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replace dir with directory where appropriate

This commit is contained in:
Axel Kohlmeyer 2020-02-21 15:08:18 -05:00
parent c144918441
commit bf3e7237c3
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12 changed files with 92 additions and 90 deletions
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2
doc/src/Build_package.rst
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@ -242,4 +242,4 @@ Type "make package-overwrite" to overwrite files in the package
sub-directories with src files.
Type "make package-diff" to list all differences between pairs of
files in both the src dir and a package dir.
files in both the source directory and the package directory.

2
doc/src/Build_settings.rst
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@ -307,7 +307,7 @@ As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
find the graphics header and library files. You must specify JPG\_LIB
with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime,
i.e. a dir in your PATH environment variable.
that is a directory in your PATH environment variable.
**CMake and make info**\ :

2
doc/src/Howto.rst
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@ -5,7 +5,7 @@ These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
`glossary <http://lammps.sandia.gov>`_ website page also lists MD
terminology with links to corresponding LAMMPS manual pages. The
example input scripts included in the examples dir of the LAMMPS
example input scripts included in the examples directory of the LAMMPS
distribution and highlighted on the :doc:`Examples <Examples>` doc page
also show how to setup and run various kinds of simulations.

2
doc/src/Howto_client_server.rst
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@ -97,7 +97,7 @@ client or server code:
* examples/COUPLE/lammps\_nwchem
* examples/COUPLE/lammps\_vasp
The examples/message dir couples a client instance of LAMMPS to a
The examples/message directory couples a client instance of LAMMPS to a
server instance of LAMMPS.
The files in the *lammps\_mc* folder show how to couple LAMMPS as

21
doc/src/Install_git.rst
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@ -1,5 +1,5 @@
Download source via Git
=======================
Download the LAMMPS source with Git
===================================
All LAMMPS development is coordinated through the "LAMMPS GitHub
site". If you clone the LAMMPS repository onto your local machine, it
@ -16,13 +16,12 @@ the public Git server for LAMMPS.
.. warning::
As of Oct 2016, the official home of public LAMMPS
development is on GitHub. The previously advertised LAMMPS git
repositories on git.lammps.org and bitbucket.org are now deprecated,
may not be up-to-date, and may go away at any time.
.. _git: http://git-scm.com
As of October 2016, the official home of public LAMMPS development is
on GitHub. The previously advertised LAMMPS git repositories on
git.lammps.org and bitbucket.org are now deprecated, may not be
up-to-date, and may go away at any time.
.. _git: https://git-scm.com
You can follow LAMMPS development on 3 different Git branches:
@ -107,15 +106,15 @@ after a patch has been installed.
If you wish to edit/change a src file that is from a
package, you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The version in
the src dir is merely a copy and will be wiped out if you type "make
the source directory is merely a copy and will be wiped out if you type "make
package-update".
.. warning::
The GitHub servers support both the "git://" and
"https://" access protocols for anonymous read-only access. If you
have a correspondingly configured GitHub account, you may also use SSH
with "git@github.com:/lammps/lammps.git".
have a correspondingly configured GitHub account, you may also use
passwordless SSH access with the URL "git@github.com:lammps/lammps.git".
The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at

10
doc/src/Install_patch.rst
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@ -56,8 +56,8 @@ up to date.
.. warning::
If you wish to edit/change a src file that is from a
package, you should edit the version of the file inside the package
sub-dir of src, then re-install the package. The version in the src
dir is merely a copy and will be wiped out if you type "make
package-update".
If you wish to edit/change a source file that is part of a package,
you should edit the version of the file inside the package folder in
src, and then re-install or update the package. The version in the
src directory is merely a copy and will be wiped out when you type
"make package-update".

8
doc/src/Install_svn.rst
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@ -85,10 +85,10 @@ after a patch has been installed.
.. warning::
If you wish to edit/change a src file that is from a
package, you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The version in
the src dir is merely a copy and will be wiped out if you type "make
If you wish to edit/change a source file that is from a package, you
should edit the version of the file inside the package sub-directory
with src, then re-install the package. The version in the src
directory is merely a copy and will be wiped out if you type "make
package-update".
The LAMMPS GitHub project is managed by Christoph Junghans (LANL,

