atomref scalar-data quickstart¶

Goal. Retrieve common atomic reference values, inspect the provenance of a transferred value, and discover the packaged scalar datasets.

Prerequisites. Install atomref; no optional dependencies or prior knowledge of its registry and policy internals are required.

A separate notebook covers the density and pairwise neutral-proatom workflows.

Setup and element discovery¶

Import the public package namespace, normalize one element symbol, and list the available reference-data quantities.

In [1]:

import atomref as ar

print(ar.get_element('Cl'))
print(ar.list_quantities())

import atomref as ar print(ar.get_element('Cl')) print(ar.list_quantities())

Element(z=17, symbol='Cl', name='Chlorine')
('covalent_radius', 'van_der_waals_radius', 'atomic_radius', 'xh_bond_length', 'proatomic_density')

Direct scalar lookups¶

The convenience get_* functions return numbers in angstrom. They are the short path when the selected value is all the caller needs.

In [2]:

r_c = ar.get_covalent_radius('C')
r_vdw = ar.get_vdw_radius('O')
print(r_c)
print(r_vdw)
assert r_c == 0.76
assert r_vdw == 1.50

r_c = ar.get_covalent_radius('C') r_vdw = ar.get_vdw_radius('O') print(r_c) print(r_vdw) assert r_c == 0.76 assert r_vdw == 1.50

0.76
1.5

A lookup with provenance¶

The preferred van der Waals table has no direct value for Pm. lookup_* returns the value together with the transfer method and source dataset.

In [3]:

lookup = ar.lookup_vdw_radius('Pm')
print(f"{lookup.value:.12f}")
print(lookup.source)
print(lookup.resolved_from)
assert lookup.source == 'transfer_linear'

lookup = ar.lookup_vdw_radius('Pm') print(f"{lookup.value:.12f}") print(lookup.source) print(lookup.resolved_from) assert lookup.source == 'transfer_linear'

2.897226539515
transfer_linear
(DatasetRef(quantity='atomic_radius', set_id='rahm2016'),)

Catalog metadata¶

Quantity and dataset metadata make units, intended role, and source choice discoverable instead of leaving them as project-local conventions.

In [4]:

quantity = ar.get_quantity_info('atomic_radius')
print(quantity.quantity, quantity.domain, quantity.units)

for info in ar.list_dataset_infos('van_der_waals_radius', usage_role='target'):
    print(info.ref.set_id, info.name, info.usage_role)

quantity = ar.get_quantity_info('atomic_radius') print(quantity.quantity, quantity.domain, quantity.units) for info in ar.list_dataset_infos('van_der_waals_radius', usage_role='target'): print(info.ref.set_id, info.name, info.usage_role)

atomic_radius element angstrom
bondi1964 Bondi van der Waals radii target
rowland_taylor1996 Rowland & Taylor nonbonded contact radii target
alvarez2013 Alvarez van der Waals radii target
chernyshov2020 Chernyshov LoS van der Waals radii target

Direct packaged-set access¶

Load a target radii table through its convenience helper and a support table through the generic dataset reference used by the registry.

In [5]:

vdw = ar.get_radii_set('van_der_waals', 'alvarez2013')
print(vdw.get('O'))

support = ar.get_builtin_set(ar.DatasetRef('atomic_radius', 'rahm2016'))
print(support.get('Pm'))

vdw = ar.get_radii_set('van_der_waals', 'alvarez2013') print(vdw.get('O')) support = ar.get_builtin_set(ar.DatasetRef('atomic_radius', 'rahm2016')) print(support.get('Pm'))

1.5
2.83

What this demonstrated and limitations¶

The scalar API supports short numeric lookups, provenance-carrying results, catalog discovery, and direct packaged-set access. A transferred value is a declared policy result, not a hidden measurement. Dataset suitability and fallback policy remain choices for the consuming scientific workflow.