From 9eaf110bdb968734f76a1a983bfe30a8fbcf32b2 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 30 Jun 2011 19:09:25 +0200
Subject: [PATCH] User doc split in several files and improved doc

I also upgraded the doxygen configuration files to 1.7.4 version
---
 developer-doc/Doxyfile         | 309 ++++------------
 developer-doc/Intro.txt        |   2 +
 src/DumpDerivatives.cpp        |  23 ++
 src/Units.cpp                  |   2 +-
 user-doc/.gitignore            |   2 +-
 user-doc/AdvancedTopics.txt    |  20 ++
 user-doc/BasicUsage.txt        |  37 ++
 user-doc/Bias.txt              |  32 ++
 user-doc/Colvar.txt            |  20 ++
 user-doc/Doc.txt               | 176 ---------
 user-doc/Doxyfile              | 635 +++++++--------------------------
 user-doc/Functions.txt         |  28 ++
 user-doc/GenericDirectives.txt |  12 +
 user-doc/InputDirectives.txt   |  65 ++++
 user-doc/Installation.txt      |  43 +++
 user-doc/Intro.txt             |  18 +
 user-doc/Makefile              |   2 +-
 user-doc/Reference.txt         |  18 +
 user-doc/Setup.txt             |  14 +
 user-doc/Tools.txt             |  12 +
 user-doc/WhatsNew.txt          |  12 +
 user-doc/extract               |  13 +-
 22 files changed, 570 insertions(+), 925 deletions(-)
 create mode 100644 user-doc/AdvancedTopics.txt
 create mode 100644 user-doc/BasicUsage.txt
 create mode 100644 user-doc/Bias.txt
 create mode 100644 user-doc/Colvar.txt
 delete mode 100644 user-doc/Doc.txt
 create mode 100644 user-doc/Functions.txt
 create mode 100644 user-doc/GenericDirectives.txt
 create mode 100644 user-doc/InputDirectives.txt
 create mode 100644 user-doc/Installation.txt
 create mode 100644 user-doc/Intro.txt
 create mode 100644 user-doc/Reference.txt
 create mode 100644 user-doc/Setup.txt
 create mode 100644 user-doc/Tools.txt
 create mode 100644 user-doc/WhatsNew.txt

diff --git a/developer-doc/Doxyfile b/developer-doc/Doxyfile
index d63aa8389..57b442c36 100644
--- a/developer-doc/Doxyfile
+++ b/developer-doc/Doxyfile
@@ -1,4 +1,4 @@
-# Doxyfile 1.5.6
+# Doxyfile 1.4.7
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project
@@ -14,18 +14,10 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 
-# This tag specifies the encoding used for all characters in the config file 
-# that follow. The default is UTF-8 which is also the encoding used for all 
-# text before the first occurrence of this tag. Doxygen uses libiconv (or the 
-# iconv built into libc) for the transcoding. See 
-# http://www.gnu.org/software/libiconv for the list of possible encodings.
-
-DOXYFILE_ENCODING      = UTF-8
-
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
 # by quotes) that should identify the project.
 
-PROJECT_NAME           =  
+PROJECT_NAME           = "Plumed 2.0: developer manual"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. 
 # This could be handy for archiving the generated documentation or 
@@ -53,15 +45,24 @@ CREATE_SUBDIRS         = NO
 # documentation generated by doxygen is written. Doxygen will use this 
 # information to generate all constant output in the proper language. 
 # The default language is English, other supported languages are: 
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
-# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek, 
-# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages), 
-# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish, 
-# Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, 
-# and Ukrainian.
+# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, 
+# Dutch, Finnish, French, German, Greek, Hungarian, Italian, Japanese, 
+# Japanese-en (Japanese with English messages), Korean, Korean-en, Norwegian, 
+# Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, 
+# Swedish, and Ukrainian.
 
 OUTPUT_LANGUAGE        = English
 
+# This tag can be used to specify the encoding used in the generated output. 
+# The encoding is not always determined by the language that is chosen, 
+# but also whether or not the output is meant for Windows or non-Windows users. 
+# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES 
+# forces the Windows encoding (this is the default for the Windows binary), 
+# whereas setting the tag to NO uses a Unix-style encoding (the default for 
+# all platforms other than Windows).
+
+USE_WINDOWS_ENCODING   = NO
+
 # If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
 # include brief member descriptions after the members that are listed in 
 # the file and class documentation (similar to JavaDoc). 
@@ -134,19 +135,11 @@ SHORT_NAMES            = NO
 # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
 # will interpret the first line (until the first dot) of a JavaDoc-style 
 # comment as the brief description. If set to NO, the JavaDoc 
-# comments will behave just like regular Qt-style comments 
-# (thus requiring an explicit @brief command for a brief description.)
+# comments will behave just like the Qt-style comments (thus requiring an 
+# explicit @brief command for a brief description.
 
 JAVADOC_AUTOBRIEF      = YES
 
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will 
-# interpret the first line (until the first dot) of a Qt-style 
-# comment as the brief description. If set to NO, the comments 
-# will behave just like regular Qt-style comments (thus requiring 
-# an explicit \brief command for a brief description.)
-
-QT_AUTOBRIEF           = NO
-
 # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
 # treat a multi-line C++ special comment block (i.e. a block of //! or /// 
 # comments) as a brief description. This used to be the default behaviour. 
@@ -196,26 +189,14 @@ ALIASES                =
 OPTIMIZE_OUTPUT_FOR_C  = NO
 
 # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
-# sources only. Doxygen will then generate output that is more tailored for 
-# Java. For instance, namespaces will be presented as packages, qualified 
-# scopes will look different, etc.
+# sources only. Doxygen will then generate output that is more tailored for Java. 
+# For instance, namespaces will be presented as packages, qualified scopes 
+# will look different, etc.
 
 OPTIMIZE_OUTPUT_JAVA   = NO
 
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran 
-# sources only. Doxygen will then generate output that is more tailored for 
-# Fortran.
-
-OPTIMIZE_FOR_FORTRAN   = NO
-
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL 
-# sources. Doxygen will then generate output that is tailored for 
-# VHDL.
-
-OPTIMIZE_OUTPUT_VHDL   = NO
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want 
-# to include (a tag file for) the STL sources as input, then you should 
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to 
+# include (a tag file for) the STL sources as input, then you should 
 # set this tag to YES in order to let doxygen match functions declarations and 
 # definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
 # func(std::string) {}). This also make the inheritance and collaboration 
@@ -223,26 +204,6 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 
 BUILTIN_STL_SUPPORT    = YES
 
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
-# enable parsing support.
-
-CPP_CLI_SUPPORT        = NO
-
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. 
-# Doxygen will parse them like normal C++ but will assume all classes use public 
-# instead of private inheritance when no explicit protection keyword is present.
-
-SIP_SUPPORT            = NO
-
-# For Microsoft's IDL there are propget and propput attributes to indicate getter 
-# and setter methods for a property. Setting this option to YES (the default) 
-# will make doxygen to replace the get and set methods by a property in the 
-# documentation. This will only work if the methods are indeed getting or 
-# setting a simple type. If this is not the case, or you want to show the 
-# methods anyway, you should set this option to NO.
-
-IDL_PROPERTY_SUPPORT   = YES
-
 # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
 # tag is set to YES, then doxygen will reuse the documentation of the first 
 # member in the group (if any) for the other members of the group. By default 
@@ -258,16 +219,6 @@ DISTRIBUTE_GROUP_DOC   = NO
 
 SUBGROUPING            = YES
 
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
-# is documented as struct, union, or enum with the name of the typedef. So 
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct 
-# with name TypeT. When disabled the typedef will appear as a member of a file, 
-# namespace, or class. And the struct will be named TypeS. This can typically 
-# be useful for C code in case the coding convention dictates that all compound 
-# types are typedef'ed and only the typedef is referenced, never the tag name.
-
-TYPEDEF_HIDES_STRUCT   = NO
-
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -302,14 +253,6 @@ EXTRACT_LOCAL_CLASSES  = YES
 
 EXTRACT_LOCAL_METHODS  = NO
 
-# If this flag is set to YES, the members of anonymous namespaces will be 
-# extracted and appear in the documentation as a namespace called 
-# 'anonymous_namespace{file}', where file will be replaced with the base 
-# name of the file that contains the anonymous namespace. By default 
-# anonymous namespace are hidden.
-
-EXTRACT_ANON_NSPACES   = 
-
 # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
 # undocumented members of documented classes, files or namespaces. 
 # If set to NO (the default) these members will be included in the 
@@ -385,12 +328,6 @@ SORT_MEMBER_DOCS       = YES
 
 SORT_BRIEF_DOCS        = NO
 
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the 
-# hierarchy of group names into alphabetical order. If set to NO (the default) 
-# the group names will appear in their defined order.
-
-SORT_GROUP_NAMES       = NO
-
 # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
 # sorted by fully-qualified names, including namespaces. If set to 
 # NO (the default), the class list will be sorted only by class name, 
@@ -452,21 +389,9 @@ SHOW_USED_FILES        = YES
 
