From ae82462569b688a29207e8f45d8e894df5c155ce Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 2 Jun 2014 16:54:31 +0100
Subject: [PATCH] Brilliantly and linearly organized documentation
---
user-doc/Doxyfile | 4 +++-
user-doc/Glossary.txt | 6 +-----
user-doc/Intro.txt | 11 -----------
user-doc/Misc.txt | 8 ++++++++
user-doc/PlumedLayout.xml | 18 ++++++++++++------
user-doc/Tools.txt | 17 +++++++++++++++++
user-doc/extract | 2 +-
7 files changed, 42 insertions(+), 24 deletions(-)
create mode 100644 user-doc/Misc.txt
create mode 100644 user-doc/Tools.txt
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index b9919b5e3..62abc0717 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -744,6 +744,8 @@ INPUT = IntroPP.txt \
GlossaryPP.txt \
TutorialsPP.txt \
ModulesPP.txt \
+ MiscPP.txt \
+ ToolsPP.txt \
RegexPP.txt \
../CHANGES \
tutorials \
@@ -1356,7 +1358,7 @@ DISABLE_INDEX = NO
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
-GENERATE_TREEVIEW = NO
+GENERATE_TREEVIEW = YES
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
diff --git a/user-doc/Glossary.txt b/user-doc/Glossary.txt
index c4c5d4247..2e9450e24 100644
--- a/user-doc/Glossary.txt
+++ b/user-doc/Glossary.txt
@@ -1,6 +1,6 @@
/**
-@page glossary Glossary of Actions
+@page glossary Index of Actions
The following page contains an alphabetically ordered list of all the Actions and command line tools
that are available in PLUMED 2. For lists of Actions classified in accordance with the
@@ -15,8 +15,4 @@ particular tasks that are being performed see:
@GLOSSARY@
-\section dictionary Dictionary
-
-@DICTIONARY@
-
*/
diff --git a/user-doc/Intro.txt b/user-doc/Intro.txt
index 5154a4ff7..cf0b0d5c0 100644
--- a/user-doc/Intro.txt
+++ b/user-doc/Intro.txt
@@ -40,17 +40,6 @@ analsyis tools that come with PLUMED are given in:
PLUMED can be used in one of two ways. It can be incorporated into any one of the MD codes listed on the
\ref Installation page and used to analyse or bias a molecular dynamics run on the fly. Alternatively, one
can use it as a standalone tool for postprocessing the results from molecular dynamics or enhanced sampling calculations.
-To use PLUMED in this second way you will issue a command something like:
-
-\verbatim
-plumed <toolname> <list of input flags for that tool>
-\endverbatim
-
-The following is a list of the various standalone tools that PLUMED contains.
-
-@TOOLS@
-
-For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.
*/
diff --git a/user-doc/Misc.txt b/user-doc/Misc.txt
new file mode 100644
index 000000000..598e617d6
--- /dev/null
+++ b/user-doc/Misc.txt
@@ -0,0 +1,8 @@
+/**
+
+\page misc Miscellaneus
+
+@DICTIONARY@
+
+
+*/
diff --git a/user-doc/PlumedLayout.xml b/user-doc/PlumedLayout.xml
index 49d7ddcc6..ccc60e87b 100644
--- a/user-doc/PlumedLayout.xml
+++ b/user-doc/PlumedLayout.xml
@@ -2,15 +2,21 @@
<!-- Navigation index tabs for HTML output -->
<navindex>
<tab type="mainpage" visible="yes" title=""/>
- <tab type="user" visible="no" url="mymodules.html" title="Modules"/>
<tab type="user" visible="yes" url="_installation.html" title="Installation"/>
- <tab type="user" visible="yes" url="tutorials.html" title="Tutorials"/>
- <tab type="user" visible="yes" url="_group.html" title="Groups and Atoms"/>
- <tab type="user" visible="yes" url="_colvar.html" title="Collective Variables"/>
- <tab type="user" visible="yes" url="_function.html" title="Functions"/>
+ <tab type="usergroup" title="Basics">
+ <tab type="user" visible="yes" url="_syntax.html" title="Input File"/>
+ <tab type="user" visible="yes" url="_group.html" title="Groups and Atoms"/>
+ </tab>
+ <tab type="usergroup" title="Collective variables">
+ <tab type="user" visible="yes" url="_colvar.html" title="Collective Variables"/>
+ <tab type="user" visible="yes" url="_function.html" title="Functions"/>
+ </tab>
<tab type="user" visible="yes" url="_analysis.html" title="Analysis"/>
<tab type="user" visible="yes" url="_bias.html" title="Bias"/>
- <tab type="user" visible="yes" url="glossary.html" title="Glossary"/>
+ <tab type="user" visible="yes" url="tools.html" title="Tools"/>
+ <tab type="user" visible="yes" url="misc.html" title="Misc"/>
+ <tab type="user" visible="yes" url="tutorials.html" title="Tutorials"/>
+ <tab type="user" visible="yes" url="glossary.html" title="Index"/>
<tab type="pages" visible="no" title="" intro=""/>
<tab type="modules" visible="yes" title="" intro=""/>
<tab type="namespaces" visible="yes" title="">
diff --git a/user-doc/Tools.txt b/user-doc/Tools.txt
new file mode 100644
index 000000000..81b7a9161
--- /dev/null
+++ b/user-doc/Tools.txt
@@ -0,0 +1,17 @@
+/**
+
+\page tools Command Line Tools
+
+To use PLUMED in this second way you will issue a command something like:
+
+\verbatim
+plumed <toolname> <list of input flags for that tool>
+\endverbatim
+
+The following is a list of the various standalone tools that PLUMED contains.
+
+@TOOLS@
+
+For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.
+
+*/
diff --git a/user-doc/extract b/user-doc/extract
index 7d221b5bf..570d9bab8 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -213,7 +213,7 @@ do
fi
done
-for file in Bias Syntax Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex
+for file in Bias Syntax Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex Misc Tools
do
cat $file.txt |
--
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