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Use this skill for generating adsorbates and reaction intermediates, standardizing molecular inputs, and preparing structures for adsorption placement.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
Proposal-first scientific writing pipeline. Three modes (compose/revise/hybrid) with four-layer QA pipeline. Enforces evidence-before-prose, argument-before-sections, and contracts-before-paragraphs.
Use this skill for managed MLFF molecular dynamics, restart-safe trajectory continuation, ensemble selection, and trajectory-health analysis when mlff_md is available.
Use only after a DPDispatcher-backed managed execution tool returns a failure with receipt/context fields, an ambiguous transport error, or evidence of a possible orphan job. Do not use for a pending synchronous call or ordinary success.
Use this skill before remote_submission or remote_submission_batch to build and verify canonical stage directories for registered DPDispatcher tasks, including deterministic MLFF SP/relax, MD, and NEB input layouts.
Use this skill for managed MLFF NEB optimization after a complete locally interpolated fixed-image path has been validated.
Use this skill for MLFF single-point screening, ranking, and geometry relaxation when choosing among enabled MACE, FairChem UMA, MatterSim, or ORB-v3 backends.
| name | adsorbate-and-intermediate-generation |
| description | 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.