Custom sets and dataset discovery¶

Goal. Build a small immutable user-provided scalar set, use it as a policy base, and inspect metadata for packaged alternatives.

Prerequisites. Familiarity with element symbols and basic scalar lookups is sufficient. The example values are illustrative covalent radii in angstrom, not a new curated dataset shipped by atomref.

Setup¶

Import the public namespace used to construct sets, policies, and dataset references.

In [1]:

import atomref as ar

import atomref as ar

Define a custom base set¶

The custom set supplies C and O directly. An explicit substitution step uses the packaged Cordero table for N, so each lookup retains whether it came from the custom base or the fallback source.

In [2]:

custom_cov = ar.ElementScalarSet.from_mapping(
    ref=ar.DatasetRef("covalent_radius", "demo_user_cov"),
    values={"C": 0.77, "O": 0.67},
    name="Demo user covalent set",
    units="angstrom",
    description="Example custom set for notebook usage.",
    notes=("Notebook example",),
)

policy = ar.RadiiPolicy(
    kind="covalent",
    base_set=custom_cov,
    transfers=(
        ar.SubstitutionTransfer(
            source=ar.DatasetRef("covalent_radius", "cordero2008")
        ),
    ),
)

for symbol in ("C", "O", "N"):
    print(symbol, ar.lookup_covalent_radius(symbol, policy=policy))

custom_cov = ar.ElementScalarSet.from_mapping( ref=ar.DatasetRef("covalent_radius", "demo_user_cov"), values={"C": 0.77, "O": 0.67}, name="Demo user covalent set", units="angstrom", description="Example custom set for notebook usage.", notes=("Notebook example",), ) policy = ar.RadiiPolicy( kind="covalent", base_set=custom_cov, transfers=( ar.SubstitutionTransfer( source=ar.DatasetRef("covalent_radius", "cordero2008") ), ), ) for symbol in ("C", "O", "N"): print(symbol, ar.lookup_covalent_radius(symbol, policy=policy))

C LookupResult(value=0.77, source='base', target=DatasetRef(quantity='covalent_radius', set_id='demo_user_cov'), resolved_from=(DatasetRef(quantity='covalent_radius', set_id='demo_user_cov'),), is_placeholder=False, fit=None, notes=(), transfer_depth=0)
O LookupResult(value=0.67, source='base', target=DatasetRef(quantity='covalent_radius', set_id='demo_user_cov'), resolved_from=(DatasetRef(quantity='covalent_radius', set_id='demo_user_cov'),), is_placeholder=False, fit=None, notes=(), transfer_depth=0)
N LookupResult(value=0.71, source='transfer_substitution', target=DatasetRef(quantity='covalent_radius', set_id='demo_user_cov'), resolved_from=(DatasetRef(quantity='covalent_radius', set_id='cordero2008'),), is_placeholder=False, fit=None, notes=('missing in base set; substituted from transfer source',), transfer_depth=1)

Discover packaged dataset metadata¶

List target van der Waals tables and inspect the scientific classification and usage role of the Rahm atomic-radius support dataset.

In [3]:

for info in ar.list_radii_set_infos("van_der_waals", usage_role="target"):
    print(info.ref.set_id, info.semantic_class, info.origin_class, info.phase_context)

rahm = ar.get_dataset_info(ar.DatasetRef("atomic_radius", "rahm2016"))
print(rahm.name)
print(rahm.semantic_class, rahm.phase_context, rahm.usage_role)

for info in ar.list_radii_set_infos("van_der_waals", usage_role="target"): print(info.ref.set_id, info.semantic_class, info.origin_class, info.phase_context) rahm = ar.get_dataset_info(ar.DatasetRef("atomic_radius", "rahm2016")) print(rahm.name) print(rahm.semantic_class, rahm.phase_context, rahm.usage_role)

bondi1964 vdw_compiled compiled_experimental mixed_or_legacy
rowland_taylor1996 vdw_structural structural condensed_phase
alvarez2013 vdw_structural structural condensed_phase
chernyshov2020 vdw_structural_typed_reduced structural condensed_phase
Rahm isodensity atomic radii (ρ=0.001 e/bohr³)
atomic_isodensity isolated_atom support

What this demonstrated and limitations¶

A custom ElementScalarSet can participate in the same scalar policy machinery as packaged tables without modifying the global registry. Users remain responsible for the provenance, units, coverage, and scientific fitness of their own values. Custom radial-profile datasets are outside the current public scope.