diff --git a/doc/src/Intro_citing.rst b/doc/src/Intro_citing.rst index a0dec35b50..0e10b7559a 100644 --- a/doc/src/Intro_citing.rst +++ b/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: diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index 3d57633df2..5f1211d093 100644 --- a/doc/src/Run_basics.rst +++ b/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_`` with +`` 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 diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt index 7e4563a1ec..f367727d20 100644 --- a/doc/utils/requirements.txt +++ b/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