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

[Ask Hjorth Larsen]

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, ...?

Best regards
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