United States
Environmental Protection
Agency
Robert S. Kerr Environmental
Research Laboratory
Ada OK 74820
Research and Development
EPA/600/S8-88/093 Feb. 1989
AEPA Project Summary
BIOPLUME II - Computer
Model of Two-Dimensional
Contaminant Transport
Under the Influence of Oxygen
Limited Biodegradation in
Ground Water (User's Manual -
Version 1.0; Preprocessor
Source Code Version 1.0;
Source Code Version 1.0)
Hanadi S. Rifai, Philip B. Bedient, Robert C. Bordon, and John F. Haasbeek
This manual presents a two-
dimensional computer model,
BIOPLUME II,that simulates the
transport of dissolved hydrocarbons
under the influence of oxygen-
limited biodegradation. BIOPLUME II
also simulates reaeration and
anaerobic biodegradation as a first
order decay in hydrocarbon con-
centrations.
The model is based on the USGS
solute transport two-dimensional
code (Konikow and Bredehoeft,
1978). The model computes the
changes in concentration over time
due to convection, dispersion,
mixing, and biodegradation. The
same numerical techniques that are
used in the USGS code are
maintained in BIOPLUME II.
BIOPLUME II solves the solute
transport equation twice: once for
hydrocarbon and once for oxygen.
As a result, two plumes are
computed at every time step. The
model assumes an instantaneous
reaction between oxygen and
hydrocarbon to simulate biode-
gradation processes. The two plumes
are combined using the principle of
superposition.
The model is extremely versatile in
that it can be used to simulate
natural biodegradation processes,
retarded plumes, and in-s/tu
biorestoration schemes. BIOPLUME II
allows injection wells to be specified
as oxygen sources into a
contaminated aquifer. This means
that alternate methods for aquifer
reclamation can be investigated to
design the most economically
feasible scheme.
The model provides three
additional sources of oxygen into an
aquifer initial dissolved oxygen In
the uncontaminated aquifer, natural
recharge of oxygen across the
boundaries, and vertical exchange of
oxygen from the unsaturated zone
(reaeration). All three sources of
oxygen can be used to simulate a
-------
contaminant plume that is being
naturally biodegraded.
BIOPLUME II runs on an IBM PC/AT
or compatible system. A menu-
driven preprocessor was developed
to assist the user in applying the
model. The preprocessor provides
three options: data input or data edit,
performing a simulation run, and
developing graphical output. A
graphics software program, SURFER,
from Golden Software, Inc. (1987),
was selected to provide the user with
contour and surface plots of
hydrocarbon and oxygen concen-
trations and water table elevations.
This Project Summary was devel-
oped by EPA's Robert S. Kerr
Environ-mental Research Laboratory,
Ada, OK, to announce key findings of
the research project that is fully
documented in a separate report of
the same title (see Project Report
ordering information at back).
Introduction
This manual describes a computer
model for simulating transport of
hydrocarbons (HC) in ground water
under the influence of oxygen (Oa)
limited biodegradation. The model core
is based on the USGS 2-D solute
transport model (Konikow and
Bredehoeft, 1978). Although this manual
is self-contained and will allow the user
to run BIOPLUME II easily, it is
recommended that the user be familiar
with the USGS code beforehand. A
user-friendly menu-driven preproces-
sor has been built in the code. The
preprocessor provides the user with
three options: (1) data input/editing; (2)
simulation run performance; and (3)
graphical representation of output. The
model is designed to run on an IBM
PC/AT or compatible system.
The purpose of the simulation model is
to compute the concentration of a
dissolved hydrocarbon that is undergoing
biodegradation in an aquifer. Changes in
chemical concentration occur primarily
due to four distinct processes: (1)
convective transport, in which dissolved
chemicals are moving with the flowing
ground water; (2) hydrodynamic dis-
persion, in which molecular and ionic
diffusion and small scale variations in the
velocity of flow through the porous media
cause spreading of the contaminant front;
(3) fluid sources or sinks, such as
pumping or injecting wells, and; (4)
reactions, in which the concentration of
the contaminant may increase or de-
crease due to chemical and physical
reactions within the ground water or
between the water and the solid aquifer
material.
The standard 2-D USGS code
assumes that no reactions occur which
affect the concentration of the species of
interest. BIOPLUME II, on the other hand,
assumes an instantaneous reaction
between HC and Oa- The instantaneous
reaction decreases the concentration of
HC by an amount that is proportional to
the available ©2 in the aquifer (it is
assumed that 3 mass units of 02 are
required to completely biodegrade 1
mass unit of HC).
