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

[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.

Jens Jørgen

>
> Best regards
> Ask
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