[ase-users] swap atoms

[Jens Jørgen Mortensen]

On 07/28/2017 03:15 PM, Ask Hjorth Larsen via ase-users wrote:
> Hi
>
> 2017-07-28 5:44 GMT+02:00 Tristan Maxson via ase-users
> <ase-users at listserv.fysik.dtu.dk>:
>> I think a function like this is reasonable, but the following can be done
>> just as easily. I can put in a pull request for the next version of ASE with
>> something like this, we can work out details on naming on the request.
>>
>> Try something like this
>>
>> atoms[i_a].position, atoms.position[i_b] = atoms.position[i_b],
>> atoms.position[i_a]
>>
>> This could get pretty ugly looking in code very quickly though and a helper
>> function makes sense. Thank you for the suggestion.
> Another way is:
>
> atoms.positions[[i, j]] = atoms.positions[[j, i]]
>
> I think this simple enough that a method is not needed.  It is a bit
> unclear what a method called swap() exactly does (does it interchange
> the species, or the position, or reorder the atoms object itself,
> ...), so it is likely more clear to do it directly on the array
> anyway.

I've added it to the "tips and tricks" page:

     https://wiki.fysik.dtu.dk/ase/dev/tips.html

Jens Jørgen

> Best regards
> Ask
>
>
>
>> Tristan Maxson
>>
>>
>> On Thu, Jul 27, 2017 at 10:42 PM, Oscar Xavier Guerrero via ase-users
>> <ase-users at listserv.fysik.dtu.dk> wrote:
>>> Hello,
>>>
>>> I am interested in swapping the positions of two atoms.
>>>
>>> This is what I'm doing right now:
>>>
>>> atoms = init_atoms.copy()
>>> atoms[i_a].position = init_atoms[i_b].get('position')
>>> atoms[i_b].position = init_atoms[i_a].get('position')
>>>
>>> Here i_a and i_b are the indices of the two atoms I want to swap. Should
>>> there be a function in the atoms object that mutates it or returns a copy?
>>> Something like:
>>>
>>> atoms.exchange(i_a, i_b)
>>> atoms.swap(i_a, i_b)
>>>
>>>
>>>
>>>
>>>
>>>
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>>> ase-users mailing list
>>> ase-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>
>>
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