Merge pull request #2962 from akohlmey/doc-updates

A few final updates to the LAMMPS manual

doc/src/Intro_citing.rst

@@ -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:

doc/src/Run_basics.rst

@@ -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

doc/utils/requirements.txt

@@ -1,7 +1,7 @@
 Sphinx==4.0.3
-sphinxcontrib-spelling
+sphinxcontrib-spelling==7.2.1
 git+git://github.com/akohlmey/sphinx-fortran@parallel-read
-sphinx_tabs
-breathe
-Pygments
-six
+sphinx_tabs==3.2.0
+breathe==4.31.0
+Pygments==2.10.0
+six==1.16.0