BIOPLUME II solves the solute
transport equation twice, once for HC
and once for 02- This allows the
simultaneous simulation of two plumes;
an HC plume and an 02 plume. The two
plumes are combined using super-
position at every particle move to
simulate the reaction between HC and
02.
BIOPLUME II is extremely versatile: it
allows the simulation of a retarded HC
plume undergoing biodegradation and it
provides the user with the capability to
simulate in-situ biorestoration schemes
such as the injection of oxygenated
water. Moreover, the model simulates
anaerobic biodegradation and reaeration
as a first order decay in HC concen-
trations.
System Requirements
To run BIOPLUME II, you need the
following:
1. IBM PC/AT or compatible
2. DOS version 2.0 (or later)
3. 640K of machine resident memory
(RAM)1
4. 80287 math co-processor chip
5. Harddisk2
Note. Specific mention of equation, page or section
numbers herein refer to the final reports which
are available from the National Technical
Information Service, as described on the last
page of this Project Summary
1 A minimum of 605K of RAM is necessary to load
the model with the menu preprocessor To check
available RAM, type the command CHKDSK If
there is less memory available, the model
(DRIVER EXE) may still be loaded without the
menu preprocessor Please contact Rice University
if you have any questions.
2 It is possible to run the model using a high-
density floppy drive if a hard disk is not available
in your system
3 The VIEW program and the VIEW option in TOPO
and SURF both require a graphics card (adapter)
However, if your system does not have a graphics
card, SURFER may still be used to generate
graphics on a graphics printer or plotter (Golden
Software, Inc, 1987)
Optional hardware includes:
6. Graphics adapter (CGA, EG/
Hercules)3
7. SURFER supported graphics prinl
plotter (see Appendix D of SUF
manual)
System Setup
In order to run the programs,
following command must be includ
the file CONFIG.SYS on your sy
disk:
DEVICE = ANSI.SYS
Note that the file ANSI.SYS, includec
the DOS package, must reside ii
same directory as CONFIG.
Otherwise a pathname must be inc
in the file. Please refer to your
reference manual for details on
command.
Overview of the Model
Description of the Program
The purpose of this section
describe the overall structure o
program and to present a de
description of the model's capabi
This section is not intended to di
the numerical methods and techr
used to solve the flow and trar
equations since these method;
discussed in detail in the USGS n
(Konikow and Bredehoeft, 197
should be noted, however, that
numerical limitations of the USGS
apply to BIOPLUME II and the
needs to be aware of these limit;
The user also needs to be aware
limitations of the method of ch
teristics for solving the tran
equation.
The major steps in the calci
procedure are summarized in Fig
which presents a simplified flow cl
the overall structure of the con
program. The flow chart illustrate
two independent sets of particle
tracer particles and HC tracer pa
are generated. Since the tracer pi
may have to be moved more thar
to complete a given time step ai
reaction between 02 and HC is as;
instantaneous, the 02 and HC
particles are moved independent)
their subsequent concentrations ai
computed independently. The re:
two plumes (HC and ©2) are cor
after every particle move time s
simulate the reaction between C
HC. In this version of the mode
-------
Read I
Input /
DataJ
Generate Uniform
Distribution of Tracer
Panicles for
Contaminant and Oxygen
Determine Length of Time
Increment for Explicit
Calculations
->
Compute Hydraulic
Gradients lor One Time
Step
Compute Ground Water
Velocities and Dispersion
Equation Coefficients
Move Contaminant
Particles
Generate or Remove
Particles at
Appropriate Boundaries
Compute Contaminant
Concentration in Cells
and at Nodes
Move Oxygen
Particles
Generate or Remove
Panicles at
Appropriate Boundaries
Compute Oxygen
Concentration in Cells
and at Nodes
Compute Mass Balance
Compute Mass Balance
Superpose Contaminant
and Oxygen Panicles
Figure 1. Simplified Flowchart of BIOPLUMEII.
assumed that three mass units of oxygen
are required to completely mineralize
one mass unit of hydrocarbon (parameter
F, equations 7 and 8, section 1.2.2).
More work is necessary before this
parameter can be defined on a
compound by compound basis.
This technique, although it probably
requires more computational time, is
extremely beneficial due mainly to the
following reasons:
1. It provides the capability to simulate
retarded HC plumes undergoing
biodegradation.
2. It allows the simulation of in-situ
biorestoration since one can model
the injection of oxygenated water.
