Abstract
Kinetic Monte Carlo generates a sequence of configurations and times when the transitions between these configurations occur. This solves the master equation in the sense that a configuration α is obtained at time t with a probability P α (t) that is a solution of the master equation. There are many algorithms that yield such a sequence of configurations and which are statistically equivalent. They all need to determine repeatedly the time that the next process will occur, the type of process that will occur, and the position on the surface where the process will occur. Each of these can be determined in a number of ways, which can be combined in even more ways. This results in many algorithms. Few of them are however efficient. We discuss in detail the Variable Step Size Method, the Random Selection Method, and the First Reaction Method. We use the Variable Step Size Method to show how to handle lists of processes, different ways to make selections of processes and process types, and how computer time and memory scales with system size. Time-dependent rate constants are discusses separately as the determination of when processes take place pose special problems. Parallelization is discussed as well as some older algorithms. Some guidelines are given of how to choose an algorithm for a simulation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
K. Binder, Monte Carlo Methods in Statistical Physics (Springer, Berlin, 1986)
D.T. Gillespie, J. Comput. Phys. 22, 403 (1976)
D.T. Gillespie, J. Phys. Chem. 81, 2340 (1977)
J. Honerkamp, Stochastische Dynamische Systeme (VCH, Weinheim, 1990)
Y. Cao, H. Li, L. Petzold, J. Chem. Phys. 121, 4059 (2004)
Y. Cao, D.T. Gillespie, L. Petzold, J. Chem. Phys. 122, 014116 (2005)
Y. Cao, D.T. Gillespie, L. Petzold, J. Comput. Phys. 206, 395 (2005)
A.P.J. Jansen, J.J. Lukkien, Catal. Today 53, 259 (1999)
D.T. Gillespie, J. Chem. Phys. 115, 1716 (2001)
H. Resat, H.S. Wiley, D.A. Dixon, J. Phys. Chem. B 105, 11026 (2001)
A. Chatterjee, D.G. Vlachos, J. Comput.-Aided Mater. Des. 14, 253 (2007)
A.B. Bortz, M.H. Kalos, J.L. Lebowitz, J. Comput. Phys. 17, 10 (1975)
F.C. Alcaraz, M. Droz, M. Henkel, V. Rittenberg, J. Phys. 230, 250 (1994)
W. Feller, An Introduction to Probability Theory and Its Applications (Wiley, New York, 1970)
D.E. Knuth, The Art of Computer Programming, Volume III: Sorting and Searching (Addison-Wesley, Reading, 1973)
T.P. Schulze, Phys. Rev. E 65, 036704 (2002)
T.P. Schulze, J. Comput. Phys. 227, 2455 (2008)
E. Hansen, M. Neurock, Chem. Eng. Sci. 54, 3411 (1999)
M. Stamatakis, D.G. Vlachos, J. Chem. Phys. 134, 214115 (2011)
J.P.L. Segers, Algorithms for the Simulation of Surface Processes (Eindhoven University of Technology, Eindhoven, 1999)
I. Mitrani, Simulation Techniques for Discrete Event Systems (Cambridge University Press, Cambridge, 1982)
A.P.J. Jansen, Comput. Phys. Commun. 86, 1 (1995)
A.P.J. Jansen, Phys. Rev. B 52, 5400 (1995)
R.M. Nieminen, A.P.J. Jansen, Appl. Catal. A, Gen. 160, 99 (1997)
M.T.M. Koper, J.J. Lukkien, A.P.J. Jansen, P.A.J. Hilbers, R.A. van Santen, J. Chem. Phys. 109, 6051 (1998)
V. Rai, H. Pitsch, A. Novikov, Phys. Rev. E 74, 046707 (2006)
C.G.M. Hermse, A.P. van Bavel, M.T.M. Koper, J.J. Lukkien, R.A. van Santen, A.P.J. Jansen, Surf. Sci. 572, 247 (2004)
C.G.M. Hermse, A.P. van Bavel, M.T.M. Koper, J.J. Lukkien, R.A. van Santen, A.P.J. Jansen, Phys. Rev. B 73, 195422 (2006)
W.H. Press, B.P. Flannery, S.A. Teukolsky, W.T. Vetterling, Numerical Recipes. The Art of Scientific Computing (Cambridge University Press, Cambridge, 1989)
S.J. Lombardo, A.T. Bell, Surf. Sci. Rep. 13, 1 (1991)
J.J. Lukkien, J.P.L. Segers, P.A.J. Hilbers, R.J. Gelten, A.P.J. Jansen, Phys. Rev. E 58, 2598 (1998)
