823R04003
vvEPA
umieu oicuca
Environmental Protection
Agency
Office of Water (4305)
EPA-823-R-04-003
January 2004
AQUATOX (RELEASE 2)
MODELING ENVIRONMENTAL FATE
AND ECOLOGICAL EFFECTS IN
AQUATIC ECOSYSTEMS
RELEASE 2
VOLUME 3: USER'S MANUAL FOR THE
BASINS (VERSION 3.1) EXTENSION TO
AQUATOX RELEASE 2
XX-
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AQUATOX (RELEASE 2)
MODELING ENVIRONMENTAL FATE
AND ECOLOGICAL EFFECTS
IN AQUATIC ECOSYSTEMS
VOLUME 3: User's Manual for the BASINS (Version 3.1)
Extension to AQUATOX Release 2
Jonathan S. Clough
JANUARY 2004
U.S. ENVIRONMENTAL PROTECTION AGENCY
OFFICE OF WATER
OFFICE OF SCIENCE AND TECHNOLOGY (MAIL CODE 4305T)
WASHINGTON DC 20460
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DISCLAIMER
This document has been approved for publication by the Office of Science and Technology, Office
of Water, U.S. Environmental Protection Agency. Mention of trade names, commercial products
or organizations does not imply endorsement or recommendation for use.
This document describes a new aquatic ecosystem simulation model. It is not intended to serve as
guidance or regulation, nor is the use of this model in any way required. This document cannot
impose legally binding requirements on EPA, States, Tribes, or the regulated community.
ACKNOWLEDGMENTS
The AQUATOX model has been developed by Dr. Richard A. Park of Eco Modeling; the
AQUATOX programming, and the BASINS Extension documentation, and additional linkage
development was performed by Jonathan S. Clough of Warren Pinnacle Consulting, Inc. under
subcontract to Eco Modeling. Additional linkage development and the programming of the
WINHSPF and ARCVIEW interfaces within BASINS was performed by Paul Duda of AQUA
TERRA Consultants. The BASINS Extension was funded with Federal funds from the U.S.
Environmental Protection Agency, Office of Science and Technology under contract number
68-C-01-0037 to AQUA TERRA Consultants, Anthony Donigian, Work Assignment Manager.
The assistance, advice, and comments of the EPA work assignment manager, Marjorie Coombs
Wellman of the Exposure Assessment Branch, Office of Science and Technology have been of great
value in developing this extension and preparing this report.
11
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TABLE OF CONTENTS
DISCLAIMER n
ACKNOWLEDGMENTS •. . ii
1 INTRODUCTION TO THE BASINS AQUATOX EXTENSION ±±
1.1 Overview and Background 1-1
1.2 System Requirements 1-3
2 WINHSPF TO AQUATOX LINKAGE 2=1
2.1 Introduction 2-1
2.2 Selection of Pollutants 2-5
2.3 AQUATOX Linkage M
2.4 Obtain HSPF Watershed Simulation 2=2
2.5 Running AQUATOX from WinHSPF 2J_
2.6 Linked Simulation 2-12
2.7 Specification of Additional State Variables and Loadings 2-13
2.8 Run AQUATOX and Plot Results 2-21
3 BASINS GIS TO AQUATOX LINKAGE 3J.
3.1 Introduction 3-1
3.2 Performing the BASINS to AQUATOX Linkage 3-1
3.3 Using AQUATOX after a BASINS to AQUATOX Linkage M
4 SWAT TO AQUATOX LINKAGE «
4.1 Introduction: 4-1
4.2 Running a SWAT Simulation 4-1
4.3 Loading SWAT data into AQUATOX 4=4
4.4 The Linkage Process 4-7
5 AQUATOX TO GENSCN LINKAGE 5^_
5.1 Introduction 5-1
5.2 Linking to GenScn 5-1
5.3 Using GenScn 5-1
in
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AQUATQX (RELEASE 2) BASINS EXTENSION
CHAPTER 1
1 INTRODUCTION TO THE BASINS AQUATOX EXTENSION
1.1 Overview and Background
It has become increasingly apparent that methods and tools are needed to analyze the combined fate
and effects of all stressors on aquatic ecosystems from all sources. Stressors may include nutrients,
organic loading, toxic organic compounds, sediments and habitat alteration; sources include point
and non point source loadings and atmospheric deposition. Stressors may affect water clarity, algae
populations, dissolved oxygen levels, fish and invertebrate communities, levels of contaminants
in fish tissue, and many other important environmental conditions. Management approaches that
focus on one stressor at a time may miss important interactions that could determine whether overall
environmental goals, such as restoration of a more natural aquatic ecosystem, are met.
Environmental management programs and activities that could benefit from additional tools for an
integrated approach include water quality criteria and standards, Total Maximum Daily Loads
(TMDLs), identification of the cause(s) of biological impairment where there are multiple stressors,
and ecological risk assessments.
AQUATOX is a time-variable ecological risk assessment model that simulates the fate and effects
of various environmental stressors in aquatic ecosystems. It simulates the fate and transfer of
pollutants from loads to the water, sediments, and biotic components, and transfer throughout the
food web. Simultaneously it predicts the effects of the stressors on the ecosystem, by simulating the
chemical, physical and biological processes that bind the ecosystem together. AQUATOX can
predict the fate and ecological effects of nutrients, organic toxicants, and bioaccumulative
compounds, as well as the expected ecosystem responses to pollution reductions. It considers
several trophic levels, including attached and planktonic algae and submerged aquatic vegetation,
invertebrates, and forage, bottom-feeding, and game fish; it also represents associated organic
toxicants.
BASINS (Better Assessment Integrating Point and Nonpoint Sources) is a combined GIS/water
quality modeling system that includes numerous national level environmental and cartographic data
layers, analytical tools, watershed loading models, and instream water quality models. One of the
main advantages of an integrated system such as BASINS is that the time consuming task of
developing input data files for the various models is reduced: watershed characteristics necessary
for the watershed models can be developed from the landscape data layers, and data can be
converted into the proper formats for model input files. BASINS Version 3 changed the system
architecture to a modularized system, and converted the models and many other functions to
Arc View "extensions." The modular setup allows the models to run either as part of BASINS or
stand alone. The modularity also makes it easier to add components, and for users to customize
BASINS for their own purposes. This new software extension links the AQUATOX ecosystem
model to the BASINS modeling system.
1-1
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER I
The extension has been developed to assist in comprehensive environmental analysis and prediction.
