Use this skill for generating adsorbates and reaction intermediates, standardizing molecular inputs, and preparing structures for adsorption placement.
Use this skill to turn SMILES-level adsorbate requests into stable 3D molecule files for later slab placement.
fmt intentionally: poscar for slab workflows, xyz for inspection, both when both are useful.output_path as a path prefix, not a final filename.xyz_file_rel or poscar_file_rel instead of reconstructing paths by hand.create_molecule_from_smilescreate_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.formula, natoms, xyz_file_rel, poscar_file_rel, and box_size.fmt convention across a comparison set so the downstream placement workflow sees a consistent input type.Return:
fmtadsorption-site-screening first, then promote the screening set to adsorption-screening.