 SHOW_DIRECTORIES       = NO
 
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
-# This will remove the Files entry from the Quick Index and from the 
-# Folder Tree View (if specified). The default is YES.
-
-SHOW_FILES             = YES
-
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the 
-# Namespaces page.  This will remove the Namespaces entry from the Quick Index
-# and from the Folder Tree View (if specified). The default is YES.
-
-SHOW_NAMESPACES        = NO
-
 # The FILE_VERSION_FILTER tag can be used to specify a program or script that 
-# doxygen should invoke to get the current version for each file (typically from 
-# the version control system). Doxygen will invoke the program by executing (via 
+# doxygen should invoke to get the current version for each file (typically from the 
+# version control system). Doxygen will invoke the program by executing (via 
 # popen()) the command <command> <input-file>, where <command> is the value of 
 # the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
 # provided by doxygen. Whatever the program writes to standard output 
@@ -534,22 +459,22 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  =  ./Intro.txt ./cvTemplate.txt ./freeTemplate.txt ./funcTemplate.txt ./mdTemplate.txt ./plmdIntro.txt ./usingDoxygen.txt ./parsing.txt ../src
-
-# This tag can be used to specify the character encoding of the source files 
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
-# also the default input encoding. Doxygen uses libiconv (or the iconv built 
-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for 
-# the list of possible encodings.
-
-INPUT_ENCODING         = UTF-8
+INPUT                  = ./Intro.txt \
+                         ./cvTemplate.txt \
+                         ./freeTemplate.txt \
+                         ./funcTemplate.txt \
+                         ./mdTemplate.txt \
+                         ./plmdIntro.txt \
+                         ./usingDoxygen.txt \
+                         ./parsing.txt \
+                         ../src
 
 # If the value of the INPUT tag contains directories, you can use the 
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
 # and *.h) to filter out the source-files in the directories. If left 
 # blank the following patterns are tested: 
 # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
 
 FILE_PATTERNS          = 
 
@@ -579,14 +504,6 @@ EXCLUDE_SYMLINKS       = NO
 
 EXCLUDE_PATTERNS       = 
 
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
-# (namespaces, classes, functions, etc.) that should be excluded from the 
-# output. The symbol name can be a fully qualified name, a word, or if the 
-# wildcard * is used, a substring. Examples: ANamespace, AClass, 
-# AClass::ANamespace, ANamespace::*Test
-
-EXCLUDE_SYMBOLS        = 
-
 # The EXAMPLE_PATH tag can be used to specify one or more files or 
 # directories that contain example code fragments that are included (see 
 # the \include command).
@@ -660,13 +577,13 @@ INLINE_SOURCES         = NO
 
 STRIP_CODE_COMMENTS    = YES
 
-# If the REFERENCED_BY_RELATION tag is set to YES 
+# If the REFERENCED_BY_RELATION tag is set to YES (the default) 
 # then for each documented function all documented 
 # functions referencing it will be listed.
 
 REFERENCED_BY_RELATION = NO
 
-# If the REFERENCES_RELATION tag is set to YES 
+# If the REFERENCES_RELATION tag is set to YES (the default) 
 # then for each documented function all documented entities 
 # called/used by that function will be listed.
 
@@ -766,44 +683,11 @@ HTML_ALIGN_MEMBERS     = YES
 
 # If the GENERATE_HTMLHELP tag is set to YES, additional index files 
 # will be generated that can be used as input for tools like the 
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
+# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 
 # of the generated HTML documentation.
 
 GENERATE_HTMLHELP      = NO
 
-# If the GENERATE_DOCSET tag is set to YES, additional index files 
-# will be generated that can be used as input for Apple's Xcode 3 
-# integrated development environment, introduced with OSX 10.5 (Leopard). 
-# To create a documentation set, doxygen will generate a Makefile in the 
-# HTML output directory. Running make will produce the docset in that 
-# directory and running "make install" will install the docset in 
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find 
-# it at startup.
-
-GENERATE_DOCSET        = NO
-
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the 
-# feed. A documentation feed provides an umbrella under which multiple 
-# documentation sets from a single provider (such as a company or product suite) 
-# can be grouped.
-
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that 
-# should uniquely identify the documentation set bundle. This should be a 
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen 
-# will append .docset to the name.
-
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
-# documentation will contain sections that can be hidden and shown after the 
-# page has loaded. For this to work a browser that supports 
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
-
-HTML_DYNAMIC_SECTIONS  = NO
-
 # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
 # be used to specify the file name of the resulting .chm file. You 
 # can add a path in front of the file if the result should not be 
@@ -824,12 +708,6 @@ HHC_LOCATION           =
 
 GENERATE_CHI           = NO
 
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file
-# content.
-
-CHM_INDEX_ENCODING     = 
-
 # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
 # controls whether a binary table of contents is generated (YES) or a 
 # normal table of contents (NO) in the .chm file.
@@ -852,20 +730,12 @@ DISABLE_INDEX          = NO
 
 ENUM_VALUES_PER_LINE   = 4
 
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information.
-# If the tag value is set to FRAME, a side panel will be generated
-# containing a tree-like index structure (just like the one that 
+# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
+# generated containing a tree-like index structure (just like the one that 
 # is generated for HTML Help). For this to work a browser that supports 
 # JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
 # Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
-# probably better off using the HTML help feature. Other possible values 
-# for this tag are: HIERARCHIES, which will generate the Groups, Directories,
-# and Class Hiererachy pages using a tree view instead of an ordered list;
-# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
-# disables this behavior completely. For backwards compatibility with previous
-# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
-# respectively.
+# probably better off using the HTML help feature.
 
 GENERATE_TREEVIEW      = NO
 
@@ -873,15 +743,7 @@ GENERATE_TREEVIEW      = NO
 # used to set the initial width (in pixels) of the frame in which the tree 
 # is shown.
 
-TREEVIEW_WIDTH         = 250
-
-# Use this tag to change the font size of Latex formulas included 
-# as images in the HTML documentation. The default is 10. Note that 
-# when you change the font size after a successful doxygen run you need 
-# to manually remove any form_*.png images from the HTML output directory 
-# to force them to be regenerated.
-
-FORMULA_FONTSIZE       = 10
+TREEVIEW_WIDTH         = 200
 
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
@@ -1231,20 +1093,11 @@ PERL_PATH              = /usr/bin/perl
 
 CLASS_DIAGRAMS         = YES
 
-# You can define message sequence charts within doxygen comments using the \msc 
-# command. Doxygen will then run the mscgen tool (see 
-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the 
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where 
-# the mscgen tool resides. If left empty the tool is assumed to be found in the 
-# default search path.
-
-MSCGEN_PATH            = 
-
 # If set to YES, the inheritance and collaboration graphs will hide 
 # inheritance and usage relations if the target is undocumented 
 # or is not a class.
 
-HIDE_UNDOC_RELATIONS   = 
+HIDE_UNDOC_RELATIONS   = YES
 
 # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
 # available from the path. This tool is part of Graphviz, a graph visualization 
@@ -1253,24 +1106,6 @@ HIDE_UNDOC_RELATIONS   =
 
 HAVE_DOT               = YES
 
-# By default doxygen will write a font called FreeSans.ttf to the output 
-# directory and reference it in all dot files that doxygen generates. This 
-# font does not include all possible unicode characters however, so when you need 
-# these (or just want a differently looking font) you can specify the font name 
-# using DOT_FONTNAME. You need need to make sure dot is able to find the font, 
-# which can be done by putting it in a standard location or by setting the 
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
-# containing the font.
-
-DOT_FONTNAME           = FreeSans
-
-# By default doxygen will tell dot to use the output directory to look for the 
-# FreeSans.ttf font (which doxygen will put there itself). If you specify a 
-# different font using DOT_FONTNAME you can set the path where dot 
-# can find it using this tag.
-
-DOT_FONTPATH           = 
-
 # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
 # will generate a graph for each documented class showing the direct and 
 # indirect inheritance relations. Setting this tag to YES will force the 
@@ -1315,19 +1150,19 @@ INCLUDE_GRAPH          = YES
 
 INCLUDED_BY_GRAPH      = YES
 
-# If the CALL_GRAPH and HAVE_DOT options are set to YES then 
-# doxygen will generate a call dependency graph for every global function 
-# or class method. Note that enabling this option will significantly increase 
-# the time of a run. So in most cases it will be better to enable call graphs 
-# for selected functions only using the \callgraph command.
+# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
+# generate a call dependency graph for every global function or class method. 
+# Note that enabling this option will significantly increase the time of a run. 
+# So in most cases it will be better to enable call graphs for selected 
+# functions only using the \callgraph command.
 
 CALL_GRAPH             = NO
 
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then 
-# doxygen will generate a caller dependency graph for every global function 
-# or class method. Note that enabling this option will significantly increase 
-# the time of a run. So in most cases it will be better to enable caller 
-# graphs for selected functions only using the \callergraph command.
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
+# generate a caller dependency graph for every global function or class method. 
+# Note that enabling this option will significantly increase the time of a run. 
+# So in most cases it will be better to enable caller graphs for selected 
+# functions only using the \callergraph command.
 
