| name | mat-db-optimade |
| description | Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures. |
| category | materials |
mat-db-optimade
Goal
To query experimental crystal structures (e.g. from the Crystallography Open Database - COD, NOMAD) using the standardized REST API provided by OPTIMADE, and to extract the structural data and metadata in a JSON format.
Instructions
Step 1. Querying an OPTIMADE Database
Use the query_optimade.py script to fetch structure data based on standard OPTIMADE query language filters.
python .agents/skills/mat-db-optimade/scripts/query_optimade.py \
results.json \
--filter 'elements HAS ALL "Na", "Cl"' \
--provider cod \
--max_results 5
Parameters:
output: Path to the output JSON file where results will be stored.--filter: The OPTIMADE filter string. (e.g., elements HAS ALL "O", "Ti").--provider: Comma-separated list of database providers. Defaults to cod.--max_results: Maximum number of structures to pull per provider. Defaults to 10.
Supported Database Providers (Common short IDs)
When using the --provider parameter, you can provide the following short string identifiers for well-known databases:
cod – Crystallography Open Database: The largest open-access collection of experimentally determined crystal structures.nmd – NOMAD: Comprehensive repository of both theoretical methods and experimental configurations.aflow – AFLOW: Automatic-FLOW Computational Materials Data Repository.mp – Materials Project: Well-known theoretical stable/unstable materials repository based on DFT.oqmd – Open Quantum Materials Database: High-throughput DFT database of thermodynamic and structural properties.jarvis – JARVIS: Joint Automated Repository for Various Integrated Simulations.
Constraints
- Environments: The scripts require the
base-agent Conda environment.
- Provider Status: Sometimes specific providers (like Aflow or NOMAD) may experience API downtime. If a provider fails, the
optimade client will log warnings.
References
- Andersen, C. W., et al. "OPTIMADE, an API for exchanging materials data." Scientific Data, 8, 217 (2021). DOI
Author: Bowen Deng
Contact: GitHub @learningmatter-mit
