BioF&T 2D/3D

Βιοαποδόμηση, Ροή και Μεταφορά σε Κορεσμένες και Μη-Κεκορεσμένες Ζώνες

BioF&T 3-D models flow and transport in the saturated and unsaturated zones in two or three dimensions in heterogeneous, anisotropic porous media or fractured media. BIOF&T allows real world modeling not available in similar packages. Model convection, dispersion, diffusion, adsorption, desorption, and microbial processes based on oxygen-limited, anaerobic, first-order, or Monod-type biodegradation kinetics as well as anaerobic or first-order sequential degradation involving multiple daughter species.


  • Transient 1-D or 2-D Cartesian (x,z) or 2-D Radial (r,z) water flow and multi-species dissolved phase transport solution in the unsaturated zone uncoupled with 2-D or 3-D flow and multicomponent aqueous phase transport in ground-water aquifers. This feature enables computationally-efficient simulations and gives due regard to the dimensionality of the problem, and is hydrogeologically defensible.
  • An option for fully coupled 3-D simulations of unsaturated and saturated zones for extremely complicated conditions.
  • Temporal and spatial variations in the source (i.e., residual dense or light nonaqueous phase liquids and/or other nonpoint contaminations) and, given the initial conditions, changes in loading to ground water are computed and updated internally.
  • Spatial variation in recharge/injection.
  • Model multiple pumping and/or injection wells, or trenches.
  • Simulation of heterogeneous and/or anisotropic porous media with (or without) fractures based on a dual porosity approach.
  • Rectangular 2-D/3-D prism or isoparametric quadrilateral/hexahedral elements to accurately model irregular domain and material boundaries, hydraulic, and physical boundaries.
  • Convection, dispersion, diffusion, adsorption, desorption, and microbial processes based on oxygen-limited, first-order, or Monod-type biodegradation kinetics, as well as anaerobic sequential degradation involving multiple daughter products. This allows real-world modeling not accomplished in similar biodegradation packages.
  • Computationally efficient matrix solution by conjugate gradient method with preconditioning.
  • BioF&T allows highly accurate representation of irregular site boundaries, uneven ground surface and complex subsurface geology with the three-dimensional mesh editor.



    Graphical user interface for Windows 3.x, Windows 95 and Windows NT


    For each species:

    BIOF&T Technical and Interface Information

    This document describes a three (two) dimensional finite element model BIOF&T-3-D (2-D) for flow of water and multicomponent aqueous phase transport in variably saturated porous media. BIOF&T has capabilities to model contaminated sites that have complex heterogeneous and/or anisotropic hydrogeology. BIOF&T models variably saturated fractured media or unfractured granular porous media based on a dual porosity approach.
    The flow and transport in the unsaturated zone is modeled either in 1-D vertical or in 2-D planar or radial symmetric vertical sections or in full 3-D. The flow and dissolved phase transport in the saturated zone are modeled as 2-D areal or a 3-D phenomenon. BIOF&T allows uncoupled solution of the unsaturated and the saturated zones. During the solution of the unsaturated zone, the time series of the spatially distributed contaminant effluent rate is computed and subsequently used to define loading to the groundwater. BIOF&T- 3-D has options for coupled three dimensional solutions of the unsaturated and saturated zones for complicated problems.
    Two-dimensional rectangular or isoparametric quadrilateral or 3-D rectangular prism or isoparametric hexahedral elements are permissible to accurately model irregular domain and material boundaries. BIOF&T incorporates convection, dispersion, diffusion, adsorption, desorption and biodegradation based on oxygen limited, anaerobic, first order, or monod type biodegradation kinetics as well sequential anaerobic or first order biodegradation involving multiple daughter products. Given the initial conditions, temporal and spatial variation in the source (i.e., nonaqueous phase liquid) is computed and updated internally by the model. Spatially variable recharge rates accounting for different hydrogeologic conditions can be specified.
    BIOF&T is accompanied by a pre-processor, a mesh editor and a post-processor. The pre-processor and mesh editor can be used to create an input data file for BIOF&T. They include tools for: mesh generation; allocating heterogeneous and anisotropic soil properties; defining fixed head, flux, source/sink boundary conditions for flow; and fixed concentration, mixed type, and injection/extraction boundary conditions for multicomponent transport; and allocating spatially variable recharge in the domain.
    Required input for flow analyses consist of initial conditions, soil hydraulic properties, time integration parameters, boundary conditions and mesh parameters. The van Genuchten constitutive model is used to define the moisture retention properties for the unsaturated zone. For transport analyses, additional input data are the porous media dispersivities, fraction of the porous media as mobile phase (needed only for fractured media analysis), species solubility, biodecay parameters, diffusion coefficient, distribution coefficient, mass transfer coefficients (needed only for fractured media analysis).
    The BIOF&T output file includes a list of the input parameters, initial and boundary conditions, and the mesh connectivity. It also includes pressure, water saturation, and velocity for each node and total volume of water versus time, recovery/injection rate for each sink/source location versus time. For transport simulations, the species concentration at each node, total mass of species in water and in the residual hydrocarbon phase are included at each printout interval. Flow and transport simulations can be performed in stages and BIOF&T creates an auxiliary file at the end of the simulated stage that can be used to define initial conditions for the next stage.

