This repository includes 5 Jupyter notebooks and corresponding folders containing sample input and output files for KMC simulations for the electrocatalysis with Zacros. The folder zacros_wrapper is from the authors of software Zacros. Units.py contains frequently used units.
Reference
Li, J.; Maresi, I.; Lum, Y.; Ager III, J. W. Effects of Surface Diffusion in Electrocatalytic CO. J. Chem. Phys. 2021. DOI:10.1063/5.0068517
Specifically,
01-parameter-CO-stripping+Goodpaster.ipynb is for parameters conversion to the form for Zacros using the samples from the CO stripping model and Goodpaster model.
02-CO-stripping-MKM.ipynb exhibits running microkinetic models for Cyclic Voltammetry（CV) and potential steps (PS). Results can be compared with KMC results.
03-PS-Multi.ipynb runs potential steps for CO stripping with multiple trajectories and provides plots for adsorbate coverage and current density. Folder 03-PS-Multi-SF contains sample simulation files and outputs.
04-CV-Multi.ipynb runs CV for CO stripping with multiple trajectories and provides plots for adsorbate coverage and current density. Note that CV requires reading the last snapshot of forward sweeping and coding that as the initial state for backward sweeping, and in the notebook includes the methods dealing with bidentate situations. Folder 04-CV-Multi-SF contains sample simulation files and outputs.
05-Isotope-Multi.ipynb runs the two-site model for CO$_2$ reduction for multiple trajectories and saves data in .csv files that can be further analyzed. Folder 05-Isotope-Multi contains sample simulation files and outputs. Note that the lattice_input.dat and state_input.dat should be changed for different region sizes.