q734738781/adsorption-site-screening

adsorption-site-screening

Overview

Use this skill to enumerate adsorption sites, place adsorbates reproducibly, and emit batch-ready adsorption structures with metadata.

Quick Start

1. Start from a validated slab and a canonical adsorbate file.
2. Run enumerate_adsorption_sites first and keep the returned sites_json_rel.
3. Use place_adsorbate for one chosen site or generate_batch_adsorption_structures for a screening set.
4. Preserve the returned ads_indices metadata for downstream relaxations and thermochemistry.

Allowed tools

• enumerate_adsorption_sites
• place_adsorbate
• generate_batch_adsorption_structures

Workflow

1. Enumerate before placing

• enumerate_adsorption_sites writes a JSON site list and returns default_site_label.
• Each enumerated site row includes Cartesian cart_coords; the ontop_0 / bridge_1 / hollow_2 labels used by place_adsorbate come from this enumeration.
• In mode=all, the candidate families are ontop, bridge, and hollow.
• For single-structure placement, do not guess the site label if the JSON has already been generated.

2. Place one structure intentionally

• place_adsorbate accepts site_label values like ontop_0; site_label=auto prefers the first available ontop, then bridge, then hollow.
• place_adsorbate also accepts site_cart_coords=[x, y, z] in Cartesian Angstrom for direct placement. site_label and site_cart_coords are mutually exclusive.
• XYZ/internal molecular geometry is preserved during placement; the tool does not automatically reorient the molecule.
• The placement point is the adsorption-site coordinate returned by ASF at the requested distance; the molecule is translated so the center of mass of its lowest-z atom layer lands on that site coordinate.
• The tool preserves slab selective dynamics and marks newly added adsorbate atoms as movable.
• Returned metadata includes ads_indices_added, merged ads_indices, metadata_rel, ads_indices_json_rel, and the chosen site coordinates.

3. Batch only the candidates you want to screen

• generate_batch_adsorption_structures supports either slab_file or slab_dir, not both.
• max_structures is a real cap; if the site count exceeds it, the batch is truncated.
• The batch output writes batch_structures.json plus ads_indices.json under output_dir.

Method-critical defaults

• If the screening is intended for quantitative ranking, preserve metadata and reference-state traceability needed for downstream consistent energy evaluation.
• Do not generate candidate structures without carrying forward the adsorbate indices and site provenance required for later interpretation.

Output Contract

Return:

• site source (sites_json_rel or explicit label)
• generated structure path or output_dir_rel
• ads_indices metadata path(s)
• whether the batch was truncated

References

• When the slab already carries adsorbate metadata, rely on the merged ads_indices returned by the tool instead of recomputing adsorbate atom indices.
• For the full screening workflow, hand off to adsorption-screening after the primitive site list is established.