 CALLER_GRAPH           = NO
 
@@ -1360,31 +1195,39 @@ DOT_PATH               =
 
 DOTFILE_DIRS           = 
 
-# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of 
-# nodes that will be shown in the graph. If the number of nodes in a graph 
-# becomes larger than this value, doxygen will truncate the graph, which is 
-# visualized by representing a node as a red box. Note that doxygen if the 
-# number of direct children of the root node in a graph is already larger than 
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note 
-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+MAX_DOT_GRAPH_WIDTH    = 1024
+
+# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
 
-DOT_GRAPH_MAX_NODES    = 50
+MAX_DOT_GRAPH_HEIGHT   = 1024
 
 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
 # graphs generated by dot. A depth value of 3 means that only nodes reachable 
 # from the root by following a path via at most 3 edges will be shown. Nodes 
 # that lay further from the root node will be omitted. Note that setting this 
 # option to 1 or 2 may greatly reduce the computation time needed for large 
-# code bases. Also note that the size of a graph can be further restricted by 
-# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# code bases. Also note that a graph may be further truncated if the graph's 
+# image dimensions are not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH 
+# and MAX_DOT_GRAPH_HEIGHT). If 0 is used for the depth value (the default), 
+# the graph is not depth-constrained.
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
-# background. This is enabled by default, which results in a transparent 
-# background. Warning: Depending on the platform used, enabling this option 
-# may lead to badly anti-aliased labels on the edges of a graph (i.e. they 
-# become hard to read).
+# background. This is disabled by default, which results in a white background. 
+# Warning: Depending on the platform used, enabling this option may lead to 
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to 
+# read).
 
 DOT_TRANSPARENT        = YES
 
diff --git a/developer-doc/Intro.txt b/developer-doc/Intro.txt
index 859128bd1..47cb2a4cc 100644
--- a/developer-doc/Intro.txt
+++ b/developer-doc/Intro.txt
@@ -2,6 +2,8 @@
 /**
 \mainpage A Plumed Clone
 
+This is the developer manual. Please first have a look at the <a href="../../user-doc/html/index.html"> user manual </a>.
+
 Plumed 2.0 is written in C++ and uses many of the advanced, object-oriented features of this language.  This structure makes the implementation of collective coordinates and free energy methods straightforward.  In fact, it should be possible to implement methods and collective coordinates (CV) by creating a single file and without touching any other part of the code. Futhermore, to implement new methodology does not require one to be some sort of C++ wizzard. Rather, the code has been specifically redisigned to make the implementation of new CVs and new free energy methods straightforward so as to encourage people to implement whatever new functionality they require.  This document serves then to provide an introduction as to how to go about implementing new functionality in plumed.   Within there are templates that give step by step explanation for how to implement new CVs, free energy methods and functions:    
 
 - \ref HowToAddACollectiveVariable
diff --git a/src/DumpDerivatives.cpp b/src/DumpDerivatives.cpp
index 03714939c..4f785ea92 100644
--- a/src/DumpDerivatives.cpp
+++ b/src/DumpDerivatives.cpp
@@ -9,6 +9,29 @@ namespace PLMD{
 
 //+PLUMEDOC GENERIC DUMPDERIVATIVES
 /**
+Dump the derivatives of one or more actions with respect to their input parameters
+on a file. For collective variables, these are the derivatives of the collective
+variable (or of one of its components) with respect to atom positions and to cell
+vectors (virial-like form). For functions, there are the the derivatives with respect
+the function arguments.
+
+\verbatim
+DISTANCE ATOM=1,2 LABEL=distance
+# this is writing on file deriv the derivatives of the
+# distance wrt atomic and cell coordinates
+DUMPDERIVATIVES ARG=distance STRIDE=100 FILE=deriv
+\endverbatim
+
+It can print at the same time derivatives of more than one object, but they should
+have the same number of parameters. Typically, this can be used to test numerical
+derivatives againts analytical ones
+
+\verbatim
+DISTANCE ATOM=1,2 LABEL=distance
+DISTANCE ATOM=1,2 LABEL=distanceN NUMERICAL_DERIVATIVES
+DUMPDERIVATIVES ARG=distance,distanceN STRIDE=1 FILE=deriv
+\endverbatim
+
 
 */
 //+ENDPLUMEDOC
diff --git a/src/Units.cpp b/src/Units.cpp
index 229dcb133..5bc6ce91c 100644
--- a/src/Units.cpp
+++ b/src/Units.cpp
@@ -6,7 +6,7 @@ using namespace std;
 
 namespace PLMD{
 
-//+PLUMEDOC GENERIC UNITS
+//+PLUMEDOC SETUP UNITS
 /**
 Sets internal units.
 
diff --git a/user-doc/.gitignore b/user-doc/.gitignore
index 628872b9e..13a384553 100644
--- a/user-doc/.gitignore
+++ b/user-doc/.gitignore
@@ -1,6 +1,6 @@
 /html
 /latex
 /*.tmp
-/DocPostproc.txt
 /automatic
+/*PP.txt
 
diff --git a/user-doc/AdvancedTopics.txt b/user-doc/AdvancedTopics.txt
new file mode 100644
index 000000000..553f4281b
--- /dev/null
+++ b/user-doc/AdvancedTopics.txt
@@ -0,0 +1,20 @@
+/**
+\page AdvancedTopics Advanced topics
+
+\section AdvancedInput Advanced input file
+
+Inclusion of other files (\ref INCLUDE)
+
+Loading libraries at runtime (\ref LOAD)
+
+\section AtomGroups Atom groups
+
+\section AtomAlignment Atom alignement
+
+\section ReplicaExchange Replica exchange
+
+Discuss the way input is provided.
+A different bias is allowed on the different replicas.
+
+*/
+
diff --git a/user-doc/BasicUsage.txt b/user-doc/BasicUsage.txt
new file mode 100644
index 000000000..2cc62f90e
--- /dev/null
+++ b/user-doc/BasicUsage.txt
@@ -0,0 +1,37 @@
+/**
+\page BasicUsage Basic usage
+
+\section HowToActivatePlumed How to activate Plumed
+
+[discuss the different options for supported codes]
+
+\section TheInputFile The input file
+
+Directives
+
+Continued lines
+
+Labeling the directives
+
+Units (see \ref UNITS).
+
+\section MonitoringSimulationsI Monitoring simulations I: Collective variables
+
+Example with \ref DISTANCE and \ref PRINT
+
+For more collective variables, see \ref Colvar
+
+\section MonitoringSimulationsII Monitoring simulations II: Functions
+
+Example with \ref COMBINE
+
+For more, see \ref Function
+
+\section BiasingSimulations Biasing simulations
+
+Example with \ref RESTRAINT
+
+For more, see \ref Bias
+
+*/
+
diff --git a/user-doc/Bias.txt b/user-doc/Bias.txt
new file mode 100644
index 000000000..0cd697401
--- /dev/null
+++ b/user-doc/Bias.txt
@@ -0,0 +1,32 @@
+/**
+
+\page Bias Bias
+
+The following keywords are available for all directives of this section:
+
+- ARG:
+  This keyword is used to specify on which variables the bias is acting.
+  It is a comma-separated list of labels. Here is an example with \ref RESTRAINT
+\verbatim
+DISTANCE  ATOMS=1,5 LABEL=d1
+DISTANCE  ATOMS=2,6 LABEL=d2
+RESTRAINT ARG=d1,d2 AT=5.0,6.0 KAPPA=100.0,50.0
+\endverbatim
+- STRIDE:
+  PLUMED implements a multiple-time-step scheme. Using the keyword STRIDE
+  one can set how frequently the bias should be applied, in units of time steps.
+  It can be used to decrease the impact of variables which are computationally heavy.
+  Here is an example with \ref RESTRAINT
+\verbatim
+DISTANCE  ATOMS=1,5 LABEL=d1
+RESTRAINT ARG=d1 AT=5.0 KAPPA=100.0 STRIDE=2
+\endverbatim
+
+\attention The rest of this page is automatically generated from the source
+files
+
+
+@BIAS@
+
+*/
+
diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt
new file mode 100644
index 000000000..e2b58f269
--- /dev/null
+++ b/user-doc/Colvar.txt
@@ -0,0 +1,20 @@
+/**
+
+\page Colvar Collective Variables
+
+The following keywords are available for all directives of this section:
+- NUMERICAL_DERIVATIVES:
+  This flag can be used to enforce calculation of derivatives with respect to
+  atom positions and cell vectors by means of numerical differences
+\verbatim
+DISTANCE  ATOMS=1,5 LABEL=d1 NUMERICAL_DERIVATIVES
+\endverbatim
+
+\attention The rest of this page is automatically generated from the source
+files
+
+
+@COLVAR@
+
+*/
+
diff --git a/user-doc/Doc.txt b/user-doc/Doc.txt
deleted file mode 100644
index 2b779464e..000000000
--- a/user-doc/Doc.txt
+++ /dev/null
@@ -1,176 +0,0 @@
-/**
-\mainpage User guide
-
-Introduction
-
-\section WhatsNew What's new
-
-\subsection NewInputSyntax New syntax for the input file
-
-Briefly describe the difference between old and new input
-
-\subsection NewFeatures List of new features
-
-List of new features
-
-\section Topics
-
-\subpage Installation
-
-\subpage BasicUsage
-
-\subpage AdvancedTopics
-
-\subpage Tools
-
-\page Reference
-
-List of directives to manipulate input: \subpage InputDirectives
-
-List of collective variables: \subpage Colvar
-
-List of functions: \subpage Function
-
-List of free energy methods: \subpage Bias
-
-List of general purpose directives: \subpage GenericDirectives
-
-\page Installation
-
-\section CompilingPlumed Compiling Plumed
-
-How to configure
-
-How to compile
-
-\section Patching Patching your MD code
-
-\section Testing Testing the installation
-
-\section InstallingPlumedOnAMainframe Installing Plumed on a mainframe
-
-Notes on shared libraries, modules, etc.
-
-\page BasicUsage Basic usage
-
-\section HowToActivatePlumed How to activate Plumed
-
-\section TheInputFile The input file
-
-Directives
-
-Continued lines
-
-Labeling the directives
-
-Units (see \ref UNITS).
-
-\section MonitoringSimulationsI Monitoring simulations I: Collective variables
-
-Example with \ref DISTANCE and \ref PRINT
-
-For more collective variables, see \ref Colvar
-
-\section MonitoringSimulationsII Monitoring simulations II: Functions
-
-Example with \ref COMBINE
-
-For more, see \ref Function
-
-\section BiasingSimulations Biasing simulations
-
-Example with \ref RESTRAINT
-
-For more, see \ref Bias
-
-\page AdvancedTopics Advanced topics
-
-\section AdvancedInput Advanced input file
-
-Inclusion of other files
-
-Loading libraries
-
-\section AtomGroups Atom groups
-
-\section AtomAlignment Atom alignement
-
-\section ReplicaExchange Replica exchange
-
-Discuss the way input is provided.
-A different bias is allowed on the different replicas.
-
-\page Tools
-
-\page InputDirectives Input directives
-
-These are directives which can be used to manipulate the input file.
-
-\section Comments
-
-\section ContinuationLines Continuation lines
-
-\section INCLUDE
-
-\section LOAD
-
-\section ENDPLUMED
-
-\page Colvar Collective Variables
-
-\attention This page should be automatically generated from the .cpp files
-
-@COLVAR@
-
-\page Function Functions
-
-The following keywords are available for all directives of this section:
-- ARG:
-  This keyword is used to specify on which variables the function is computed
-  It is a comma-separated list of labels. Here is an example with \ref COMBINE
-\verbatim
-DISTANCE  ATOMS=1,5 LABEL=d1
-DISTANCE  ATOMS=2,6 LABEL=d2
-COMBINE   ARG=d1,d2 POWERS=2
-\endverbatim
-
-\attention This page should be automatically generated from the .cpp files
-
-@FUNCTION@
-
-\page Bias 
-
-The following keywords are available for all directives of this section:
-
-- ARG:
-  This keyword is used to specify on which variables the bias is acting.
-  It is a comma-separated list of labels. Here is an example with \ref RESTRAINT
-\verbatim
-DISTANCE  ATOMS=1,5 LABEL=d1
-DISTANCE  ATOMS=2,6 LABEL=d2
-RESTRAINT ARG=d1,d2 AT=5.0,6.0 KAPPA=100.0,50.0
-\endverbatim
-- STRIDE:
-  PLUMED implements a multiple-time-step scheme. Using the keyword STRIDE
-  one can set how frequently the bias should be applied, in units of time steps.
-  It can be used to decrease the impact of variables which are computationally heavy.
-  Here is an example with \ref RESTRAINT
-\verbatim
-DISTANCE  ATOMS=1,5 LABEL=d1
-RESTRAINT ARG=d1 AT=5.0 KAPPA=100.0 STRIDE=2
-\endverbatim
-
-\attention This page should be automatically generated from the .cpp files
-
-@BIAS@
-
-\page GenericDirectives Generic directives
-
-\attention The following pages should be automatically generated from the .cpp files
-
-@GENERIC@
-
-
-
-*/
-
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index d119df1d3..49804fd5b 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -1,4 +1,4 @@
-# Doxyfile 1.7.2
+# Doxyfile 1.4.7
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project
@@ -14,24 +14,16 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 
-# This tag specifies the encoding used for all characters in the config file 
-# that follow. The default is UTF-8 which is also the encoding used for all 
-# text before the first occurrence of this tag. Doxygen uses libiconv (or the 
-# iconv built into libc) for the transcoding. See 
-# http://www.gnu.org/software/libiconv for the list of possible encodings.
-
-DOXYFILE_ENCODING      = UTF-8
-
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
 # by quotes) that should identify the project.
 
