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muon-spectroscopy-computational-project / pymuon-suite

Collection of scripts and utilities for muon spectroscopy
GNU General Public License v3.0
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DFTB read doesn't pick up custom masses #57

Closed elichad closed 11 months ago

elichad commented 2 years ago

When reading the output DFTB+ file geo_end.gen using ASE, masses are set to the default atomic mass of the element symbol's prefix, as the custom mass is set in dftb_in.hsd (the DFTB+ input file) which isn't read simultaneously. For example, if the muon is treated as an H with a custom mass, it is given a mass of 1.008 when loaded by ASE.

I'm not sure this is a big issue for us as it happens after the relaxation stage, but something to be aware of.

Similar issue exists for CASTEP but I've raised that as an ASE issue since the mass & element info is all contained in the same file and should be picked up by ASE https://gitlab.com/ase/ase/-/issues/1079 . For DFTB+ perhaps it's on us to set the mass ourselves if we need it in the clustering stage.

leandro-liborio commented 11 months ago

We will not be using DFTB+ in the near future.