Exact distributed kinetic Monte Carlo simulations for on-lattice chemical kinetics: lessons learnt from medium- and large-scale benchmarks

被引:5
作者
Savva, Giannis D. [1 ]
Benson, Raz L. [1 ]
Christidi, Ilektra-Athanasia [2 ]
Stamatakis, Michail [1 ]
机构
[1] UCL, Thomas Young Ctr, Dept Chem Engn, Torrington Pl, London WC1E7JE, England
[2] UCL, Adv Res Comp Ctr, Res Software Dev Grp, Gower St, London WC1E6BT, England
来源
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES | 2023年 / 381卷 / 2250期
基金
英国工程与自然科学研究理事会;
关键词
kinetic Monte Carlo; lattice; time-warp algorithm; catalysis; materials science; distributed simulation; CO OXIDATION; OSCILLATORY REACTIONS; TRANSITION; FRAMEWORK; PATTERNS;
D O I
10.1098/rsta.2022.0235
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Kinetic Monte Carlo (KMC) simulations have been instrumental in multiscale catalysis studies, enabling the elucidation of the complex dynamics of heterogeneous catalysts and the prediction of macroscopic performance metrics, such as activity and selectivity. However, the accessible length- and time-scales have been a limiting factor in such simulations. For instance, handling lattices containing millions of sites with 'traditional' sequential KMC implementations is prohibitive owing to large memory requirements and long simulation times. We have recently established an approach for exact, distributed, lattice-based simulations of catalytic kinetics which couples the Time-Warp algorithm with the Graph-Theoretical KMC framework, enabling the handling of complex adsorbate lateral interactions and reaction events within large lattices. In this work, we develop a lattice-based variant of the Brusselator system, a prototype chemical oscillator pioneered by Prigogine and Lefever in the late 60s, to benchmark and demonstrate our approach. This system can form spiral wave patterns, which would be computationally intractable with sequential KMC, while our distributed KMC approach can simulate such patterns 15 and 36 times faster with 625 and 1600 processors, respectively. The medium- and large-scale benchmarks thus conducted, demonstrate the robustness of the approach, and reveal computational bottlenecks that could be targeted in further development efforts.This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
引用
收藏
页数:18
相关论文
共 53 条
  • [1] [Anonymous], 1971, Thermodynamics of structure stability and fluctuations
  • [2] Quantifying Pore Width Effects on Diffusivity via a Novel 3D Stochastic Approach with Input from Atomistic Molecular Dynamics Simulations
    Apostolopoulou, Maria
    Santos, Mirella S.
    Hamza, Muhammad
    Bui, Tai
    Economou, Ioannis G.
    Stamatakis, Michail
    Striolo, Alberto
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (12) : 6907 - 6922
  • [3] Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms
    Arampatzis, Giorgos
    Katsoulakis, Markos A.
    Plechac, Petr
    Taufer, Michela
    Xu, Lifan
    [J]. JOURNAL OF COMPUTATIONAL PHYSICS, 2012, 231 (23) : 7795 - 7814
  • [4] The kinetic Monte Carlo method: Foundation, implementation, and application
    Battaile, Corbett C.
    [J]. COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, 2008, 197 (41-42) : 3386 - 3398
  • [5] Belousov B.P., 1959, PERIODIC REACTION IT, P145
  • [6] An overview of spatial microscopic and accelerated kinetic Monte Carlo methods
    Chatterjee, Abhijit
    Vlachos, Dionisios G.
    [J]. JOURNAL OF COMPUTER-AIDED MATERIALS DESIGN, 2007, 14 (02): : 253 - 308
  • [7] Accurate acceleration of kinetic Monte Carlo simulations through the modification of rate constants
    Chatterjee, Abhijit
    Voter, Arthur F.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2010, 132 (19)
  • [8] Chemical Wave Computing from Labware to Electrical Systems
    Chatzinikolaou, Theodoros Panagiotis
    Fyrigos, Iosif-Angelos
    Ntinas, Vasileios
    Kitsios, Stavros
    Tsompanas, Michail-Antisthenis
    Bousoulas, Panagiotis
    Tsoukalas, Dimitris
    Adamatzky, Andrew
    Sirakoulis, Georgios Ch
    [J]. ELECTRONICS, 2022, 11 (11)
  • [9] A DFT and KMC based study on the mechanism of the water gas shift reaction on the Pd(100) surface
    Chutia, Arunabhiram
    Thetford, Adam
    Stamatakis, Michail
    Catlow, C. Richard A.
    [J]. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2020, 22 (06) : 3620 - 3632
  • [10] Spontaneous isothermal oscillations in N2O decomposition over a Cu-ZSM5 catalyst
    Ciambelli, P
    Di Benedetto, A
    Garufi, E
    Pirone, R
    Russo, G
    [J]. JOURNAL OF CATALYSIS, 1998, 175 (02) : 161 - 169