Update ase.py: To avoid errors in writing to the .extxyz format from an Atom object coverted from .npy with dpdata. #717

ZhouXY-PKU · 2024-09-04T01:58:37Z

Stress store in an ASE SinglePointCalculator should be an 1×6 array, not be a 3×3 matrix.

Summary by CodeRabbit

New Features
- Enhanced stress value calculations to provide a more structured representation of the stress tensor components in results.
- Improved handling of stress tensor components for better accuracy in subsequent calculations.

…an Atom object coverted from .npy with dpdata. Stress store in an ASE SinglePointCalculator should be an 1×6 array, not be a 3×3 matrix. Signed-off-by: Levi Zhou <[email protected]>

coderabbitai · 2024-09-04T01:58:45Z

Walkthrough

The changes in the to_labeled_system method of the dpdata/plugins/ase.py file involve a modification in the calculation and storage of stress values in the results dictionary. The stress is now computed as a structured NumPy array that includes both diagonal and off-diagonal components of the stress tensor, improving the organization of stress data.

Changes

Files	Change Summary
`dpdata/plugins/ase.py`	Updated the `to_labeled_system` method to calculate stress as a structured NumPy array, incorporating specific components of the stress tensor. No changes to the function signature.

Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 9de727e and 9a92619.

Files selected for processing (1)

dpdata/plugins/ase.py (1 hunks)

Files skipped from review as they are similar to previous changes (1)

dpdata/plugins/ase.py

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codspeed-hq · 2024-09-04T02:00:17Z

CodSpeed Performance Report

Merging #717 will not alter performance

_{Comparing ZhouXY-PKU:patch-1 (9a92619) with master (c685e62)}

Summary

✅ 2 untouched benchmarks

codecov · 2024-09-04T02:00:24Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.51%. Comparing base (c685e62) to head (9a92619).
Report is 33 commits behind head on devel.

Additional details and impacted files

@@           Coverage Diff           @@
##            devel     #717   +/-   ##
=======================================
  Coverage   84.50%   84.51%           
=======================================
  Files          81       81           
  Lines        7152     7153    +1     
=======================================
+ Hits         6044     6045    +1     
  Misses       1108     1108

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

njzjz · 2024-09-04T04:57:45Z

dpdata/plugins/ase.py

+                        stress33[1][1],
+                        stress33[2][2],
+                        stress33[1][2],
+                        stress33[2][0],


should be 0,2 though

https://gitlab.com/ase/ase/-/blob/bfd2381a/ase/calculators/cp2k.py#L362

But actually the value of (2,0) always equals to (0,2)......changing it is okay.

Signed-off-by: Levi Zhou <[email protected]>

Update ase.py: To avoid errors in writing to the .extxyz format from …

7a10ae6

…an Atom object coverted from .npy with dpdata. Stress store in an ASE SinglePointCalculator should be an 1×6 array, not be a 3×3 matrix. Signed-off-by: Levi Zhou <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

9de727e

for more information, see https://pre-commit.ci

ZhouXY-PKU mentioned this pull request Sep 4, 2024

[Feature Request] We need another LabeledSystem input and output format, such as extxyz #708

Open

njzjz requested changes Sep 4, 2024

View reviewed changes

Update ase.py: Stress zx to xz

9a92619

Signed-off-by: Levi Zhou <[email protected]>

njzjz approved these changes Sep 4, 2024

View reviewed changes

njzjz changed the base branch from master to devel September 4, 2024 13:49

njzjz merged commit 976cf16 into deepmodeling:devel Sep 4, 2024
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Update ase.py: To avoid errors in writing to the .extxyz format from an Atom object coverted from .npy with dpdata. #717

Update ase.py: To avoid errors in writing to the .extxyz format from an Atom object coverted from .npy with dpdata. #717

ZhouXY-PKU commented Sep 4, 2024 •

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ZhouXY-PKU Sep 4, 2024

Update ase.py: To avoid errors in writing to the .extxyz format from an Atom object coverted from .npy with dpdata. #717

Update ase.py: To avoid errors in writing to the .extxyz format from an Atom object coverted from .npy with dpdata. #717

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ZhouXY-PKU commented Sep 4, 2024 •

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