HPx is a multicomponent reactive transport model which uses HYDRUS as the flow and transport solver and PHREEQC-3 as the biogeochemical solver. Some recent adaptations have significantly increased the flexibility of the software for different environmental and engineering applications. This paper gives an overview of the most significant changes of HPx, such as coupling transport properties to geochemical state variables, gas diffusion, and transport in two and three dimensions. OpenMP allows for parallel computing using shared memory. Enhancements for scripting may eventually simplify input definitions and create possibilities for defining templates for generic (sub)problems. We included a discussion of root solute uptake and colloid-affected solute transport to show that most or all of the comprehensive features of HYDRUS can be extended with geochemical information. Finally, an example is used to demonstrate how HPx, and similar reactive transport models, can be helpful in implementing different factors relevant for soil organic matter dynamics in soils. HPx offers a unique framework to couple spatial-temporal variations in water contents, temperatures, and water fluxes, with dissolved organic matter and CO2 transport, as well as bioturbation processes.
If the inline PDF is not rendering correctly, you can download the PDF file here.
Aagaard P. Helgeson H.C. 1982. Thermodynamic and kinetic constraints on reaction rates among minerals and aqueous solutions 1. Theoretical considerations. Am. J. Sci. 282 237–285.
Amos R.T. Mayer K.U. 2006. Investigating the role of gas bubble formation and entrapment in contaminated aquifers: Reactive transport modelling. J. Cont. Hydrol. 87 123–154.
Appelo C.A.J. Parkhurst D.L. Post V.E.A. 2014. Equations for calculating hydrogeochemical reactions of minerals and gases such as CO2 at high pressures and temperatures. Geochim. Cosmochim. Acta 125 49–67.
Appelo C.A.J. Wersin P. 2007. Multicomponent diffusion modeling in clay systems with application to the diffusion of tritium iodide and sodium in Opalinus Clay. Env. Sci. Tech. 41 5002–5007.
Batlle-Aguilar J. Brovelli A. Porporato A. Barry D.A. 2011. Modelling soil carbon and nitrogen cycles during land use change: A review. Agron. Sust. Devel. 31 251–274.
Bennacer L. Ahfir N.D. Alem A. Wang H.Q. 2017. Coupled effects of ionic strength particle size and flow velocity on transport and deposition of suspended particles in saturated porous media. Transp. Por. Med. 118 251–269.
Bessinger B.A. Marks C.D. 2010. Treatment of mercurycontaminated soils with activated carbon: A laboratory field and modeling study. Remed. 21 115–135.
Bloom S.A. Mansell R.S. 2001. An algorithm for generating cation exchange isotherms from binary selectivity coefficients. Soil Sci. Soc. Am. J. 65 1426–1429.
Bond W.J. 1995. On the Rothmund-Kornfeld description of cation exchange. Soil Sc. Soc. Am. J. 59 436–443.
Borkovec M. Westall J. 1983. Solution of the Poisson-Boltzmann equation for surface excesses of ions in the diffuse layer at the oxide electrolyte interface. J. Elect. Chem. 150 325–337.
Bozorg A. Gates I.D. Sen A. 2015a. Impact of biofilm on bacterial transport and deposition in porous media. J. Cont. Hydrol.183 109–120.
Bozorg A. Gates I.D. Sen A. 2015b. Using bacterial bioluminescence to evaluate the impact of biofilm on porous media hydraulic properties. J. Microb. Meth. 109 84–92.
Braakhekke M.C. Beer C. Hoosbeek M.R. Reichstein M. Kruijt B. Schrumpf M. Kabat P. 2011. SOMPROF: A vertically explicit soil organic matter model. Ecol. Mod. 222 1712–1730.
Brantley S. Goldhaber M.B. Ragnarsdottir K.V. 2007. Crossing disciplines and scales to understand the critical zone. Elements 3 307–314.
Brooks R.H. Corey A. 1964. Hydraulic properties of porous media. Hydrol. Paper No. 3 Colorado State Univ. Fort Collins CO.
Carles Brangarí A. Sanchez-Vila X. Freixa A. M. Romaní A. Rubol S. Fernàndez-Garcia D. 2017. A mechanistic model (BCC-PSSICO) to predict changes in the hydraulic properties for bio-amended variably saturated soils. Water Resour. Res. 53 93–109.
