United States Robert S. Kerr
Environmental Protection Environmental Research Laboratory
Agency Ada, OK 74820
EPA/600/8-90/039
Feb. 1990
Research and Development
OASIS: Parameter
Estimation System for
Aquifer Restoration
Models
User's Manual Version 2.0
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EPA/600/8-90/039
February 1990
OASIS: PARAMETER ESTIMATION SYSTEM
FOR AQUIFER RESTORATION MODELS
User's Manual Version 2.0
by
Charles J. Newell
John F. Haasbeek
Loren P. Hopkins
Sarah E. Alder-Schaller
Hanadi S. Rifai
Philip B. Bedient
G. Anthony Gorry
Department of Environmental Science and Engineering
Rice University
P.O. Box 1892
Houston, Texas 77251-1892
CR-814495
Project Officer
J. R. Williams
Robert S. Kerr Environmental Research Laboratory
U.S. Environmental Protection Agency
Ada, Oklahoma 74820
ROBERT S. KERR ENVIRONMENTAL RESEARCH LABORATORY
OFFICE OF RESEARCH AND DEVELOPMENT
U.S. ENVIRONMENTAL PROTECTION AGENCY
ADA, OKLAHOMA 74820
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DISCLAIMER
The information in this document has been funded wholly or in part by the United States
Envkonmental Protection Agency under Assistance Agreement No. CR-814495 to Rice
University. It has been subjected to the Agency's peer and administrative review, and it has
been approved for publication as an EPA document. Mention of trade names or commercial
products does not constitute an endorsement or recommendation for use.
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FOREWORD
EPA is charged by Congress to protect the Nation's land, air and water systems. Under
a mandate of national environmental laws focused on air and water quality, solid waste
management and control of toxic substances, pesticides, noise and radiation, the agency strives
to formulate and implement actions which lead to a compatible balance between human
activities and the ability of natural systems to support and nurture life.
The Robert S. Kerr Environmental Research Laboratory is the Agency's center of
expertise for investigation of the soil and subsurface environment. Personnel at the laboratory
are responsible for management of research programs to: (a) determine the fate, transport and
transformation rates of pollutants in the soil, the unsaturated and the saturated zones of the
subsurface environment; (b) define the processes to be used in characterizing the soil and
subsurface environment as a receptor of pollutants; (c) develop techniques for predicting the
effect of pollutants on ground water, soil, and indigenous organisms; (d) define and
demonstrate the applicability and limitations of using natural processes, indigenous to the soil
and subsurface environment, for the protection of this resource.
This user's manual instructs the user in the execution of the software package OASIS, a
decision support system for ground water contaminant modeling. This guide should give the
user access to critical information for analyzing ground water contamination problems.
Clinton W. Hall
Director
Robert S. Kerr Environmental
Research Laboratory
111
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ABSTRACT
OASIS, a decision support system for ground water contaminant modeling, has been
developed for the EPA by Rice University, through the National Center for Ground Water
Research. As a decision support system, OASIS was designed to provide a set of tools which
will help scientists and modelers assess ground water contamination problems. OASIS is a
graphical decision support system and was developed around BIOPLUME II (Rifai et al.,
1988), a numerical model which simulates the aerobic degradation of dissolved hydrocarbons
in ground water.
The OASIS system was developed in the HyperCard environment and, unlike
traditional software, contains extensive documentation and help onscreen. Question mark
icons throughout OASIS lead the user to further discussion and definitions, thereby allowing
the system to be fully operational without the aid of paper documentation.
The information in OASIS includes documentation, a hydrogeologic database, two
chemical databases, several simple hydrogeologic models, and the BIOPLUME II model with
preprocessors and postprocessors. The system was developed for use on Macintosh personal
computers and now contains over 1600 screens and 9 megabytes (Mb) of information. The
installation of the software requires 10 Mb of disk space.
IV
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CONTENTS
Disclaimer ii
Foreword iii
Abstract iv
Figures vi
1.0 Introduction 1
2.0 HyperCard 3
3.0 OASIS System Contents 4
General Information 4
Notebook 8
Reference Library 8
Hydrogeologic Database 10
General Chemical Database 12
Specific Chemical Database 12
Darcy's Law 14
Analytical Models 14
BIOPLUME II Model 14
BIOPLUME II Preprocessor 15
Run Model 19
OASIS Example 20
4.0 OASIS System Requirements 24
5.0 Instructions for Installing the OASIS Software 25
6.0 OASIS Installation Procedure for Experienced Users 28
7.0 Using OASIS 30
8.0 General OASIS Exercises 31
9.0 BioGraph User's Manual 46
References 50
Software Disclaimer 51
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FIGURES
Number Page
1 The system outline card for OASIS 5
2 Card from the specific chemical database, benzene 6
3 Key to common button symbols and icons in OASIS 7
4 Flowchart from the source by industry reference stack 9
5 Decision process for selecting a hydrogeologic setting 11
6 Card from the general chemical database, benzene 13
7 First card from the BIOPLUME II preprocessor 16
8 Transmissivity card 18
9 Hydrogeologic setting card 21
10 Output from the BioGraph postprocessor 23
VI
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OASIS: PARAMETER ESTIMATION SYSTEM FOR AQUIFER
RESTORATION MODELS
1.0 INTRODUCTION
OASIS, a decision support system for ground water contaminant modeling, has been
developed for the EPA by Rice University, through the National Center for Ground Water
Research. As a decision support system, OASIS was designed to provide scientists and
modelers with a collection of tools to help assess and analyze ground water contamination
problems. New types of software are being developed for problems that have traditionally
been difficult to implement using conventional computer technology. Decision Support
Systems (DSS) are a class of software that help people deal with broad problems that do not
have a clearly defined solution procedure. The use of a ground water contaminant transport
model is a semi-structured problem which requires the scientist to make a series of decisions
related to representation of the site, application of available data, and types of simulations to be
performed.
OASIS is a graphical decision support system and was developed around the BIOPLUME
II model (Rifai et al., 1988). OASIS contains an extensive amount of information designed to
facilitate the task of ground water modeling. The reference stack incorporated in the system
contains libraries of information related to the field ground water. OASIS contains a general
chemical database containing 117 chemicals, with one card of information per chemical, and a
specific chemical database which contains 18 chemicals, with 25 cards of information per
chemical. Also contained in OASIS is a hydrogeologic database, which was developed
through an extensive technical survey of ground water professionals. Data from 400 field
sites across the country was obtained from ground water professionals and incorporated into
this database.
The OASIS system allows the user ro perform three different levels of modeling. At the
lowest level, the Darcy's law stack calculates the ground water velocity in a system where
hydraulic conductivity, gradient, and porosity are known. At the next level, ODAST,
(Javandel, Doughty, and Tsang, 1984), a one-dimensional solute transport model, considers
advection, dispersion, solute decay, source decay, and adsorption in a ground water system.
Finally, OASIS contains BIOPLUME II, a two-dimensional computer model 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 concentrations.
Unlike traditional software, the OASIS system contains extensive documentation and help
onscreen. Throughout the system, question mark icons lead the user to further discussion and
definitions. Thus, the system has been designed to be fully operational without the aid of
1
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paper documentation. The OASIS system was developed using HyperCard on Macintosh
personal computers and now contains over 1600 screens and 9 megabytes (Mb) of
information, thus requiring the use of a 20 Mb hard disk. It is noted that the installation of the
software actually requires 10 Mb of disk space.
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2.0 HYPERCARD®
OASIS was built using HyperCard, a software package provided with the Apple
Macintosh. In the HyperCard environment, each different screen of information is called a
"card," and cards are collected into groups called "stacks." The cards within a stack are
connected to each other by "links." These links may take many forms. For example, a link
may consist of a "button" which sends the user to a particular card or a "field" which displays
data taken from another card. In HyperCard, fields and buttons link together cards, stacks,
and other files and programs in the computer. The user is able to navigate through large
amounts of information using a series of mouse clicks on active buttons. Thus, instead of
going screen by screen through the computer (or similarly page by page in a book), a user is
allowed nonsequential access to information in the system. The first card in the OASIS system
(the OASIS Home card) contains an Intro button which gives more information about
HyperCard. The user is also referred to the HyperCard user's manual for any additional
questions.
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3.0 OASIS SYSTEM CONTENTS
The OASIS system consists of documentation, a hydrogeologic database, two chemical
databases, several simple hydrogeologic models, and the BIOPLUME II model with
preprocessors and postprocessors. Figure 1 shows an overall outline of the system that is
shown on the computer screen to users of OASIS. Each round rectangle is a "button" that the
user can click on with the mouse to go to a particular part of the system.
General Information
Each card in OASIS consists of one screen of information on a picture background.
Cards are organized into stacks of related information, with most cards in a stack having
similar backgrounds. Several different backgrounds are used in the OASIS system. These
backgrounds include pictures of tab cards, open books, notebooks, etc. The background of
the card pictured in Figure 2, from the specific chemical database, is a spiral notebook.
Text in a card is entered into a text field. Text fields take many different forms:
rectangular, opaque (on a white background), shadowed, transparent (only the text can be
seen, not the field) or scrolling. In Figure 2, the physical data is entered into transparent fields,
whereas the fire hazard data is entered into a scrolling field. In a scrolling field, all the
information cannot be viewed at the same time, and to see additional information the user clicks
the mouse on the up or down arrow at the right of the field. The field scrolls in the direction of
the arrows, thereby displaying previously hidden information.
At the bottom of Figure 2 are examples of several button types used in the OASIS
system. Buttons connect information within the OASIS system, thereby providing links
between cards. Clicking on a button takes the user to another card within the system or
performs some operation on data entered in a field. In the OASIS system, there is a convention
for each of the button styles used. Figure 3 shows a key for the common button symbols and
icons. The check box button pictured in Figure 3 is used when a multiple choice of items in a
list can be checked at the same time. The radio button shown in the figure is used when only
one item in a list can be viewed at a time. The palm tree icon returns the user to the OASIS
system outline.
