[bobbypaton]

Summary

This keeps the ORCA outputs from the stale feat/goodvibes-integration branch before that branch is deleted.

That branch has 18 commits that were never merged. I compared them with master. Every feature on it has since been reimplemented on master, often more generally:

• GoodVibes-based parsing and scaling factors;
• ORCA support and ORCA mass normalization;
• the Bell crossover guard and Skodje–Truhlar tunnelling;
• packaging, the publish workflow and the module split.

Only three things are missing from master: these ORCA files, a Rich-table terminal output that master never adopted, and a warning for KIEs above 1.5 or below 0.67.

The files are also the real ORCA fixtures that tests/data/orca/README.md and the implementation plan (Phase 5) asked for. Until now the ORCA tests ran on Gaussian Hessians rewritten in ORCA's format.

The data (tests/data/orca/, ORCA 6.1.0)

• pentane_TT / pentane_GG (.out, .hess): the anti,anti and gauche,gauche conformers of n-pentane, r2SCAN-3c optimization and frequencies.
• hat_gs_freq / hat_ts_freq (.out, .hess, .inp): the reactant and transition structure of a hydrogen-atom transfer.
  • Level of theory: broken-symmetry M06-2X-D3(0)/6-31+G** with SMD(dichloromethane), a triplet guess flipped to M_S = 0.
  • H26 moves from C13 to C6 in the transition mode (1974.9i cm⁻¹). I checked this from the imaginary mode and the C–H distances: 1.106 Å in the reactant, 1.238 and 1.667 Å at the transition structure.
  • The parabolic-barrier crossover temperature is therefore 438 K, so 298 K is in the deep-tunnelling regime.

The .out files are kept whole, not trimmed to the sections Kinisot reads. The point is to keep the data, and the plan's "< 100 kB" guideline is the trade-off.

Tests (tests/test_orca.py)

• test_real_orca_conformer_eqe:
  • The level of theory is detected as r2SCAN-3c/def2-mTZVPP; it has no scaling factor, so none is applied.
  • The EQE for ²H at atom 6 is 1.0077302, with no warnings.
  • Reading the .hess files directly gives the same number.
• test_real_orca_deep_tunnelling_hat:
  • The scaling factor 0.968 is detected from ORCA's ! input line.
  • At 298 K the KIEs are: primary ²H 3.18884 (4.46248 with Wigner), ³H 5.11494, secondary ²H at H24 1.037178.
  • Kinisot refuses the Bell correction below the 437.8 K crossover temperature; the Skodje–Truhlar correction stays finite.
  • At 500 K, Bell gives 5.67082 and Skodje–Truhlar 4.85377, less tunnelling from the truncated parabola, as expected.

These values reproduce the ones first pinned on the old branch within 1.5 × 10⁻⁵ (relative). The pentane EQE differs by 7.5 × 10⁻⁸, which comes from slightly different isotope masses.

Docs

• tests/data/orca/README.md describes the new files and their provenance. A linear molecule is still wanted.
• The implementation plan (Phase 5 note) and CHANGELOG ("Unreleased") are updated.

Verification

• ruff check . and ruff format --check . are clean.
• pytest tests/: 255 passed, 1 skipped.
• The wheel is unchanged (87 KB). The sdist grows from 1.05 to 1.36 MB, because MANIFEST.in ships tests/**/*.out; as for the existing ORCA fixtures, the .hess files aren't in it.

Once this merges, feat/goodvibes-integration holds nothing that isn't on master, and it can be deleted.

Summary by CodeRabbit

• Tests
  • Added validation using real ORCA 6.1.0 calculations for pentane conformer equilibrium isotope effects and hydrogen-atom-transfer isotope effects.
  • Coverage checks isotope-specific results, automatic scaling, consistency between output and Hessian inputs, and tunneling corrections across temperatures.
• Documentation
  • Updated fixture notes to describe the new ORCA calculation data and clarify the source and format of existing fixtures.

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⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Essentials

Run ID: 5afc13e9-08ad-41d7-a0a2-af3e4c30dc6c

📥 Commits

Reviewing files that changed from the base of the PR and between d536cc8 and e5fdfb6.

⛔ Files ignored due to path filters (4)

• tests/data/orca/hat_gs_freq.out is excluded by !**/*.out
• tests/data/orca/hat_ts_freq.out is excluded by !**/*.out
• tests/data/orca/pentane_GG.out is excluded by !**/*.out
• tests/data/orca/pentane_TT.out is excluded by !**/*.out

📒 Files selected for processing (10)

• CHANGELOG.md
• IMPLEMENTATION_PLAN.md
• tests/data/orca/README.md
• tests/data/orca/hat_gs_freq.hess
• tests/data/orca/hat_gs_freq.inp
• tests/data/orca/hat_ts_freq.hess
• tests/data/orca/hat_ts_freq.inp
• tests/data/orca/pentane_GG.hess
• tests/data/orca/pentane_TT.hess
• tests/test_orca.py

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📝 Walkthrough

Walkthrough

The change adds ORCA 6.1.0 hydrogen-atom-transfer frequency inputs, documents the pentane and hydrogen-atom-transfer fixtures, and adds tests for conformer equilibrium isotope effects, hydrogen-atom-transfer isotope effects, scaling, and tunneling behavior.

Changes

ORCA fixture tests

Layer / File(s)	Summary
Frequency inputs and fixture documentation tests/data/orca/hat_gs_freq.inp, tests/data/orca/hat_ts_freq.inp, tests/data/orca/README.md, IMPLEMENTATION_PLAN.md	Adds frequency calculation inputs for the hydrogen-atom-transfer reactant and transition state. Documents the pentane and hydrogen-atom-transfer fixtures and notes that a linear-molecule fixture is still wanted.
Isotope-effect and tunneling tests tests/test_orca.py, CHANGELOG.md	Adds tests for pentane conformer equilibrium isotope effects and hydrogen-atom-transfer isotope effects, scaling, and tunneling behavior. The changelog records the test expectations.

Priority: ⬇️ Low

Estimated code review effort: 2 (Simple) | ~15 minutes

Change: Other

Suggested reviewers: claude

Merge Risk: ⚪ Minimal · up to e5fdf

The changes add ORCA fixtures, regression tests, and provenance documentation without an identified behavioral regression. Mergeable subject to normal test checks.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 3 functions across 1 files. (5 skipped: 5 …	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely identifies the main change: adding real ORCA 6.1.0 test data for pentane conformer EQE and deep-tunnelling HAT.

Full details: Docstring Coverage

Explanation

Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 3 functions across 1 files. (5 skipped: 5 unsupported.)

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