-PROJECT_NAME           =  "A PLUMED CLONE"
+PROJECT_NAME           = "Plumed 2.0: user manual"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. 
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         =
+PROJECT_NUMBER         = 
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
 # base path where the generated documentation will be put. 
@@ -53,15 +45,24 @@ CREATE_SUBDIRS         = NO
 # documentation generated by doxygen is written. Doxygen will use this 
 # information to generate all constant output in the proper language. 
 # The default language is English, other supported languages are: 
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
-# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, 
-# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English 
-# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, 
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, 
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, 
+# Dutch, Finnish, French, German, Greek, Hungarian, Italian, Japanese, 
+# Japanese-en (Japanese with English messages), Korean, Korean-en, Norwegian, 
+# Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, 
+# Swedish, and Ukrainian.
 
 OUTPUT_LANGUAGE        = English
 
+# This tag can be used to specify the encoding used in the generated output. 
+# The encoding is not always determined by the language that is chosen, 
+# but also whether or not the output is meant for Windows or non-Windows users. 
+# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES 
+# forces the Windows encoding (this is the default for the Windows binary), 
+# whereas setting the tag to NO uses a Unix-style encoding (the default for 
+# all platforms other than Windows).
+
+USE_WINDOWS_ENCODING   = NO
+
 # If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
 # include brief member descriptions after the members that are listed in 
 # the file and class documentation (similar to JavaDoc). 
@@ -126,7 +127,7 @@ STRIP_FROM_PATH        =
 STRIP_FROM_INC_PATH    = 
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
-# (but less readable) file names. This can be useful if your file system 
+# (but less readable) file names. This can be useful is your file systems 
 # doesn't support long names like on DOS, Mac, or CD-ROM.
 
 SHORT_NAMES            = NO
@@ -134,19 +135,11 @@ SHORT_NAMES            = NO
 # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
 # will interpret the first line (until the first dot) of a JavaDoc-style 
 # comment as the brief description. If set to NO, the JavaDoc 
-# comments will behave just like regular Qt-style comments 
-# (thus requiring an explicit @brief command for a brief description.)
+# comments will behave just like the Qt-style comments (thus requiring an 
+# explicit @brief command for a brief description.
 
 JAVADOC_AUTOBRIEF      = NO
 
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will 
-# interpret the first line (until the first dot) of a Qt-style 
-# comment as the brief description. If set to NO, the comments 
-# will behave just like regular Qt-style comments (thus requiring 
-# an explicit \brief command for a brief description.)
-
-QT_AUTOBRIEF           = NO
-
 # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
 # treat a multi-line C++ special comment block (i.e. a block of //! or /// 
 # comments) as a brief description. This used to be the default behaviour. 
@@ -155,6 +148,13 @@ QT_AUTOBRIEF           = NO
 
 MULTILINE_CPP_IS_BRIEF = NO
 
+# If the DETAILS_AT_TOP tag is set to YES then Doxygen 
+# will output the detailed description near the top, like JavaDoc.
+# If set to NO, the detailed description appears after the member 
+# documentation.
+
+DETAILS_AT_TOP         = NO
+
 # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
 # member inherits the documentation from any documented member that it 
 # re-implements.
@@ -189,65 +189,21 @@ ALIASES                =
 OPTIMIZE_OUTPUT_FOR_C  = NO
 
 # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
-# sources only. Doxygen will then generate output that is more tailored for 
-# Java. For instance, namespaces will be presented as packages, qualified 
-# scopes will look different, etc.
+# sources only. Doxygen will then generate output that is more tailored for Java. 
+# For instance, namespaces will be presented as packages, qualified scopes 
+# will look different, etc.
 
 OPTIMIZE_OUTPUT_JAVA   = NO
 
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran 
-# sources only. Doxygen will then generate output that is more tailored for 
-# Fortran.
-
-OPTIMIZE_FOR_FORTRAN   = NO
-
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL 
-# sources. Doxygen will then generate output that is tailored for 
-# VHDL.
-
-OPTIMIZE_OUTPUT_VHDL   = NO
-
-# Doxygen selects the parser to use depending on the extension of the files it 
-# parses. With this tag you can assign which parser to use for a given extension. 
-# Doxygen has a built-in mapping, but you can override or extend it using this 
-# tag. The format is ext=language, where ext is a file extension, and language 
-# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C, 
-# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make 
-# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C 
-# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions 
-# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
-
-EXTENSION_MAPPING      = 
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want 
-# to include (a tag file for) the STL sources as input, then you should 
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to 
+# include (a tag file for) the STL sources as input, then you should 
 # set this tag to YES in order to let doxygen match functions declarations and 
 # definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
-# func(std::string) {}). This also makes the inheritance and collaboration 
+# func(std::string) {}). This also make the inheritance and collaboration 
 # diagrams that involve STL classes more complete and accurate.
 
