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pyiron / pyiron_workflow_atomistics / 25943564275
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Ran 15 May 2026 10:14PM UTC
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15 May 2026 10:02PM UTC coverage: 89.987% (+0.9%) from 89.094%
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feat(free_energy): consolidate harmonic / QHA / anharmonic into physics.free_energy (#46)

* docs: spec + implementation plan for free-energy consolidation

Design and plan for adding harmonic / quasiharmonic / anharmonic free-energy
entry points under physics.free_energy, wrapping phonopy, dynaphopy, and the
existing calphy nodes. Import-and-wrap consolidation; no physical relocation
of phonon plumbing.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(free_energy): extend FreeEnergyOutput for harmonic/QHA/dynaphopy modes

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(free_energy): add _free_energy_from_spectrum helper

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(free_energy): symmetric expm1 guard + tighten S/Cv assertions

Code-review follow-up to a4750d7:
- _free_energy_from_spectrum: entropy now guards np.expm1(x)==0 the same
  way the Cv branch does, so an ultra-soft non-acoustic mode cannot leak
  inf via the np.errstate suppression.
- Einstein test now cross-checks S and Cv against analytic closed forms
  instead of only F (and a weak Cv>0).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(free_energy): add harmonic_free_energy macro

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* refactor(free_energy): clarify harmonic.py reading order + simfolder side effect

Code-review follow-up to d62f33e:
- Move _Phono3pyShim definition above _pack_harmonic_output, its only
  caller. Functionally identical (lookup happens at call time) but
  reads top-to-bottom now.
- Update _resolve_simfolder docstring to make the mkdir side effect
  explicit; the node both resolves and creates the directory.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(free_energy): add _fit_qha + _check_qha_volume_range helpers

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(free_e... (continued)

2768 of 3076 relevant lines covered (89.99%)

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