One of the benefits of kinetic Monte Carlo is that it coarse-grains physical space: the reacting molecules are no longer moving and interacting in the 3D space but on a lattice. Thus, diffusion, for instance, is not captured as a continuous (x,y,z)-trajectory but rather as a transition whereby a molecule hops from one site of the lattice to another. Choosing how to map a catalytic surface onto a lattice is relatively simple, but one has to make some decisions that may be important in correctly capturing the relevant physics. This tutorial provides guidance on this matter and explains how to set up the input for a periodic lattice in Zacros. As a working example we will consider a FCC(100) surface.
Within the Graph-Theoretical KMC framework, a lattice is a collection of connected sites. Each site can be of a particular type, making it possible to represent for instance, the atop, bridge, and hollow sites of an FCC metal surface. The information about a periodic lattice is therefore “encoded” in the sites contained unit cell and the connectivity of these sites within the cell, as well as the sites of the neighbouring cells. In the following, we will explain how one can set up the lattice_input.dat in Zacros for a FCC(100) surface input for files.