Geochemical and Biogeochemical Modeling in Low- and High-temperature Aquifers

Geochemical modeling is an important tool in environmental studies, and in the areas of subsurface and surface hydrology, pedology, water resources management, mining geology, geothermal resources, hydrocarbon geology, and related areas dealing with the exploration and extraction of natural resources.

The book fills a gap in the literature through its discussion of geochemical modeling, which simulates the chemical and physical processes affecting the distribution of chemical species in liquid, gas, and solid phases. Geochemical modeling applies to a diversity of subsurface environments, from the vadose zone close to the Earth’s surface, down to deep-seated geothermal reservoirs.

This book provides the fundamental thermodynamic concepts of liquid-gas-solid phase systems. It introduces the principal types of geochemical models, such as speciation, reaction-path or forward, inverse- and reactive-transport models, together with examples of the most common codes and the best-practices for constructing geochemical models. The physical laws describing homogeneous and heterogeneous chemical reactions, their kinetics, and the transport of reactive solutes are presented. The partial differential or algebraic equations representing these laws, and the principal numerical methods that allow approximate solutions of these equations that can provide useful solutions to model different geochemical processes, are discussed in detail. Case studies applying geochemical models in different scientific areas and environmental settings, conclude the book.

The book is addressed to students, teachers, other professionals, and to the institutions involved in water, geothermal and hydrocarbon resources, mining, and environmental management. The book should prove useful to undergraduate and graduate students, postgraduates, professional geologists and geophysicists, engineers, environmental scientists, soil scientists, hydrochemists, and others interested in water and geochemistry. More

