Abstract
Equilibrium chemistry computations and reactive transport modelling require the intensive use of a linear solver under very specific conditions. The systems to be solved are small or very small (4 × 4 to 20 × 20, occasionally larger) and are very ill-conditioned (condition number up to 10100). These specific conditions have never been investigated in terms of the robustness, accuracy, and efficiency of the linear solver. In this work, we present the specificity of the linear system to be solved. Several direct and iterative solvers are compared using a panel of chemical systems, including or excluding the formation of mineral species. We show that direct and iterative solvers can be used for these problems and propose computational keys to improve the chemical solvers.
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Walter, A.L., et al.: Modeling of multicomponent reactive transport in groundwater. 2. Metal mobility in aquifers impacted by acidic mine tailings discharge. Water Resour. Res. 30(11), 3149–3158 (1994)
Arora, B., et al.: A reactive transport benchmark on heavy metal cycling in lake sediments Computational Geosciences (2014)
De Windt, L., Leclercq, S., Van der Lee, J.: Assessing the durability of nuclear glass with respect to silica controlling processes in a clayey underground disposal. In: 29th International Symposium on the Scientific Basis for Nuclear Waste Management XXIX. Materials Research Society Symposium Proceedings, Ghent; Belgium (2005)
Hoteit, H., Ackerer, P., Mose, R.: Nuclear waste disposal simulations: Couplex test cases. Comput. Geosci. 8(2), 99–124 (2004)
Tompson, A.F.B., et al.: On the evaluation of groundwater contamination from underground nuclear tests. Environ. Geol. 42(2-3), 235–247 (2002)
Andre, L., et al.: Numerical modeling of fluid-rock chemical interactions at the supercritical CO2-liquid interface during CO2 injection into a carbonate reservoir, the Dogger aquifer (Paris Basin, France). Energy Convers. Manag. 48(6), 1782–1797 (2007)
Kang, Q., et al.: Pore scale modeling of reactive transport involved in geologic CO2 sequestration. Transp. Porous Media 82(1), 197–213 (2010)
Navarre-Sitchler, A.K., et al.: Elucidating geochemical response of shallow heterogeneous aquifers to CO2 leakage using high-performance computing: implications for monitoring of CO2 sequestration. Adv. Water Resour. 53(0), 45–55 (2013)
Pruess, K., et al.: Code intercomparison builds confidence in numerical simulation models for geologic disposal of CO2. Energy 29(9-10), 1431–1444 (2004)
Regnault, O., et al.: Etude experimentale de la reactivite du CO2 supercritique vis-a-vis de phases minerales pures. Implications pour la sequestration geologique de CO2. Compt. Rendus Geosci. 337(15), 1331–1339 (2005)
Valocchi, A.J., Street, R.L., Roberts, P.V.: Transport of ion-exchanging solutes in groundwater: chromatographic theory and field simulation. Water Resour. Res. 17, 1517–1527 (1981)
Lichtner, P.C.: Continuum model for simultaneous chemical reactions and mass transport in hydrothermal systems. Geochim. Cosmochim. Acta 49(3), 779–800 (1985)
Appelo, C.A.J.: Hydrogeochemical transport modelling. Proceed. Inf.—Comm. Hydrol. Res. TNO 43, 81–104 (1990)
Yeh, G.T., Tripathi, V.S.: A critical evaluation of recent developments in hydrogeochemical transport models of reactive multichemical components. Water Resour. Res. 25, 93–108 (1989)
Carrayrou, J., et al.: Comparison of numerical methods for simulating strongly nonlinear and heterogeneous reactive transport problems—the MoMaS benchmark case. Computational Geosciences 14(3), 483–502 (2010)
Hammond, G.E., Valocchi, A.J., Lichtner, P.C.: Modeling multicomponent reactive transport on parallel computers using Jacobian-Free Newton Krylov with operator-split preconditioning. In: Hassanizadeh, S.M. (ed.) Developments in water science, computational methods in water resources, Proceedings of the XIVth International Conference on Computational Methods in Water Resources (CMWR XIV), pp 727–734. Elsevier (2002)
