From 9dbd5bb27da9a97850a5e4055a944ed401e5aaa1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 27 Sep 2021 16:49:29 -0400 Subject: [PATCH 1/4] copy request to mention lammps.org form home page instructions for citing --- doc/src/Intro_citing.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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: From 9c4a82f2864e56a7c6cc0c1d33c8a8842a558adb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 27 Sep 2021 16:50:25 -0400 Subject: [PATCH 2/4] be more specific about what the name of the LAMMPS executable can be also provide a few more examples without a machine suffix --- doc/src/Run_basics.rst | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index 3d57633df2..bd8cbc6d2d 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -2,15 +2,22 @@ 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. 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 + $ mpirun -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 From 913ce25a01bc1bf35c50fff0148673e56344e639 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 27 Sep 2021 17:13:32 -0400 Subject: [PATCH 3/4] small tweak --- doc/src/Run_basics.rst | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index bd8cbc6d2d..5f1211d093 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -3,11 +3,12 @@ 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 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: +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 @@ -17,9 +18,9 @@ but optional when using CMake to configure and build LAMMPS: $ lmp < in.file $ /path/to/lammps/src/lmp_serial -i in.file $ mpirun -np 4 lmp_mpi -in in.file - $ mpirun -np 4 lmp -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 @@ -30,7 +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 From 34fe792fad73d370362cf68b8442fb52656c5db0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 27 Sep 2021 18:31:46 -0400 Subject: [PATCH 4/4] freeze versions of pip packages for processing the manual of the stable version this way we avoid surprises in case one of the packages get updated to an incompatible new version. these are know-to-work versions. --- doc/utils/requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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