Added tutorials directory to documentation

This funcitonality allows you to add tutorials written in Doxygen
and links to external websites.  They are called How Tos though

user-doc/Doxyfile

@@ -469,6 +469,8 @@ INPUT                  = IntroPP.txt \
                          WhatsNew.txt \
                          GlossaryPP.txt \
                          Transition.txt \
+                         TutorialsPP.txt \
+                         tutorials \
                          automatic
 
 # If the value of the INPUT tag contains directories, you can use the 

user-doc/Intro.txt

@@ -13,9 +13,6 @@ features available in plumed 2.0 and to work out how to install plumed 2.0 in yo
 - \subpage WhatsNew
 - \subpage Installation 
 
-If you are experienced with Plumed 1, you migh find this useful:
-- \subpage Transition
-
 \section qintro A quick introduction
 
 To run plumed 2.0 you need to provide one input file.  In this file you specify what it

user-doc/PlumedLayout.xml

@@ -2,7 +2,8 @@
   <!-- Navigation index tabs for HTML output -->
   <navindex>
     <tab type="mainpage" visible="yes" title=""/>
-    <tab type="user" visible="yes" url="@ref glossary" title="Glossary"/>
+    <tab type="user" visible="yes" url="glossary.html" title="Glossary"/>
+    <tab type="user" visible="yes" url="tutorials.html" title="How-tos"/>
     <tab type="pages" visible="no" title="" intro=""/>
     <tab type="modules" visible="yes" title="" intro=""/>
     <tab type="namespaces" visible="yes" title="">

user-doc/Tutorials.txt

+/**
+
+@page tutorials How-tos
+
+The following pages describe how to perform a variety of tasks using plumed 2.0
+
+@TUTORIALS@
+
+In addition, the following websites contain resources that might be helpful  
+
+@WEBSITES@
+
+*/

user-doc/extract

@@ -83,6 +83,26 @@ awk 'BEGIN{gfile="automatic/GLOSSARY1.list"; dfile="automatic/DICTIONARY1.list";
 sort automatic/GLOSSARY1.list > automatic/GLOSSARY.list 
 sort automatic/DICTIONARY1.list > automatic/DICTIONARY.list
 
+# Generate links to tutorial pages
+for file in ./tutorials/*.txt ; do
+
+    link=`grep link: $file | sed -e 's/link://'`
+    describe=`grep description: $file | sed -e 's/description://'`
+
+    echo "<tr> <td> $link </td> <td> $describe </td> </tr>" >> automatic/TUTORIALS.list  
+
+done
+
+# Generate links to websites
+for file in ./tutorials/*.site; do
+
+   link=`grep link: $file | sed -e 's/link://'`
+   describe=`grep description: $file | sed -e 's/description://'`
+
+   echo "<tr> <td> $link </td> <td> $describe </td> </tr>" >> automatic/WEBSITES.list
+
+done
+
 # Generate all the documentation from keywords
 source ../sourceme.sh
 for file in automatic/*.tmp
@@ -113,7 +133,7 @@ do
     } > automatic/$flag.txt
 done
 
-for file in Bias Colvar Functions Installation Intro Analysis Glossary
+for file in Bias Colvar Functions Installation Intro Analysis Glossary Tutorials
 do
 
 cat $file.txt |
@@ -150,6 +170,16 @@ cat $file.txt |
     echo "<table align=center frame=void width=95%% cellpadding=5%%>"
     cat automatic/DICTIONARY.list
     echo "</table>"
+  elif [ "$LINE" = "@TUTORIALS@" ]
+  then
+    echo "<table align=center frame=void width=95%% cellpadding=5%%>"
+    cat automatic/TUTORIALS.list
+    echo "</table>"
+  elif [ "$LINE" = "@WEBSITES@" ]
+  then
+    echo "<table align=center frame=void width=95%% cellpadding=5%%>"
+    cat automatic/WEBSITES.list
+    echo "</table>"
   elif [ "$LINE" = "@FUNCTION@" ]
   then
     echo "<table align=center frame=void width=95%% cellpadding=5%%>"

