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FAIRmat-NFDI / nomad-simulations
86%

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DEFAULT BRANCH: develop
Repo Added 02 Jan 2026 09:31AM UTC
Token NlHfzWOWVbn6VpwLJzAj4wHjNVcmQ4tGZ regen
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  • 240-disambiguate-crystal-symmetry-symbols-port
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09 Jul 2026 07:51PM UTC coverage: 86.096% (+0.2%) from 85.94%
29045851850

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Fix high-symmetry k-point normalization crashes via SeeKpath (#403, closes #401)

`KMesh.high_symmetry_points` resolution relied on ASE's Bravais-lattice objects, whose attributes did not always match NOMAD's stored Pearson/Bravais label; the uncaught `AttributeError`s surfaced as "could not normalize section" failures on non-conventional lattices. The PR began as a defensive fallback around those mismatches, but since the root cause is ASE classifying the cell from its geometry alone, it resolves the problem by replacing that path entirely.

High-symmetry points are now derived from the full crystal structure (lattice and atomic positions) via SeeKpath/HPKOT, using the same `symmetry_tolerance` as MatID, so the k-points and the stored `bravais_lattice` agree by construction; coordinates are expressed in the input cell's reciprocal basis, and resolution degrades to a warning instead of crashing.

Adds the `seekpath`/`spglib` dependencies, regression tests, and primitive-cell reference fixtures.

Co-authored-by: Nathan Daelman <ndaelman@physik.hu-berlin.de>

108 of 115 new or added lines in 4 files covered. (93.91%)

9864 of 11457 relevant lines covered (86.1%)

2.58 hits per line

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Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
29045851850 develop Fix high-symmetry k-point normalization crashes via SeeKpath (#403, closes #401) `KMesh.high_symmetry_points` resolution relied on ASE's Bravais-lattice objects, whose attributes did not always match NOMAD's stored Pearson/Bravais label; the unca... push 09 Jul 2026 07:53PM UTC web-flow github
86.1
29044829132 fix-kmesh-high-symmetry-ase-lattice-mismatch Explain in-code why only GAMMA is remapped to Gamma Expand the comment on the label conversion: SeeKpath's native HPKOT labels are kept as-is, with GAMMA -> Gamma the sole deliberate exception for downstream name-matching compatibility; the full ... Pull #403 09 Jul 2026 07:35PM UTC ndaelman-hu github
86.07
29044006682 fix-kmesh-high-symmetry-ase-lattice-mismatch Feed SeeKpath from the schema directly, dropping the ASE round-trip resolve_high_symmetry_points built an ASE Atoms via to_ase_atoms only to immediately unpack it into the (cell, scaled_positions, numbers) tuple SeeKpath needs; no ASE algorithm w... Pull #403 09 Jul 2026 07:22PM UTC ndaelman-hu github
86.07
29043135066 fix-kmesh-high-symmetry-ase-lattice-mismatch Keep SeeKpath native label spelling; defer label conventions to #409 Revert the title-casing of spelled-out Greek k-point labels. The wider label convention question (capitalization of SIGMA/DELTA/... and HPKOT vs Setyawan-Curtarolo naming) is ha... Pull #403 09 Jul 2026 07:07PM UTC ndaelman-hu github
86.1
29042927576 fix-kmesh-high-symmetry-ase-lattice-mismatch Normalize all spelled-out Greek k-point labels, not only Gamma SeeKpath spells Greek-letter high-symmetry points in upper case (GAMMA, SIGMA, ...). The conversion only title-cased GAMMA, leaving labels such as SIGMA_0 upper case and inconsistent.... Pull #403 09 Jul 2026 07:04PM UTC ndaelman-hu github
86.1
29029973558 fix-kmesh-high-symmetry-ase-lattice-mismatch Document the shared symmetry_tolerance and its schema-wide effect Annotate the Symmetry Information section of the ModelSystem explanation with the meaning of configuration.symmetry_tolerance (spglib symprec, 0.01 angstrom default), its effect on... Pull #403 09 Jul 2026 03:34PM UTC ndaelman-hu github
86.1
29029754016 fix-kmesh-high-symmetry-ase-lattice-mismatch Derive SeeKpath k-points at the same tolerance as MatID symmetry MatID's symmetry_tol and SeeKpath's symprec are the same spglib parameter, but the stored bravais_lattice used configuration. symmetry_tolerance (0.1) while resolve_high_symmetry_po... Pull #403 09 Jul 2026 03:31PM UTC ndaelman-hu github
86.1
29027032505 fix-kmesh-high-symmetry-ase-lattice-mismatch Address Copilot review on merged SeeKpath k-point resolution - Catch SymmetryDetectionError (raised by seekpath.get_path when spglib cannot detect symmetry; does not derive from ValueError) so it no longer escapes and crashes normalization - ... Pull #403 09 Jul 2026 02:51PM UTC ndaelman-hu github
86.09
29016415064 fix-kmesh-high-symmetry-ase-lattice-mismatch Use SeeKpath for high-symmetry k-point resolution (#405) Replace the ASE-based high-symmetry k-point resolution with SeeKpath (HPKOT recipe). ASE classifies the bare cell from its metrics alone and cannot accept an external symmetry analysis, so ... Pull #403 09 Jul 2026 12:01PM UTC web-flow github
86.06
29015941064 develop Add geometry optimization tests for flat trajectories and untimed outputs (#408) - Parametrize `test_energies` with a fully flat trajectory (all energies identical): `energies` is recorded but `final_energy_difference` stays unset. - Add an end... push 09 Jul 2026 11:47AM UTC web-flow github
85.94
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