aromatic-skill

name

aromatic-skill

description

Multiwfn aromaticity and electron-delocalization workflow skill. Use when the user includes --aromatic or asks for aromaticity, antiaromaticity, NICS, ICSS, HOMA, HOMAc, HOMER, Bird index, multicenter bond order, MCI, AV1245, PDI, FLU, FLU-pi, PLR, ITA aromaticity, Shannon aromaticity, ring critical point properties, ELF/LOL pi analysis, or LOLIPOP from SMILES, structures, wavefunction files, Gaussian NMR outputs, or Multiwfn outputs.

Aromatic Skill

Use this skill to explain and prepare Multiwfn aromaticity analyses, then run or resume the selected workflow when the required files are available.

Required Behavior

Always start aromaticity requests by giving a concise overview of the available method families unless the user explicitly names a method and asks to skip explanation.

Use references/aromatic-methods.yml for method cards, required inputs, outputs, and caveats. Use references/multiwfn-aromatic-recipes.md when a generated Multiwfn recipe needs inspection or repair.

Quick Start

Explain all supported methods and create a dry-run plan:

python3 skills/aromatic-skill/scripts/aromatic_pipeline.py --aromatic --explain --workdir <project-dir>

Prepare a specific workflow:

python3 skills/aromatic-skill/scripts/aromatic_pipeline.py \
  --aromatic \
  --method homa \
  --input molecule.xyz \
  --ring-atoms 1-6

Prepare NICS-1D from SMILES by calling input-skill for a Gaussian NMR template:

python3 skills/aromatic-skill/scripts/aromatic_pipeline.py \
  --aromatic \
  --method nics-1d \
  --smiles 'c1ccccc1' \
  --charge 0 \
  --multiplicity 1 \
  --ring-atoms 1-6

After the user runs the generated Gaussian job, resume with:

python3 skills/aromatic-skill/scripts/aromatic_pipeline.py \
  --aromatic \
  --method nics-1d \
  --resume-manifest aromatic-skill-run/<run>/manifest.json \
  --gaussian-output NICS_1D.out \
  --ring-atoms 1-6

Add --execute only when the recipe has no placeholders and a valid Multiwfn input file is available.

Workflow

1. Run the pipeline with --aromatic --explain or read references/aromatic-methods.yml to present all methods briefly.
2. Identify the user's target method. If unspecified, ask which method family they want after explaining the options.
3. Inspect provided files. Gaussian NMR outputs containing GIAO Magnetic shielding tensor and Bq should be treated as NICS/ICSS-ready and the user should be asked whether to continue aromaticity analysis.
4. For SMILES-only requests, call aromatic_pipeline with --smiles; it delegates structure/input preparation to input-skill. Collect charge and multiplicity first rather than silently inferring them.
5. For ring-dependent analyses, suggest ring candidates when possible, but require user confirmation via --ring-atoms before production calculations. Multi-ring systems must never proceed with a silent default ring.
6. For FLU-pi, ELF/LOL-pi, and LOLIPOP, require confirmed --pi-orbitals.
7. For NICS/ICSS, use the Gaussian two-stage flow: generate template/Bq input first, wait for the user to run Gaussian, then resume from .out or .log.
8. Return aromatic_summary.md, manifest.json, generated recipes, any parsed result files, and warnings.

Output Contract

Each run writes aromatic-skill-run/<name>-YYYYMMDD-HHMMSS/ unless --outdir is provided.

Expected outputs:

• method_overview.md
• aromatic_plan.md
• aromatic_results.json
• aromatic_summary.md
• manifest.json
• multiwfn_aromatic.inp
• multiwfn_aromatic.log
• NICS/ICSS intermediate inputs and parsed text/cube/PDF outputs when available.

Do not claim a numeric result was produced unless aromatic_results.json or manifest.json records an existing parsed result or a successful Multiwfn execution.

Scientific Guardrails

• Treat RDKit SMILES geometries as starting structures only.
• Confirm ring atom order follows connectivity for HOMA, Bird, FLU, AV1245, and multicenter methods.
• Confirm pi orbitals explicitly for pi-resolved methods.
• Report that ORCA NMR output parsing is not a v1 target; NICS/ICSS resume expects Gaussian NMR output.
• For topology/fuzzy methods, report partition scheme, critical point, or grid caveats when relevant.