|
||||
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
|
||||
Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft
|
||||
materials (biomolecules, 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
|
||||
.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 http://lammps.sandia.gov/ for documentation.
|
||||
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
|
||||
See https://lammps.sandia.gov/doc/Run_options.html for details on
|
||||
command-line options.
|
||||
|
||||
.SH COPYRIGHT
|
||||
© 2003--2018 Sandia Corporation
|
||||
.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 as published by
|
||||
the Free Software Foundation; either version 2 of the License, or
|
||||
(at your option) any later version.
|
||||
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
|
||||
|
||||
111
doc/msi2lmp.1
Normal file
111
doc/msi2lmp.1
Normal file
@ -0,0 +1,111 @@
|
||||
.TH MSI2LMP "v3.9.9" "2018-11-05"
|
||||
.SH NAME
|
||||
.B MSI2LMP
|
||||
\- Converter for Materials Studio files to LAMMPS
|
||||
|
||||
.SH SYNOPSIS
|
||||
.B msi2lmp
|
||||
<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
|
||||
|
||||
.SH DESCRIPTION
|
||||
.PP
|
||||
.B MSI2LMP
|
||||
is a tool bundled with LAMMPS to aide in the conversion of simulation
|
||||
inputs from Biovia's Materials Studio software for use with LAMMPS.
|
||||
It is a standalone program that generates a LAMMPS data file based on
|
||||
the information in an MS .car file (atom coordinates), an .mdf file
|
||||
(molecular topology and atom types) and an .frc (forcefield parameters)
|
||||
file. The .car and .mdf files are specific to a molecular system while
|
||||
the .frc file is specific to a forcefield (variant). The only coherency
|
||||
needed between .frc and .car/.mdf files are the atom types.
|
||||
.PP
|
||||
|
||||
.SH OPTIONS
|
||||
.TP
|
||||
\fB\<ROOTNAME>\fR
|
||||
This has to be the first argument and is a
|
||||
.B mandatory
|
||||
argument. It defines the root of the file names; i.e. for a
|
||||
.B <ROOTNAME>
|
||||
of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
|
||||
in the current working directory.
|
||||
.B msi2lmp
|
||||
will then read and process those files according to its remaining settings.
|
||||
All other settins are optional and have defaults as listed.
|
||||
.TP
|
||||
\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
|
||||
The \-c or \-class option selects the force field class, i.e which pair
|
||||
styles and bond styles and so on are required in the LAMMPS input file.
|
||||
Class I or class 1 uses similar combination of functional forms as Amber
|
||||
and Charmm force field and support the force fields
|
||||
.B cvff
|
||||
and
|
||||
.B clayff.
|
||||
Class II or class 2 corresponds to the more complex force fields
|
||||
.B COMPASS
|
||||
and
|
||||
.B pcff.
|
||||
Class O or class 0 finally is an experimental and incomplete extension
|
||||
and supports generating output for
|
||||
.B OPLS-AA
|
||||
.TP
|
||||
\fB\-f <ffname>\fR, \fB\-frc <ffname>\fR
|
||||
The \-c or \-frc option allows the selection of the force field parameter
|
||||
file
|
||||
.B<ffname>.frc.
|
||||
Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug,
|
||||
pcff, compass_published, cff91, and oplsaa. If the argument is a pathname,
|
||||
i.e. it starts with a '.' or a '/', then this absolute path is used to read
|
||||
the force field, otherwise
|
||||
.B msi2lmp
|
||||
will look in the folder pointed to by the environment variable
|
||||
$MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current
|
||||
directory. The extension '.frc' is appended, if missing.
|
||||
Default is to look for the cvff.frc force field file.
|
||||
.TP
|
||||
\fB\-p <loglevel>\fR, \fB\-print <loglevel>\fR,
|
||||
Selects the amount of information messages about the progress of the
|
||||
conversion printed to the screen.
|
||||
.B <loglevel>
|
||||
can be a number from 0 (silent except for errors) to 3 (very detailed).
