replace dir with directory where appropriate

doc/src/Build_package.rst

@@ -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.

doc/src/Build_settings.rst

@@ -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**\ :
 

doc/src/Howto.rst

@@ -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.
 

doc/src/Howto_client_server.rst

@@ -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

doc/src/Install_git.rst

@@ -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
+   As of October 2016, the official home of public LAMMPS development is
-   development is on GitHub.  The previously advertised LAMMPS git
+   on GitHub.  The previously advertised LAMMPS git repositories on
-   repositories on git.lammps.org and bitbucket.org are now deprecated,
+   git.lammps.org and bitbucket.org are now deprecated, may not be
-   may not be up-to-date, and may go away at any time.
+   up-to-date, and may go away at any time.
-
-.. _git: http://git-scm.com
 
+.. _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
+   have a correspondingly configured GitHub account, you may also use
-   with "git@github.com:/lammps/lammps.git".
+   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

doc/src/Install_patch.rst

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

doc/src/Install_svn.rst

@@ -85,10 +85,10 @@ after a patch has been installed.
 
 .. warning::
 
-   If you wish to edit/change a src file that is from a
+   If you wish to edit/change a source file that is from a package, you
-   package, you should edit the version of the file inside the package
+   should edit the version of the file inside the package sub-directory
-   sub-directory with src, then re-install the package.  The version in
+   with src, then re-install the package.  The version in the src
-   the src dir is merely a copy and will be wiped out if you type "make
+   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,

doc/src/Manual_build.rst

@@ -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.
+a. You can "fetch" the current HTML and PDF files from the LAMMPS web
-   Just type "make fetch".  This should create a html\_www dir and
+   site.  Just type "make fetch".  This should download a html\_www
-   Manual\_www.pdf/Developer\_www.pdf files.  Note that if new LAMMPS features
+   directory and Manual\_www.pdf/Developer\_www.pdf files.  Note that if
-   have been added more recently than the date of your version, the fetched
+   new LAMMPS features have been added more recently than the date of
-   documentation will include those changes (but your source code will not, unless
+   your LAMMPS version, the fetched documentation will include those
-   you update your local repository).
+   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
+b. You can build the HTML and PDF files yourself, by typing "make html"
-   html" followed by "make pdf".  This requires various tools including
+   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
+   automatically into a virtual environment in the folder doc/docenv, if
-   available.  See more details below.  To generate the PDF version of
+   not already available.  See more details below.  To generate the PDF
-   the manual, additionally PDFLaTeX and several LaTeX packages are required.
+   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
+Same as for HTML. This uses mostly the same tools and configuration
-files as the HTML tree.
+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.

doc/src/Modify_contribute.rst

@@ -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
+changes in core LAMMPS files, you should `communicate with the
-not want to make those changes.  An example of a trivial change is
+developers <http://lammps.sandia.gov/authors.html>`_, since we may or
-making a parent-class method "virtual" when you derive a new child
+may not want to include those changes for some reason.  An example of a
-class from it.
+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
+both you and us time. Please have a look at the existing files in
-examples. If you are uncertain, please ask.
+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
+* You **must** also create a **documentation** file for each new command
-  style you are adding to LAMMPS. For simplicity and convenience, the
+  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
+  files with a .rst extension using the `reStructuredText <rst_>`_
-  `reStructuredText <rst_>`_ markup language, that are then converted to HTML
+  markup language, that are then converted to HTML and PDF using the
-  and PDF using the `Sphinx <sphinx_>`_ documentation
+  `Sphinx <sphinx_>`_ documentation generator tool.  Running Sphinx with
-  generator tool.   Running Sphinx with the included configuration
+  the included configuration requires Python 3.x.  Configuration
-  requires Python 3.x.  Configuration
+  settings and custom extensions for this conversion are included in the
-  settings and custom extensions for this conversion are included in
+  source distribution, and missing python packages will be transparently
-  the source distribution, and missing python packages will be
+  downloaded into a virtual environment via pip. Thus, if your local
-  transparently downloaded into a virtual environment via pip. Thus,
+  system is missing required packages, you need access to the
-  if your local system is missing required packages, you need access
+  internet. The translation can be as simple as doing "make html pdf" in
-  to the internet. The translation can be as simple as doing
+  the doc folder.  As appropriate, the text files can include inline
-  "make html pdf" in the doc folder.
+  mathematical expression or figures (see doc/JPG for examples).
-  As appropriate, the text files can include inline mathematical
+  Additional PDF files with further details (see doc/PDF for examples)
-  expression or figures (see doc/JPG for examples).  Additional PDF
+  may also be included.  The doc page should also include literature
-  files with further details (see doc/PDF for examples) may also be
+  citations as appropriate; see the bottom of doc/fix\_nh.rst for
-  included.  The doc page should also include literature citations as
+  examples and the earlier part of the same file for how to format the
-  appropriate; see the  bottom of doc/fix\_nh.rst for examples and
+  cite itself.  Citation labels must be unique across all .rst files.
-  the earlier part of the same file for how to format the cite itself.
+  The "Restrictions" section of the doc page should indicate if your
-  Citation labels must be unique across all .rst files.
+  command is only available if LAMMPS is built with the appropriate
-  The "Restrictions" section of the doc page should indicate if
+  USER-MISC or USER-FOO package.  See other user package doc files for
-  your command is only available if LAMMPS is built with the
+  examples of how to do this.  Please run at least "make html" and "make
-  appropriate USER-MISC or USER-FOO package.
+  spelling" and carefully inspect and proofread the resulting HTML
-  See other user package doc files for examples of how to do this.
+  format doc page before submitting your code.  Upon submission of a
-  Please run at least "make html" and carefully inspect and proofread
+  pull request, checks for error free completion of the HTML and PDF
-  the resulting HTML format  doc page before submitting your code.
+  build will be performed and also a spell check, a check for correct
-  Upon submission of a pull request, checks for error free completion
+  anchors and labels, and a check for completeness of references all
-  of the HTML and PDF build will be performed and also a spell check,
+  styles in their corresponding tables and lists is run.  In case the
-  a check for correct anchors and labels, and a check for completeness
+  spell check reports false positives they can be added to the file
-  of references all styles in their corresponding tables and lists is
+  doc/utils/sphinx-config/false_positives.txt
-  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

doc/src/Modify_overview.rst

@@ -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
+page require you to write a new C++ derived class (except for exceptions
-exceptions described below, where you can make small edits to existing
+described below, where you can make small edits to existing files).
-files).  Creating a new class requires 2 files, a source code file
+Creating a new class requires 2 files, a source code file (\*.cpp) and a
-(\*.cpp) and a header file (\*.h).  The derived class must provide
+header file (\*.h).  The derived class must provide certain methods to
-certain methods to work as a new option.  Depending on how different
+work as a new option.  Depending on how different your new feature is
-your new feature is compared to existing features, you can either
+compared to existing features, you can either derive from the base class
-derive from the base class itself, or from a derived class that
+itself, or from a derived class that already exists.  Enabling LAMMPS to
-already exists.  Enabling LAMMPS to invoke the new class is as simple
+invoke the new class is as simple as putting the two source files in the
-as putting the two source files in the src dir and re-building LAMMPS.
+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

doc/src/fix_client_md.rst

@@ -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.

doc/src/pair_polymorphic.rst

@@ -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
+included in the potentials directory of the LAMMPS distribution.  They
-"poly" suffix.
+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