Accurate acceleration of kinetic Monte Carlo simulations through the modification of rate constants

被引:88
作者
Chatterjee, Abhijit [1 ]
Voter, Arthur F. [2 ]
机构
[1] Indian Inst Technol Kanpur, Dept Chem Engn, Kanpur 208016, Uttar Pradesh, India
[2] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA
基金
美国能源部;
关键词
STOCHASTIC SIMULATION; ALGORITHMS; SYSTEMS;
D O I
10.1063/1.3409606
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
We present a novel computational algorithm called the accelerated superbasin kinetic Monte Carlo (AS-KMC) method that enables a more efficient study of rare-event dynamics than the standard KMC method while maintaining control over the error. In AS-KMC, the rate constants for processes that are observed many times are lowered during the course of a simulation. As a result, rare processes are observed more frequently than in KMC and the time progresses faster. We first derive error estimates for AS-KMC when the rate constants are modified. These error estimates are next employed to develop a procedure for lowering process rates with control over the maximum error. Finally, numerical calculations are performed to demonstrate that the AS-KMC method captures the correct dynamics, while providing significant CPU savings over KMC in most cases. We show that the AS-KMC method can be employed with any KMC model, even when no time scale separation is present (although in such cases no computational speed-up is observed), without requiring the knowledge of various time scales present in the system. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3409606]
引用
收藏
页数:12
相关论文
共 35 条
[1]   NEW ALGORITHM FOR MONTE-CARLO SIMULATION OF ISING SPIN SYSTEMS [J].
BORTZ, AB ;
KALOS, MH ;
LEBOWITZ, JL .
JOURNAL OF COMPUTATIONAL PHYSICS, 1975, 17 (01) :10-18
[2]   The slow-scale stochastic simulation algorithm [J].
Cao, Y ;
Gillespie, DT ;
Petzold, LR .
JOURNAL OF CHEMICAL PHYSICS, 2005, 122 (01)
[3]   Multiscale spatial Monte Carlo simulations: Multigriding, computational singular perturbation, and hierarchical stochastic closures [J].
Chatterjee, A ;
Vlachos, DG .
JOURNAL OF CHEMICAL PHYSICS, 2006, 124 (06)
[4]   Binomial distribution based τ-leap accelerated stochastic simulation -: art. no. 024112 [J].
Chatterjee, A ;
Vlachos, DG ;
Katsoulakis, MA .
JOURNAL OF CHEMICAL PHYSICS, 2005, 122 (02)
[5]   An overview of spatial microscopic and accelerated kinetic Monte Carlo methods [J].
Chatterjee, Abhijit ;
Vlachos, Dionisios G. .
JOURNAL OF COMPUTER-AIDED MATERIALS DESIGN, 2007, 14 (02) :253-308
[6]   Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains [J].
Deuflhard, P ;
Huisinga, W ;
Fischer, A ;
Schütte, C .
LINEAR ALGEBRA AND ITS APPLICATIONS, 2000, 315 (1-3) :39-59
[7]  
Eick S. G., 1993, ACM Transactions on Modeling and Computer Simulation, V3, P287, DOI 10.1145/159737.159744
[8]   Efficient exact stochastic simulation of chemical systems with many species and many channels [J].
Gibson, MA ;
Bruck, J .
JOURNAL OF PHYSICAL CHEMISTRY A, 2000, 104 (09) :1876-1889
[9]   GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS [J].
GILLESPIE, DT .
JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (04) :403-434
[10]   Approximate accelerated stochastic simulation of chemically reacting systems [J].
Gillespie, DT .
JOURNAL OF CHEMICAL PHYSICS, 2001, 115 (04) :1716-1733