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Use this skill for generating adsorbates and reaction intermediates, standardizing molecular inputs, and preparing structures for adsorption placement.
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Basé sur la classification professionnelle SOC
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.