diff --git a/src/MultiColvarCoordination.cpp b/src/MultiColvarCoordination.cpp index 533ab128abd3bc37a2312294c06eddac3df43daa..451c18a7937f8f5565cf938cdcd9290fa8e74012 100644 --- a/src/MultiColvarCoordination.cpp +++ b/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. diff --git a/src/MultiColvarDensity.cpp b/src/MultiColvarDensity.cpp index c7b26fa582b944463782d3081f8c3f879603e841..24a93e1f3d71556284d06e701dc639a4a97dc550 100644 --- a/src/MultiColvarDensity.cpp +++ b/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. diff --git a/src/MultiColvarDistance.cpp b/src/MultiColvarDistance.cpp index ec4646d02a254ee7af41dfb63a66bae35d576abd..7d2bf8300467563ba1efae33be03c5c97bd34cad 100644 --- a/src/MultiColvarDistance.cpp +++ b/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. diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt index 4015dd43586b7597ef0282aed298cff398d60df3..47b929b319d3abeed4ff934bba7ce718af399370 100644 --- a/user-doc/Colvar.txt +++ b/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@ + */ diff --git a/user-doc/extract b/user-doc/extract index 284a54e351e71a52275ed5fd7fa7b0f78625442b..3d4faaf464bcaf97eeea9293bca825ee42a054af 100755 --- a/user-doc/extract +++ b/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%%>"