A fast and spectrally accurate Ewald summation method for the evaluation of stokeslet, stresslet and rotlet potentials of three-dimensional Stokes flow is presented. This work extends the previously developed Spectral Ewald method for Stokes flow to periodic boundary conditions in any number (three, two, one, or none) of the spatial directions, in a unified framework. The periodic potential is split into a short-range and a long-range part, where the latter is treated in Fourier space using the fast Fourier transform. A crucial component of the method is the modified kernels used to treat singular integration. We derive new modified kernels, and new improved truncation error estimates for the stokeslet and stresslet. An automated procedure for selecting parameters based on a given error tolerance is designed and tested. Analytical formulas for validation in the doubly and singly periodic cases are presented. We show that the computational time of the method scales like O(N log N) for N sources and targets, and investigate how the time depends on the error tolerance and window function, i.e. the function used to smoothly spread irregular point data to a uniform grid. The method is fastest in the fully periodic case, while the run time in the free-space case is around three times as large. Furthermore, the highest efficiency is reached when applying the method to a uniform source distribution in a primary cell with low aspect ratio. The work presented in this paper enables efficient and accurate simulations of three-dimensional Stokes flow with arbitrary periodicity using e.g. boundary integral and potential methods.
Fast Ewald Summation with Prolates for Charged Systems in the NPT Ensemble
Center for Computational Mathematics, Flatiron Institute(西蒙斯基金会平顿研究所计算数学中心);School of Mathematical Sciences, Shanghai Jiao Tong University(上海交通大学数学科学学院)
Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates
Center for Computational Mathematics, Flatiron Institute(计算数学中心,Flatiron研究所);School of Mathematical Sciences, Shanghai Jiao Tong University(上海交通大学数学科学学院);Courant Institute of Mathematical Sciences, New York University(纽约大学柯朗数学科学研究所)
Bashkir State University(巴什基尔国立大学);Center for Micro and Nanoscale Dynamics of Dispersed Systems, Bashkir State University(巴什基尔国立大学分散系统微纳动力学中心);Fantalgo, LLC.(Fantalgo有限责任公司);Institute for Advanced Computer Studies(高级计算机研究所);Department of Computer Science(计算机科学系);University of Maryland, College Park(马里兰大学帕克分校)
An Adaptive Fast Algorithm for Periodic Coulomb Lattice Sums in Arbitrary Unit Cells
Center for Computational Mathematics, Flatiron Institute(计算数学中心,平顿研究所);Simons Foundation(西蒙斯基金会);Courant Institute of Mathematical Sciences, New York University(纽约大学柯朗数学科学研究所)
Universal image systems for non-periodic and periodic Stokes flows above a no-slip wall
Center for Computational Biology, Flatiron Institute(Flatiron研究所计算生物学中心);Courant Institute of Mathematical Sciences, New York University(纽约大学柯朗数学科学研究所)