3. It maintains the modular structure of
the program which makes future
updates relatively simple.
For the case of retarded HC plumes
undergoing biodegradation, the model
automatically computes the maximum
time increments allowable for the explicit
calculations for the retarded HC plume
and for the non-retarded 02 plume. The
model then uses the smaller of the two
time steps for the explicit solution of the
solute transport equation (i.e., the larger
number of particle moves is used to
complete the given time step).
The flow chart also illustrates that
hydraulic gradients are computed once
for the aquifer in question. The flowrates
specified for pumping or injection wells
are used in the computation. However, if
one specifies an injection well, then that
well can be used to simulate a
contaminant source, an oxygen source,
or both, by specifying the concentration
of HC and/or Oa in the injected water.
Mass balance computations are
performed for both 02 and HC
independently at the end of every particle
move. The mass balance computations
-------
are then adjusted to account for the
mass loss due to biodegradation after the
two plumes have been superimposed.
The amount of mass loss due to
biodegrada-tion is printed as part of the
chemical mass balance output. This is
extremely useful since one can correlate
the simulated mass loss with the
observed mass loss from field data. The
mass balance computations for C>2 are
necessary to ensure the accuracy of the
numerical technique when one is
simulating an 02 injection scheme
In addition to aerobic biodegradation,
the model provides two other sources for
biodegradation: anaerobic decay and
reaeration. Both are simulated as a first
order decay in HC concentrations, and
the only input requirement is the
coefficient of decay. The decay terms
are applied at the nodes and not at the
particles. This provides more numerical
stability in case the coefficient of decay
is much smaller than the move time step.
The chemical balance output also
provides the user with the amount of
mass loss due to reaeration and
anaerobic decay.
It should be mentioned that the model
can be used to simulate plumes without
biodegradation terms. The user would
have to set all the oxygen sources in the
model to 2ero. The output for the oxygen
plume is not suppressed. Instead, a null
plume for oxygen is printed.
Use of the Preprocessor
A user-friendly menu-driven pre-
processor has been written for
BIOPLUME II. This Preprocessor allows
a user to create and/or edit data files, run
the BIOPLUME II program and prepare
graphics files. The preprocessor can be
executed by typing the command:
This command will cause a title screen to
be displayed on the terminal. When the
enter or carriage return key is pressed, a
second title screen will appear. Pressing
the enter key again will cause the mam
menu to be displayed:
1. Edit/Create an Input Data File
2. Run BIOPLUME II
3. Prepare Graphics Files
4. QUIT
To choose an option, simply type the
number of the option and press the enter
or return key (indicated by < ENTER >
or ). Each of the options of the
main menu are discussed in more detail
in the following sections.
Throughout the remainder of this
manual, messages which the computer
displays on the screen will be indicated
in boldface type, such as that used
above in the main menu. Commands or
responses entered by the user will be
indicated in smaller type such as the
command
Responses to the program may be made
in either upper or lower case. The
program will recognize an
N
and an
n
as the same response. You may stop at
any point in the program simply by
pressing CTRL C (hold down the CTRL
key and press C at the same time). The
following message will appear on the
screen:
Press the < ENTER > key to con-
tinue...
Pressing the < ENTER > key will return
you to the main menu.
Option 1: Edit/Create an Input
Data File
Option 1 of the main menu allows one
to either edit an existing data file or
create a new data file. The editing
program is structured to allow editing of
an entire data file or any portion of a data
file. When option 1 is selected, a
message will appear on the screen which
indicates the version of the editing.
Pressing the return key will cause the
next item in the data file to appear on the
screen. For instance, if you have just
entered a new title card, the next item for
editing would be the variables on Card 1
Entering an
M
and pressing the return key will return
the editing menu to the screen.
Option 2: Run BIOPLUME II
Option 2 allows a user to run the
BIOPLUME II model from the mam
menu. When this option is selected, the
program will prompt:
Enter name of input file-
Type in the name of an input file. 1
can be a file which was created using
Edit/Create option or by some ot
means. If the file does not exist,
program will display a message tel
you that the file does not exist and ref
the prompt for the input file nai
(Remember that CTRL C will return
to the main menu.) If the file does e:
the program will prompt:
Enter name of output file...
If this file name already exists,
program will ask if you wish to rep
the existing file. If a negative respons
received, the prompt for the output
name is repeated.
Once the proper input and output
names have been entered, BIOPLUtv
is run using the data from the input
Output is written to the output file.
program does take a few minutes to
so please be patient.