Charlton S.R. Parkhurst D.L. 2011. Modules based on the geochemical model PHREEQC for use in scripting and programming languages. Comp. & Geosc. 37 1653–1663.
Durner W. 1994. Hydraulic conductivity estimation for soils with heterogeneous pore structure. Water Resour. Res. 30 211–223.
Dzombak D.A. Morel F.M.M. 1990. Surface Complexation Modeling – Hydrous Ferric Oxide. John Wiley New York.
Freedman V.L. Bacon D.H. Saripalli K.P. Meyer P.D. 2004. A film depositional model of permeability for mineral reactions in unsaturated media. Vadose Zone J. 3 1414–1424.
Greskowiak J. Gwo J. Jacques D. Yin J. Mayer K.U. 2015. A benchmark for multi-rate surface complexation and 1D dual-domain multi-component reactive transport of U(VI). Comp. Geosc. 19 585–597.
Haggerty R. Gorelick S.M. 1995. Multiple-rate mass transfer for modeling diffusion and surface reactions in media with pore-scale heterogeneity. Water Resour. Res. 31 2383–2400.
Hiemstra T. VanRiemsdijk W.H. 1996. A surface structural approach to ion adsorption: The charge distribution (CD) model. J. Col. Int. Sci. 179 488–508.
Hommel J. Lauchnor E. Phillips A. Gerlach R. Cunningham A.B. Helmig R. Ebigbo A. Class H. 2015. A revised model for microbially induced calcite precipitation: Improvements and new insights based on recent experiments. Water Resour. Res. 51 3695–3715.
Jacques D. 2009. Benchmarking of the cement model and detrimental chemical reactions including temperature dependent parameters. Project near surface disposal of category A waste at Dessel NIRAS-MP5-03 DATA-LT(NF) Version 1.
Jacques D. Šimůnek J. 2005. User Manual of the Multicomponent Variably-Saturated Flow and Transport Model HP1. SCK•CEN-BLG-998.
Jacques D. Šimůnek J. Mallants D. van Genuchten M.T. 2006. Operator-splitting errors in coupled reactive transport codes for transient variably saturated flow and contaminant transport in layered soil profiles. J. Contam. Hydrol. 88 197–218.
Jacques D. Šimůnek J. Mallants D. van Genuchten M.T. 2008a. Modeling coupled hydrologic and chemical processes: Long-term uranium transport following phosphorus fertilization. Vadose Zone J. 7 698–711.
Jacques D. Šimůnek J. Mallants D. van Genuchten M.T. 2008b. Modelling coupled water flow solute transport and geochemical reactions affecting heavy metal migration in a podzol soil. Geoderma 145 449–461.
Jacques D. Smith C. Simůnek J. Smiles D. 2012. Inverse optimization of hydraulic solute transport and cation exchange parameters using HP1 and UCODE to simulate cation exchange. J. Contam. Hydrol. 142–143 109–125.
Jarvis N.J. Taylor A. Larsbo M. Etana A. Rosen K. 2010. Modelling the effects of bioturbation on the re-distribution of 137Cs in an undisturbed grassland soil. Eur. J. Soil Sci. 61 24–34.
Jenkinson D.S. Andrew S.P.S. Lynch J.M. Goss J.M. Tinker P.B. 1990. The turnover of organic carbon and nitrogen in soil. Philosoph. Trans. 329 361–368.
Kosugi K. 1996. Lognormal distribution model for unsaturated soil hydraulic properties. Water Resour. Res. 32 2697–2703.
Laliberté M. 2007. Model for calculating the viscosity of aqueous solutions. J. Chem. Eng. Data 52 321-335.
Laliberté M. Cooper W.E. 2004. Model for calculating the density of aqueous electrolyte solutions. J. Chem. Eng. Data 49 1141–1151.
Leterme B. Blanc P. Jacques D. 2014. A reactive transport model for mercury fate in soil—application to different anthropogenic pollution sources. Environ. Sci. Pollut. Res. 12279–12293.
Leterme B. Jacques D. 2015. A reactive transport model for mercury fate in contaminated soil-sensitivity analysis. Environ. Sci. Pollut. Res. 22 16830–16842.
Li L. Maher K. Navarre-Sitchler A. Druhan J. Meile C. Lawrence C. Moore J. Perdrial J. Sullivan P. Thompson A. Jin L. Bolton E.W. Brantley S.L. Dietrich W.E. Mayer K.U. Steefel C.I. Valocchi A. Zachara J. Kocar B. McIntosh J. Tutolo B.M. Kumar M. Sonnenthal E. Bao C. Beisman J. 2017. Expanding the role of reactive transport models in critical zone processes. Earth Sci. Rev. 165 280–301.