When linked to BASINS, AQUATOX can be used to track ecological effects of point and non
point source loadings of organic and nutrient loadings, organic chemicals and pesticides, and
changes in hydrology. Specifically, the extension has been designed so that AQUATOX can be run
with site characteristics and loadings input directly from the BASINS GIS data layers or from the
HSPF and SWAT watershed models. The extension makes possible the direct linkage- of the
following types of data from BASINS to AQUATOX:
Site Physical Characteristics (source: GIS Layer, HSPF, SWAT)
• Dynamic Water Volume Data (source: HSPF, SWAT)
• Nutrient & BOD time-series Loadings (source: HSPF, SWAT)
• Plankton Time-Series Loadings (source: HSPF)
• Organic Chemical or Pesticide Loadings (source: HSPF, SWAT)
Time Varying TSS Concentrations (source HSPF, SWAT)
For each of the time-series that are linked, the extension converts units and integrates data to an
appropriate time-step automatically. Additionally, the extension allows AQUATOX output to be
linked to GenScn, the post-processor within BASINS. GenScn offers several statistical functions
that are not available through the AQUATOX output screen such as comparison of predicted and
observed time-series and duration analysis.
1-2
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 1
The following diagram illustrates how the BASINS AQUATOX extension integrates AQUATOX
into the previously existing BASINS framework:
Linkages Between Models
SWAT
BASINS CIS Layer
^ I ^\
AQUATOX
GenScn
HSPF
Previously Existing Linkage
New Linkage
1.2 System Requirements
The BASINS AQUATOX extension requires Microsoft Windows 98, NT, 2000, or XP. Because
Arc View and the constituent models are resident in memory, 256 MB of RAM or higher is highly
recommended. A user may be able to use the extension with less RAM by setting up a significant
virtual memory file within the Windows control panel, although that will necessitate frequent disk
access and increase simulation run times. See section 3 of the BASINS 3.0 Users Manual (EPA-823-
B-01 -001, or see the BASINS web site at http://www.epa.gov/OST/BASINS/) for more information
about BASINS Hardware and software requirements. Within BASINS, Arcview's Spatial Analyst
extension is required to run the SWAT model and to automatically delineate rivers within the
BASINS modeling system.
1-3
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
2 WINHSPF TO AQUATOX LINKAGE
2,1 Introduction
Data from HSPF (Hydrological Simulation Program- FORTRAN) can be linked to the
AQUATOX ecosystem model through the BASINS AQUATOX Extension. HSPF is a model
that simulates the hydrologic processes, and associated water quality processes, on pervious and
impervious land surfaces and in streams and well-mixed impoundments. AQUATOX accepts
data from HSPF assuming that a single HSPF river reach is equivalent to a single AQUATOX
riverine segment. Using the results of an HSPF simulation, AQUATOX accepts input for the
water volume of the system, nutrient time-series loadings, plankton time-series loadings, organic
chemical time-series loadings, and physical characteristics of the system.
To link HSPF data to AQUATOX the following steps are undertaken:
• WinHSPF is executed
• An HSPF simulation is loaded from disk (or using the BASINS interface)
• Appropriate pollutants for linkage to AQUATOX are selected within WinHSPF
The WinHSPF software is told to produce specialized AQUATOX output files
The HSPF simulation is executed
• AQUATOX is invoked from the WinHSPF interface, causing the linkage process
to take place
Additional parameters are specified within AQUATOX to complete the
AQUATOX simulation
• The AQUATOX simulation is run
To link HSPF data to AQUATOX, the WinHSPF interface must be used. This program can be
found under the BASINS Start menu as shown below.
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
Aquatox
^^^^i
Hardware
Microsoft Office Tools
ModelMaker 4
One-Write Plus
Perl
Startup
SYSTAT1Q
Microsoft Access
Microsoft Excel
Microsoft FrontPage
Microsoft PowerPoint
Microsoft Publisher
Microsoft Word
PhotoWise
Windows NT Explorer
WordPerfect 9
BASINS
Basins Projector
Data Extraction
GenScn
Project Builder
QUAL2E
1$ WDMUtil
As an illustrative example, this documentation will walk through the steps required to link the
tutorial.uci file that comes with the BASINS installation set to AQUATOX. To ensure that this
file has not changed during previous uses of WinHSPF, we will start by using the "Create"
option to restore the tutorial.uci file to its original state. (Note: If you wish to retain your
existing tutorial.uci file, please backup the file found in the /basins/data/tutorial/hspf directory to
a different name.)
To open the create project window within WinHSPF go to the "File" menu and select "Create."
The Create Project window contains Select buttons for three types of files, a list for selecting a
meteorological station (met station), and a set of radio buttons for choosing between two land
surface segmentation options.
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AQUATQX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
•: WinHSPF - Create Project
r Fi)es
Select [ BASINS Watershed File |C:\BASIHS\data\tulorial\HSPF\tutQriai?W^d"
Select | Mel WDM Files |C:\BASIHS\data\met data\tutorial.¥Jdm
c&fflaaul Piojecl WDM File
C:\BASlNS\data\tutorial\HSPF\oulpul2. wdm
-Initial Met Station-
PAOQ4390:PA JOHNSTOWN 2
PA007229:PA PUTNEYVILLE 2 SE DAM
pModel Segmentation
(• Grouped
C Individual
OK
Cancel
Start by selecting the tutorial watershed file. Select the
"BASINS\data\tutorial\HSPF\tutorial.wsd" file as shown above. Next, select the Met WDM file.
Select the "BASINS\data\met_data\ tutorial.wdm" file. Finally, specify the project WDM file.
This file is used to store model output and does not have to be a previously existing file.
Once the met WDM file has been specified, the "Initial Met Station" list will be populated with
the identifier corresponding to met stations available for use in the new HSPF project. One item
from this list should be selected in order to have some met data included in the HSPF simulation.
Select the first met station on the list (Johnstown) as shown above.
In the Model Surface Segmentation radio buttons, the Grouped option creates a single model
segment for all collective subbasins, and the Individual creates a single model segment for each
subbasin. For this tutorial leave the selection set to Grouped. Then click the OK button to call
the algorithms that build the new UCI file. The new UCI file will be written to the
"BASINS\data\tutorial\HSPF\" directory.
For more information on using the "Create" screen within WinHSPF, see Lesson 1 in the
Tutorial within the WinHSPF manual (found in the BASINSVdocs directory).
2-3
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
After you have left the "Create" screen, the UCI file will have been created and opened. In the
future, you may open this UCI by clicking on "File," then "Open.," and then selecting the file.
Ffe Ecfe -unctions Help,
D
flv
Acs_
For Imp
Onfii Ci niert
Lookb; | ^ HSPF
Mbase.ud
S^^ffi
|*)tutoif
Type: UCI File
Size: 39,5 KB
File name:
Rci of type:
rfatial uci
f=lr^.I?.--~i L--^~:r -- - -
i-[JSy.--r_-i;-:--:r -•.
JJJSl
«•
User Control Input Files |*.uci]
Open
Cancel
--w
2-4
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
2.2 Selection of Pollutants
In order to pass water quality data to AQUATOX, a user must include several water quality
categories within their HSPF simulation. Click on the Pollutant Selection button. Add NH3.
