Merge branch 'v2.3'

CHANGES/v2.3.txt

@@ -155,6 +155,8 @@ See branch \branch{v2.3} on git repository.
 - Fixed bug in if condition in \ref PCAVARS so that you can run with only one eigenvector defined in input 
 - Fixed but with timers in \ref sum_hills \issue{194}.
 - Fixed bug when using \ref MOVINGRESTRAINT with periodic variables such as \ref TORSION \issue{225}.
+- Fixed bug in \ref HBONDS that used to apear when you used DONORNS and ACCEPTORS with same numbers of atoms 
+- Fixed bug in \ref DISTANCES that appears when using BETWEEN and link cells.
 
 For developers:
 - plumedcheck validation has been made stricter. All the checks are now described in the developer manual.

src/adjmat/AdjacencyMatrixBase.cpp

@@ -149,8 +149,15 @@ void AdjacencyMatrixBase::retrieveTypeDimensions( unsigned& nrows, unsigned& nco
 void AdjacencyMatrixBase::finishMatrixSetup( const bool& symmetric, const std::vector<AtomNumber>& all_atoms ){
   std::string param;
   if( symmetric && ablocks[0].size()==ablocks[1].size() ) param="SYMMETRIC";
-  if( !symmetric && ablocks[0].size()==ablocks[1].size() ) param="HBONDS";
-
+  if( !symmetric ){
+      bool usehbonds=( ablocks[0].size()==ablocks[1].size() );
+      if( usehbonds ){
+          for(unsigned i=0;i<ablocks[0].size();++i){
+              if( ablocks[0][i]!=ablocks[1][i] ){ usehbonds = false; break; } 
+          } 
+          if( usehbonds ) param="HBONDS";       
+      } 
+  }
 
   vesselbase::VesselOptions da("","",0,param,this);
   Keywords keys; AdjacencyMatrixVessel::registerKeywords( keys );

src/multicolvar/Distances.cpp

@@ -174,7 +174,7 @@ MultiColvarBase(ao)
          use_link=true; rcut=lt->getCutoff();
      } else {
          vesselbase::Between* bt=dynamic_cast<vesselbase::Between*>( getPntrToVessel(0) );
-         if( bt ) use_link=true; rcut=bt->getCutoff();
+         if( bt ){ use_link=true; rcut=bt->getCutoff(); }
      }
      if( use_link ){
          for(unsigned i=1;i<getNumberOfVessels();++i){