The cards in HyperCard are in black and white. It is suggested that users with color
monitors switch off the color when using OASIS because the system's visual effects will only
function in black and white.
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' References
[source by IndustryJ*
Rokey
'.^Remediation
Hydrogeology J:'\_ Chemical J$t Prey's Law
Intro
//.\ Regicns
PRASTIC
Specific );-;•( Preprocessor J*^*
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Figure 1. The system outline card for OASIS.
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Figure 2.
Physical data
Physical State
Melting Point
Boiling Point
Specific Gravity
Taper Pressure
Vapor Density
Solubility in ffater
Solubility in Common
Organic Solvents
Fire Hazard Data
liquid
5.5 - 6°C
80°C
0.88
75-76 mm Hg at 20°C
2.7 - 2.8
0.07 - 0.19 wt *
«alc,CS2,eth,ac a,
ace,CHC13,and CC14
Benzene
2,3,6,7,206
1,2,3,4,206
2,3,4,6,8,206
1,14,200,206
6,8,10,14,200
3,186,187,205,206,210,226
2,4,6,7
Flash Point - Open Cup 21°F
Closed Cup 12°F
Autoignition Temperature 1000°F - 1076°F
Flammability Limits in Air (fc by vol)
Lower 1.3
14
3,5,6,8,10,48,206
3,5,6,7,8,10,13,206
8.13,14,207
ID info
Properties
Reactions
ToHicology
Modeling
References
Figure 2. Card from the specific chemical database, benzene.
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Figures.
Key to Common Button Symbols and Icons |
Note: Host stacks contain individual keys to their own buttons
Go Back to Where You Were
These button styles
Instructions or Explanation
fora Card or a Stack
Click for More Information
Go to Previous Card
Go to Next Card
Go to OASIS
are used:
Button
D Check BOK
O Radio Button
Important Note
Try a button or an icon to see what it does
Return
button
Figure 3. Key to common symbols and icons in OASIS.
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Notebook
The notebook is a system within OASIS that allows the user to transfer information
between stacks or from the support system to the models. For example, parameter data can be
taken from the chemical or hydrogeologic stacks and put into the notebook for later use in the
preprocessor. To activate the notebook, either type Command-M (the command key has an
apple/cloverleaf on it and is located on the left-hand side of the keyboard) or use the mouse to
choose the Message option under the Go menu. The message box will appear at the bottom of
the screen. To operate the notebook, type one of the following three commands into the
message box and hit return.
on : For Open Notebook - brings up a text field into which the user may type
information. The chemical and hydrogeologic databases contain a "notebook
button" which, when activated, will automatically enter the relevant data from the
card into the notebook.
en : For Close Notebook - hides the text field with the information saved within it.
Always close the notebook before leaving a card.
cln : For Clear Notebook - erases all information in the notebook.
(Note: Clear notebook only works when the notebook is closed.)
To see the whole notebook, close the message box.
WARNING: Be careful when operating the notebook. If the en command is given and
the notebook is not open, the notebook will be altered. If this occurs, the notebook can be
repaired by clicking the About the Notebook button on the OASIS system outline (a routine
has been placed in this button to fix the notebook if it has been altered as described).
Portions of the hydrogeologic and chemical databases also contain a button called
Notebook. Clicking the Notebook button will automatically enter data from the card into the
notebook and then open the notebook.
Reference Library
The reference stack contains libraries of information related to the field ground water.
Figure 4 shows the flowchart for the Source by Industry reference stack. Clicking on any of
the terms in the flowchart takes the user to contaminant information related to that source. The
references stack also contains information on source by zone, a glossary of terms, the Rokey
database (McClymont and Schwartz, 1987) which provides discussion of parameters used in
ground water modeling, and a Remediation stack. The Remediation stack contains information
on different remediation techniques for contaminated ground water aquifers and also presents
BIOPLUME II simulations which demonstrate the importance of well placement and source
term definition.
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FLOWCHART: SOURCES BY INDUSTRY^
g!^f^^^!^«^¥^^?«^?f»5^^^^-*^^T'^'
S S?' ';
Introduction
Manufacturin
flgriculture
Aluminum
Batter g
Electrical components
Electroplating
Fertilizers
Inorganic chemicals
Iron and steel
Organic chemicals
Paper and pulp
Pesticides
Petro refining
Photo supplies
Plastic, synthetics
Steam Electric Pover
Cattle feeding
Dairy operations
Poultry raising
Swine raising
The high-lighted name shews where you came from.
Togo to any section, press on the appropriate name.
References
Figure 4. Flowchart from the source by industry reference stack.
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Hydrogeologic Database
The hydrogeologic database was developed to take advantage of the large number of
hydrogeologic investigations that have been conducted at waste sites but have not been reported
in the technical literature. An extensive technical survey of ground water professionals was
conducted with funding from the American Petroleum Institute and assistance from the
National Water Well Association. Data from 400 field sites across the country was obtained
from ground water professionals and incorporated into a database.
The database was structured using the concept of hydrogeologic settings developed for
the EPA's DRASTIC system, an aquifer vulnerability index using hydrogeologic settings. The
database is used by determining the hydrogeologic setting that best matches a site or area of
interest. The hydrogeologic setting is selected by determining the ground water region, aquifer
media, and then the setting which best describes the site in question. Figure 5 shows the
decision process for selecting a hydrogeologic setting. The setting is used to access the
database; the database statistics can then be used for ground water modeling or for general site
characterization purposes.
After selecting the hydrogeologic setting for a site, the user is presented with two options:
Calculate DRASTIC Index or See Hydrogeologic Statistics. The DRASTIC manual is
presented on the Calculate DRASTIC Index card in the "Click for More Information" button.
The See Hydrogeologic Statistics option provides the mean, median, and number of
cases for six parameters (hydraulic conductivity, seepage velocity, penetration depth, gradient,
saturated thickness, and depth to water). The Raw Data and Transformed Statistics buttons at
the bottom of the card will take the user to spreadsheets containing the data collected in the
survey. Each of the six parameters exhibit a log-normal distribution, and the median values or
the transformed data are probably more appropriate for most problems. The spreadsheets can
be viewed using either Microsoft Excel, which does not come with the OASIS software and
must be supplied by the user, or EDIT, which is supplied with OASIS. To return to the
database (and HyperCard) from the spreadsheets, choose Quit on the pull-down menu under
File on the menu bar. The Hydrogeologic Statistics section also contains a Notebook button
which places information from the card into the notebook (for more information on the
notebook see the previous discussion).
The first card in the Hydrogeologic Statistics section contains an Index button. The Index
button gives the user four options: See Data by Environment, See Data by Parameter,
Collection and Analysis methods, or Return to Hydrogeologic DB. The See Data by
Environment button allows the user to view the mean, median, and number of cases for each
of the six parameters once a hydrogeologic environment has been selected.
10
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See Decision Process Rgain
Decision Process
Vifcr Rtyten Map
Select Ground
Water Region
Select Aquifer Media
Select the Hgdrogeologic
Setting That Matches Site
Ground Wster
DRASTIC
index
See Statistics in
Database
Statistics
(Or: Use DRASTIC
Use Models)
Figure 5. Decision process for selecting a hydrogeologic setting.
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The See Data by Parameter button allows the user to select one of the six parameters and
see the mean, median, and number of cases for that parameter for all the hydrogeologic
environments. The log data and data plot buttons at the top of the card show the user box
plots of the statistical information. If the mouse is held down on any portion of a box plot, the
value at that point is displayed in a pop-up field which disappears when the mouse is released.
The help button on the card explains the box plots.
The Collection and Analysis Methods button accesses "Hydrogeologic Database for
Ground Water Modeling" (Newell, Hopkins, and Bedient, 1988), a report which discusses the
database in more detail. The Return to Hydrogeologic DB option returns the user to the
Calculate Drastic Index/See Hydrogeologic Statistics card.
General Chemical Database
The general chemical database contains 117 chemicals with one card of information per
chemical and was taken from the ROKEY database by McClymont and Schwartz, 1987
(original source: Federal Register, 1982). Chemical information can be accessed in four ways:
by category, by name, by EPA number, or by CAS number (Chemical Abstract Service
number). The general chemical database contains a Notebook button which enters data from
the card into the notebook (for more information on the notebook see the previous discussion).
Figure 6 shows the benzene card from the database.
Specific Chemical Database
The specific chemical database contains 18 chemicals with 25 cards of information per
chemical. The first card of the database has buttons which access information related to
Identification, Physical Properties, Fire Hazard Data, Chemical Reactions, and Toxicology.
These terms are defined as they are used to describe the various chemicals in the database
The Choose Chemical button allows the user to select, by name, a chemical from the
database. Figure 2 shows a card from the specific chemical database for benzene. The
physical and fire hazard data are given. A list of numbers is shown to the right of the data.
These numbers are the reference numbers related to each piece of information. Clicking on a
number will take the user to that reference in the reference list. Please note, however, that
words and phrases which are not reference numbers can also be chosen with the mouse for the
reference search. Should this happen, an appropriate error message will occur.
The first card of the specific chemical database also contains a button named Find a
Phrase. This button will search the stack and take the user to the first card in which the phrase
is referenced. Hitting return after a reference is found will continue the search procedure.
12
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Benzene
solubility 1800.00mg/l
toxicity
limit
abiotic
hydrolysis
half-life no data
cancer-risk
limit 6.6 MP/1
aerobic
half-life
taste and odor
limit 31.3ppm
anaerobic
half-life
( Alternate Names}
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Darcy's Law
The Darcy's law stack calculates the ground water velocity in a system where hydraulic
conductivity, gradient, and porosity are known. The help button (question mark icon) gives
information for each of the parameters needed in the calculation.
