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Detailed Description




BIOF&T 3-D models biodegradation, 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 multispecies dissolved phase transport solution in the unsaturated zone uncoupled with 2-D or 3-D flow and multi-component aqueous phase transport in ground-water aquifers. This feature enables computationally-efficient simulations and gives due regard to the dimensionally of the problem and is hydrogeological 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 non point contamination) 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.


  • Mesh discretization data
  • Initial conditions for flow: water
  • Boundary conditions for flow: specified head boundaries, flux boundaries, and sources and sinks
  • Soil hydraulic properties: van Genuchten parameters, hydraulic conductivity distribution and porosity
  • Initial conditions for transport: species concentration
  • Boundary conditions for transport: specified concentration boundary, specified mass flux, and spatial distribution of contaminant loading
  • Dispersivities
  • Mass transfer rate coefficient between oil and water phase
  • Distribution coefficient
  • Bulk density
  • Diffusion coefficient for species
  • Biodegradation parameters for each species
  • Fraction of the mobile phase



  • Spatial distribution of water pressure with time
  • Spatial distribution of water saturation with time
  • Velocity distribution with time
  • Pumping/injection rates and volume vs. time


For each species:

  • Spatial distribution of concentration with time
  • Mass dissolved in water vs. time
  • Mass remaining in NAPL phase vs. time
  • Mass adsorbed on the solid phase vs. time


BIOF&T (2-D/3-D) is a three (two) dimensional finite element model for flow of water and multi-component 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 as 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 multi-component transport; and allocating spatially variable recharge in the domain.

Required input for flow analyses consists 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.

Equations (.pdf file)


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 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 the 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 concentration for every slice

(2) a nonuniform aqueous phase species concentration 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].


BIOF&T comes with a Windows 3.x/95/NT 4.0-based Pre-processor, Post-processor and Mesh Editor. Following is a brief description of these.

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 BIOF&T Flow and Transport code. After installing BIOF&T for Windows, there will be four icons in the Windows Group: BIOF&T Model, BIOF&T Pre-processor, Mesh Editor, and 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 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.

Using the BIOF&T Pre-processor


BIOF&T Control Parameters

The BIOF&T Pre-processor runs under Windows 3.X, Windows 95 and Windows NT. The Pre-processor uses a familiar tabbed notebook interface to allow quick editing of input files. The main program has two sets of tabs: one along the bottom which separates major sections of the interface, and, on some of the large notebook pages, tabs along the top that separate subsections to make the most use of available screen space. For example, clicking on the bottom tab "Boundary Schedules" takes the user to the boundary schedule notebook. Here there is a tabbed notebook for editing type 1 and type 2 boundary condition schedules.

Opening and Saving Projects

A BIOF&T project file is similar to a multi-table database. Data for the Pre-processor is stored in ASCII text files, as is data for the Mesh Editor and Post-processor. When a new project is created and saved to file, the Pre-processor prompts the user for a project name (a .bfp file extension is the default type). The Pre-processor will then create sub-data files for species data and materials data.

What is the Mesh Editor?

The Mesh Editor was designed to work with these numerical models to create and edit finite element meshes. The Mesh Editor allows designing irregular quadrilateral meshes in two dimensions 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.

Speed Buttons



Panning allows the mesh to be moved in the Mesh Editor window. This puts the Mesh Editor into its "pan" state. You can then hold down the left mouse button and move the mesh on the screen. Letting go of the left mouse button "drops" the mesh in place. Nodes cannot be selected individually in this state.



The rotate button is the leftmost red button on the tool bar. It puts the Mesh Editor into a "rotate" state, where the mouse can be used to rotate the mesh in three dimensions. The mouse will rotate the mesh on the XYZ axis intersection. Rotating the Mesh Editor takes a little getting used to, but if you ever get lost, the handy X-Y, Y-Z, and Z-X buttons will snap the mesh back into place.



The rightmost red button called Node Control puts the Mesh Editor in its "editing" state. Now a node or group of nodes can be selected to have values assigned to them or to be moved in the X, Y and/or Z direction. To edit associations (i.e., soil type, recharge zones, type-1 boundary conditions, etc.) for a node, select the node, then right click the mouse. This will bring up a list of available associations. Clicking on an association will bring up a secondary list of associations that can be assigned to the node.

Moving Nodes

Nodes can be moved by holding down the Ctrl key (control) and the left mouse button and 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 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 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.


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. 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. The 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 the 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

BIOF&T Requirements: (1,500 nodes) Windows 95/98/2000/NT and 8 MB RAM. BIOF&T 3-D requires Windows95/98/2000/NT and 16 MB RAM.

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