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chem-db-qmof

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Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.

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Source SKILL.md: https://github.com/learningmatter-mit/AtomisticSkills/blob/HEAD/.agents/skills/chem-db-qmof/SKILL.md

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chem-db-qmof

Goal

To retrieve computational data and relaxed crystal structures (.cif) for roughly 20,000 Metal-Organic Frameworks (MOFs) that have been thoroughly characterized using DFT. QMOF is hosted by the Materials Project under the "MPContribs" project (qmof). This skill allows you to retrieve relaxed CIF structures by reference name, CSD refcode, or specific structural/electronic properties like bandgap.

Prerequisites

  • Dependency: mpcontribs-client must be installed.
  • Environment: Execution happens in the base-agent environment.
  • Credentials: Requires the standard Materials Project API key exported as MP_API_KEY.

Instructions

  1. Query Database: Use the provided script query_qmof.py to search by formula or identifier.
# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --formula "Zn" \
    --max-results 5 \
    --output-dir ./research/qmof_results

Available Arguments:

  • --formula: Search by chemical formula or elements (e.g., Zn,O,C).
  • --identifier: Search by specific CSD refcode or MOF common name (e.g., KAXQIL).
  • --max-results: Maximum number of structures to download (default: 5).
  • --output-dir: Directory to save the resulting .cif files.

Examples

Example 1: Automated testing script (Zinc MOF)

# Env: base-agent
bash .agents/skills/chem-db-qmof/examples/test_qmof.sh

Example 2: Query for 5 MOFs containing Zinc manually

# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --formula "Zn" \
    --max-results 5 \
    --output-dir ./results/qmof_zn

Example 2: Retrieve a specific MOF by identifier

# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --identifier "KAXQIL" \
    --max-results 1 \
    --output-dir ./results/qmof_kaxqil

Constraints

  • API Limits: The Materials Project/MPContribs API has rate limits. Do not use extremely large values for --max-results unless necessary.
  • Availability: If you cannot find a MOF in QMOF via the script, or if the API query is overly complex, you can also search the QMOF database manually through the Materials Project web interface under the "Contributions" section.

Author: Bowen Deng Contact: GitHub @learningmatter-mit