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Merge pull request #2962 from akohlmey/doc-updates

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A few final updates to the LAMMPS manual
This commit is contained in:
Axel Kohlmeyer
2021-09-27 20:39:06 -04:00
committed by GitHub
parent 9d5aa757c3 34fe792fad
commit c4616d4a11
3 changed files with 19 additions and 10 deletions
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3
doc/src/Intro_citing.rst
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@ -21,7 +21,8 @@ users and developers have contributed to LAMMPS is:
So a project using LAMMPS or a derivative application that uses LAMMPS
as a simulation engine should cite this paper. The paper is expected to
be published in its final form under the same DOI in the first half
of 2022.
of 2022. Please also give the URL of the LAMMPS website in your paper,
namely https://www.lammps.org.
The original publication describing the parallel algorithms used in the
initial versions of LAMMPS is:

16
doc/src/Run_basics.rst
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@ -2,17 +2,25 @@ Basics of running LAMMPS
========================
LAMMPS is run from the command line, reading commands from a file via
the -in command line flag, or from standard input.
Using the "-in in.file" variant is recommended:
the -in command line flag, or from standard input. Using the "-in
in.file" variant is recommended (see note below). The name of the
LAMMPS executable is either ``lmp`` or ``lmp_<machine>`` with
`<machine>` being the machine string used when compiling LAMMPS. This
is required when compiling LAMMPS with the traditional build system
(e.g. with ``make mpi``), but optional when using CMake to configure and
build LAMMPS:
.. code-block:: bash
$ lmp_serial -in in.file
$ lmp_serial < in.file
$ lmp -in in.file
$ lmp < in.file
$ /path/to/lammps/src/lmp_serial -i in.file
$ mpirun -np 4 lmp_mpi -in in.file
$ mpiexec -np 4 lmp -in in.file
$ mpirun -np 8 /path/to/lammps/src/lmp_mpi -in in.file
$ mpirun -np 6 /usr/local/bin/lmp -in in.file
$ mpiexec -n 6 /usr/local/bin/lmp -in in.file
You normally run the LAMMPS command in the directory where your input
script is located. That is also where output files are produced by
@ -23,7 +31,7 @@ executable itself can be placed elsewhere.
.. note::
The redirection operator "<" will not always work when running
in parallel with mpirun; for those systems the -in form is required.
in parallel with mpirun or mpiexec; for those systems the -in form is required.
As LAMMPS runs it prints info to the screen and a logfile named
*log.lammps*\ . More info about output is given on the