N02 and NO3, Ortho P, BOD, DO, and Sediment. Click "OK" when finished.
File Edit Functions Help
D
VI
CD
Ol
lf>
"3
11
o
j Point Sources |
Land Surf a
Land
Per
B
Imp
Forest Land
Agri cultural
v 1
Use
•®«IP Eriaft n=
^1 F
^J4- J
I V
IH%. WinHSPF - Pollutant Selection
Be
*-i
ll
* X
Available: Selected:
F.COLIFORM i Add"-7 "I
WATERTEMP
<- Remove
NH3
N02 N03
ORTHO P
BOD
SEDIMENT
DO
1
t
Total
0.
OK
Cancel
2-5
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
2.3 AQUATOX Linkage
Specify AQUATOX output by clicking on the Output Manager button, choosing the
"AQUATOX Linkage" radio button, and clicking on "Add." Choose one or more reaches in the
next dialog, click "OK," and "Close." (Note: If "AQUATOX linkage"is not visible in the
Output Manager window, then the AQUATOX extension has not been installed. Obtain a copy
of the AQUATOX extension and install it. To do this, the file "b3mo_aquatox.avx" must be
obtained and installed into the BASINS\etc\Extensions\Models\ directory)
Hydroloqical Simulation Program -JFWtNHFtHSW;
Fit Edi: Functions Help
D
Fi=li
Per Imp
g Fortft Lind
Agricultural
WmllbPF - Output Manager
-101 x|
Output Tjrpa
Hydrology Calibration
Flow
4? AQUATOX Linkagoj
r Other
Output wB be generated at each 'AQUAT OX Linkage' output location
(a inflow, discharge, surface atea, mean depth, water temperature,
tutpended sedment, otganic chemicals fif available], and inflowt of
nut'ient?, DO, BOD, leffactotv organic carbon, algae, and sediment
Output Locations:
Name
jDwcibtion
RCHRES 3
STREAM 3
Add
JjeiBiiyii
RCHRES1
(Acr««)
2-6
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
2.4 Obtain HSPF Watershed Simulation
Click on the Run HSPF button to obtain a simulation of the watershed.
£xecuting
Now
17*
Complete
EiUmatad time left 16 seconds
Pauie I Cancel
Qutput
Agricultural
Land ETsa |V«fc
Total
cbas |laplnd (Aciras)
0.0
| Pa rind {Adas}
O.D
| Total (Astss)
0.0
2.5 Running AQUATOX from WinHSPF
From the Functions menu choose AQUATOX.
*" Hv.lrn!n™ral Simulation Program- Fortran (H5PH): tutorial -:•, .^v>-X^:;H%l^^%^
Fte Edit j Functions Hdp . .
Ream • y^T7^ f HUt H ""^^-w J«^ T* prn • ^^— i
j P< Control
I1 1 | • Polutant
<* = • _ .
s i = • ^°nT
3lsi FO Eta
_|5! output
J*| RUN
liS View
2 ! J at
^| • BMP
1; ! I Starter
*"( _ HSyPamn
Laad Use |Raae
1 a ^ 1 J
RCHRES2 ^ RCHRES 1
I S
RCHRES 3
has jlmjfltid (Acres) j Pa rind {Acres) Total (Acres)
Tutsi 0.0 ' 0.0 0.0
2-7
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
In the WinHSPF-AQUATOX Linkage dialog window, select the reach to link (only one at a
time). Also, check to make sure the BASINS Watershed File is specii d. If you are running the
tutorial and WinHSPF does not find the default, use "tutorial.wsd" from
\basins\data\tutorial\hspf\. Otherwise, choose the Watershed File that is relevant to the HSPF
simulation you are running. If no watershed file is specified, AQUATOX will not be able to
locate the BASINS GIS files that are relevant to this particular HSPF simulation. In this case,
Channel Length, Channel Slope, Channel Depth, and Maximum Depth data will not be read from
the GIS data.
WnrtlSPI - AQUATOX Linkage
BASINS Wateiified File |c:\bti«nt\dala\hrioiia^tpfViutiirial-md |
Select| Project WDM File |c:VbatmtWirta\tmoriat\h»pfVQUtput.*dm |
Select RCHRES lo Link: IRCHFES 3
jtart AQUATOX | Caned
Land U*«
Total
1 R**ch*»
jlkplnd (Acv«<)
P triad 4Acc*>)
Toc»l (Acir«*>
0.0 0.0 0.0
To initiate AQUATOX, click the "Start AQUATOX" button. (If AQUATOX was installed after
BASINS, you may need to locate the "AQUATOX.EXE" program file in the "PROGRAM"
directory of your AQUATOX installation.) After AQUATOX has started, you will be asket; if
you wish to create a new simulation or modify an existing AQUATOX simulation. To continue
stepping through this tutorial, you should choose a "blank" simulation.
2-8
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AQUATQX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
AQUATOX Base Simulation
Do you wish to load this linkage data into
a "blank" AQUATOX simulation or do you
wish to modify the channel geometry,
organics and nutrient loadings, and
toxicant loadings of an existing
simulation?
Use "Blank" Simulation jl Modify Existing Simulation
If you choose to use a "blank" simulation, the only parameters within the AQUATOX simulation
will be taken from the BASINS linkage. If you choose to modify an existing AQUATOX
simulation, data from BASINS will be used to overwrite variables and time-series from the
original simulation. Note: if you choose to modify an existing AQUATOX simulation,
AQUATOX will rename the file-name of the simulation so that the original simulation remains
intact. You will be able to see exactly which variables in the original simulation were
overwritten by examining the linkage log file as discussed below.
Modifying an existing simulation can be quite useful because BASINS simulations contain little
information about plants and no information about animals within a simulation. Therefore a user
can take an existing AQUATOX simulation with extensive information about plants and animals
and see how it will respond to the flow, nutrient, and toxicant regime found in the BASINS
simulation.
Additionally, a user can perform experiments and see how a particular set of plants and animals
will respond to a different set of flow and nutrient parameters from different reaches within
BASINS or different calibrations of the same BASINS river reach,
Next, you will be asked for which dates you wish to import loadings from the HSPF simulation.
2-9
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
HSPF-AQUATOX- SelertDalttx I o Import
The HSPF simulation has loadings for the following date range:
1/1/1990 to 12/31/1995
You may import the entire date range into AQUATOX or import a subset of loadings.
Loading many years of data that you do not plan to simulate in AQUATOX will slow
the linkage procedure and increase AQUATOX's run time.
Please select the date range to load and press OK:
to 12/31/1995
O.K.
If the HSPF sin ;ulation is fairly long in length, you may wish to reduce the amount of loadings
you bring into AQUATOX. The more years of loadings that you import into AQUATOX, the
longer the linkage process will take, the larger the AQUATOX simulation will be on disk, and
the slower the AQUATOX simulation will run.
