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Hydrogeochem 1 & 2

Detailed Description

Hydrogeochem 1 & 2

Hydrogeochem 1 & 2





INTRODUCTION TO HYDROGEOCHEM

The purpose of HYDROGEOCHEM is to simulate transient and/or steady-state density-dependent flow fields and temperature distribution and to compute transient and/or steady-state distribution of reactive multispecies chemical concentrations in subsurface media.

HYDROGEOCHEM computes and predicts the distribution of pressure head, moisture content, flow velocity, and total head over a three-dimensional plane in either completely saturated, completely unsaturated, partially unsaturated, or partially saturated subsurface media. It also computes and predicts the spatial-temporal distribution of multi-chemical components. The media may consist of as many types of soils and geologic units as desired with different material properties. Each soil type may be isotropic or anisotropic. The processes governing the distribution of chemical distribution include (1) geochemical equilibrium of aqueous complexation, reduction-oxidation, sorption, and precipitation and dissolution, and (2) hydrological transport by flow advection, dispersion, and effect of unsaturation.

The generalized Richards' equation and Darcy's law governing pressure distribution and water flow in saturated-unsaturated media are simulated with the Galerkin finite-element method subject to appropriate initial and four types of boundary conditions. The hydrological transport equations (a set of PDEs) are derived based on the principle of conservation of mass, and the geochemical equilibrium equations (a set of AEs) are derived based on the mass balance and mass action. The coupled set of PDEs and AEs are simulated with either the conventional finite-element methods or the hybrid Langrangian-Eulerian finite-element method with peak capturing scheme subject to appropriate initial and four types of boundary conditions. Hexahedral elements, triangular prism, and tetrahedral elements are used to facilitate the discretization of the region of interest.

HYDROGEOCHEM is a coupled model of hydrologic transport and geochemical reaction in saturated-unsaturated media. It is designed to simulate transient and/or steady-state transport of Na, aqueous components and transient and/or steady-state mass balance of Ns adsorbent components and ion-exchange sites. Along the transport path, HYDROGEOCHEM computes the species distribution of N component species, Mx complexed species, My adsorbed species. Mz ion-exchanged species, and Mp potentially precipitated species. The physical, hydrological and chemical settings are as follows.

  • Media: Heterogeneous and Anisotropic.
  • Flow Conditions: Saturated-Unsaturated Flows.
  • Hydrologic Processes: Advection, Dispersion and Diffusion.
  • Chemical Processes: Aqueous Complexation, Adsorption/Desorption (Surface Complexation, Constant Capacitance, and Double Layer Approaches), Ion-Exchange, Precipitation/Dissolution, Redox, and Acid-Base Reactions.
  • Source/Sink: Spatially- and Temporally-Dependent Element and Point Sources/Sinks.
  • Initial Conditions: Prescribed Initial Condition or the Simulated Steady-State Solution as the Initial Condition.
  • Boundary Conditions: Prescribed Total Analytical Concentrations on Dirichlet Boundaries, Prescribed Fluxes on Flow-In Boundaries, Natural Advective Fluxes on Flow-Out Boundaries - All Boundary Values (Concentrations or Fluxes) are Spatially- and Temporally-Dependent.
  • Numerical Discretization: Finite-Element Methods with Quadrilateral Elements, Triangular Elements, or the Mixtures of These Two Types.
  • Approximation Options: Consistent Matrix or Mass Lumping, Nodal Quadrature or Gaussian Quadrature for Surface and Element Integrations.
  • Solvers: Direct Band Matrix Solver, Basic Point Iterations, and 4 PCG Methods (polynomial PCG, Incomplete Cholesky PCG, Modified Incomplete Cholesky PCG, and Symmetric Successive Over-Relaxation PCG).
  • Time Stepping: Implicit Difference, Crank-Nicholson Central Difference, or Mid-Difference.
  • Solution Methods for Geochemical Reactions: Newton-Raphson with Full Pivoting to Solve the Jacobian Matrix Equation and Constraints on Species Concentrations.

HYDROGEOCHEM is the only commercially-available model for the simulation of reactive multispecies-multicomponent chemical transport through saturated-unsaturated media. It is not a path model; it is a true transport model coupled with homogeneous and heterogeneous geochemical reactions.


