AMSkinetics (MKMCXX and Zacros)¶
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¶
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]