AMSkinetics (MKMCXX and Zacros)

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

To search menu commands, input panels, and documentation, click the search icon in the notebook’s top-right corner, or press Cmd+F or Cmd+Shift+F on macOS (Ctrl+F or Ctrl+Shift+F on Windows and Linux). This works in both MKMCXX and Zacros mode. See Menu command search for keyboard navigation and matching details.

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]