@article{fc684bd49d6644c486985cdf5b134184,
title = "Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units",
abstract = "We present an algorithm based on linear bounding volume hierarchies (LBVHs) for computing neighbor (Verlet) lists using graphics processing units (GPUs) for colloidal systems characterized by large size disparities. We compare this to a GPU implementation of the current state-of-the-art CPU algorithm based on stenciled cell lists. We report benchmarks for both neighbor list algorithms in a Lennard-Jones binary mixture with synthetic interaction range disparity and a realistic colloid solution. LBVHs outperformed the stenciled cell lists for systems with moderate or large size disparity and dilute or semidilute fractions of large particles, conditions typical of colloidal systems.",
keywords = "Bounding volume hierarchy, Colloid, GPU, Molecular simulation, Neighbor list, Non-uniform, Size disparity",
author = "Howard, {Michael P.} and Anderson, {Joshua A.} and Arash Nikoubashman and Glotzer, {Sharon C.} and Panagiotopoulos, {Athanassios Z.}",
note = "Funding Information: MPH, AN, and AZP acknowledge financial support from the Princeton Center for Complex Materials (PCCM) , a U.S. National Science Foundation Materials Research Science and Engineering Center (awards DMR-0819860 and DMR-1420541 ). MPH received Government support under contract FA9550-11-C-0028 awarded by the Department of Defense, Air Force Office of Scientific Research, National Defense Science and Engineering Graduate (NDSEG) Fellowship , 32 CFR 168a. JAA and SCG acknowledge support by the National Science Foundation, Division of Materials Research , award DMR-1409620 and by NVIDIA Corp. under their NVIDIA GPU Research Center Awards program. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant Number ACI-1053575 . Publisher Copyright: {\textcopyright} 2016 Elsevier B.V. All rights reserved.",
year = "2016",
month = jun,
day = "1",
doi = "10.1016/j.cpc.2016.02.003",
language = "English (US)",
volume = "203",
pages = "45--52",
journal = "Computer Physics Communications",
issn = "0010-4655",
publisher = "Elsevier",
}