A wrapped pair

Two points near opposite faces of a 10-wide box sit 9.2 apart in Cartesian space and 0.8 apart under the minimum image.

use minimage::Cell;

let cell = Cell::ortho(10.0, 10.0, 10.0)?;
assert!((cell.dist2([0.2, 0.0, 0.0], [9.4, 0.0, 0.0]) - 0.64).abs() < 1e-12);

A sheared LAMMPS dump uses bound spans, not lx, ly, lz. The a-image pair (0.2, 0.1, 1) and (9.7, 0.1, 1) on

box = 15  8.660254037844386  10  5  0  0

has squared distance 0.25.

let sheared = Cell::from_lammps_bounds(
    15.0, 8.660254037844386, 10.0, 5.0, 0.0, 0.0, 0.0, 0.0, 0.0,
)?;
assert!((sheared.dist2([0.2, 0.1, 1.0], [9.7, 0.1, 1.0]) - 0.25).abs() < 1e-12);

vesin can list a particle as its own neighbour through an image. reduce_pairs keeps each ordered pair once and drops the self image.

use minimage::reduce_pairs;

let pairs = [[0, 1], [0, 0], [0, 1]];
let mut kept = Vec::new();
reduce_pairs(&pairs, &mut kept)?;
assert_eq!(kept, vec![[0, 1]]);