structure adapter ase convertor can not deal with symbol with index

[unkcpz]

It is allowed in the specification that the symbol of species_at_sites can have an index for the symbol https://github.com/Materials-Consortia/OPTIMADE/blob/develop/optimade.rst#species-at-sites.
However, ase.Atom do not accept this as symbol https://wiki.fysik.dtu.dk/ase/ase/atom.html#ase.atom.Atom.
The function standardize_chemical_symbol is introduced to convert it to the regular specie symbol.

Here is the trackback of failed test:

tests/adapters/structures/test_ase.py:24: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
optimade/adapters/structures/ase.py:91: in get_ase_atoms
    atoms.append(Atom(symbol=species_name, position=site, mass=mass))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <[AttributeError('atoms') raised in repr()] Atom object at 0x7f1b8cb83d40>, symbol = 'O0', position = [2.4472140189034, 3.0912417710884, 3.985872061678], tag = None, momentum = None
mass = 15.9994, magmom = None, charge = None, atoms = None, index = None

    def __init__(self, symbol='X', position=(0, 0, 0),
                 tag=None, momentum=None, mass=None,
                 magmom=None, charge=None,
                 atoms=None, index=None):
    
        self.data = d = {}
    
        if atoms is None:
            # This atom is not part of any Atoms object:
            if isinstance(symbol, str):
>               d['number'] = atomic_numbers[symbol]
E               KeyError: 'O0'

[JPBergsma]

Dear unkcpz,

Thank you for pointing out this issue with the ase adaptor.
The species in optimade can be an arbitrary string, so there is no guarantee that after stripping the digits, you will have a valid element symbol. So I do not think the solution you have here will work. Instead, you would need to read the element from the species.

I'll try to make a hot fix for this issue asap.

[JPBergsma]

I have created a quick fix (PR#1571) and merged it with the develop master branch.
I'll let @ml-evs check it before making a release.

[unkcpz]

Okay, thanks. I close this one.