Agent skill
catalysis-electrochem
Install this agent skill to your Project
npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/other/other/catalysis-electrochem
SKILL.md
Catalysis and Electrochemistry Toolkit
Overview
This skill group covers computational catalysis and electrochemistry workflows corresponding to VASPKIT menu 05 (tasks 501-509). It provides tools for computing thermodynamic corrections to DFT energies, analyzing reaction pathways (NEB), extracting d-band descriptors for catalytic activity, and applying transition state theory for reaction kinetics.
Sub-Skills
| Sub-Skill | Directory | Description |
|---|---|---|
| Thermal Corrections | thermal-corrections/ |
Zero-point energy, thermal corrections for adsorbates and gas-phase molecules (VASPKIT 501-502). Uses ASE thermochemistry, ideal gas, and harmonic approximations. |
| NEB Analysis | neb-analysis/ |
NEB path analysis, converting NEB paths to PDB trajectories, interpolating NEB images (VASPKIT 504-505). Uses ASE NEB, pymatgen, QE NEB. |
| d-Band Center | band-center/ |
d-band center calculation from projected DOS (VASPKIT 503). Parse QE/VASP PDOS data for catalytic activity descriptors. |
| Reaction Kinetics | reaction-kinetics/ |
Imaginary frequency correction (VASPKIT 507), half-life calculation (VASPKIT 509). Transition state theory rate constants and kinetic analysis. |
| Implicit Solvation | implicit-solvation/ |
Implicit solvation models for electrode-electrolyte interfaces. VASPsol, QE+Environ, and ASE-based Born/GBSA corrections. Solvation free energies, pKa, electrochemical reaction energetics with solvent effects. |
Method Decision Guide
Need free energy corrections for reaction energetics?
YES --> thermal-corrections/ (ZPE + thermal + entropy from vibrational frequencies)
Need to analyze an NEB calculation result?
YES --> neb-analysis/ (extract energies, interpolate images, convert to trajectory)
Need a catalytic activity descriptor?
YES --> band-center/ (d-band center from PDOS data)
Need reaction rate constants or half-lives?
YES --> reaction-kinetics/ (transition state theory, Eyring equation)
Need to correct for imaginary frequencies at a transition state?
YES --> reaction-kinetics/ (project out imaginary mode from ZPE sum)
Need solvation effects for electrode-electrolyte interfaces?
YES --> implicit-solvation/ (VASPsol, QE+Environ, or Born/GBSA corrections)
Need solvation free energies or pKa values?
YES --> implicit-solvation/ (implicit solvent models, Born model for ions)
Common Prerequisites
- ASE: Thermochemistry modules (
ase.thermochemistry), NEB tools - pymatgen: Structure manipulation, DOS parsing
- MACE: Fast frequency calculations via finite displacements
- Quantum ESPRESSO: DFT-quality frequencies via DFPT or finite differences
- numpy, scipy, matplotlib: Numerical analysis and plotting
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