HYDROGEOCHEM SPECIAL FEATURES

The special features of HYDROGEOCHEM are its flexibility and versatility in modeling as wide a range of problems as possible. The model is designed to (1) treat heterogeneous and anisotropic media, (2) consider spatially and temporally-distributed as well as point sources/sinks, (3) accept the prescribed initial conditions or obtain initial conditions by simulating the steady-state version of the system under consideration, (4) deal with prescribed transient concentrations distributed over a Dirichlet boundary, (5) handle time-dependent fluxes over variable boundaries, (6) deal with time-dependent total fluxes over Cauchy boundaries, (7) include the off-diagonal dispersion coefficient tensor components in the governing equation for dealing with cases when the coordinate system does not coincide with the principal directions of the dispersion coefficient tensor, (8) provide two options for treating the mass matrix - consistent and lumping, (9) give three options (exact relaxation, under- and over-relaxation) for estimating the nonlinear matrix, (10) include two options (direct solution with Gaussian elimination method and successive point iterations) for solving the linearized matrix equations, (11) include both quadrilateral and triangular elements to facilitate the discretization of the region, (12) automatically reset time step size when boundary conditions or sources/sinks change abruptly, and (13) include simultaneous chemical processes of aqueous complexation, precipitation/dissolution, adsorption, ion exchange, redox, and acid-base reactions.

HYDROGEOCHEM INPUT

(1) Geometry in terms of nodes and elements, and boundaries in terms of nodes and segments; (2) soil properties including (a) saturated hydraulic conductivities or permeabilities; (b) compressibility of water and the media, respectively; (c) bulk density; (d) three soil characteristic curves for each type of soil or geologic unit which are the retention curve, relative conductivity vs head curve, and water capacity curve; (e) effect porosity; and (f) dispersivities, and effective molecular diffusion coefficient for each soil type or geologic unit; (3) initial distribution of pressure head over the region of interest; (4) net precipitation, allowed ponding depth, potential evaporation, and allowed minimum pressure head in the soil; (5) prescribed head on Dirichlet boundaries; (6) prescribed fluxes on Cauchy and/or Neumann boundaries; (7) artificial withdrawals or injections of water; (8) number of chemical components as well as chemical species and their thermodynamic data base; (9) artificial sources/sinks of water and all chemical components; (10) prescribed total concentrations of all chemical components on Dirichlet boundaries; (11) prescribed fluxes of all chemical components on variable boundaries; and (12) initial distribution of all chemical component concentrations. All inputs in items 4 through 11 can be time-dependent or constant with time.

HYDROGEOCHEM OUTPUT

(1) pressure head, total head, moisture content, and flow velocity over the two-dimensional grid at any desired time; (2) water fluxes through all types of boundaries and amount of water accumulated in the media at any desired time; (3) distribution of total analytical concentrations, total dissolved concentrations, total sorbed concentrations, total precipitated concentrations, and free ion concentrations of all chemical components over a three-dimensional grid at any desired time; (4) amount of waste fluxes through the variable boundary; and (5) equivalent kds as a function of time and space in the region of interest.

HYDROGEOCHEM Requirements: Pentium with 16 MB RAM and FORTRAN Compiler, any Workstation, e.g., IBM RS6000, DEC Alpha, Silicon Graphics, Sun SparcStation, and HP 9000 Series.


HYDROGEOCHEM Equations (pdf file)

Requires the Adobe Acrobat Reader to view pdf file.

HYDROGEOCHEM 2 INTRODUCTION

HYDROGEOCHEM 2 is a modification of HYDROGEOCHEM 1.0 (Yeh et al., 1991), a general purpose computer program written in FORTRAN 77 which was designed to solve coupled hydrologic transport and geochemical equilibrium problems. The modification includes replacement of the EQMOD chemical equilibrium subroutines by a mixed chemical Kinetic and Equilibrium model (KEMOD) to deal with species whose concentrations are controlled by either thermodynamics or kinetics.

HYDROGEOCHEM 2 is a coupled model of hydrologic transport and geochemical reaction in saturated-unsaturated media. HYDROGEOCHEM 2 comprises two basic modules: the transport module and the geochemical reaction module. The transport module is designed to simulate: (1) transient and/or steady-state transport of Ns aqueous components, (2) transient and/or steady-state mass balance of Ns adsorbent components and NSITE ion-exchange sites. The geochemical reaction module is designed to compute the species distribution of N = (Na+ Ns) component species, Mx-Kx equilibrium-controlled complexed species, (My Ky) equilibrium-controlled adsorbed species, Ky kinetic-controlled adsorbed species, (Mz Kz) equilibrium-controlled ion-exchanged species, Kz kinetic-controlled ion exchanged species, (Mp Kp) equilibrium-controlled potentially-precipitated species, and Kp kinetic-controlled precipitated species. The two modules are solved iteratively with three options: (1) a complete iteration, (2) an operator splitting, and (3) a predictor-corrector method. The transport module includes advection, dispersion/diffusion, and slight deformation. In the geochemical reaction module, nine types of reactions are included to generate the aforementioned eight types of product species.


