Add reaction free energy and reduction potential helpers - #79
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Introduce ThermoScreening.thermo.reactions with two pure post-processing helpers that combine per-species absolute Gibbs free energies (Thermo.total_EeGtot) computed by any engine: - reaction_free_energy(reactants, products, unit): dG = sum(products) - sum(reactants), with (coefficient, Thermo) stoichiometry tuples and H / eV / kcal / kJ output units. - reduction_potential(oxidized, reduced, n_electrons, reference_potential): E = -dG_red / n, referenced to the SHE by default (override for a calibrated reference or 0.0 for the absolute potential). Both are exported from ThermoScreening.thermo. Adds CI-safe exact-math tests plus a skippable native-xtb benzoquinone end-to-end test, and docs (API reference + a usage section) with a prominent caveat that GFN-xTB/DFTB absolute redox potentials are quantitatively poor and best used for relative trends or with a calibrated reference.
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## main #79 +/- ##
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+ Coverage 96.80% 96.85% +0.05%
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Files 25 26 +1
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Misses 52 52
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Address review feedback: raise ValueError for n_electrons == 0 rather than an opaque ZeroDivisionError, add a kJ/mol unit assertion, and derive the kcal factor from PhysicalConstants['cal'] for codebase consistency.
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What
Adds
ThermoScreening.thermo.reactions, two pure post-processing helpers that combine per-species absolute Gibbs free energies (Thermo.total_EeGtot(), electronic + thermal) into reaction thermochemistry. Compute each species with any engine (dftbplus_thermo/xtb_thermo/xtb_cli_thermo) under matched conditions, then combine:reaction_free_energy(reactants, products, unit="kcal")— ΔG = Σ(products) − Σ(reactants). Species entries are aThermo(coefficient 1) or a(coefficient, Thermo)tuple; output inH/eV/kcal/kJ.reduction_potential(oxidized, reduced, n_electrons=1, reference_potential=SHE_ABSOLUTE_POTENTIAL)—E = -ΔG_red / n(electron free energy taken as zero), referenced to the SHE (4.44 V, IUPAC) by default. Passreference_potential=0.0for the absolute potential.Both are exported from
ThermoScreening.thermo.This directly serves charged / open-shell / solvated workflows (radical anions in solution) enabled by the native-xtb backend.
Tests
ValueError, absolute + vs-SHE potentials,n_electrons, public API export.xtbbenzoquinone reduction end-to-end test (gated onxtb/XTB_COMMAND) that checks the pipeline runs and the reduction is favorable — not experimental accuracy.Docs
API reference entries plus a "Reactions and redox" usage section with a worked example and a prominent
.. warning::that GFN-xTB / DFTB absolute redox potentials are quantitatively poor (benzoquinone GFN2 EA ~7 eV vs ~1.9 eV experimental) and are best used for relative trends or with a calibrated reference.