×

ParCrunchFlow: an efficient, parallel reactive transport simulation tool for physically and chemically heterogeneous saturated subsurface environments. (English) Zbl 1392.86005

Summary: Understanding the interactions between physical, geochemical, and biological processes in the shallow subsurface is integral to the development of effective contamination remediation techniques, or the accurate quantification of nutrient fluxes and biogeochemical cycling. Hydrology is a primary control on the behavior of shallow subsurface environments and must be realistically represented if we hope to accurately model these systems. ParCrunchFlow is a new parallel reactive transport model that was created by coupling a multicomponent geochemical code (CrunchFlow) with a parallel hydrologic model (ParFlow). These models are coupled in an explicit operator-splitting manner. ParCrunchFlow can simulate three-dimensional multicomponent reactive transport in highly resolved, field-scale systems by taking advantage of ParFlow’s efficient parallelism and robust hydrologic abilities, and CrunchFlow’s extensive geochemical abilities. Here, the development of ParCrunchFlow is described and two simple verification simulations are presented. The parallel performance is evaluated and shows that ParCrunchFlow has the ability to simulate very large problems. A series of simulations involving the biologically mediated reduction of nitrate in a floodplain aquifer were conducted. These floodplain simulations show that this code enables us to represent more realistically the variability in chemical concentrations observed in many field-scale systems. The numerical formulation implemented in ParCrunchFlow minimizes numerical dispersion and allows the use of higher-order explicit advection schemes. The effects that numerical dispersion can have on finely resolved, field-scale reactive transport simulations have been evaluated. The smooth gradients produced by a first-order advection scheme create an artificial mixing effect, which decreases the spatial variance in solute concentrations and leads to an increase in overall reaction rates. The work presented here is the first step in a larger effort to couple these models in a transient, variably saturated surface-subsurface framework, with additional geochemical abilities.

MSC:

86-08 Computational methods for problems pertaining to geophysics
86A05 Hydrology, hydrography, oceanography
74F25 Chemical and reactive effects in solid mechanics
PDF BibTeX XML Cite
Full Text: DOI

References:

[1] Li, L; Peters, CA; Celia, MA, Upscaling geochemical reaction rates using pore-scale network modeling, Adv. Water Resour., 29, 1351-1370, (2006)
[2] White, AF; Brantley, SL, The effect of time on the weathering of silicate minerals: why do weathering rates differ in the laboratory and field, Chem. Geol., 202, 479-506, (2003)
[3] Maher, K; Steefel, CI; DePaolo, DJ; Viani, BE, The mineral dissolution rate conundrum: insights from reactive transport modeling of U isotopes and pore fluid chemistry in marine sediments, Geochim. Cosmochim. Acta., 70, 337-363, (2006)
[4] Navarre-Sitchler, A; Brantley, S, Basalt weathering across scales, Earth Planet. Sci. Lett., 261, 321-334, (2007)
[5] Lichtner, PC, Continuum model for simultaneous chemical reactions and mass transport in hydrothermal systems, Geochim. Cosmochim. Acta., 49, 779-800, (1985)
[6] Steefel, CI; Lasaga, AC, A coupled model for transport of multiple chemical species and kinetic precipitation/dissolution reactions with application to reactive flow in single phase hydrothermal systems, Am. J. Sci., 294, 529-592, (1994)
