This chapter presents the development of the latest version of HYDROGEOCHEM a multidimensional numerical model of coupled fluid flow, thermal transport, hydrologic transport, and biogeochemical kinetic/equilibrium reactions in saturated/unsaturated media. It iteratively solves the Richards equation for fluid flow, the thermal transport equation for temperature fields, and reactive biogeochemical transport equations for concentration distributions. For the latter, the advectivedispersive- reactive transport equations are solved for mobile components and kinetic variables. The biogeochemical reaction equations along with the component- and kinetic-variable equations are solved for concentration distributions of all species. This version of HYDROGEOCHEM is designed for generic applications to reactive transport problems under non-isothermal conditions in subsurface media. It considers all types of reactions (aqueous complexation, adsorption-desorption, precipitationdissolution, ion-exchange, hydrolysis, and abiotic and biotic-mediated redox) as both fast/equilibrium and/or slow/kinetic processes, using a consistent definition of fast/equilibrium reaction rates. Input to the program includes the finite element numerical representation of the system, the properties of the media, reaction network, and initial and boundary conditions. Output includes the spatial distributions of pressure and total heads, velocity fields, moisture contents, temperature, and biogeochemical concentrations at user specified times and locations (finite element nodes). Six examples are employed to demonstrate the design capabilities of HYDROGEOCHEM, to illustrate the calculations of fast/equilibrium reaction rates, and to highlight the non-intuitive notion that the rates of slow/kinetic reactions are not necessarily smaller than those of fast/equilibrium reactions.

In this work, we describe a number of efficient and locally conservative methods for subsurface flow and reactive transport that have been or are currently being implemented in the IPARS (Integrated Parallel and Accurate Reservoir Simulator). For flow problems, we consider discontinuous Galerkin (DG) methods and mortar mixed finite element methods. For transport problems, we employ discontinuous Galerkin methods and Godunov-mixed methods. For efficient treatment of reactive transport simulations, we present a number of state-of-the-art dynamic mesh adaptation strategies and implementations. Operator splitting approaches and iterative coupling techniques are also discussed. Finally, numerical examples are provided to illustrate the capability of IPARS to treat general biogeochemistry as well as the effectivity of mesh adaptations with DG for transport.

TOUGHREACT is a numerical simulation program for chemically reactive non-isothermal flows of multiphase fluids in porous and fractured media. The program was written in Fortran 77 and developed by introducing reactive chemistry into the multiphase fluid and heat flow simulator TOUGH2. A variety of subsurface thermo-physical-chemical-biological processes are considered under a wide range of conditions of pressure, temperature, water saturation, ionic strength, and pH and Eh. Reactions among aqueous species and interactions between mineral assemblages and fluids can occur under local equilibrium or via kinetically controlled rates. The gas phase can be chemically active. Precipitation and dissolution reactions can change formation porosity and permeability. Intra-aqueous kinetics, biodegradation and surface complexation have recently been incorporated. The program can be applied to one-, two- or three-dimensional porous and fractured media with physical and chemical heterogeneity. It can accommodate any number of chemical species present in liquid, gas and solid phases. TOUGHREACT can be applied to many geologic systems and environmental problems, including subsurface storage of nuclear waste and CO2, geothermal systems, diagenetic and weathering processes, acid mine drainage remediation, contaminant transport, and groundwater quality. The methods and approaches used in TOUGHREACT have been extensively published over the last decade. Here we give a general description and summary of the program, including the main features, scope, processes, and solution method. To illustrate its applicability, we present four examples: (1) Denitrification and sulfate reduction, (2) long-term fate of injected CO2 for geological sequestration, (3) bentonite alteration due to THC processes in a nuclear waste repository, and (4) chemical stimulation of an enhanced geothermal system.

RT3D is a Fortran-based software for simulating three-dimensional, multi-species, reactive transport of chemical compounds (solutes) in groundwater. RT3D is a MODFLOW-based solute transport code derived from MT3DMS, but with greatly expanded reaction capabilities. Although RT3D is often discussed in the context of accelerated in situ bioremediation (ISB) and natural/enhanced attenuation scenarios, RT3D is a general-purpose reactive transport code suitable for simulating a multitude of scenarios. Potential capabilities include simulation of inorganic reactions, geochemistry reactions, NAPL dissolution, mobile/immobile dual porosity, colloid transport, virus transport, heat transport, and risk analysis. With some degree of effort, RT3D can be linked to other codes to include time-varying porosity, interaction with the unsaturated zone, or full geochemistry. Commercial thirdparty graphical user interface software is typically used to define RT3D simulation model configurations and to visualize contours or isosurfaces of results. Results consist of whole-grid data sets at points in time and location-specific time series data sets. Multiple examples of RT3D application in the published literature are discussed, with a more in depth look at case studies for a monitored natural attenuation application and the design of an active remediation system.