Table of contents
About the book series Editorial board of the book seriesContributors Foreword Editors’ prefaceAbout the editors Acknowledgements
Section 1: Introduction to groundwater geochemistry and fundamentals of hydrogeochemical modeling
1 Hydrogeochemistry principles for geochemical modeling(J. Bundschuh & O. Sracek)1.1 Sampling and analysis of water, solids and gases 1.1.1 Measurement of field parameters 1.1.2 Filtration and preservation of water samples 1.1.3 Sampling of solid materials 1.1.4 Sampling of gases 1.2 Introduction to thermodynamics 1.3 Chemical composition of precipitation 1.4 Hydrochemical processes 1.4.1 Introduction 1.4.2 Oxidation-reduction reactions 1.4.3 Organic matter decomposition, photosynthesis and aerobic respiration 1.4.4 Nitrification and denitrification 1.4.5 Sorption 1.5 Kinetics
2 Thermodynamics of gas and mineral solubility in the unsaturated-zone water(L. Mercury & M. Zilberbrand) 2.1 Introduction2.2 Background2.2.1 Capillary water 2.2.2 “Capillarizing” the water by the dryness of the soil atmosphere 2.2.3 Capillarity and size of pores 2.2.4 Capillary water: stable or metastable? 2.3 Capillary thermodynamics 2.3.1 Capillary solutions and the gas-solutions equilibria 2.3.2 Solids in capillary situations 2.3.3 Thermodynamic modeling of reactions in capillary systems 2.3.4 Simplified modeling of salt solubility in capillary systems 2.4 Illustrations in natural settings 2.4.1 Capillarity and mineralogy of desert roses 2.4.2 Capillarity and the dissolution of gases 2.5 Hydrogeochemical modeling in the unsaturated zone 2.6 Conclusions
3 Governing equations and solution algorithms for geochemical modeling(C. Ayora, M.W. Saaltink & J. Carrera) 3.1 The formulation of reactions 3.1.1 Species, reactions and stoichiometric coefficients 3.1.2 Equilibrium reactions in terms of the stoichiometric matrix 3.1.3 Primary and secondary species 3.1.4 Components and component matrix 3.1.4.1 Method 1 (aqueous components) 3.1.4.2 Method 2 (eliminate constant activity species) 3.1.4.3 Other methods 3.2 Homogeneous reactions 3.2.1 Speciation calculations 3.2.1.1 Algorithm 1 3.2.1.2 Algorithm 2 3.3 Heterogeneous reactions 3.3.1 Surface complexation reactions 3.3.2 Cation exchange reactions 3.3.3 Reactions with a solid phase 3.3.4 Reactions with a gas phase 3.4 Reaction paths 3.5 Formulation of kinetic reactions
4 Fluid flow, solute and heat transport equations(M.W. Saaltink, A. Yakirevich, J. Carrera & C. Ayora) 4.1 Introduction 4.2 Groundwater flow equations 4.2.1 Single phase flow 4.2.1.1 The conservation mass for the fluid 4.2.1.2 The momentum mass balance equations for the fluid 4.2.1.3 Flow equations 4.2.2 Multiphase flow 4.2.2.1 Multiphase system 4.3 Transport of conservative solutes 4.3.1 Advection, diffusion and dispersion 4.3.1.1 Advection 4.3.1.2 Diffusion 4.3.1.3 Dispersion 4.3.2 Transport equations of conservative solutes 4.4 Heat transport equations 4.4.1 Conduction and convection 4.4.1.1 Heat conduction 4.4.1.2 Heat convection 4.4.2 Heat transport in single fluid phase systems 4.4.3 Heat transport in multiple fluid phases systems 4.5 Reactive transport 4.5.1 The need for reactive transport: calcite dissolution in the fresh-salt water mixing zone4.5.2 Mass balance equations 4.5.3 Constant activity species 4.5.4 Analytical solution for a binary system: equilibrium reaction rates 4.5.4.1 Problem statement 4.5.4.2 Methodology of solution 4.5.4.3 An analytical solution: pulse injection in a binary system 4.6 The effect of heterogeneity and non-local formulations 4.6.1 The limitations of traditional formulations and the need for upscaling 4.6.2 Solution of reactive transport in MRMT formulations
5 Numerical solutions of reactive transport equations(M.W. Saaltink, J. Carrera & C. Ayora) 5.1 Introduction 5.2 Methods for discretizing space and time 5.2.1 Finite differences 5.2.1.1 Fundamentals 5.2.1.2 Application to conservative transport 5.2.2 Finite elements 5.2.3 Instability and numerical dispersion 5.3 Methods for solving reactive transport equations 5.3.1 Sequential Iteration Approach (SIA) 5.3.2 Direct Substitution Approach (DSA) 5.3.3 Comparison between SIA and DSA
6 Elaboration of a geochemical model(M. Zilberbrand) 6.1 Introduction 6.2 Model types and the most popular existing software packages 6.2.1 Speciation-solubility models 6.2.2 Reaction-path models 6.2.3 Inverse (mass-balance) models 6.2.4 Reactive transport models 6.3 Data required for geochemical modeling 6.3.1 Data for speciation-solubility models 6.3.2 Data for reaction-path models 6.3.3 Data for inverse (mass-balance) models 6.3.4 Data for reactive transport models 6.4 Schematization and choice of thermodynamic database 6.5 Modeling and interpretation of its results 6.6 Possible errors and misconceptions in model elaboration
