Neighbors

neighbors(structure, cutoff) returns every periodic pair within cutoff Angstrom as Neighbor { i, j, image, distance }, where image is the lattice translation of atom j relative to atom i. neighbors_of filters the list for one atom. The structure is expanded to P1 first.

rust

use xtalforge::core::neighbors;

let found = neighbors(&structure, 3.2)?;
for neighbor in &found {
    println!("{} - {} at {:.3} A", neighbor.i, neighbor.j, neighbor.distance);
}

The search uses a linked-cell index in fractional space. Bins are sized from the perpendicular widths of the cell, so triclinic cells are exact; each candidate pair then enumerates the integer images that can reach the cutoff. Small cells and skewed cells include the repeated images inside the cutoff. Results are sorted by (i, j, image), which makes them deterministic. Self-images (i == j, nonzero image) are included; the zero image is not.

The benchmark target covers 10^3, 10^4 and 10^5 atoms:

bash

cargo bench -p xtalforge-core --bench neighbors

See Periodic neighbor search for the index construction, the complexity and the comparison with the Crystal-Builder implementation.

Neighbors ​

Neighbors