Analytical Models
Currently, only one analytical model is contained in this stack. ODAST (Javandel,
Doughty, and Tsang, 1984) is a one-dimensional solute transport model, which considers
advection, dispersion, solute decay, source decay, and adsorption. Output from the model is
provided as a two-way table of dimensionless concentration versus time and distance. The
ODAST model is a useful tool for providing preliminary estimates of solute transport in a
ground water system.
To run ODAST, the user first enters data into the ODAST data input card. The help button
(question mark icon) contains definitions for the input variables, as well as the equations used
by ODAST. After entering the data, the user must save the data to an input file. After hitting
the "Save" button, a standard save-file dialog box will appear onscreen. This box allows the
user to decide where to save the input file on the hard disk. ODAST input data sets must be in
the Analytical Models folder to be accessed by the program. The system will also prompt the
user to enter a title for the file being saved to disk. The "Run ODAST" button will open the
program. The user will be prompted to enter an input data set name and an output data set
name. The "View Data" button on the ODAST input data card opens the Edit application, and
allows the user to see the input or output file for an ODAST run. The help button on the input
data card also explains the procedure for running ODAST.
BIOPLUME II Model
BIOPLUME II is a two-dimensional computer model 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
concentrations. The model is based on the USGS solute transport two-dimensional code
(Konikow and Bredehoeft, 1978). BIOPLUME II computes the changes in concentration over
time due to advection, dispersion, mixing, and biodegradation.
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
biodegradation 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-situ biorestoration schemes. BIOPLUME II allows
injection wells to be specified as oxygen sources into a contaminated aquifer, and the model
can be used to evaluate alternate methods for aquifer reclamation.
14
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BIOPLUME II Preprocessor
A graphical preprocessor for the BIOPLUME II model has been developed to facilitate
data entry. Figure 7 shows the first card of the BIOPLUME II Preprocessor. This card is
divided into three sections, from left to right across the screen. These sections are Start Here,
Enter Data for Model, and Run Model.
Start Here
The Start Here section contains two buttons: Clear Preprocessor and Import existing file.
Clear Preprocessor. HyperCard automatically saves changes made to the preprocessor.
Any previous work which has been done and not cleared will be stored in the preprocessor.
Therefore, to begin a completely new data set, the user must use the Clear Preprocessor
button. Otherwise, the existing preprocessor file may be edited.
Import a File. The Import a File button imports to the preprocessor a data set which has
been saved previously. Warning: Importing a file is a slow process (up to 35 minutes for a
Mac SE), and it may be faster to re-enter the data by hand.
Enter Data for Model
Data is entered in six sections: Configuration, Timing Parameters, Physical Parameters,
Initial Conditions, Boundary Conditions, and Numerical Parameters. Note: Data must be
entered in decimal format; exponential notation cannot be read by the preprocessor.
The first card of the preprocessor contains a "New Users Click Here!" button (question
mark icon). This button contains important information for running the BIOPLUME n model.
This button contains a Read This First section, a BIOPLUME II summary, BIOPLUME II
assumptions, a Troubleshooting section (i.e., what to do about long run times and high mass
balance errors, and the run time error codes for the model), a Guided Tour of the Array Maker,
and a Disclaimer for BIOPLUME II. Every user is strongly urged to read through the new
user's information. Also, the BIOPLUME II user's manual can be accessed from the first card
of the preprocessor ("BIOPLUME II Manuel" button).
The Configuration card must be completed before data is entered on any other card. The
Configuration card defines the model grid to be used in the simulation. When each data section
is complete, the corresponding button on the first card of the preprocessor will be highlighted,
as seen in Figure 7. All six data sections must be completed before the preprocessor file is
Saved to Disk and used as an input data set for the model. Also, the user must enter data for
every variable in the preprocessor. If the value for a variable is left blank, a run time error will
result.
15
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CTi
BIOPLUME II Preprocessor
Enter feta for f-fatef:
Clear
Preprocessor
3. Physical Parameters
4. Initial Conditions
Import
Existing File
5. Boundary Conditions
6. Numerical Parameters
!-• Users
Click Here!
( BIOPLUME ii f-fanuai J
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Figure 7. First card from the BIOPLUME II preprocessor.
-------
All cards in the preprocessor contain help buttons (question mark icon), which assist the
user in completing the data set. Help buttons
next to the parameter will give a definition and
typical values for a given parameter. The user is strongly urged to use the help buttons
whenever she or he has questions.
Using the Array Maker. Certain parameters in the model require that a value be entered
for every grid cell. A 10 x 10 grid, for exampl
z, would require 100 values to be entered for the
parameter; the group of data values is referred to as an array. An array may have a different
i
value for every grid cell, blocks of areas with the same value, or a constant value over the
entire grid. Entering a large number of values into an array can be tedious. However, the
BIOPLUME II Preprocessor has an easy, graphical approach for entering data into arrays (the
array maker), which helps facilitate the process^.
Figure 8 shows the transmissivity card from the preprocessor. A 20 x 20 grid is shown,
with different patterns displayed over the grid.
transmissivity. The key to the transmissivity
Each pattern corresponds to a different value of
values is shown to the right of the grid. To use
the chosen area (see Figure 8). When the mou:
area. The patterns on the grid are automatically
the array maker, the user first selects a value for transmissivity (see the white arrow pointing at
a value of 0.001 ft^/s in Figure 8). The mouse is then clicked at the upper left-hand corner of
the area which will be described by the selected value of transmissivity. Without releasing, the
user drags the mouse to the lower right-hand corner of the area. A flashing rectangle will show
,e is released, the appropriate pattern will fill the
convened into a numerical array.
Important: Simply clicking on a value in the grid key will not enter data into the
numerical array, which is used in the BIOPLUME II model. The user must go through the
click and drag procedure. Similarly, if any changes are made to the grid key values, the user
must click and drag after the changes have been made, or the numerical array will not reflect the
changes. Also, if the number entered for a variable is not on the list of pattern values, the
default pattern will be black. Black patterns may occur when importing a file, if the user
manually changes values in the list of pattern values, or if the user enters data with the Other
Data Entry Options button (below), and the values entered do not correspond to the pattern
values. To change black patterns, the user needs to change the values in the pattern list to
correspond to the values entered for the variable. Then the click and drag procedure must be
performed before the grid patterns will change. See the Troubleshooting section (accessed
through the help button on the first page of the preprocessor) for more information.
The numerical array can be seen at any time by clicking the Other Data Entry Options
button on the card (see Figure 8). This button not only allows the user to view the array, but
also allows him/her to enter data in one of two ways: as a constant value over the entire grid by
typing a single number or as discreet values, entered one at a time, directly into the array.
17
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-------
The help button (question mark icon, see Figure 8) gives information about
transmissivity and also shows a guided tour of the array maker. On the first card of the
preprocessor, also, there is a New Users Click Here! button, which contains the guided tour
of the array maker. It is strongly urged that first time users watch the guided tour before
entering data into the array cards.
The following parameters require that data be entered as a numerical array:
Physical Parameters
• Transmissivity
• Saturated thickness
• Diffuse recharge
Initial Conditions
• Initial water table
• Initial contaminant concentration
• Initial oxygen concentration (only if aerobic degradation)
Boundary Conditions
• Constant head cells
• Area sources
The default value for parameters entered as an array is zero, (i.e., a value of zero is
entered into the arrays until the user makes changes). For all non-array variables, the user
must enter a value; there is no assumed default.
Run Model
The Run Model section contains four buttons: Save to Disk, Run Model, Run Biograph,
and, View Data.
Save to Disk. The Save to Disk button saves the current preprocessor file in a format
which can be used by the BIOPLUME II model as an input data set. The user must Save to
Disk before using a preprocessor file to run the model. After hitting the "Save to Disk"
button, a standard save-file dialog box will appear onscreen. This box allows the user to
decide where to save the input file on the hard disk. The best place to save the input file is in
the BIOPLUME II folder. If the user opens the BIOPLUME II folder in the minifinder (save
file dialog box) before hitting the save button, the file will be saved in that folder.
Run the Model. The Run Model button accesses BIOPLUME II. The user needs to
supply an input file name (created by Saving to Disk). The user will then be prompted for
names for an output file and for a BioGraph file (the default name for the postprocessor file
will be "input file name Biograph" file). The BioGraph file created during the BIOPLUME II
run is used as input for the postprocessor. To return to HyperCard when the run is finished,
the user simply needs to hit the carriage return on the keyboard.
19
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A BIOPLUME n run can take anywhere from a few minutes to a few hours. To estimate
the time required to complete a BIOPLUME run, see the "Long Run Times" in the
Troubleshooting section (accessed by clicking on the help button on the first card of the
preprocessor). To cancel a run before completion, type command (the apple/cloverleaf key )
and a period at the same time.
Run BioGraph. The Run BioGraph button accesses BioGraph, a graphical post-
processor for the BIOPLUME II model. The input for BioGraph is the BioGraph file created
during the model run. To return to HyperCard when finished in the postprocessor, the user
must choose Quit on the pull-down menu under File on the menu bar. For more information
on BioGraph, see the BioGraph user's manual in Section 9.0.
View Data. The View Data button takes the user to the Edit application. Edit allows the
user to see the data set which will be used as input for BIOPLUME II. Edit also will allow the
user to view the output data set created by BIOPLUME II. To use the View Data button, the
user needs to click the button and supply a file name. To return to the preprocessor when
finished, the user must choose Quit on the pull-down menu under File on the menu bar.
Note: The data must be saved (using the Save to Disk button) before the View Data button can
be used to view the input data set.
OASIS Example
As an example of the way in which OASIS can be used as a support tool for the
BIOPLUME II model, consider a gasoline leak at a service station located in the western
mountain ranges. The following steps might occur when using the system.
