docs: define HDF5 trajectory storage

[njzjz-bot]

Summary

• define use_hdf5 as dflow HDF5 dataset artifact storage
• explain that LAMMPS continues to produce aligned standard dump and model-deviation data
• distinguish this supported contract from native LAMMPS dump h5md
• document extra_output_files for users who also need a native H5MD artifact
• cover normalization of the public HDF5 option

Tests

• PYTHONPATH=tests python -m unittest -v tests.op.test_run_lmp.TestRunLmp.test_hdf5_storage_option_is_normalized
• python -m py_compile on changed Python files
• isort --check-only on changed Python files
• git diff --check

Closes #7

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

[coderabbitai]

Warning

Review limit reached

Next included review available in 59 minutes.

View limit details

Limit details: You’ve used the included review currently available.

You've used all free OSS reviews for now. Wait for the free limit to reset to keep reviewing this public repository.

Learn how review limits work.

Review configuration:

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 6db7349a-05a1-4592-ab1e-b061cdfa3811

📥 Commits

Reviewing files that changed from the base of the PR and between 6b01f29 and 989e592.

📒 Files selected for processing (4)

• docs/input.md
• dpgen2/entrypoint/args.py
• dpgen2/op/run_lmp.py
• tests/op/test_run_lmp.py

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.43%. Comparing base (6b01f29) to head (989e592).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #402   +/-   ##
=======================================
  Coverage   84.43%   84.43%           
=======================================
  Files         104      104           
  Lines        6110     6110           
=======================================
  Hits         5159     5159           
  Misses        951      951           

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

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.