@article{9fac3a97d24b48d7916806f35480eaf8,
title = "Quantized bounding volume hierarchies for neighbor search in molecular simulations on graphics processing units",
abstract = "We present an algorithm for neighbor search in molecular simulations on graphics processing units (GPUs) based on bounding volume hierarchies (BVHs). The BVH is compressed into a low-precision, quantized representation to increase the BVH traversal speed compared to a previous implementation. We find that neighbor search using the quantized BVH is roughly two to four times faster than current state-of-the-art methods using uniform grids (cell lists) for a suite of benchmarks for common molecular simulation models. Based on the benchmark results, we recommend using the BVH instead of a single cell list for neighbor list generation in molecular simulations on GPUs.",
keywords = "Bounding volume hierarchy, GPU, Molecular simulation, Neighbor search",
author = "Howard, {Michael P.} and Antonia Statt and Felix Madutsa and Truskett, {Thomas M.} and Panagiotopoulos, {Athanassios Z.}",
note = "Funding Information: We gratefully acknowledge the NVIDIA Corporation for providing access to the PSG Cluster to perform the benchmarks on Tesla K80, P100, and V100. M.P.H. and T.M.T. acknowledge support from the Welch Foundation (Grant No. F-1696). Financial support for this work (A.S. A.Z.P.) was partially provided by the Princeton Center for Complex Materials, a U.S. National Science Foundation Materials Research Science and Engineering Center (Award No. DMR-1420541). Funding Information: We gratefully acknowledge the NVIDIA Corporation for providing access to the PSG Cluster to perform the benchmarks on Tesla K80, P100, and V100. M.P.H. and T.M.T. acknowledge support from the Welch Foundation (Grant No. F-1696 ). Financial support for this work (A.S., A.Z.P.) was partially provided by the Princeton Center for Complex Materials , a U.S. National Science Foundation Materials Research Science and Engineering Center (Award No. DMR-1420541). Publisher Copyright: {\textcopyright} 2019 Elsevier B.V.",
year = "2019",
month = jun,
day = "15",
doi = "10.1016/j.commatsci.2019.04.004",
language = "English (US)",
volume = "164",
pages = "139--146",
journal = "Computational Materials Science",
issn = "0927-0256",
publisher = "Elsevier",
}