Added two new methods to get all the close pairs (not checking for duplicates at this time).

getClosePairs to get the indexes in the positions array, getClosePairsAtomicIndex to get the atomic indexes instead

src/NeighborList.cpp

@@ -118,6 +118,30 @@ vector<unsigned> NeighborList::getNeighborsAtomicIndex(unsigned iatom)
  return neigh; 
 }
 
+vector<pair <unsigned, unsigned> > NeighborList::getClosePairs()
+{
+ vector<pair <unsigned, unsigned> > pairs;
+ for(unsigned int i=0;i<getNumberOfAtoms();++i){
+  for(unsigned int j=0;j<getNumberOfNeighbors(i);++j){
+   unsigned jatom=neighbors_[i][j];
+   pairs.push_back(pair <unsigned,unsigned> (i,indexes_[jatom]));
+  }
+ }
+ return pairs;
+}
+
+vector<pair <unsigned, unsigned> > NeighborList::getClosePairsAtomicIndex()
+{
+ vector<pair <unsigned, unsigned> > pairs;
+ for(unsigned int i=0;i<getNumberOfAtoms();++i){
+  unsigned iatom=list0_[i];
+  for(unsigned int j=0;j<getNumberOfNeighbors(i);++j){
+   pairs.push_back(pair <unsigned,unsigned> (iatom,neighbors_[i][j]));
+  }
+ }
+ return pairs;
+}
+
 unsigned NeighborList::getNumberOfNeighbors(unsigned index)
 {
  return neighbors_[index].size();
@@ -125,5 +149,5 @@ unsigned NeighborList::getNumberOfNeighbors(unsigned index)
 
 unsigned NeighborList::getNumberOfAtoms() const
 {
- return neighbors_.size();
+ return list0_.size();
 }

src/NeighborList.h

@@ -22,6 +22,8 @@ public:
   void update();
   std::vector<unsigned> getNeighbors(unsigned index);
   std::vector<unsigned> getNeighborsAtomicIndex(unsigned iatom);
+  std::vector<std::pair <unsigned, unsigned> > getClosePairs();
+  std::vector<std::pair <unsigned, unsigned> > getClosePairsAtomicIndex();
   unsigned getStride() const;
   unsigned getNumberOfAtoms() const;
   unsigned getNumberOfNeighbors(unsigned index);