facebookresearch / facebookresearch/all-atom-diffusion-transformer

Potential unit issue with StructureMatcher.get_rms_dist() in evaluation

Open
#28 3 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
317
Forks
43
PR merge metrics
No merged PRs in 30d

Description

https://github.com/facebookresearch/all-atom-diffusion-transformer/blob/b9ce505f170597a7c8ca50d13ce8e15df21cf8c9/src/eval/crystal_reconstruction.py#L98C13-L98C79

This method might return a volume-normalized dimensionless value rather than actual distances in Ångstroms. The normalization seems to be (volume/nsites)^(1/3).

However, in your paper, it appears to treat these values as Ångstrom units.

Could you clarify this, thank you!

Contributor guide

Open the contributing guide

Research direction

Start at src/eval/crystal_reconstruction.py around line 98 and inspect how StructureMatcher.get_rms_dist() is used in evaluation. Check the method's documented units and the apparent (volume/nsites)^(1/3) normalization, then compare the result with the paper's stated Ångstrom interpretation; done means the unit question is resolved and the evaluation is documented or corrected accordingly.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.