AMSkinetics (MKMCXX and Zacros)

The AMSkinetics GUI module provides an graphical interface to set up microkinetics or kinetic Monte Carlo (KMC) simulations.

MKMCXX Microkinetics

GUI Tutorial: Microkinetics: CO oxidation

Microkinetics simulations can be done via the MKMCXX program by Filot, I.A.W., Zijlstra, B. and Hensen, E.J.M.. The AMSkinetics GUI module was initially developed by Micha Davids. For a description of the MKMCXX program and an overview of the microkinetics method, we refer the reader to the following pages:

When you publish results in the scientific literature which were obtained with the MKMCXX program you should include the following reference:
Ivo A. W. Filot, Prof. Dr. Rutger A. van Santen, Prof. Dr. Emiel J. M. Hensen, The Optimally Performing Fischer–Tropsch Catalyst, Angew. Chem. Int. Ed., 53: 12746-12750 (2014)

Zacros Kinetic Monte Carlo

Note

To use Zacros, you need a valid Zacros license that you can obtain from SCM (it is separate from the general Amsterdam Modeling Suite license).

GUI tutorial: Zacros Kinetic Monte Carlo

The kinetic Monte Carlo tools in the Amsterdam Modeling Suite based on Zacros include

  • The Zacros program itself
  • pyZacros : a Python library for running and analyzing Zacros simulations
  • AMSkinetics : a GUI for setting up Zacros calculations (jobs can be submitted via AMSjobs)
  • Zacros-post: a GUI for viewing Zacros results. Installable via the package manager (SCM → Packages).

When you publish results in the scientific literature which were obtained with the Zacros program you should include the following reference:

  • Stamatakis, M. and D. G. Vlachos (2011). “A Graph-Theoretical Kinetic Monte Carlo Framework for on-Lattice Chemical Kinetics.” The Journal of Chemical Physics, 134(21): 214115.
  • Nielsen, J., M. d’Avezac, J. Hetherington and M. Stamatakis (2013). “Parallel Kinetic Monte Carlo Simulation Framework Incorporating Accurate Models of Adsorbate Lateral Interactions.” The Journal of Chemical Physics, 139(22): 224706.
  • Ravipati, S., Nielsen, J., d’Avezac, M., Hetherington, J. and M. Stamatakis (2020). “A Caching Scheme to Accelerate Kinetic Monte Carlo Simulations of Catalytic Reactions”. The Journal of Physical Chemistry A, 124(35): 7140-7154. [please cite if you are using the caching scheme]
  • Savva, G. D. and M. Stamatakis (2020). “Comparison of Queueing Data-Structures for Kinetic Monte Carlo Simulations of Heterogeneous Catalysts”. The Journal of Physical Chemistry A, 124(38): 7843-7856. [please cite if you are using the skip-list or the pairing heap queueing system]
  • Ravipati, S., Savva, G. D., Christidi, I.-A., Guichard, R., Nielsen, J., Réocreux, R., and Stamatakis, M. (2022). “Coupling the Time-Warp algorithm with the Graph-Theoretical Kinetic Monte Carlo framework for distributed simulations of heterogeneous catalysts”. Computer Physics Communications, 270: 108148 [please cite if you are using the MPI Time- Warp algorithm implementation]