Update shuffle_poscar feature in run.py

[ztzkz]

numpy.random.Generator.shuffle() performs the intended operation of shuffling the order of atoms. numpy.random.Generator.permuted() permutes the elements along the given axis, which mixes the coordinates of all atoms
shuffle

permuted

Summary by CodeRabbit

• Refactor
  • Improved the process that randomizes system coordinates when a specific option is enabled, enhancing internal data handling and consistency.

[coderabbitai]

📝 Walkthrough

Walkthrough

The change updates the make_model_devi function in the coordinate generation process. When the shuffle_poscar flag is set to True, the function now uses rng.shuffle to shuffle the system coordinates in place instead of generating a permuted copy with rng.permuted. This update modifies the internal handling of the coordinates during the model generation process.

Changes

File	Change Summary
dpgen/generator/run.py	In the make_model_devi function, replaced rng.permuted(system.data["coords"], axis=1) with rng.shuffle(system.data["coords"], axis=1) to shuffle coordinates in place.

Sequence Diagram(s)

sequenceDiagram
    participant Caller
    participant make_model_devi
    participant RNG

    Caller->>make_model_devi: Call with shuffle_poscar=True
    make_model_devi->>RNG: rng.shuffle(system.data["coords"], axis=1)
    RNG-->>make_model_devi: Return shuffled coordinates
    make_model_devi-->>Caller: Return modified system

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Possibly related PRs

• fix: support shuffle_poscar for other formats #1610: Alters the shuffling method in the make_model_devi function and removes the poscar_shuffle function, representing a code-level modification closely tied to this change.

Suggested reviewers

• wanghan-iapcm

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📥 Commits

Reviewing files that changed from the base of the PR and between 9b5fab4 and 752ed21.

📒 Files selected for processing (1)

• dpgen/generator/run.py (1 hunks)

🔇 Additional comments (1)

dpgen/generator/run.py (1)

1308-1308: Good change: Using shuffle instead of permuted for atomic coordinates

This change correctly modifies the behavior to shuffle atom order rather than mixing atom coordinates. Using rng.shuffle() in-place instead of rng.permuted() ensures that whole atoms (with their x, y, z coordinates intact) are shuffled in their positions, rather than permuting individual coordinate values across atoms.

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[codecov]

Codecov Report

Attention: Patch coverage is 52.87770% with 131 lines in your changes missing coverage. Please review.

Project coverage is 49.40%. Comparing base (e02e6a2) to head (752ed21).
Report is 17 commits behind head on devel.

Files with missing lines	Patch %	Lines
dpgen/auto_test/lib/vasp.py	6.25%	15 Missing ⚠️
dpgen/generator/run.py	48.14%	14 Missing ⚠️
dpgen/auto_test/lib/mfp_eosfit.py	0.00%	12 Missing ⚠️
dpgen/data/gen.py	57.69%	11 Missing ⚠️
dpgen/generator/lib/run_calypso.py	0.00%	8 Missing ⚠️
dpgen/auto_test/lib/lammps.py	36.36%	7 Missing ⚠️
dpgen/auto_test/lib/siesta.py	0.00%	7 Missing ⚠️
dpgen/auto_test/lib/pwscf.py	0.00%	5 Missing ⚠️
dpgen/tools/relabel.py	0.00%	5 Missing ⚠️
dpgen/auto_test/lib/lmp.py	0.00%	4 Missing ⚠️
... and 24 more

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #1730      +/-   ##
==========================================
- Coverage   49.51%   49.40%   -0.11%     
==========================================
  Files          83       83              
  Lines       14863    14770      -93     
==========================================
- Hits         7359     7297      -62     
+ Misses       7504     7473      -31     

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