Introduction
BIOF&T 3D 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 oxygenlimited, anaerobic, firstorder, or Monodtype biodegradation kinetics as well as anaerobic or firstorder sequential degradation involving multiple daughter species.
BIOF&T 3D FEATURES

Transient 1D or 2D Cartesian (x,z) or 2D Radial (r,z) water flow and multispecies dissolved phase transport solution in the unsaturated zone uncoupled with 2D or 3D flow and multicomponent aqueous phase transport in groundwater aquifers. This feature enables computationallyefficient simulations and gives due regard to the dimensionally of the problem and is hydrogeological defensible.

An option for fullycoupled 3D 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 2D/3D 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 oxygenlimited, firstorder, or Monodtype biodegradation kinetics, as well as anaerobic sequential degradation involving multiple daughter products. This allows realworld modeling not accomplished in similar biodegradation packages.

Computationallyefficient matrix solution by conjugate gradient method with preconditioning.

BIOF&T allows highlyaccurate representation of irregular site boundaries, uneven ground surface and complex subsurface geology with the threedimensional Mesh Editor.
BIOF&T 3D INPUT

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
BIOF&T 3D OUTPUT
Flow

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
Transport
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 TECHNICAL INFORMATION
BIOF&T (2D/3D) is a three (two) dimensional finite element model for flow of water and multicomponent aqueous phase transport in variablysaturated porous media. BIOF&T has capabilities to model contaminated sites that have complex heterogeneous and/or anisotropic hydrogeology. BIOF&T models variablysaturated 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 1D vertical or in 2D planar or radial symmetric vertical sections or in full 3D. The flow and dissolved phase transport in the saturated zone are modeled as 2D areal or a 3D 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 spatiallydistributed contaminant effluent rate is computed and subsequently used to define loading to the groundwater. BIOF&T 3D has options for coupled threedimensional solutions of the unsaturated and saturated zones for complicated problems.
Twodimensional rectangular or isoparametric quadrilateral or 3D 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, firstorder, or Monodtype biodegradation kinetics as well as sequential anaerobic or firstorder 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. Spatiallyvariable recharge rates accounting for different hydrogeologic conditions can be specified.
BIOF&T is accompanied by a Preprocessor, a Mesh Editor and a Postprocessor. The Preprocessor 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 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)
BIOF&T 3D 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 xdirection of the model domain, soil porosity, irreducible water saturation Sm, van Genuchten retention parameters and n. SOILPARA, 1995, a proprietary computer model provides an easytouse 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 USDArecommended 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 (type1) boundary conditions can be defined at selected nodes versus time. Type2 (specified flux) and source/sink boundary conditions are defined by specifying the flow rate [L3 T1] versus time for respective nodes. For a type2 boundary condition when flux [L T1] 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 type1 and type3 boundary conditions for transport is similar to that for flow type1 and type2/source/sink boundary conditions. The default boundary condition for transport is type2, which implies zero normal concentration gradient (i.e., zero dispersive flux). A type1 boundary condition defines the time dependent variation in concentration at a specified node for each species. For a type3 and a source/sink boundary condition, the user specifies the time dependent water injection (or withdrawal) rate [L3 T1] and the concentration of the species in the injected fluid. BIOF&T internally computes the time dependent total mass injection (or withdrawal) rate [MT1].
BIOF&T 3D WINDOWS INTERFACE
BIOF&T comes with a Windows 3.x/95/NT 4.0based Preprocessor, Postprocessor and Mesh Editor. Following is a brief description of these.
What is the BIOF&T Preprocessor?
The BIOF&T Preprocessor was designed to store data and create input data files for BIOF&T numerical model runs. The Preprocessor works in concert with the Mesh Editor and with the Postprocessor 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 Preprocessor, Mesh Editor, and Postprocessor. Each program has distinct functions, but all rely on one another for data input by the user.
The BIOF&T Preprocessor 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 Preprocessor are used in the Mesh Editor. Values like nonuniform water heads are defined in the Preprocessor, 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 Preprocessor
