feat(hessian): Implement Method D/E eigenvalue fitting#83
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ericchansen merged 1 commit intomasterfrom Mar 20, 2026
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Add Method D (natural eigenvalue) and building blocks for Method E (hybrid) from Lime & Norrby (J. Comput. Chem. 2015, 36, 1130): - keep_natural_eigenvalue(): Method D -- returns eigenvalues unchanged - detect_problematic_params(): find zero/negative force constants - lock_params(): copy reference values to lock problematic params - invert_ts_curvature() now accepts method='C'|'D' parameter - Fix circular import: Atom type hint via TYPE_CHECKING guard 24 new tests covering synthetic and real SN2 TS Hessians. Method D preserves the negative reaction coordinate eigenvalue while Method C replaces it with ~9376 kJ/mol/A^2/amu. Ref #75 Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
This was referenced Mar 20, 2026
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Summary
Implement Method D (natural eigenvalue fitting) and building blocks for Method E (hybrid) from Lime & Norrby (J. Comput. Chem. 2015, 36, 1130, DOI:10.1002/jcc.23797).
Ref #75
Background
The current
replace_neg_eigenvalue()implements Method C -- forcing the reaction coordinate eigenvalue to ~9376 kJ/mol/A^2/amu. Lime & Norrby showed Method D (keeping the natural eigenvalue) gives ~13x lower RMS error, though it may produce unstable FFs with zero/negative bending constants.Changes
New functions in
q2mm/models/hessian.pykeep_natural_eigenvalue()detect_problematic_params()lock_params()Modified functions
invert_ts_curvature()now acceptsmethod="C"(default) ormethod="D"Atomtype hint viaTYPE_CHECKINGguard +from __future__ import annotationsNew tests:
test/test_method_d_e.py(24 tests)TestMethodD(4): copy safety, negative preservation, multi-neg handlingTestInvertTSCurvature(5): C vs D via unified interface, default is CTestDetectProblematicParams(5): zero/negative/custom threshold detectionTestLockParams(4): lock/preserve/empty scenariosTestMethodDOnSN2(6): real SN2 TS Hessian -- eigenvalue structure, C vs D behaviorTesting
251 passed, 20 skipped. All existing tests unaffected. Ruff clean.