fix(dftbplus): parse all geometry and force rows

[njzjz-bot]

Fixes #991.

Use the declared DFTB+ atom count instead of a four-row state machine for geometry and force blocks.

Tests: cd tests && python -m unittest test_dftbplus

Why existing tests missed it: The only fixture was ammonia with exactly four atoms, matching the accidental hard-coded limits.

Coding agent: Codex
Codex version: codex-cli 0.144.4
Model: gpt-5.6-sol
Reasoning effort: xhigh

[coderabbitai]

Warning

Review limit reached

@njzjz-bot, you've reached your PR review limit, so we couldn't start this review.

Next review available in: 59 minutes

Enable usage-based reviews in Billing to review now. Otherwise, wait until the next included review is available.
You're only billed for reviews past your plan's rate limits ($0.25/file).

How can I continue?

After more reviews become available, a review can be triggered using the @coderabbitai review command as a PR comment. Alternatively, push new commits to this PR.

To avoid repeated limits, reduce automatic review volume by pausing incremental auto-reviews earlier, using label-based review opt-in, excluding WIP or generated PR titles, or requesting reviews manually when the PR is ready. If your team needs uninterrupted high-volume reviews, an organization admin can enable usage-based reviews.

How do review limits work?

CodeRabbit enforces per-developer PR review limits for each organization. Most developers receive the normal plan review availability.

For paid Pro and Pro+ PR reviews, CodeRabbit uses adaptive limits for sustained high-volume activity. When a developer's recent PR review activity reaches the 95th percentile or higher among CodeRabbit users, additional reviews become available more gradually as earlier reviews age out of the rolling window.

Please refer docs for additional details.

Review details

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 779e0f62-e4d1-45d1-8f8f-eb0c4ef88ae2

📥 Commits

Reviewing files that changed from the base of the PR and between 0416b54 and eff5b61.

📒 Files selected for processing (2)

• dpdata/formats/dftbplus/output.py
• tests/test_dftbplus.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.}

[codspeed-hq]

Merging this PR will not alter performance

⚠️ Unknown Walltime execution environment detected

Using the Walltime instrument on standard Hosted Runners will lead to inconsistent data.

For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

✅ 2 untouched benchmarks

---

_{Comparing njzjz-bot:fix/issue-991 (eff5b61) with master (0416b54)}

[codecov]

Codecov Report

❌ Patch coverage is 94.44444% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 86.84%. Comparing base (0416b54) to head (eff5b61).
⚠️ Report is 5 commits behind head on master.

Files with missing lines	Patch %	Lines
dpdata/formats/dftbplus/output.py	94.44%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1018      +/-   ##
==========================================
- Coverage   86.87%   86.84%   -0.03%     
==========================================
  Files          89       89              
  Lines        8266     8256      -10     
==========================================
- Hits         7181     7170      -11     
- Misses       1085     1086       +1     

☔ 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.

[wanghan-iapcm]

Approving: correct rewrite of the DFTB+ parser (#991). Reading natoms from the GenFormat header and looping dynamically fixes the accidental hard-coded 4-row limit (which was invisible only because the sole fixture, ammonia, had exactly 4 atoms). Verified: count line's field 0 is the atom count, exactly natoms geometry+force rows are read, columns/units unchanged, the 4-atom fixture is unaffected, and the new 5-atom test genuinely fails on the pre-fix truncating parser. Build CI green (docs/readthedocs red is the unrelated emscripten-forge outage, handled in #1035). Minor non-blocking follow-ups exist for malformed input (unbound natoms if no Geometry block) and the F/fractional GenFormat flag, both pre-existing edge cases.