Added glossary of Actions to the manual

imd/ActionIMD.cpp

@@ -15,10 +15,11 @@ extern "C" {
 namespace PLMD {
 
 //+PLUMEDOC GENERIC IMD
-/**
+/*
 Use interactive molecular dynamics with VMD
 
 \par Examples
+
 \verbatim
 # listen to port 1112 of localhost
 IMD PORT=1112

src/GenericPrint.cpp

@@ -34,7 +34,7 @@ Print quantities to a file.
 
 This directive can be used multiple times
 in the input so you can print files with different strides or print different quantities 
-to different files.  You can control the buffering of output using the \ref FLUSH keyword.
+to different files.  You can control the buffering of output using the \subpage FLUSH keyword.
 
 \par Examples
 The following input instructs plumed to print the distance between atoms 3 and 5 on a file 

user-doc/Bias.txt

@@ -8,5 +8,8 @@ The list of available enhanced sampling algorithms contains:
 
 @BIAS@
 
+You can also use plumed in conjunction with VMD's interactive MD module by taking
+advantage of the \subpage IMD action.
+
 */
 

user-doc/Colvar.txt

@@ -37,7 +37,7 @@ how these shortcuts can be used can be found in the documentation for the variou
 
 Lastly, if you have a list of colvar that is particularly laborious to write out that you need to use multiple times in the 
 input you can create a static group of atoms and then use the label of the group to specify the correpsonding list of 
-atoms in your various colvars.  For more details see \ref GROUP.
+atoms in your various colvars.  For more details see \subpage GROUP.
 
 \section vatoms Virtual Atoms
 

user-doc/Doxyfile

@@ -463,11 +463,11 @@ INPUT                  = IntroPP.txt \
                          BiasPP.txt \
                          AnalysisPP.txt \
                          ColvarPP.txt \ 
-                         GenericPP.txt \
                          FunctionsPP.txt \
                          ToolsPP.txt \ 
                          InstallationPP.txt \
                          WhatsNew.txt \
+                         GlossaryPP.txt \
                          automatic
 
 # If the value of the INPUT tag contains directories, you can use the 

user-doc/Generic.txt

-/**
-
-\page Generic Generic
-
-Here you can find other possible plumed directives
-which do not fall in any of the other groups.
-
-@GENERIC@
-
-*/
-

user-doc/Glossary.txt

+/**
+
+\page Glossary Glossary of Actions 
+
+The following page contains alphabetically ordered list of all the Actions and command line tools 
+that are available in plumed 2.0. For lists of Actions classified in accordance with the 
+particular tasks that are being performed see:
+
+- \ref Colvar
+- \ref Function
+- \ref Analysis
+- \ref Bias
+
+\section ActionList Full list of actions
+
+@GLOSSARY@
+
+*/

user-doc/Intro.txt

@@ -6,7 +6,7 @@ to analyse features of the dynamics on-the-fly or to perform a wide variety of f
 The original plumed 1.0 was highly successful and had over 1000 users.  Plumed 2.0 constitues an 
 extensive rewrite of the original in a way that makes it more modular and thus easier to implement 
 new methods, more straightforward to add it to MD codes and hopefully simpler to use.  
-This is the user manual -  i f you want to modify PLUMED or to understand how it works internally, have a look at the 
+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>.  Alternatively, to look at a list of the new 
 features available in plumed 2.0 and to work out how to install plumed 2.0 in your MD code check out:
 
@@ -26,7 +26,6 @@ analsyis tools that come with plumed are given in:
 - \subpage Function
 - \subpage Analysis
 - \subpage Bias
-- \subpage Generic
 
 Plumed can be used in one of two ways.  It can be incorporated into any one of the MD codes listed on the
 \ref Installation page and used to analyse or bias a molecular dynamics run on the fly.  Alternatively, one
@@ -49,7 +48,8 @@ which provide plumed with more details as to how the action is to be performed.
 (in which they tell plumed to do the calculation in a particular way - for example NOPBC tells plumed to not use the periodic
 bounadry conditions when calculating a particular colvar) or they can be words followed by an equals sign and a comma separated 
 list - WITH NO SPACES - of numbers or characters (so for example ATOMS=1,2,3,4 tells plumed to use atom numbers 1,2,3 and 4 in 
-the calculation of a particular colvar).  
+the calculation of a particular colvar). Details on all the actions that are available in plumed can be found in the \ref
+Glossary. 
 
