Past Projects

M. Stamatakis (PI), J. Hetherington (co-I), B. Silva (co-I), "Zacros Software Package Development: Pushing the Frontiers of Kinetic Monte Carlo Simulation in Catalysis". 2014-2015. Sponsored by the Edinburgh Parallel Computing Centre by an Embedded CSE support grant (eCSE01-001). Read the end-of-project report on the ARCHER website.

This project focused on algorithmic implementations to improve the performance and scalability of Zacros. The main research objective was the incorporation of spatial decomposition schemes for parallelising the simulation to an arbitrary number of processors, successfully harnessing the power of ARCHER. We thus employed distributed-memory (MPI) parallelism making it possible for Zacros to run simulations of large domains, with each core tackling a different part of the domain. An approximate scheme was implemented that resulted in 23× speedup using 24 computers. Future work will enable us to exploit an ever increasing number of machines.


M. Stamatakis, "Graph Theoretical Kinetic Monte Carlo: Preliminary Investigation of Approaches to Parallelisation". Jan-Mar 2013. Sponsored by the RITS Department, under the termly call for software development proposals.

The energetic models were extended to tackle arbitrarily complex adsorbate-adsorbate lateral interactions, involving long-range and many-body contributions. Brønsted-Evans-Polanyi relations were implemented for capturing the effect of local coverage on the activation energies of elementary processes. As part of this project, Zacros's continuous integration and testing framework was developed on the RSDT Jenkins server. This allows the testing of new features of the code as they are being developed. Memory allocation on Zacros was optimised, thereby speeding up KMC simulations involving short-range lateral interactions. OpenMP shared memory parallelisation was further implemented, providing significant speed up for problems that involve long-range interactions. Speedups of 10x were verified on the Legion@UCL cluster with up to 12 cores.

Relevant publication:


M. Stamatakis, D. G. Vlachos, "Graph Theoretical Kinetic Monte Carlo Method Development". 2010-2012. Carried out as part of M. Stamatakis's post-doc at D. G. Vlachos's lab at the University of Delaware, USA.

This project laid out the foundations of the Graph-Theoretical KMC method which is implemented in Zacros. This method enables the representation and treatment of arbitrarily complex reactions, involving many sites in specific neighbouring arrangements, potentially occupied by multi-dentate species. Energetic interactions were limited to pairwise additive contributions in this original implementation. The first reaction to be modelled with this framework was the water-gas shift on flat and stepped Pt surfaces, followed by a study of CO oxidation on Au6 nanoclusters. Both systems involve complicated catalytic structures and reactions in which multi-dentate species participate.

Relevant publications:

  • Stamatakis, M. and D. G. Vlachos (2011). “A Graph-Theoretical Kinetic Monte Carlo Framework for on-Lattice Chemical Kinetics”. Journal of Chemical Physics 134(21): 214115. (doi: 10.1063/1.3596751)
  • Stamatakis, M., Chen, Y. and D. G. Vlachos (2011). “First Principles-Based Kinetic Monte Carlo Simulation of the Structure-Sensitivity of the Water-Gas Shift Reaction on Platinum Surfaces”. Journal of Physical Chemistry C 115(50): 24750-24762. (doi: 10.1021/jp2071869)
  • Stamatakis, M., Christiansen, M., D. G. Vlachos and G. Mpourmpakis (2012). “Multiscale Modeling Reveals Poisoning Mechanisms on MgO-supported Au Catalysts in CO Oxidation”. Nano Letters 2(7): 3621-3626. (doi: 10.1021/nl301318b)