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update man page with missing flags and correct URLs

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This commit is contained in:
Axel Kohlmeyer
2021-09-05 12:07:18 -04:00
parent 0c2d8ad210
commit b34a3cec1e
3 changed files with 59 additions and 14 deletions
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51
doc/lammps.1
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@ -54,7 +54,7 @@ using
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
without a suffix. In this man page we will use
.B lmp
to represent any of those names.
@ -94,7 +94,7 @@ 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
at: https://docs.lammps.org/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.
@ -122,6 +122,38 @@ to perform client/server messaging with another application.
.B LAMMPS
can act as either a client or server (or both).
.TP
\fB\-mdi '<mdi_flags>'\fR
This flag is only recognized and used when
.B 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
.B 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
.TP
\fB\-c\fR or \fB\-cite <style or filename>\fR
Select how and where to output a reminder about citing contributions
to the
.B 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
.B LAMMPS
.
.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
@ -218,8 +250,19 @@ 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.
.TP
\fB\-sr\fR or \fB\-skiprun\fR
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
.B 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://lammps.sandia.gov/doc/Run_options.html for additional
See https://docs.lammps.org/Run_options.html for additional
details and discussions on command-line options.
.SH LAMMPS BASICS
@ -254,7 +297,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2020 Sandia Corporation
© 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

2
doc/msi2lmp.1
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@ -98,7 +98,7 @@ msi2lmp decane -c 0 -f oplsaa
.SH COPYRIGHT
© 2003--2019 Sandia Corporation
© 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

20
doc/src/Run_options.rst
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@ -242,10 +242,11 @@ links with from the lib/message directory. See the
**-cite style** or **file name**
Select how and where to output a reminder about citing contributions
to the LAMMPS code that were used during the run. Available styles are
"both", "none", "screen", or "log". Any flag will be considered a file
name to write the detailed citation info to. Default is the "log" style
where there is a short summary in the screen output and detailed citations
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
@ -537,13 +538,14 @@ partition screen files file.N.
**-skiprun**
Insert the command :doc:`timer timerout 0 every 1 <timer>` at the
Insert the command :doc:`timer timeout 0 every 1 <timer>` at the
beginning of an input file or after a :doc:`clear <clear>` command.
This has the effect that the entire LAMMPS input script is processed
without executing actual runs or minimizations (their main loops are
skipped). This can be helpful and convenient to test input scripts for
long running calculations to avoid having them crash after a long time
due to a typo or syntax error.
without executing actual :doc:`run <run>` or :doc:`minimize <minimize>`
and 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.
----------