HYDROGEOCHEM 2 REACTIONS

  • Basic equilibrium complexation reaction: reactants are any number of aqueous components, and the product is an equilibrium-controlled complexed species.
  • Basic kinetic complexation reaction: reactants are any number of aqueous components, and the product is a kinetic-controlled complexed species.
  • Basic equilibrium adsorption/desorption reaction: reactants are any number of aqueous and adsorbed components, and the product is an equilibrium-controlled adsorbed species.
  • Basic kinetic adsorption/desorption reaction: reactants are any number of aqueous and adsorbed components, and the product is a kinetic-controlled adsorbed species.
  • Basic equilibrium ion-exchange reaction: reactants are one of the aqueous and complexed species and of the ion-exchanges species, and the products are one of the equilibrium-controlled ion-exchanges species and one of the aqueous and complexed species.
  • Basic kinetic ion-exchange reaction: reactants are one of the aqueous and complexed species and one of the ion-exchanges species, and the products are one of the kinetic-controlled ion-exchanged species and one of the aqueous and complexed species.
  • Basic equilibrium precipitation/dissolution reaction: reactants are aqueous components, and the product is an equilibrium-controlled precipitated species.
  • Basic kinetic precipitation/dissolution reaction: reactants are aqueous components, and the product is a kinetic-controlled precipitated species.
  • Parallel kinetic reaction: reactants, and the products can involve all species.

HYDROGEOCHEM 2 is designed for generic application to reactive transport problems controlled by both kinetic and equilibrium reactions in subsurface media. Input to the program includes the geometry of the system, the spatial distribution of finite elements and nodes, the properties of the media, the potential chemical reactions, and the initial and boundary conditions. Output includes the spatial distribution of chemical concentrations as a function of time and space and the chemical speciation at user-specified nodes.

The program must be run with a consistent set of units. Units of mass (M), length (L), and time (T) are indicated in the input description. The unit of length should be decimeter (dm), and the unit of mass for any chemical species should be mole. The density of water and solid should be expressed in kg/dm3 (liter). The ion-exchange capacity is in equivalents/Mass of solid. The corresponding concentration unit of all species (aqueous, sorbed, and precipitated species) is mole/liter of fluid (Molar); the corresponding unit for the sorption distribution coefficient is dm3/kg (= ml/g). Any units of time may be used as long as the same unit is used throughout the input file.


HYDROGEOCHEM 2 APPLICATIONS

  • Treat heterogeneous and anisotropic media.
  • Consider spatially- and temporally-distributed sources/sinks as well as point sources/sinks.
  • Accept the prescribed initial conditions or obtain initial conditions by simulating the steady-state version of the system under consideration.
  • Deal with prescribed transient concentrations distributed over a Dirichlet boundary.
  • Handle time-dependent fluxes over variable boundaries.
  • Include the off-diagonal dispersion coefficient tensor components in the governing equation for dealing with cases in which the coordinate system does not coincide with the principal directions of the dispersion coefficient tensor.
  • Provide two options for treating the mass matrix (consistent and lumping).
  • Give three options for estimating the nonlinear matrix (exact relaxation, under-relaxation, and over-relaxation).
  • Include six options for solving the linearized matrix equations (direct solution with the Gaussian elimination method, successive point iterations, and four preconditioned conjugate gradient methods).
  • Include both quadrilateral and triangular elements to facilitate the discretization of the region.
  • Automatically reset the time-step size when boundary conditions or sources/sinks change abruptly.
  • Include chemical processes of aqueous complexation, precipitation/dissolution, adsorption, ion-exchange, redox, and acid-base reactions.
  • Handle multiple adsorption sites and multiple ion-exchange sites.
  • Include colloid transport.


HYDROGEOCHEM 2 LIMITATIONS

  • Inability to simulate co-precipitation (solid solution).
  • Inability to simulate microbiological reactions which may transform pollutants in the subsurface environment.
  • The need to import hydrologic variables of flow velocity, moisture content, and pressure head generated by a subsurface flow model.
  • The assumption of isothermal conditions.
  • Applications limited to two-dimensional problems.
  • Applications limited to single-fluid phase flows.

HYDROGEOCHEM 2 is the only commercially-available model for the simulation of reactive multispecies-multicomponent chemical transport controlled by both kinetic and equilibrium reactions.


HYDROGEOCHEM 2 Requirements: Pentium with 16 MB RAM and Fortran compiler, any Workstation, e.g., IBM RS6000, DEC Alpha, Silicon Graphics, Sun SparcStation, and HP 9000 Series.

HYDROGEOCHEM 2 Manual - Part 1 (pdf file)

HYDROGEOCHEM 2 Manual - Part 2 (pdf file)

Requires the Adobe Acrobat Reader to view pdf file.

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