Carrayrou, J., Mosé, R., Behra, P.: New efficient algorithm for solving thermodynamic chemistry. AIChE J. 48(4), 894–904 (2002)
Amir, L., Kern, M.: A global method for coupling transport with chemistry in heterogeneous porous media. Comput. Geosci. 14(3), 465–481 (2010)
Quarteroni, A., Sacco, R., Saleri, F.: Numerical mathematics. In: Marsden, J.E., Sirovich, L., Antman. S.S. (eds.) Texts in Applied Mathematics. 2nd edn. Springer, Heidelberg (2007)
Axelsson, O., et al.: Direct solution and incomplete factorization preconditioned conjugate gradient methods. Comparison of algebraic solution methods on a set of benchmark problems in linear elasticity, in STW report. 2000, Department of Mathematics, Catholic University of Nijmegen: Nijmegen, The Netherlands. pp. 1-36
Barrett, R., Berry, M., Chan, T.F., Demmel, J., Donato, J., Dongarra, J., Eijkhout, V., Pozo, R., Romine, C., Van Der Vorst, H.: Templates for the solution of linear systems: building blocks for iterative methods, 2nd edn. SIAM, Philadelphia (1994)
Gould, N.I.M., Hu, Y., Scott, J.A.: A numerical evaluation of sparse direct solvers for the solution of large sparse, symmetric linear systems of equations. 2005, Council for the Central Laboratory of the Research Councils
Allaire, G., Kaber, S.M. In: Marsden, J.E., Sirovich, L., Antman, S.S. (eds.) : Numerical linear algebra. Texts in applied mathematics. Springer, New York (2008)
Baldwin, C., et al.: Iterative linear solvers in a 2D radiation-hydrodynamics code: methods and performance. J. Comput. Phys. 154(1), 1–40 (1999)
Chao B.T., L.H.L., Scott, E.J.: On the solution of ill-conditioned, simultaneous, linear, algebraic equations by machine computation, in University of Illinois Bulletin. 1961, University of Illinois
Hadjidimos, A.: Successive overrelaxation (SOR) and related methods. J. Comput. Appl. Math. 123(1-2), 177–199 (2000)
Kalambi, I.B.: A comparison of three iterative methods for the solution of linear equations. J. Appl. Sci. Environ. Manag. 12(4), 53–55 (2008)
Klisinski, M., Runesson, K.: Improved symmetric and non-symmetric solvers for FE calculations. Adv. Eng. Softw. 18(1), 41–51 (1993)
Schenk, O., Gartner, K.: Solving unsymmetric sparse systems of linear equations with PARDISO. Fut. Gener. Comput. Syst. 20(3), 475–487 (2004)
Xue, X.J., et al.: A direct algorithm for solving ill-conditioned linear algebraic systems. JCPDS-Int. Centre Diffract. Data Adv. X-ray Anal. 42, 629–633 (2000)
Pyzara, A., Bylina, B., Bylina, J.: The influence of a matrix condition number on iterative methods’ convergence (2011)
Hoffmann, J., Kras̈utle, S., Knabner, P.: A parallel global-implicit 2-D solver for reactive transport problems in porous media based on a reduction scheme and its application to the MoMaS benchmark problem. Comput. Geosci. 14(3), 421–433 (2010)
Soleymani, F.: A new method for solving ill-conditioned linear systems. Opuscula Math. 33(2), 337–344 (2013)
Morel, F., Morgan, J.: A numerical method for computing equilibria in aqueous chemical systems. Environ. Sci. Technol. 6(1), 58–67 (1972)
Morel, F.M.M.: Principles of aquatic chemistry. Wiley Interscience, New York (1983)
De Windt, L., et al.: Intercomparison of reactive transport models applied to UO2 oxidative dissolution and uranium migration. J. Contam. Hydrol. 61(1-4), 303–312 (2003)
Jauzein, M., et al.: A flexible computer code for modelling transport in porous media: impact. Geoderma 44(2–3), 95– 113 (1989)
Parkhurst, D.L., Appelo, C.A.J.: User’s guide to PHREEQC (version 2)—a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations. Water Resour. Invest., Editor. 1999: Denver. p. 312
Van der Lee, J.: CHESS another speciation and surface complexation computer code. E.d.M.d. Paris, Editor. 1993: Fontainebleau. p. 85
Westall, J.C.: MICROQL: a chemical equilibrium program in BASIC. Computation of adsorption equilibria in BASIC. S.F.I.o.T. EAWAG, Editor. 1979: Dübandorf. p. 42
Westall, J.C.: FITEQL ver. 2.1. 1982: Corvallis
Westall, J.C., Zachary, J.L., Morel, F.M.M.: MINEQL: a computer program for the calculation of chemical equilibrium composition of aqueous system. R.M.P. Laboratory, Editor. 1976: Cambridge. p. 91
