q734738781/adsorption-screening

adsorption-screening

Overview

Use this skill to build, run, and rank a controlled adsorption screen while preserving site labels and adsorbate atom indices for later thermochemistry.

Quick Start

1. Start from one accepted slab and one canonical adsorbate file.
2. Enumerate sites first; keep the site JSON as the ledger.
3. Generate only the adsorption candidates you actually plan to relax.
4. Prepare and dispatch one consistent adsorption batch.
5. Use analyze_vasp_results for ranking and keep ads_indices metadata for any later frequency correction work.

Allowed tools

• enumerate_adsorption_sites
• place_adsorbate
• generate_batch_adsorption_structures
• vasp_prepare
• vasp_execute_batch
• analyze_vasp_results
• vaspkit_adsorbate_thermo_correction
• render_structure_views

Workflow

1. Preserve adsorption provenance

• Always enumerate sites before broad placement.
• Treat generate_batch_adsorption_structures as a convenience wrapper over site enumeration plus placement, not as a separate scientific abstraction.

2. Build a controlled candidate set

• Use one adsorbate geometry source across the whole screen.
• If only one site is under study, use place_adsorbate directly and keep the chosen site label explicit.
• Use render_structure_views when collisions or orientation ambiguity need a visual check before DFT.

3. Run one comparable relaxation stage

• Prepare adsorption candidates with one consistent slab regime and method policy.
• Keep clean slab, gas reference, and adsorbed systems method-aligned if adsorption energies will be compared later.

4. Rank, then branch

• Use analyze_vasp_results to detect failed or unconverged candidates before ranking.
• Run vaspkit_adsorbate_thermo_correction only on the retained adsorption states that genuinely need thermal corrections.

Method-critical defaults

• Do not compare adsorption energies if the clean slab or gas reference was prepared under a different spin, dispersion, or DFT+U contract.
• Preserve and report ads_indices; they are part of the downstream thermochemistry contract.
• Do not silently accept truncated candidate batches from the wrapper if the ranking depends on full site coverage.

Output Contract

Return:

• site JSON path
• generated adsorption structure root
• retained candidate list
• VASP analysis summary path
• adsorbate thermochemistry artifact path when used

References

• Use the primitive skills adsorption-site-screening and adsorbate-and-intermediate-generation when only the front half of the workflow is needed.