القائمة
Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Quantify prediction uncertainty of MACE MLIPs using committee (ensemble) models; flag high-uncertainty structures for DFT verification.
Compute phonon-limited carrier mobility and mode-resolved electron-phonon coupling in 2D materials from first principles with Quantum ESPRESSO and EPW.
GPU-accelerated batched inference for MACE, MatGL (TensorNet/M3GNet/CHGNet), and FairChem MLIPs using NValchemi, enabling parallel static, relax, and MD workflows across multiple structures simultaneously.
Extract structured synthesis procedures from a folder of PDFs using the LeMat-Synth GeneralSynthesisOntology schema, producing one JSON file per paper with per-material synthesis records.
Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.
Match an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation. Supports local catalog lookup, public database fallback, and pluggable similarity metrics.
| name | mat-db-optimade |
| description | Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures. |
| category | materials |
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.
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.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.base-agent Conda environment.optimade client will log warnings.Author: Bowen Deng Contact: GitHub @learningmatter-mit