catalysis-electrochem

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