Next you will need to characterize the organic matter loadings that are being read into
AQUATOX from HSPF. AQUATOX models organic matter in the water column as four
compartments by splitting organic matter into refractory and labile fractions and dissolved and
paniculate fractions.
AQUATOX has a single parameter that characterizes the percentage of inflow loadings that are
labile versus refractory. This parameter remains constant throughout the course of an
AQUATOX simulation. From HSPF, AQUATOX can obtain two different daily loadings (BOD
and organic refractory carbon) with different refractory to labile splits. BOD is assumed to be
mostly labile in nature, while refractory organic carbon is refractory by definition. If a user has
additional information about the refractory and labile split of BOD modeled within HSPF, the
next dialog screen allows this information to be incorporated into the linkage. To get the best
representation of organic matter coming into the system, the linkage software sums these two
loadings. Then, using a weighted average, AQUATOX determines the most representative
percentage of labile vs. refractory for this total mass of incoming organic matter. In this manner,
the total labile and refractory loadings will be averaged out over the course of the entire
AQUATOX simulation.
2-10
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
Organic matter loadings must also be broken down into paniculate and dissolved fractions for
use in AQUATOX. This percentage may also be entered in the dialog screen shown below. The
default value of 10% particulate is a generally accepted percentage, but this can vary depending
on site-specific conditions.
BASINS-AQUATOX Linkage: Please Characterize Organic Carbon Loadings
AQUATOX will import BOD from the HSPF simulation. This must be characterized as
Labile or Refractory organic matter. It is generally assumed that BOD is predominantly
Labile in nature.
AQUATOX will assume that 10% of the BOD is Refractoiy (90% Labile) unless a different
number using is specified using this screen.
% of BOD that is Refractory
[To
Additionally, AQUATOX must characterize incoming toads of organic matter (BOD and
Refractory Organic Carbon) as Dissolved or Particulate in nature.
AQUATOX will assume thatthe organic loadings are 10% particulate unless a different
number is specified with this screen:
% of Organic Loadings that are Particulate
ho
O.K.
2.6 Linked Simulation
At this point, the linkage procedure should complete itself and the below screen will be
displayed. You may wish to click on "View Log File" to see what actions were taken; the log
file name and location is also copied into the set of notes associated with the AQUATOX study.
These notes can be displayed by clicking on the "Notes" button from that main study screen
(Note: the Notes button is not available when the linkage windows or the Wizard is open).
2-11
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AQUATQX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
, AQI)AfllX — Mrtin Winilnw
L'brwy Scutr? *virtd*/i Msip
n
Study Name; JTU1
Model Run Statu
Toxics Run: I
Conlrol Run: /
Dala Operations:
gg[ InltMComts.
Site
Satup
Holes
Edit With Wli
You have linked an HSPf simulation to AQUATQX.
The tallowing categories of dataware brought into AOUATOXIf they were available;
Simulation Star! and End Time
Dynamic Water Volume Data
Nutrient Time-Series Loadings
Plankton Time-Series Loadings
Organic Chemical Time-Series Loadings
Site Physical Characteristics
To see the detailed lag of the model linkage, please dick the button here—> View Log Fife
You may ttll wish to specify tha tallowing categories of data which are unavailable from the linkage:
Nutrient Initial Conditions
Organic Matter in the Sediment Bed
Additional Plants and or Animals
Wind and Light Loadmgs
Additional Organic Chemicals
Additional Model Characterintics may fan specified using the AOUATOX Simutatton-
Satap Wiiard which is designed for user-friandly input ol modal parameters
10:20 AM
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
2.7 Specification of Additional State Variables and Loadings
Especially if linking to a blank simulation, the user is advised to click the "Continue to Wizard"
button to facilitate specification of state variables and loadings that are not available from the
linkage. There are 19 steps with context-sensitive help. Unless discussed below, the default
values are appropriate for the initial simulation. This section will discuss how a user can set up
the basic ecosystem variables after linking to a blank simulation. You may also reference the
AQUATOX Users Manual (EPA-823-R-04-001) for more information on using the AQUATOX
wizard.
SsfeSi*r - .-date
^ Step 1 . Siinulalwi Type
Step 2: Simulation Period
Step 3. Nutrients
Step 4: Ddntus
Step 5- Plants
Step 6 Invertebrates
Step 7- Flih
Step B. Site Characteristics
Step 9- W«er Volume
Step 1ft Water Temperature
Step 11 :V*d Loadins
Step 12. Light Loading
Step 13: Water pH
Step 14: Inorganc Solds
Step 15: Chemicals
Step 16: inflow Loadings
Step17: D«d Preelpitatkxi
Step 18: Pomt.MUfce Loadings
Step 1 9: Norpolnt-source Loads
(double dicK on an/ step to jump there)
Heto I I WdeProgrN* 1
jfr Edh With Wizard
CffoV
ShKfttlonNaine: TUTOWAUSTREAMS
Stnufston Type: Stream
Step 1: Simulation Type
Enter a Name for the Simulation:
Select The Type of System to be Simulated:
I 8l*>tonSystemDoclm j |?Wo.dPerfea9-IoV...|
Professi
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
Note: While the AQUATOX linkage reads BOD data from HSPF, it converts these data into
organic matter and then adds the data to the time-series of organic refractory carbon data for a
complete set of organic carbon loadings. Therefore, the user should maintain a selection of
"organic matter" in Wizard Step 4.
If diatoms loadings have been linked from the PLANK submodel in HSPF, you will see diatoms
included in Step 5 as shown below ("Diatoms'! :[Diatoms]") , otherwise no animals or plants
will be included in your simulation. If planktonic diatoms have been linked from HSPF thi^
variable should be retained within AQUATOX as this will most closely link the algal simulation
routines within the two modeling frameworks. Although phytoplankton are seldom important in
streams, such a linkage could be important in exporting algae to receiving waters downstream.
Step 1 : Simulation Type
Step 2. Simulation Period
Step 3; Nutrlerrts
Step 4: Detritus
Step 5: Plants
Step 6: ^vertebrates
Step 7: Flstl
Step ft Sile Char*
Step a Water V<*
Step 10: Water Tei
Step 11: Wind Loa
PMVIHmKTi.
dx,t
m.
Step 13: Water pH
Step 14: Inoroanc
Step 15: Chemical!
Step 16: Inflow Lo
Step 17: Direct Pre
Step 18. Point-sou
Step19:Nofinoirit-
(Oouttte click on any
Step 5: Plants to Simulate (Diatoms)
Within AQUATOX, plants are classified as Diatoms, Greens, BlueGreens, Other
Algae, and Macrophytes.
To add a Diatoms Cmnpartment to the simulation, drag Its name front the list of
available Diatoms to the simulation box on the right. To remove a Diatoms
Compartment from the simulation, select It and click the Remove button below.