First, the user might consult one of the two chemical databases contained in OASIS.
The user could refer to the specific chemical database to examine physical data on benzene
(Figure 2).
If the user is unfamiliar with the hydrogeology of the area, he or she can enter the
hydrogeologic database. The correct ground water region is selected first, then the aquifer
media, and then the hydrogeologic setting, as pictured in Figure 9. Once the setting is known,
the user can examine data from sites with a similar hydrogeologic setting. The hydrogeologic
data is designed to be used as a general educational tool and is not designed to be a substitute
for field work.
At this point, the user can run the analytical model to help set up the problem or enter
directly into the BIOPLUME II Preprocessor. The preprocessor was designed to do three
things: structure the data entry process, give immediate access to ground water and data entry
help, and provide a graphical method for entering and viewing the spatial information used by
the model.
20
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Region: Western ^fountain Ranges
Setting: GLACIATED MOUNTAIN
VALLEYS
This setting is characterized by moderate
topographic relief and very coarse grained
deposits associated with the near mountain
glacial features such as cirques and paternoster
lakes. These deposits may serve as localized
sources of water. Water tables are typically
shallow with coarse grained deposits present at
the surface. Mountain glaciers may be present
in some areas. Although precipitation may not be
great, recharge is relatively high when
compared to other settings in the region because
of the large vol umes of water produced from the
glaciers during the summer melting cycle. These
recent glacial deposits are underlain by
fractured bedrock.
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Figure 9. Hydrogeologic setting card,
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Once the user finishes entering the data, the preprocessor makes a text file corresponding
to the format required by BIOPLUME II. The model is run and the graphical postprocessor,
BioGraph, displays the output from the model (contaminant concentrations over the area of the
aquifer) in the form of patterns. Darker patterns correspond to higher concentrations. The
development of the plume over time can be seen with an animation option in BioGraph.
Concentration profiles over time or over distance (Figure 10) can be examined also. The
preprocessor and the postprocessor for BIOPLUME II were designed to facilitate model
calibration and data evaluation.
22
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* File Modes Time Windows Other Info Color
Hydrocarbon Plume
M
U>
IUI Hydrocarbon From 11,2 to 11,17
[Figure 10.
Figure 10. Output from the BioGraph postprocessor.
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4.0 OASIS SYSTEM REQUIREMENTS
The OASIS system will run on an Apple Macintosh SE, Macintosh II, Hx, Hex, or SE/30
computer. The system requires 9 Mb of hard disk storage and 1 Mb of RAM. If your
computer has insufficient internal memory to run OASIS, the BIOPLUME II Preprocessor
will not run properly. Indications of memory problems include the following:
• Dialog boxes which inform you that there is not enough memory to use the paint tools
• Dialog boxes which inform you that a picture cannot be saved
If your computer experiences memory problems while running OASIS, make sure that
your computer's RAM cache is turned off. To check the RAM cache, look in the Control Panel
which is located in the pull-down menu under the apple on the menu bar. Also, no networking
software or applications such as multifinder should be in operation.
The Macintosh SE may not be suitable for running BIOPLUME II for many problems
due to the lack of a math co-processor in the SE. Problems involving high ground water
velocities, large grid sizes, pumping wells, or injection wells may required excessive run times
on a Mac SE. See the Troubleshooting section (accessed through the help button on the first
card of the preprocessor) for information on:
• How to estimate run times
• How to cancel runs
• How to speed up runs
The Macintosh II, IIx, Ilex, and SE/30 are much faster at performing heavy numerical
calculations and can handle more numerically intensive simulations.
24
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5.0 INSTRUCTIONS FOR INSTALLING THE OASIS SOFTWARE
These instructions are fairly comprehensive and will ensure proper operation of the OASIS
system on your computer. Please follow them closely and make sure you complete each step.
Do not hesitate to call for assistance if you have any questions or problems (Rice University,
Department of Environmental Science and Engineering, (713) 527-4951). If at any time during
the installation you encounter a situation not covered in these instructions, please note the
circumstances and call for assistance. If the system is not properly installed, you may
encounter problems with its operation. If you accidentally throw a file or stack away, you may
have to re-install the whole system. If you are an experienced Macintosh user, an abbreviated
version of the installation procedures follows this section.
1. Remove ALL old OASIS files from your hard disk. If you are unsure if some files
are pan of the old OASIS system, please make a list of them and call us.
2. Move to the desktop level and note the name of your hard disk. The desktop is explained
in the Macintosh user's manuals. The easiest way to move to the desktop is to hold
down the option key and click in the close box in the upper left-hand corner of the front-
most window. This will close all open windows. You should see a trash can icon and
the hard disk icon. Make a note of the hard disk name, which appears at the bottom of
the disk icon. Be sure to include any spaces or other special characters, as they are
important. Now double-click the hard disk icon to open it. The window which appears
is called the desktop window.
3. Make sure there is no folder on the desktop called "OASIS Folder" or "Temporary
OASIS Folder." If there is, either throw it away (if it contains nothing you want to keep)
or rename it to something else. Also make sure that Multifinder is turned off
when loading OASIS. If Multifinder is on or you are unsure, choose the Restart
command from the Special menu while holding down the command key (the command
key has the §€ icon on it). Hold down the command key until the computer has
completely finished rebooting.
4. Check to see that there are at least 10 Mb free on your hard disk. You must have at least
10 Mb to use the system. The free space is shown in the upper right of the window, just
below the title. 10 Mb is equal to 10240 K. If there is not enough space, you will have
to remove other items. If this is the case, when you have cleared at least 10 Mb on your
disk, please return to the desktop level (as described in step 2) and continue with the
installation.
5. Find the HD Backup application that came with your Macintosh computer. If it is already
on your hard disk, skip to step 7. If not, continue with step 6.
6. HD Backup can be found on the Utilities disk or disks that come with every Macintosh
computer. Insert these disks until you find one with the application HD Backup, then
copy it to your hard drive by clicking on its icon and dragging it onto the desktop
window of your hard disk.
7. Double-click the application icon named "HD Backup." This will start the HD Backup
application.
25
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8. Click the button labeled "Restore a single file.", then click the button labeled "OK."
9. Insert the first disk, labeled "OASIS Part 1 - Disk 1". The file "1.OASIS Pan 1
(Compressed)" should be highlighted (if not, click on that file name). Click "Open."
10. Insert each of the Part 1 disks as they are requested from 2 through 6.
11. When the restoration is completed, click on the button "Quit." The application may ask
for the last disk inserted. If so, insert the disk OASIS Part 1 - Disk 6 as directed.
12. At the desktop level, there will be a compressed file on your hard drive called "OASIS
Part 1 (Compressed)". Open it by double-clicking on it. The computer will proceed to
decompress the file. This takes approximately 20 minutes on a Macintosh SE.
13. There will now be a folder on the hard drive called "OASIS Folder" in addition to the file
"OASIS Part 1 (Compressed)." Put "OASIS Part 1 (Compressed)" in the trash can by
clicking its icon and dragging it over the trash can on the lower-right side of the screen.
Click on the menu button Special at the top of the screen, drag down to the command
"Empty Trash," and release the mouse button. From now on in the instructions, when a
menu and a command are given, do them in this manner.
14. Double-click the application icon named "HD Backup." This will start the HD Backup
application again.
15. Click the button labeled "Restore a single file.", then click the button labeled "OK."
16. Insert the first disk, labeled "OASIS Part 2 - Disk 1." The file "1.OASIS Part 2
(Compressed)" should be highlighted (if not, click on that file name). Click "Open."
17. When requested, enter the disk labeled "OASIS Part 2 - Disk 2."
18. When the restore is completed, click on the button "Quit." The application may ask for
the last disk inserted. If so, insert the disk OASIS Part 2 - Disk 2 as directed.
19. There are now two OASIS icons on your hard disk, "OASIS Folder" and "OASIS Part 2
(Compressed)." Open "OASIS Part 2 (Compressed)" by double-clicking on it. The
computer will proceed to decompress the file. This takes approximately six minutes on a
Macintosh SE.
20. There will now be a folder on the hard drive called "Temporary OASIS Folder" in
addition to the file "OASIS Part 2 (Compressed)" and "OASIS Folder." Put "OASIS
Part 2 (Compressed)" in the trash can by clicking its icon and dragging it over the trash
can on the lower-right side of the screen. Do the "Empty Trash" command from the
Special menu.
21. Open the Temporary OASIS Folder by double-clicking on it. Make sure the window
showing the files in the Temporary OASIS Folder does not cover the icon of the OASIS
Folder. If it does, resize or move the Temporary OASIS Folder window until it does
not. Choose the "By Kind" command from the View menu. Choose the "Select All"
command from the Edit menu. Put all of the files in the Temporary OASIS Folder into
the OASIS Folder by clicking on any of the small, darkened icons in the Temporary
OASIS Folder window, drag them over the OASIS Folder icon until it is darkened, and
then release the mouse button, dropping the files into the OASIS Folder.
22. Close the Temporary OASIS Folder window by clicking on the small square in the
upper-left corner of the window.
26
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23. Throw away the Temporary OASIS Folder by dragging it into the trash can and choosing
the "Empty Trash" command from the Special menu.
24. Open the OASIS Folder by double-clicking on its icon. Choose the "By Kind" command
from the View menu.
25. The OASIS folder contains your OASIS software. Please do not move this folder,
rename it, or otherwise change the file structure. Please do not change
the names or locations of any of the files inside the folder, except input and
output files for the BIOPLUME and BioGraph programs.
26. You will see one icon, named "HyperCardvl.2.2.," at the top of the list. Double click
this icon to start the OASIS system. Even if you do not wish to use the software at this
point, you must start it up in order to initialize the file structures.
