RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) [1] where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library [2, 3]. Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12, 288 cores, while achieving approximately 54% strong-scaling efficiency.
@article{arxiv.1711.02976,
title = {RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations},
author = {W. Guan and X. Cheng and J. Huang and G. Huber and W. Li and J. A. McCammon and B. Zhang},
journal= {arXiv preprint arXiv:1711.02976},
year = {2018}
}