Available Diatoms:
Actorimella
Diatoms In Simulation:
(Maximum qfTwo)
Sim nation Name: TUTORIAL: STREAM 3
Simulation Type: Stream
Stata Variables in Simulation:
Ammonia u H
NltritO *• H
PhoiphMe as P
Carbon dioxide
Oxygen
Tot. Sutp. Solid!
Rofrac. «ed. detritus
Labile Bed. detrttua
Suep. and diMOlued detritus
BurtedRefrDetr
BurtedLiblleDMr
DIatomBi: [DMonMl
Water Volume
Temperature
Wind Loading
Light
PH
man Summary
2-14
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
For a typical stream you should add periphytic Diatoms, Greens, and Blue-greens, and
Macrophytes. Set their initial conditions to 1 g\m2 in a subsequent screen (unless of course you
have site specific data). You should run the model for several years to "spin up" the model and
avoid transient conditions from the initial guesses; you can then take the end conditions and
substitute them for the original initial conditions in subsequent simulations.
MaHmnmaren
jn|.x|
Step 1: Simulation Type
Step 2: Simulation Period
Step 3: Nutrients
Step 4: Detritus
• Step 5 Plants
Step T. Fish
Step 8: Site Characteristics
Step a Water Volume
Step 10: Water Temperature
Step 11 :Wrid Loading
Step 12: Light Loading
^InjxJ
Simulation Name- TUTORIAL: STREAM I
Simulation Type Stream
State Variable: in Simulation:
AUUA I UK- bimuwcion beiuo wizard
Step 14: Inorganic Solids
Step 15: Chemicals
Step 16: Inflow Loadings
Step 17: Direct Preciptstion
Step 1 8: Point-source Loadings
Step 19: Nonpoint -source Loads
(double click on any step to jump trieiej
Hide Progress |
Step 5: Plant Initial Conditions:
Enter initial conditions for each of the plants in this simulation:
Diatnmsl: [Diatoms]^^
g/sqjn
g/sqjn
S/sqjfl
[StigeocloMiuin,peii.] I
Bl-greEBl: [Attached [7~
blue-greens] I
Mtcrepfcyiel: 17"
[MyriophyllunJ I1
Nitrate as H
-
t
•itus
lUB
Ived detritus
r
ms]
iclonium, perl.]
;hed blue-greens]
lyriopbyllum]
lironomid]
goehaete]
(Baetis)]
idg_m2]
lata]
Edit With Wizard
[Shiner]
NueoJII]
[Stoneroller]
argefnouth BIBS, Lg]
Hide Summary
2-15
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
Several invertebrates should be chosen, and their initial conditions also set to 1, as shown.
Step 1: StnuMlon Type
Step ? Simulation Period
Step 3: Nutrients
Step t: Detritus
Step 5; pitnts
Step 6 Invertebrates
Step? Fish
^IfljJC]
£ Study Information
Version 1*1
nri Plriulnn WartvhloB In Cti irtu
Step 3: Water Volume
Step ID. Water Tempe
Step 11: Wire) Loadns
Step 12. Light LoaOnf
St»p! 3; Water pH
Step 14: Inorganic Sol
Step 15 Chemicals
Step t& Inflow Uadir
Step 17: DireO Free*
Step 16 Pott-source
Step 16. NonpoJrit-soi
HWutte cNck on any Me
Itetp
ftOUA)UX-- MniuldLion Setup Wi/«d
Step 6: Invertebrate Initial Confflttoiu:
Enter Initial conditions fbr aach of die tnvertobratei In this simulation:
S«iF«mbrl
[CUrnwMH]
IF
Cnxerh [bb^tlj |
(
5MHh[Gi
tnrri
^IBJ^J
SknuMtonMame TUTOHALi STREAM 3
State VarMMw h StraJaton:
Ammont*
HKrale
Carbon dtoK
Tat. SiMp. Solid*
Refrtc, «ed. dMrttu*
LtbHe ««L iMtrHu*
Suap. »rnJ dtevohrad dalittui
BurteiffiorrPatr
BMtedLabHeDotr
MatorMt: [Poriphyton, Diftonw]
: [Stlgmdonluni, pMi.]
BI-grMnl: (AMachad bliw-arew»l
Macrophytel: [Myiloptqrihim]
SedFeederl! (diironomidj
itl; [OHgactMBte]
Sntill: CGaKropod Q_m?
PredfrwM: |0danat«]
SmF«*goH*h1i [Mnnaw]
LgFongBFtchl: IBhiaglB]
SmBattamFMMi [StanwnHerl
LnGwmFMHi [LBroatnouUi B«M, La)
arVolurna 2.
m> I
Likewise, several fish would usually be chosen. Initial conditions of 0.2 g\m2 are suggested.
2-16
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
.JO*!
Etepl: SfcnUalfonType
Step 2. Simulation Period
Step 3: Nutrients
Step 4; Detritus
Step 5: Harts
Step 6; Invertebrates
• aep 7: Foh
Step 8: Site Characteristics
Step 9: Water Volume
Step 10 Water Temperature
mt
esseH
' ^H'/Jfftri^^iK3'?*^ jUfilisJ
- StnUstwiNsme: TUTORIAL! STREAM 3
ShmJation Type strewn
Stale Vwh&tes in Smtlatlon.
— <>imutation 5ptup wizard
' Slep 12. LigH Loading
Slop 13. Water pH
Step1fl:horgant Solids
Step IS1 Cheincals
Step 16 Inflow Loadings
Step 17 Drecl Precipitation
Step 16 Pairt-source Losttngs
Step 19 NonpOnt-sauice Loads
(double eick on any step to lump there)
Step?: Fish Initial Conditions:
Enter initial candttUms for these fish in tills simulation:
(/(*»
[StencnDer]
Ammonia »
HMrtte
Hu*
lUB
hwd detritus
r
hyton, DMoma]
KlonJum, peri.]
ihed bkie-greensl
lyrtophyllumt
lironomld]
igoductc]
Hkto Prouren
EdHVflth Wljard
[Shiner]
[Bluegll]
: (Stonero!ler|
MrgomoiMt &*st, Lgj
In the wizard step 8, site characteristics that have been imported from HSPF will be displayed.
Note that the stream bottom is assumed to be 100% run. If the site has significant riffle and pool
features, change these parameters accordingly.
Next, water volume data will be loaded from HSPF so that the water volume in the AQUATOX
reach is identical to the HSPF water volume over the course of the simulation. To make this
possible, the inflow water loaded into AQUATOX has been adjusted for the evaporation and
precipitation predicted by HSPF.
To use the HSPF water volume data, the "Vary Given Inflow and Outflow" option should remain
checked as shown below. For more information about the other water volume modeling choices
on this screen, you can select the "Help" button from this wizard step.
