update documentation for contributing files and building the manual to using rst files

doc/src/Manual_build.rst

@@ -30,10 +30,11 @@ a. You can "fetch" the current HTML and PDF files from the LAMMPS web site.
    you update your local repository).
 
 b. You can build the HTML and PDF files yourself, by typing "make
-   html" followed by "make pdf".  Note that the PDF make requires the
+   html" followed by "make pdf".  This requires various tools including
-   HTML files already exist.  This requires various tools including
    Sphinx, which the build process will attempt to download and install
-   on your system, if not already available.  See more details below.
+   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.
 
 ----------
 
@@ -56,7 +57,7 @@ the doc dir.
    make clean        # remove intermediate RST files created by HTML build
    make clean-all    # remove entire build folder and any cached data
    make anchor_check # check for duplicate anchor labels
-   style_check       # check for complete and consistent style lists
+   make style_check  # check for complete and consistent style lists
    make spelling     # spell-check the manual
 
 

doc/src/Modify_contribute.rst

@@ -92,6 +92,7 @@ examples. If you are uncertain, please ask.
   need to test compiling LAMMPS from scratch with -DLAMMPS\_BIGBIG
   set in addition to the default -DLAMMPS\_SMALLBIG setting. Your code
   will need to work correctly in serial and in parallel using MPI.
+
 * For consistency with the rest of LAMMPS and especially, if you want
   your contribution(s) to be added to main LAMMPS code or one of its
   standard packages, it needs to be written in a style compatible with
@@ -114,12 +115,14 @@ examples. If you are uncertain, please ask.
   structures, performs its operations, and is formatted similar to other
   LAMMPS source files, including the use of the error class for error
   and warning messages.
+
 * If you want your contribution to be added as a user-contributed
   feature, and it's a single file (actually a \*.cpp and \*.h file) it can
   rapidly be added to the USER-MISC directory.  Send us the one-line
   entry to add to the USER-MISC/README file in that dir, along with the
   2 source files.  You can do this multiple times if you wish to
   contribute several individual features.
+
 * If you want your contribution to be added as a user-contribution and
   it is several related features, it is probably best to make it a user
   package directory with a name like USER-FOO.  In addition to your new
@@ -132,7 +135,7 @@ examples. If you are uncertain, please ask.
   and Install.sh files in other USER directories as examples.  Send us a
   tarball of this USER-FOO directory.
 
-  Your new source files need to have the LAMMPS copyright, GPL notice,
+* Your new source files need to have the LAMMPS copyright, GPL notice,
   and your name and email address at the top, like other
   user-contributed LAMMPS source files.  They need to create a class
   that is inside the LAMMPS namespace.  If the file is for one of the
@@ -142,14 +145,15 @@ examples. If you are uncertain, please ask.
   same stylistic format and syntax as other LAMMPS files, though that
   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
   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
-  :ref:`reStructuredText <https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html>`_ markup language, that are then converted to HTML
+  `reStructuredText <rst_>`_ markup language, that are then converted to HTML
-  and PDF using the :ref:`Sphinx <https://sphinx-doc.org>`_ documentation
+  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
@@ -177,6 +181,7 @@ examples. If you are uncertain, please ask.
   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
   more than a couple minutes, even on a single processor, and not require
@@ -184,6 +189,7 @@ examples. If you are uncertain, please ask.
   examples of input scripts other users provided for their packages.
   These example inputs are also required for validating memory accesses
   and testing for memory leaks with valgrind
+
 * If there is a paper of yours describing your feature (either the
   algorithm/science behind the feature itself, or its initial usage, or
   its implementation in LAMMPS), you can add the citation to the \*.cpp
@@ -204,3 +210,6 @@ Finally, as a general rule-of-thumb, the more clear and
 self-explanatory you make your documentation and README files, and the
 easier you make it for people to get started, e.g. by providing example
 scripts, the more likely it is that users will try out your new feature.
+
+.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
+.. _sphinx: https://sphinx-doc.org

doc/utils/sphinx-config/false_positives.txt

@@ -634,6 +634,7 @@ dnf
 DNi
 Dobson
 Dodds
+docenv
 dodgerblue
 dof
 doi
@@ -2510,6 +2511,7 @@ Rr
 rRESPA
 Rspace
 rsq
+rst
 rstyle
 Rubensson
 Rubia