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Fast Ewald summation for electrostatic potentials with arbitrary periodicity
KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0003-0067-2731
KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-6953-8058
KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-4290-1670
2021 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 16, article id 164109Article in journal (Refereed) Published
Abstract [en]

A unified treatment for the fast and spectrally accurate evaluation of electrostatic potentials with periodic boundary conditions in any or none of the three spatial dimensions is presented. Ewald decomposition is used to split the problem into real-space and Fourier-space parts, and the Fast Fourier Transform (FFT)-based Spectral Ewald (SE) method is used to accelerate computation of the latter, yielding the total runtime O(N log N) for N sources. A key component is a new FFT-based solution technique for the free-space Poisson problem. The computational cost is further reduced by a new adaptive FFT for the doubly and singly periodic cases, allowing for different local upsampling factors. The SE method is most efficient in the triply periodic case where the cost of computing FFTs is the lowest, whereas the rest of the algorithm is essentially independent of periodicity. We show that removing periodic boundary conditions from one or two directions out of three will only moderately increase the total runtime, and in the free-space case, the runtime is around four times that of the triply periodic case. The Gaussian window function previously used in the SE method is compared with a new piecewise polynomial approximation of the Kaiser–Bessel window, which further reduces the runtime. We present error estimates and a parameter selection scheme for all parameters of the method, including a new estimate for the shape parameter of the Kaiser–Bessel window. Finally, we consider methods for force computation and compare the runtime of the SE method with that of the fast multipole method.

Place, publisher, year, edition, pages
AIP Publishing , 2021. Vol. 154, no 16, article id 164109
National Category
Computational Mathematics
Research subject
Applied and Computational Mathematics, Numerical Analysis
Identifiers
URN: urn:nbn:se:kth:diva-296966DOI: 10.1063/5.0044895ISI: 000692814300001PubMedID: 33940832Scopus ID: 2-s2.0-85105146195OAI: oai:DiVA.org:kth-296966DiVA, id: diva2:1564853
Note

QC 20210614

Available from: 2021-06-12 Created: 2021-06-12 Last updated: 2023-05-16Bibliographically approved
In thesis
1. Accurate quadrature and fast summation in boundary integral methods for Stokes flow
Open this publication in new window or tab >>Accurate quadrature and fast summation in boundary integral methods for Stokes flow
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis concerns accurate and efficient numerical methods for the simulation of fluid flow on the microscale, known as Stokes flow or creeping flow. Such flows are important, for example, in understanding the swimming of microorganisms, spreading of dust particles, as well as in developing new nano-materials, and microfluidic devices that can be used for on-the-fly analysis of blood samples, among other things.

Flow on the microscale is dominated by viscous forces, meaning that a fluid such as water or air will behave as a very viscous fluid, like e.g. honey. The equations governing the flow, known as the Stokes equations, are linear PDEs, which permits the use of boundary integral methods (BIMs). In these methods, the PDE is reformulated as a boundary integral equation, thus reducing the dimensionality of the computational problem from three dimensions to two dimensions. The boundary integral formulation is well-conditioned, so that high accuracy can be achieved.

We consider two main challenges related to BIMs. The first challenge is that the integrals in the formulation contain integrands that vary rapidly for evaluation points close to the boundary, and cannot be accurately resolved using a standard method for numerical integration. Therefore, special quadrature methods are needed. We consider two such methods: quadrature by expansion (QBX) and the “line extrapolation/interpolation method” (also known as the Hedgehog method). In particular, we consider these methods applied to simulations involving rigid rodlike particles and surrounding walls.

The second challenge is that discretizing the boundary integral formulation leads to a dense linear system, which requires O(N2) operations to solve iteratively, where N is the number of unknowns. This becomes too expensive for large systems. A fast summation method, such as the Spectral Ewald (SE) method considered in this thesis, reduces the number of operations required, for example to O(N log N). The SE method can also be used for problems with periodic boundary conditions in any number of the spatial directions (arbitrary periodicity).

We also consider an application of these methods to a flow problem involving an inertial spheroid in a parabolic flow profile, and analyze the lateral drift of this spheroidal particle.

The numerical methods studied in this thesis enable fast and accurate computer simulations of e.g. suspensions of rigid particles in three-dimensional Stokes flow, including surrounding walls and arbitrary periodicity.

Abstract [sv]

Denna avhandling behandlar noggranna och effektiva numeriska metoder för att simulera strömning på mikroskalan, känt som Stokesflöde eller krypande flöde. Sådana flöden är viktiga till exempel för att förstå hur mikroorganismer simmar och stoftpartiklar sprider sig, liksom för att utveckla nya nanomaterial samt mikrofluidiska enheter för omedelbar blodanalys, bland annat.

Strömning på mikroskalan domineras av viskösa krafter, vilket innebär att en fluid såsom vatten eller luft kommer att bete sig som en mycket viskös fluid, som till exempel honung. De ekvationer som styr strömningen kallas Stokes ekvationer och är linjära PDE:er, vilket innebär att randintegralmetoder kan användas. I dessa metoder omformuleras PDE:n som en randintegralekvation, så att beräkningsproblemets dimensionalitet minskar från tre till två dimensioner. Randintegralformuleringen är välkonditionerad, så att hög noggrannhet kan uppnås.

Vi behandlar två huvudsakliga utmaningar kopplade till randintegralmetoder. Den första utmaningen är att integralerna i formuleringen innehåller integrander som varierar snabbt för evalueringspunkter nära randen, och inte kan lösas upp noggrannt med en standardmetod för numerisk integration. Därmed behövs speciella kvadraturmetoder. Vi betraktar två sådana metoder: expansionskvadratur (eng. quadrature by expansion) och ”linje-extrapolation/interpolation” (även känt som igelkottsmetoden, eng. Hedgehog method). Metoderna tillämpas specifikt på strömningsproblem innehållande stela stavlika partiklar och omgivande väggar.

Den andra utmaningen är att diskretiseringen av randintegralformuleringen leder till ett tätt linjärt system, som kräver O(N2) operationer att lösa iterativt, där N är antalet okända. Detta blir alltför kostsamt för stora system. En snabb summeringsmetod, såsom den spektrala Ewald-metoden som behandlas i denna avhandling, minskar antalet operationer som krävs till exempelvis O(N log N). Den spektrala Ewald-metoden kan även användas för problem med periodiska randvillkor i godtyckligt antal rumsriktningar.

Vi tillämpar även dessa metoder på ett strömningsproblem med en trög sfäroid i en parabolisk strömningsprofil, och analyserar driften i sidled hos denna sfäroidiska partikel.

De numeriska metoder som studeras i denna avhandling möjliggör snabba och noggranna datorsimuleringar av exempelvis suspensioner av stela partiklar i tredimensionellt Stokesflöde, inklusive omgivande väggar och godtycklig periodicitet.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2023. p. 70
Series
TRITA-SCI-FOU ; 2023:30
National Category
Computational Mathematics
Research subject
Applied and Computational Mathematics, Numerical Analysis
Identifiers
urn:nbn:se:kth:diva-326997 (URN)978-91-8040-608-6 (ISBN)
Public defence
2023-06-14, https://kth-se.zoom.us/j/63845616516, Sal F3, Lindstedtsvägen 26, Stockholm, 14:00 (English)
Opponent
Supervisors
Funder
Göran Gustafsson Foundation for Research in Natural Sciences and MedicineSwedish Research Council
Note

QC 2023-05-17

Available from: 2023-05-17 Created: 2023-05-16 Last updated: 2023-06-02Bibliographically approved

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Saffar Shamshirgar, DavoodBagge, JoarTornberg, Anna-Karin

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