2-17
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
Step 1 :'->.' -"Ifpe
Step I: SnfeMnn Period
Step 3; Nutrients
Step 4 Detritus
Step 5- Ptonts
Step 6- invertebrates
Step 7- F»h
Step S: Sde Ctmiacter ji
> Step 9 Walsr Volume
Step 10 Water Temp*
Step 11 V*ldLoodln!
Step 12 Ughl Loaflms
Stop 13 Water pH
Step 14 Inorganic Set
Step IS. Chemicals
Step 16 Inflow Loadlr
Step 17 Direct Pracip
Step 16 Point-source
Step IS Nonpoint-ioL
(double ctck on any ste
HMp
-inlxi
V Study Information
Version 1.81
»nrl Driulnn \/«ri»KI« In
AGIJAIOX- Simulation Setup Wizard
Step 9: Water Volume Data
AQUATOX cut simulate tha mtar volume in i ereral diOkrant ways:
- The water volume c» be kept constant given an Inflow volume.
- The water Dow can vary dynamically given an Inflow and a discharge.
- The volume can be *et to known value* given an Inflow of water.
- Fora stream, Manning's Equation can be uied to calculate the water volume,
Select a method tor modeling water volume:
Keep Vohune Constant
Vary Given Inflow and Outflow
Set to Known Values
StnuMfonNimK TUTOWAUSTREAM3
SmMnn Type: Mrawn
Stale VirlaOU ti SknuMMi
AmmonM
Nitrite
Ctrbon dioildo
Oxygen
Tot. Sinp. SoHd*
Bnfrtt, *0d detrttuc
Ldrile «ott. detrHtiB
Stop. *od dtaaolv
BurtodRDfrDotr
DMoriMl: [Periphyton, DMunw)
Groanvt: (Sllomclonium, parL]
H-greonl: [At1*chnd
M«njptiyto1: [
SedFoedarl: (Ctilronomld]
Gr»wiM;|M*yfly(»«rtl*)]
Sntfll: (CiMropod o_m2]
Prndlmrtl: |0donitt]
SfnFw«a*FI*h1: [Minnow]
LgFortgeFiihl: (Huaoilll
SmBattomFMH: IStoneroUer]
LgGwneFlthl: [L«nj«iiouth B
W«ter Volume
Because a time-series of water temperature is generally imported from the HSPF linkage, the
user should select the option "Use time-varying temperature" in Wizard Step 10.
Stream simulations are generally nof. sensitive to wind, so use the default with a mean value of 3
m\s.
Wizard step 14 displays inorganic solids loadings within the AQUATOX simulation. Currently
TSS concentrations are linked from HSPF as the summation of modeled sand, silt, and clay.
TSS concentrations can affect light extinction within a simulation, affecting algal growth. A
user can also choose to model sand, silt, and clay as state variables within AQUATOX, but not
directly through the linkage at this time. (As light extinction is currently the only feedback
between inorganic sediments and modeled biota, HSPF simulated TSS concentrations provide a
sufficient source of data. In the future, if more complex feedbacks between sand silt and clay
and the biotic components within AQUATOX are developed, linkage to categorized sand, silt,
and clay data from HSPF will be .ippropriate.)
2-18
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
Oxygen loadings have been converted from kg\hr as predicted by HSPF into mg\L of inflow
water for integration into the AQUATOX interface. Because of this translation, the oxygen
concentration predicted within the AQUATOX reach will be essentially identical to the oxygen
concentration predicted by HSPF. Because of the translation from kg\hr to mg\L of inflow
water, in some cases the inflow loading value may appear to be too high within AQUATOX.
However, when these loadings are brought into the system, and matched with the volume of
inflow water in that time-step, the oxygen concentration within the AQUATOX reach will match
the oxygen concentration predicted by HSPF at that time.
AQUATQX Simulation Setup Wizard j
st
ep 16: Inflow Loadings
The below list shows the modeled components c
simulation. Yon can specify constant or dynamic
components. To do so, select a component Iron
I" Ignore
Inflow Loadings in Simulation:
Inflow NH4
Inflow NO3
Inflow P04 ff
Inflow CO2
In 11 n»' Uw
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
There are usually many modeled components of the water that directly flow into each
AQUATOX simulation. This wizard step is provided so that you may check and edit inflow
loadings for each of these inflow components. You can scroll through the list to see which of
these items have already had dynamic data loaded into them from the HSPF to AQUATOX
linkage. As mentioned above, for several of the new animals you added to the simulation within
the wizard, a "seed" loading may also be appropriate.
Step 1: Simulation Type
Step 2. Simulation Period
Step 3: Nutrients
Step 4: Detrtus
Step £: Plants
Step 6: Invertebrates
Step 7: Fish
Step B: Site Characteristics
Step 9: Water Volume
Step 10: Watei Temperature
Step 11 Wind Loading
Step 12. Light Loading
Step 13: Water pH
Step 14; Inorganic SolWs
Slep 15 Chemicals
> Step 16: Inflow Loadings
Step 17: Direct Precipitation
Step 19. Point-source Loadings
Step 19: Nonpoint-source Loads
(double dick an any step to |Ltrip there)
simulation Name TUTORIAL: STREAM 2
Simulation Type stream
State Variables in Simulation:
Ammonia at H
Hitrato am tt
Halp | I Htde ProgtBag
Hates
Edit With Wizard
AtJUAHIX-- Sinuil.ll IUM Set M|i Wl/*llil ... ,..'.• iif.tja.
st
;p 16: Inflow Loadings
The below list shows the modeled com
simulation. You can specify constant n
components. To do so, select a compo
Inflow Loadings In Simulation:
Inflow NH4
Inflow N03
Inflow PO4
Inflow C02
Inflow Oxygen
Inflow SdgMcIonlum,
Inflow Attache* blue-
Inflow Myriophyllum
Inflow CUronomld
Inflow OUc«chutt
Inflow Mayfly (Baetts
Inflow Gastropod { _m2
iHflnw OidiMflta —
lonents afthe water directly flowing Into the
r dynamic loadings for each of these
nent from the list and enter the loading below:
r list Constant Lf adlii| «f
|" »f fL
(•* Use Dynamic Loalingi
I
Date
12/27/1995
12/28/1995
12/29/1995
12/30/199*
12/31/1995
* I -
Loading 1 ±J
011000
OJfflOO
itis/L
00)00
OWJOO
ODOOO H
-*. Impoft
About Dynmnlc Dtti |
lUh
hcd doirltu*
r
nv»]
Klonium, pnri.]
hod blUB-greena)
jyrlDptQfllum]
ilronomid]
Igochaate]
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
2.8 Run AQUATOX and Plot Results
Run the model for several years and plot the results to see what changes may need to be made.
The "Change Variables" button allows you to select which AQUATOX variables are currently
plotted and whether to plot variables on one or two axes. For further information on the
AQUATOX output capabilities, please see the Users' Manual (referenced below).