    BIOF&T 3-D Input Parameters
    Estimation of Soil Properties
    Soil properties needed for BIOF&T flow simulation are: saturated hydraulic conductivity Kij in principal flow directions, anisotropy angle of the main principal flow direction in the areal plane with the x-direction of the model domain, soil porosity , irreducible water saturation Sm, van Genuchten retention parameters and n. SOILPARA 1995 a proprietary computer model developed by DAEM provides an easy to use tool for estimating soil hydraulic parameters from soil texture based on: 1) the public domain model RETC developed by M. Th. van Genuchten, 2) the work of Shirazi and Boersma, 1984 and Campbell, 1985, and 3) a selection of USDA recommended typical parameter values for various texture classes available in the SOILPARA database that are included in the BIOF&T document .

    Physicochemical Properties
    Physicochemical properties of various NAPL species can be found in Handbooks like Lyman et al., 1982. A Table has been furnished in BIOF&T document giving properties for chemicals of concern commonly found in soil and groundwater.

    Creating Input Data Files
    The sequence of the input parameters and their definitions have been furnished in Appendix D of the BIOF&T document. Here is a brief description of the procedure for spatial discretization and mesh generation, defining initial conditions, and boundary conditions.

    Initial Conditions for Flow
    Initial head distribution in the domain can be specified by
    1) using bilinear interpolation with heads defined on the left and right boundary of each slice
    2) a nonuniform head distribution defining the head at each node in every slice

    Initial Conditions for Transport
    Initial aqueous phase concentrations for each species in the domain can be specified by
    1) defining a uniform aqueous species concentrations for every slice
    2) a nonuniform aqueous phase species concentrations at each node in every slice

    Boundary Conditions for Flow
    Specified pressure head (type-1) boundary conditions can be defined at selected nodes versus time. Type-2 (specified flux) and source/sink boundary conditions are defined by specifying the flow rate [L3 T-1] versus time for respective nodes. For a type-2 boundary condition when flux [L T-1] is known at a node, the user should multiply flux with the area represented by the node in a plane perpendicular to the flux.

    Boundary Conditions for Transport
    The procedure to define type-1 and type-3 boundary conditions for transport is similar to that for flow type-1 and type-2/source/sink boundary conditions. The default boundary condition for transport is type-2, which implies zero normal concentration gradient (i.e., zero dispersive flux). A type-1 boundary condition defines the time dependent variation in concentration at a specified node for each species. For a type-3 and a source/sink boundary condition, the user specifies the time dependent water injection (or withdrawal) rate [L3 T-1] and the concentration of the species in the injected fluid. BIOF&T internally computes the time dependent total mass injection (or withdrawal) rate [MT-1].

    Windows Interface
    BIOF&T comes with a Windows 3.X, Windows 95/NT 4.0 based pre-processor, post-processor and mesh editor. Following is a brief description of those interfaces.

    What is the BIOF&T Pre-processor?
    The BIOF&T pre-processor was designed to store data and create input data files for BIOF&T numerical model runs. The pre-processor works in concert with the Mesh Editor and with the Post-processor to make a complete graphical interface to the DAEM's Bio Flow and Transport code. After installing BIOF&T for Windows there will be four icons in the DAEM Windows Group: BIOF&T Model, BIOF&T Pre-processor, DAEM Mesh Editor, DAEM Post-processor. Each program has distinct functions, but all rely on one another for data input by the user.
    The BIOF&T Pre-processor allows for entry of Control Parameters (for example, whether or not transport will be solved for in the run), Initial Conditions (initial heads of water), Species Properties for up to five species, Boundary Schedules, and Material Properties for up to ten soils. Many values entered in the pre-processor are used in the DAEM Mesh Editor. Values like non-uniform water heads are defined in the pre-processor, then later assigned to nodes in the Mesh Editor. Material Properties, Boundary Conditions, and Recharge Zones are all assigned to nodes in the mesh editor.

