Different behavior for neighbors.periodic_nearest_neighbors_by_atom() and neighbors.periodic_nearest_neighbors_by_atom_large()

[adamphil]

Using all the same arguments, some atoms are excluded when computing neighbors using the _large version of the function. Seems to have to do with the passing of kwargs regarding bond thresholds and molecule computation.

[avmarchenko]

Thanks for this issue report. Would it be possible to give a minimal working example perhaps? Including the commands run and a snapshot (xyz or similar) where the behavior is observed would help debug. It is possible that there is a bug in the code or (more nefariously) that the algorithm has nuances that haven't been uncovered. Either way, the commands run and an example snapshot are necessary to investigate.

[adamphil]

exatomic-issue#133.py.txt
example.txt

Don't think I did this properly but w/e