Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Period group embedding #331

Merged
merged 13 commits into from
Jan 16, 2025

Conversation

chrisiacovella
Copy link
Member

@chrisiacovella chrisiacovella commented Dec 23, 2024

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).

Key changes

Notable points that this PR has either accomplished or will accomplish.

  • Adds atomic group and period to featurization (computed if requested)

Associated Issue(s)

Pull Request Checklist

  • Issue(s) raised/addressed and linked
  • Includes appropriate unit test(s)
  • Appropriate docstring(s) added/updated
  • Appropriate .rst doc file(s) added/updated
  • PR is ready for review

@chrisiacovella chrisiacovella added enhancement New feature or request WIP Work in Progress labels Dec 23, 2024
…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).
@codecov-commenter
Copy link

codecov-commenter commented Dec 26, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 79.01%. Comparing base (8120b70) to head (d2a0ff4).

Additional details and impacted files

@chrisiacovella chrisiacovella removed the WIP Work in Progress label Jan 6, 2025
@chrisiacovella chrisiacovella merged commit 54962ca into choderalab:main Jan 16, 2025
10 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants