Effects of chemical reactions on density-dependent fluid flow: on the numerical formulation and the development of instabilities

A three-dimensional, reactive numerical flow model is developed that couples chemical reactions with density-dependent mass transport and fluid flow. The model includes equilibrium reactions for the aqueous species, kinetic reactions between the solid and aqueous phases, and full coupling of porosity and permeability changes that result from precipitation and dissolution reactions in porous media. A one-step, global implicit approach is used to solve the coupled flow, transport and reaction equations with a fully implicit upstream-weighted control volume discretization. The Newton–Raphson method is applied to the discretized non-linear equations and a block ILU-preconditioned CGSTAB method is used to solve the resulting Jacobian matrix equations. This approach permits the solution of the complete set of governing equations for both concentration and pressure simultaneously affected by chemical and physical processes. A series of chemical transport simulations are conducted to investigate coupled processes of reactive chemical transport and density-dependent flow and their subsequent impact on the development of preferential flow paths in porous media. The coupled effects of the processes driving flow and the chemical reactions occurring during solute transport is studied using a carbonate system in fully saturated porous media. Results demonstrate that instability development is sensitive to the initial perturbation caused by density differences between the solute plume and the ambient groundwater. If the initial perturbation is large, then it acts as a “trigger” in the flow system that causes instabilities to develop in a planar reaction front. When permeability changes occur due to dissolution reactions occurring in the porous media, a reactive feedback loop is created by calcite dissolution and the mixed convective transport of the system. Although the feedback loop does not have a significant impact on plume shape, complex concentration distributions develop as a result of the instabilities generated in the flow system.     

Computational methods for reactive transport modeling: An extended law of mass-action,xLMA, method for multiphase equilibrium calculations

We present an extended law of mass-action (xLMA) method for multiphase equilibrium calculations and apply it in the context of reactive transport modeling. This extended LMA formulation differs from its conventional counterpart in that (i) it is directly derived from the Gibbs energy minimization (GEM) problem (i.e., the fundamental problem that describes the state of equilibrium of a chemical system under constant temperature and pressure); and (ii) it extends the conventional mass-action equations with Lagrange multipliers from the Gibbs energy minimization problem, which can be interpreted as stability indices of the chemical species. Accounting for these multipliers enables the method to determine all stable phases without presuming their types (e.g., aqueous, gaseous) or their presence in the equilibrium state. Therefore, the here proposed xLMA method inherits traits of Gibbs energy minimization algorithms that allow it to naturally detect the phases present in equilibrium, which can be single-component phases (e.g., pure solids or liquids) or non-ideal multi-component phases (e.g., aqueous, melts, gaseous, solid solutions, adsorption, or ion exchange). Moreover, our xLMA method requires no technique that tentatively adds or removes reactions based on phase stability indices (e.g., saturation indices for minerals), since the extended mass-action equations are valid even when their corresponding reactions involve unstable species. We successfully apply the proposed method to a reactive transport modeling problem in which we use PHREEQC and GEMS as alternative backends for the calculation of thermodynamic properties such as equilibrium constants of reactions, standard chemical potentials of species, and activity coefficients. Our tests show that our algorithm is efficient and robust for demanding applications, such as reactive transport modeling, where it converges within 1–3 iterations in most cases. The proposed xLMA method is implemented in Reaktoro, a unified open-source framework for modeling chemically reactive systems.     

An efficient numerical model for multicomponent compressible flow in fractured porous media

An efficient and accurate numerical model for multicomponent compressible single-phase flow in fractured media is presented. The discrete-fracture approach is used to model the fractures where the fracture entities are described explicitly in the computational domain. We use the concept of cross flow equilibrium in the fractures. This will allow large matrix elements in the neighborhood of the fractures and considerable speed up of the algorithm. We use an implicit finite volume (FV) scheme to solve the species mass balance equation in the fractures. This step avoids the use of Courant–Freidricks–Levy (CFL) condition and contributes to significant speed up of the code. The hybrid mixed finite element method (MFE) is used to solve for the velocity in both the matrix and the fractures coupled with the discontinuous Galerkin (DG) method to solve the species transport equations in the matrix. Four numerical examples are presented to demonstrate the robustness and efficiency of the proposed model. We show that the combination of the fracture cross-flow equilibrium and the implicit composition calculation in the fractures increase the computational speed 20–130 times in 2D. In 3D, one may expect even a higher computational efficiency.     

Coupling water flow and solute transport into a physically-based surface-subsurface hydrological model

A distributed-parameter physically-based solute transport model using a novel approach to describe surface-subsurface interactions is coupled to an existing flow model. In the integrated model the same surface routing and mass transport equations are used for both hillslope and channel processes, but with different parametrizations for these two cases. For the subsurface an advanced time-splitting procedure is used to solve the advection-dispersion equation for transport and a standard finite element scheme is used to solve Richards equation for flow. The surface-subsurface interactions are resolved using a mass balance-based surface boundary condition switching algorithm that partitions water and solute into actual fluxes across the land surface and changes in water and mass storage. The time stepping strategy allows the different time scales that characterize surface and subsurface water and solute dynamics to be efficiently and accurately captured. The model features and performance are demonstrated in a series of numerical experiments of hillslope drainage and runoff generation.     

Transport in chemically and mechanically heterogeneous porous media. I: Theoretical development of region-averaged equations for slightly compressible single-phase flow

Transport processes in heterogeneous porous media are often treated in terms of one-equation models. Such treatment assumes that the velocity, pressure, temperature, and concentration can be represented in terms of a single large-scale averaged quantity in regions having significantly different mechanical, thermal, and chemical properties. In this paper we explore the process of single-phase flow in a two-region model of heterogeneous porous media. The region-averaged equations are developed for the case of a slightly compressible flow which is an accurate representation for a certain class of liquid-phase flows. The analysis leads to a pair of transport equations for the region averaged pressures that are coupled through a classic exchange term, in addition to being coupled by a diffusive cross effect. The domain of validity of the theory has been identified in terms of a series of length and timescale constraints.In Part II the theory is tested, in the absence of adjustable parameters, by comparison with numerical experiments for transient, slightly compressible flow in both stratified and nodular models of heterogeneous porous media. Good agreement between theory and experiment is obtained for nodular and stratified systems, and effective transport coefficients for a wide range of conditions are presented on the basis of solutions of the three closure problems that appear in the theory. Part III of this paper deals with the principle of large-scale mechanical equilibrium and the region-averaged form of Darcy's law. This form is necessary for the development and solution of the region-averaged solute transport equations that are presented in Part IV. Finally, in Part V we present results for the dispersion tensors and the exchange coefficient associated with the two-region model of solute transport with adsorption.     

Flux-Corrected Transport with MT3DMS for Positive Solution of Transport with Full-Tensor Dispersion

Solute transport is usually modeled by the advection-dispersion-reaction equation. In the standard approach, mechanical dispersion is a tensor with principal directions parallel and perpendicular to the flow vector. Since realistic scenarios include nonuniform and unsteady flow fields, the governing equation has full tensor mechanical dispersion. When conventional grid-based numerical methods are used, approximation of the cross terms arising from the off-diagonal terms cause nonphysical solution with oscillations. As an example, for the common scenario of contaminant input into a domain with zero initial concentration, the cross-dispersion terms can result in negative concentrations that can wreak havoc in reactive transport applications. To address this issue, we use the well-known flux-corrected-transport (FCT) technique for a standard finite volume method. Although FCT has most often been used to eliminate oscillations resulting from discretization of the advection term for explicit time stepping, we show that it can be adapted for full-tensor dispersion and implicit time stepping. Unlike other approaches based on new discretization techniques (e.g., mimetic finite difference, nonlinear finite volume), FCT has the advantage of being flexible and widely applicable. Implementation of FCT requires solving an additional system of equations at each time step, using a modified “low order” matrix and a modified right-hand-side vector. To demonstrate the flexibility of FCT, we have modified the well-known and widely used groundwater solute transport simulator, MT3DMS. We apply the new simulator, MT3DMS-FCT, to several benchmark problems that suffer from negative concentrations when using MT3DMS. The new results are mass conservative and strictly nonnegative.     

