Import QM outputs (Gaussian, Turbomole, ORCA, ...) via cclib - #101
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Add an optional `qm` extra (cclib) and a cclib-backed reader that consumes a frequency calculation from any cclib-supported program (Gaussian, Turbomole, ORCA, Psi4, NWChem, ...): - read_cclib(path) -> (ase.Atoms, frequencies cm^-1, energy Hartree), using cclib's atomcoords (Angstrom), vibfreqs (cm^-1) and best available energy (ccenergies/mpenergies/scfenergies, converted eV -> Hartree). - cclib_thermo(output_file, energy=None, ...) runs the RRHO thermochemistry via run_thermo (energy defaults to cclib's, overridable). cclib is imported lazily, so the core install (and the conda-forge recipe) is unchanged; a clear error asks for `thermoscreening[qm]` when it's absent. Closes #100
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cclib 2.0 is a breaking rearchitecture (data model / units); cap the qm (and test) extra below it since the reader targets the 1.x model. Note in read_cclib that cclib supplies only the real modes, so the geometry's linearity classification must match the QM program's mode count.
galjos
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PySCF is a Python library, so its results are in memory rather than a file. This adds `pyscf_thermo(mean_field, ...)` to complete the QM-import set (Gaussian/Turbomole/ORCA via cclib in #101; ORCA `.hess` in #99). - Reads the geometry (Bohr → Å) and energy (`mean_field.e_tot`) from a converged PySCF mean-field object. - Vibrational frequencies come from `frequencies=` (cm⁻¹) or are derived from `hessian=` via `pyscf.hessian.thermo.harmonic_analysis`. - Optional `pyscf` extra (`pip install thermoscreening[pyscf]`); **pyscf is imported lazily** so the core install and conda-forge recipe are unaffected, with a clear error when it's needed but missing. So `reduction_potential(pyscf_thermo(mf_ox, hessian=h_ox), pyscf_thermo(mf_red, hessian=h_red))` works for a PySCF redox pair. Tested with a duck-typed fake mean field (no real pyscf needed): frequencies path + energy-from-`e_tot`, energy override, the hessian branch (helper mocked), the requires-frequencies-or-hessian error, and the missing-pyscf error (forced via `sys.modules`). Docs + full patch coverage. Closes #102
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Consume DFT frequency calculations from many programs through cclib, which auto-detects the format — so Gaussian and Turbomole (and ORCA, Psi4, NWChem, …) are covered by one reader.
qmextra (pip install thermoscreening[qm]→ cclib). cclib is imported lazily, soimport ThermoScreening, the core deps, and the conda-forge recipe are all unchanged; a clear error asks for the extra when it's missing.read_cclib(path)→(ase.Atoms, frequencies cm⁻¹, energy Hartree)using cclib'satomcoords(Å),vibfreqs(cm⁻¹) and the best available energy (ccenergies→mpenergies→scfenergies, converted eV → Hartree).cclib_thermo(output_file, energy=None, ...)runs the RRHO thermochemistry viarun_thermo(energy defaults to cclib's, overridable).So
reduction_potential(cclib_thermo("ox.log"), cclib_thermo("red.log"))works for a Gaussian (or Turbomole/ORCA/…) redox pair on DFT energetics.Verified against cclib 1.8.1's documented units (
atomcoordsÅ,vibfreqscm⁻¹,scfenergieseV). Tested (parse + eV→Hartree, energy priority cc/mp/scf, unparseable/no-frequency/missing-dependency errors, end-to-endcclib_thermo+ override + requires-energy). Docs + full patch coverage on the new code.Closes #100