From 9030c987e60430a0a82f2691d7d04ebfb9e418be Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 19 Sep 2020 00:54:54 -0400
Subject: [PATCH] tweak formatting and style setting to have the desired
 structure and layout

---
 doc/Makefile                                  |  6 ++----
 doc/src/Manual.rst                            | 20 +++++++++++--------
 .../sphinx-config/_static/css/lammps.css      |  4 ++++
 .../_themes/lammps_theme/theme.conf           |  2 +-
 4 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/doc/Makefile b/doc/Makefile
index ac1b8b6ba2..d1afa95030 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -166,14 +166,12 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		deactivate ;\
 	)
 	@cd latex && \
-		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
-		mv temp Makefile && \
 		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
 		mv tmp.tex LAMMPS.tex && \
 		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
 		mv tmp.tex LAMMPS.tex && \
-		$(MAKE) $(MFLAGS) && \
-		$(MAKE) $(MFLAGS) && \
+		sed 's/\\contentsname}{.*}}/\\contentsname}{LAMMPS Documentation}}/g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
 		$(MAKE) $(MFLAGS) && \
 		mv LAMMPS.pdf ../Manual.pdf && \
 		cd ../;
diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst
index 8351f5ebbd..ddc2b2daa8 100644
--- a/doc/src/Manual.rst
+++ b/doc/src/Manual.rst
@@ -23,25 +23,28 @@ The content for this manual is part of the LAMMPS distribution.  You
 can build a local copy of the Manual as HTML pages or a PDF file, by
 following the steps on the :doc:`Manual build <Manual_build>` doc page.
 The manual is organized in two parts:
-1) A :ref:`User documentation <user_documentation>` for how to install
-and use LAMMPS and 2) a :ref:`Programmer documentation <programmer_documentation>`
-for how to write programs using the LAMMPS library or how to modify LAMMPS.
+1) the :ref:`User documentation <user_documentation>` for how to install
+and use LAMMPS and 2) the :ref:`Programmer documentation <programmer_documentation>`
+for how to write programs using the LAMMPS library from different
+programming languages and how to modify and extend LAMMPS.
 
-----------
+.. only:: html
 
-Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands_all>` since it gives quick access to a doc page for
-every LAMMPS command.
+   Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands_all>` since it gives quick access to a doc page for
+   every LAMMPS command.
 
 .. _lws: https://lammps.sandia.gov
 
+----------
+
 User Documentation
 ******************
 
-..   :caption: User Documentation
 .. _user_documentation:
 .. toctree::
    :maxdepth: 2
    :numbered: 3
+   :caption: User Documentation
    :name: userdoc
    :includehidden:
 
@@ -61,11 +64,12 @@ User Documentation
 
 Programmer Documentation
 ************************
-..   :caption: Programmer Documentation
+
 .. _programmer_documentation:
 .. toctree::
    :maxdepth: 2
    :numbered: 3
+   :caption: Programmer Documentation
    :name: progdoc
    :includehidden:
 
diff --git a/doc/utils/sphinx-config/_static/css/lammps.css b/doc/utils/sphinx-config/_static/css/lammps.css
index 79d3aa36f6..279b089a0a 100644
--- a/doc/utils/sphinx-config/_static/css/lammps.css
+++ b/doc/utils/sphinx-config/_static/css/lammps.css
@@ -27,6 +27,10 @@ hr {
      margin-bottom: 12px !important;
 }
 
+.section h2 {
+     display: none;
+}
+
 .ui.tabular.menu .item {
     padding-right: 1em;
     padding-left: 1em;
diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/theme.conf b/doc/utils/sphinx-config/_themes/lammps_theme/theme.conf
index fadb472b81..37dc1185b7 100644
--- a/doc/utils/sphinx-config/_themes/lammps_theme/theme.conf
+++ b/doc/utils/sphinx-config/_themes/lammps_theme/theme.conf
@@ -14,5 +14,5 @@ titles_only =
 logo_only =
 display_version = True
 prev_next_buttons_location = both
-style_external_links = False
+style_external_links = True
 style_nav_header_background =