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  4. Large-scale benchmarks of the time-warp/graph-theoretical kinetic Monte Carlo approach for distributed on-lattice simulations of catalytic kinetics
 
research article

Large-scale benchmarks of the time-warp/graph-theoretical kinetic Monte Carlo approach for distributed on-lattice simulations of catalytic kinetics

Savva, Giannis D.  
•
Benson, Raz L.
•
Christidi, Ilektra A.
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January 6, 2023
Physical Chemistry Chemical Physics

Motivated by the need to perform large-scale kinetic Monte Carlo (KMC) simulations, in the context of unravelling complex phenomena such as catalyst reconstruction and pattern formation, we extend the work of Ravipati et al. [S. Ravipati, G. D. Savva, I.-A. Christidi, R. Guichard, J. Nielsen, R. Reocreux and M. Stamatakis, Comput. Phys. Commun., 2022, 270, 108148] in benchmarking the performance of a distributed-computing, on-lattice KMC approach. The latter, implemented in our software package Zacros, combines the graph-theoretical KMC framework with the Time-Warp algorithm for parallel discrete event simulations, and entails dividing the lattice into subdomains, each assigned to a processor. The cornerstone of the Time-Warp algorithm is the state queue, to which snapshots of the simulation state are saved regularly, enabling historical KMC information to be corrected when conflicts occur at subdomain boundaries. Focusing on three model systems, we highlight the key Time-Warp parameters that can be tuned to optimise performance. The frequency of state saving, controlled by the state saving interval, delta(snap), is shown to have the largest effect on performance, which favours balancing the overhead of re-simulating KMC history with that of writing state snapshots to memory. Also important is the global virtual time (GVT) computation interval, Delta tau(GVT), which has little direct effect on the progress of the simulation but controls how often the state queue memory can be freed up. We also find that pre-allocating memory for the state queue data structure favours performance. These findings will guide users in maximising the efficiency of Zacros or other distributed KMC software, which is a vital step towards realising accurate, meso-scale simulations of heterogeneous catalysis.

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Type
research article
DOI
10.1039/d2cp04424b
Web of Science ID

WOS:000928686800001

Author(s)
Savva, Giannis D.  
Benson, Raz L.
Christidi, Ilektra A.
Stamatakis, Michail
Date Issued

2023-01-06

Published in
Physical Chemistry Chemical Physics
Subjects

Chemistry, Physical

•

Physics, Atomic, Molecular & Chemical

•

Chemistry

•

Physics

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
THEOS  
Available on Infoscience
March 13, 2023
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/195747
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