Small cleanup in WholeMolecules

* Eliminated a possible tricky method to modify atom by relative index
* Eliminated duplicates in requested atom list

I also added a operators to AtomNumber, so it can be sorted with STL
algorithms

src/AtomNumber.h

@@ -20,6 +20,8 @@ public:
   void setIndex(unsigned);
   static AtomNumber serial(unsigned);
   static AtomNumber index(unsigned);
+  friend bool operator<(const AtomNumber&,const AtomNumber&);
+  friend bool operator==(const AtomNumber&,const AtomNumber&);
 };
 
 inline
@@ -62,6 +64,16 @@ AtomNumber AtomNumber::index(unsigned i){
   return a;
 }
 
+inline
+bool operator<(const AtomNumber&a,const AtomNumber&b){
+  return a.index_<b.index_;
+}
+
+inline
+bool operator==(const AtomNumber&a,const AtomNumber&b){
+  return a.index_==b.index_;
+}
+
 
 }
 

src/GenericWholeMolecules.cpp

@@ -3,6 +3,7 @@
 #include "ActionRegister.h"
 #include "Vector.h"
 #include "AtomNumber.h"
+#include "Tools.h"
 
 #include <vector>
 #include <string>
@@ -56,11 +57,6 @@ Vector & GenericWholeMolecules::modifyPosition(AtomNumber i){
   return plumed.getAtoms().positions[i.index()];
 }
 
-inline
-Vector & GenericWholeMolecules::modifyPosition(unsigned i){
-  return plumed.getAtoms().positions[getAbsoluteIndex(i).index()];
-}
-
 GenericWholeMolecules::GenericWholeMolecules(const ActionOptions&ao):
 Action(ao),
 ActionPilot(ao),
@@ -77,6 +73,7 @@ ActionAtomistic(ao)
     merge.insert(merge.end(),group.begin(),group.end());
   }
   checkRead();
+  Tools::removeDuplicates(merge);
   requestAtoms(merge);
 }