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deepmodeling / dpdata

Manipulating multiple atomic simulation data formats, including DeePMD-kit, VASP, LAMMPS, ABACUS, etc.
https://docs.deepmodeling.com/projects/dpdata/
GNU Lesser General Public License v3.0
188 stars 128 forks source link

improve ASE traj #633

Closed thangckt closed 1 month ago

thangckt commented 3 months ago

add functions to convert from others formats to ASE traj format

Summary by CodeRabbit

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 84.31%. Comparing base (1d87e82) to head (77fb18a). Report is 1 commits behind head on devel.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #633 +/- ## ========================================== + Coverage 84.06% 84.31% +0.25% ========================================== Files 81 81 Lines 7122 7141 +19 ========================================== + Hits 5987 6021 +34 + Misses 1135 1120 -15 ```

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coderabbitai[bot] commented 1 month ago

Walkthrough

The recent changes enhance the functionality of the dpdata/plugins/ase.py module by updating the return types of several methods and adding new parameters for improved flexibility. Additionally, the Python version matrix for testing has been streamlined, and new test classes have been introduced to ensure the robustness of the changes.

Changes

File Change Summary
dpdata/plugins/ase.py Updated return types, added new parameters, and modified functionality in several methods.
.github/workflows/test.yml Updated Python version matrix to include only version "3.11".
tests/test_ase_traj.py Added new test classes TestASEtraj4 and TestASEtraj4Labeled to test trajectory-related operations.

Sequence Diagram(s) (Beta)

sequenceDiagram
    participant User
    participant ASEPlugin
    participant ASEIO
    participant TestSuite

    User->>ASEPlugin: Call to_system(data, file_name="confs.traj")
    ASEPlugin->>ASEIO: Save data to trajectory file
    ASEIO-->>ASEPlugin: Trajectory file saved
    ASEPlugin-->>User: Return List[ase.Atoms]

    User->>ASEPlugin: Call to_labeled_system(data, file_name="labeled_confs.traj")
    ASEPlugin->>ASEIO: Save labeled data to trajectory file
    ASEIO-->>ASEPlugin: Labeled trajectory file saved
    ASEPlugin-->>User: Return List[ase.Atoms]

    TestSuite->>ASEPlugin: Run TestASEtraj4
    ASEPlugin-->>TestSuite: Test results
    TestSuite->>ASEPlugin: Run TestASEtraj4Labeled
    ASEPlugin-->>TestSuite: Test results

[!TIP]

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codspeed-hq[bot] commented 1 month ago

CodSpeed Performance Report

Merging #633 will not alter performance

Comparing thangckt:PR (bb0640f) with devel (c5b36bb)

Summary

✅ 2 untouched benchmarks