Liu S. Jacques D. Govaerts J. Wang L. 2014. Conceptual model analysis of interaction at a concrete-Boom Clay interface. Phys. Chem. Earth 70–71 150–159.
Maes N. Wang L. Hicks T. Bennett D. Warwick P. Hall T. Walker G. Dierckx A. 2006. The role of natural organic matter in the migration behaviour of americium in the Boom Clay - Part I: Migration experiments. Phys. Chem. Earth 31 541–547.
Makselon J. Zhou D. Engelhardt I. Jacques D. Klumpp E. 2017. Experimental and numerical investigations of silver nanoparticle transport under variable flow and ionic strength in soil. Envir. Sci. Techn. 51 2096–2104.
Mallants D. Šimůnek J. van Genuchten M.T. Jacques D. 2017. Simulating the fate and transport of coal seam gas chemicals in variably-saturated soils using HYDRUS. Water 9 6 385.
Manzoni S. Porporato A. 2009. Soil carbon and nitrogen mineralization: Theory and models across scales. Soil Biol. Biochem. 41 1355–1379.
Martinez B.C. DeJong J.T. Ginn T.R. 2014. Biogeochemical reactive transport modeling of microbial induced calcite precipitation to predict the treatment of sand in one-dimensional flow. Comp. Geotech. 58 1–13.
Mayer K.U. Alt-Epping P. Jacques D. Arora B. Steefel C.I. 2015. Benchmark problems for reactive transport modeling of the generation and attenuation of acid rock drainage. Comp. Geosci. 19 599–611.
Mayer K.U. Frind E.O. Blowes D.W. 2002. Multicomponent reactive transport modeling in variably saturated porous media using a generalized formulation for kinetically controlled reactions. Water Resour. Res. 38 1174 DOI: 1110.1029/2001WR000862.
Mays D.C. Hunt J.R. 2007. Hydrodynamic and chemical factors in clogging by montmorillonite in porous media. Envir. Sci. Techn. 41 5666–5671.
Meysman F.J.R. Boudreau B.P. Middelburg J.J. 2003a. Relations between local nonlocal discrete and continuous models of bioturbation. J. Mar. Res. 61 391–410.
Meysman F.J.R. Boudreau B.P. Middelburg J.J. 2005. Modeling reactive transport in sediments subject to bioturbation and compaction. Geochim. Cosmochim. Acta 69 3601–3617.
Meysman F.J.R. Middelburg J.J. Herman P.M.J. Heip C.H.R. 2003b. Reactive transport in surface sediments. I. Model complexity and software quality. Comp. Geosci. 29 291–300.
Nowack B. Mayer K.U. Oswald S.E. van Beinum W. Appelo C.A.J. Jacques D. Seuntjens P. Gérard F. Jaillard B. Schnepf A. Roose T. 2006. Verification and intercomparison of reactive transport codes to describe rootuptake. Plant and Soil 285 305–321.
Or D. Smets B.F. Wraith J.M. Dechesne A. Friedman S.P. 2007. Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review. Adv. Wat. Res. 30 1505–1527.
Paradelo M. Perez-Rodriguez P. Fernandez-Calvino D. Arias-Estevez M. Lopez-Periago J.E. 2012. Coupled transport of humic acids and copper through saturated porous media. Eur. J. Soil Sci. 63 708–716.
Parkhurst D.L. Appelo C.A.J. 2013. Description of Input and Examples for PHREEQC Version 3 – A Computer Program for Speciation Batch-Reaction One-Dimensional Transport and Inverse Geochemical Calculations. Chapter 43 of Section A. Groundwater Book 6 Modeling Techniques.
Parkhurst D.L. Wissmeier L. 2015. PhreeqcRM: A reaction module for transport simulators based on the geochemical model PHREEQC. Adv. Wat. Res. 83 176–189.
Patel R. Phung Q.T. Seetharam S.C. Perko J. Jacques D. Maes N. De Schutter G. Ye G. van Breugel K. 2016. Diffusivity of saturated ordinary Portland cement-based materials: A critical review of experimental and analytical modelling approaches. Cem. Con. Res. 90 52–72.
