diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt
index 04784399d790c75e30bd4ba34b3563a14813f5f8..4015dd43586b7597ef0282aed298cff398d60df3 100644
--- a/user-doc/Colvar.txt
+++ b/user-doc/Colvar.txt
@@ -71,7 +71,11 @@ in a wide variety of MD codes. Consequentially, we have implemented a more prag
in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run. In plumed 1.0 this was done
using the ALIGN_ATOMS keyword. In plumed 2.0 the same effect can be acchieved using any one from the following list of commands
-- \subpage WHOLEMOLECULES
+<table align=center frame=void width=95%% cellpadding=5%%>
+<tr>
+<td width=5%> \subpage WHOLEMOLECULES </td> <td> With this command you can specify the atoms in each of your molecules </td>
+</tr>
+</table>
@TOPOLOGY@
The most general of these is the \ref WHOLEMOLECULES keywords. However, there are advantages in using the others as oftentimes
diff --git a/user-doc/extract b/user-doc/extract
index 5a4c4ddf72bcb1dd3e910cced466558fa3a8adeb..cddbe0bda8ec0e8a57f296909e5fac08231b639d 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -3,7 +3,7 @@ rm -rf automatic
mkdir automatic
# Check for files that register actions with no documentation
-touch errors
+rm errors
for file in ../src/*.cpp
do
nreg=`grep "PLUMED_REGISTER_ACTION" $file | wc -l | awk '{print $1}'`
@@ -30,23 +30,27 @@ done
# fi
#done
-# Generate all the documentation pages for colvar modifiers
-#rm -f modifier_file
-#echo "\\section mod Working with distributions" > modifier_file
-#echo "As described above you can use this colvar to calculate one or multiple CVs. Obviously, if you have calculated multiple CVs then you have a distribution of CVs. As such plumed allows you to calculate a number of functions of this distribution. These quantities and their derivatives are then stored as the values of the colvar. N.B. You cannot calcualte the values of the colvars and these functions of the distribution from a single line in input. You can however calculate multiple functions of the distribution." >> modifier_file
-#cat ../*/*cpp |
-#awk '{
-# if($1=="//+ENDPLUMEDOC"){
-# inside=0
-# }
-# if(inside && $1!="/**" && $1!="*/") print $0 >> "modifier_file"
-# if($1=="//+PLUMEDOC"){
-# if($2=="MODIFIER"){
-# print "\\par " $3 >> "modifier_file"
-# inside=1;
-# }
-# }
-#}'
+# Generate all the documentation for colvar modifiers
+rm -f modifier_file
+echo "\\section mod Working with distributions" > modifier_file
+echo "As described above you can use this colvar to calculate one or multiple CVs. Obviously, if you have calculated multiple CVs then you have a distribution of CVs. Plumed allows you to calculate a number of functions of this distribution. These quantities and their derivatives are then stored as the values of the colvar. N.B. You cannot calcualte the values of the colvars and these functions of the distribution from a single line in input. You can however calculate multiple functions of the distribution." >> modifier_file
+echo "<table align=center frame=void width=95%% cellpadding=5%%>" >> modifier_file
+cat ../*/*cpp |
+awk '{
+ if($1=="//+ENDPLUMEDOC" && inside==1){
+ print "</td> </tr>" >> "modifier_file"
+ inside=0
+ }
+ if(inside && $1!="/**" && $1!="*/") print $0 >> "modifier_file"
+ if($1=="//+PLUMEDOC"){
+ if($2=="MODIFIER"){
+ print "<tr> <td width=5%> <b> ", $3, " </b></td>" >> "modifier_file"
+ print "<td>" >> "modifier_file"
+ inside=1;
+ }
+ }
+}'
+echo "</table>" >> modifier_file
# Generate all the documentation pages from comments
cat ../*/*cpp |
@@ -55,16 +59,25 @@ awk '{
inside=0;
print "*/" >output
}
- if(inside && $1!="/**" && $1!="*/") print $0 >output
+ if(inside==2 && NF==0){
+ print "</td> </tr>" > lfile
+ inside=1
+ }
+ if(inside==1 && $1!="/**" && $1!="*/") print $0 >output
+ if(inside==2 && $1!="/**" && $1!="*/" ){
+ print $0 > output
+ print $0 > lfile
+ }
if($1=="//+PLUMEDOC"){
if( $2=="TOPOLOGY" || $2=="COLVAR" || $2=="FUNCTION" || $2=="ANALYSIS" || $2=="BIAS" || $2=="VATOM" || $2=="GENERIC" || $2=="TOOLS" ){
lfile="automatic/"$2".list"
- print "- \\subpage "$3 > lfile
+
+ print "<tr> <td width=5%> \\subpage ", $3,"</td> <td>" > lfile
output="automatic/"$3".tmp";
print "/**" > output
print "\\page "$3 > output
print "\\section "$3 >output
- inside=1;
+ inside=2;
}
}
}'
@@ -94,7 +107,7 @@ do
iscol=`grep $flag automatic/COLVAR.list | wc -l`
if [ $iscol -gt 0 ] ; then
fname=`grep PLUMED_REGISTER_ACTION ../src/*.cpp | grep $flag | sed -e 's/:/ /g' | awk '{print $1}'`
- hasmod=`grep ColvarWithModifiers $fname | wc -l | awk '{print $1}'`
+ hasmod=`grep MultiColvar $fname | wc -l | awk '{print $1}'`
if [ $hasmod -gt 0 ] ; then
cat modifier_file
fi
@@ -116,28 +129,44 @@ cat $file.txt |
do
if [ "$LINE" = "@COLVAR@" ]
then
+ echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/COLVAR.list
+ echo "</table>"
elif [ "$LINE" = "@ANALYSIS@" ]
then
+ echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/ANALYSIS.list
+ echo "</table>"
elif [ "$LINE" = "@BIAS@" ]
then
+ echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/BIAS.list
+ echo "</table>"
elif [ "$LINE" = "@FUNCTION@" ]
then
+ echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/FUNCTION.list
+ echo "</table>"
elif [ "$LINE" = "@TOPOLOGY@" ]
then
+ echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/TOPOLOGY.list
+ echo "</table>"
elif [ "$LINE" = "@VATOM@" ]
then
+ echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/VATOM.list
+ echo "</table>"
elif [ "$LINE" = "@TOOLS@" ]
then
+ echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/TOOLS.list
+ echo "</table>"
elif [ "$LINE" = "@CODES@" ]
then
+ echo "<table align=center frame=void width=95%% cellpadding=5%%>"
cat automatic/codes.list
+ echo "</table>"
else
echo -E "$LINE"
fi