radius_graph for periodic structure

❓ Questions & Help

Do you have a radius_graph function for periodic structure? Otherwise I will think how I can implement one and propose a PR, any suggestions? So far we are using pymatgen.core.structure.Structure.get_all_neighbors to do that.

[mariogeiger]

Yes I will try to make something. I plan to look at it this week or maybe the week after. I’d love to contribute

[APJansen]

Any update on this issue? I would also like to create a radius graph that takes into account periodic boundary conditions. It is possible to do so by several times shifting the original positions and remapping them to the original domain, and computing the edges for each shift.

More elegant, and perhaps with unrelated applications as well, would be if one can provide a custom difference function to radius_graph. For example below is a difference for a box with periodicity in all directions.

I don’t know if that’s feasible though as I don’t know how radius_graph works internally, and found it very difficult to track down, as there are several imports between torch geometric and torch_cluster and vice versa.

def periodic_difference(x_i, x_j, domain):
    """
    Compute x_i - x_j taking into account the periodic boundary conditions.
    """
    diff = x_i - x_j
    smaller_one = x_i < x_j  # component-wise check which is bigger
    domain_shift = (1 - 2 * smaller_one) * domain
    diff_shifted = diff - domain_shift
    # boolean indicating in which component to use the original difference
    use_original = torch.abs(diff) < torch.abs(diff_shifted)
    periodic_diff = use_original * diff + ~use_original * diff_shifted
    return periodic_diff