pymatgen.optimization.neighbors module

compute_offset_vectors()[source]
find_points_in_spheres()[source]

For each point in center_coords, get all the neighboring points in all_coords that are within the cutoff radius r. All the coordinates should be in Cartesian.

Parameters:

  • all_coords – (np.ndarray[double, dim=2]) all available points. When periodic boundary is considered, this is all the points in the lattice.

  • center_coords – (np.ndarray[double, dim=2]) all centering points

  • r – (float) cutoff radius

  • pbc – (list of bool) whether to set periodic boundaries

  • lattice – (np.ndarray[double, dim=2]) 3x3 lattice matrix

  • tol – (float) numerical tolerance

  • min_r – (float) minimal cutoff to calculate the neighbor list directly. If the cutoff is less than this value, the algorithm will calculate neighbor list using min_r as cutoff and discard those that have larger distances.

Returns:

index1 (n, ), index2 (n, ), offset_vectors (n, 3), distances (n, ). index1 of center_coords, and index2 of all_coords that form the neighbor pair

offset_vectors are the periodic image offsets for the all_coords.