Quantized bounding volume hierarchies for neighbor search in molecular simulations on graphics processing units
MP Howard and A Statt and F Madutsa and TM Truskett and AZ Panagiotopoulos, COMPUTATIONAL MATERIALS SCIENCE, 164, 139-146 (2019).
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.
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