£_; AQUATQX- For Windows
Fte Viet* Library 3:jdy Window Hdp
© e
mi&9r*iNr
*]
AQUATOX: Study Information
Wordnn 1 fli
; Oulpul Window— lulu rial ,aps
Study
Mod* Perturbed Simulation j Control Simulation ! Pertutbed Grapli | Control Graph j Difference Graph | Uncaf
CnphSBtup I Chwme VtftaWw I Cow I Print Setup j PrMCnphl Hoto
DalaO
TUTORIAL: STREAM 3 (PERTURBED) 1/31/20029:16:59 AM
m2)
• Qllgochaele (g/m2)
Odonata (g/m2)
Maytly (Baetis (g/m2)
• G astro pod g_m2 (g/m2J
• Bluegill (g/m2)
Shiner (g/mZ)
• Stoneroller (g/m2)
largamou>h Basfg/mZ)
1/2&fl990 1Q6fl9St
1/2SH993 1/2&1394 1K5199S 1/25A1996
(Note: Plotted results above are given as an example only. Your results -will vary depending on the
specific data libraries utilized, the stream reach modeled and the initial conditions chosen)
A site-specific parameter that often needs to be adjusted is mortality for the fish. As mentioned
previously, it may be desirable to take the end biomass values and use them as initial conditions
to avoid a transient response in the first year or two due to inappropriate values. In this
example, all fish started with initial conditions that are too high, and the shiners and stonerollers
attained even higher levels before crashing. (Reasons for the decline can be determined by
saving and plotting the rates.) The decline of all state variables toward the end of the simulation
is the result of declining water levels.
2-21
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 2
For more information on how to use AQUATOX see:
AQUATOX (Release 2)—Modeling Environmental Fate and Ecological Effects in Aquatic
Ecosystems. Volume 1: User's Manual, January 2004, 823-R-04-001.
It is available on-line at: http:\\www.epa.gov\waterscience\models\aQuatox\
2-22
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 3
3 BASINS CIS TO AQUATOX LINKAGE
3.1 Introduction
A user may link data from the BASINS GIS data layer directly to AQUATOX through the
ArcView interface. This can be helpful for gathering information about a site even when there is
no related HSPF or SWAT simulation. The categories of data that are relevant to AQUATOX
within the BASINS GIS layers are listed below:
* Reach Name
• Channel Length
• Mean Depth of Reach
• Channel Slope
• Channel Depth
The steps that are required to link BASINS GIS data to AQUATOX are as follows
• Verify that the AQUATOX and delineation extensions are active.
• Manually or automatically delineate the watershed sub-basins.
• Select the stream segment to be modeled within AQUATOX.
Execute AQUATOX from the BASINS interface.
• Setup and Run the AQUATOX simulation.
3.2 Performing the BASINS to AQUATOX Linkage
Performing this linkage is very similar to linking a stream reach from the BASINS GIS data
layer to HSPF, except that it starts from the BASINS interface rather than the WinHSFP
interface. The following steps are required:
3-1
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 3
Open a BASINS project by selecting BASINS from the'Trograms" menu as shown.
LjjJ, Hardware
E£J, Microsoft Office Tools
LgJ MowlMaket 4
Fart
Slarup
5YSTAT 10
Mmomlt
Mtowoft Pubfohcr
p|j Basins Projector
BASINS
Data Extraction
1 Ws GenScn
Project Builder
QLJAL2E
Uninstall BASINS Pate
WDMUtil
WinHSPF
WinHSPFU
t
Maoia..j
Open "TUTORIAL.APR" or whichever BASINS project file you wish to work with.
Next, verify that the AQUATOX extension is active in your BASINS project by typing Ctrl+B
from the BASINS View and selecting the Models item from the Extension Categories drop-down
list. The AQUATOX entry in the BASINS Extensions list should be visible and selected.
3-2
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 3
BASINS Extension Manager
Select an Extension Category:
[Models
BASINS Extensions:
|? HSPF
|7 PLOAD
7 SWAT
|7 Qual2e
OK
Cancel
Load All Extensions I
About:
AQUATOX Extension, Version 1.0
Adds AQUATOX to the Models menu.
AQUA TERRA Consultants, Decatur, GA.
If AQUATOX is not visible in the BASINS Extensions list when the Models item has been
selected, then the AQUATOX extension has not been installed. Obtain a copy of the AQUATOX
extension and install it. (To do this, the file "b3mo_aquatox.avx" must be obtained and installed
into the BASINS\etc\Extensions\Models\ directory)
If AQUATOX is not selected (checked), click on it to select it.
Also, to use the AQUATOX extension to create an AQUATOX simulation, you must first run
the manual or automatic delineation extensions to create the watershed, sub-basins, streams, and
outlets themes. See section 8 of the BASINS User Manual for details on watershed delineation.
This step requires that the automatic or manual watershed delineation tools are selected in the
"Delineate" extension category within the BASINS Extension Manager. (Note: automatic
delineation requires the Arcview Spatial Analyst software package.)
When delineating the watershed sub-basins, a user should keep in mind that the primary stream
in each sub-basin will become the AQUATOX reach simulated. On an ecological basis, fast-
flowing upstream river segments may be significantly different than downstream slow-flowing
3-3
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 3
backwaters. Therefore, a user should try to keep the size of the reaches small enough so that
dramatically different ecosystems are not simulated within a single AQUATOX reach.
After the watershed has been delineated, the user must select the stream segment that is to
become an AQUATOX stream simulation. Select the "streams" theme and use the "select
feature" tool to make the relevant stream reach turn yellow. Then, select AQUATOX from the
"Models" menu at the top of the screen.
As shown below, you will next be asked whether you wish to "Open AQUATOX with Linked
BASINS Stream data." (Note: Screen capture based on TUTORIAL APR)
Be Edit \Bew Iheme Analysis Surface Graphics Data Assess Delineate Reports Utilities Models Window Help ASCII Tool
BASINS View
Stra ams
A/
SoilClass
HPA022
PA033
PAQS1
PA052
PA053
PA054
PA055
PAOSB
SwjtLandUseClass
HAGRL
_____ FRSD
[""I FRSE
FRST
UCOM
UIDU
URLD
URMO
UTRH
WATR
OutUts
• Llnklngstisim jddid Out I
Paimlt Compliance Systen
Subbaslns
Wattnh«d
Open AQUATOX with Linked-BASINS Stisam data?
Selecting "Yes from this dialog" will open AQUATOX with linked data. Selecting "No"will
open AQUATOX but with no linked data.
3.3 Using AQUATOX after a BASINS to AQUATOX Linkage
3-4
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 3
As was the case for the HSPF linkage, a user may choose to link to a blank AQUATOX
simulation or overwrite relevant parameters and loadings in an existing AQUATOX simulation.
