fix(corrections): swap defect/bulk site potentials in get_efnv_correction#226
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…tion (GH#219) Lines 96-97 of kumagai.py had defect_potentials and bulk_potentials sourced from the wrong structures. For antisite defects (defect.num_sites == bulk.num_sites) the swap was silent but produced incorrect alignment; for vacancies and interstitials it raised IndexError downstream in pydefect's make_efnv_correction. - Restore correct ordering: potentials are read from the structure they describe. - The pre-existing test_kumagai assertion (q=+1 correction > 0) was effectively locking in the buggy behavior — the correct value with proper ordering is approximately -0.49 eV. Updated to assert the new reference value. - Add test_kumagai_vacancy regression test that synthesizes a vacancy (different num_sites between defect and bulk) and exercises the bug directly. Without the fix this raises the same IndexError reported in GH#219. Reported by user in GH issue #219; the issue body identifies the swap and the verified-against-legacy KumagaiCorrection value.
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Closes #219.
Summary
get_efnv_correctionwas extracting site potentials from the wrong structures:For antisites (
defect.num_sites == bulk.num_sites) the swap was silent but inverted the sign of the alignment term. For vacancies/interstitials it raisedIndexErrordownstream inpydefect.make_efnv_correction. Reported in #219.Tests
test_kumagai: invariant assertions (isfinite,< 0) + a snapshot value (-0.4898778 eV) for regression detection. The pre-fix code asserted> 0, which was implicitly locking in the buggy behavior.test_kumagai_vacancy: synthesizes a vacancy by removing a site from the bundled q=0 structure sodefect.num_sites != bulk.num_sites. Without the fix this reproduces the originalIndexError; with the fix it returns cleanly.