36
doc/src/Manual_build.rst
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@ -22,25 +22,27 @@ If you downloaded LAMMPS from the public SVN or Git repositories, then
the HTML and PDF files are not included. Instead you need to create
them, in one of two ways:
a. You can "fetch" the current HTML and PDF files from the LAMMPS web site.
Just type "make fetch". This should create a html\_www dir and
Manual\_www.pdf/Developer\_www.pdf files. Note that if new LAMMPS features
have been added more recently than the date of your version, the fetched
documentation will include those changes (but your source code will not, unless
you update your local repository).
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type "make fetch". This should download a html\_www
directory and Manual\_www.pdf/Developer\_www.pdf files. Note that if
new LAMMPS features have been added more recently than the date of
your LAMMPS version, the fetched documentation will include those
changes (but your source code will not, unless you update your local
repository).
b. You can build the HTML and PDF files yourself, by typing "make
html" followed by "make pdf". This requires various tools including
b. You can build the HTML and PDF files yourself, by typing "make html"
followed by "make pdf". This requires various tools including
Sphinx, which the build process will attempt to download and install
into a virtual environment in the folder doc/docenv, if not already
available. See more details below. To generate the PDF version of
the manual, additionally PDFLaTeX and several LaTeX packages are required.
automatically into a virtual environment in the folder doc/docenv, if
not already available. See more details below. To generate the PDF
version of the manual, additionally the PDFLaTeX software and several
LaTeX packages are required.
----------
The generation of all documentation is managed by the Makefile in
the doc dir.
the doc directory.
.. code-block:: bash
@ -60,7 +62,6 @@ the doc dir.
make style_check # check for complete and consistent style lists
make spelling # spell-check the manual
----------
@ -127,11 +128,14 @@ Installing prerequisites for epub build
ePUB
----
Same as for HTML. This uses the same tools and configuration
files as the HTML tree.
Same as for HTML. This uses mostly the same tools and configuration
files as the HTML tree. In addition it uses LaTeX to convert embedded
math expressions transparently into embedded images.
For converting the generated ePUB file to a MOBI format file
(for e-book readers like Kindle, that cannot read ePUB), you
(for e-book readers, like Kindle, that cannot read ePUB), you
also need to have the 'ebook-convert' tool from the "calibre"
software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
You first create the ePUB file and then convert it with 'make mobi'
On the Kindle readers in particular, you also have support for
PDF files, so you could download and view the PDF version as an alternative.

