Separated multicolvars from regular colvars in manual

src/MultiColvarCoordination.cpp

@@ -10,7 +10,7 @@ using namespace std;
 
 namespace PLMD{
 
-//+PLUMEDOC COLVAR COORDINATIONNUMBER
+//+PLUMEDOC MCOLVAR COORDINATIONNUMBER
 /**
 Calculate the coordination numbers of atoms so that  you can then calculate functions of the distribution of
 coordination numbers such as the minimum, the number less than a certain quantity and so on.   

src/MultiColvarDensity.cpp

@@ -9,7 +9,7 @@ using namespace std;
 
 namespace PLMD{
 
-//+PLUMEDOC COLVAR DENSITY
+//+PLUMEDOC MCOLVAR DENSITY
 /**
 Calculate functions of the density of atoms as a function of the box.  This allows one to calculate
 density gradients, number of atoms in half the box and so on.

src/MultiColvarDistance.cpp

@@ -9,7 +9,7 @@ using namespace std;
 
 namespace PLMD{
 
-//+PLUMEDOC COLVAR DISTANCES
+//+PLUMEDOC MCOLVAR DISTANCES
 /**
 Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of
 distances such as the minimum, the number less than a certain quantity and so on. 

user-doc/Colvar.txt

@@ -88,5 +88,12 @@ The following list contains all the colvars that are currently implemented in pl
 
 @COLVAR@
 
+Often you do not need one of these collective variables directly.  What you want instead is a function of a distribution of
+collective variables of a particular type.  For instance you might need to calculate a minimum distance or the number of 
+coordination numbers greater than a 3.0.  Descriptions as to how to use plumed to calculate these kinds of CVs are given
+below:
+
+@MCOLVAR@
+
 */
 

user-doc/extract

@@ -47,7 +47,7 @@ awk '{
      print $0 > lfile
   }
   if($1=="//+PLUMEDOC"){
-    if( $2=="TOPOLOGY" || $2=="COLVAR" || $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=="VATOM" || $2=="GENERIC" || $2=="TOOLS" ){
       lfile="automatic/"$2".list"
       
       print "<tr> <td width=5%> \\subpage ", $3,"</td> <td>" > lfile
@@ -102,6 +102,11 @@ cat $file.txt |
     echo "<table align=center frame=void width=95%% cellpadding=5%%>"
     cat automatic/COLVAR.list
     echo "</table>"
+  elif [ "$LINE" = "@MCOLVAR@" ]
+  then
+    echo "<table align=center frame=void width=95%% cellpadding=5%%>"
+    cat automatic/MCOLVAR.list
+    echo "</table>"
   elif [ "$LINE" = "@ANALYSIS@" ]
   then
     echo "<table align=center frame=void width=95%% cellpadding=5%%>"