How to load structures including Deuterium with ASE

ASE
1

When I use ase.AseAtomsAdaptor.get_atoms to convert pymatgen.core.structure.Structure object to Atom object, I always see error loading structures that include Deuterium, as I show in the attached picture. Do you know how to read the .mcif files with Deuterium?

picture

2

Dear Ryotaro,

This is an issue with pymatgen, as it tries to create an Atoms object with the element D.

To create the Atoms object, you (or the pymatgen code) will need to set the masses explicitly and then make sure the symbol is H rather than D.

Best regards
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