pele.mindist.periodic_mindist

class pele.mindist.periodic_mindist.MinDistBulk

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class MinDistBulk:

Obtain the best alignment between two configurations of a periodic system

MinDistBulk.align_fragments()

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def align_fragments(self, x1, x2):

Obtain the best alignment between two configurations of a periodic system

Parameters:

coords1, coords2np.array

the structures to align. X2 will be aligned with X1 Both structures are arrays of cartesian coordinates

Returns:

a triple of (dist, coords1, coords2). coords1 are the unchanged coords1

and coords2 are brought in best alignment with coords2

MinDistBulk.finalize_best_match()

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def finalize_best_match(self, x1, best_x2):

do final processing of the best match