[7] Steefel, CI; DePaolo, DJ; Lichtner, PC, Reactive transport modeling: an essential tool and a new research approach for the Earth sciences, Earth. Planet. Sci. Lett., 240, 539-558, (2005)
[8] Dagan, G, Statistical theory of groundwater flow and transport: pore to laboratory, laboratory to formation, and formation to regional scale, Water Resour. Res., 22, 120s-134s, (1986)
[9] Dagan, G, The significance of heterogeneity of evolving scales to transport in porous formations, Water Resour. Res., 30, 3327-3336, (1994)
[10] Cushman, J.H.: Dynamics of Fluids in Hierarchical Porous Media. Academic Press Inc. Ltd., London (1990)
[11] Gutiérrez, JL; Jones, CG, Physical ecosystem engineers as agents of biogeochemical heterogeneity, Bioscience, 56, 227-236, (2006)
[12] Zhou, J; Xia, B; Huang, H; Palumbo, AV; Tiedje, JM, Microbial diversity and heterogeneity in sandy subsurface soils, Appl. Environ. Microbiol., 70, 1723-1734, (2004)
[13] Englert, A; Hubbard, S; Williams, K; Li, L; Steefel, C, Feedbacks between hydrological heterogeneity and bioremediation induced biogeochemical transformations, Environ. Sci. Technol., 43, 5197-5204, (2009)
[14] Neuman, SP; Zhang, YK, A quasi-linear theory of non-fickian and Fickian subsurface dispersion: 1. theoretical analysis with application to isotropic media, Water Resour. Res., 26, 887-902, (1990)
[15] Li, L; Steefel, CI; Yang, L, Scale dependence of mineral dissolution rates within single pores and fractures, Geochim. Cosmochim. Acta., 72, 360-377, (2008)
[16] Navarre-Sitchler, A., Steefel, C.I., Yang, L., Tomutsa, L., Brantley, S.L.: Evolution of porosity and diffusivity associated with chemical weathering of a basalt clast. J. Geophys. Res. (Earth Surf.) 114(F2) (2009). doi:10.1029/2008JF001060
[17] Yabusaki, SB; Steefel, CI; Wood, B, Multidimensional, multicomponent, subsurface reactive transport in nonuniform velocity fields: code verification using an advective reactive streamtube approach, J. Contam. Hydrol., 30, 299-331, (1998)
[18] Steefel, C.I.: New directions in hydrogeochemical transport modeling: incorporating multiple kinetic and equilibrium reaction pathways. In: Lawrence Livermore National Lab., CA (US) (2000)
[19] Velbel, MA, Constancy of silicate-mineral weathering-rate ratios between natural and experimental weathering: implications for hydrologic control of differences in absolute rates, Chem. Geol., 105, 89-99, (1993)
[20] Clow, D; Drever, J, Weathering rates as a function of flow through an alpine soil, Chem. Geol., 132, 131-141, (1996)
[21] Maher, K, The dependence of chemical weathering rates on fluid residence time, Earth Planet. Sci. Lett., 294, 101-110, (2010)
[22] Navarre-Sitchler, A; Steefel, CI; Sak, PB; Brantley, SL, A reactive-transport model for weathering rind formation on basalt, Geochim. Cosmochim. Acta., 75, 7644-7667, (2011)
[23] Siirila, E.R., Maxwell, R.M.: Evaluating effective reaction rates of kinetically driven solutes in large-scale, statistically anisotropic media: human health risk implications. Water Resour. Res. 48(4) (2012). doi:10.1029/2011WR011516
[24] Frei, S; Fleckenstein, J; Kollet, S; Maxwell, R, Patterns and dynamics of river-aquifer exchange with variably-saturated flow using a fully-coupled model, J. Hydrology, 375, 383-393, (2009)
[25] Maxwell, RM; Kollet, SJ, Quantifying the effects of three-dimensional subsurface heterogeneity on Hortonian runoff processes using a coupled numerical, stochastic approach, Adv. Water Resour., 31, 807-817, (2008)
[26] Ashby, SF; Falgout, RD, A parallel multigrid preconditioned conjugate gradient algorithm for groundwater flow simulations, Nucl. Sci. Eng., 124, 145-159, (1996)
[27] Jones, JE; Woodward, CS, Newton-Krylov-multigrid solvers for large-scale, highly heterogeneous, variably saturated flow problems, Adv. Water Resour., 24, 763-774, (2001)
