Upscaling geochemical reaction rates using pore-scale network modeling

Geochemical reaction rate laws are often measured using crushed minerals in well-mixed laboratory systems that are designed to eliminate mass transport limitations. Such rate laws are often used directly in reactive transport models to predict the reaction and transport of chemical species in consolidated porous media found in subsurface environments. Due to the inherent heterogeneities of porous media, such use of lab-measured rate laws may introduce errors, leading to a need to develop methods for upscaling reaction rates. In this work, we present a methodology for using pore-scale network modeling to investigate scaling effects in geochemical reaction rates. The reactive transport processes are simulated at the pore scale, accounting for heterogeneities of both physical and mineral properties. Mass balance principles are then used to calculate reaction rates at the continuum scale. To examine the scaling behavior of reaction kinetics, these continuum-scale rates from the network model are compared to the rates calculated by directly using laboratory-measured reaction rate laws and ignoring pore-scale heterogeneities. In this work, this methodology is demonstrated by upscaling anorthite and kaolinite reaction rates under simulation conditions relevant to geological CO₂ sequestration. Simulation results show that under conditions with CO₂ present at high concentrations, pore-scale concentrations of reactive species and reaction rates vary spatially by orders of magnitude, and the scaling effect is significant. With a much smaller CO₂ concentration, the scaling effect is relatively small. These results indicate that the increased acidity associated with geological sequestration can generate conditions for which proper scaling tools are yet to be developed. This work demonstrates the use of pore-scale network modeling as a valuable research tool for examining upscaling of geochemical kinetics. The pore-scale model allows the effects of pore-scale heterogeneities to be integrated into system behavior at multiple scales, thereby identifying important factors that contribute to the scaling effect.     

Direct numerical simulation of pore-scale flow in a bead pack: Comparison with magnetic resonance imaging observations

A significant body of current research is aimed at developing methods for numerical simulation of flow and transport in porous media that explicitly resolve complex pore and solid geometries, and at utilizing such models to study the relationships between fundamental pore-scale processes and macroscopic manifestations at larger (i.e., Darcy) scales. A number of different numerical methods for pore-scale simulation have been developed, and have been extensively tested and validated for simplified geometries. However, validation of pore-scale simulations of fluid velocity for complex, three-dimensional (3D) pore geometries that are representative of natural porous media is challenging due to our limited ability to measure pore-scale velocity in such systems. Recent advances in magnetic resonance imaging (MRI) offer the opportunity to measure not only the pore geometry, but also local fluid velocities under steady-state flow conditions in 3D and with high spatial resolution. In this paper, we present a 3D velocity field measured at sub-pore resolution (tens of micrometers) over a centimeter-scale 3D domain using MRI methods. We have utilized the measured pore geometry to perform 3D simulations of Navier–Stokes flow over the same domain using direct numerical simulation techniques. We present a comparison of the numerical simulation results with the measured velocity field. It is shown that the numerical results match the observed velocity patterns well overall except for a variance and small systematic scaling which can be attributed to the known experimental uncertainty in the MRI measurements. The comparisons presented here provide strong validation of the pore-scale simulation methods and new insights for interpretation of uncertainty in MRI measurements of pore-scale velocity. This study also provides a potential benchmark for future comparison of other pore-scale simulation methods. © 2012 Elsevier Science. All rights reserved.     

Comparison of an algebraic multigrid algorithm to two iterative solvers used for modeling ground water flow and transport

Numerical solution of large-scale ground water flow and transport problems is often constrained by the convergence behavior of the iterative solvers used to solve the resulting systems of equations. We demonstrate the ability of an algebraic multigrid algorithm (AMG) to efficiently solve the large, sparse systems of equations that result from computational models of ground water flow and transport in large and complex domains. Unlike geometric multigrid methods, this algorithm is applicable to problems in complex flow geometries, such as those encountered in pore-scale modeling of two-phase flow and transport. We integrated AMG into MODFLOW 2000 to compare two- and three-dimensional flow simulations using AMG to simulations using PCG2, a preconditioned conjugate gradient solver that uses the modified incomplete Cholesky preconditioner and is included with MODFLOW 2000. CPU times required for convergence with AMG were up to 140 times faster than those for PCG2. The cost of this increased speed was up to a nine-fold increase in required random access memory (RAM) for the three-dimensional problems and up to a four-fold increase in required RAM for the two-dimensional problems. We also compared two-dimensional numerical simulations of steady-state transport using AMG and the generalized minimum residual method with an incomplete LU-decomposition preconditioner. For these transport simulations, AMG yielded increased speeds of up to 17 times with only a 20% increase in required RAM. The ability of AMG to solve flow and transport problems in large, complex flow systems and its ready availability make it an ideal solver for use in both field-scale and pore-scale modeling.     

