Unstable `_bbox_intersect()`

[chenzhaiyu]

Unexpected AssertionError while initial bound should be fine:

AssertionError: intersection failed! check the initial bound

Degenerate cases found, likely due to arithmetic error of bounds (ndarray): https://github.com/chenzhaiyu/abspy/blob/91310f21d98451290364b04a721a747c5dfb3602/abspy/complex.py#L410 One possible fix is to stick to the rational ring, which however might harm the performance.

[chenzhaiyu]

Happening in the middle of partitioning from a complex model (with VertexGroupReference):

 59%|█████▉    | 192/326 [00:15<00:10, 12.67it/s]

[chenzhaiyu]

A simple distance tolerance was introduced rather than changing to the rational ring in favor of performance.