PyMKMKit documentation

Purpose

This toolkit standardizes how microkinetic modeling data from plane-wave DFT (VASP) calculations are collected, stored, and reproduced. It extracts energies and vibrational frequencies to compute activation energies and pre-exponential factors for reaction steps. Data are stored in human-readable YAML files, with separate files for each thermodynamic state and a master file defining the full reaction network.

Features

• VASP output parsing: Convert frequency and geometry optimization OUTCAR files into structured YAML data.

• Standardized data generation: Automatically produce consistent, reusable YAML representations of thermodynamic states.

• Reaction network evaluation: Compute activation barriers and adsorption energies from a network definition.

• Reaction pathway analysis: Calculate overall reaction energies for defined pathways.

• Potential energy diagrams: Generate potential energy profiles for selected reaction paths.

Contents

• Installation
  • Why use a virtual environment?
  • Create and activate a virtual environment
  • Install pymkmkit
• Tutorials
  • Converting OUTCAR to YAML file
  • Building network.yaml file
• API reference
  • Classes overview
  • Functions overview
  • Module details
• CLI reference
  • Command overview
  • CLI module API