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Validation: src/calliope/chemistry.py

This page tracks the @pytest.mark.reference_pinned tests that anchor the behaviour of calliope.chemistry against published sources.

Test id Reference Source page Scope
tests/test_chemistry.py::test_modified_keq_janaf_H2_matches_closed_form_at_2000K_with_oneill NIST JANAF Thermochemical Tables1 (4th ed.), fits for H2O = H2 + 0.5 O2 over 1500-3000 K src/calliope/chemistry.py:41-43 (janaf_H2) Pins Geq(janaf_H2) at T = 2000 K under the O'Neill 20022 IW buffer against the closed-form 10^(Keq - 0.5 * log10_fO2); includes a wrong-reaction discrimination guard against schaefer_H3 at the same conditions.

Re-derivation note

ModifiedKeq returns Geq = 10^(Keq(T) - fO2_stoich * log10_fO2(T, dIW)). For janaf_H2 the coefficients (a = -13152.48, b = 3.038586, stoich = 0.5) fit the JANAF tables for H2O = H2 + 0.5 O2 over the documented 1500-3000 K CALLIOPE-use range.

At T = 2000 K, fO2_model='oneill', fO2_shift = 0:

Keq = 10^(-13152.48 / 2000 + 3.038586)
    = 10^(-6.5762 + 3.0386)
    = 10^-3.5376
    ~ 2.901e-4

The O'Neill 2002 IW buffer at the same T:

log10(fO2) = 2 * (-244118 + 115.559 * 2000 - 8.474 * 2000 * ln(2000))
             / (ln(10) * 8.31441 * 2000)
           ~ -7.4078

Combining:

log10(Geq) = -3.5376 - 0.5 * (-7.4078) = 0.1663
Geq = 10^0.1663 ~ 1.467

The test reconstructs the closed form symbolically (without intermediate rounding) and pins to rel=1e-6 precision.

Wrong-reaction discrimination guard: schaefer_H at the same T:

Keq_schaefer = 10^(-12794 / 2000 + 2.7768)
             = 10^-3.6202 ~ 2.398e-4
Geq_schaefer = 10^(-3.6202 + 3.7039) = 10^0.0837 ~ 1.213

The 0.25 difference between Geq_janaf_H2 ~ 1.467 and Geq_schaefer_H ~ 1.213 exceeds the test's discrimination guard threshold (abs(g - wrong) > 0.2).

Anchor type

Published benchmark (JANAF tables) plus cross-reaction discrimination (janaf vs schaefer) plus a separate buffer-flip-propagation test (test_modified_keq_fO2_model_choice_changes_result) that asserts switching from O'Neill to Fischer changes Geq beyond rel=1e-6.

Cross-references

  • src/calliope/chemistry.py:11-22: ModifiedKeq constructor and __call__.
  • src/calliope/chemistry.py:24-62: per-reaction coefficient methods.
  • docs/Explanations/equilibrium_chemistry.md: user-facing concept page.

References

  1. M. W. Chase, NIST-JANAF Thermochemical Tables, 4th edition, Journal of Physical and Chemical Reference Data Monograph 9, 1998. ↩

  2. H. St. C. O'Neill, S. M. Eggins, The effect of melt composition on trace element partitioning: an experimental investigation of the activity coefficients of FeO, NiO, CoO, MoO\(_2\) and MoO\(_3\) in silicate melts, Chemical Geology, 186, 151-181, 2002. SciX. ↩

  3. L. Schaefer, B. Fegley, Redox states of initial atmospheres outgassed on rocky planets and planetesimals, The Astrophysical Journal, 843(2), 120, 2017. SciX. ↩