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cosmetic changes for consistency

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This commit is contained in:
Axel Kohlmeyer
2021-09-07 19:12:59 -04:00
parent 36eb2e30df
commit c1dbc110d9
15 changed files with 54 additions and 50 deletions
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6
doc/lammps.1
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@ -54,7 +54,7 @@ using
this <machine name> 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 <file name> 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 name>" file, the remainder is written in a
per-partition file "screen.N" or "<file name>.N"
per-partition file "screen.N" or "<file name>.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

2
doc/msi2lmp.1
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@ -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

4
doc/src/Build_manual.rst
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@ -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

2
doc/src/Errors_messages.rst
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@ -714,7 +714,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*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

4
doc/src/Examples.rst
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@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the
:doc:`dump image <dump_image>` doc page.
Animations of many of the examples can be viewed on the Movies section
of the `LAMMPS web site <https://www.lammps.org/movies.html>`_.
of the `LAMMPS website <https://www.lammps.org/movies.html>`_.
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 <https://www.lammps.org/viz.html>`_ page of the LAMMPS
web site.
website.
If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
script a series of JPG images will be produced by the run (assuming

2
doc/src/Install_windows.rst
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@ -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.

26
doc/src/Packages_details.rst
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@ -915,7 +915,7 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu
* :doc:`package gpu <package>`
* :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)
for styles followed by (g)
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
----------
@ -1027,7 +1027,7 @@ This package has :ref:`specific installation instructions <intel>` on the :doc:`
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)
* src/INTEL/TEST
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
----------
@ -1164,7 +1164,7 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (k)
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ 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 <latte-home_>`_. A brief technical
description is given with the :doc:`fix latte <fix_latte>` command.
@ -2017,7 +2017,7 @@ the :doc:`Build extras <Build_extras>` page.
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (o)
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
----------
@ -2051,7 +2051,7 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
* :doc:`OPT package <Speed_opt>`
* :doc:`Section 2.6 -sf opt <Run_options>`
* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
.. _PKG-ORIENT:
@ -2248,16 +2248,16 @@ PYTHON package
A :doc:`python <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 <Python_call>` page for an overview of using Python from
LAMMPS in this manner and all the :doc:`Python <Python_head>` manual pages
for other ways to use LAMMPS and Python together.
embedded in the input script itself. See the :doc:`Python call
<Python_call>` page for an overview of using Python from LAMMPS in this
manner and all the :doc:`Python <Python_head>` 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:**

20
doc/src/Run_options.rst
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@ -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 <timer>` at the
Insert the command :doc:`timer timeout 0 every 1 <timer>` at the
beginning of an input file or after a :doc:`clear <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 <run>` or :doc:`minimize <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.
----------

2
doc/src/Speed.rst
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@ -13,7 +13,7 @@ for certain kinds of hardware, including multi-core CPUs, GPUs, and
Intel Xeon Phi co-processors.
The `Benchmark page <https://www.lammps.org/bench.html>`_ 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 <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

2
doc/src/Speed_gpu.rst
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@ -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 <https://www.lammps.org/bench.html>`_ 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

2
doc/src/Speed_kokkos.rst
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@ -407,7 +407,7 @@ Generally speaking, the following rules of thumb apply:
by switching to single or mixed precision mode.
See the `Benchmark page <https://www.lammps.org/bench.html>`_ 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

2
doc/src/Speed_packages.rst
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@ -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 <https://www.lammps.org/bench.html>`_ of the LAMMPS web site gives
As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ 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.

26
doc/src/compute_angle.rst
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@ -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 <angle_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 <angle_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 <angle_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 <angle_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 <angle_style>` 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 <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 <angle_style>` 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 <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
""""""""""""""""

2
doc/src/fix_wall_gran_region.rst
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@ -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 <https://www.lammps.org/movies.html#granregion>`_
of the LAMMPS web site.
of the LAMMPS website.
.. |wallgran1| image:: img/gran_funnel.png
:width: 48%

2
src/memory.h
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@ -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.
*/