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Implementation of sparse matrix algorithms in an advection-diffusion-chemistry module. (English) Zbl 1228.65184

Summary: A two-dimensional advection-diffusion-chemistry module of a large-scale environmental model is taken. The module is described mathematically by a system of partial differential equations. Sequential splitting is used in the numerical treatment. The non-linear chemistry is the most time-consuming part and it is handled by six implicit algorithms for solving ordinary differential equations. This leads to the solution of very long sequences of systems of linear algebraic equations. It is crucial to solve these systems efficiently. This is achieved by applying four different algorithms. The numerical results indicate that the algorithms based on a preconditioned sparse matrix technique and on a specially designed algorithm for the particular problem under consideration perform best.

MSC:

65M20 Method of lines for initial value and initial-boundary value problems involving PDEs
92E20 Classical flows, reactions, etc. in chemistry
92D40 Ecology
35Q92 PDEs in connection with biology, chemistry and other natural sciences
35K55 Nonlinear parabolic equations

Software:

RODAS; CGS; LAPACK; SuperLU
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Full Text: DOI

References:

[1] Zlatev, Z., Computer Treatment of Large Air Pollution Models (1995), Kluwer Academic Publishers: Kluwer Academic Publishers Dordrecht-Boston-London · Zbl 0852.65058
[2] Zlatev, Z.; Dimov, I., Computational and numerical challenges in environmental modelling, (Studies in Computational Mathematics 13 (2006), Elsevier: Elsevier Amsterdam-Boston-Heidelberg-London-New York-Oxford-Paris-San Diego-San Francisco-Singapore-Sydney-Tokyo) · Zbl 1120.65103
[3] Crowley, W. P., Numerical advection experiments, Monthly Weather Review, 96, 1-11 (1968) · Zbl 0177.56504
[4] Molenkampf, C. R., Accuracy of finite-difference methods applied to the advection equation, Journal of Applied Meteorology, 7, 160-167 (1968)
[5] Hov, Ø.; Zlatev, Z.; Berkowicz, R.; Eliassen, A.; Prahm, L. P., Comparison of numerical techniques for use in air pollution models with non-linear chemical reactions, Atmospheric Environment, 23, 967-983 (1988)
[6] Strikwerda, J. C., Finite Difference Schemes and Partial Differential Equations (2004), SIAM: SIAM Philadelphia · Zbl 1071.65118
[7] Bui, T. D., Some A-Stable and L-Stable Methods for the Numerical Integration of Stiff Ordinary Differential Equations, JACM, 26, 3, 483-493 (1979) · Zbl 0403.65033
[8] Butcher, J. C., The Numerical Analysis of Ordinary Differential Equations. Runge-Kutta Methods and General Linear Methods (1987), Wiley: Wiley Chichester-New York-Brisbane-Toronto-Singapore · Zbl 0616.65072
[9] Hairer, E.; Nørsett, S. P.; Wanner, G., Solving Ordinary Differential Equations, I: Nonstiff Problems (1987), Springer: Springer Berlin-Heidelberg-New York-London · Zbl 0638.65058
[10] Lambert, J. D., Numerical Methods for Ordinary Differential Equations (1991), Wiley: Wiley Chichester-New York-Brisbane-Toronto-Singapore · Zbl 0745.65049
[11] Hairer, E.; Wanner, G., Solving Ordinary Differential Equations, II: Stiff and Differential-Algebraic Problems (1991), Springer: Springer Berlin-Heidelberg-New York-London · Zbl 0729.65051
[12] Zlatev, Z., Modified diagonally implicit Runge-Kutta methods, SIAM Journal on Scientific and Statistical Computing, 2, 321-334 (1981) · Zbl 0475.65040
[13] Zlatev, Z., Computational Methods for General Sparse Matrices (1991), KLUWER Academic Publishers: KLUWER Academic Publishers Dordrecht-Boston-London · Zbl 0746.65041
[14] Hundsdorfer, W.; Verwer, J. G., Numerical Solution of Time-Dependent Advection-Diffusion-Reaction Equations (2003), Springer: Springer Berlin · Zbl 1030.65100
[15] Golub, G. H.; Ortega, J. M., Scientific Computing and Differential Equations (1992), Academic Press: Academic Press Boston-San Diego-New York-London-Sydney-Tokyo-Toronto · Zbl 0749.65041
[16] Anderson, E.; Bai, Z.; Bischof, C.; Demmel, J.; Dongarra, J.; Du Croz, J.; Greenbaum, A.; Hammarling, S.; McKenney, A.; Ostrouchov, S.; Sorensen, D., LAPACK: Users’ Guide (1992), SIAM: SIAM Philadelphia · Zbl 0843.65018
[17] Alexandrov, V. N.; Sameh, A.; Siddique, Y.; Zlatev, Z., Numerical integration of chemical ODE problems arising in air pollution models, Environmental Modelling and Assessment, 2, 365-377 (1997)
