Simulation tool for variably saturated flow with comprehensive geochemical reactions in two and three-dimensional domains

We present a software tool for simulations of flow and multi-species solute transport in two and three-dimensional domains in combination with comprehensive intra-phase and inter-phase geochemistry. The software uses IPhreeqc, the coupling version of the geochemical modelling framework PHREEQC, as a reaction engine to the multi-purpose finite element solver COMSOL Multiphysics® for flow and transport simulations. Here we used COMSOL to solve Richards’ equation for aqueous phase flow in variably saturated porous media. The coupling procedure presented is in principle applicable to any simulation of aqueous phase flow and solute transport in COMSOL. The coupling with IPhreeqc gives major advantages over COMSOL’s built-in reaction capabilities, i.e., the soil solution is speciated from its element composition according to thermodynamic mass action equations with ion activity corrections. State-of-the-art adsorption models such as surface complexation with diffuse double layer calculations are accessible. In addition, IPhreeqc provides a framework to integrate user-defined kinetic reactions with possible dependencies on solution speciation (i.e., pH, saturation indices, and ion activities), allowing for modelling of microbially mediated reactions. Extensive compilations of geochemical reactions and their parameterization are accessible through associated databases

The HPx software for multicomponent reactive transport during variably-saturated flow: Recent developments and applications

Abstract 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

RETRASO, a code for modeling reactive transport in saturated and unsaturated porous media

The code RETRASO (REactive TRAnsport of SOlutes) simulates reactive transport of dissolved and gaseous species in non-isothermal saturated or unsaturated problems. Possible chemical reactions include aqueous complexation (including redox reactions), sorption, precipitation-dissolution of minerals and gas dissolution. Various models for sorption of solutes on solids are available, from experimental relationships (linear KD, Freundlich and Langmuir isotherms) to cation exchange and surface complexation models (constant capacitance, diffuse layer and triple layer models). Precipitation-dissolution and aqueous complexation can be modelled in equilibrium or according to kinetic laws. For the numerical solution of the reactive transport equations it uses the Direct Substitution Approach. The use of the code is demonstrated by three examples. The first example models various sorption processes in a smectite barrier. The second example models a complex chemical system in a two dimensional cross-section. The last example models pyrite weathering in an unsaturated medium

Recent Developments and Applications of the HYDRUS Computer Software Packages

The HYDRUS-1D and HYDRUS (2D/3D) computer software packages are widely used finite-element models for simulating the one- and two- or three-dimensional movement of water, heat, and multiple solutes in variably saturated media, respectively. In 2008, Šimůnek et al. (2008b) described the entire history of the development of the various HYDRUS programs and related models and tools such as STANMOD, RETC, ROSETTA, UNSODA, UNSATCHEM, HP1, and others. The objective of this manuscript is to review selected capabilities of HYDRUS that have been implemented since 2008. Our review is not limited to listing additional processes that were implemented in the standard computational modules, but also describes many new standard and nonstandard specialized add-on modules that significantly expanded the capabilities of the two software packages. We also review additional capabilities that have been incorporated into the graphical user interface (GUI) that supports the use of HYDRUS (2D/3D). Another objective of this manuscript is to review selected applications of the HYDRUS models such as evaluation of various irrigation schemes, evaluation of the effects of plant water uptake on groundwater recharge, assessing the transport of particle-like substances in the subsurface, and using the models in conjunction with various geophysical methods

Nernst-Planck Based Description of Transport, Coulombic Interactions and Geochemical Reactions in Porous Media: Modeling Approach and Benchmark Experiments

Transport of multicomponent electrolyte solutions in saturated porous media is affected by the electrostatic interactions between charged species. Such Coulombic interactions couple the displacement of the different ions in the pore water and remarkably impact mass transfer not only under diffusion, but also under advection-dominated flow regimes. To accurately describe charge effects in flow-through systems, we propose a multidimensional modeling approach based on the Nernst-Planck formulation of diffusive/dispersive fluxes. The approach is implemented with a COMSOL-PhreeqcRM coupling allowing us to solve multicomponent ionic conservative and reactive transport problems, in domains with different dimensionality (1-D, 2-D, and 3-D), and in homogeneous and heterogeneous media. The Nernst-Planck-based coupling has been benchmarked with analytical solutions, numerical simulations with another code, and high-resolution experimental data sets. The latter include flow-through experiments that have been carried out in this study to explore the effects of electrostatic interactions in fully three-dimensional setups. The results of the simulations show excellent agreement for all the benchmarks problems, which were selected to illustrate the capabilities and the distinct features of the Nernst-Planck-based reactive transport code. The outcomes of this study illustrate the importance of Coulombic interactions during conservative and reactive transport of charged species in porous media and allow the quantification and visualization of the specific contributions to the diffusive/dispersive Nernst-Planck fluxes, including the Fickian component, the term arising from the activity coefficient gradients, and the contribution due to electromigration

