adsorbate-placement

To place adsorbates on a slab surface for DFT geometry optimization, you can use this Skill to automate finding adsorption sites and orienting molecules using Rodrigues rotation. It outputs a structure JSON ready for geo_opt pipelines.

Finding adsorption sites on a catalyst surface is automated by this Skill using ferrox to locate sites. It supports configuring site_type, height, and site_index for accurate adsorbate placement prior to calculations.

Yes, you can place multi-dentate adsorbates on surfaces. The Skill supports multi-dentate configurations and includes overlap detection to ensure the generated slab and adsorbate models are physically valid.

The best way to prepare a slab and adsorbate model for DFT workflows is using this Skill to construct the structure. It configures placement parameters like species, site, and height to output a JSON ready for your pipeline.

Yes, the adsorbate placement tool handles molecule orientation on surfaces by applying Rodrigues rotation. This ensures the adsorbate is correctly oriented relative to the identified adsorption site on the slab.