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warn for unknown element symbols #63

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ltalirz opened this issue Apr 22, 2021 · 0 comments
Open

warn for unknown element symbols #63

ltalirz opened this issue Apr 22, 2021 · 0 comments

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@ltalirz
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ltalirz commented Apr 22, 2021

Another point discovered with CIFs from the CSD: pymatgen spits out the symbol "D0+" when the structure contains deuterium, which is then not understood by zeo++

Unable to find radius for D0+ in table. Please provide it

zeo++ actually has a radius for deuterium, so it's not really its fault (more pymatgen's).

However, it might make sense to add a check in aiida-zeopp in prepare_for_submission:
if no radiifile is provided, one could try to parse the CIF file and check whether there are any element symbols unknown to zeo++ (see link above for the known ones).

In any case, this issue is mostly for reference - it's probably best to fix this at the pymatgen side

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