Lattice Boltzmann based multicomponent reactive transport model coupled with geochemical solver for pore scale simulations

A Lattice Boltzmann (LB) based reactive transport model intended to capture reactions and solid phase changes occurring at the pore scale is presented. The proposed approach uses LB method to compute multi component mass transport. The LB multicomponent transport model is then coupled with the well-established geochemical reaction code PHREEQC which solves for thermodynamic equilibrium in mixed aqueous-solid phase system with homogenous and heterogeneous reactions. This coupling enables us to update solid phases volumes based on dissolution or precipitation using static update rules which, on pore scale, affects the change of potentially pore network geometry. Unlike conventional approach, heterogeneous reactions are conceptualized as volumetric reactions by introducing additional source term in the fluid node next to solid node, and not as flux boundaries. To demonstrate the validity of this approach several examples are presented in this paper

Reactive transport modeling at hillslope scale with high performance computing methods

Reactive transport modeling is an important approach to understand water dynamics, mass transport and biogeochemical processes from the hillslope to the catchment scale. It has a wide range of applications in the fields of e.g. water resource management, contaminanted site remediation and geotechnical engineering. To simulate reactive transport processes at a hillslope or larger scales is a challenging task, which involves interactions of complex physical and biogeochemical processes, huge computational expenses as well as difficulties in numerical precision and stability. The primary goal of the work is to develop a practical, accurate and efficient tool to facilitate the simulation techniques for reactive transport problems towards hillslope or larger scales. The first part of the work deals with the simulation of water flow in saturated and unsaturated porous media. The capability and accuracy of different numerical approaches were analyzed and compared by using benchmark tests. The second part of the work introduces the coupling of the scientific software packages OpenGeoSys and IPhreeqc by using a character-string-based interface. The accuracy and computational efficiency of the coupled tool were discussed based on three benchmarks. It shows that OGS#IPhreeqc provides sufficient numerical accuracy to simulate reactive transport problems for both equilibrium and kinetic reactions in variably saturated porous media. The third part of the work describes the algorithm of a parallelization scheme using MPI (Message Passing Interface) grouping concept, which enables a flexible allocation of computational resources for calculating geochemical reaction and the physical processes such as groundwater flow and transport. The parallel performance of the approach was tested by three examples. It shows that the new approach has more advantages than the conventional ones for the calculation of geochemically-dominated problems, especially when only limited benefit can be obtained through parallelization for solving flow or solute transport. The comparison between the character-string-based and the file-based coupling shows, that the former approach produces less computational overhead in a distributed-memory system such as a computing cluster. The last part of the work shows the application of OGS#IPhreeqc for the simulation of the water dynamic and denitrification process in the groundwater aquifer of a study site in Northern Germany. It demonstrates that OGS#IPhreeqc is able to simulate heterogeneous reactive transport problems at a hillslope scale within an acceptable time span. The model results shows the importance of functional zones for natural attenuation process.Modellierung des reaktiven Stofftranports ist ein wichtiger Ansatz um die Wasserströmung, den Stofftransport und die biogeochemischen Prozesse von der Hang- bis zur Einzugsgebietsskala zu verstehen. Es gibt umfangreiche Anwendungsgebiete, z.B. in der Wasserwirtschaft, Umweltsanierung und Geotechnik. Die Simulation der reaktiven Stofftransportprozesse auf der Hangskala oder auf größeren Maßstäbe ist eine anspruchsvolle Aufgabe, da es sich um die Wechselwirkungen komplexer physikalischer und biogeochemischen Prozesse