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

[Michael Walter]

2016-10-05 8:06 GMT+02:00 Jens Jørgen Mortensen via ase-users <
ase-users at listserv.fysik.dtu.dk>:

> 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 can agree also.

In particular the restriction of the chemical symbols was annoying when one
is working with eg. force fields, where different "versions" of the same
element appear.

Nevertheless flexibility always comes with the price of complexity. Maybe
we can create a more flexible Atoms base class (eg. named Structure) and
can keep the simpler Atoms class as it is now in addition. A "Structure"
could then consist of virtually anything that is connected to a potential
and/or forces.

Michael


>
> Jens Jørgen
>
>
>
>> Best regards
>> Ask
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>
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PD Dr Michael Walter
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