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

DOI10.1016/J.CPC.2018.02.005MaRDI QIDQ2102473zbMATHOpenAlexWikidataFDO

Authors Yanyan Li

Publication date 28 November 2022

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

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

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)

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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Cites work

• scientific article; zbMATH DE number 1069612 (Why is no real title available?)
• A Fast Adaptive Multipole Algorithm for Particle Simulations
• A fast adaptive multipole algorithm in three dimensions
• A fast algorithm for Brownian dynamics simulation with hydrodynamic interactions
• A fast algorithm for particle simulations
• A fast multipole method for the Rotne-Prager-Yamakawa tensor and its applications
• A fast multipole method for the three-dimensional Stokes equations
• Brownian diffusion of particles with hydrodynamic interaction
• Communications overlapping in fast multipole particle dynamics methods
• DASHMM: dynamic adaptive system for hierarchical multipole methods
• Generalization of the Rotne-Prager-Yamakawa mobility and shear disturbance tensors
• Revision of DASHMM: dynamic adaptive system for hierarchical multipole methods

Cited in

(5)

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

Describes a project that uses

Uses Software

• RPYFMM

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