Fixed cluster diameter business and added test

regtest/adjmat/rt-dfg2/plumed.dat

@@ -12,6 +12,7 @@ OUTPUT_CLUSTER CLUSTERS=dfs CLUSTER=1 FILE=dfs.dat
 
 clust2a: CLUSTER_WITHSURFACE CLUSTERS=dfs RCUT_SURF=0.3 
 size2a: CLUSTER_NATOMS CLUSTERS=clust2a CLUSTER=2
+dia2a: CLUSTER_DIAMETER CLUSTERS=clust2a CLUSTER=2
 OUTPUT_CLUSTER CLUSTERS=clust2a CLUSTER=2 FILE=dfs2.dat
 
-PRINT ARG=size2a FILE=size
+PRINT ARG=size2a,dia2a FILE=size FMT=%8.4f 

regtest/adjmat/rt-dfg2/size.reference

-#! FIELDS time size2a
- 0.000000 78.000000
+#! FIELDS time size2a dia2a
+ 0.000000  78.0000   2.3294

src/adjmat/ClusterAnalysisBase.cpp

@@ -41,12 +41,6 @@ myclusters(NULL)
   if(!found_cluster) error("unable to interpret input clusters " + matname[0] );
   myclusters = dynamic_cast<ClusteringBase*>( mybasemulticolvars[0] );
   if( !myclusters ) error("input label is not that of a DFS object");
-
-  // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
-  for(unsigned i=0;i<myclusters->getNumberOfNodes();++i) addTaskToList(i);
-
-  // And now finish the setup of everything in the base
-  setupAtomLists();
 }
 
 void ClusterAnalysisBase::turnOnDerivatives(){ 

src/adjmat/ClusterDiameter.cpp

@@ -72,7 +72,7 @@ ClusterAnalysisBase(ao)
        for(unsigned j=0;j<i;++j) addTaskToList( i*getNumberOfNodes() + j );
    }
    // Now create a higest vessel
-   addVessel("HIGHEST", "", -1); readVesselKeywords();
+   addVessel("HIGHEST", "", -1); setupAtomLists();
 }
 
 void ClusterDiameter::turnOnDerivatives(){
@@ -93,22 +93,10 @@ void ClusterDiameter::calculate(){
 }
 
 void ClusterDiameter::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const { 
-  unsigned iatom=current/getNumberOfNodes(), jatom = current - iatom*getNumberOfNodes();
+  unsigned iatom=std::floor(current/getNumberOfNodes()), jatom = current - iatom*getNumberOfNodes();
   Vector distance=getSeparation( getPosition(iatom), getPosition(jatom) );
-  double dd = distance.modulo(), inv = 1.0/dd ; myvals.setValue( 1, dd ); 
-  if( !doNotCalculateDerivatives() ){
-      myvals.addDerivative( 1, 3*iatom + 0, -inv*distance[0] );
-      myvals.addDerivative( 1, 3*iatom + 1, -inv*distance[1] );
-      myvals.addDerivative( 1, 3*iatom + 2, -inv*distance[2] );
-      myvals.addDerivative( 1, 3*jatom + 0, +inv*distance[0] );
-      myvals.addDerivative( 1, 3*jatom + 1, +inv*distance[1] );
-      myvals.addDerivative( 1, 3*jatom + 2, +inv*distance[2] );
-      Tensor vir = -inv*Tensor(distance,distance);
-      unsigned vbase = myvals.getNumberOfDerivatives() - 9;
-      for(unsigned i=0;i<3;++i){
-          for(unsigned j=0;j<3;++j) myvals.addDerivative( 1, vbase+3*i+j, vir(i,j) );
-      }
-  }
+  double dd = distance.modulo(), inv = 1.0/dd ; 
+  myvals.setValue( 0, 1.0 ); myvals.setValue( 1, dd ); 
 }
 
 }

src/adjmat/ClusterDistribution.cpp

@@ -78,8 +78,11 @@ nderivatives(0)
    parseFlag("INVERSE_TRANSFORM",inverse);
    if( inverse && !use_switch ) error("INVERSE_TRANSFORM option was specified but no TRANSOFRM switching function was given");
 
-   // Setup the various things this will calculate
-   readVesselKeywords();
+   // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
+   for(unsigned i=0;i<getNumberOfNodes();++i) addTaskToList(i);
+
+   // And now finish the setup of everything in the base
+   setupAtomLists();
 }
 
 void ClusterDistribution::calculate(){

src/adjmat/ClusterProperties.cpp

@@ -165,8 +165,11 @@ ClusterAnalysisBase(ao)
    if( clustr<1 ) error("cannot look for a cluster larger than the largest cluster");
    if( clustr>getNumberOfNodes() ) error("cluster selected is invalid - too few atoms in system");
 
-   // Setup the various things this will calculate
-   readVesselKeywords();
+   // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
+   for(unsigned i=0;i<getNumberOfNodes();++i) addTaskToList(i);
+
+   // And now finish the setup of everything in the base
+   setupAtomLists();
 }
 
 void ClusterProperties::calculate(){

src/adjmat/ClusterSize.cpp

@@ -68,7 +68,10 @@ ClusterAnalysisBase(ao)
    if( clustr<1 ) error("cannot look for a cluster larger than the largest cluster");
    if( clustr>getNumberOfNodes() ) error("cluster selected is invalid - too few atoms in system");
 
-   addValue(); setNotPeriodic();
+   // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
+   for(unsigned i=0;i<getNumberOfNodes();++i) addTaskToList(i);
+   // And now finish the setup of everything in the base
+   setupAtomLists(); addValue(); setNotPeriodic();
 }
 
 void ClusterSize::turnOnDerivatives(){