How do I install the Mat DB Optimade skill?

Run npx skillmds@latest add learningmatter-mit/mat-db-optimade in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Mat DB Optimade safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts, makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Mat DB Optimade?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Mat DB Optimade free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Mat DB Optimade?

learningmatter-mit (@learningmatter-mit) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Mat DB Optimade by learningmatter-mit

Name: Mat DB Optimade
Rating: 4.2 (5 reviews)
Author: learningmatter-mit

File contents

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.

# Env: base-agent
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

---name: mat-db-optimadedescription: Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.---# mat-db-optimade## GoalTo 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 DatabaseUse the `query_optimade.py` script to fetch structure data based on standard OPTIMADE query language filters.```bash# Env: base-agentpython .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](https://doi.org/10.1038/s41597-021-00974-z)---**Author:** Bowen Deng**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)

Frequently asked questions

Mat DB Optimade