If an error occurs, you can disc
where it occurred by looking at the 01
data file. The DOS editor EDLIN or
other text editor may be used to exai
the output file. (See your DOS manu<
more information on EDLIN.) Find
point at which the program stoppei
any input variable which was not
properly. Check the input data fil
make sure that it contains the pr
data. If you cannot locate the sour<
the error, call the phone number list
the front of the manual or send ir
preaddressed card at the back witl
problem described in as much det<
possible.
Option 3: Prepare Graphics
Files
Option 3 is used to convert the c
from BIOPLUME II into files which c;
plotted using SURFER (Golden Soft
1987). The format for SURFER coi
of three columns of data. This data
form X, Y, Z and could be used wit
other plotting package which use;
format.
BIOPLUME II automatically v
output data to three files n;
HEADS.BIO, HPLUME.BIO
OPLUME.BIO. The file HEDŁ
contains the array of computed
values at the end of each time
HPLUME.BIO and OPLUME.BIO c
the HC and Oa plumes, respectively
The first line of the file HPLUMI
contains the variables NTIM, NPMI
NY, NPNT, and NPNTMV. This I
read before converting any of th<
from the files HEADS.BIO, HPLUM
and OPLUME.BIO into the graphic;
-------
format. It informs the program how often
he chemical and hydraulic output was
requested by the user. In other words, it
tells the program just how many plumes
can be converted for use with SURFER.
The files with the HC and 02 plumes
also contain a line of data before each
plume. This line contains the pumping
period number, time step number, and
number of moves completed. This allows
the program to determine which plume is
being requested for conversion. It also
allows you to convert and plot several
plumes from the same output data.
Option 4: QUIT
Selecting Option 4 will stop the
program and return you to DOS.
Summary
BIOPLUME II simulates hydrocarbon
transport under the influence of oxygen
limited biodegradation. A dual particle
mover concept is used to compute an
oxygen plume and a hydrocarbon plume.
An instantaneous reaction between the
solute (hydrocarbon) and the substrate
(oxygen) is assumed and the method of
superposition is utilized to represent the
reaction between the two. An
independent mass balance is performed
for oxygen and hydrocarbon and is
adjusted to account for the mass loss
due to biodegradation.
The model can be used to simulate
naturally occurring biodegradation
processes and to simulate in-situ
restoration processes. Injection wells can
be used as oxygen sources in the model.
Three other sources of oxygen are
included in BIOPLUME II: (1) dissolved
oxygen in the aquifer; (2) natural
recharge, and; (3) oxygen exchange from
the unsaturated zone.
The biodegraded mass in the model is
most sensitive to hydraulic conductivity,
the coefficient of reaeration, and the
coefficient of anaerobic decay. The
model has been applied to two sites: a
wood creosoting process waste site in
Conroe, Texas (Borden et al., 1986) and
a jet fuel spill site in Traverse City,
Michigan. The model application to the
Traverse City site is in press. The model
provided a good match to field conditions
at both sites. BIOPLUME II is presently
being used to design an in-situ
bioreclamation field experiment at the
Traverse City field site. Results from the
experiment will also be published in the
literature.
-------
Hanadi S. Rifai, Philip B. Bedient, and John F. Haasbeek are with Rice University,
Houston, TX; Robert C. Bordon is with North Carolina State University, Raleigh,
NC 27695-7908.
John T. Wilson., is the EPA Project Officer (see below).
The complete report consists of paper copy and software, entitled, "BIOPLUMEII
- Computer Model of Two-Dimensional Contaminant Transport Under the
Influence of Oxygen Limited Biodegradation in Ground Water (User's Manual -
Version 1.0; Preprocessor Source Code Version 1.0; Source Code Version
1.0),"
Paper Copy (Order No. PB 89-151 120/AS; Cost: $28.95)
Software (Order No. PB 89-151 1121 AS; Cost: $350.00, cost of software
includes paper copy)
The above items will be available only from: (costsubject to change)
National Technical Information Service
5285 Port Royal Road
Springfield, VA 22161
Telephone: 703-487-4650
The EPA Project Officer can be contacted at:
Robert S. Kerr Environmental Research Laboratory
U.S. Environmental Protection Agency
Ada, OK 74820
United States
Environmental Protection
Agency
Center for Environmental Research
Information
Cincinnati OH 45268
BULK RATE
POSTAGE & FEES PAID
EPA
PERMIT No. G-35
Official Business
Penalty for Private Use $300
EPA/600/S8-88/093
000Q32? PS
60604
------- |