Multilayer shallow water flow using lattice Boltzmann method with high performance computing

A multilayer lattice Boltzmann (LB) model is introduced to solve three-dimensional wind-driven shallow water flow problems. The multilayer LB model avoids the expensive Navier–Stokes equations and obtains stratified horizontal flow velocities as vertical velocities are relatively small and the flow is still within the shallow water regime. A single relaxation time BGK method is used to solve each layer coupled by the vertical viscosity forcing term. To increase solution stability, an implicit step is suggested to obtain flow velocities. The main advantage of using the LBM is that after selecting appropriate equilibrium distribution functions, the LB algorithm is only slightly modified for each layer and retains all the simplicities of the LBM within the high performance computing (HPC) environment. The performance of the parallel LB model for the multilayer shallow water equations is investigated on CPU-based HPC environments using OpenMP. We found that the explicit loop control with cache optimization in LBM gives better performance on execution time, speedup and efficiency than the implicit loop control as the number of processors increases. Numerical examples are presented to verify the multilayer LB model against analytical solutions. We demonstrate the model’s capability of calculating lateral and vertical distributions of velocities for wind-driven circulation over non-uniform bathymetry.     

A split operator approach to reactive transport with the forward particle tracking Eulerian Lagrangian localized adjoint method

A forward particle tracking Eulerian Lagrangian localized adjoint method (ELLAM) is applied to the multicomponent reactive transport problem using a split operator approach. Two split operator algorithms are compared, the Strang algorithm and the sequential non-iterative algorithm (SNIA). The reaction equations are integrated using a coupled predictor corrector algorithm with adaptive time stepping. Reaction time steps are adjusted at the inflow boundary to reflect the actual time of transport inside the solution domain.Results show that split operator ELLAM formulations are competitive with direct or fully coupled ELLAM solutions for reactive transport problems. The SNIA algorithm is more accurate than the Strang splitting algorithm when large time steps are used. The reaction algorithm employed dominates computational effort in runs with large time step sizes. To illustrate the use of the method in practical problems, the model is fitted to aerobic aniline degradation data from laboratory scale column experiments. Model inversion is achieved using non-linear regression with a shuffled complex evolution optimization algorithm and parameter uncertainty is assessed using a Bayesian uncertainty analysis procedure.     

Eulerian-Lagrangian formulation of the equations for groundwater denitrification using bacterial activity

A mathematical model for groundwater denitrification using bacterial activity is presented. The model includes the momentum and mass balance equations for water and nitrogen, substrate and bacteria, and chemical reactions between them. The resulting multiphase, multicomponent, flow and transport governing equations, are coupled and nonlinear. A Eulerian-Lagrangian formulation of the equations is developed. The water and gas flow and transport equations are split into forward advection along characteristics, and a residual at a fixed frame of reference. Discontinuities, sharp fronts and steep gradients of the dependent variables are imposed on the advection mode and solved exactly. It is believed that this novel method will avoid numerical artifacts for the solution of the multiphase flow equations (e.g., upstream permeability) and numerical dispersion for the transport equation.     

Proper orthogonal decomposition reduced model for mass transport in heterogenous media

Numerical models with fine discretization normally demand large computational time and space, which lead to computational burden for state estimations or model parameter inversion calculation. This article presented a reduced implicit finite difference scheme that based on proper orthogonal decomposition (POD) for two-dimensional transient mass transport in heterogeneous media. The reduction of the original full model was achieved by projecting the high-dimension full model to a low-dimension space created by POD bases, and the bases are derived from the snapshots generated from the model solutions of the forward simulations. The POD bases were extracted from the ensemble of snapshots by singular value decomposition. The dimension of the Jacobian matrix was then reduced after Galerkin projection. Thus, the reduced model can accurately reproduce and predict the original model’s transport process with significantly decreased computational time. This scheme is practicable with easy implementation of the partial differential equations. The POD method is illustrated and validated through synthetic cases with various heterogeneous permeability field scenarios. The accuracy and efficiency of the reduced model are determined by the optimal selection of the snapshots and POD bases.     

基于耦合反射/透射系数单程波传播算子的地震波模拟研究

单程波近似实际上是一种多次前向散射和单次后向散射近似.利用单程波近似来描述波传播可以极大地节省地震数值模拟的计算时间和内存,实现地震波长距离传播模拟和三维地震模拟快速计算.本文基于单程波近似和波动积分方程的分离变量逼近,从广义Lippmann-Schwinger波动积分方程推导出耦合反射/透射系数的单程波传播算子.该算子由两部分构成：分离变量Fourier单程波传播算子和薄板间的反射/透射系数表达.前者将常规的Fourier分裂步单程波传播算子(SSF)推广适应横向强速度变化介质和大角度传播波场.后者是利用垂直波数来表示反射/透射系数,自然耦合到波场传播的计算过程中,其为地质界面倾角的隐式表达,精确描述振幅随入射角的变化,能适应任意复杂的模型.通过两个数值算例和一个实际地质模型的计算,本文将该方法和边界元法进行了比较,结果表明：在算例给出的介质横向速度变化情况下,本文提出的方法在相位和振幅方面与全波数值方法基本吻合.     

