Merge branch 'v2.1' into v2.2

[makedoc]

src/multicolvar/Distances.cpp

@@ -72,6 +72,52 @@ DISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
 PRINT ARG=d1.gt0.1 
 \endverbatim
 (See also \ref PRINT \ref switchingfunction)
+
+
+\par Calculating minimum distances
+
+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.lessthan,d1.morethan,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.
+
 */
 //+ENDPLUMEDOC
 

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.lessthan,d1.morethan,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/tutorials/moving.txt

@@ -126,7 +126,7 @@ equivalent.  You should read the documentation for the Plumed 2 Action.
 </TR>
 <TR>
   <TD> MINDIST </TD>
-  <TD> \ref DISTANCES with keyword MIN (See also \ref mindist) </TD>
+  <TD> \ref DISTANCES with keyword MIN </TD>
 </TR>
 <TR>
   <TD> ANGLE </TD>