Effects of compound-specific dilution on transient transport and solute breakthrough: A pore-scale analysis

This pore-scale modeling study in saturated porous media shows that compound-specific effects are important not only at steady-state and for the lateral displacement of solutes with different diffusivities but also for transient transport and solute breakthrough. We performed flow and transport simulations in two-dimensional pore-scale domains with different arrangement of the solid grains leading to distinct characteristics of flow variability and connectivity, representing mildly and highly heterogeneous porous media, respectively. The results obtained for a range of average velocities representative of groundwater flow (0.1–10 m/day), show significant effects of aqueous diffusion on solute breakthrough curves. However, the magnitude of such effects can be masked by the flux-averaging approach used to measure solute breakthrough and can hinder the correct interpretation of the true dilution of different solutes. We propose, as a metric of mixing, a transient flux-related dilution index that allows quantifying the evolution of solute dilution at a given position along the main flow direction. For the different solute transport scenarios we obtained dilution breakthrough curves that complement and add important information to traditional solute breakthrough curves. Such dilution breakthrough curves allow capturing the compound-specific mixing of the different solutes and provide useful insights on the interplay between advective and diffusive processes, mass transfer limitations, and incomplete mixing in the heterogeneous pore-scale domains. The quantification of dilution for conservative solutes is in good agreement with the outcomes of mixing-controlled reactive transport simulations, in which the mass and concentration breakthrough curves of the product of an instantaneous transformation of two initially segregated reactants were used as measures of reactive mixing.     

Modeling non-equilibrium mass transport in biologically reactive porous media

We develop a one-equation non-equilibrium model to describe the Darcy-scale transport of a solute undergoing biodegradation in porous media. Most of the mathematical models that describe the macroscale transport in such systems have been developed intuitively on the basis of simple conceptual schemes. There are two problems with such a heuristic analysis. First, it is unclear how much information these models are able to capture; that is, it is not clear what the model's domain of validity is. Second, there is no obvious connection between the macroscale effective parameters and the microscopic processes and parameters. As an alternative, a number of upscaling techniques have been developed to derive the appropriate macroscale equations that are used to describe mass transport and reactions in multiphase media. These approaches have been adapted to the problem of biodegradation in porous media with biofilms, but most of the work has focused on systems that are restricted to small concentration gradients at the microscale. This assumption, referred to as the local mass equilibrium approximation, generally has constraints that are overly restrictive. In this article, we devise a model that does not require the assumption of local mass equilibrium to be valid. In this approach, one instead requires only that, at sufficiently long times, anomalous behaviors of the third and higher spatial moments can be neglected; this, in turn, implies that the macroscopic model is well represented by a convection–dispersion–reaction type equation. This strategy is very much in the spirit of the developments for Taylor dispersion presented by Aris (1956). On the basis of our numerical results, we carefully describe the domain of validity of the model and show that the time-asymptotic constraint may be adhered to even for systems that are not at local mass equilibrium.     

