Check Generalization of unit cells in ASE
Check to see if this is important for us in Amp?
https://listserv.fysik.dtu.dk/pipermail/ase-users/2016-November/003212.html
See also messages following it in the thread...
Comments (4)
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reporter -
repo owner I just saw your comment on ASE, but it looks like you put it on the closed merge request. I tried your test script with the newest master version of ASE and it breaks with a different error. You probably need to create an issue on the ASE gitlab page instead of on the merge request.
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reporter -
repo owner - changed status to resolved
I see. Actually it looks like you were specifying both the pbc and the cell wrong, because the new way of defining the unit cell is now defaulting to [0, 0, 0] if you don't otherwise specify. (Previously it was [1, 1, 1].) So a 0-sided cell with periodic boundary conditions should break with a divide by zero message when calculating neighborlists -- infinite neighbors!
Anyway, I think this is behaving as we want if we write a script like
from ase import Atoms from ase.neighborlist import NeighborList image = Atoms('H', pbc=True, cell=[1.5, 1.5, 1.5]) nl = NeighborList(cutoffs=[3.0,], self_interaction=False, bothways=True, skin=0.) nl.update(image)
so we can close this issue.
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This recent change in pbc of ASE seems to break the update (or build) method of NeighborList. If we do
it will crash here with the message "IndexError: index 1 is out of bounds for axis 0 with size 1".
I am not sure what they desire to do with this new implementation to go ahead and fix it. Therefore, I just put a comment under the merge request. Lets postpone this issue for now until we hear back from them.