 BUILTIN_STL_SUPPORT    = NO
 
-# If you use Microsoft's C++/CLI language, you should set this option to YES to 
-# enable parsing support.
-
-CPP_CLI_SUPPORT        = NO
-
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. 
-# Doxygen will parse them like normal C++ but will assume all classes use public 
-# instead of private inheritance when no explicit protection keyword is present.
-
-SIP_SUPPORT            = NO
-
-# For Microsoft's IDL there are propget and propput attributes to indicate getter 
-# and setter methods for a property. Setting this option to YES (the default) 
-# will make doxygen replace the get and set methods by a property in the 
-# documentation. This will only work if the methods are indeed getting or 
-# setting a simple type. If this is not the case, or you want to show the 
-# methods anyway, you should set this option to NO.
-
-IDL_PROPERTY_SUPPORT   = YES
-
 # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
 # tag is set to YES, then doxygen will reuse the documentation of the first 
 # member in the group (if any) for the other members of the group. By default 
@@ -263,32 +219,6 @@ DISTRIBUTE_GROUP_DOC   = NO
 
 SUBGROUPING            = YES
 
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
-# is documented as struct, union, or enum with the name of the typedef. So 
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct 
-# with name TypeT. When disabled the typedef will appear as a member of a file, 
-# namespace, or class. And the struct will be named TypeS. This can typically 
-# be useful for C code in case the coding convention dictates that all compound 
-# types are typedef'ed and only the typedef is referenced, never the tag name.
-
-TYPEDEF_HIDES_STRUCT   = NO
-
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to 
-# determine which symbols to keep in memory and which to flush to disk. 
-# When the cache is full, less often used symbols will be written to disk. 
-# For small to medium size projects (<1000 input files) the default value is 
-# probably good enough. For larger projects a too small cache size can cause 
-# doxygen to be busy swapping symbols to and from disk most of the time 
-# causing a significant performance penality. 
-# If the system has enough physical memory increasing the cache will improve the 
-# performance by keeping more symbols in memory. Note that the value works on 
-# a logarithmic scale so increasing the size by one will roughly double the 
-# memory usage. The cache size is given by this formula: 
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, 
-# corresponding to a cache size of 2^16 = 65536 symbols
-
-SYMBOL_CACHE_SIZE      = 0
-
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -323,14 +253,6 @@ EXTRACT_LOCAL_CLASSES  = YES
 
 EXTRACT_LOCAL_METHODS  = NO
 
-# If this flag is set to YES, the members of anonymous namespaces will be 
-# extracted and appear in the documentation as a namespace called 
-# 'anonymous_namespace{file}', where file will be replaced with the base 
-# name of the file that contains the anonymous namespace. By default 
-# anonymous namespaces are hidden.
-
-EXTRACT_ANON_NSPACES   = NO
-
 # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
 # undocumented members of documented classes, files or namespaces. 
 # If set to NO (the default) these members will be included in the 
@@ -387,12 +309,6 @@ HIDE_SCOPE_NAMES       = NO
 
 SHOW_INCLUDE_FILES     = YES
 
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen 
-# will list include files with double quotes in the documentation 
-# rather than with sharp brackets.
-
-FORCE_LOCAL_INCLUDES   = NO
-
 # If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
 # is inserted in the documentation for inline members.
 
@@ -412,27 +328,11 @@ SORT_MEMBER_DOCS       = YES
 
 SORT_BRIEF_DOCS        = NO
 
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen 
-# will sort the (brief and detailed) documentation of class members so that 
-# constructors and destructors are listed first. If set to NO (the default) 
-# the constructors will appear in the respective orders defined by 
-# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. 
-# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO 
-# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
-
-SORT_MEMBERS_CTORS_1ST = NO
-
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the 
-# hierarchy of group names into alphabetical order. If set to NO (the default) 
-# the group names will appear in their defined order.
-
-SORT_GROUP_NAMES       = NO
-
 # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
 # sorted by fully-qualified names, including namespaces. If set to 
 # NO (the default), the class list will be sorted only by class name, 
 # not including the namespace part. 
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. 
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
 # Note: This option applies only to the class list, not to the 
 # alphabetical list.
 
@@ -468,10 +368,10 @@ GENERATE_DEPRECATEDLIST= YES
 ENABLED_SECTIONS       = 
 
 # The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
-# the initial value of a variable or macro consists of for it to appear in 
+# the initial value of a variable or define consists of for it to appear in 
 # the documentation. If the initializer consists of more lines than specified 
 # here it will be hidden. Use a value of 0 to hide initializers completely. 
-# The appearance of the initializer of individual variables and macros in the 
+# The appearance of the initializer of individual variables and defines in the 
 # documentation can be controlled using \showinitializer or \hideinitializer 
 # command in the documentation regardless of this setting.
 
@@ -489,21 +389,9 @@ SHOW_USED_FILES        = YES
 
 SHOW_DIRECTORIES       = NO
 
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page. 
-# This will remove the Files entry from the Quick Index and from the 
-# Folder Tree View (if specified). The default is YES.
-
-SHOW_FILES             = YES
-
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the 
-# Namespaces page.  This will remove the Namespaces entry from the Quick Index 
-# and from the Folder Tree View (if specified). The default is YES.
-
-SHOW_NAMESPACES        = YES
-
 # The FILE_VERSION_FILTER tag can be used to specify a program or script that 
-# doxygen should invoke to get the current version for each file (typically from 
-# the version control system). Doxygen will invoke the program by executing (via 
+# doxygen should invoke to get the current version for each file (typically from the 
+# version control system). Doxygen will invoke the program by executing (via 
 # popen()) the command <command> <input-file>, where <command> is the value of 
 # the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
 # provided by doxygen. Whatever the program writes to standard output 
@@ -511,15 +399,6 @@ SHOW_NAMESPACES        = YES
 
 FILE_VERSION_FILTER    = 
 
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed 
-# by doxygen. The layout file controls the global structure of the generated 
-# output files in an output format independent way. The create the layout file 
-# that represents doxygen's defaults, run doxygen with the -l option. 
-# You can optionally specify a file name after the option, if omitted 
-# DoxygenLayout.xml will be used as the name of the layout file.
-
-LAYOUT_FILE            = 
-
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
@@ -548,7 +427,7 @@ WARN_IF_UNDOCUMENTED   = YES
 
 WARN_IF_DOC_ERROR      = YES
 
-# The WARN_NO_PARAMDOC option can be enabled to get warnings for 
+# This WARN_NO_PARAMDOC option can be abled to get warnings for 
 # functions that are documented, but have no documentation for their parameters 
 # or return value. If set to NO (the default) doxygen will only warn about 
 # wrong or incomplete parameter documentation, but not about the absence of 
@@ -580,23 +459,26 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = DocPostproc.txt
-
-# This tag can be used to specify the character encoding of the source files 
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
-# also the default input encoding. Doxygen uses libiconv (or the iconv built 
-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for 
-# the list of possible encodings.
-
-INPUT_ENCODING         = UTF-8
+INPUT                  = Intro.txt \
+                         WhatsNew.txt \
+                         Installation.txt \
+                         BasicUsage.txt \
+                         AdvancedTopics.txt \
+                         Tools.txt \
+                         Reference.txt \
+                         InputDirectivesPP.txt \
+                         SetupPP.txt \
+                         ColvarPP.txt \
+                         FunctionsPP.txt \
+                         BiasPP.txt \
+                         GenericDirectivesPP.txt
 
 # If the value of the INPUT tag contains directories, you can use the 
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
 # and *.h) to filter out the source-files in the directories. If left 
 # blank the following patterns are tested: 
-# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh 
-# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py 
-# *.f90 *.f *.vhd *.vhdl
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
 
 FILE_PATTERNS          = 
 
@@ -626,14 +508,6 @@ EXCLUDE_SYMLINKS       = NO
 
 EXCLUDE_PATTERNS       = 
 
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
-# (namespaces, classes, functions, etc.) that should be excluded from the 
-# output. The symbol name can be a fully qualified name, a word, or if the 
-# wildcard * is used, a substring. Examples: ANamespace, AClass, 
-# AClass::ANamespace, ANamespace::*Test
-
-EXCLUDE_SYMBOLS        = 
-
 # The EXAMPLE_PATH tag can be used to specify one or more files or 
 # directories that contain example code fragments that are included (see 
 # the \include command).
@@ -707,22 +581,22 @@ INLINE_SOURCES         = NO
 
 STRIP_CODE_COMMENTS    = YES
 
-# If the REFERENCED_BY_RELATION tag is set to YES 
+# If the REFERENCED_BY_RELATION tag is set to YES (the default) 
 # then for each documented function all documented 
 # functions referencing it will be listed.
 
 REFERENCED_BY_RELATION = NO
 
-# If the REFERENCES_RELATION tag is set to YES 
+# If the REFERENCES_RELATION tag is set to YES (the default) 
 # then for each documented function all documented entities 
 # called/used by that function will be listed.
 
 REFERENCES_RELATION    = NO
 
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) 
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from 
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will 
-# link to the source code.  Otherwise they will link to the documentation.
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code.  Otherwise they will link to the documentstion.
 
