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.