Walter, L.J., Wolery, T.J.: A monotone-sequences algorithm and FORTRAN IV program for calculation of equilibrium distributions of chemical species. Comput. Geosci. 1, 57–63 (1975)
Wigley, T.M.L.: WATSPEC: a computer program for determining the equilibrium speciation of aqueous solutions. B.G.R.G. Tech. Bull., Editor. 1977. p. 49
Jennings, A.A., Kirkner, D.J., Theis, T.L.: Multicomponent equilibrium chemistry in groundwater quality models. Water Resour. Res. 18, 1089–1096 (1982)
Cederberg, A., Street, R.L., Leckie, J.O.: A groundwater mass transport and equilibrium chemistry model for multicomponent systems. Water Resour Res. 21, 1095–1104 (1985)
Yeh, G.T., Tripathi, V.S.: A model for simulating transport of reactive multispecies components: model development and demonstration. Water Resour. Res. 27(12), 3075–3094 (1991)
Carrayrou, J.: Looking for some reference solutions for the reactive transport benchmark of MoMaS with SPECY. Comput. Geosci. 14(3), 393–403 (2010)
Brassard, P., Bodurtha, P.: A feasible set for chemical speciation problems. Comput. Geosci. 26(3), 277–291 (2000)
Carrayrou, J., Kern, M., Knabner, P.: Reactive transport benchmark of MoMaS. Comput. Geosci. 14 (3), 385–392 (2010)
Fendorf, S.E., Li, G.: Kinetics of chromate reduction by ferrous iron. Environ. Sci. Technol. 30(5), 1614–1617 (1996)
Chilakapati, A., et al.: Groundwater flow, multicomponent transport and biogeochemistry: development and application of a coupled process model. J. Contam. Hydrol. 43(3-4), 303–325 (2000)
Knight, P., Ruiz, D., Ucar, B.: A symmetry preserving algorithm for matrix scaling. SIAM J. Matrix Anal. Appl. 35(3), 931–955 (2014)
Golub, H.V., Van Loan, C.F.: Matrix computations. 3rd ed. The Johns Hopkins University Press, Baltimore (1996)
Davis, T.A., Duff, I.S.: A combined unifrontal/multifrontal method for unsymmetric sparse matrices. ACM Trans. Math. Softw. 25(1), 1–20 (1999)
Woźnicki, Z.: On performance of SOR method for solving nonsymmetric linear systems. J. Comput. Appl. Math. 137(1), 145–176 (2001)
Saad, Y., Van Der Vorst, H.A.: Iterative solution of linear systems in the 20th century. J. Comput. Appl. Math. 123(1-2), 1–33 (2000)
Diersch, H.J.G.: FEFLOW reference manual. DHI-WASY GmbH, Berlin (2009)
Van der Lee, J., et al.: Presentation and application of the reactive transport code HYTEC. In: Hassanizadeh, S.M. (ed.) Developments in Water Science, Computational Methods in Water Resources, Proceedings of the XIVth International Conference on Computational Methods in Water Resources (CMWR XIV), pp 599–606. Elsevier (2002)
Press, W.H., S.A.T., Vettering, W.T., Flannery, B.P.: Numerical recipes in FORTRAN: the art of scientific computation, 2nd edn., pp 123–124. Cambridge University Press, New Yor (1992)
The Linear Algebra Package (LAPACK) can be obtained free of charge from the address listed here: http://www.netlib.org/lapack
Kincaid, D., Cheney, W.: Numerical analysis: mathematics of scientific computing, 3rd edn. American Mathematical Society (2002)
HSL: A collection of Fortran codes for large scale scientific computation. http://www.hsl.rl.ac.uk (2013)
Chapter 8 Systems of nonlinear equations. In: Studies in computational mathematics, Claude, B. Editor. 1997, Elsevier. pp. 287–336
Soleymani, F.: A rapid numerical algorithm to compute matrix inversion. Int. J. Math. Math. Sci. 2012 (2012)
Soleymani, F.: On a fast iterative method for approximate inverse of matrices. Commun. Korean Math. Soc. 28(2), 407–418 (2013)
Morin, K.A.: Simplified explanations and examples of computerized methods for calculating chemical equilibrium in water. Comput. Geosci. 11, 409–416 (1985)
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Machat, H., Carrayrou, J. Comparison of linear solvers for equilibrium geochemistry computations. Comput Geosci 21, 131–150 (2017). https://doi.org/10.1007/s10596-016-9600-5
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DOI: https://doi.org/10.1007/s10596-016-9600-5