coordinates inside displacement function about pybinding HOT 1 CLOSED

The onsite_modifier-function will compute the changed positions first, and only then take the appropriate shape. The larger number of sites comes from all the other sites that are first computed, but lie outside the polygon. The function is also called twice, for the A and B sublattice of graphene. The original, distorted and all the sites before the cutout are shown in following figure:

We are working on a better implementation of the model class such that this could be used to read out the updated positions from a .xyz-file. This work is still at the first stages, but this will help with the problem you are encountering. Right now, it is harder to tackle this problem. Right now, I just suggest you to print out the values and the sublattice that they correspond to, then, you can change the values manually for that system.
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from pybinding.