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A Fast Direct Solver for a Class of 3-D Elliptic Partial Differential Equation with Variable Coefficient

Published online by Cambridge University Press:  20 August 2015

Beibei Huang*
Affiliation:
Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and System Sciences, Academy of Science, Beijing 100190, P.R. China Departament d’Enginyeria Química, Universitat Rovira i Virgili, Av. dels Päısos Catalans, 26 Tarragona 43007, Spain
Bin Tu*
Affiliation:
Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and System Sciences, Academy of Science, Beijing 100190, P.R. China
Benzhuo Lu*
Affiliation:
Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and System Sciences, Academy of Science, Beijing 100190, P.R. China
*
Corresponding author.Email:hbb21st@lsec.cc.ac.cn
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Abstract

We propose a direct solver for the three-dimensional Poisson equation with a variable coefficient, and an algorithm to directly solve the associated sparse linear systems that exploits the sparsity pattern of the coefficient matrix. Introducing some appropriate finite difference operators, we derive a second-order scheme for the solver, and then two suitable high-order compact schemes are also discussed. For a cube containing N nodes, the solver requires arithmetic operations and memory to store the necessary information. Its efficiency is illustrated with examples, and the numerical results are analysed.

Type
Research Article
Copyright
Copyright © Global Science Press Limited 2012

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References

[1]Martinsson, P.‐G., A fast direct solver for a class of elliptic partial differential equations, J. Sci. Comput. 38 (2009), pp. 316–330.Google Scholar
[2]Engquist, B. and Ying, L., Sweeping preconditioner for the Helmholtz equation: Moving perfectly matched layers, Multiscale Model. Sim. 9(2) (2011), 686–710.Google Scholar
[3]Chandrasekaran, S., Gu, M., and Lyons, W., A fast adaptive solver for hierarchically semisep-arable representations, Calcolo 42(3-4) (2005), pp. 171–185.Google Scholar
[4]Chandrasekaran, S., Gu, M., and Lyons, W., Superfast multifrontal method for structured linear systems of equations, Private Communication (2007).Google Scholar
[5]Grasedyck, L., Kriemann, R., and Le Borne, S., Domain-decomposition based H-matrix pre-conditioners, Proceedings of DD16. LNSCE, Vol. 55, Springer, Berlin (2006), pp. 661–668, pp. 471–476.Google Scholar
[6]Le Tallec, P., Domain decomposition methods in computational mechanical, Computational Mechanics Advances (1986), pp. 121–220.Google Scholar
[7]Pack, G.R., Garrett, G.A., Wong, L., and Lamm, G., The Effect of a variable dielectric coefficient and finite Ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems, Biophysical J. 65 (1993), pp. 1363–1370.Google Scholar
[8]Warwicker, J. and Watson, H.C., Calculation of the electric potential in the active site cleft due to α-helical dipoles, J. Mol. Biol. 157 (1982), pp. 671–679.CrossRefGoogle Scholar
[9]Lu, B.Z. and McCammon, J.A., Molecular surface-free continuum model for electrodiffusion processes, Chem. Phys. Lett. 451(4-6) 2008, pp. 282–286.Google Scholar
[10]Warming, R.F. and Hyett, B.J., The modified equation approach to the stability and accuracy analysis of finite-difference methods, J. Comput. Phys. 14(2) (1974), pp. 159–179.Google Scholar
[11]Hackbusch, W., Elliptic Differential Equations Theory and Numerical Treatment, Springer-Verlag Berlin Heidelberg, Berlin, 1992, pp. 40–72. (Electronic).Google Scholar
[12]Iserles, A., A First Course in the Numerical Analysis of Differential Equations, Tinghua University Press, 2005, pp. 101–127. (Chinese version).Google Scholar
[13]Yu, D.H. and Tang, H.Z., Numerical Solution of Differential Equations, Science Press, 2007, pp. 300–307. (Chinese version).Google Scholar
[14]Liberty, E., Woolfe, F., Martinsson, P., Rokhlin, V., and Tygert, M., Randomized algorithms for the low-rank approximation of matrices, Proc. Natl. Acad. Sci. USA 104 (2007), pp. 20167– 0172.Google Scholar
[15]Woolfe, F., Liberty, E., Rokhlin, V., and Tygert, M., A fast randomized algorithm for the approximation of matrices, Appl. Comput. Harmon. Anal. 25 (2008), pp. 335–366.Google Scholar
[16]Lin, L., Lu, J., and Ying, L., Fast construction of hierarchical matrix representation from matrix-vector multiplication, J. Comput. Phys. 230(10) (2010), pp. 4071–4087.Google Scholar
[17]Spotz, W.F. and Carey, G.F., A high-order compact formulation for the 3-D Poisson equation, Numer. Methods Part. Diff. Eqs. 12 (1996), pp. 235–243.Google Scholar
[18]Spotz, W. F. and Carey, G. F., High-order compact scheme for the steady stream-function vorticity equations, Int. J. Numer. Methods Eng. 38 (1995), pp. 3497–3512.CrossRefGoogle Scholar
[19]Gupta, M.M. and Kouatchou, J., Symbolic derivation of finite difference approximations for three dimensional Poisson equation, Int. J. Numer. Methods Part. Diff. Eqs. 14(5) (1998), pp. 593–606.Google Scholar
[20]Ananthakrishnaiah, U., Manohar, R., and Stephenson, J. W., Fourth-order finite difference for three-dimensional general elliptic problems with variable coefficients, Numer. Methods Part. Diff. Eqs. 3 (1987), pp. 229–240.Google Scholar
[21]Zhang, J., An explicit fourth-order compact finite difference scheme for three dimensional convection-diffusion equation, Commun. Numer. Methods Eng. 14 (1997), pp. 263–280.Google Scholar