RPYFMM: parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations

DOI10.1016/J.CPC.2018.02.005zbMATH Open1498.76002arXiv1711.02976OpenAlexW2768002686WikidataQ91149608 ScholiaQ91149608MaRDI QIDQ2102473FDOQ2102473

Authors: Yanyan Li 

Publication date: 28 November 2022

Published in: Computer Physics Communications (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1711.02976

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zbMATH Keywords

distributed computingBrownian dynamicsfast multipole methodRotne-Prager-Yamakawa tensordashmmhydrodynamics interactions

Mathematics Subject Classification ID

Software, source code, etc. for problems pertaining to fluid mechanics (76-04)

Cites Work

• DASHMM: dynamic adaptive system for hierarchical multipole methods
• A fast algorithm for particle simulations
• Title not available (Why is that?)
• A fast adaptive multipole algorithm in three dimensions
• A Fast Adaptive Multipole Algorithm for Particle Simulations
• Brownian diffusion of particles with hydrodynamic interaction
• A fast multipole method for the three-dimensional Stokes equations
• A fast multipole method for the Rotne-Prager-Yamakawa tensor and its applications
• Generalization of the Rotne-Prager-Yamakawa mobility and shear disturbance tensors
• A fast algorithm for Brownian dynamics simulation with hydrodynamic interactions
• Communications overlapping in fast multipole particle dynamics methods
• Revision of DASHMM: dynamic adaptive system for hierarchical multipole methods

Cited In (5)

• A scalable computational platform for particulate Stokes suspensions
• A kernel-independent treecode for general Rotne-Prager-Yamakawa tensor
• Kernel aggregated fast multipole method. Efficient summation of Laplace and Stokes kernel functions
• A hierarchical matrix approach for computing hydrodynamic interactions
• A fast multipole method for the Rotne-Prager-Yamakawa tensor and its applications

Uses Software

• RPYFMM

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