 REFERENCES_LINK_SOURCE = YES
 
@@ -805,91 +679,15 @@ HTML_FOOTER            =
 
 HTML_STYLESHEET        = 
 
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. 
-# Doxygen will adjust the colors in the stylesheet and background images 
-# according to this color. Hue is specified as an angle on a colorwheel, 
-# see http://en.wikipedia.org/wiki/Hue for more information. 
-# For instance the value 0 represents red, 60 is yellow, 120 is green, 
-# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. 
-# The allowed range is 0 to 359.
-
-HTML_COLORSTYLE_HUE    = 220
-
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of 
-# the colors in the HTML output. For a value of 0 the output will use 
-# grayscales only. A value of 255 will produce the most vivid colors.
-
-HTML_COLORSTYLE_SAT    = 100
-
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to 
-# the luminance component of the colors in the HTML output. Values below 
-# 100 gradually make the output lighter, whereas values above 100 make 
-# the output darker. The value divided by 100 is the actual gamma applied, 
-# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, 
-# and 100 does not change the gamma.
-
-HTML_COLORSTYLE_GAMMA  = 80
-
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML 
-# page will contain the date and time when the page was generated. Setting 
-# this to NO can help when comparing the output of multiple runs.
-
-HTML_TIMESTAMP         = YES
-
 # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
 # files or namespaces will be aligned in HTML using tables. If set to 
 # NO a bullet list will be used.
 
 HTML_ALIGN_MEMBERS     = YES
 
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
-# documentation will contain sections that can be hidden and shown after the 
-# page has loaded. For this to work a browser that supports 
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
-
-HTML_DYNAMIC_SECTIONS  = NO
-
-# If the GENERATE_DOCSET tag is set to YES, additional index files 
-# will be generated that can be used as input for Apple's Xcode 3 
-# integrated development environment, introduced with OSX 10.5 (Leopard). 
-# To create a documentation set, doxygen will generate a Makefile in the 
-# HTML output directory. Running make will produce the docset in that 
-# directory and running "make install" will install the docset in 
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find 
-# it at startup. 
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html 
-# for more information.
-
-GENERATE_DOCSET        = NO
-
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the 
-# feed. A documentation feed provides an umbrella under which multiple 
-# documentation sets from a single provider (such as a company or product suite) 
-# can be grouped.
-
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that 
-# should uniquely identify the documentation set bundle. This should be a 
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen 
-# will append .docset to the name.
-
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify 
-# the documentation publisher. This should be a reverse domain-name style 
-# string, e.g. com.mycompany.MyDocSet.documentation.
-
-DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
-
-# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
-
-DOCSET_PUBLISHER_NAME  = Publisher
-
 # If the GENERATE_HTMLHELP tag is set to YES, additional index files 
 # will be generated that can be used as input for tools like the 
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
+# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 
 # of the generated HTML documentation.
 
 GENERATE_HTMLHELP      = NO
@@ -914,12 +712,6 @@ HHC_LOCATION           =
 
 GENERATE_CHI           = NO
 
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING 
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file 
-# content.
-
-CHM_INDEX_ENCODING     = 
-
 # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
 # controls whether a binary table of contents is generated (YES) or a 
 # normal table of contents (NO) in the .chm file.
@@ -931,171 +723,32 @@ BINARY_TOC             = NO
 
 TOC_EXPAND             = NO
 
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and 
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated 
-# that can be used as input for Qt's qhelpgenerator to generate a 
-# Qt Compressed Help (.qch) of the generated HTML documentation.
-
-GENERATE_QHP           = NO
-
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can 
-# be used to specify the file name of the resulting .qch file. 
-# The path specified is relative to the HTML output folder.
-
-QCH_FILE               = 
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating 
-# Qt Help Project output. For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#namespace
-
-QHP_NAMESPACE          = org.doxygen.Project
-
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating 
-# Qt Help Project output. For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#virtual-folders
-
-QHP_VIRTUAL_FOLDER     = doc
-
-# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to 
-# add. For more information please see 
-# http://doc.trolltech.com/qthelpproject.html#custom-filters
-
-QHP_CUST_FILTER_NAME   = 
-
-# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the 
-# custom filter to add. For more information please see 
-# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters"> 
-# Qt Help Project / Custom Filters</a>.
-
-QHP_CUST_FILTER_ATTRS  = 
-
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this 
-# project's 
-# filter section matches. 
-# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes"> 
-# Qt Help Project / Filter Attributes</a>.
-
-QHP_SECT_FILTER_ATTRS  = 
-
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can 
-# be used to specify the location of Qt's qhelpgenerator. 
-# If non-empty doxygen will try to run qhelpgenerator on the generated 
-# .qhp file.
-
-QHG_LOCATION           = 
-
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files  
-# will be generated, which together with the HTML files, form an Eclipse help 
-# plugin. To install this plugin and make it available under the help contents 
-# menu in Eclipse, the contents of the directory containing the HTML and XML 
-# files needs to be copied into the plugins directory of eclipse. The name of 
-# the directory within the plugins directory should be the same as 
-# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before 
-# the help appears.
-
-GENERATE_ECLIPSEHELP   = NO
-
-# A unique identifier for the eclipse help plugin. When installing the plugin 
-# the directory name containing the HTML and XML files should also have 
-# this name.
-
-ECLIPSE_DOC_ID         = org.doxygen.Project
-
 # The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
 # top of each HTML page. The value NO (the default) enables the index and 
 # the value YES disables it.
 
 DISABLE_INDEX          = NO
 
-# This tag can be used to set the number of enum values (range [0,1..20]) 
-# that doxygen will group on one line in the generated HTML documentation. 
-# Note that a value of 0 will completely suppress the enum values from
-# appearing in the overview section.
+# This tag can be used to set the number of enum values (range [1..20]) 
+# that doxygen will group on one line in the generated HTML documentation.
 
 ENUM_VALUES_PER_LINE   = 4
 
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index 
-# structure should be generated to display hierarchical information. 
-# If the tag value is set to YES, a side panel will be generated 
-# containing a tree-like index structure (just like the one that 
+# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
+# generated containing a tree-like index structure (just like the one that 
 # is generated for HTML Help). For this to work a browser that supports 
-# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). 
-# Windows users are probably better off using the HTML help feature.
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
+# probably better off using the HTML help feature.
 
 GENERATE_TREEVIEW      = YES
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, 
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
 # used to set the initial width (in pixels) of the frame in which the tree 
 # is shown.
 
 TREEVIEW_WIDTH         = 200
 
-# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open 
-# links to external symbols imported via tag files in a separate window.
-
-EXT_LINKS_IN_WINDOW    = NO
-
-# Use this tag to change the font size of Latex formulas included 
-# as images in the HTML documentation. The default is 10. Note that 
-# when you change the font size after a successful doxygen run you need 
-# to manually remove any form_*.png images from the HTML output directory 
-# to force them to be regenerated.
-
-FORMULA_FONTSIZE       = 10
-
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images 
-# generated for formulas are transparent PNGs. Transparent PNGs are 
-# not supported properly for IE 6.0, but are supported on all modern browsers. 
-# Note that when changing this option you need to delete any form_*.png files 
-# in the HTML output before the changes have effect.
-
-FORMULA_TRANSPARENT    = YES
-
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax 
-# (see http://www.mathjax.org) which uses client side Javascript for the 
-# rendering instead of using prerendered bitmaps. Use this if you do not 
-# have LaTeX installed or if you want to formulas look prettier in the HTML 
-# output. When enabled you also need to install MathJax separately and 
-# configure the path to it using the MATHJAX_RELPATH option.
-
-USE_MATHJAX            = NO
-
-# When MathJax is enabled you need to specify the location relative to the 
-# HTML output directory using the MATHJAX_RELPATH option. The destination 
-# directory should contain the MathJax.js script. For instance, if the mathjax 
-# directory is located at the same level as the HTML output directory, then 
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the
-# mathjax.org site, so you can quickly see the result without installing 
-# MathJax, but it is strongly recommended to install a local copy of MathJax 
-# before deployment.
-
-MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
-
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box 
-# for the HTML output. The underlying search engine uses javascript 
-# and DHTML and should work on any modern browser. Note that when using 
-# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets 
-# (GENERATE_DOCSET) there is already a search function so this one should 
-# typically be disabled. For large projects the javascript based search engine 
-# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
-
-SEARCHENGINE           = NO
-
-# When the SERVER_BASED_SEARCH tag is enabled the search engine will be 
-# implemented using a PHP enabled web server instead of at the web client 
-# using Javascript. Doxygen will generate the search PHP script and index 
-# file to put on the web server. The advantage of the server 
-# based approach is that it scales better to large projects and allows 
-# full text search. The disadvantages are that it is more difficult to setup 
-# and does not have live searching capabilities.
-
-SERVER_BASED_SEARCH    = NO
-
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
@@ -1112,10 +765,7 @@ GENERATE_LATEX         = YES
 LATEX_OUTPUT           = latex
 
 # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
-# invoked. If left blank `latex' will be used as the default command name. 
-# Note that when enabling USE_PDFLATEX this option is only used for 
-# generating bitmaps for formulas in the HTML output, but not in the 
-# Makefile that is written to the output directory.
+# invoked. If left blank `latex' will be used as the default command name.
 