K.A. Fichthorn, W.H. Weinberg, J. Chem. Phys. 95, 1090 (1991)
V. Privman, Nonequilibrium Statistical Mechanics in One Dimension (Cambridge University Press, Cambridge, 1997)
B. Meng, W.H. Weinberg, J. Chem. Phys. 100, 5280 (1994)
J. Mai, W. von Niessen, Phys. Rev. A 44, R6165 (1991)
J. Mai, W. von Niessen, J. Chem. Phys. 98, 2032 (1993)
R. Danielak, A. Perera, M. Moreau, M. Frankowicz, R. Kapral, Physica A 229, 428 (1996)
J.P. Boon, B. Dab, R. Kapral, A. Lawniczak, Phys. Rep. 273, 55 (1996)
J.R. Weimar, Simulation with Cellular Automata (Logos Verlag, Berlin, 1997)
S. Wolfram, A New Kind of Science (Wolfram Media, Champaign, 2002)
B. Drossel, Phys. Rev. Lett. 76, 936 (1996)
G. Korniss, M.A. Novotny, P.A. Rikvold, J. Comput. Phys. 153, 488 (1999)
G. Korniss, C.J. White, P.A. Rikvold, M.A. Novotny, Phys. Rev. E 63, 016120 (2000)
G. Korniss, Z. Toroczkai, M.A. Novotny, P.A. Rikvold, Phys. Rev. Lett. 84, 1351 (2000)
G. Korniss, M.A. Novotny, Z. Toroczkai, P.A. Rikvold, in Computer Simulations in Condensed Matter Physics XIII, ed. by D.P. Landau, S. Lewis, H.B. Schütler (Springer, Berlin, 2001), pp. 183–188
A. Kolakowska, M.A. Novotny, G. Korniss, Phys. Rev. E 67, 046703 (2003)
S.V. Nedea, Analysis and simulations of catalytic reactions. Ph.D. thesis, Eindhoven (2003)
Y. Shim, J.G. Amar, Phys. Rev. B 71, 115436 (2005)
Y. Shim, J.G. Amar, Phys. Rev. B 71, 125432 (2005)
Y. Shim, J.G. Amar, J. Comput. Phys. 212, 305 (2006)
M. Merrick, K.A. Fichthorn, Phys. Rev. E 75, 011606 (2007)
F. Shi, Y. Shim, J.G. Amar, Phys. Rev. E 76, 031607 (2007)
E. Martínez, J. Marian, M.H. Kalos, J.M. Perlado, J. Comput. Phys. 227, 3804 (2008)
G. Nandipati, Y. Shim, J.G. Amar, A. Karim, A. Kara, T.S. Rahman, O. Trushin, J. Phys., Condens. Matter 21, 084214 (2009)
M.J. Quinn, Parallel Computing: Theory and Practice (McGraw-Hill, New York, 1994)
R.M. Fujimoto, Commun. ACM 33, 31 (1990)
B.D. Lubachevsky, J. Comput. Phys. 75, 103 (1988)
D.E. Knuth, The Art of Computer Programming, Volume I: Fundamental Algorithms (Addison-Wesley, Reading, 1973)
Carlos is a general-purpose program, written in C by J.J. Lukkien, for simulating reactions on surfaces that can be represented by regular lattices: an implementation of the First Reaction Method, the Variable Step Size Method, and the Random Selection Method. http://www.win.tue.nl/~johanl/projects/Carlos/
R.M. Ziff, E. Gulari, Y. Barshad, Phys. Rev. Lett. 56, 2553 (1986)
A.P.J. Jansen, Phys. Rev. B 69, 035414 (2004)
M.T.M. Koper, J.J. Lukkien, A.P.J. Jansen, R.A. van Santen, J. Phys. Chem. B 103, 5522 (1999)
C.G.M. Hermse, A.P. van Bavel, A.P.J. Jansen, L.A.M.M. Barbosa, P. Sautet, R.A. van Santen, J. Phys. Chem. B 108, 11035 (2004)
R.J. Gelten, A.P.J. Jansen, R.A. van Santen, J.J. Lukkien, J.P.L. Segers, P.A.J. Hilbers, J. Chem. Phys. 108, 5921 (1998)
C.G.M. Hermse, F. Frechard, A.P. van Bavel, J.J. Lukkien, J.W. Niemantsverdriet, R.A. van Santen, A.P.J. Jansen, J. Chem. Phys. 118, 7081 (2003)
W.K. Offermans, A.P.J. Jansen, R.A. van Santen, Surf. Sci. 600, 1714 (2006)
W.K. Offermans, A.P.J. Jansen, R.A. van Santen, G. Novell-Leruth, J.M. Ricart, J. Pérez-Ramirez, J. Phys. Chem. C 111, 17551 (2007)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Jansen, A.P.J. (2012). Kinetic Monte Carlo Algorithms. In: An Introduction to Kinetic Monte Carlo Simulations of Surface Reactions. Lecture Notes in Physics, vol 856. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29488-4_3
Download citation
DOI: https://doi.org/10.1007/978-3-642-29488-4_3
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-29487-7
Online ISBN: 978-3-642-29488-4
eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)