 The most important of these keywords is the label keyword as it is only by using these labels that we can pass data 
 from one action to another.  As an example if you do:
@@ -169,5 +169,10 @@ LOAD library.so
 N.B.  If your system uses a different suffix for dynamic libraries (e.g. macs use .dylib) then PLUMED will try to 
 automatically adjust the suffix accordingly.
 
+\section degub Debugging the code
+
+The \subpage DEBUG action provides some functionality for debugging the code that may be useful if you are doing 
+very intensive development of the code of if you are running on a computer with a strange architecture.
+
 */
 

user-doc/extract

@@ -32,25 +32,29 @@ done
 
 # Generate all the documentation pages from comments
 cat ../*/*cpp |
-awk '{
+awk 'BEGIN{gfile="automatic/GLOSSARY1.list"}{
   if($1=="//+ENDPLUMEDOC"){
      inside=0;
      print "*/" >output
   }
   if(inside==2 && NF==0){
      print "</td> </tr>" > lfile
+     printf "</td> </tr>\n" > gfile
      inside=1
   }
   if(inside==1 && $1!="/*" && $1!="*/") print $0 >output
   if(inside==2 && $1!="/*" && $1!="*/" ){
      print $0 > output
      print $0 > lfile
+     printf "%s", $0 > gfile
   }
   if($1=="//+PLUMEDOC"){
-    if( $2=="TOPOLOGY" || $2=="COLVAR" || $2=="MCOLVAR" || $2=="FUNCTION" || $2=="ANALYSIS" || $2=="BIAS" || $2=="VATOM" || $2=="GENERIC" || $2=="TOOLS" ){
+    if( $2=="TOPOLOGY" || $2=="COLVAR" || $2=="MCOLVAR" || $2=="FUNCTION" || $2=="ANALYSIS" || $2=="BIAS" || $2=="GENERIC" || $2=="VATOM" || $2=="TOOLS" ){
       lfile="automatic/"$2".list"
       
       print "<tr> <td width=5%> \\subpage ", $3,"</td> <td>" > lfile
+      printf "<tr> <td width=5%> \\ref %s </td><td> %s </td><td>",$3, $2 > gfile
+
       if(output!="")close(output);
       output="automatic/"$3".tmp";
       print "/**" > output
@@ -61,6 +65,9 @@ awk '{
   }
 }'
 
+# Now put the glossary in alphabetical order
+sort automatic/GLOSSARY1.list > automatic/GLOSSARY.list 
+
 # Generate all the documentation from keywords
 source ../sourceme.sh
 for file in automatic/*.tmp
@@ -91,7 +98,7 @@ do
     } > automatic/$flag.txt
 done
 
-for file in Bias Colvar Functions Installation Intro Analysis Generic
+for file in Bias Colvar Functions Installation Intro Analysis Glossary
 do
 
 cat $file.txt |
@@ -113,15 +120,15 @@ cat $file.txt |
     echo "<table align=center frame=void width=95%% cellpadding=5%%>"
     cat automatic/ANALYSIS.list
     echo "</table>"
-  elif [ "$LINE" = "@GENERIC@" ]
+  elif [ "$LINE" = "@BIAS@" ]
   then
     echo "<table align=center frame=void width=95%% cellpadding=5%%>"
-    cat automatic/GENERIC.list
+    cat automatic/BIAS.list
     echo "</table>"
-  elif [ "$LINE" = "@BIAS@" ]
+  elif [ "$LINE" = "@GLOSSARY@" ]
   then
     echo "<table align=center frame=void width=95%% cellpadding=5%%>"
-    cat automatic/BIAS.list
+    cat automatic/GLOSSARY.list
     echo "</table>"
   elif [ "$LINE" = "@FUNCTION@" ]
   then