 LATEX_CMD_NAME         = latex
 
@@ -1132,7 +782,7 @@ MAKEINDEX_CMD_NAME     = makeindex
 COMPACT_LATEX          = NO
 
 # The PAPER_TYPE tag can be used to set the paper type that is used 
-# by the printer. Possible values are: a4, letter, legal and 
+# by the printer. Possible values are: a4, a4wide, letter, legal and 
 # executive. If left blank a4wide will be used.
 
 PAPER_TYPE             = a4wide
@@ -1175,13 +825,6 @@ LATEX_BATCHMODE        = NO
 
 LATEX_HIDE_INDICES     = NO
 
-# If LATEX_SOURCE_CODE is set to YES then doxygen will include 
-# source code with syntax highlighting in the LaTeX output. 
-# Note that which sources are shown also depends on other settings 
-# such as SOURCE_BROWSER.
-
-LATEX_SOURCE_CODE      = NO
-
 #---------------------------------------------------------------------------
 # configuration options related to the RTF output
 #---------------------------------------------------------------------------
@@ -1333,7 +976,7 @@ PERLMOD_PRETTY         = YES
 PERLMOD_MAKEVAR_PREFIX = 
 
 #---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
+# Configuration options related to the preprocessor   
 #---------------------------------------------------------------------------
 
 # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
@@ -1399,7 +1042,7 @@ EXPAND_AS_DEFINED      =
 SKIP_FUNCTION_MACROS   = YES
 
 #---------------------------------------------------------------------------
-# Configuration::additions related to external references
+# Configuration::additions related to external references   
 #---------------------------------------------------------------------------
 
 # The TAGFILES option can be used to specify one or more tagfiles. 
@@ -1411,9 +1054,9 @@ SKIP_FUNCTION_MACROS   = YES
 #   TAGFILES = file1=loc1 "file2 = loc2" ... 
 # where "loc1" and "loc2" can be relative or absolute paths or 
 # URLs. If a location is present for each tag, the installdox tool 
-# does not have to be run to correct the links. 
-# Note that each tag file must have a unique name 
-# (where the name does NOT include the path) 
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
 # If a tag file is not located in the directory in which doxygen 
 # is run, you must also specify the path to the tagfile here.
 
@@ -1442,26 +1085,18 @@ EXTERNAL_GROUPS        = YES
 PERL_PATH              = /usr/bin/perl
 
 #---------------------------------------------------------------------------
-# Configuration options related to the dot tool
+# Configuration options related to the dot tool   
 #---------------------------------------------------------------------------
 
 # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
 # generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base 
 # or super classes. Setting the tag to NO turns the diagrams off. Note that 
-# this option also works with HAVE_DOT disabled, but it is recommended to 
-# install and use dot, since it yields more powerful graphs.
+# this option is superseded by the HAVE_DOT option below. This is only a 
+# fallback. It is recommended to install and use dot, since it yields more 
+# powerful graphs.
 
 CLASS_DIAGRAMS         = YES
 
-# You can define message sequence charts within doxygen comments using the \msc 
-# command. Doxygen will then run the mscgen tool (see 
-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the 
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where 
-# the mscgen tool resides. If left empty the tool is assumed to be found in the 
-# default search path.
-
-MSCGEN_PATH            = 
-
 # If set to YES, the inheritance and collaboration graphs will hide 
 # inheritance and usage relations if the target is undocumented 
 # or is not a class.
@@ -1473,38 +1108,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # toolkit from AT&T and Lucent Bell Labs. The other options in this section 
 # have no effect if this option is set to NO (the default)
 
-HAVE_DOT               = NO
-
-# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is 
-# allowed to run in parallel. When set to 0 (the default) doxygen will 
-# base this on the number of processors available in the system. You can set it 
-# explicitly to a value larger than 0 to get control over the balance 
-# between CPU load and processing speed.
-
-DOT_NUM_THREADS        = 0
-
-# By default doxygen will write a font called FreeSans.ttf to the output 
-# directory and reference it in all dot files that doxygen generates. This 
-# font does not include all possible unicode characters however, so when you need 
-# these (or just want a differently looking font) you can specify the font name 
-# using DOT_FONTNAME. You need need to make sure dot is able to find the font, 
-# which can be done by putting it in a standard location or by setting the 
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
-# containing the font.
-
-DOT_FONTNAME           = FreeSans
-
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
-# The default size is 10pt.
-
-DOT_FONTSIZE           = 10
-
-# By default doxygen will tell dot to use the output directory to look for the 
-# FreeSans.ttf font (which doxygen will put there itself). If you specify a 
-# different font using DOT_FONTNAME you can set the path where dot 
-# can find it using this tag.
-
-DOT_FONTPATH           = 
+HAVE_DOT               = YES
 
 # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
 # will generate a graph for each documented class showing the direct and 
@@ -1518,7 +1122,7 @@ CLASS_GRAPH            = YES
 # indirect implementation dependencies (inheritance, containment, and 
 # class references variables) of the class with other documented classes.
 
-COLLABORATION_GRAPH    = YES
+COLLABORATION_GRAPH    = NO
 
 # If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen 
 # will generate a graph for groups, showing the direct groups dependencies
@@ -1534,7 +1138,7 @@ UML_LOOK               = NO
 # If set to YES, the inheritance and collaboration graphs will show the 
 # relations between templates and their instances.
 
-TEMPLATE_RELATIONS     = NO
+TEMPLATE_RELATIONS     = YES
 
 # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
 # tags are set to YES then doxygen will generate a graph for each documented 
@@ -1550,36 +1154,36 @@ INCLUDE_GRAPH          = YES
 
 INCLUDED_BY_GRAPH      = YES
 
-# If the CALL_GRAPH and HAVE_DOT options are set to YES then 
-# doxygen will generate a call dependency graph for every global function 
-# or class method. Note that enabling this option will significantly increase 
-# the time of a run. So in most cases it will be better to enable call graphs 
-# for selected functions only using the \callgraph command.
+# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
+# generate a call dependency graph for every global function or class method. 
+# Note that enabling this option will significantly increase the time of a run. 
+# So in most cases it will be better to enable call graphs for selected 
+# functions only using the \callgraph command.
 
 CALL_GRAPH             = NO
 
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then 
-# doxygen will generate a caller dependency graph for every global function 
-# or class method. Note that enabling this option will significantly increase 
-# the time of a run. So in most cases it will be better to enable caller 
-# graphs for selected functions only using the \callergraph command.
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
+# generate a caller dependency graph for every global function or class method. 
+# Note that enabling this option will significantly increase the time of a run. 
+# So in most cases it will be better to enable caller graphs for selected 
+# functions only using the \callergraph command.
 
 CALLER_GRAPH           = NO
 
 # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
-# will generate a graphical hierarchy of all classes instead of a textual one.
+# will graphical hierarchy of all classes instead of a textual one.
 
 GRAPHICAL_HIERARCHY    = YES
 
 # If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES 
 # then doxygen will show the dependencies a directory has on other directories 
-# in a graphical way. The dependency relations are determined by the #include 
+# in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
 
 DIRECTORY_GRAPH        = YES
 
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
-# generated by dot. Possible values are png, jpg, or gif. 
+# generated by dot. Possible values are png, jpg, or gif
 # If left blank png will be used.
 
 DOT_IMAGE_FORMAT       = png
@@ -1595,37 +1199,39 @@ DOT_PATH               =
 
 DOTFILE_DIRS           = 
 
-# The MSCFILE_DIRS tag can be used to specify one or more directories that 
-# contain msc files that are included in the documentation (see the 
-# \mscfile command).
+# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
 
-MSCFILE_DIRS           = 
+MAX_DOT_GRAPH_WIDTH    = 1024
 
-# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of 
-# nodes that will be shown in the graph. If the number of nodes in a graph 
-# becomes larger than this value, doxygen will truncate the graph, which is 
-# visualized by representing a node as a red box. Note that doxygen if the 
-# number of direct children of the root node in a graph is already larger than 
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note 
-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
 
-DOT_GRAPH_MAX_NODES    = 50
+MAX_DOT_GRAPH_HEIGHT   = 1024
 
 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
 # graphs generated by dot. A depth value of 3 means that only nodes reachable 
 # from the root by following a path via at most 3 edges will be shown. Nodes 
 # that lay further from the root node will be omitted. Note that setting this 
 # option to 1 or 2 may greatly reduce the computation time needed for large 
-# code bases. Also note that the size of a graph can be further restricted by 
-# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# code bases. Also note that a graph may be further truncated if the graph's 
+# image dimensions are not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH 
+# and MAX_DOT_GRAPH_HEIGHT). If 0 is used for the depth value (the default), 
+# the graph is not depth-constrained.
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
-# background. This is disabled by default, because dot on Windows does not 
-# seem to support this out of the box. Warning: Depending on the platform used, 
-# enabling this option may lead to badly anti-aliased labels on the edges of 
-# a graph (i.e. they become hard to read).
+# background. This is disabled by default, which results in a white background. 
+# Warning: Depending on the platform used, enabling this option may lead to 
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to 
+# read).
 
 DOT_TRANSPARENT        = YES
 
@@ -1647,3 +1253,12 @@ GENERATE_LEGEND        = YES
 # the various graphs.
 
