How do I install the Catalysis Electrochem skill?

Run npx skillmds add majiayu000/catalysis-electrochem in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Catalysis Electrochem safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Catalysis Electrochem?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Catalysis Electrochem free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Catalysis Electrochem?

majiayu000 (@majiayu000) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Catalysis Electrochem by majiayu000

Name: Catalysis Electrochem
Rating: 4.2 (5 reviews)
Author: majiayu000

Catalysis Electrochem

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.

majiayu000 4529cd0 2 files · 4.2 KB Updated Sep 9, 2026 567 repo stars

File contents

name: catalysis-electrochem description: Catalysis and Electrochemistry Toolkit (6 sub-skills: band-center, imaginary-freq-correction, implicit-solvation, neb-analysis, reaction-kinetics, thermal-corrections)

Catalysis and Electrochemistry Toolkit

Overview

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

---name: catalysis-electrochemdescription: 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.--- --- name: catalysis-electrochem description: Catalysis and Electrochemistry Toolkit (6 sub-skills: band-center, imaginary-freq-correction, implicit-solvation, neb-analysis, reaction-kinetics, thermal-corrections) --- # 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

Frequently asked questions