vesin

import numpy as np from vesin import NeighborList # Define positions and box (example for a 2-atom system in a cubic box) positions = np.array([ (0.0, 0.0, 0.0), (0.5, 0.0, 0.0) ]) box = 3.0 * np.eye(3) # 3x3 Angstrom cubic box cutoff = 1.0 # Angstroms # Initialize the NeighborList calculator calculator = NeighborList(cutoff=cutoff, full_list=True) # Compute the neighbor list, requesting indices (i, j), periodic shifts (S), and distances (d) i, j, S, d = calculator.compute( points=positions, box=box, periodic=True, # Enable periodic boundary conditions quantities="ijSd" ) print(f"Neighbor indices (i): {i}") print(f"Neighbor indices (j): {j}") print(f"Periodic shifts (S): {S}") print(f"Distances (d): {d}") # Example with ASE (requires 'ase' to be installed) # try: # import ase # from vesin import ase_neighbor_list # atoms = ase.Atoms('H2', positions=[(0,0,0), (0,0,0.74)], cell=[10,10,10], pbc=True) # i_ase, j_ase, S_ase, d_ase = ase_neighbor_list("ijSd", atoms, cutoff=1.0) # print(f"\nASE-compatible Neighbor indices (i): {i_ase}") # except ImportError: # print("\nASE not installed, skipping ase_neighbor_list example.")