 DOT_CLEANUP            = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to the search engine   
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be 
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE           = NO
diff --git a/user-doc/Functions.txt b/user-doc/Functions.txt
new file mode 100644
index 000000000..64b4e8f72
--- /dev/null
+++ b/user-doc/Functions.txt
@@ -0,0 +1,28 @@
+/**
+\page Function Functions
+
+The following keywords are available for all directives of this section:
+- ARG:
+  This keyword is used to specify on which variables the function is computed
+  It is a comma-separated list of labels. Here is an example with \ref COMBINE
+\verbatim
+DISTANCE  ATOMS=1,5 LABEL=d1
+DISTANCE  ATOMS=2,6 LABEL=d2
+COMBINE   ARG=d1,d2 POWERS=2
+\endverbatim
+- NUMERICAL_DERIVATIVES:
+  This flag can be used to enforce calculation of derivatives with respect to
+  function arguments by means of numerical differences
+\verbatim
+DISTANCE  ATOMS=1,5 LABEL=d1
+DISTANCE  ATOMS=2,6 LABEL=d2
+COMBINE   ARG=d1,d2 POWERS=2 NUMERICAL_DERIVATIVES
+\endverbatim
+
+\attention The rest of this page is automatically generated from the source
+files
+
+
+@FUNCTION@
+*/
+
diff --git a/user-doc/GenericDirectives.txt b/user-doc/GenericDirectives.txt
new file mode 100644
index 000000000..93d55ebee
--- /dev/null
+++ b/user-doc/GenericDirectives.txt
@@ -0,0 +1,12 @@
+/**
+
+\page GenericDirectives Generic directives
+
+\attention The rest of this page is automatically generated from the source
+files
+
+
+@GENERIC@
+
+*/
+
diff --git a/user-doc/InputDirectives.txt b/user-doc/InputDirectives.txt
new file mode 100644
index 000000000..a8ac21825
--- /dev/null
+++ b/user-doc/InputDirectives.txt
@@ -0,0 +1,65 @@
+/**
+
+\page InputDirectives Input directives
+
+These are directives which can be used to manipulate the input file.
+
+\section Comments
+
+Comments can be added with # syntax
+\verbatim
+# This is the distance between two atoms:
+DISTANCE ATOM=1,2
+\endverbatim
+
+\section ContinuationLines Continuation lines
+
+Directives with many keywords can be splitted for convenience on multiple
+lines using "..." syntax:
+This:
+\verbatim
+DISTANCE ...
+  ATOMS=1,300
+  NOPBC
+... DISTANCE
+\endverbatim
+is equivalent to this:
+\verbatim
+DISTANCE ATOMS=1,300 NOPBC
+\endverbatim
+
+\section INCLUDE
+
+Other file can be included with the INCLUDE directive. A single "plumed.dat"
+file:
+\verbatim
+DISTANCE ATOMS=0,1 LABEL=dist
+RESTRAINTG ARG=dist
+\endverbatim
+can be equivalently splitted as
+\verbatim
+DISTANCE ATOMS=0,1 LABEL=dist
+INCLUDE toBeIncluded.dat
+\endverbatim
+plus a "toBeIncluded.dat" file
+\verbatim
+RESTRAINTG ARG=dist
+\endverbatim
+
+\section LOAD
+
+[How to load external dynamic libraries]
+
+\section ENDPLUMED
+
+Reading is killed when the directive ENDPLUMED is found. Thus, subsequent
+lines can be used to store comments or other unread information
+\verbatim
+DISTANCE ATOMS=0,1 LABEL=dist
+ENDPLUMED
+lines here are not parsed
+\endverbatim
+
+
+*/
+
diff --git a/user-doc/Installation.txt b/user-doc/Installation.txt
new file mode 100644
index 000000000..399acf0ce
--- /dev/null
+++ b/user-doc/Installation.txt
@@ -0,0 +1,43 @@
+/**
+
+\page Installation Installation
+
+\section CompilingPlumed Compiling Plumed
+
+[Configuration]
+
+[Compilation]
+
+[Installation?]
+
+[How to test plumed without MD engine]
+
+\section Patching Patching your MD code
+
+To patch your MD code, you should have PLUMED already installed and properly
+working. In particular, you should have the command "plumed" in your execution
+path. Then, follow these steps
+- Configure and compile your MD enginge
+- Test if it is working properly
+- Go to the root diretory of the MD engine
+- Patch:
+\verbatim
+> plumed patch
+\endverbatim
+The script will interactively ask which MD engine you are patching.
+- Recompile the MD code (if dependencies are set up properly in the MD engine,
+  only modified files will be recompiled)
+
+If your MD code is not supported, you may want to implement an interface for
+it. Refer to the <a href="../../developer-doc/html/index.html"> developer
+manual </a>.
+
+[How to test if interface has been installed properly]
+
+\section InstallingPlumedOnAMainframe Installing Plumed on a mainframe
+
+[Notes on shared libraries, modules, etc.]
+
+
+*/
+
diff --git a/user-doc/Intro.txt b/user-doc/Intro.txt
new file mode 100644
index 000000000..3e0f6da00
--- /dev/null
+++ b/user-doc/Intro.txt
@@ -0,0 +1,18 @@
+/**
+\mainpage User guide
+
+This is the user manual. If you want to modify PLUMED or to understand how it works internally,
+have a look at the <a href="../../developer-doc/html/index.html"> developer manual </a>.
+
+PLUMED 2.0 is a major rewriting of PLUMED. (...)
+
+- \subpage WhatsNew
+- \subpage Installation
+- \subpage BasicUsage
+- \subpage AdvancedTopics
+- \subpage Tools
+- \subpage Reference
+
+
+*/
+
diff --git a/user-doc/Makefile b/user-doc/Makefile
index e41a54dae..bf7678d5a 100644
--- a/user-doc/Makefile
+++ b/user-doc/Makefile
@@ -6,4 +6,4 @@ all:
 	doxygen
 
 clean:
-	rm -fr html latex automatic DocPostproc.txt *~
+	rm -fr html latex automatic *~ *PP.txt
diff --git a/user-doc/Reference.txt b/user-doc/Reference.txt
new file mode 100644
index 000000000..6c673d9e5
--- /dev/null
+++ b/user-doc/Reference.txt
@@ -0,0 +1,18 @@
+/**
+\page Reference Reference
+
+List of directives to manipulate input: \subpage InputDirectives
+
+List of directives to setup plumed: \subpage Setup
+
+List of collective variables: \subpage Colvar
+
+List of functions: \subpage Function
+
+List of free energy methods: \subpage Bias
+
+List of general purpose directives: \subpage GenericDirectives
+
+
+*/
+
diff --git a/user-doc/Setup.txt b/user-doc/Setup.txt
new file mode 100644
index 000000000..05978a7aa
--- /dev/null
+++ b/user-doc/Setup.txt
@@ -0,0 +1,14 @@
+/**
+
+\page Setup Setup directives
+
+These are directives which set global PLUMED parameters at the beginning of
+the simulation. They must preceed all the non-setup directives, and they are
+inactive during MD simulation.
+
+\attention The rest of this page is automatically generated from the source files
+
+@SETUP@
+
+*/
+
diff --git a/user-doc/Tools.txt b/user-doc/Tools.txt
new file mode 100644
index 000000000..2f1c556aa
--- /dev/null
+++ b/user-doc/Tools.txt
@@ -0,0 +1,12 @@
+/**
+\mainpage User guide
+
+\page Tools Tools
+
+\section Driver
+
+How to compute the collective variables on an input trajectory.
+
+
+*/
+
diff --git a/user-doc/WhatsNew.txt b/user-doc/WhatsNew.txt
new file mode 100644
index 000000000..aa6d93ccd
--- /dev/null
+++ b/user-doc/WhatsNew.txt
@@ -0,0 +1,12 @@
+/**
+\page WhatsNew What's new
+
+\section NewFeatures List of new features
+
+[List of new features]
+
+\section NewInputSyntax New syntax for the input file
+
+[Briefly describe the difference between old and new input]
+
+*/
diff --git a/user-doc/extract b/user-doc/extract
index 83fca78cd..2d09ac595 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -6,7 +6,7 @@ awk '{
   if($1=="//+ENDPLUMEDOC") inside=0;
   if(inside && $1!="/**" && $1!="*/") print $0 >output
   if($1=="//+PLUMEDOC"){
-    if($2=="COLVAR" || $2=="FUNCTION" || $2=="BIAS" || $2=="GENERIC"){
+    if($2=="COLVAR" || $2=="FUNCTION" || $2=="BIAS" || $2=="GENERIC" || $2=="SETUP"){
       output="automatic/"$2".txt";
       print "\\section "$3 > output
       inside=1;
@@ -14,7 +14,10 @@ awk '{
   }
 }'
 
-cat Doc.txt |
+for file in Bias Colvar Functions GenericDirectives InputDirectives Setup
+do
+
+cat $file.txt |
 {
   while read -r LINE ;
   do
@@ -30,9 +33,13 @@ cat Doc.txt |
   elif [ "$LINE" = "@GENERIC@" ]
   then
     cat automatic/GENERIC.txt
+  elif [ "$LINE" = "@SETUP@" ]
+  then
+    cat automatic/SETUP.txt
   else
     echo -E "$LINE"
   fi
   done
-} > DocPostproc.txt
+} > ${file}PP.txt
+done
 
-- 
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