Add NEBCalculator with M3GNet and CHGNet example notebook
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I don't see you loading all these trajectory files in the test nor example notebook you added. Were they committed by accident?
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These can be deleted. They are truly not used anywhere. I will remove them from the PR.
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I have removed the traj files, and users can reproduce them with the notebook if needed. Now the NEB_data is below 1MB that majorly comes from the two png files in the notebook. Let me know if we need to futher downsize it or not.
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Could you replace the PNGs with vector graphics if those are smaller (PDF will be smaller but might not work in notebook, so could try SVG as well).
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I just tried and the pdf file (~2.5MB for each) extracted from VESTA would be >5 times larger than the png snapshot. Directly transferring the png snapshots to pdf version would not change the size much, e.g., from 284 to 276 KB. If the storage space is of concern, maybe we can just remove all NEB_data?
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Just use the PNG. Don't be silly. there are instances where vector formats are better and there are those where non-vector are better. this is one instance. Though 2.5 Mb is really nothing.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #13 +/- ##
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+ Coverage 99.11% 100.00% +0.88%
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Files 7 8 +1
Lines 227 271 +44
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+ Hits 225 271 +46
+ Misses 2 0 -2 ☔ View full report in Codecov by Sentry. |
| if self.traj_folder is not None: | ||
| os.makedirs(self.traj_folder, exist_ok=True) | ||
| for i in range(len(self.images)): | ||
| self.optimizer.attach( |
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We need some more tests for uncovered lines (see the codecov comments).
janosh
added
enhancement
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Thanks @JiQi535, really nice contribution! |
janosh
changed the title
NEBCalculator with M3GNet and CHGNet example notebook
Summary
Added NEBCalc for NEB calculations with universal potentials. LiFePO4 is used as an example system, where M3GNet-MS, M3GNet-DIRECT, and CHGNet provide reasonable agreements to each other and to literature.
Major changes:
Checklist
ruff.mypy.duecredit@due.dcitedecorators to reference relevant papers by DOI (example)