adsorption-site-screening

Enumerate adsorption sites and generate batch adsorbate placements for screening workflows.

13|1|Updated Nov 27, 2025
One-click install
npx skills add https://github.com/q734738781/CatMaster --skill adsorption-site-screening
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: adsorption-site-screening
Source: https://github.com/q734738781/CatMaster/tree/main/skills/adsorption-site-screening
Command: npx skills add https://github.com/q734738781/CatMaster --skill adsorption-site-screening

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill helps researchers enumerate adsorption sites on slabs, reproducibly place adsorbates, and generate batch adsorption structures for screening campaigns.

Core Features & Use Cases

  • Site enumeration: Compute and list candidate adsorption sites (ontop, bridge, hollow) for given slabs.
  • Controlled adsorption placement: Place adsorbates at chosen sites with consistent coordinates and preserve slab dynamics.
  • Batch generation: Produce batch of adsorption structures with metadata for downstream relaxations and thermochemistry.

Quick Start

Start from a validated slab and an adsorbate file, run enumerate_adsorption_sites to obtain a sites_json_rel, then use place_adsorbate for a single site or generate_batch_adsorption_structures for screening.

Frequently Asked Questions about adsorption-site-screening

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I enumerate adsorption sites on a slab for catalysis screening?

Batch adsorption structure generation provides metadata with each generated structure to ensure reproducibility and traceability of site labels and indices. This metadata is required for tracking structures through downstream relaxations and thermochemistry analysis.

How do I batch generate adsorption structures for surface science screening?

Batch adsorption structure generation produces multiple adsorbate placements across enumerated sites with associated metadata. This output supports downstream relaxations and thermochemistry analysis, ensuring reproducibility and traceability of site labels and indices.

How do I place adsorbates on a slab for catalysis screening?

Site enumeration with this workflow requires a validated slab and an adsorbate file. You run the enumeration function to obtain a sites metadata reference, then use placement functions to generate single or batch adsorption structures for screening.

Does adsorption site screening integrate with CatMaster tools for thermochemistry analysis?

Adsorption site screening integrates with CatMaster tools and provides site metadata plus batch outputs for downstream relaxations and thermochemistry analysis. This satisfies reproducibility and traceability requirements for materials screening campaigns involving slabs.

What adsorption site types are supported for slab enumeration?

Adsorption site screening handles ontop, bridge, and hollow site types for slabs. It places adsorbates at chosen sites with consistent coordinates while preserving slab dynamics, supporting controlled placement for surface science workflows.

Why is metadata needed when generating batch adsorption structures?

Batch adsorption structure generation provides metadata with each generated structure to ensure reproducibility and traceability of site labels and indices. This metadata is required for tracking structures through downstream relaxations and thermochemistry analysis.