[ase-users] Sorting the atoms by type is ASE Atoms object

[Ask Hjorth Larsen]

Hi,

2018-01-08 17:48 GMT+01:00 Spencer Hills via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> Hello,
>
> I am taking two atoms objects and combining them together in ASE. When I
> combine the atoms objects together, the atoms in it become ordered based on
> the atoms object that they came from, not the atom type. Is there a method
> in the atoms object that will sort the atoms based in type?
>
> For example, say I have a little IrO2 cluster:
>
> Ir  22.6334501337769005 19.6996362359443431 21.0784105283482646
>
> Ir  20.2595762079976787 22.4702461104581452 20.7038624595503258
>
> O  19.3965392350654007 23.4514891890007426 22.1970325117515728
>
> O  24.0620720990382466 21.0803337056451703 21.1448758079263861
>
> O  15.7084192410784240 19.4294461605727591 20.5780672191905865
>
> O  19.7168563866926618 21.1123958649343066 24.2764522228896453
>
> Ir  21.3230402254681302 16.6020447883440561 17.0235124864985607
>
> O  23.2085293491334674 22.2830325778158311 19.4895699171266834
>
> O  18.7714791811689601 19.4119976460262293 16.9011321089083033
>
>
> But I want it to look like this:
>
> Ir  22.6334501337769005 19.6996362359443431 21.0784105283482646
>
> Ir  20.2595762079976787 22.4702461104581452 20.7038624595503258
>
> Ir  21.3230402254681302 16.6020447883440561 17.0235124864985607
>
> O  19.3965392350654007 23.4514891890007426 22.1970325117515728
>
> O  24.0620720990382466 21.0803337056451703 21.1448758079263861
>
> O  15.7084192410784240 19.4294461605727591 20.5780672191905865
>
> O  19.7168563866926618 21.1123958649343066 24.2764522228896453
>
> O  23.2085293491334674 22.2830325778158311 19.4895699171266834
>
> O  18.7714791811689601 19.4119976460262293 16.9011321089083033
>
>
> Is there a way to do that?

import numpy as np
permutation = np.argsort(atoms.numbers)
atoms = atoms[permutation]

You may wish to map the atomic numbers to a different set of numbers
to customize the sort; for example map Ir to something smaller than O
if that is important.

Best regards
Ask

>
>
> Thanks,
>
> Spencer
>
>
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