27. Click on the button labeled "Read This First." Then click "Update Hard Disk Name."
28. You will be asked if you know the name of your hard disk. If you wrote the name down
in step 2, click yes. Otherwise click Help and follow the instructions on how to get the
name of your hard disk. When you do know the name, return to this step.
29. In the next dialog box, type in the name of your hard disk, including any spaces, etc.,
then click OK.
30. Use the "Update Hard Disk Name" button anytime you change the name of
your hard disk. You may now click on the OASIS button to enter the system or use
the "Quit" button to quit HyperCard.
Note: You may keep HyperCard on your hard disk for other uses, but you must use a
separate copy of the program file, and that copy must be in a different folder. None of the
OASIS files can be merged into other HyperCard environments at this point. Do not leave
any of your own HyperCard stacks in the OASIS folder.
27
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6.0 OASIS INSTALLATION PROCEDURE FOR EXPERIENCED USERS
This installation procedure is for users who are already familiar with the Macintosh
environment. If you are unsure or have questions about any part of this procedure, use the
more detailed instructions in the user's manual. First, make sure that your hard drive meets
these four conditions:
1. Does not contain any old OASIS files.
2. Does not have a folder called "OASIS Folder" or "Temporary OASIS Folder."
3. Has at least 10 Mb of free disk space.
4. Multifinder is turned off (do this temporarily by restarting the Mac with the command key
down).
Procedure
1. Find the copy of the program HD Backup which comes with every Macintosh computer
on the Utilities disk(s). Put it on your hard drive if it is not there already.
2. Run the HD Backup application.
3. Click "Restore a single file." and "OK."
4. Insert the first disk, labeled "OASIS Part 1 - Disk 1". Open the file " 1 .OASIS Part 1
Compressed)."
5. Insert each of the Part 1 disks as they are requested from 2 through 6.
6. Quit the HD Backup application.
7. There will be a compressed file on your hard drive called OASIS Part 1 (Compressed).
Open it. The computer will proceed to decompress the file. This takes approximately
20 minutes on a Macintosh SE.
8. There will now be a folder on the hard drive called OASIS Folder in addition to the file
OASIS Part 1 (Compressed). Put OASIS Pan 1 (Compressed) in the trash can and do
the Empty Trash command from the Special menu.
9. Run the HD Backup application again.
10. Click "Restore a single file." and "OK."
11. Insert the disk labeled "OASIS Pan 2 - Disk 1." Open the file " 1 .OASIS Part 2
(Compressed)."
12. Insert the disk labeled "OASIS Part 2 - Disk 2" when requested.
13. Quit the HD Backup application.
28
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14. There will be a compressed file on your hard drive called OASIS Part 2 (Compressed).
Open it. The computer will proceed to decompress the file. This will take
approximately six minutes on a Macintosh SE.
15. There will now be a folder on the hard drive called Temporary OASIS Folder in
addition to the file OASIS Part 2 (Compressed). Put OASIS Part 2 (Compressed) in
the trash can and do the Empty Trash command from the Special menu.
16. Open the Temporary OASIS Folder, choose "By Kind" from the View menu, choose
the "Select All" command from the Edit menu, and drag all four files at once from the
Temporary OASIS Folder and drop them into the OASIS Folder.
17. Put Temporary OASIS Folder in the trash can and do the Empty Trash command from
the Special menu.
18. Open the OASIS Folder and select the "By Kind" command from the View menu. At
the top of the list should be Hypercardvl .2.2. Opening this will start OASIS.
19. Run HyperCardv 1.2.2 inside the OASIS Folder and follow the instructions given by
the "Read This First" button.
Note: Never change the name of the OASIS Folder and never change the name or location of
any of the items inside the folder, except for input and output files that you make yourself.
29
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7.0 USING OASIS
Whenever you wish to use the OASIS software, use the following simple procedure to
enter the system:
1. Close all open windows. You can do this easily by holding down the option key and
closing the front-most window. All other windows will automatically close.
2. Open the hard disk icon - this will get you to the desktop window.
3. Open the folder named "OASIS Folder."
4. Double-click the HyperCardv 1.2.2 icon which will appear in the OASIS Folder window.
5. If you have changed the name of your hard disk, use the button labeled "Update Hard
Disk Name."
6. Click the button labeled "OASIS" to enter the system.
If you encounter any problems while using the software, please refer first to the
Macintosh user's manual. Many "problems" are actually just standard operating system
procedures. If you seem to be getting a lot of standard file dialog boxes asking "Where is ...,"
you may need to update the name of your hard disk, as described above. If you need to leave
the system at any time or the system appears to be "hung," you can exit by holding down the
command (apple/cloverleaf) key and typing a "q." This will return you to the desktop level. If
this does not work, try holding down the command key and typing a period (.). If all else fails,
simply turn off the computer. You can re-enter the system after you restart the machine. If
you ever become lost in the system, the OASIS palm tree icon will return you to the system
outline. Also, selecting "Home" on the pull-down menu under "Go" on the menu bar will take
you to the OASIS Home card.
30
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8.0 GENERAL OASIS EXERCISES
The following questions and exercises are intended to help you navigate through the
OASIS system. Begin at the system outline. The italicized words in the answers show the
sequence of button selections needed to arrive at the correct information. The first word
preceding the italicized button selections is the stack name.
Reference Library
1. Question: What is the difference between Total porosity' and 'Effective porosity'?
Answer: References, Rokey, Porosity.
• Total porosity = total void space in porous material
• Effective porosity = that portion of total porosity which is interconnected
Chemical Database
2. Question: What are two other names for the eighth monocyclic aromatic compound
listed? What is its toxicity limit?
Answer: Databases, Chemical, General Chemical Database, Category, Monocyclic
aromatic. Go to the eighth chemical.
• Phenylethane, ethylbenzol
• 1400 mg/1
3. Question: What is the aerobic half-life of naphthalene?
Answer: Databases, Chemical, General Chemical Database, Name. Enter
naphthalene.
• 0.20 days
4. Question: What chemical is CAS #110-75-8?
Answer: Databases, Chemical, General Chemical Database, CAS number. Enter
number.
• 2-chloroethyl vinyl ether
5. Question: Under what condition would pentachlorophenol corrode rubber?
Answer: Databases, Chemical, Specific Chemical Database, Choose Chemical. Select
pentachlorophenol. Reactions, Corrosion.
• When dissolved in oil
6. Question: What is the vapor density of 1,2-dichloropropane?
Answer: Databases, Chemical, Specific Chemical Database, Choose Chemical. Select
dichloropropane. 1,2 isomers, Proper ties.
•3.9
31
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7. Question: Who are the editors of a book containing information on the
photodecomposition of ethylene dibromide?
Answer: Databases, Chemical, Specific Chemical Database, Choose Chemical. Select
ethylene dibromide. Reactions, Photochemical.
To access the reference stack, click on the reference number (1311).
• Ramond E. Kirk, and Donald F. Othmer
8. Question: s xylene carcinogenic?
Answer: Databases, Chemical, Specific Chemical Database, Choose Chemical. Select
xylene. Toxicology.
•No
Hydrogeologic Database
Problem
Suppose a plastics manufacturer had buried drums of scrap material on their plant site in
the past and recent fish kills in the river near the burial indicate there may be a leak. The site is
located in the Gulf Coast region of Texas and the drums were buried in clayey loam underlain
by a silty sand aquifer. The area is very swampy. You have the following field data for the
aquifer:
Hydraulic conductivity = 10"^ cm/sec
Saturated thickness = 15 ft
Hydraulic gradient = .003 ft/ft
Depth to water = -5 ft
9. Question: Determine the region, the hydrogeologic setting, and the environment
associated with this site.
Answer: Databases, Hydrogeology, Begin: Access Database.
• Region: Atlantic and Gulf Coastal Plain
• Setting: Swamp
• To see the hydrogeologic environment, click on See Hydrogeologic Statistics.
• Environment: Sand and Gravel
10. Question: What is the DRASTIC Index for this site?
Answer: After selecting the Region and the Setting for the site, click on. Calculate
Drastic Index.
• 202; This index is high, which implies a high susceptibility to contamination.
32
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11. Question: You are not sure about the accuracy of the hydraulic conductivity data that
you obtained from the field. What is the mean and median values for the hydraulic
conductivity found for sites similar to this?
Answer: After selecting the Region and the Setting for the site, click on See
Hydrogeologic Statistics.
• mean = 0.0915 cm/s
• median = 0.008 cm/s
Modeling
Analytical model
Go to the analytical model section of OASIS by clicking on the words "Analytical Model"
on the system flowchart. The first card shows ODAST, a 1-D analytical model. We hope to
include others in a future version of the system. To see how the 1-D model works, read the
help screen (? button) and run the example problem.
BIOPLUME II
Test Case 1: Create a plume
This test case involves only the BIOPLUME 11 section of OASIS. To begin, access the
BIOPLUME II Preprocessor by clicking on "Preprocessor" in the system flowchart. You
should now be on the first card of the stack titled "BIOPLUME II Preprocessor." Click the
button in the lower left of the screen entitled "New Users Click Here," then select "Read This
First" to get crucial information about how the preprocessor works. The input data for a
simple problem is listed below. Before entering any data, hit the "Clear Preprocessor" button
on the right-hand side of the screen. Select "Yes" in the following dialog box which prompts
you as follows, "Clear Previous Graphical Patterns?". If you cannot find the information on
this sheet to fill in a blank, it is either not needed or can be entered using a default button on the
appropriate card.
Configuration Card
Enter a grid size of 10 columns and 10 rows with cells of 60 x 60.
Note: The BIOPLUME II program adds a row (or column) of zeroes along each edge of
the grid. Thus, the actual grid size will be 12 x 12 instead of 10 x 10.
