pymatgen.optimization.neighbors module¶
-
compute_offset_vectors
()¶
-
find_points_in_spheres
()¶ 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
numerical_tol – (float) numerical tolerance
- 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.