q734738781/adsorbate-and-intermediate-generation

adsorbate-and-intermediate-generation

Overview

Use this skill to turn SMILES-level adsorbate requests into stable 3D molecule files for later slab placement.

Quick Start

1. Normalize the requested species name and canonical SMILES before generation.
2. Choose fmt intentionally: poscar for slab workflows, xyz for inspection, both when both are useful.
3. Set output_path as a path prefix, not a final filename.
4. Carry forward the returned xyz_file_rel or poscar_file_rel instead of reconstructing paths by hand.

Allowed tools

• create_molecule_from_smiles

Workflow

1. Normalize chemistry first

• Resolve ambiguous protonation, charge, or radical assumptions before calling the tool.
• If the SMILES is chemically wrong, the generated structure will still be wrong.

2. Generate one canonical molecule file per species

• create_molecule_from_smiles builds a 3D conformer with deterministic embedding.
• fmt=poscar writes a boxed .vasp; fmt=xyz writes .xyz; fmt=both writes both.
• box_padding controls the cubic POSCAR box size for isolated-molecule references.

3. Use returned paths as the handoff contract

• The tool returns formula, natoms, xyz_file_rel, poscar_file_rel, and box_size.
• Downstream adsorption workflows should use the returned molecule path directly.

Method-critical defaults

• Keep protonation, charge, and radical assumptions explicit because they change the generated molecule, not just the file name.
• Use the same fmt convention across a comparison set so the downstream placement workflow sees a consistent input type.

Output Contract

Return:

• canonical molecule file path(s)
• chosen fmt
• any charge or species assumptions that remain unresolved

References

• For slab placement, hand off the returned molecule file to adsorption-site-screening first, then promote the screening set to adsorption-screening.