user-doc/tutorials/mindist.txt

+/**
+\page mindist Calculating a minimum distance 
+
+To calculate and print the minimum distance between two groups of atoms you use the following commands
+
+\verbatim
+d1: DISTANCES GROUPA=1-10 GROUPB=11-20 MIN={BETA=500.} 
+PRINT ARG=d1.min FILE=colvar STRIDE=10
+\endverbatim
+(see \ref DISTANCES and \ref PRINT)
+
+In order to ensure differentiability the minimum is calculated using the following function:
+
+\f[
+s = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) }
+\f]
+
+where \f$\beta\f$ is a user specified parameter.
+
+This input is used rather than a separate MINDIST colvar so that the same routine and the same input style can be 
+used to calculate minimum coordinatetion numbers (see \ref COORDINATIONNUMBER), minimum 
+angles (see \ref ANGLES) and many other variables.  
+
+This new way of calculating mindist is part of plumed 2's multicolvar functionality.  These special actions
+allow you to calculate multiple functions of a distribution of simple collective variables.  As an example you 
+can calculate the number of distances less than 1.0, the minimum distance, the number of distances more than
+2.0 and the number of distances between 1.0 and 2.0 by using the following command:
+
+\verbatim
+DISTANCES ...
+ GROUPA=1-10 GROUPB=11-20 
+ LESS_THAN={RATIONAL R_0=1.0} 
+ MORE_THAN={RATIONAL R_0=2.0} 
+ BETWEEN={GAUSSIAN LOWER=1.0 UPPER=2.0} 
+ MIN={BETA=500.}
+... DISTANCES
+PRINT ARG=d1.less_than,d1.more_than,d1.between,d1.min FILE=colvar STRIDE=10
+\endverbatim
+(see \ref DISTANCES and \ref PRINT)
+
+A calculation performed this way is fast because the expensive part of the calculation - the calculation of all the distances - is only 
+done once per step.  Furthermore, it can be made faster by using the TOL keyword to discard those distance that make only a small contributions 
+to the final values together with the NL_STRIDE keyword, which ensures that the distances that make only a small contribution to the final values aren't
+calculated at every step.
+
+*/
+
+link: @subpage mindist
+
+description: This tutorial explains how to calculate the minimum distance between groups of atoms and serves as an introduction to MultiColvars

user-doc/Transition.txt → user-doc/tutorials/moving.txt

 /**
-\page Transition Plumed 1 to Plumed 2: quick transition guide
+\page moving Moving from Plumed 1 to Plumed 2
 
-We here provide a sort of quick reference for Plumed 1 users so as to
-translate their plumed.dat files into the new Plumed 2 syntax.
-
-\section Groups
-
-In Plumed 1 groups were used, depending on the specific collective variable, for two tasks:
-- To provide centers of masses to collective variables such as distances, angles, etc. This can
-  be done now defining virtual atoms with \ref CENTER or \ref COM
+In Plumed 1 groups (lists) were used for two tasks:
+- To provide centers of masses to collective variables such as distances, angles, etc. This is 
+  now done by defining virtual atoms using either \ref CENTER or \ref COM
 - To provide lists of atoms to collective variables such as coordination, gyration radius, etc.
-  This can be done now directly in the line which defines the collective variable. To increase
-  readability of the plumed.dat file, it is possible to define \ref GROUP.
+  This is now done directly in the line that defines the collective variable. 
+
+If you would still like to use groups you can use the \ref GROUP commands.  Whenever the label
+for a \ref GROUP action appears in the input it is replaced by the list of atoms that were 
+specified in the \ref GROUP.
 
 \section Directives
 
-For all the documented directives of Plumed 1 you find hiere the corresponding
-action in Plumed 2. Please take into consideration that syntax is not totally equivalent,
-so taht you have to read the documentation of the Plumed 2 Action.
+What follows is a list of all the documented directives of Plumed 1 together with their 
+plumed 2 equivalents.  Be aware that the input syntaxes for these directives are not totally 
+equivalent.  You should read the documentation for the Plumed 2 Action.
 
 <TABLE>
 <TR> 
@@ -115,7 +113,7 @@ so taht you have to read the documentation of the Plumed 2 Action.
 </TR>
 <TR>
   <TD> MINDIST </TD>
-  <TD> \ref DISTANCES with keyword MIN </TD>
+  <TD> \ref DISTANCES with keyword MIN (See also \ref mindist) </TD>
 </TR>
 <TR>
   <TD> ANGLE </TD>
@@ -225,3 +223,6 @@ so taht you have to read the documentation of the Plumed 2 Action.
 
 */
 
+link: @subpage moving
+
+description: This tutorial explains how plumed 1 input files can be translated into the new plumed 2 syntax.

user-doc/tutorials/wiki.site

+link: http://en.wikipedia.org/wiki/Metadynamics
+
+description: A wikipedia article on metadynamics