code: public List<Contact> getContactsWithinCell(){
  
  		List<Contact> contacts = new ArrayList<Contact>();
  
  		Point3d[] iAtoms = grid.getIAtoms();
  		Point3d[] jAtoms = grid.getJAtoms();
  		double cutoff = grid.getCutoff();
  
  		if (jAtoms==null) {
  			for (int i:iIndices) {
  				for (int j:iIndices) {
  					if (j>i) {
  						double distance = iAtoms[i].distance(iAtoms[j]);
  						if (distance<cutoff) contacts.add(new Contact(i, j, distance));
  					}
  				}
  			}
  
  		} else {
  			for (int i:iIndices) {
  				for (int j:jIndices) {
  					double distance = iAtoms[i].distance(jAtoms[j]);
  					if (distance<cutoff) contacts.add(new Contact(i, j, distance));
  				}
  			}
  		}
  
  		return contacts;
  	}
docs: Calculates all distances of atoms within this cell returning those that are within the given cutoff
  as a list of Contacts containing the indices of the pair and the calculated distance.
  
  If {@link Grid#getJAtoms()} is null, distances are within the iAtoms only
  @return