[28] Kollet, SJ; Maxwell, RM, Integrated surface-groundwater flow modeling: a free-surface overland flow boundary condition in a parallel groundwater flow model, Adv. Water Resour., 29, 945-958, (2006)
[29] Bell, JB; Dawson, CN; Shubin, GR, An unsplit, higher order Godunov method for scalar conservation laws in multiple dimensions, J. Comput. Phys., 74, 1-24, (1988) · Zbl 0684.65088
[30] Steefel, C., Yabusaki, S.: OS3D/GIMRT, software for multicomponent-multidimensional reactive transport. User manual and programmer’s guide, PNL-11166. Pacific Northwest National Laboratory, Richland, WA 99352 (1996)
[31] Steefel, CI; Appelo, CAJ; Arora, B; Jacques, D; Kalbacher, T; Kolditz, O; Lagneau, V; Lichtner, PC; Mayer, KU; Meeussen, JCL; Molins, S; Moulton, D; Parkhurst, DL; Shao, H; Šimůnek, J; Spycher, N; Yabusaki, SB; Yeh, GT, Reactive transport codes for subsurface environmental simulation, Computat. Geosci., (2014) · Zbl 1323.86002
[32] Maher, K; Steefel, CI; White, AF; Stonestrom, DA, The role of reaction affinity and secondary minerals in regulating chemical weathering rates at the santa cruz soil chronosequence, California, Geochim. Cosmochim. Acta., 73, 2804-2831, (2009)
[33] Atchley, AL; Maxwell, RM; Navarre-Sitchler, AK, Using streamlines to simulate stochastic reactive transport in heterogeneous aquifers: kinetic metal release and transport in CO2 impacted drinking water aquifers, Adv. Water Resour., 52, 93-106, (2013)
[34] Chang, H-s; Um, W; Rod, K; Serne, RJ; Thompson, A; Perdrial, N; Steefel, CI; Chorover, J, Strontium and cesium release mechanisms during unsaturated flow through waste-weathered hanford sediments, Environ. Sci. Technol., 45, 8313-8320, (2011)
[35] Wanner, C; Eggenberger, U; Mäder, U, A chromate-contaminated site in southern Switzerland-part 2: reactive transport modeling to optimize remediation options, Appl. Geochem., 27, 655-662, (2012)
[36] Yeh, G; Tripathi, V, A critical evaluation of recent developments in hydrogeochemical transport models of reactive multichemical components, Water Resour. Res., 25, 93-108, (1989)
[37] Walter, A; Frind, E; Blowes, D; Ptacek, C; Molson, J, Modeling of multicomponent reactive transport in groundwater: 1. model development and evaluation, Water Resour. Res., 30, 3137-3148, (1994)
[38] Steefel, CI; MacQuarrie, KT, Approaches to modeling of reactive transport in porous media, Rev. Mineral. Geochem., 34, 85-129, (1996)
[39] Maxwell, R; Putti, M; Meyerhoff, S; Delfs, J-O; Ferguson, I; Ivanov, V; Kim, J; Kolditz, O; Kollet, S; Kumar, M; Lopez, S; Niu, J; Paniconi, C; Park, Y-J; Phanikumar, M; Shen, C; Sudicky, E; Sulis, M, Surface-subsurface model intercomparison: a first set of benchmark results to diagnose integrated hydrology and feedbacks, Water Resour. Res., 50, 1531-1549, (2014)
[40] Reed, MH, Calculation of multicomponent chemical equilibria and reaction processes in systems involving minerals, gases and an aqueous phase, Geochim. Cosmochim. Acta, 46, 513-528, (1982)
[41] Kirkner, DJ; Reeves, H, Multicomponent mass transport with homogeneous and heterogeneous chemical reactions: effect of the chemistry on the choice of numerical algorithm: 1, Theory. Water Resour. Res., 24, 1719-1729, (1988)
[42] Lasaga, A.C.: Rate laws of chemical reactions. Rev. Mineralology Geochemistry 8 (1981)
[43] Lasaga, AC, Chemical kinetics of water-rock interactions, J. Geophys. Res. (Solid Earth), 89, 4009-4025, (1984)
[44] Aagaard, P; Helgeson, HC, Thermodynamic and kinetic constraints on reaction rates among minerals and aqueous solutions; I, theoretical considerations, Am. J. Sci., 282, 237-285, (1982)
[45] Strang, G, On the construction and comparison of difference schemes, SIAM J. Numer. Anal., 5, 506-517, (1968) · Zbl 0184.38503
