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arXiv · 1711.02976

RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations

W. Guan·X. Cheng·J. Huang·G. Huber·W. Li·J. A. McCammon·B. Zhang
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Abstract

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.

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W. Guan, X. Cheng, J. Huang, G. Huber, W. Li, J. A. McCammon, B. Zhang. 2017-11-08. RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations. https://doi.org/10.1016/j.cpc.2018.02.005

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