Peng D.-Y. Robinson D.B. 1976. A new two-constant equation of state. Ind. Eng. Chem. Fund. 15 59–64.
Phung Q.T. Maes N. Jacques D. De Schutter G. Ye G. Perko J. 2016. Modelling the carbonation of cement pastes under a CO2 pressure gradient considering both diffusive and convective transport. Const. Build. Mat. 114 333–351.
Porporato A. D'Odorico P. Laio F. Rodriguez-Iturbe I. 2003. Hydrologic controls on soil carbon and nitrogen cycles. I. Modeling scheme. Adv. Wat. Res. 26 45–58.
Puigdomènech I. Rard J.A. Plyasunov A.V. Grenthe I. 1997. Temperature corrections to thermodynamic data and enthalpy calculations. In: Grenthe I. PuigdomSnech I. (Eds.): OECD Nuclear Chemistry Paris pp. 427–493.
Riley W.J. Maggi F. Kleber M. Torn M.S. Tang J.Y. Dwivedi D. Guerry N. 2014. Long residence times of rapidly decomposable soil organic matter: application of a multi-phase multi-component and vertically resolved model (BAMS1) to soil carbon dynamics. Geosci. Model Dev. 7 1335–1355.
Rockhold M.L. Yarwood R.R. Niemat M.R. Bottomley P.J. Selker J.S. 2002. Considerations for modeling bacterial-induced changes in hydraulic properties of variably saturated porous media. Adv. Wat. Res. 25 477–495.
Schmidt M.W.I. Torn M.S. Abiven S. Dittmar T. Guggenberger G. Janssens I.A. Kleber M. Kogel-Knabner I. Lehmann J. Manning D.A.C. Nannipieri P. Rasse D.P. Weiner S. Trumbore S.E. 2011. Persistence of soil organic matter as an ecosystem property. Nature 478 49–56.
Seuntjens P. Nowack B. Schulin R. 2004. Root-zone modeling of heavy metal uptake and leaching in the presence of organic ligands. Plant and Soil 265 61–73.
Sharqawy M.H. Lienhard V J.H. Zubair S.M. 2010. Thermophysical properties of seawater: A review of existing correlations and data. Desal. Wat. Treat. 16 354–380.
Sierra C.A. Müller M. Trumbore S.E. 2012. Models of soil organic matter decomposition: the SoilR package version 1.0. Geosci. Model Dev. 5 1045–1060.
Silberbush M. Ben-Asher J. Ephrath J.E. 2005. A model for nutrient and water flow and their uptake by plants grown in a soilless culture. Plant and Soil 271 309–319.
Šimůnek J. He C. Pang L. Bradford S.A. 2006. Colloidfacilitated solute transport in variably saturated porous media: Numerical model and experimental verification. Vadose Zone J. 5 1035–1047.
Šimůnek J. Hopmans J.W. 2009. Modeling compensated root water and nutrient uptake. Ecol. Mod. 220 505–521.
Šimůnek J. Jacques D. Šejna M. van Genuchten M.T. 2012. The HP2 Program for HYDRUS (2D/3D). A Coupled Code for Simulating Two-Dimensional Variably-Saturated Water Flow Head Transport Solute Transport Flow and Biogeochemistry in Porous Media. (HYDRUS+PHREEQC+2D) Version 1.
Simunek J. Sejna M. Saito H. Sakai K. van Genuchten M.T. 2013. The HYDRUS-1D Software Package for Simulating the Movement of Water Heat and Multiple Solutes in Variably Saturated Media. Version 4.17. HYDRUS Software Series 3. Department of Environmental Sciences University of California Riverside Riverside California USA.
Šimůnek J. van Genuchten M.T. 2008. Modeling nonequilibrium flow and transport processes using HYDRUS. Vadose Zone J. 7 782–797.
Šimůnek J. van Genuchten M.T. Šejna M. 2016. Recent developments and applications of the HYDRUS Computer Software Packages. Vadose Zone J. 15 DOI: 10.2136/vzj2016.04.0033.
Steefel C.I. Appelo C.A.J. Arora B. Jacques D. Kalbacher T. Kolditz O. Lagneau V. Lichtner P.C. Mayer K.U. Meeussen J.C.L. Molins S. Moulton D. Shao H. Šimůnek J. Spycher N. Yabusaki S.B. Yeh G.T. 2015. Reactive transport codes for subsurface environmental simulation. Comp. Geosci. 19 445–478.