handelt, die riesigen Berechnungsaufwand sowie numerischen Schwierigkeiten bezogen auf die Genauigkeit und die Stabilität nach sich ziehen. Das Hauptziel dieser Arbeit besteht darin, ein praktisches, genaues und effizientes Werkzeug zu entwickeln, um die Simulationstechnik für reaktiven Stofftransport auf der Hangskala und auf größeren Skalen zu verbessern. Der erste Teil der Arbeit behandelt die Simulation der Wasserströmung in gesättigten und ungesättigten porösen Medien. Das Anwendungspotential und die Genauigkeit verschiedener numerischer Ansätze wurden mittels einiger Benchmarks analysiert und miteinander verglichen. Der zweite Teil der Arbeit stellt die Kopplung der wissenschaftlichen Softwarepakete OpenGeoSys und IPhreeqc mit einer stringbasierten Schnittstelle dar. Die Genauigkeit und die Recheneffizienz des gekoppelten Tools OGS#IPhreeqc wurden basierend auf drei Benchmark-Tests diskutiert. Das Ergebnis zeigt, dass OGS#IPhreeqc die ausreichende numerische Genauigkeit für die Simulation reaktiven Stofftransports liefert, welcher sich sowohl auf die Gleichgewichtsreaktion als auch auf die kinetische Reaktion in variabel gesättigten porösen Medien beziehen. Der dritte Teil der Arbeit beschreibt zuerst den Algorithmus der Parallelisierung des OGS#IPhreeqc basierend auf dem MPI (Message Passing Interface) Gruppierungskonzept, welcher eine flexible Verteilung der Rechenressourcen für die Berechnung der geochemischen Reaktion und der physikalischen Prozesse wie z.B. Wasserströmung oder Stofftransport ermöglicht. Danach wurde die Leistungsfähigkeit des Algorithmus anhand von drei Beispielen getestet. Es zeigt sich, dass der neue Ansatz Vorteile gegenüber die konventionellen Ansätzen für die Berechnung von geochemisch dominierten Problemen bringt. Dies ist vor allem dann der Fall, wenn nur eingeschränkter Nutzen aus der Parallelisierung für die Berechnung der Wasserströmung oder des Stofftransportes gezogen werden kann. Der Vergleich zwischen der string- und der dateibasierten Kopplung zeigt, dass die erstere weniger Rechenoverhead in einem verteilten Rechnersystem, wie z.B. Cluster erzeugt. Der letzte Teil der Arbeit zeigt die Anwendung von OGS#IPhreeqc für die Simulation der Wasserdynamik und der Denitrifikation im Grundwasserleiter eines Untersuchungsgebietes in NordDeutschland. Es beweist, dass OGS#IPhreeqc in der Lage ist, reaktiven Stofftransport auf der Hangskala innerhalb akzeptabler Zeitspanne zu simulieren. Die Simulationsergebnisse zeigen die Bedeutung der funktionalen Zonen für die natürlichen Selbstreinigungsprozesse

Multiphase fluid flow and subsequent geochemical transport invariably saturated fractured rocks: 1. Approaches

Reactive fluid flow and geochemical transport in unsaturated fractured rocks has received increasing attention for studies of contaminant transport, groundwater quality, waste disposal, acid mine drainage remediation, mineral deposits, sedimentary diagenesis, and fluid-rock interactions in hydrothermal systems. This paper presents methods for modeling geochemical systems that emphasize: (1) involvement of the gas phase in addition to liquid and solid phases in fluid flow, mass transport and chemical reactions, (2) treatment of physically and chemically heterogeneous and fractured rocks, (3) the effect of heat on fluid flow and reaction properties and processes, and (4) the kinetics of fluid-rock interaction. The physical and chemical process model is embodied in a system of partial differential equations for flow and transport, coupled to algebraic equations and ordinary differential equations for chemical interactions. For numerical solution, the continuum equations are discretized in space and time. Space discretization is based on a flexible integral finite difference approach that can use irregular gridding to model geologic structure; time is discretized fully implicitly as a first-order finite difference. Heterogeneous and fractured media are treated with a general multiple interacting continua method that includes double-porosity, dual-permeability, and multi-region models as special cases. A sequential iteration approach is used to treat the coupling between fluid flow and mass transport on the one hand, chemical reactions on the other. Applications of the methods developed here to variably saturated geochemical systems are presented in a companion paper (part 2, this issue)