BIOMOD 3-D

Bioremediation, Fate and Transport for MODFLOW


BIOMOD 3-D (Bioremediation Fate and Transport Simulator) is a 2-D/3-D finite-element fate and multicomponent transport model that is linked to the USGS finite-difference MODFLOW 3-D model. BIOMOD has the following key features:
  • Simulate fractured media or granular porous media.
  • Convection, dispersion, diffusion, adsorption, desorption, and microbial processes based on oxygen-limited, first-order, Monod, anaerobic biodegradation kinetics as well as anaerobic or first-order sequential degradation involving multiple daughter products are simulated. This allows real-world modeling not accomplished in other fate and transport packages.
  • Results of transient/steady state MODFLOW simulations are used to obtain velocity distribution for use in BIOMOD.
  • Temporal and spatial variations in the source (i.e., residual dense or light nonaqueous phase liquids and/or other nonpoint contaminations) is allowed, and, given the initial conditions, changes in loading to ground water are computed and updated internally.
  • Restart capabilities for multistage simulations.
  • Computationally-efficient matrix solution by conjugate gradient method with preconditioning.
  • Simulation of heterogeneous and/or anisotropic porous media (includes cross derivative terms in dispersive tensor), 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/layers and material boundaries, hydraulic and physical boundaries.
  • Modeling transport in subdomain(s) within a large regional MODFLOW domain is allowed for accurate results and computational efficiency.

    OUTPUT (For each species)


    BIOMOD Technical and Interface Information

    This document describes a three-dimensional finite element model BIOMOD for multicomponent aqueous phase transport in porous media. BIOMOD 3-D (Bioremediation, Fate and transport simulator) is a 2-D/3-D finite element multicomponent transport model that is linked to the USGS model MODFLOW. BIOMOD simulates convection, dispersion, diffusion, adsorption, desorption, and microbial processes based on oxygen limited, first order, Monod, anaerobic biodegradation kinetics, as well as anaerobic or first order sequential degradation involving multiple daughter products. It uses results of transient/steady state MODFLOW simulations to obtain velocity distributions for use in BIOMOD. The model allows temporal and spatial variations in the source (i.e., residual DNAPL/LNAPL or other nonpoint contaminations), and, given the initial conditions, computes and updates changes in loading to groundwater internally. It also models spatial variation in contaminant injection and/or extraction.
    BIOMOD simulates heterogeneous and/or anisotropic porous media (includes cross derivative terms in dispersive tensor), with (or without) fractures. It allows rectangular 2-D/3-D prism or isoparametric quadrilateral/hexahedral elements to accurately model irregular domain/layers and material boundaries. BIOMOD can also model transport in sub-domain(s) within a large regional MODFLOW domain for accurate results and computational efficiency. It has restart capabilities for multistage simulations. BIOMOD has capabilities to model contaminated sites that have complex heterogeneous and/or anisotropic hydrogeology. BIOMOD models granular porous media or fractured media based on a dual porosity approach. BIOMOD is accompanied by a MODFLOW to BIOMOD data converter, a velocity calculation module, 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 BIOMOD. They include tools for: mesh generation; allocating heterogeneous soil properties; assigning prescribed concentration, and mixed type injection/extraction boundary conditions for multicomponent transport; and allocating spatially variable recharge in the domain. The pre-processor also contains a model runner for all DOS executables.
    The BIOMOD output file includes a list of the input parameters, initial and boundary conditions, and the mesh connectivity. It also includes the species (organic/inorganic) concentration at each node, total mass of species in water and in the residual hydrocarbon phase (if present) are included at each printout interval. Simulations can be performed in stages and BIOMOD creates an auxiliary file at the end of the simulated stage that can be used to define initial conditions for the next stage.

    BIOMOD Input Parameters
    Estimation of Soil Properties
    Soil properties needed for a BIOMOD simulation are: soil porosity , irreducible water saturation Sm = r s, bulk density, and the distribution coefficient (Kd = Koc foc). 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. These tables have been included in the BIOMOD document.

    Physicochemical Properties
    Physicochemical properties of various NAPL species can be found in Handbooks like Lyman et al., 1982. A Table has been included in the document that gives properties for chemicals of concern commonly found in soil and groundwater.

    Creating Input Data Files
    Initial Conditions
    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
    The procedure to define type-1 (prescribed concentration) and type-3 (prescribed injection/extraction rates) boundary conditions for transport is similar. 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. BIOMOD internally computes the time dependent total mass injection (or withdrawal) rate [MT-1].

    Windows Interface
    BIOMOD 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 BIOMOD Pre-processor?
    The BIOMOD pre-processor was designed to store data and create input data files for BIOMOD numerical model runs, and coordinate data translation through two DOS executable codes: mod2bio.exe and mod_vel.exe. 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 Biological Fate and Transport code for MODFLOW. Each program has distinct functions, but all rely on one another for data input by the user.

    BIOMOD Control Parameters

    The BIOMOD Pre-processor allows for entry of Control Parameters (for example, whether or not areal recharge is variable or uniform), 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 material properties are defined in the pre-processor, then later assigned to nodes in the Mesh Editor.

    Using the BIOMOD pre-processor

    Creating a new mesh for BIOF&T 3D with the Mesh Expert

    The BIOMOD 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 sub-sections 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 3 boundary condition schedules.
    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 and 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.

    Post-processor
    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 nine verification problems included in the BIOMOD 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 BIOMOD 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 BIOMOD 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

    Transport of a non-conservative solute with oxygen limited biodegradation

    The following figure shows a variation in the concentration of hydrocarbon and oxygen with distance at 11,000 days. There is reasonable agreement between BIOMOD 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.
    Example: Three-dimensional transport in an unconfined aquifer from a disposal pit
    This example (Huyakorn et al., 1986) demonstrates the application of BIOMOD to simulate contaminant transport from a small disposal pit on the top of a shallow unconfined homogeneous aquifer (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
    Contaminant transport from a surface disposal pit

    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. BIOMOD concentration distribution results are compared in the last two figures with results of Huyakorn et al., 1986. The BIOMOD solution is in good agreement with solution of Huyakorn et al., 1986.

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

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

    Requirements

    (1,500 nodes) Any version of MODFLOW which includes the BCF2 Pkg, 486 or higher with 16 MB RAM, and Windows 95/NT for pre/postprocessing.

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