Cell List algorithms for nonequilibrium molecular dynamics

DOI10.1016/J.JCP.2016.03.056MaRDI QIDQ2375181zbMATH OpenOpenAlexFDO

Authors M. Dobson, Ian Fox, Alexandra Saracino

Publication date 5 December 2016

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1412.3784

zbMATH Keywords

molecular dynamicsnonequilibriumelongational flowcell List

Mathematics Subject Classification ID

Kinetic theory of gases in time-dependent statistical mechanics (82C40) Rarefied gas flows, Boltzmann equation in fluid mechanics (76P05)

Abstract: We present two modifications of the standard cell list algorithm for nonequilibrium molecular dynamics simulations of homogeneous, linear flows. When such a flow is modeled with periodic boundary conditions, the simulation box deforms with the flow, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. For the typical case of short-ranged, pairwise interactions, the cell list algorithm reduces computational complexity of the force computation from O($N^2$) to O($N$), where $N$ is the total number of particles in the simulation box. The new versions of the cell list algorithm handle the dynamic, deforming simulation geometry. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.

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Cites work

• Extensional motions of spatially periodic lattices
• Heterogeneous multiscale method for the modeling of complex fluids and micro-fluidics

Cited in

(5)

• Neighbor list collision-driven molecular dynamics simulation for nonspherical hard particles. I: Algorithmic details
• Objective molecular dynamics for atomistic simulation of macroscopic fluid motion
• A multilevel-skin neighbor list algorithm for molecular dynamics simulation
• An efficient linked list for molecular simulations on a spherical surface
• A GENERALIZED CELL METHOD FOR HARD DISK MOLECULAR DYNAMICS SIMULATION OF POLYDISPERSE SYSTEMS

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