[18] Gallivan, K. A.; Sameh, A. H.; Zlatev, Z., Comparison of ten methods for the solution of large and sparse linear algebraic systems, (Dimov, I.; Lirkov, I.; Margenov, S.; Zlatev, Z., Numerical Methods and Applications. Numerical Methods and Applications, Lecture Notes in Computer Science, 2542 (2003), Spinger-Verlag: Spinger-Verlag Berlin), 24-35 · Zbl 1032.65030
[19] Duff, I. S.; Erisman, A. M.; Reid, J. K., Direct Methods for Sparse Matrices (1986), Oxford University Press: Oxford University Press Oxford-London · Zbl 0604.65011
[20] Demmel, J. W., Applied Numerical Linear Algebra (1997), SIAM: SIAM Philadelphia · Zbl 0879.65017
[21] Demmel, J. W.; Eisenstat, S. C.; Gilbert, J. R.; Li, X. S.; Liu, J. W.H., A supernodal approach to sparse partial pivoting, SIAM Journal of Matrix Analysis and Applications, 20, 720-755 (1999) · Zbl 0931.65022
[22] Demmel, J. W.; Gilbert, J. R.; Li, X. S., An asynchronous parallel supernodal algorithm for sparse Gaussian elimination, SIAM Journal of Matrix Analysis and Applications, 20, 915-952 (1999) · Zbl 0939.65036
[23] Zlatev, Z., On some pivotal strategies in Gaussian elimination by sparse technique, SIAM Journal on Numerical Analysis, 17, 18-30 (1980) · Zbl 0427.65016
[24] Zlatev, Z., Use of iterative refinement in the solution of sparse linear systems, SIAM Journal on Numerical Analysis, 17, 381-399 (1982) · Zbl 0485.65022
[25] Zlatev, Z.; Wasniewski, J.; Schaumburg, K., Comparison of two algorithms for solving large linear systems, SIAM Journal on Scientific and Statistic Computing, 3, 486-501 (1982) · Zbl 0491.65017
[26] P. Vinsome, ORTHOMIN, an iterative method for solving sparse sets of simultaneous linear equations, Proc. Fourth Sympos. on Reservoir Simulation, Society of Petr. Eng. of AIME, 1976.; P. Vinsome, ORTHOMIN, an iterative method for solving sparse sets of simultaneous linear equations, Proc. Fourth Sympos. on Reservoir Simulation, Society of Petr. Eng. of AIME, 1976.
[27] Sonneveld, P., CGS, a fast Lanczos-type solver for nonsymmetric linear systems, SIAM Journal on Scientific and Statistical Computing, 10, 36-52 (1989) · Zbl 0666.65029
[28] van der Vorst, H. A., BI-CGSTAB: a fast and smoothly converging variant of BI-CG for the solution of nonsymmetric linear systems, SIAM Journal on Scientific and Statistical Computing, 13, 631-644 (1992) · Zbl 0761.65023
[29] Freund, R. W., A transpose-free quasi-minimal residual algorithm for non-Hermitian linear systems, SIAM Journal on Scientific and Statistical Computing, 14, 470-482 (1993) · Zbl 0781.65022
[30] Saad, Y.; Schultz, M. H., GMRES: a generalized minimal residual algorithm for solving nonsymmetric linear systems, SIAM Journal on Scientific and Statistical Computing, 7, 856-869 (1986) · Zbl 0599.65018
[31] Eirola, T.; Nevanlinna, O., Accelerating with rank-one updates, Linear Algebra with Applications, 121, 511-520 (1989) · Zbl 0683.65018
[32] Vuik, C.; van der Vorst, H. A., A comparison of some GMRES-like methods, Linear Algebra with Applications, 160, 131-160 (1992) · Zbl 0749.65027
[33] Yang, U. M.; Gallivan, K., A family of preconditioned iterative solvers for sparse linear systems, Applied Numerical Mathematics, 30, 155-173 (1999) · Zbl 0930.65023
[34] Willoughby, R. A., Sparse matrix algorithms and their relation to problem classes and computer architecture, (Reid, J, J. K., Large Sparse Sets of Linear Equations (1970), Academic Press: Academic Press London-New York), 255-277
[35] Sandu, A.; Verwer, J. G.; Bloom, J. G.; Spee, E. J.; Carmichael, G. R., Benchmarking stiff ODE systems for atmospheric chemistry problems: II. Rosenbrock solvers, Atmospheric Environment, 31, 3459-3472 (1997)
[36] Swart, J.; Blom, J., Experience with sparse matrix solvers in parallel ODE software, Computers and Mathematics Applications, 31, 43-55 (1996) · Zbl 0859.65072
[37] WEB-site of the Danish Centre for Scientific Computing at the Technical University of Denmark: Sun High Performance Computing Systems. http://www.hpc.dtu.dk; WEB-site of the Danish Centre for Scientific Computing at the Technical University of Denmark: Sun High Performance Computing Systems. http://www.hpc.dtu.dk
[38] WEB-site for OPEN MP tools: http://www.openmp.org; WEB-site for OPEN MP tools: http://www.openmp.org
[39] Zlatev, Z., Impact of future climate changes on high ozone levels in European suburban areas, Climatic Change, 101, 447-483 (2010)
[40] Zlatev, Z.; Moseholm, L., Impact of climate changes on pollution levels in Denmark, Environmental Modelling, 22, 203-222 (2008)
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