From c1dbc110d9c64e74722437cc96ce03286e8d4334 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Sep 2021 19:12:59 -0400 Subject: [PATCH] cosmetic changes for consistency --- doc/lammps.1 | 6 +++--- doc/msi2lmp.1 | 2 +- doc/src/Build_manual.rst | 4 ++-- doc/src/Errors_messages.rst | 2 +- doc/src/Examples.rst | 4 ++-- doc/src/Install_windows.rst | 2 +- doc/src/Packages_details.rst | 26 +++++++++++++------------- doc/src/Run_options.rst | 20 +++++++++++--------- doc/src/Speed.rst | 2 +- doc/src/Speed_gpu.rst | 2 +- doc/src/Speed_kokkos.rst | 2 +- doc/src/Speed_packages.rst | 2 +- doc/src/compute_angle.rst | 26 ++++++++++++++------------ doc/src/fix_wall_gran_region.rst | 2 +- src/memory.h | 2 +- 15 files changed, 54 insertions(+), 50 deletions(-) diff --git a/doc/lammps.1 b/doc/lammps.1 index 03dfd27734..40d4295b7e 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -54,7 +54,7 @@ using this 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. @@ -234,7 +234,7 @@ the standard output. If is "none", (most) screen output will be suppressed. In multi-partition mode only some high-level all-partition information is written to the screen or "" file, the remainder is written in a -per-partition file "screen.N" or ".N" +per-partition file "screen.N" or ".N" with "N" being the respective partition number, and unless overridden by the \-pscreen flag (see above). .TP @@ -297,7 +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 diff --git a/doc/msi2lmp.1 b/doc/msi2lmp.1 index e1a8c8a2f3..91916fb3a5 100644 --- a/doc/msi2lmp.1 +++ b/doc/msi2lmp.1 @@ -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 diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index 185734a1c7..d12c6dc498 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -74,8 +74,8 @@ folder. The following ``make`` commands are available: .. code-block:: bash make html # generate HTML in html dir using Sphinx - make pdf # generate PDF as Manual.pdf using Sphinx and pdflatex - make fetch # fetch HTML pages and PDF files from LAMMPS web site + make pdf # generate PDF as Manual.pdf using Sphinx and PDFLaTeX + make fetch # fetch HTML pages and PDF files from LAMMPS website # and unpack into the html_www folder and Manual_www.pdf make epub # generate LAMMPS.epub in ePUB format using Sphinx make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index a26857ebf5..02b9edd466 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -714,7 +714,7 @@ Doc page with :doc:`WARNING messages ` *Cannot create/grow a vector/array of pointers for %s* LAMMPS code is making an illegal call to the templated memory - allocaters, to create a vector or array of pointers. + allocators, to create a vector or array of pointers. *Cannot create_atoms after reading restart file with per-atom info* The per-atom info was stored to be used when by a fix that you may diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 649be52ab7..f91ca2db11 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the :doc:`dump image ` doc page. Animations of many of the examples can be viewed on the Movies section -of the `LAMMPS web site `_. +of the `LAMMPS website `_. There are two kinds of sub-directories in the examples folder. Lower case named directories contain one or a few simple, quick-to-run @@ -169,7 +169,7 @@ Running the simulation produces the files *dump.indent* and *log.lammps*\ . You can visualize the dump file of snapshots with a variety of third-party tools highlighted on the `Visualization `_ page of the LAMMPS -web site. +website. If you uncomment the :doc:`dump image ` line(s) in the input script a series of JPG images will be produced by the run (assuming diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index 1e5c9684ac..108c03c249 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -12,7 +12,7 @@ Note that each installer package has a date in its name, which corresponds to the LAMMPS version of the same date. Installers for current and older versions of LAMMPS are available. 32-bit and 64-bit installers are available, and each installer contains both a serial -and parallel executable. The installer web site also explains how to +and parallel executable. The installer website also explains how to install the Windows MPI package (MPICH2 from Argonne National Labs), needed to run in parallel with MPI. diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index b4e50fad75..5474d0fff9 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -915,7 +915,7 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * :doc:`package gpu ` * :doc:`Commands ` pages (:doc:`pair `, :doc:`kspace `) for styles followed by (g) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of website ---------- @@ -1027,7 +1027,7 @@ This package has :ref:`specific installation instructions ` on the :doc:` * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) * src/INTEL/TEST -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of website ---------- @@ -1164,7 +1164,7 @@ This package has :ref:`specific installation instructions ` on the :doc: * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (k) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of website ---------- @@ -1242,7 +1242,7 @@ A fix command which wraps the LATTE DFTB code, so that molecular dynamics can be run with LAMMPS using density-functional tight-binding quantum forces calculated by LATTE. -More information on LATTE can be found at this web site: +More information on LATTE can be found at this website: `https://github.com/lanl/LATTE `_. A brief technical description is given with the :doc:`fix latte ` command. @@ -2017,7 +2017,7 @@ the :doc:`Build extras ` page. * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (o) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of website ---------- @@ -2051,7 +2051,7 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * :doc:`OPT package ` * :doc:`Section 2.6 -sf opt ` * Search the :doc:`pair style ` page for styles followed by (t) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of website .. _PKG-ORIENT: @@ -2248,16 +2248,16 @@ PYTHON package A :doc:`python ` command which allow you to execute Python code from a LAMMPS input script. The code can be in a separate file or -embedded in the input script itself. See the :doc:`Python call ` page for an overview of using Python from -LAMMPS in this manner and all the :doc:`Python ` manual pages -for other ways to use LAMMPS and Python together. +embedded in the input script itself. See the :doc:`Python call +` page for an overview of using Python from LAMMPS in this +manner and all the :doc:`Python ` manual pages for other +ways to use LAMMPS and Python together. .. note:: - Building with the PYTHON package assumes you have a Python - shared library available on your system, which needs to be a Python 2 - version, 2.6 or later. Python 3 is not yet supported. See the - lib/python/README for more details. + Building with the PYTHON package assumes you have a Python development + environment (headers and libraries) available on your system, which needs + to be either Python version 2.7 or Python 3.5 and later. **Install:** diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index b07c9b2529..96015b1613 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -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 ` at the +Insert the command :doc:`timer timeout 0 every 1 ` at the beginning of an input file or after a :doc:`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 ` or :doc:`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. ---------- diff --git a/doc/src/Speed.rst b/doc/src/Speed.rst index ccabc0adb6..02eae1f3fa 100644 --- a/doc/src/Speed.rst +++ b/doc/src/Speed.rst @@ -13,7 +13,7 @@ for certain kinds of hardware, including multi-core CPUs, GPUs, and Intel Xeon Phi co-processors. The `Benchmark page `_ of the LAMMPS -web site gives performance results for the various accelerator +website gives performance results for the various accelerator packages discussed on the :doc:`Speed packages ` doc page, for several of the standard LAMMPS benchmark problems, as a function of problem size and number of compute nodes, on different diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index 656ce08bbc..9015bff9ef 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -153,7 +153,7 @@ usually resulting in inferior performance compared to using LAMMPS' native threading and vectorization support in the OPENMP and INTEL packages. See the `Benchmark page `_ of the -LAMMPS web site for performance of the GPU package on various +LAMMPS website for performance of the GPU package on various hardware, including the Titan HPC platform at ORNL. You should also experiment with how many MPI tasks per GPU to use to diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 400db9585c..14c2ec680e 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -407,7 +407,7 @@ Generally speaking, the following rules of thumb apply: by switching to single or mixed precision mode. See the `Benchmark page `_ of the -LAMMPS web site for performance of the KOKKOS package on different +LAMMPS website for performance of the KOKKOS package on different hardware. Advanced Kokkos options diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index be3f205f4b..74d470c9fd 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -144,7 +144,7 @@ sub-directories with Make.py commands and input scripts for using all the accelerator packages on various machines. See the README files in those directories. -As mentioned above, the `Benchmark page `_ of the LAMMPS web site gives +As mentioned above, the `Benchmark page `_ of the LAMMPS website gives performance results for the various accelerator packages for several of the standard LAMMPS benchmark problems, as a function of problem size and number of compute nodes, on different hardware platforms. diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index 93677b4953..b4a7d9a060 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -23,22 +23,23 @@ Examples Description """"""""""" -Define a computation that extracts the angle energy calculated by each -of the angle sub-styles used in the doc:`angle_style hybrid ` -command. These values are made accessible -for output or further processing by other commands. The group -specified for this command is ignored. +Define a computation that extracts the angle energy calculated by each of the +angle sub-styles used in the :doc:`angle_style hybrid ` command. +These values are made accessible for output or further processing by other +commands. The group specified for this command is ignored. -This compute is useful when using :doc:`angle_style hybrid ` if you want to know the portion of the total -energy contributed by one or more of the hybrid sub-styles. +This compute is useful when using :doc:`angle_style hybrid ` if +you want to know the portion of the total energy contributed by one or more of +the hybrid sub-styles. Output info """"""""""" -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the :doc:`angle_style hybrid ` command, which can be accessed by indices -1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output +This compute calculates a global vector of length N where N is the number of +sub_styles defined by the :doc:`angle_style hybrid ` command, +which can be accessed by indices 1-N. These values can be used by any command +that uses global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy @@ -46,7 +47,8 @@ The vector values are "extensive" and will be in energy Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 95634238aa..5a4c983554 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -66,7 +66,7 @@ non-granular particles and simpler wall geometries, respectively. Here are snapshots of example models using this command. Corresponding input scripts can be found in examples/granregion. Movies of these simulations are `here on the Movies page `_ -of the LAMMPS web site. +of the LAMMPS website. .. |wallgran1| image:: img/gran_funnel.png :width: 48% diff --git a/src/memory.h b/src/memory.h index b42f1e0866..f7ea3bc4a7 100644 --- a/src/memory.h +++ b/src/memory.h @@ -738,6 +738,6 @@ smaller simulation or on more processors. E: Cannot create/grow a vector/array of pointers for %s LAMMPS code is making an illegal call to the templated memory -allocaters, to create a vector or array of pointers. +allocators, to create a vector or array of pointers. */