    BIOF&T Control Parameters
    What is the Mesh Editor?
    The mesh editor was designed to work with DAEM's numerical models to create and edit finite element meshes. The mesh editor allows designing irregular quadrilateral meshes in two dimension and hexahedral meshes in three dimensions. Working with a numerical model pre-processor, the mesh editor provides a graphical interface for assigning properties to a mesh like initial concentrations of contaminants, soil properties, boundary conditions, etc.
    Moving Nodes
    Nodes can be moved by holding down the Ctrl key (control) and the left mouse button, then moving the cursor on the screen. Nodes move according to the dimension displayed on the screen, so that two dimensional meshes should be in the default X-Y view for node movement. Nodes can only be moved when the mesh editor is in its "editing" state.

    DXF Import
    Version 1.1 of the DAEM Mesh Editor introduced DXF import. This tool allows for .dxf files to be placed on a mesh. This way, site files in CAD programs can be exported to the mesh editor, then used to aid mesh refinement and adjustment.

    The DAEM post-processor is a data parsing tool, graphing package and contour export tool for DAEM numerical models. The post-processor is designed to be a user-friendly tool for quickly discerning model results. Users of these models can also review model text output files for a more detailed view of model results.

    Verification Problems
    There are twelve verification problems included in the BIOF&T user guide. Following are two of the verification problems that highlight biodegradation and 3-D application.

    Example: Oxygen limited biodegradation
    Bordent and Bedient, 1986 suggested that many biodegradation reactions between oxygen and hydrocarbon can be assumed instantaneous. This example shows the application of BIOF&T to model an instantaneous biodegradation reaction. The length of the domain is 500m and is discretized into 5m long for a total of 100 elements. The numerical simulation was performed for 11,000 days in 1100, 10 day time steps. The transport parameters, initial and boundary conditions are
    Initial concentration = 0.0
    Groundwater velocity = 0.015m/day
    Porosity = 0.26
    (Darcy velocity = 0.0039m/day)
    Longitudinal dispersivity = 9.1m
    (Borden and Bedient, 1986, minimized the effect of numerical dispersion by reducing the longitudinal dispersivity by a factor (dx-v dt) / 2. The BIOF&T simulation was performed with a longitudinal dispersivity of 7.9m).
    Transverse dispersivity = 1.8m
    Influent hydrocarbon concentration = 4.5mg/L
    Influent oxygen concentration = 3.0mg/L
    Ratio of oxygen to hydrocarbon consumed = 3.0
    The following figure shows a variation in the concentration of hydrocarbon and oxygen with distance at 11,000 days. There is reasonable agreement between BIOF&T results and the solution of Borden and Bedient, 1986, in most parts of the domain. There are some differences between the two solutions at the lower part of the plume, which may be due to different numerical dispersion in these models.

    Transport of a nonconservative solute with oxygen limited biodegradation
    Example: Three-dimensional transport in an unconfined aquifer from a disposal pit
    This example (Huyakorn et al., 1986) demonstrates the application of BIOF&T to simulate contaminant transport from a small disposal pit on the top of a shallow unconfined homogeneous aquifer (the following figure). Since the domain is symmetrical about the horizontal x-axis, only half of the domain was simulated. Domain was discretized with 11 horizontal slices. Uniform grid spacings of 6m, 3m, and 2m, in x, y, z directions, respectively were used (total nodes = 4961). The transport parameters, initial and boundary conditions are
    Initial concentration = 0
    Darcy velocity = 0.0161m/day
    Porosity = 0.35
    Longitudinal dispersivity = 4.0m
    Transverse dispersivity = 0.8m
    Contaminant mass flux = 140.8g/day
    Concentration at the upstream boundary = 0
    The simulation was started with an initial time step of 10 days and increased to 50 days with an incremental factor of 1.2. BIOF&T concentration distribution results are compared in the last two figures with results of Huyakorn et al., 1986. The BIOF&T solution is in good agreement with solution of Huyakorn et al., 1986.

    Contaminant transport from a surface disposal pit

    Concentration versus longitudinal distance (y = 0, z = 0) at 2000 days

    Concentration versus transverse distance (y = 0, z = 0) at 2000 days


    (1,500 nodes) Windows 3.x/Windows 95/Windows NT and 4 MB RAM. BioF&T 3-D requires Windows95/NT and 16 MB RAM.

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