Effective macroscopic transport parameters between parallel plates with constant concentration boundaries

A macroscopic transport model is developed, following the Taylor shear dispersion analysis procedure, for a 2D laminar shear flow between parallel plates possessing a constant specified concentration. This idealized geometry models flow with contaminant dissolution at pore-scale in a contaminant source zone and flow in a rock fracture with dissolving walls. We upscale a macroscopic transient transport model with effective transport coefficients of mean velocity, macroscopic dispersion, and first-order mass transfer rate. To validate the macroscopic model the mean concentration, covariance, and wall concentration gradient are compared to the results of numerical simulations of the advection–diffusion equation and the Graetz solution. Results indicate that in the presence of local-scale variations and constant concentration boundaries, the upscaled mean velocity and macrodispersion coefficient differ from those of the Taylor–Aris dispersion, and the mass transfer flux described by the first-order mass transfer model is larger than the diffusive mass flux from the constant wall. In addition, the upscaled first-order mass transfer coefficient in the macroscopic model depends only on the plate gap and diffusion coefficient. Therefore, the upscaled first-order mass transfer coefficient is independent of the mean velocity and travel distance, leading to a constant pore-scale Sherwood number of 12. By contrast, the effective Sherwood number determined by the diffusive mass flux is a function of the Peclet number for small Peclet number, and approaches a constant of 10.3 for large Peclet number.     

Simulating dispersion in porous media and the influence of segmentation on stagnancy in carbonates

Understanding the transport of chemical components in porous media is fundamentally important to many reservoir processes such as contaminant transport and reactive flows involved in CO₂ sequestration. Carbonate rocks in particular present difficulties for pore-scale simulations because they contain large amounts of sub-micron porosity. In this work, we introduce a new hybrid simulation model to calculate hydrodynamic dispersion in pore-scale images of real porous media and use this to elucidate the origins and behaviour of stagnant zones arising in transport simulations using micro-CT images of carbonates. For this purpose a stochastic particle model for simulating the transport of a solute is coupled to a Lattice-Boltzmann algorithm to calculate the flow field. The particle method incorporates second order spatial and temporal resolution to resolve finer features of the domain. We demonstrate how dispersion coefficients can be accurately obtained in capillaries, where corresponding analytical solutions are available, even when these are resolved to just a few lattice units. Then we compute molecular displacement distributions for pore-spaces of varying complexity: a pack of beads; a Bentheimer sandstone; and a Portland carbonate. Our calculated propagator distributions are compared directly with recent experimental PFG-NMR propagator distributions (Scheven et al., 2005; Mitchell et al., 2008), the latter excluding spin relaxation mechanisms. We observe that the calculated transport propagators can be quantitatively compared with the experimental distribution, provided that spin relaxations in the experiment are excluded, and good agreement is found for both the sandstone and the carbonate. However, due to the absence of explicit micro-porosity from the carbonate pore space image used for flow field simulations we note that there are fundamental differences in the physical origins of the stagnant zones for micro-porous rocks between simulation and experiment. We show that for a given micro-CT image of a carbonate, small variations in the parameters chosen for the segmentation process lead to different amounts of stagnancy which diffuse away at different rates. Finally, we use a filtering method to show that this is due to the presence of spurious isolated pores which arise from the segmentation process and suggest an approach to overcome this limitation.     

Efficient flow and transport simulations in reconstructed 3D pore geometries

Upscaling pore-scale processes into macroscopic quantities such as hydrodynamic dispersion is still not a straightforward matter for porous media with complex pore space geometries. Recently it has become possible to obtain very realistic 3D geometries for the pore system of real rocks using either numerical reconstruction or micro-CT measurements. In this work, we present a finite element–finite volume simulation method for modeling single-phase fluid flow and solute transport in experimentally obtained 3D pore geometries. Algebraic multigrid techniques and parallelization allow us to solve the Stokes and advection–diffusion equations on large meshes with several millions of elements. We apply this method in a proof-of-concept study of a digitized Fontainebleau sandstone sample. We use the calculated velocity to simulate pore-scale solute transport and diffusion. From this, we are able to calculate the a priori emergent macroscopic hydrodynamic dispersion coefficient of the porous medium for a given molecular diffusion D_m of the solute species. By performing this calculation at a range of flow rates, we can correctly predict all of the observed flow regimes from diffusion dominated to convection dominated.     

