docs: def remove_collisions(self, min_dist=0.5):
          """
          Remove vnodes that are too close to existing atoms in the structure
  
          Args:
              min_dist(float): The minimum distance that a vertex needs to be
                  from existing atoms.
          """
          vfcoords = [v.frac_coords for v in self.vnodes]
          sfcoords = self.structure.frac_coords
          dist_matrix = self.structure.lattice.get_all_distances(vfcoords,
                                                                 sfcoords)
          all_dist = np.min(dist_matrix, axis=1)
          new_vnodes = []
          for i, v in enumerate(self.vnodes):
              if all_dist[i] > min_dist:
                  new_vnodes.append(v)
          self.vnodes = new_vnodes