7 Advances in geochemical modeling for geothermal applications(P. Birkle) 7.1 Introduction 7.2 Development of geothermal reservoir tools 7.3 Types of geochemical models for geothermal systems 7.4 Requirements for geochemical simulations of geothermal reservoirs 7.5 Popular computer software for geothermal system modeling 7.6 Flow and geochemical model calibration 7.7 Selection of recent applications (2000–2010)—Case studies 7.7.1 General applications 7.7.2 Conceptual reservoir models 7.7.3 Lumped parameter models 7.7.4 Advanced numerical modeling 7.7.4.1 Reservoir design and magnitude—Reconstruction of reservoir parameters 7.7.4.2 Origin of acidity for reservoir fluids 7.7.4.3 Mineral-fluid equilibria 7.7.4.4 Fluid reinjection—Scaling effects 7.7.4.5 Hot-Dry Rock (HDR) systems (Soultz-sous-Forêts, France) 7.7.4.6 CO2 injection into geothermal reservoirs 7.8 Conclusions—Future challenges
Section 2: Cases studies
8 Integrating field observations and inverse and forward modeling: application at a site with acidic, heavy-metal-contaminated groundwater(P. Glynn & J. Brown) 8.1 Introduction 8.2 Geochemical modeling: computer codes, theory and assumptions 8.2.1 Inverse geochemical modeling 8.2.1.1 Principles, codes and theory 8.2.1.2 Assumptions used in inverse modeling 8.2.2 Forward geochemical modeling 8.2.2.1 Principles and codes 8.3 The Pinal Creek basin site: brief description 8.3.1 Geology 8.3.2 Hydrology and groundwater flow 8.4 Inverse geochemical modeling at the Pinal Creek site 8.4.1 Examination of end-member waters and their conservative constituents 8.4.2 The thermodynamic state of the end-member waters 8.4.3 NETPATH inverse modeling: simulation results 8.4.4 Inverse geochemical modeling with PHREEQC 8.5 Reactive-transport modeling at the Pinal Creek site 8.5.1 Summary of previous reactive-transport modeling 8.5.2 A reactive-transport sensitivity analysis on the movement of pH and pe-controlling mineral fronts 8.5.2.1 A simple model for advective transport of a reactive front: the MnO2 dissolution front 8.5.2.2 Determination of the initial MnO2,s and carbonate mineral concentrations 8.5.2.3 Setup of the 1-D reactive-transport simulations 8.5.2.4 Simulation results: movement of the Fe(II)-rich waters and of the MnO2 dissolution front 8.5.2.5 Simulation results: evolution of the low-pH waters 8.5.2.6 The effect of the initial carbonate to initial MnO2 ratio on the evolution of the low-pH waters 8.5.2.7 Influence of the aluminum mineral allowed to precipitate on the evolution of the low-pH waters 8.5.2.8 Effects of the irreversible dissolution of Ca and Mg silicates on the evolution of low-pH Fe(II)-rich waters 8.5.2.9 The effect of not allowing rhodochrosite precipitation 8.5.2.10 The CO2 open system simulations 8.5.2.11 The effect of longitudinal dispersion 8.5.2.12 The influence of cation exchange and surface-complexation sorption processes 8.5.2.13 Other minor effects on the evolution of the low-pH waters 8.5.2.14 Comparison of the reactive transport simulation results with observations at the Pinal Creek site 8.6 Conclusions 8.7 The Senior Author’s fifteen year perspective on the Glynn and Brown (1996) paper
9 Models and measurements of porosity and permeability evolution in a sandstone formation(S. Emmanuel, J.J. Ague & O. Walderhaug) 9.1 Introduction 9.2 Porosity measurements in mineralized rock 9.3 Theory and numerical modeling of porosity evolution 9.3.1 Conceptual model of the porous medium 9.3.2 Reaction kinetics 9.3.3 Reactive transport equations 9.3.4 Numerical solution and model optimization 9.4 Comparison between numerical models and measurements 9.5 Implications for bulk reaction rates 9.6 Implications for permeability evolution in aquifers 9.7 Concluding remarks
10 Geochemical modeling of water chemistry evolution in the Guarani Aquifer System in São Paulo, Brazil(O. Sracek & R. Hirata)
11 Modeling of reactive transport at a site contaminated by petroleum hydrocarbons at Hnevice, Czech Republic(O. Sracek & Z. Vencelides) 11.1 Site characterization and conceptual model 11.2 Speciation and inverse geochemical modeling 11.3 Modeling of reactive transport
12 Numerical modeling for preliminary assessment of natural remediation of phosphorus in variably saturated soil in a peri-urban settlement in Kampala, Uganda(R.N. Kulabako, R. Thunvik, M. Nalubega & L.A. Soutter) 12.1 Introduction 12.2 Setting 12.3 Numerical model 12.3.1 Flow model 12.3.2 Solute model 12.3.2.1 Soil phosphorus sorption 12.3.2.2 Solute transport model 12.4 Simulations 12.5 Results and discussion 12.5.1 Field measurements 12.5.2 Pollution and remediation simulation scenarios 12.5.3 Sensitivity analyses 12.5.3.1 Impact of change of sorption coefficients (KL and Kplin) on pollution time 12.5.3.2 Impact of change of the pore size distribution values on pollution time 12.5.3.3 Impact of change of the air entry values on pollution time 12.6 Conclusions
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