Algorithms for staggered-grid computations for poroelastic,elastic, acoustic,and scalar wave equations

Heterogeneous wave equations are more complicated numerically than homogeneous wave equations, but are necessary for physical validity. A wide variety of numerical solutions of seismic wave equations is available, but most produce strong numerical artefacts and local instabilities where model parameters change rapidly. Accuracy and stability of heterogeneous equations is achieved through staggered-grid formulations. A new pseudospectral staggered-grid algorithm is developed for the poroelastic (Biot) equations. The algorithm may be reduced to handle the elastic and acoustic limits of the Biot equations. Comparisons of results from poroelastic, elastic, acoustic and scalar computations for a 2D model show that porous medium parameters may affect amplitudes significantly. The use of homogeneous wave equations for modelling of a heterogeneous medium, or of a centred rather than a staggered grid, or of simplified (e.g. acoustic) wave equations when elastic or poroelastic media are synthesized, may produce erroneous or ambiguous interpretations.     

Numerical modelling of alternate bar formation,development and sediment sorting in straight channels

A two‐dimensional shallow water hydro‐sediment‐morphodynamic model is applied to investigate alternate bar formation, development and sediment sorting in straight channels. The model is coupled, explicitly incorporating the flow–sediment–bed interactions by using the full mass and momentum conservation equations, which are numerically solved by a well‐balanced version of the finite volume Slope Limiter Centred (SLIC) scheme. The model is first tested against a flume experiment on alternate bars formed over a uniform sediment bed, which clearly exhibits processes of bar formation, migrating and finally approaching an equilibrium state. Then it is applied to another flume experiment on alternate bars due to non‐uniform sediment transport. The computational results are evaluated, with a focus on the longitudinal and vertical sediment sorting. It is argued for the first time that the inconsistent sediment sorting patterns observed in previous studies are determined by different sediment transport conditions, i.e. full versus partial transport. When a condition of full transport is achieved, under which all size fractions are fully mobilized and transported, the longitudinal surface sediment shows a sorting pattern of coarse‐on‐head and fine‐in‐pool, and the vertical substrate sediment exhibits an immobile‐fine‐coarse structure upwards. In contrast, for a partial transport condition, under which only finer fraction participates in the transport process, an opposite longitudinal pattern (i.e. fine‐on‐head and coarse‐in‐pool) and a different vertical structure (i.e. immobile‐coarse‐fine) are observed. Concurrently, numerical experiments with specified conditions show that the critical aspect ratio for the formation of migrating alternate bars is approximately equal to 12. With the increase of the aspect ratio, the bar length grows gradually, while the bar height increases rapidly for moderate values of the aspect ratio and then keeps nearly stable. The bar celerity, however, is weakly sensitive to the variation of this ratio. Copyright © 2016 John Wiley & Sons, Ltd.     

Numerical calculation for bed variation in compound-meandering channel using depth integrated model without assumption of shallow water flow

In a compound meandering channel, patterns of flow structures and bed variations change with increasing water depth owing to complex momentum exchange between high-velocity flow in a main channel and low-velocity flows in flood plains. We have developed a new quasi-three-dimensional model without the shallow water assumption, i.e., hydrostatic pressure distribution; our method is known as the general bottom velocity computation (BVC) method. In this method, a set of depth-integrated equations, including depth-integrated momentum and vorticity equations, are prepared for evaluating bottom velocity and vertical velocity distributions. The objective of this study is to develop a bed variation calculation method for both single and compound meandering channels by using the BVC method coupled with a sediment transport model. This paper shows that the BVC method can reproduce the pattern change of bed variation in a compound meandering channel flow with increasing relative depth. The variation in sediment transport rate due to overbank flow is explained by experimental and computational results.     

