mat-db-optimade

Files (8)

• SKILL.md
• README.md · examples/query-aflow/
• results_aflow.json · examples/query-aflow/
• README.md · examples/query-cod/
• results.json · examples/query-cod/
• README.md · examples/query-nomad/
• results_nomad.json · examples/query-nomad/
• query_optimade.py · scripts/

SKILL.md (first lines)

# 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.

```bash
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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 `cpu` 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](https://doi.org/10.1038/s41597-021-00974-z)

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**Author:** Bowen Deng
**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)

From learningmatter-mit/AtomisticSkills, MIT.

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