Timing Parameters
One pumping period that lasts ten years and only one time step under steady state
conditions. You may enter the rest of the information in this section or default.
33
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Physical Parameters
Porosity = 0.3
Anisotropic ratio =1.0
Longitudinal dispersivity = 10.0 ft
Ratio of transverse to longitudinal dispersivity = 0.3
Transmissivity = 0.001 ft2/s
Saturated thickness = 10.0 ft
Diffuse recharge = 0.0
No decay or aerobic degradation
Retardation factor = 1
Initial Conditions
Initial water table = 100
Initial contaminant cone = 0.0
Boundary Conditions
You have a row of constant heads of 100 at the top and 99.15 at the bottom and the
direction of flow is north to south. You do not have any other constant head cells. You have
an injection well at (5,3) with a rate of 2.47 xlO-6 cfs and a concentration of 15,000 mg/1.
You do not have any area sources.
Numerical Parameters
Default
Run the model
First, save your data to disk by hitting the "save to disk" button on the Preprocessor card.
After hitting the "Save to Disk" button, you will see a standard save-file dialog box. This box
allows you to decide where you would like to save your input file on the hard disk. If you
have any questions about the procedure for saving a file, consult the Macintosh user's
manuals. The system will also prompt you to enter a title for the file you are saving to disk.
Please remember the location and name of the file you have just saved. The whole process will
take around six minutes on an SE and about three minutes on a Mac II.
Once the data has been saved to disk, you are ready to run the model. Hit the "run the
model" button on the Preprocessor card. After you have hit the "run the model" button, the
system will ask you whether you are running on a Mac SE or a Mac II. After making the
proper selection, the screen will go blank for a few seconds before a standard open-file dialog
box appears on your screen. Select the folder in the dialog box which contains your input data
set and open your input file. If you have any questions on the procedures for opening a file,
please consult the Macintosh user's guide. The system will provide you with an output file
name and BioGraph file name for your approval. Run time for the Trial 1 test problem is a
little over three minutes on a Macintosh SE.
34
-------
To run BioGraph, hit the "Run BioGraph" button on the first card of the preprocessor.
Pull down the menu titled "file" and select "open" from the menu. Now open the BioGraph
file you made when you ran the model (for example, Test Case 1. BioGraph). Pull down the
"time" menu and select "forward" or "animate." BioGraph output is shown on the following
page. For the output shown, the concentration limits for the patterns have been changed from
the default limits set by BioGraph. For more detailed instructions, see the enclosed BioGraph
User's Manual (Section 9.0).
To see the input or output file for your BIOPLUME II run, click the "View Data" button
on the first card of the preprocessor. This button will open the Edit application. Click on the
name of your input or output file to see the data.
Check your results with the results for test case, Trial 1, on the next page.
35
-------
Contaminant Plume
Time Step
Legend : Values represent upper limits for corresponding pattern.
Concentration
D
D
l.OOe-1
3.25e+l
6.49e+l
9.74e+l
1.30e+2
1.62e+2
1.95e+2
2.27e+2
2.60e+2
2.92e+2
1
|
1
~~1
~~l
|
|
36
Triall Contaminant Plume
-------
1 BIOPLUME II
1CONTAMINANT TRANSPORT UNDER THE INFLUENCE OF OXYGEN LIMITED BIODEGRADATION
INPUT DATA
GRID DESCRIPTORS
(NUMBER OF COLUMNS) =
(NUMBER OF ROWS)
(X-DISTANCE IN FEET) =
(Y-DISTANCE IN FEET) =
TIME PARAMETERS
12
12
60.0
60.0
(MAX. NO. OF TIME STEPS)
(NO. OF PUMPING PERIODS)
(PUMPING PERIOD IN YEARS)
(TIME INCREMENT MULTIPLIER)
(INITIAL TIME STEP IN SEC.)
NX
NY
XDEL
YDEL
NTIM
NPMP
PINT
TIMX
TINIT . . ... ,
HYDROLOGIC AND CHEMICAL PARAMETERS
S (STORAGE COEFFICIENT)
POROS (EFFECTIVE POROSITY)
BETA (LONGITUDINAL DISPERSIVITY) ••
DLTRAT (RATIO OF TRANSVERSE TO
LONGITUDINAL DISPERSIVITY) >
ANFCTR (RATIO OF T-YY TO T-XX)
EXECUTION PARAMETERS
NITP (NO. OF ITERATION PARAMETERS,
TOL (CONVERGENCE CRITERIA - AD IP)
ITMAX (MAX.NO.OF ITERATIONS - ADIP)
CELDIS (MAX.CELL DISTANCE PER MOVE
OF PARTICLES - M.O.C.)
NPMAX (MAX. NO. OF PARTICLES)
NPTPND (NO. PARTICLES PER NODE)
PROGRAM OPTIONS
NPNT (TIME STEP INTERVAL FOR
COMPLETE PRINTOiJT)
NPNTMV (MOVE INTERVAL FOR CHEM.
CONCENTRATION PRINTOUT) =
NPNTVL (PRINT OPTION-VELOCITY
0=NO; 1=FIRST TIME STEP;
2=ALL TIME STEPS)
NPNTD (PRINT OPTION-DISP.COEF.
0=NO; 1=FIRST TIME ST3P;
2=ALL TIME STEPS)
NUMOBS (NO. OF OBSERVATION WELLS
FOR HYDROGRAPH PRINTOUT) =
NREC (NO. OF PUMPING WELLS)
NCODES (FOR NODE IDENT.)
NPNCHV (PUNCH VELOCITIES)
NPDELC (PRINT DPI. -CONC. CHANGE) =-
REACTION TERMS
1
1
10.000
.00
0.
.000000
.300
10.0
.30
1.000000
.0010
= 200
.500
93CO
9
DK
RHOB
RF
THALF
DECAY
(DISTRIBUTION COEFUCIENT) = 3.0COOO:>&0
(BULK DENSITY OF SOLIDS) = 0.17SOOE+01
(RETARDATION FACTOR) - 0.10000E+01
(HALF LIFE OF DECAY, IN SEC)= O.OOOOOE+00
(DECAY CONSTANT=LN 2/THALF)
DECAY TERMS
O.OOOOOE+00
DEC1 (ANAEROBIC DECAY COEFF . ) = O.OOOOOE+00
DEC2 (REAERATION DECAY COEFF.) = O.OOOOOE+00
STEADY-STATE FLOW
TIME INTERVAL (IN SEC) FOR SOLUTE-TRANSPORT SIMULATION = 0.31558E+09
LOCATION OF PUMPING WELLS
X Y RATE (IN CFS) CONC.
-0.20E-05 15000.00
CONC (02)
.00
0 AREA OF ONE CELL =
0 X-Y SPACING:
60.000
60.000
1TRANSMISSIVITY MAP (FT*FT/SEC)
O.'OOE-OI I'.ool-Ol °-°°E"01
?:00°E-03 0.'o0OE-00l :-°°E~03
?."00°E-03 I'.oot" 1-°°E~03
?.1oE-o3 I'.on-n
1.'OOE-03 0.'OOE-0°1
3600.
°-OOE-01 O.OOE-01 C.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
1-OOE-°3 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
i'00^03 LOOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
i'00^03 LOOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
1'°°E~03 1-°°E"03 i'°OE"03 1-OOE"03 1-OOE-°3 1-OOE-°3 1-OOE-°3
i-OOE-OS l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
37
-------
O.OOE-01 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
l.OOE-03 O.OOE-01
O.OOE-01 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
l.OOE-03 O.OOE-01
O.OOE-01 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
l.OOE-03 O.OOE-01
O.OOE-01 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
l.OOE-03 O.OOE-01
O.OOE-01 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03 l.OOE-03
l.OOE-03 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
1AQUIFER THICKNESS (FT)
.0 .0 .0 .0 .0 .0 .0 .0 .0 .0 .0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 .0
.0 .0 .0 .0 .0 .0 .0 .0 .0 .0 .0 .0
1DIFFUSE RECHARGE AND DISCHARGE (FT/SEC)
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 D.OOE-Cu O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.DOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.DOE-OJ O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-C1 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
1PERMEABILTY MAP (FT/SEC)
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OHE-34 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.COE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04 l.OOE-04
l.OOE-04 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-0: O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
0 NO. OF FINITE-DIFFERENCE CELLS IN AQUIFER = 100
AREA OF AQUIFER IN MODEL = 0.36000E+06 SQ. FT.
NZCRIT (MAX. NO. OF CELLS THAT CAN BE VOID OF
PARTICLES; IF EXCEEDED, PARTICLES ARE REGENERATED)
1NODE IDENTIFICATION MAP
000000000000
011111111110 _Q
000000000000 -JO
-------
coooocoooooo
coooooooo'ooo
000000000000
000000000000
000000000000
000000000000
000000000000
011111111110
000000000000
0 NO. OF NODE IDENT. CODES SPECIFIED = 1
0 THE FOLLOWING ASSIGNMENTS HAVE BEEN MADE:
CODE NO. LEAKANCE SOURCE CONC. 02 CONC RECHARGE
0 1 0.100E+01 .00 .00
1VERTICAL PERMEABILITY/THICKNESS (FT/(FT*SEC))
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 l.OOE+00 l.OOE+00 l.OOE+00 l.OOE+00 l.OOE+00 l.OOE+00 l.OOE+00 l.OOE+00 l.OOE+00
l.OOE+00 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOZ-01 0.00£-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.COE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
O.OOE-01 l.OOE+00 l.OOE+00 1. OOE+CO l.OOEi-00 l.OOE+00 l.OOE+00 l.OOE + 00 l.OOE + 00 l.OOE+00
l.OOE+00 O.OOE-01
O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01 O.OOE-01
O.OOE-01 O.OOE-01
1WATER TABLE
0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. 100. 100. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. 100. 100. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. 100. 100. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. 100. 100. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. 100. 100. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. 100. 100. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. IOC. 100. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. 100. 100. 0.
