Efficiency of linked cell algorithms

DOI10.1016/J.CPC.2010.11.002zbMATH Open1215.82002arXiv1006.1239OpenAlexW2083641704MaRDI QIDQ538540FDOQ538540

Guido Germano, Ulrich Welling

Publication date: 25 May 2011

Published in: Computer Physics Communications (Search for Journal in Brave)

Abstract: The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its efficiency, because a large part of CPU time is spent to identify the interacting particles. Several recent publications proposed improvements to the algorithm and investigated their efficiency by applying them to particular setups. In this publication we develop a general method to evaluate the efficiency of these algorithms, which is mostly independent of the parameters of the simulation, and test it for a number of linked cell list algorithms. We also propose a combination of linked cell reordering and interaction sorting that shows a good efficiency for a broad range of simulation setups.

Full work available at URL: https://arxiv.org/abs/1006.1239

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zbMATH Keywords

Monte Carlomolecular dynamicsmolecular simulationinteraction sortinglinked cell listlinked cell reorderingneighbour list

Mathematics Subject Classification ID

Analysis of algorithms (68W40) Interacting particle systems in time-dependent statistical mechanics (82C22)

Cites Work

• Fast parallel algorithms for short-range molecular dynamics
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• General purpose molecular dynamics simulations fully implemented on graphics processing units
• Parallel atomistic simulations
• Faster neighbour list generation using a novel lattice vector representation
• Algorithm optimization in molecular dynamics simulation

Cited In (4)

• A multilevel-skin neighbor list algorithm for molecular dynamics simulation
• Spectral accuracy in fast Ewald-based methods for particle simulations
• An efficient linked list for molecular simulations on a spherical surface
• Fast neighbor lists for adaptive-resolution particle simulations

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