atomRDF#

Note

atomRDF was previously called pyscal-rdf.

atomRDF is a Python tool for ontology-based creation, manipulation and querying of atomic-scale structures and the simulation workflows that produce them.

The data model is implemented as Pydantic classes generated from the Conceptual Dictionary for Computational Materials Science ontologies maintained by OCDO:

Ontology

What it covers

CMSO

Computational Material Sample Ontology

CDCO

Crystallographic Defect Core Ontology

PODO

Point-defect Ontology

PLDO

Planar-defect Ontology

LDO

Line-defect Ontology

ASMO

Atomistic Simulation Methods Ontology

Every object created by atomRDF is round-trippable between Python, JSON/YAML and RDF, with ontology-conformant semantics out of the box.

Where to next#

  • Installation — install and run your first example.

  • Examples — worked notebooks (bulk structures, grain boundaries, defects, SPARQL queries, working with data, …).

  • Migration guide — upgrading from 0.12.x.

  • API Reference — full API reference.

  • Support — contribute / extend.

Citing atomRDF#

If you use atomRDF in academic work, please cite:

Guzmán, A. A., Menon, S., Hickel, T., & Sandfeld, S. (2026). Ontology-based knowledge graph infrastructure for interoperable atomistic simulation data. arXiv:2604.06230. https://arxiv.org/abs/2604.06230