cosmetic changes for consistency

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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@ -297,7 +297,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible. manual gives some additional information about error messages, if possible.
.SH COPYRIGHT .SH COPYRIGHT
© 2003--2020 Sandia Corporation © 2003--2021 Sandia Corporation
This package is free software; you can redistribute it and/or modify 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 it under the terms of the GNU General Public License version 2 as

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@ -98,7 +98,7 @@ msi2lmp decane -c 0 -f oplsaa
.SH COPYRIGHT .SH COPYRIGHT
© 2003--2019 Sandia Corporation © 2003--2021 Sandia Corporation
This package is free software; you can redistribute it and/or modify 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 it under the terms of the GNU General Public License version 2 as

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@ -74,7 +74,7 @@ folder. The following ``make`` commands are available:
.. code-block:: bash .. code-block:: bash
make html # generate HTML in html dir using Sphinx make html # generate HTML in html dir using Sphinx
make pdf # generate PDF as Manual.pdf using Sphinx and pdflatex make pdf # generate PDF as Manual.pdf using Sphinx and PDFLaTeX
make fetch # fetch HTML pages and PDF files from LAMMPS website make fetch # fetch HTML pages and PDF files from LAMMPS website
# and unpack into the html_www folder and Manual_www.pdf # and unpack into the html_www folder and Manual_www.pdf
make epub # generate LAMMPS.epub in ePUB format using Sphinx make epub # generate LAMMPS.epub in ePUB format using Sphinx

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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* *Cannot create/grow a vector/array of pointers for %s*
LAMMPS code is making an illegal call to the templated memory 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* *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 The per-atom info was stored to be used when by a fix that you may

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@ -2248,16 +2248,16 @@ PYTHON package
A :doc:`python <python>` command which allow you to execute Python code 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 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 embedded in the input script itself. See the :doc:`Python call
LAMMPS in this manner and all the :doc:`Python <Python_head>` manual pages <Python_call>` page for an overview of using Python from LAMMPS in this
for other ways to use LAMMPS and Python together. manner and all the :doc:`Python <Python_head>` manual pages for other
ways to use LAMMPS and Python together.
.. note:: .. note::
Building with the PYTHON package assumes you have a Python Building with the PYTHON package assumes you have a Python development
shared library available on your system, which needs to be a Python 2 environment (headers and libraries) available on your system, which needs
version, 2.6 or later. Python 3 is not yet supported. See the to be either Python version 2.7 or Python 3.5 and later.
lib/python/README for more details.
**Install:** **Install:**

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@ -242,10 +242,11 @@ links with from the lib/message directory. See the
**-cite style** or **file name** **-cite style** or **file name**
Select how and where to output a reminder about citing contributions Select how and where to output a reminder about citing contributions
to the LAMMPS code that were used during the run. Available styles are to the LAMMPS code that were used during the run. Available keywords
"both", "none", "screen", or "log". Any flag will be considered a file for styles are "both", "none", "screen", or "log". Any other keyword
name to write the detailed citation info to. Default is the "log" style will be considered a file name to write the detailed citation info to
where there is a short summary in the screen output and detailed citations 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 in BibTeX format in the logfile. The option "both" selects the detailed
output for both, "none", the short output for both, and "screen" will 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 write the detailed info to the screen and the short version to the log
@ -537,13 +538,14 @@ partition screen files file.N.
**-skiprun** **-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. beginning of an input file or after a :doc:`clear <clear>` command.
This has the effect that the entire LAMMPS input script is processed This has the effect that the entire LAMMPS input script is processed
without executing actual runs or minimizations (their main loops are without executing actual :doc:`run <run>` or :doc:`minimize <minimize>`
skipped). This can be helpful and convenient to test input scripts for and similar commands (their main loops are skipped). This can be
long running calculations to avoid having them crash after a long time helpful and convenient to test input scripts of long running
due to a typo or syntax error. 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.
---------- ----------

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@ -23,22 +23,23 @@ Examples
Description Description
""""""""""" """""""""""
Define a computation that extracts the angle energy calculated by each Define a computation that extracts the angle energy calculated by each of the
of the angle sub-styles used in the doc:`angle_style hybrid <angle_hybrid>` angle sub-styles used in the :doc:`angle_style hybrid <angle_hybrid>` command.
command. These values are made accessible These values are made accessible for output or further processing by other
for output or further processing by other commands. The group commands. The group specified for this command is ignored.
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 This compute is useful when using :doc:`angle_style hybrid <angle_hybrid>` if
energy contributed by one or more of the hybrid sub-styles. you want to know the portion of the total energy contributed by one or more of
the hybrid sub-styles.
Output info Output info
""""""""""" """""""""""
This compute calculates a global vector of length N where N is the This compute calculates a global vector of length N where N is the number of
number of sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command, which can be accessed by indices sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command,
1-N. These values can be used by any command that uses global scalar which can be accessed by indices 1-N. These values can be used by any command
or vector values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output 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. options.
The vector values are "extensive" and will be in energy The vector values are "extensive" and will be in energy
@ -46,6 +47,7 @@ The vector values are "extensive" and will be in energy
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands Related commands

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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 E: Cannot create/grow a vector/array of pointers for %s
LAMMPS code is making an illegal call to the templated memory 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.
*/ */