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.

Hydrogeochemical Modelling of Variably Saturated Soils

Laurin Wissmeier

This thesis is about the simulation of flow, transport and geochemical reactions in variably saturated soils. Motivated by the problematic disposal and revegetation of residue from aluminium refining, novel modelling tools for general geochemical reactions in variably saturated flow conditions were developed. In addition, a new model for the effect of mineral reactions on unsaturated hydraulic properties was established. The most sophisticated of the presented series of models was applied in a comprehensive simulation of the geochemical evolution of residue from aluminium refining in response to rainfall- and evaporation-induced leaching. Model development commenced with the direct implementation of the one-dimensional moisture-based form of Richards' equation into the geochemical modelling framework PHREEQC for the simulation of biogeochemical reactions in the vadose zone. The implementation gives access to the full suite of reactions in PHREEQC with activity corrected solution speciation, advanced adsorption models and the flexible definition of kinetic mineral reactions. The numerical approach is based on the conceptual treatment of liquid phase flow and solute transport as time- and space-dependent reactions. The accuracy of the applied finite difference scheme profits from the Kirchhoff transformation on the diffusivity term. In case of the van Genuchten hydraulic model, the integration of soil moisture diffusivity led to analytical series solutions that necessitate numerical approximation. The model's novel capabilities for the simulation of unsaturated flow and ion complexation with variable charge surface sites as well as water content modifying mineral reactions, such as dissolution of hydrated minerals were demonstrated in examples. In a second step, the applicability of this simulation tool was extended to soil profiles with heterogeneous hydraulic properties and variably saturated conditions where parts of the domain may be fully saturated. For this, the head-based form of Richards' equation was implemented using a mass balancing, implicit finite difference scheme with Picard iteration. The use of a total variation-diminishing scheme for solute transport yields second order accurate yet oscillation free solutions for the advective transport of sharp concentration fronts. Applications of the scheme were illustrated for (i) infiltration with saturation-dependent cation exchange capacity, (ii) changes in hydraulic properties due to mineral reactions and (iii) transport of mobile organic substances with complexation of heavy metals. Using this extended simulation tool, an advanced model for the effect of mineral reactions on unsaturated hydraulic properties was developed. The selective radius shift model accounts for the fact that mineral reactions in unsaturated conditions only affect the water filled pore size fraction. In addition, the volume change in each pore due to dissolution/precipitation is proportional to the pore volume. Changes in mineral volume according to geochemical speciation are translated to the pore-size distribution considering the actual moisture content. The resulting discontinuous pore-size distribution is related to the water retention curve by the pore-bundle concept. From the updated discontinuous water retention curve, a smooth water retention function is deduced by means of parameter optimization. Applications of the selective radius shift model were presented for kinetic halite dissolution and calcite precipitation as a consequence of cation exchange. In a further development, the simulation of geochemical reactions in variably saturated soils was extended to two and three-dimensional domains by coupling the general finite element solver COMSOL Multiphysics® to IPhreeqc. IPhreeqc is an object-oriented version of PHREEQC that is specifically designed for couplings to flow and solute transport simulators. The resulting model combines COMSOL's capabilities for the computation of variably saturated flow and solute transport in domains of arbitrary complexity with the full suite of geochemical reaction calculations in PHREEQC. Code verification was performed for point source infiltration and degradation of the pesticide Aldicarb via a kinetic reaction chain. An application example of the new software features subsurface irrigation and fertigation, with cation exchange, proton adsorption and pressure- and space dependent root-water uptake. Using the coupled software, the coarse fraction of the leftover from aluminium refining using Bayer's process was investigated as a covering substrate for residue disposal areas and substrate for plant growth. The solid phase mineral assembly in the residue sand was derived from measured acid neutralization curves. Ion adsorption was modelled and parameterized as an exchange process. A column experiment under saturated flow conditions partially validated the model. The parameterized model was used to predict the geochemical evolution of fertigated and gypsum amended residue sand as response to rainfall- and evaporation-induced leaching in the climatic conditions of southwest Western Australia. Scenarios were calculated for a vertical flow lysimeter and a sloping cover layer for a disposal facility with dimensions 3 m × 50 m. Results show poor long-term retention of fertilizers and the stabilization of the pH at around 10 for at least 5 years of leaching. Soil moisture conditions in the cover layer could be ameliorated by appropriate design of the layer thickness, slope and distance between lateral drains.

EPFL2010

Implementation of variably saturated flow into PHREEQC for the simulation of biogeochemical reactions in the vadose zone

David Andrew Barry, Laurin Wissmeier

A software tool for the simulation of one-dimensional unsaturated flow and solute transport together with biogeochemical reactions in the vadose zone was developed by integrating a numerical solution of Richards' equation into the geochemical modelling framework PHREEQC. Unlike existing software, the new simulation tool is fully based on existing capabilities of PHREEQC without source code modifications or coupling to external software packages. Because of the direct integration, the full set of PHREEQC's geochemical reactions with connected databases for reaction constants is immediately accessible. Thus, unsaturated flow and solute transport can be simulated together with complex solution speciation, equilibrium and kinetic mineral reactions, redox reactions, ion exchange reactions and surface adsorption including diffuse double layer calculations. Liquid phase flow is solved as a result of element advection, where the Darcy flux is calculated according to Richards' equation. For accurate representation of advection-dominated transport, a total- variation-diminishing scheme was implemented. Dispersion was simulated with a standard approach; however, PHREEQC's multicomponent transport capabilities can be used to simulate species-dependent diffusion. Since liquid phase saturation is recalculated after every reaction step, biogeochemical processes that modify liquid phase saturation, such as dissolution or precipitation of hydrated minerals are considered a priori. Implementation of the numerical schemes for flow and solute transport have been described, along with examples of the extensive code verification, before illustrating more advanced application examples. These include (i) the simulation of infiltration with saturation-dependent cation exchange capacity, (ii) changes in hydraulic properties due to mineral reactions and (iii) transport of mobile organic substances with complexation of heavy metals in varying geochemical conditions.

Elsevier2010

Buffering soil-water acidity in chlorinated solvent bioremediation schemes

David Andrew Barry, Alessandro Brovelli, Christof Holliger, Elsa Marina Lacroix, Clare Robinson

Chlorinated solvents form a significant part of groundwater contamination worldwide. They are difficult to remove via physical means, and anaerobic source-zone remediation based on provision of fermentable e-donor is an attractive clean-up dechlorination option. However, organic acids and HCl lower the groundwater pH and thereby stall the microbial consortia responsible for the biodegradation process. Often, the soil’s natural buffering capacity will be exceeded, in which case a strategy of adding buffer to the groundwater is a priori beneficial to maintain dechlorination. Geochemical modelling was used to investigate the feasibility of adding naturally occurring buffering minerals to the groundwater for pH control. The simulations revealed that anorthite has the potential to be used as a sustainable pH buffering mineral.