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:

* MKMCXX website

* MKMCXX wiki

* Introduction to microkinetic modeling by I.A.W. Filot

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]