SEAWAT‐Based Simulation of Axisymmetric Heat Transport

Simulation of heat transport has its applications in geothermal exploitation of aquifers and the analysis of temperature dependent chemical reactions. Under homogeneous conditions and in the absence of a regional hydraulic gradient, groundwater flow and heat transport from or to a well exhibit radial symmetry, and governing equations are reduced by one dimension (1D) which increases computational efficiency importantly. Solute transport codes can simulate heat transport and input parameters may be modified such that the Cartesian geometry can handle radial flow. In this article, SEAWAT is evaluated as simulator for heat transport under radial flow conditions. The 1971, 1D analytical solution of Gelhar and Collins is used to compare axisymmetric transport with retardation (i.e., as a result of thermal equilibrium between fluid and solid) and a large diffusion (conduction). It is shown that an axisymmetric simulation compares well with a fully three dimensional (3D) simulation of an aquifer thermal energy storage systems. The influence of grid discretization, solver parameters, and advection solution is illustrated. Because of the high diffusion to simulate conduction, convergence criterion for heat transport must be set much smaller (10^?10) than for solute transport (10^?6). Grid discretization should be considered carefully, in particular the subdivision of the screen interval. On the other hand, different methods to calculate the pumping or injection rate distribution over different nodes of a multilayer well lead to small differences only.     

A parallel,fully coupled,fully implicit solution to reactive transport in porous media using the preconditioned Jacobian-Free Newton-Krylov Method

Modeling large multicomponent reactive transport systems in porous media is particularly challenging when the governing partial differential algebraic equations (PDAEs) are highly nonlinear and tightly coupled due to complex nonlinear reactions and strong solution-media interactions. Here we present a preconditioned Jacobian-Free Newton-Krylov (JFNK) solution approach to solve the governing PDAEs in a fully coupled and fully implicit manner. A well-known advantage of the JFNK method is that it does not require explicitly computing and storing the Jacobian matrix during Newton nonlinear iterations. Our approach further enhances the JFNK method by utilizing physics-based, block preconditioning and a multigrid algorithm for efficient inversion of the preconditioner. This preconditioning strategy accounts for self- and optionally, cross-coupling between primary variables using diagonal and off-diagonal blocks of an approximate Jacobian, respectively. Numerical results are presented demonstrating the efficiency and massive scalability of the solution strategy for reactive transport problems involving strong solution-mineral interactions and fast kinetics. We found that the physics-based, block preconditioner significantly decreases the number of linear iterations, directly reducing computational cost; and the strongly scalable algebraic multigrid algorithm for approximate inversion of the preconditioner leads to excellent parallel scaling performance.     

Finite-difference solution of the transport equation: First results

The ray-theoretical transport equation for inhomogeneous isotropic media (2D-SH case) is solved by the method of finite differences on a rectangular grid, both for an incident plane wave (explicit scheme) and a line source (implicit scheme). Results for homogeneous models and for heterogeneous models with structural discontinuities are discussed. First-arrival travel times calculated by various techniques serve as input for the solution of the transport equation and the computation of amplitudes of first arrivals. To obtain correct amplitudes the travel times must be highly accurate and the discontinuities must be smoothed out; the reason is that the spatial second derivatives of the travel time field enter the transport equation. In the simple cases studied, finite differences provide a fast and efficient tool for the computation of first-arrival amplitudes.     

Modelling dam-break flows over mobile beds using a 2D coupled approach

Dam-break flows usually propagate along rivers and floodplains, where the processes of fluid flow, sediment transport and bed evolution are closely linked. However, the majority of existing two-dimensional (2D) models used to simulate dam-break flows are only applicable to fixed beds. Details are given in this paper of the development of a 2D morphodynamic model for predicting dam-break flows over mobile beds. In this model, the common 2D shallow water equations are modified, so that the effects of sediment concentrations and bed evolution on the flood wave propagation can be considered. These equations are used together with the non-equilibrium transport equations for graded sediments and the equation of bed evolution. The governing equations are solved using a matrix method, thus the hydrodynamic, sediment transport and morphological processes can be jointly solved. The model employs an unstructured finite volume algorithm, with an approximate Riemann solver, based on the Roe-MUSCL scheme. A predictor–corrector scheme is used in time stepping, leading to a second-order accurate solution in both time and space. In addition, the model considers the adjustment process of bed material composition during the morphological evolution process. The model was first verified against results from existing numerical models and laboratory experiments. It was then used to simulate dam-break flows over a fixed bed and a mobile bed to examine the differences in the predicted flood wave speed and depth. The effects of bed material size distributions on the flood flow and bed evolution were also investigated. The results indicate that there is a great difference between the dam-break flow predictions made over a fixed bed and a mobile bed. At the initial stage of a dam-break flow, the rate of bed evolution could be comparable to that of water depth change. Therefore, it is often necessary to employ the turbid water governing equations using a coupled approach for simulating dam-break flows.