New equations for binary gas transport in porous media,: Part 1: equation development

A rigorous understanding of the mass and momentum conservation equations for gas transport in porous media is vital for many environmental and industrial applications. We utilize the method of volume averaging to derive Darcy-scale, closure-level coupled equations for mass and momentum conservation. The up-scaled expressions for both the gas-phase advective velocity and the mass transport contain novel terms which may be significant under flow regimes of environmental significance. New terms in the velocity expression arise from the inclusion of a slip boundary condition and closure-level coupling to the mass transport equation. A new term in the mass conservation equation, due to the closure-level coupling, may significantly affect advective transport. Order of magnitude estimates based on the closure equations indicate that one or more of these new terms will be significant in many cases of gas flow in porous media.     

Intercomparison of 3D pore-scale flow and solute transport simulation methods

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based on the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for confidence in a variety of pore-scale modeling methods and motivates further development and application of pore-scale simulation methods.     

Reactive transport in disordered media: Role of fluctuations in interpretation of laboratory experiments

We review the analysis of the dynamics of reactive transport in disordered media, emphasizing the nature of the chemical reactions and the role of small-scale fluctuations induced by the structure of the porous medium. We are motivated by results and interpretations of laboratory-scale experiments, for which detailed characterization of the system is possible. Modeling approaches based on continuum and particle tracking (PT) schemes are examined critically, highlighting how fluctuations are incorporated. The continuum approach spans a large literature. Traditional formats of reactive transport equations, such as the advection–dispersion–reaction equation (ADRE), are based on a series of assumptions related mainly to scale separation and relative magnitude of time scales involved in the reactive transport setting. These assumptions as well as further developments are assessed in depth. PT methods offer an alternative means of accounting for pore-scale dynamics, wherein space–time transitions are drawn from appropriate probability distributions that have been tested to account for anomalous transport. While PT methods have been employed for many years to describe conservative transport, their application to laboratory-scale reactive transport problems in the context of both Fickian and non-Fickian regimes is relatively recent. We concentrate on experimental observations of different types of reactions in disordered media: (1) the dynamics of a bimolecular reactive transport (A + B → C) in passive (non-reactive) media, and (2) a multi-step chemical reaction, as exemplified in the process of dedolomitization involving both dissolution and precipitation. The fluctuations in a number of the key variables controlling the processes prove to have a dominant role; elucidation of this role forms the basis of the present study and the comparison of methods.     

Micro-computed tomography pore-scale study of flow in porous media: Effect of voxel resolution

A fundamental understanding of flow in porous media at the pore-scale is necessary to be able to upscale average displacement processes from core to reservoir scale. The study of fluid flow in porous media at the pore-scale consists of two key procedures: Imaging - reconstruction of three-dimensional (3D) pore space images; and modelling such as with single and two-phase flow simulations with Lattice-Boltzmann (LB) or Pore-Network (PN) Modelling. Here we analyse pore-scale results to predict petrophysical properties such as porosity, single-phase permeability and multi-phase properties at different length scales. The fundamental issue is to understand the image resolution dependency of transport properties, in order to up-scale the flow physics from pore to core scale. In this work, we use a high resolution micro-computed tomography (micro-CT) scanner to image and reconstruct three dimensional pore-scale images of five sandstones (Bentheimer, Berea, Clashach, Doddington and Stainton) and five complex carbonates (Ketton, Estaillades, Middle Eastern sample 3, Middle Eastern sample 5 and Indiana Limestone 1) at four different voxel resolutions (4.4 µm, 6.2 µm, 8.3 µm and 10.2 µm), scanning the same physical field of view. Implementing three phase segmentation (macro-pore phase, intermediate phase and grain phase) on pore-scale images helps to understand the importance of connected macro-porosity in the fluid flow for the samples studied. We then compute the petrophysical properties for all the samples using PN and LB simulations in order to study the influence of voxel resolution on petrophysical properties. We then introduce a numerical coarsening scheme which is used to coarsen a high voxel resolution image (4.4 µm) to lower resolutions (6.2 µm, 8.3 µm and 10.2 µm) and study the impact of coarsening data on macroscopic and multi-phase properties. Numerical coarsening of high resolution data is found to be superior to using a lower resolution scan because it avoids the problem of partial volume effects and reduces the scaling effect by preserving the pore-space properties influencing the transport properties. This is evidently compared in this study by predicting several pore network properties such as number of pores and throats, average pore and throat radius and coordination number for both scan based analysis and numerical coarsened data.