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Period group embedding #331
Merged
chrisiacovella
merged 13 commits into
choderalab:main
from
chrisiacovella:period_group_embedding
Jan 16, 2025
Merged
Period group embedding #331
chrisiacovella
merged 13 commits into
choderalab:main
from
chrisiacovella:period_group_embedding
Jan 16, 2025
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…re just based on atomic number, moved the assignment into featurization, to minimize including additional things in NNPInput (since using slots now and no longer dynamic).
…r some reason; fixing that seems to fix issues).
MarshallYan
reviewed
Jan 10, 2025
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Pull Request Summary
This adds in the ability to do embedding with the atomic group and period along with atomic number, as mentioned in issue #330. Like atomic number, we can specify number of features (i.e, the size of the tensor), as opposed to be a singular value like charge.
Initially I added period and group to the NNPInput, but decided to change this to being set in featurization just based on atomic number. Adding to NNPInput breaks a lot of other things (since it uses slots and is no longer dynamic) and we should really only really need this this if it is requested in featurization (so it's a waste of memory to set this for each batch). For things that don't have a group (specifically the Lanthanoid series) likely need to return a default value of zero. Currently I have Lanthanum set to be group 3, only because it is in TMQM and thus needed a definition (from a chemistry perspective I'm not sure if that makes sense to group it in there, but since Sc or Y in the dataset I'm not sure it matters).
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