find k nearest neighbors within r_cutoff

[yzchen08]

Can vesin find k nearest neighbors within r_cutoff and output idx_i, idx_j, shifts? For now I can only calculate all neighbors within r_cutoff.

calculator = vesin.NeighborList(cutoff=self.r_cutoff, full_list=True)
idx_i, idx_j, shifts, distances = calculator.compute(
    points=atoms.positions, 
    box=atoms.cell.array, 
    periodic=True, 
    quantities="ijSd"
    )

[Luthaf]

In the current state, you'll need to do some post-processing to get the k nearest neighbors: sorting the distances array; sorting the (i, j, S) arrays in the same way; and then taking the first k elements.

It could make sense to add an option on vesin side to do the sorting according to distances (the current sorted argument sorts the pair indices); and then you would only have to slice the arrays to get the data you need.