Cleanup

      # make sure duplicate neighbors are ignored. Convert back to list before

      # returning. 

      neighbor_list[atom] = set()

      ####################################################### DEBUG

      all_nbrs = set()

      print("self.neighbor_cutoff")

      print(self.neighbor_cutoff)

      ####################################################### DEBUG

      for neighbor_cell in neighbor_cells:

        atoms_in_cell = cell_to_atoms[neighbor_cell]

        for neighbor_atom in atoms_in_cell:

          # account for periodic boundary conditions?

          if np.linalg.norm(coords[atom] - coords[neighbor_atom]) < self.neighbor_cutoff:

            neighbor_list[atom].add(neighbor_atom)

          ########################################################### DEBUG

          all_nbrs.add(neighbor_atom)

          ########################################################### DEBUG

      ########################################################### DEBUG

      print("All neighbor-cell atoms for %d = %s" % (atom, str(all_nbrs)))

      neighbor_list[atom] = list(neighbor_list[atom])

    return neighbor_list