dpdata feat: do not output spin info for lmp format

fix issue #885 in dpdata and issue #312 in dpgen2

However, adding an additional parameter is not the best method. Please provide another way to fix this issue, thanks.

Summary by CodeRabbit

New Features
- Optional setting to include per-atom spin information (direction and magnitude) in exported LAMMPS data; disabled by default and only emitted when explicitly enabled and spin data exists.
Tests
- Tests updated to parameterize and verify spin output behavior (on/off) and corresponding expected file contents.

Aug 30 '25 09:08 OutisLi

📝 Walkthrough

Walkthrough

Adds an optional output_spins flag to the LAMMPS writer path; the plugin reads and forwards this flag, and the writer emits per-atom spin columns only when spins exist and output_spins=True. Default behavior (no spins) is unchanged.

Changes

Cohort / File(s)	Summary of edits
LAMMPS writer spin gating `dpdata/lammps/lmp.py`	Added `output_spins` parameter to `from_system_data(f_idx=0, output_spins=False)`. Guarded spin-related coordinate formatting, `spins_norm` calculation, and per-atom spin output behind checks for both presence of spins and `output_spins`.
Plugin plumb-through `dpdata/plugins/lammps.py`	`LAMMPSLmpFormat.to_system` reads `output_spins = bool(kwargs.pop("output_spins", False))` and forwards it to `from_system_data(data, frame_idx, output_spins=output_spins)`. Call formatting adjusted; public API unchanged.
Tests updated for flag `tests/test_lammps_spin.py`	Parameterized tests to pass `output_spins` through `dpdata.System.to(..., output_spins=...)`. Adjusted expected coordinate blocks and signatures for tests that assert spin output presence/absence.

Sequence Diagram(s)

sequenceDiagram
  participant User
  participant Plugin as LAMMPSLmpFormat.to_system
  participant Writer as lammps.lmp.from_system_data
  participant File as "LAMMPS Data File"

  User->>Plugin: to_system(data, file_name, frame_idx, output_spins)
  Plugin->>Writer: from_system_data(system, f_idx, output_spins)
  alt spins present AND output_spins == true
    Writer->>File: write per-atom coords + spin vectors & magnitudes
  else
    Writer->>File: write per-atom coords (no spin columns)
  end

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

deepmodeling/dpdata#738 — Also modifies LAMMPS spin handling and writer/plugin interactions; directly related to gating or altering spin output.

Suggested reviewers

wanghan-iapcm
njzjz

Pre-merge checks (2 passed, 1 warning)

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 33.33% which is insufficient. The required threshold is 80.00%.	You can run `@coderabbitai generate docstrings` to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	The title succinctly describes the primary change of disabling spin output for the LAMMPS format, accurately reflecting the addition of a flag to gate spin data and the default behavior change without including extraneous details.

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📜 Recent review details

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📥 Commits

Reviewing files that changed from the base of the PR and between 80ef876bcab1a83f9efb10d6840be27aa3b5c784 and 5589f809df77c9ae287853810a319db6a981afa2.

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