|
||||
.TP
|
||||
\fB\-i\fR, \fB\-ignore\fR,
|
||||
Ignore errors about missing parameters and use 0.0 for the respective
|
||||
force constants making these no-ops. Is correct to be used for a few
|
||||
molecules and settings, but often an indication, that either the atom
|
||||
type assignment have errors, or the force field file is missing entries.
|
||||
.TP
|
||||
\fB\-n\fR, \fB\-nocenter\fR,
|
||||
Do not center the box around the (geometrical) center of the atoms,
|
||||
but around the origin. Default is to recenter.
|
||||
.TP
|
||||
\fB\-o\fR, \fB\-oldstyle\fR,
|
||||
Write out a data file without style hint comments to be compatible
|
||||
with old LAMMPS versions. Default is to write out those comments.
|
||||
.TP
|
||||
\fB-s <x> <y> <z>\fR, \fB-shift <x> <y> <z>\fR,
|
||||
Shift the entire system (box and coordinates) by a vector
|
||||
(default: 0.0 0.0 0.0).
|
||||
.TP
|
||||
|
||||
.SH EXAMPLES
|
||||
|
||||
msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
|
||||
|
||||
msi2lmp benzene-class1 -c I
|
||||
|
||||
msi2lmp decane -c 0 -f oplsaa
|
||||
|
||||
|
||||
.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.
|
||||
|
||||
@ -159,6 +159,8 @@ cmake -C ../cmake/presets/most.cmake \[OPTIONS\] ../cmake |
|
||||
enable most common packages |
|
||||
cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake |
|
||||
disable packages that do require extra libraries or tools |
|
||||
cmake -C ../cmake/presets/clang.cmake \[OPTIONS\] ../cmake |
|
||||
change settings to use the Clang compilers by default |
|
||||
cmake -C ../cmake/presets/mingw.cmake \[OPTIONS\] ../cmake |
|
||||
enable all packages compatible with MinGW compilers :tb(c=2,s=|,a=l)
|
||||
|
||||
|
||||
@ -79,7 +79,7 @@ stdin.
|
||||
Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
|
||||
package. Even if LAMMPS is built with this package, as described
|
||||
in "Speed kokkos"_Speed_kokkos.html, this switch must be set to enable
|
||||
running with the KOKKOS-enabled styles the package provides. If the
|
||||
running with KOKKOS-enabled styles the package provides. If the
|
||||
switch is not set (the default), LAMMPS will operate as if the KOKKOS
|
||||
package were not installed; i.e. you can run standard LAMMPS or with
|
||||
the GPU or USER-OMP packages, for testing or benchmarking purposes.
|
||||
@ -448,7 +448,7 @@ partition screen files file.N.
|
||||
[-suffix style args] :link(suffix)
|
||||
|
||||
Use variants of various styles if they exist. The specified style can
|
||||
be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These
|
||||
be {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These
|
||||
refer to optional packages that LAMMPS can be built with, as described
|
||||
in "Accelerate performance"_Speed.html. The "gpu" style corresponds to the
|
||||
GPU package, the "intel" style to the USER-INTEL package, the "kk"
|
||||
|
||||
@ -357,6 +357,13 @@ The {meam/c} style is provided in the USER-MEAMC package. It is
|
||||
only enabled if LAMMPS was built with that package.
|
||||
See the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
The maximum number of elements, that can be read from the MEAM
|
||||
library file, is determined at compile time. The default is 5.
|
||||
If you need support for more elements, you have to change the
|
||||
define for the constant 'maxelt' at the beginning of the file
|
||||
src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no
|
||||
limit on the number of atoms types.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html,
|
||||
|
||||
@ -349,6 +349,7 @@ Cii
|
||||
Cij
|
||||
cis
|
||||
civ
|
||||
Clang
|
||||
clearstore
|
||||
Cleary
|
||||
Clebsch
|
||||
@ -1543,6 +1544,7 @@ Mattox
|
||||
Mattson
|
||||
maxangle
|
||||
maxbond
|
||||
maxelt
|
||||
maxeval
|
||||
maxfiles
|
||||
Maxfoo
|
||||
|
||||
Reference in New Issue
Block a user