fix(dprc): count local atoms in qm-only maps

[njzjz-bot]

Summary

• count local QM atoms before iterating over MM fragments
• preserve correct QM and QM/MM atom metadata when a frame contains only one non-placeholder fragment
• add direct C++ coverage for a QM fragment with local atoms, ghosts, and -1 placeholders
• add mixed-frame TensorFlow coverage for local padding, ghost offsets, QMMM row omission, and frame indices

Why existing tests missed the bug

• The C++ mapper test used four fragments, so the MM-fragment loop always ran and overwrote the incorrect nloc initialization with the real local-QM count.
• The TensorFlow op test duplicated the same multi-fragment fixture, so it never exercised an empty QMMM map or the out-of-bounds forward-map copy.
• Existing fragment-index inputs did not combine a single QM fragment with ignored -1 placeholders, leaving the one-fragment branch uncovered.

Validation

• cmake --build source/build --target runUnitTests_lib -j2
• source/build/lib/tests/runUnitTests_lib --gtest_filter='TestGroupAtoms.*:TestPairwiseMap.*' (3 passed)
• pytest source/tests/tf/test_pairwise_dprc.py::TestPairwiseOP::test_op_single_fragment_with_placeholders source/tests/tf/test_pairwise_dprc.py::TestPairwiseOP::test_op_single_frame -q (2 passed)
• ruff format .
• ruff check .

Fixes #5649

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

Summary by CodeRabbit

• Bug Fixes

  • Fixed QM atom counting for single-fragment inputs that include placeholder entries.
  • Corrected pairwise QM/QMMM map generation when there are no additional QMMM map rows to populate.

• Tests

  • Added new test coverage for placeholder handling in the native CPU pairwise-map computation.
  • Added a TensorFlow op test to verify exact QM/QMMM maps, atom counts, padding behavior, and frame indexing.

[coderabbitai]

Caution

Review failed

An error occurred during the review process. Please try again later.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

---

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 78.32%. Comparing base (6c3b985) to head (65f3bf1).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #5843      +/-   ##
==========================================
- Coverage   78.58%   78.32%   -0.26%     
==========================================
  Files        1050     1050              
  Lines      120637   120644       +7     
  Branches     4356     4355       -1     
==========================================
- Hits        94801    94500     -301     
- Misses      24278    24583     +305     
- Partials     1558     1561       +3     

☔ 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.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.