Quantized bounding volume hierarchies for neighbor search in molecular simulations on graphics processing units
arXiv:1901.08088 · doi:10.1016/j.commatsci.2019.04.004
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.
arXiv comment28 pages, 8 figures
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