Update to AtomsBase 0.4 #77
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Luthaf
reviewed
Oct 23, 2024
| velocity_arg = (Chemfiles.velocities(frame)[:, i]u"Å/ps", ) | ||
| end | ||
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| species = AtomsBase.ChemicalSpecies(Chemfiles.atomic_number(atom)) |
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in case where the atomic number is unknown, this function will return 0. Does AtomsBase.ChemicalSpecies handle this?
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| if Symbol(species) != Symbol(Chemfiles.name(atom)) | ||
| @warn "Ignoring non-standard atom name $(Chemfiles.name(atom)) for atom $i." |
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should this check on the atom type instead? Atom name could be something like CA, while atom type would be C
https://chemfiles.org/Chemfiles.jl/latest/reference/atom/#Chemfiles.type-Tuple{Chemfiles.Atom}
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Thanks for your review @Luthaf. This triggered some internal discussion in AtomsBase aboutChemicalSpecies, so this will stall a while. |
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Updates the AtomsBase conversion layer to AtomsBase 0.4.
Requires JuliaMolSim/AtomsBase.jl#121 to be merged and AtomsBaseTesting released before tests pass.