[46] Valocchi, AJ; Malmstead, M, Accuracy of operator splitting for advection-dispersion-reaction problems, Water Resour. Res., 28, 1471-1476, (1992)
[47] Kanney, JF; Miller, CT; Kelley, C, Convergence of iterative split-operator approaches for approximating nonlinear reactive transport problems, Adv. Water Resour., 26, 247-261, (2003)
[48] Navarre-Sitchler, AK; Maxwell, RM; Siirila, ER; Hammond, GE; Lichtner, PC, Elucidating geochemical response of shallow heterogeneous aquifers to CO2 leakage using high-performance computing: implications for monitoring of CO2 sequestration, Adv. Water Resour., 53, 45-55, (2013)
[49] Hammond, G., Lichtner, P., Mills, R.: Evaluating the performance of parallel subsurface simulators: an illustrative example with PFLOTRAN. Water Resour. Res. (2014). doi:10.1002/2012WR013483
[50] Hammond, G.E., Lichtner, P.C.: Field-scale model for the natural attenuation of uranium at the Hanford 300 Area using high-performance computing. Water Resour. Res. 46(9) (2010). doi:10.1029/2009WR008819
[51] Hammond, G., Lichtner, P., Lu, C.: Subsurface multiphase flow and multicomponent reactive transport modeling using high-performance computing. In: Journal of Physics: Conference Series 2007, vol. 1, p 012025. IOP Publishing, doi:10.1088/1742-6596/78/1/012025
[52] Kollet, S.J., Maxwell, R.M., Woodward, C.S., Smith, S., Vanderborght, J., Vereecken, H., Simmer, C.: Proof of concept of regional scale hydrologic simulations at hydrologic resolution utilizing massively parallel computer resources. Water Resour. Res. 46(4) (2010). doi:10.1029/2009WR008730
[53] Maxwell, RM, A terrain-following grid transform and preconditioner for parallel, large-scale, integrated hydrologic modeling, Adv. Water Resour., 53, 109-117, (2013)
[54] Knoll, DA; Keyes, DE, Jacobian-free Newton-Krylov methods: a survey of approaches and applications, J. Comput. Phys., 193, 357-397, (2004) · Zbl 1036.65045
[55] Li, L; Steefel, CI; Kowalsky, MB; Englert, A; Hubbard, SS, Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during biostimulation experiments at rifle, colorado, J. Contam. Hydrol., 112, 45-63, (2010)
[56] Hyun, SP; Fox, PM; Davis, JA; Campbell, KM; Hayes, KF; Long, PE, Surface complexation modeling of U (VI) adsorption by aquifer sediments from a former mill tailings site at rifle, colorado, Environ. Sci. Technol., 43, 9368-9373, (2009)
[57] N’Guessan, AL; Vrionis, HA; Resch, CT; Long, PE; Lovley, DR, Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction, Environ. Sci. Technol., 42, 2999-3004, (2008)
[58] Mouser, PJ; N’Guessan, AL; Elifantz, H; Holmes, DE; Williams, KH; Wilkins, MJ; Long, PE; Lovley, DR, Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater, Environ. Sci. Technol., 43, 4386-4392, (2009)
[59] Carle, S.F.: T-PROGS: Transition probability geostatistical software. University of California, Davis (1999)
[60] Smith, MS, Dissimilatory reduction of NO2- to NH4 + and N2O by a soil citrobacter sp, Appl. Environ. Microbiol., 43, 854-860, (1982)
[61] Caskey, WH; Tiedje, JM, Evidence for clostridia as agents of dissimilatory reduction of nitrate to ammonium in soils, Soil Sci. Soc. Am. J., 43, 931-936, (1979)
[62] Kaspar, HF; Tiedje, JM; Firestone, RB, Denitrification and dissimilatory nitrate reduction to ammonium in digested sludge, Can. J. Microbiol., 27, 878-885, (1981)
[63] Cirpka, OA; Frind, EO; Helmig, R, Numerical simulation of biodegradation controlled by transverse mixing, J. Contam. Hydrol., 40, 159-182, (1999)
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. It attempts to reflect the references listed in the original paper as accurately as possible without claiming the completeness or perfect precision of the matching.