Software

Released

Flexibly Periodic Kernel Independent FMM

This package computes KIFMM in a unified codebase, for free-space singly, doubly, and triply periodic geometries. The method is described in this paper W Yan, M Shelley, 2018, Flexibly imposing periodicity in kernel independent FMM: A multipole-to-local operator approach, Journal of Computational Physics 355, 214-232 .

This is a fork of the high performance package PVFMM to perform KIFMM in periodic boundary conditions.  This fork computes the near field, and the far field is completed by this extra wrapper: PeriodicFMM .

SafeFFT

This is a simple thread safe wrapper around FFTW/MKL. It supports creating and executing FFT plans simultaneously on multiple openmp threads. Nested threading is also supported. The internal structure is a hash map and some openmp locks to allow insert and reuse already created plans.

Conventional Stokesian Dynamics

This is a pedagogical Stokesian Dynamics package in Fortran 90/95, implementing the algorithm described in Durlofsky, L., Brady, J. F. & Bossis, G. Dynamic Simulation of Hydrodynamically Interacting Particles. Journal of Fluid Mechanics 180, 21–49 (1987).

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To Be Released

Fiber Simulator

This is for simulating a large number of rigid slender fibers in Stokes flow, with spectral resolution of the structure-flow interaction, and highly stable fiber-fiber collision resolving methods coupled to the Stokes flow solver. Mixed OpenMP + MPI parallelization is implemented.

Sphere Simulator

This is for simulating a large number of spherical objects in general elliptic PDE problems, with boundary integral method to spectrally resolve the elliptic PDE field. Highly stable sphere-sphere collision resolving method is also implemented and coupled to the PDE solver. Mixed OpenMP + MPI parallelization is implemented.

Accelerated Laplacian Dynamics

This is for simulating a large number of active Brownian particles with catalytic surface chemical reactions. The chemical reaction field is resolved with an efficient FFT-based solver on CUDA GPUs. The method is described in W Yan, JF Brady, 2016, The behavior of active diffusiophoretic suspensions: An accelerated Laplacian dynamics study, Journal of Chemical Physics 145 (13), 134902 .