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Element symbols are now used when generating an ase atom. #1571

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merged 1 commit into from
Mar 25, 2023
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Element symbols are now used when generating an ase atom. #1571

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4 changes: 3 additions & 1 deletion optimade/adapters/structures/ase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,9 @@ def get_ase_atoms(optimade_structure: OptimadeStructure) -> Atoms:
if current_species.mass:
mass = current_species.mass[0]
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@ml-evs ml-evs Mar 26, 2023 •
edited

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Could probably do with an additional check for partial/multiple occupancy here, e.g.,

Suggested change
mass = current_species.mass[0]
mass = current_species.mass[0]
if len(current_species.chemical_symbols) != 1:
raise RuntimeError

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@JPBergsma JPBergsma Mar 27, 2023 •
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In principle, the disorder flag should be set in the structure_features when more than 1 element is present in a species.chemical_symbols.
And we already check for this. Do you want me to make an additional check for the fields that could potentially have more than 1 value ? i.e. mass and chemical symbols ?

PS. I do not think it is possible to generate a StructureResource object which has multiple entries for chemical_symblos or mass without also setting disorder. So I do not think this test is necessary.


atoms.append(Atom(symbol=species_name, position=site, mass=mass))
atoms.append(
Atom(symbol=current_species.chemical_symbols[0], position=site, mass=mass)
)

info = {}
for key in attributes.dict().keys():
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15 changes: 12 additions & 3 deletions optimade/server/data/test_structures.json
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Expand Up @@ -267,7 +267,16 @@
"concentration": [
1.0
],
"name": "Ac"
"name": "Ac1"
},
{
"chemical_symbols": [
"Ac"
],
"concentration": [
1.0
],
"name": "Ac2"
},
{
"chemical_symbols": [
Expand All @@ -289,8 +298,8 @@
}
],
"species_at_sites": [
"Ac",
"Ac",
"Ac1",
"Ac2",
"Ag",
"Pb"
],
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