Parallel accelerated Stokesian dynamics with Brownian motion

JOURNAL OF COMPUTATIONAL PHYSICS

卷:442

Article

Ouaknin, Gaddiel Y.¹  Su, Yu¹  Zia, Roseanna N.¹ 

[1] Stanford Univ, Dept Chem Engn, Stanford, CA 94305 USA

关键词: Stokesian dynamics;    Hydrodynamics;    Stochastic calculus;    Parallel algorithms;    Brownian motion;    Stokes flow;   

DOI  :  10.1016/j.jcp.2021.110447

来源: Elsevier

【 摘 要 】

We present scalable algorithms to simulate large-scale stochastic particle systems amenable for modeling dense colloidal suspensions, glasses and gels. To handle the large number of particles and consequent many-body interactions present in such systems, we leverage an Accelerated Stokesian Dynamics (ASD) approach, for which we developed parallel algorithms in a distributed memory architecture. We present parallelization of the sparse near-field (including singular lubrication) interactions, and of the matrix-free many body far-field interactions, along with a strategy for communicating and mapping the distributed data structures between the near-and far field. Scaling to up to tens of thousands of processors for a million particles is demonstrated. In addition, we propose a novel algorithm to efficiently simulate correlated Brownian motion with hydrodynamic interactions. The original Accelerated Stokesian Dynamics approach requires the separate computation of far-field and near-field Brownian forces. Recent advancements propose computation of a far-field velocity using positive spectral Ewald decomposition. We present an alternative approach for calculating the far-field Brownian velocity by implementing the fluctuating force coupling method and embedding it using a nested scheme into ASD. This straightforward and flexible approach reduces the computational time of the Brownian far field force construction from O(NlogN)(1+vertical bar alpha vertical bar) to O(NlogN). (C) 2021 Elsevier Inc. All rights reserved.

【 授权许可】

Free