Setting up a kinetic Monte Carlo (KMC) simulation with Zacros is relatively easy, but requires some background knowledge to ensure that things are done correctly. The material made available here contains a Lecture and 4 Tutorials, and is intended as a crash-course on KMC simulation and the use of Zacros, assuming one is familiar with basic concepts of statistical mechanics. Hands-on activities on Zacros are provided as well, at the end of each Tutorial.
The material available below is intended as a "crash-course" on KMC simulation and the use of Zacros. At the end of each Tutorial there is an activity that covers the corresponding learning outcomes. To complete the activity you have to download and install Zacros on your computer or a High Performance Computing facility that you have access to. To download the files of the latest Zacros release, please follow the instructions under menu item Software.
A broader overview of background concepts of statistical mechanics underpinning KMC, is given in the video lectures of tutorial "Fundamentals of Statistical Mechanics and KMC".
Lecture: Kinetic Monte Carlo Simulations of Surface Reactions
Learning outcomes:
- Fundamentals of Transition State Theory (TST) for calculating rates of elementary events.
- Fundamentals of the Kinetic Monte Carlo (KMC) approach for simulating reactions at the mesoscopic level.
- Elements of advanced KMC simulation as implemented in Zacros.
Lecture slides in pdf format (opens in a new window).
Tutorial 1: Demonstration of Ethylene Hydrogenation Example
Learning outcomes:
- Compiling Zacros with CMake.
- Preparing the four compulsory simulation files for a simple catalytic system.
- Running the simulation and visualizing the results.
Tutorial slides in pdf format (opens in a new window).
Zip file with the Zacros input for the ethylene hydrogenation example.
Tutorial 2: Creating Lattice Input for Pt(100)
Learning outcomes:
- Preparing lattice input files for Zacros simulations.
Tutorial slides in pdf format (opens in a new window).
Matlab script for plotting the lattice structure (opens in a new window).
Tutorial 3: Energetics Input for CO Oxidation on Pt(100)
Learning outcomes:
- Mapping raw energies (obtained from ab initio calculations) into formation energies.
- Preparing energetics input files for Zacros simulations.
Tutorial slides in pdf format (opens in a new window).
Tutorial 4: Mechanism Input for CO Oxidation on Pt(100)
Learning outcomes:
- Calculating pre-exponential factors of rate constants via TST, for representative elementary steps.
- Preparing mechanism input files for Zacros simulations.
Tutorial slides in pdf format (opens in a new window).
Zip file with a model solution for the CO oxidation simulation of Tutorials 2-4.
Part of the material made available here has been delivered in the context of Courses and Workshops outlined below. The Zacros Team and Dr Michail Stamatakis are grateful to the co-organizers and hosts of these courses and events.
- PHAS0076 "TYC Materials Modelling" course offered by the Thomas Young Centre.
- Workshop on KMC modelling at the University of Pittsburgh (July 2018) hosted by the Computer-Aided Nano and Energy Lab (CANELa), led by Prof. Giannis Mpourmpakis.
- "Workshop on Multiscale Computational Catalysis and Materials Science" and 1st International symposium on Computational and Experimental Solid Catalysis - Dynamics & Kinetics - both held at the National Institute of Technology, Akashi College, Akashi, Japan (March 2020), hosted by Prof. Hideaki Kasai, Prof. Hiroshi Nakanishi, Dr Ryan Arevalo and the members of the Nano-Design Lab.
- Online Workshop on "Theory, Applications, and Tools for Multiscale Kinetic Modeling", co-organized by Politecnico di Milano, University College London, and the University of Delaware (July 2020). A recording of the KMC session can be found on YouTube.