ECKEChem (Equilibrium, Conservation, Kinetic Equation Chemistry) is a reactive transport module for the STOMP suite of multifluid subsurface flow and transport simulators that was developed using an engineering perspective. STOMP comprises a suite of operational modes with capabilities for a variety of subsurface applications (e.g., environmental remediation and stewardship, geologic sequestration of greenhouse gases, gas hydrate production, and oil shale production). The ECKEChem module was designed to provide integrated reactive transport capabilities across the suite of STOMP simulator operational modes. The initial application for the ECKEChem module was for the simulation of mineralization reactions that were predicted to occur with the injection of supercritical carbon dioxide into deep Columbia River basalt formations, using STOMP-CO2 which solves sequestration flow and transport problems for deep saline formations. The STOMP-ECKEChem solution approach to modeling reactive transport in multifluid geologic media is founded on an engineering perspective: 1) geochemistry can be expressed, input and solved as a system of coupled nonlinear equilibrium, conservation and kinetic equations, 2) the number of kinetic equation forms used in geochemical practice are limited, 3) sequential non-iterative coupling between the flow and reactive transport is sufficient, 4) reactive transport can be modeled by operator splitting with local geochemistry and global transport. This chapter describes the conceptual approach to converting a geochemical reaction network into a series of equilibrium, conservation and kinetic equations, the implementation of ECKEChem in STOMP, the numerical solution approach, and a demonstration of the simulator on a complex application involving desorption of uranium from contaminated sediments.

PFLOTRAN, a next-generation reactive flow and transport code for modeling subsurface processes, has been designed from the ground up to run efficiently on machines ranging from leadership-class supercomputers to laptops. Based on an object-oriented design, the code is easily extensible to incorporate additional processes. It can interface seamlessly with Fortran 9X, C and C++ codes. Domain decomposition parallelism is employed, with the PETSc parallel framework used to manage parallel solvers, data structures and communication. Features of the code include a modular input file, implementation of high-performance I/O using parallel HDF5, ability to perform multiple realization simulations with multiple processors per realization in a seamless manner, and multiple modes for multiphase flow and multicomponent geochemical transport. Chemical reactions currently implemented in the code include homogeneous aqueous complexing reactions and heterogeneous mineral precipitation/dissolution, ion exchange, surface complexation and a multirate kinetic sorption model. PFLOTRAN has demonstrated petascale performance using 217 processor cores on problems composed of over 2 billion degrees of freedom. The code is currently being applied to simulate uranium transport at the Hanford 300 Area and CO2 sequestration in deep geologic formations.

Understanding natural groundwater quality patterns, quantifying groundwater pollution and assessing the performance of waste disposal facilities require modeling tools accounting for water flow, transport of heat and dissolved species as well as their complex interactions with solid and gaseous phases. Here we present, CORE2D V4, a COde for modeling partly or fully saturated water flow, heat transport and multicomponent REactive solute transport under both local chemical equilibrium and kinetic conditions. It can handle abiotic reactions including acid-base, aqueous complexation, redox, mineral dissolution/precipitation, gas dissolution/exsolution, ion exchange and sorption reactions (linear Kd, Freundlich and Langmuir isotherms, and surface complexation using constant capacitance, diffuse layer and triple layer models) and microbial processes. Hydraulic parameters may change in time due to mineral precipitation/dissolution reactions. A sequential iterative approach is used for the numerical solution of coupled reactive transport equations. The capabilities of CORE2D V4 are illustrated with six selected applications involving: 1) A laboratory concrete degradation experiment, 2) The long-term geochemical evolution of the near field of a High Level Radioactive Waste (HLW) repository in clay, 3) Cation exchange in a physically and geochemically heterogeneous medium, 4) An experiment of CO2 injection in the vadose zone, 5) The prediction of the water quality of an open pit lake, and 6) Coupled thermo-hydro-chemical processes of compacted bentonite after FEBEX in situ test.

MIN3P was developed as a general purpose multicomponent reactive transport code for variably saturated media. The basic version of the code includes Richard’s equation for the solution of variably-saturated flow, and solves mass balance equations for advective-diffusive solute transport and diffusive gas transport. Biogeochemical reactions are described by a partial equilibrium approach, using equilibrium-based law-of-mass-action relationships for fast reactions, and a generalized kinetic framework for reactions that are relatively slow in comparison to the transport time scale. MIN3P has been used to support multiple field and laboratory investigations involving the fate of inorganic and organic substances and has served as a platform for additional code development: MIN3P-Bubble, an enhanced version to simulate gas generation and exsolution in the saturated zone, as well as gas entrapment and release due to water table fluctuations; MIN3P-Dusty, a version of the code that includes gas advection and multicomponent gas diffusion based on the Dusty Gas Model (DGM); and MIN3P-Soil, a version that includes plant-soil interactions. The capabilities of the basic code and the follow-up developments are demonstrated by simulating the oxidation of pyrite in mine waste, associated metal release, and subsequent attenuation processes; the interactions between the formation of “excess air” and biogeochemical reactions in the vadose zone and below the water table; the evolution of vadose zone gas composition and transport processes at a petroleum hydrocarbon spill site undergoing natural attenuation; and the effect of plant-soil interactions on mineral weathering and secondary mineral formation in soils and surficial sediments.

Sophisticated and robust numerical modeling is essential to developing a good understanding of complex physical and chemical phenomena in the subsurface. In this chapter we provide a general overview of NUFT (Nonisothermal Unsaturated-saturated Flow and Transport) code, which is a highly flexible computer software package for modeling multiphase, multi-component heat and mass flow and reactive transport in unsaturated and saturated porous media. An integrated finite difference method is used for numerical discretization. Several mathematical models are implemented in order to address various flow and reactive transport processes in porous media. The governing equations for each submodel are solved by implicit time-integration. In particular a globally implicit approach is employed to solve transport and reaction equations simultaneously. The code is designed based on object-oriented principles, and equipped with efficient solvers and massively parallel computation capability. We present two examples involving reactive transport modeling to demonstrate capabilities of the code.