0. 100. 100. 100. 100. 100. 100. 100. 100. 100. 100. 0.
0. 99. 99. 99. 99. 99. 99. 99. 99. 99. 99. 0.
0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
1HEAD DISTRIBUTION - ROW
NUMBER OF TIME STEPS = 0
TIME(SECONDS) = .00000
TIME(DAYS) = O.OOOOOE+00
TIME(YEARS) = O.OOOOOE+00
0 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000
0 .0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000
0 100.0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.000COOO 100.0000000 100.0000000 100.0000000 100.0000000 100 OOOOOOC
0 100.0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000
0 100.0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000
0 100.0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000
0 100.0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100 0000000
0 100.0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 TOO 0000000
0 100.0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000
0 100.0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000
0 100.0000000 .0000000
0 .0000000 99.1500020 99.1500020 99.1500020 99.1500020 99.1500020 99.1500020 99.1500020 99.1500020 99 1500020
0 99.1500020 .0000000
0 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000 .0000000 0000000
0 .0000000 .0000000
1 ITERATION PARAMETERS
0.171347E-01
0.337467E-01
0.664638E-01
.130900
.257806
.507746
1.00000
.000000
.000000
39
-------
.000000
.000000
.000000
.000000
.000000
.000000
.000000
.000000
.000000
.000000
.000000
1CONCENTRATION OF CONTAMINANT
NUMBER OF TIME STEPS = 0
TIME (SECONDS) = .00000
CHEM. TIME (SECONDS) = O.OOOOOE
CHEM. TIME (DAYS) = O.OOOOOE
TIME (YEARS) = O.OOOOOE
CHEM. TIME (YEARS) = O.OOOOOE
NO. MOVES COMPLETED =
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
+00
+00
+00
+00
0
0
0
n
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
c
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
c
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
N = 1
NUMBER OF ITERATIONS = 7
1HEAD DISTRIBUTION - ROW
NUMBER OF TIME STEPS = 1
TIME (SECONDS) = 0.31558E+09
TIME (DAYS) = 0.36525E+04
TIME(YEARS) = 0.10000E+02
0 .0000000 .0000000 .0000000
0 .0000000 .0000000
0 .0000000 100.0000000 100.0000000 100.
0 100.0000000 .0000000
0 .0000000 99.9056718 99.9057666 99.
0 99.9056425 .0000000
0 .0000000 99.8109144 99.8110042 99.
0 99.8108646 .0000000
0 .0000000 99.7158946 99.7158591 99.
C 99.7158391 .0000000
0 .0000000 99.6214249 99.6213181 9?.
0 99.6213743 .0000000
0 .0000000 99.5276136 99.5277115 99.
0 99.5275728 .0000000
0 .0000000 99.4322738 99.4324187 99.
0 99.4322440 .0000000
0 .0000000 99.3379827 99.3375890 99.
0 99.3379635 .0000000
0 .0000000 99.2441941 99.2444506 99.
0 99.2441847 .0000000
0 .0000000 99.1500020 99.1500020 99.
0 99.1500020 .0000000
0 .0000000 .0000000 .0000000
0 .0000000 .0000000
1HEAD DISTRIBUTION - ROW
NUMBER OF TIME STEPS = 1
TIME (SECONDS) = 0.31558E+09
TIME(DAYS) = 0.36525E+04
TIME (YEARS)
0
0
0
0
0
0
0
0
0
0
0
0
0 0
0 100
0 100
0 100
0 100
0 100
0 100
0 99
0 99
0 99
0 99
0 0
0
100
100
100
100
100
100
99
99
99
99
0
0 0
100 100
100 100
100 100
100 100
100 100
100 100
99 99
99 99
99 99
99 99
0 0
= O.lOOOOE-i
0 0
100 100
100 100
100 100
100 100
100 100
100 100
99 99
99 99
99 99
99 99
0 0
0
100
100
100
100
100
100
99
99
99
99
0
-02
0 0
100 100
100 100
100 100
100 100
100 100
100 100
99 99
99 99
99 99
99 99
0 0
,0000000
ooooooo :
9058762
.8111490
7158975
.6212379
5277019
,4326111
3373373
.2445276
,1500020
,0000000
0
100
105
100
100
100
100
99
99
99
99
0
0
0
0
0
0
0
0
0
0
0
0
0
.0000000 .0000000 .0000000 .0000000 .0000000 .0000000
.00.0000000 100.0000000 100.0000000 100.0000000 100.0000000 100.0000000
99.9060070 99.9061432 99.9060262 99.9059122 99.9058170 99.9057283
99.8113892 99.8119025 99.8114124 99.8111865 99.8110452 99.8109397
99.7160059 99.7161384 99.7160073 99.7158837 99.7158086 99.7157930
99.6212195 99.6212273 99.6211842 99.6211531 99.6211746 99.6212627
9S. 5276669 99.5276426 99.5276248 99.5276300 99.5276595 99.5276695
99.4326908 99.4327130 99.4327043 99.4326697 99.4325838 99.4323893
99.3373325 99.3373549 99.3373504 99.3373207 99.3373210 99.3375706
99.2444599 99.2444405 99.2444385 99.2444546 99.2445199 99.2444418
99.1500020 99.1500020 99.1500020 99.1500020 99.1500020 99.1500020
.0000000 .0000000 .0000000 .0000000 .0000000 .0000000
1DRAWDOWN
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
40
-------
0
0
0
0
0
1
1
1
0
0
1
1
1
0
0
1
1
1
0
0
1
1
1
0
0
1
1
1
0
0
1
1
1
0
0
1
1
1
0
0
1
1
1
0
0
1
1
1
0
0
1
1
1
0
0
0
0
0
0
0
0 CUMULATIVE MASS BALANCE — (IN FT** 3)
RECHARGE AND INJECTION
PUMPAGE AND E-T WITHDRAWAL
CUMULATIVE NET PUMPAGE
WATER RELEASE FROM STORAGE
LEAKAGE INTO AQUIFER
LEAKAGE OUT OF AQUIFER
CUMULATIVE NET LEAKAGE
MASS BALANCE RESIDUAL
ERROR (AS PERCENT)
-0.63115E+03
O.OOOOOE+00
-0.63115E+03
O.OOOOOE+00
29709E+06
-0.29793E+06
-0.84691E+03
-215.75
-0.72442E-01
= 0
0 RATE MASS BALANCE — (IN C.F.S.)
LEAKAGE INTO AQUIFER = 0.94141E-03
LEAKAGE OUT OF AQUIFER = -0.94409E-03
NET LEAKAGE (QNET) = -0.26835E-05
RECHARGE AND INJECTION = -0.20000E-05
PUMPAGE AND E-T WITHDRAWAL = O.OOOOOE+00
NET WITHDRAWAL (TPUM) = -0.20000E-05
STABILITY CRITERIA M.O.C.
FLUID VELOCITIES
VMAX = 2.09E-09
VMXBD= 2.85E-09
0 TMV (MAX. INJ.) =
TIMV (CELDIS)
0 TIMV = 5.64E+07
VMAY = 5.30E-07
VMYBD= 5.32E-07
0.11446E+09
0.56389E+08
NTIMV = 5 NMOV
TIM (N) = 0.31558E+09
TIMEVELO = 0.52596E+08
TIMEDISP = 0.26073E+09
0 TIMV = 5.26E+07 NTIMD = 1 iXIMOV = 6
0 THE LIMITING STABILITY CRITERION IS CELDIS
0 NO. OF PARTICLE MOVES REQUIRED TO COMPLETE THIS TIME STEP =
0 NP = 1151 IMOV
TIM(N) = 0.31558E+09 TIMV
0 NP = 1157 IMOV
TIM(N) = 0.31558E+09 TIMV
0 NP = 1157 IMOV
TIM(N) = 0.31558E+09 TIMV
0 NP = 1166 IMOV
TIM(N) = 0.31558E+09 TIMV
0 NP = 1184 IMOV
TIM(N) = 0.31558E+09 TIMV
0 NP = 1193 IMOV
TIM(N) = 0.31558E+09 TIMV
1CONCENTRATION OF CONTAMINANT
NUMBER OF TIME STEPS = 1
DELTA T = 0.31558E+09
TIME(SECONDS) = 0.31558E+09
CHEM.TIME(SECONDS) = 0.31558E+09
CHEM. TIME (DAYS) = 0.36525E+04
TIME(YEARS) = 0.10000E+02
CHEM. TIME (YEARS) = 0.10000E+02
NO. MOVES COMPLETED = 6
0000000000
0000002000
000001 25 100
000009 292 900
0 0 0 0 1 16 247 16 1 0
0 0 0 0 0 14 179 14 0 0
000005 78 500
000001 13 100
0000001000
0000000000
0000000000
0000000000
CHEMICAL MASS BALANCE
MASS IN BOUNDARIES = O.OOOOOE+00
MASS OUT BOUNDARIES = -0.27079E+02
MASS PUMPED IN = 0.94673E+07
MASS PUMPED OUT = -O.OOOOOE+00
MASS LOST W. BIODEG. = 0.21958E-02
MASS LOST BY RADIO. DCY= O.OOOOOE+00
MASS LOST BY ANAER. DCY= O.OOOOOE+00
MASS LOST BY REAER. DCY= O.OOOOOE+00
MASS ADSORBED ON SOLIDS* O.OOOOOE+00
INITIAL MASS ADSORBED = O.OOOOOE+00
1
0.52596E+08
2
0.52596E+08
3
0.52596E+08
C.5
4
2596E+08
5
0.52596°:- 08
6
0.52596E+08
0
0
0
C
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
SUMTCH =
SUMTCH =
SUMTCH =
SUMTCH =
SUMTCH =
SUMTCK =
0.52596E+08
0.10519E+09
0.15779E+09
0.21038E+09
0.26298E+09
0.31558E+09
41
-------
INFLOW MINUS OUTFLOW - 0.94673E+07
INITIAL MASS DISSOLVED - O.OOOOOE+00
PRESENT MASS DISSOLVED - 0.10092E+08
CHANGE MASS DISSOLVED - 0.10092E+08
CHANGE TOTL.MASS STORED- 0.10092E+08
COMPARE RESIDUAL WITH NET FLUX AND MASS ACCUMULATION:
MASS BALANCE RESIDUAL - -0.62455E+06
ERROR (AS PERCENT) • -0.65970E+01
ITriall
42
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000000000000
000000000000
000000000000
000000000000
-------
J3L1
Graphical Analysis
for
Bioplume II
by John F. Haasbeek
June 1989
45
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9.0 DESCRIPTION OF THE PROGRAM
The goal of the BioGraph program is to facilitate the examination of output from the
BIOPLUME model and to present as much of the output information in a graphical manner as
is possible. The program is fully interactive and is controlled by mouse operations. It centers
around the display of output variables such as contaminant and oxygen concentrations using
patterns to represent the output graphically on a grid. In addition, the program provides several
tools with which the user can view the data in many ways.
