fix: support shuffle_poscar for other formats

[njzjz]

Fix #1570.

Summary by CodeRabbit

• New Features

  • Enhanced efficiency in handling atomic configurations by directly modifying coordinates in memory, eliminating the need for intermediate files.
  • Simplified logic for shuffling atomic indices.

• Bug Fixes

  • Removed obsolete function that may have caused confusion in the workflow related to POSCAR file management.

[coderabbitai]

Walkthrough

Walkthrough

The recent changes to the dpgen/generator/run.py script primarily involve the removal of the poscar_shuffle function and a streamlined approach for handling atomic configuration shuffling. The code now directly modifies atomic coordinates in-memory without the need for intermediate file operations, thus enhancing efficiency and addressing previously identified bugs related to POSCAR file handling.

Changes

Files	Change Summary
dpgen/generator/run.py	Removed poscar_shuffle function; modified make_model_devi to shuffle atomic coordinates directly in-memory using rng.permuted.

Assessment against linked issues

Objective	Addressed	Explanation
Support formats other than POSCAR when using shuffle_poscar (#1570)	❌	The underlying logic for handling formats is not improved; only POSCAR format is still addressed.

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Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between c4552bd and 0382152.

Files selected for processing (1)

• dpgen/generator/run.py (3 hunks)

Additional comments not posted (4)

dpgen/generator/run.py (4)

1262-1262: Initialize the random number generator once.

The random number generator rng is initialized once at the beginning of the function, which is a good practice for consistency.

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1282-1283: Shuffling atomic coordinates in-memory.

The atomic coordinates are shuffled in-memory using rng.permuted, which is more efficient than previous file-based operations.

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1262-1262: Initialize the random number generator once.

The random number generator rng is initialized once at the beginning of the function, which is a good practice for consistency.

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1282-1283: Shuffling atomic coordinates in-memory.

The atomic coordinates are shuffled in-memory using rng.permuted, which is more efficient than previous file-based operations.

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[codecov]

Codecov Report

Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 49.56%. Comparing base (c4552bd) to head (0382152).
Report is 21 commits behind head on devel.

Files with missing lines	Patch %	Lines
dpgen/generator/run.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #1610      +/-   ##
==========================================
+ Coverage   49.52%   49.56%   +0.03%     
==========================================
  Files          83       83              
  Lines       14872    14860      -12     
==========================================
- Hits         7366     7365       -1     
+ Misses       7506     7495      -11     

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

[njzjz]

I hope I have understood what shuffle_poscar is. The documentation for shuffle_poscar is unclear.

[wanghan-iapcm]

Yes, poscar_shuffle shuffles the coordinates of the atoms in a frame, which creates randomness in solid solution systems.

At the time when it was written, we even did not have dpdata.