Incorporating first-principles quantum chemistry data in kinetic Monte Carlo simulations has proven to be a powerful approach in investigating the behaviour of catalytic systems at the molecular level. Such first-principles KMC frameworks were pioneered by M. Neurock, M. Scheffler and co-workers [M. Neurock, E. W. Hansen (1998), Comp. Chem. Eng. 22: S1045-S1060; K. Reuter, D. Frenkel, M. Scheffler (2004), Phys. Rev. Lett. 93(11): 116105], and make use of the energies computed typically from density functional theory (DFT) for stable molecular species and transition states, in order to calculate rate constants. This tutorial explains how to map quantum chemistry data into energetics input in Zacros. As a working example we will consider water-gas shift pathways on Pt(111).
Adsorbate lateral interactions have recently attracted significant focus in the computational catalysis field, as they are responsible for ordering in the adsorbate overlayer, but also influence the activation energies of elementary events. Zacros treats such interactions within the general framework of cluster expansion Hamiltonians. This enables us to include long-range and many-body contributions in a simulation. Brønsted-Evans-Polanyi relations are used to correlate the activation energy of an elementary event with its reaction energy, thereby capturing the influence of neighbouring spectator adsorbates on barriers. This tutorial deals with setting up the Zacros input for a detailed cluster expansion Hamiltonian for O on Pt developed by Schneider and co-workers [J. Catal. (2012) 286: 88-94].
Zacros parses text files that follow a specific keyword-based syntax and can be generated by a text editor such as Notepad++ or Textpad. Such editors support syntax highlighting to make it easier for the user to read and modify the input. Within the Zacros distribution one can find the files that define the Zacros input language keywords for Notepad++ or Textpad. In this tutorial you will learn how to import these files and enable syntax highlighting for Zacros input files.
Ziff, Gulari and Barshad were the first to demonstrate kinetic phase transitions in a conceptual model for CO oxidation on the surface of a heterogeneous catalyst [R. M. Ziff, E. Gulari, Y. Barshad (1986) Phys. Rev. Lett. 56: 2553]. Using a mechanism that includes the non-dissociative adsorption of CO, the dissociative adsorption of O2, and the fast CO oxidation reaction Ziff et al., found a second order phase transition from an O-poisoned regime to a reactive regime, and a first order transition from the reactive to the CO-poisoned regime. Such a model can be easily set up in Zacros: this tutorial explains how to create the necessary input files.