The input files for the program are written by the BIOPLUME model. Each time the
model is run, it writes a duplicate set of output to a file. You specify the name for this file
when you run the model. Please note that at this time the BioGraph program can only display
data from a steady-state BIOPLUME run for one pumping period only In addition, the head
map should only be written for the first time step. These restrictions are present to simplify
the development process and will be removed at a later stage.
If you get a system error while reading an input file, especially error number 16, this
means that the file you have selected is not correctly formatted. Restart the computer and re-
run the BIOPLUME model making sure you have followed the above restrictions.
Starting
You can transfer to BioGraph from the Model Options card, from the system outline, or
from the preprocessor. When the program begins, you will see a large blank window and
several menus. This window is referred to as the main window, and this is where the grid
patterns are displayed. Program operation is controlled by commands located in pull-down
menus. The first step in using BioGraph is to open a BIOPLUME output file. The command
to do this is located in the File menu and is called Open. Selecting this command will allow
you access to the standard file selection dialog. If you do not know how to use this to locate
the file you are looking for, please read the Macintosh user's manual supplied with your
computer. Once a file has been opened, the program will read in the data and display initial
contaminant concentrations in the main window. When the cursor is over the grid, the cell
coordinates and the cell value are displayed at the top of the grid. Other variables can be
displayed, and mouse clicks within the grid access graphs versus time or distance. The
operation of the program is described below as each of the commands are listed and explained.
Remember, the best way to see what a command does is to try it.
Menus
In this section, the menus are described and each command is explained. Many of the
menu commands have keyboard equivalents - these are described under the Open command.
Note that these are all of the program commands - everything the program does is accessible
through menu commands.
46
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Apple Menu
The first menu in the menu area is the Apple menu. It allows access to all desk
accessories installed in the system and also includes the "About BioGraph ..." command.
File Menu
The File menu contains commands which control the general operation of the program.
The "Open" command brings up the standard file selection box, from which you can
select an input file for BioGraph. Most of the other menu commands will be dimmed (and thus
inaccessible) until you have selected an input file. The cloverleaf symbol followed by a letter at
the right of a command indicates that a keyboard command exists which is equivalent to
choosing that command from the menu. The apple/cloverleaf symbol represents the Command
key or Control key on the keyboard. For example, a shortcut for opening files is to hold down
the Command/Control key and type "o." There are many keyboard shortcuts included in the
menus.
The "Options" command allows you to set various options for program operation.
These include animation speed and graph scaling. To change an option, simply check the
corresponding box. Once the options are set, click the button marked OK.
The "Calibration Data" command is currently disabled, pending further review.
"Print Plume," as the name implies, allows you to print the plume on any attached
printer. There are three dialog boxes associated with printing: the first requests the printing
scale in terms of cell length in inches. Thus, if you have a model cell size of 50 feet on a side,
you would specify 0.25 to print at 1":200'. The next two dialogs are the standard Macintosh
printing dialog boxes.
Also, you may hit command - shift - 3 to save a copy of the current screen as a picture
file. The saved files will be named sequentially ScreenO through Screen9 and will be found on
the desktop. Any paint program will open the saved picture file and allow you to edit the
picture.
The "Quit" command exits the program.
Modes Menu
When the model grid is displayed in the main window, the program operates in one of
three modes. These modes are selected by the corresponding command in the "Modes" menu.
The cursor shape indicates which mode you are in as well as a check mark in the menu next to
the current mode. In Time mode, a mouse click in a grid cell calls up a graph of the current
variable versus time in that cell. The current variable depends on what is currently being
displayed in the grid - see the "Windows" menu. This option has no effect while displaying
heads unless the file contains data from a transient run. In the Options dialog, you may choose
if you want both oxygen and contaminant graphs to appear for each mouse click.
47
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The Distance mode is different from the Time mode in that it requires two grid cells for
input. Graphs of concentrations or heads are then drawn as a cross section between the two
grid cells at the current time step. The grid cells which will comprise the ends of the cross
section are selected by pressing the mouse button down in the first grid cell, dragging the
cursor to the second grid cell keeping the mouse button down, and then releasing the button
over the second cell. Note that the cells must form a horizontal or vertical line. Again, you
may choose in the Options dialog whether to display both contaminant and oxygen cross
sections or only the current variable. Note also that while the cross sections are displayed, you
may change time step (see Time menu) and the graphs will automatically be updated.
In Both mode, you select a cross section in the same manner as described above, but
when the graphs appear, cross sections are drawn for each time step.
The last two options in this menu, Patterns and Contours, toggle between the
corresponding display modes. Use these commands to select display of patterns or contours
representing data in the grid. Note that the contour display routine is still very much under
development, and so is not perfect. If you switch to contours, you will probably want to set
the contour values differently than the pattern limits. The commands to do this are in the
rightmost menu. The rightmost menu title will be "Patterns" when in pattern mode and
"Contours" when in contour mode.
Time Menu
The Time menu is used to control which time step is being displayed. In the main
window and the various graph windows, data is displayed for the current time step. If you
wish to display data for the next time step, simply choose "Forward." Similarly, to display
data for the previous time step, choose "Backward." The "Animate" command displays all
data sequentially starting at the first time step. You may adjust animation speed in the Options
dialog.
Windows Menu
The Windows menu contains commands which control what is to be displayed in the
main window, and consequently which is the "current" variable. The "Contaminant,"
"Oxygen," and "Head Map" commands select the corresponding variable for display. The
"Base Map" and "Combined" commands are currently disabled.
Other Info Menu
The Other Info menu contains only one command. This command, "Mass Balance," is
also currently disabled.
48
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Color Menu
The Color menu only appears when the program is running on a Mac II. It allows you to
select a color for the main window display. The currently selected color has a check mark next
to it.
Patterns Menu
Each pattern represents concentrations or head values less than or equal to a certain limit.
These are set by default by the program when input is read, but you can set the limits through
the Limits command in the Patterns menu. When selected, a dialog box will appear in
which you may fill in limits of your choice. Click Cancel to return to the previous pattern
limits.
Contours Menu
The default contour values are the current pattern limits. To change them (which you will
definitely want to do to see nice contours) use the Intervals command in the Contours
menu. The method is the same as for changing pattern limits; however, the numbers now
represent values to contour. Note - 0 is a bad number to contour. To see the edge of the
plume, contour a concentration of 1 or 0.1. If you set the highest contour to 0.1 and all the
others to -1, you will get a single contour of the edge of the plume. This will make for fast
contouring over time. The Sequence command creates a snapshot of the contour picture for
each time step and records them in a sequence. Every time you select this command after the
first, the sequence will be played back, saving lots of time. The sequence will have to be
redrawn if you change window sizing or contour values, etc.
49
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10.0 REFERENCES
Aller, L., T. Bennett, J. Lehr, R. J. Petty, and G. Hackett. 1987. DRASTIC: A Standardized
System for Evaluating Ground Water Pollution Potential Using Hydrogeologic Settings.
U.S. EPA. EPA-600/2-87-035.
Javandel L., C. Doughty, C. F. Tsang. 1984. Groundwater Transport: Handbook of
Mathematical Models. American Geophysical Union, Washington, DC.
Konikow, L. F. and Bredehoeft, J. D. 1978. Computer model of two-dimensional solute
transport and dispersion in ground water. In: Automated Data Processing and
Computations, Techniques of Water Resources Investigations.
McClymont, G.L. and F. W. Schwartz. 1987. Development and Application of an Expert
System in Contaminant Hydrogeology: The Expert ROKEY System. National
Hydrology Research Institute. DSS File No.: 52SS. KN107-5-4334. Serial No.:
OSS85-00149.
Newell, C.J., L.P. Hopkins, and P.B. Bedient. 1988. Hydrogeologic Database for Ground
Water Modeling. Report for the American Petroleum Institute.
Newell, C. J., J. F. Haasbeek and P. B. Bedient. Accepted for March 1990. OASIS: A
Graphical Decision Support System for Ground Water Contamination Modeling.
Groundwater.
Rifai, H. S., P. B. Bedient, J. T. Wilson, K. M. Miller, and J. M. Armstrong. 1988.
Biodegradation Modeling at a Jet Fuel Spill Site. J. Environmental Engineering Division,
ASCE Environmental Engineering Division. Vol. 114, No. 5, pp 1007-1028.
50
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SOFTWARE DISCLAIMER
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THE APPLE SOFTWARE. APPLE DOES NOT WARRANT, GUARANTEE OR MAKE
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51
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