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Data curation

Packaged scalar tables are CSV files indexed by atomic number. The neutral radial dataset is a shared-grid CSV payload inside a deterministic single-file ZIP. Dataset metadata, storage declarations, provenance, aliases, coverage, and attribution live in src/atomref/data/registry.json.

Generated scientific data must not be hand-edited.

Classification

The registry keeps several concerns separate:

  • quantity — the operational lookup target, such as covalent_radius or proatomic_density;
  • semantic_class — what the dataset scientifically represents;
  • origin_class — how its values were obtained;
  • usage_role — whether it is a direct target or transfer support;
  • phase_context — the physical context of the values;
  • storage.kind — the validated packaged payload shape.

This is why atomic_radius:rahm2016 remains an isolated-atom isodensity dataset even when a radii policy uses it as support for a fitted van der Waals value.

Neutral proatomic snapshot

proatomic_density:pbe0_sfx2c_dyallv4z_h-lr_neutral_v2 is a deterministic packaged snapshot of the atomref-proatoms 2.0.0 dataset pbe0_sfx2c_dyallv4z_h-lr_spherical_v2. It selects the neutral H–Lr profiles, retains the source grid through the first point above 20 bohr so the public endpoint remains bracketed, and does not interpolate or alter stored density values during curation.

The registry records the upstream release and dataset identity, PBE0/spherical fractional-occupation UKS/sf-X2C/dyall-v4z method summary, source and basis hashes, public domain and interpolation contract, CC BY 4.0 data license, and the concept and version-specific Zenodo DOIs. Package code remains under its own LGPL license.

The maintainer-only builder reads a separately obtained immutable upstream source tree; atomref-proatoms is not a runtime or build dependency:

python tools/build_proatomic_density_snapshot.py \
  --source-dir ../atomref-proatoms-reference-v2.0.0/upstream/data/profiles/pbe0_sfx2c_dyallv4z_h-lr_spherical_v2 \
  --check

Write mode is reserved for deliberate snapshot regeneration after a separately reviewed data change. It is not part of ordinary documentation or release builds.

Validation

Run the registry validator after any metadata or payload change:

python tools/check_registry.py

It cross-checks metadata against every scalar and radial payload. Distribution validation independently checks required members, attribution markers, and the exact outer ZIP and inner CSV fingerprints in both source and wheel artifacts.