`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.
- — install and run your first example.
- — worked notebooks (bulk structures, grain boundaries, defects, SPARQL queries, working with data, …).
- — full API reference.
- — contribute / extend.
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