Steefel C.I. DePaolo D.J. Lichtner P.C. 2005. Reactive transport modeling: An essential tool and a new research approach for the Earth sciences. Earth Plan. Sci. Let. 240 539–558.
Tang J. Riley W.J. 2015. Weaker soil carbon-climate feedbacks resulting from microbial and abiotic interactions. Nature Clim. Change 5 56–60.
Tang J.Y. Riley W.J. Koven C.D. Subin Z.M. 2013. CLM4-BeTR a generic biogeochemical transport and reaction module for CLM4: model development evaluation and application. Geosci. Model Dev. 6 127–140.
Thaysen E.M. Jacques D. Jessen S. Andersen C.E. Laloy E. Ambus P. Postma D. and Jakobsen I. 2014. Inorganic carbon fluxes across the vadose zone of planted andunplanted soil mesocosms. Biogeosci. 11 7179–7192.
Todd-Brown K.E.O. Randerson J.T. Post W.M. Hoffman F.M. Tarnocai C. Schuur E.A.G. Allison S.D. 2013. Causes of variation in soil carbon simulations from CMIP5 Earth system models and comparison with observations. Biogeosci. 10 1717–1736.
Valdes-Abellan J. Jiménez-Martínez J. Candela L. Jacques D. Kohfahl C. Tamoh K. 2017. Reactive transport modelling to infer changes in soil hydraulic properties induced by non-conventional water irrigation. J. Hydrol. 549 114–124.
van Genuchten M.T. 1980. Closed-form equation for predicting the hydraulic conductivity of unsaturated soils. Soil Sci. Soc. Am. J. 44 892–898.
Vereecken H. Schnepf A. Hopmans J.W. Javaux M. Or D. Roose T. Vanderborght J. Young M.H. Amelung W. Aitkenhead M. Allison S.D. Assouline S. Baveye P. Berli M. Brüggemann N. Finke P. Flury M. Gaiser T. Govers G. Ghezzehei T. Hallett P. Hendricks Franssen H.J. Heppell J. Horn R. Huisman J.A. Jacques D. Jonard F. Kollet S. Lafolie F. Lamorski K. Leitner D. McBratney A. Minasny B. Montzka C. Nowak W. Pachepsky Y. Padarian J. Romano N. Roth K. Rothfuss Y. Rowe E.C. Schwen A. Šimůnek J. Tiktak A. Van Dam J. van der Zee S.E.A.T.M. Vogel H.J. Vrugt J.A. Wöhling T. Young I.M. 2016. Modeling soil processes: Review key challenges and new perspectives. Vadose Zone J. 15 1–57.
Vogel T. Cislerova M. Hopmans J.W. 1991. Porous media with linearly variable hydraulic properties. Water Resour. Res. 27 2735–2741.
Wissmeier L. Barry D.A. 2009. Effect of mineral reactions on the hydraulic properties of unsaturated soils: Model development and application. Adv. Wat. Res. 32 1241–1254.
Wissmeier L. Barry D.A. 2010. Implementation of variably saturated flow into PHREEQC for the simulation of biogeochemical reactions in the vadose zone. Env. Mod. Soft. 25 526–538.
Wutzler T. Reichstein M. 2008. Colimitation of decomposition by substrate and decomposers - a comparison of model formulations. Biogeosci. 5 749–759.
Xie M. Mayer K.U. Claret F. Alt-Epping P. Jacques D. Steefel C. Chiaberge C. Šimůnek J. 2015. Implementation and evaluation of permeability-porosity and tortuosity-porosity relationships linked to mineral dissolution-precipitation. Comp. Geosci. 19 655–671.
Yarwood R.R. Rockhold M.L. Niemet M.R. Selker J.S. Bottomley P.J. 2006. Impact of microbial growth on water flow and solute transport in unsaturated porous media. Water Resour. Res. 42 W10405 1–11.
Yu C. Muñoz-Carpena R. Gao B. Perez-Ovilla O. 2013. Effects of ionic strength particle size flow rate and vegetation type on colloid transport through a dense vegetation saturated soil system: Experiments and modeling. J. Hydrol. 499 316–323.
Zhou D. Thiele-Bruhn S. Arenz-Leufen M.G. Jacques D. Lichtner P. Engelhardt I. 2016. Impact of manure-related DOM on sulfonamide transport in arable soils. J. Contam. Hydrol. 192 118–128.