fix: serialize LAMMPS HDF5 trajectories

[njzjz-bot]

Summary

• route trajectory output through a backend hook
• keep filesystem paths for standard LAMMPS runs
• return trajectory text for HDF5 serialization
• test both HDF5 output values and the unchanged standard path behavior

Tests

• PYTHONPATH=tests python -m unittest -v tests.op.test_run_lmp.TestRunLmp.test_hdf5_outputs_dataset_values tests.op.test_run_lmp.TestRunLmp.test_success
• isort --check-only dpgen2/op/run_lmp.py tests/op/test_run_lmp.py
• git diff --check

Closes #355

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

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Review configuration:

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 1e539106-5efa-4af5-a734-2dc5e21546eb

📥 Commits

Reviewing files that changed from the base of the PR and between 6b01f29 and 22146e4.

📒 Files selected for processing (2)

• dpgen2/op/run_lmp.py
• tests/op/test_run_lmp.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.52%. Comparing base (6b01f29) to head (22146e4).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #381      +/-   ##
==========================================
+ Coverage   84.43%   84.52%   +0.09%     
==========================================
  Files         104      104              
  Lines        6110     6114       +4     
==========================================
+ Hits         5159     5168       +9     
+ Misses        951      946       -5     

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Retracted. This review was produced without running the mandated /code-review fan-out (the loop skill's section 2); the substitute process used instead has since been shown to miss findings and, in one case, to state a verified-sounding falsehood. Re-reviewing properly.