[ase-users] 'Compatibility' of Atoms object with other codes

Jens Jørgen Mortensen jensj at fysik.dtu.dk
Wed Oct 5 08:32:21 CEST 2016


Den 05-10-2016 kl. 08:06 skrev Jens Jørgen Mortensen:
> Den 03-10-2016 kl. 18:39 skrev Ask Hjorth Larsen via ase-users:
>> Hello
>>
>> Maybe we have discussed this before, but I am not quite sure.
>>
>> With ASE you can call other codes, and this is never much of a problem
>> when ASE defines what the code should do.  However, for reading data
>> produced with other codes, the Atoms object frequently falls short on
>> two counts:
>>
>>    1) The Atoms object always has a 3x3 cell, and many codes have
>> either no cell, irregular shapes, or something else.
>>    2) In ASE, each atom has a chemical symbol which corresponds
>> one-to-one with an atomic number.  Many codes allows arbitrary names
>> for species or something entirely different.
>>
>> I suggest somehow improving these two things.
>>
>> We could allow the 'cell' could be None.  This will undoubtedly be an
>> annoyance, although only when something wrong was happening in the
>> first place.  One could also define a boolean or something more
>> complex to describe the cell when an array is not appropriate.
>>
>> An extra optional array of 'labels' could represent names when
>> something more than the chemical symbol is necessary.  I know we
>> already have 'tags', which are numbers.
>>
>> Suggestions, protests, ...?
>
> I like both suggestions.  It will be nice to get rid of the default 
> [[1,0,0],[0,1,0],[0,0,1]] cell we have now.

I once did some work on the cell-thing:

     https://gitlab.com/jensj/ase/tree/cell

but never finished it ...

Jens Jørgen

>
> Jens Jørgen
>
>>
>> Best regards
>> Ask
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>



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