75
doc/src/Modify_contribute.rst
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@ -77,15 +77,16 @@ one or more new class files which are invoked as a new style within a
LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you'll need to `communicate with the developers <http://lammps.sandia.gov/authors.html>`_, since we may or may
not want to make those changes. An example of a trivial change is
making a parent-class method "virtual" when you derive a new child
class from it.
changes in core LAMMPS files, you should `communicate with the
developers <http://lammps.sandia.gov/authors.html>`_, since we may or
may not want to include those changes for some reason. An example of a
trivial change is making a parent-class method "virtual" when you derive
a new child class from it.
Here is a checklist of steps you need to follow to submit a single file
or user package for our consideration. Following these steps will save
both you and us time. See existing files in packages in the src dir for
examples. If you are uncertain, please ask.
both you and us time. Please have a look at the existing files in
packages in the src directory for examples. If you are uncertain, please ask.
* All source files you provide must compile with the most current
version of LAMMPS with multiple configurations. In particular you
@ -146,41 +147,39 @@ examples. If you are uncertain, please ask.
would be nice for developers as well as users who try to read your
code.
* You **must** also create a **documentation** file for each new command or
style you are adding to LAMMPS. For simplicity and convenience, the
* You **must** also create a **documentation** file for each new command
or style you are adding to LAMMPS. For simplicity and convenience, the
documentation of groups of closely related commands or styles may be
combined into a single file. This will be one file for a single-file
feature. For a package, it might be several files. These are text
files with a .rst extension using the
`reStructuredText <rst_>`_ markup language, that are then converted to HTML
and PDF using the `Sphinx <sphinx_>`_ documentation
generator tool. Running Sphinx with the included configuration
requires Python 3.x. Configuration
settings and custom extensions for this conversion are included in
the source distribution, and missing python packages will be
transparently downloaded into a virtual environment via pip. Thus,
if your local system is missing required packages, you need access
to the internet. The translation can be as simple as doing
"make html pdf" in the doc folder.
As appropriate, the text files can include inline mathematical
expression or figures (see doc/JPG for examples). Additional PDF
files with further details (see doc/PDF for examples) may also be
included. The doc page should also include literature citations as
appropriate; see the bottom of doc/fix\_nh.rst for examples and
the earlier part of the same file for how to format the cite itself.
Citation labels must be unique across all .rst files.
The "Restrictions" section of the doc page should indicate if
your command is only available if LAMMPS is built with the
appropriate USER-MISC or USER-FOO package.
See other user package doc files for examples of how to do this.
Please run at least "make html" and carefully inspect and proofread
the resulting HTML format doc page before submitting your code.
Upon submission of a pull request, checks for error free completion
of the HTML and PDF build will be performed and also a spell check,
a check for correct anchors and labels, and a check for completeness
of references all styles in their corresponding tables and lists is
run. In case the spell check reports false positives they can be
added to the file doc/utils/sphinx-config/false_positives.txt
files with a .rst extension using the `reStructuredText <rst_>`_
markup language, that are then converted to HTML and PDF using the
`Sphinx <sphinx_>`_ documentation generator tool. Running Sphinx with
the included configuration requires Python 3.x. Configuration
settings and custom extensions for this conversion are included in the
source distribution, and missing python packages will be transparently
downloaded into a virtual environment via pip. Thus, if your local
system is missing required packages, you need access to the
internet. The translation can be as simple as doing "make html pdf" in
the doc folder. As appropriate, the text files can include inline
mathematical expression or figures (see doc/JPG for examples).
Additional PDF files with further details (see doc/PDF for examples)
may also be included. The doc page should also include literature
citations as appropriate; see the bottom of doc/fix\_nh.rst for
examples and the earlier part of the same file for how to format the
cite itself. Citation labels must be unique across all .rst files.
The "Restrictions" section of the doc page should indicate if your
command is only available if LAMMPS is built with the appropriate
USER-MISC or USER-FOO package. See other user package doc files for
examples of how to do this. Please run at least "make html" and "make
spelling" and carefully inspect and proofread the resulting HTML
format doc page before submitting your code. Upon submission of a
pull request, checks for error free completion of the HTML and PDF
build will be performed and also a spell check, a check for correct
anchors and labels, and a check for completeness of references all
styles in their corresponding tables and lists is run. In case the
spell check reports false positives they can be added to the file
doc/utils/sphinx-config/false_positives.txt
* For a new package (or even a single command) you should include one or
more example scripts demonstrating its use. These should run in no

18
doc/src/Modify_overview.rst
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@ -10,15 +10,15 @@ computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
Most of the new features described on the :doc:`Modify <Modify>` doc
page require you to write a new C++ derived class (except for
exceptions described below, where you can make small edits to existing
files). Creating a new class requires 2 files, a source code file
(\*.cpp) and a header file (\*.h). The derived class must provide
certain methods to work as a new option. Depending on how different
your new feature is compared to existing features, you can either
derive from the base class itself, or from a derived class that
already exists. Enabling LAMMPS to invoke the new class is as simple
as putting the two source files in the src dir and re-building LAMMPS.
page require you to write a new C++ derived class (except for exceptions
described below, where you can make small edits to existing files).
Creating a new class requires 2 files, a source code file (\*.cpp) and a
header file (\*.h). The derived class must provide certain methods to
work as a new option. Depending on how different your new feature is
compared to existing features, you can either derive from the base class
itself, or from a derived class that already exists. Enabling LAMMPS to
invoke the new class is as simple as putting the two source files in the
src directory and re-building LAMMPS.
The advantage of C++ and its object-orientation is that all the code
and variables needed to define the new feature are in the 2 files you

2
doc/src/fix_client_md.rst
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@ -61,7 +61,7 @@ specify boundary conditions or force constraints in the usual way,
which will be added to the per-atom forces returned by the server
code.
See the examples/message dir for example scripts where LAMMPS is both
See the examples/message directory for example scripts where LAMMPS is both
the "client" and/or "server" code for this kind of client/server MD
simulation. The examples/message/README file explains how to launch
LAMMPS and another code in tandem to perform a coupled simulation.

4
doc/src/pair_polymorphic.rst
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@ -114,8 +114,8 @@ LAMMPS atom types:
See the pair\_coeff doc page for alternate ways to specify the path for
the potential file. Several files for polymorphic potentials are
included in the potentials dir of the LAMMPS distribution. They have a
"poly" suffix.
included in the potentials directory of the LAMMPS distribution. They
have a "poly" suffix.
As an example, imagine the SiC\_tersoff.polymorphic file has tabulated
functions for Si-C tersoff potential. If your LAMMPS simulation has 4