See Section 2.5 for more information about this choice.
Next, the AQUATOX Linkage Information screen becomes visible. This screen shows the types
of information that have been linked to AQUATOX and the additional parameters that are
required to fully specify an AQUATOX simulation.
Basins Linkage Information
You have linked BASINS GIS Data to AQUATOX.
The-followrng categories of data were brought into AQUATOX if they were available:
Site Name
Site Physical Characteristics
To see the detailed log of the model linkage, please click the button here —> View Log File
AQUATOX Requires many parameters that are not available from the BASINS GIS Data Layers.
Some of these parameters are summarized below:
Simulation Start and End Time
Organic Matter in the Sediment Bed
Additional Plants and or Animals
Wind and Light Loadings
Additional Organic Chemicals
Nutrient Time-Series Loadings
Organic Chemical Time-Series Loadings
Nutrient Initial Conditions.
Additional Model Characteristics may be specified using the AQUATOX Simulation-
Setup Wizard which is designed for user-friendly input of model parameters
Bypass Wizard
Continue to-Wizard
All parameters that are loaded from the GIS data layers are logged in a text file. The user may
view and print the log file from this screen by selecting the "View Log File" button. (If a user
wishes to refer to the log file at a later time, the location of this log file is written into the
"Notes" dialog, available through the main screen of the AQUATOX interface.)
3-5
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 3
An expert AQUATOX user may choose to bypass the user-friendly AQUATOX simulation setup
wizard. Beginning users are encouraged to continue to the wizard to finish specifying the
required parameters.
3-6
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 4
4 SWAT TO AQUATOX LINKAGE
4.1 Introduction:
AQUATOX has the capability to read input and output data from SWAT (Soil and Water
Assessment Tool) version 2000. AQUATOX will read data about channel geometry, nutrient
and pesticide loadings, simulation period, water flow, and organic and inorganic sediment
loadings.
To perform this linkage, the following steps must take place.
• The user must complete the specification and calibration of a SWAT 2000 simulation
using the BASINS 3.0 interface. (This requires the Arcview Spatial Analyst software
package.)
• The user must start AQUATOX and select the SWAT output file that contains the
relevant data.
• The SWAT sub-basin the user wishes to gather data from will then be selected.
AQUATOX will read all relevant data from the SWAT input and output files.
• Finally, the user is required to fill in AQUATOX parameters that are not available
through the SWAT linkage.
When the process is complete an AQUATOX simulation that corresponds to the main channel
within a SWAT sub-basin will have been created. This SWAT to AQUATOX linkage process is
described in more detail below.
4.2 Running a SWAT Simulation
This section will outline some relevant points about running SWAT if a user intends to link the
SWAT simulation to the AQUATOX model. Complete documentation as to how to run the
SWAT 2000 model can be found in the B2SWAT.chm file located in the BASINS\DOCS
directory following the installation of BASINS 3.0.
The steps required to run a SWAT model are roughly outlined below:
» Automatically delineate the watershed.
* Define land use and soil themes for the SWAT model
• Define the HRUs (hydrologic response units) distribution for the SWAT model
"Edit Input" within the SWAT view
Write all input data files within the SWAT view (under the "Input" menu)
Run the SWAT model
4-1
-------
AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 4
At each step of the above process, a user should bear in mind that the main reach within a single
SWAT sub-basin will later correspond to a single AQUATOX reach. This may affect a user's
choices within the automatic delineation or input choices for the SWAT model. Smaller sub-
basins are generally most appropriate for an AQUATOX simulation so that the ecosystem does
not change dramatically within a single sub-basin.
When a user has completed all the steps required above, and has chosen to "Run SWAT," the
following dialog box appears:
iiel Up and Run SWAT model simulation
reuuu ui simuidiiuri.
Starting date
(January .zj |1 jd |1993 .r
Month Day Year
Ending date
| | December jj 1 31 jd 1 1 995 ^J
Month Day Year
| Daily rain /CN / Daily jj (* Skewed no
C ! Mitred! e>tpa
**" Priestley-Taylor method
rmal _,
" Penman-Monteith method
f" Read in
e+ i ti 01 1 i .• .1 J r-l i J j .• 1 > L i i i > .
P1 Not active (? Variable Storage
r Active r Muskingum
r». . . t o .• r» .- ^
r Daily
_ [Weed-B-Gon
(• Monthly
r Yearly
--...,,,. Quality Processes: Quality Processes:
i* Not Active
- , ". ;T Not Active T Not Active
C Active • ; .
. ^Active & Active.
•..> . 1 J L
^_^_- Rpinin Input Fil^1 Bsn
General Water Quality Input File: . Wwq
•; •. ,. -V.-- . ^ • - - :
Chekttiput Ranges
Help |,:; Exit 1 SetupSWATRun 1 - - .
HunbWAl
As can be seen from the lower left portion of this screen, the SWAT model can produce output in
"daily," "monthly," or" yearly" time steps. To link the model to AQUATOX, daily or monthly
time-steps must be chosen. Annual time-steps do not provide the data resolution required by
AQUATOX.
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 4
A user also can select the SWAT simulation period at the top of this screen. If the SWAT model
has many sub-basins and is being run for many years, choosing monthly time-steps is probably
the best choice as output file sizes become unwieldy otherwise.
When run with monthly time steps, SWAT sums mass loadings over the course of each month
and averages concentrations over the course of each month. In the case of summed mass
loadings, AQUATOX divides the total loading by the days in the month to get an average daily
loading. Then, in order to prevent interpolation between data-points, AQUATOX loads these
values as data points at the beginning and the end of each month. This creates some "stair-
stepping" of input data into AQUATOX, but presents the best accounting for mass-and
concentration data as provided by SWAT.
While the SWAT model can track several pesticides over land within a simulation, it only tracks
the movement of a single pesticide through the main channel. This means only a single pesticide
may be passed from SWAT to AQUATOX at a given time. The choice of which pesticide to
move into the main channel can be seen under the "Routing Pesticide" header within the screen
shown above. If the user wishes to track a specific pesticide from SWAT within AQUATOX, it
must be selected within this dialog box.
Because AQUATOX only models organic chemicals, the linkage assumes that any pesticide data
passed to AQUATOX is in the form of an organic chemical. The user will later be asked to
specify the organic chemical being modeled from a list of available chemicals, or will be
required to input chemical-specific data about the organic chemical utilized.
Finally, a user may select to have "Stream Water Quality Processes" be "active" or "not-active"
within a SWAT simulation. Within SWAT, nutrient transformations in the stream are controlled
by the in-stream water quality component of the model. Even if active nutrient transformations
within the stream are not utilized, SWAT still calculates the movement of nutrients through the
system due to inflow loadings, and loadings from point and non-point sources. More
information about SWAT's modeling of nutrients within a stream may be found in Chapter 25 of
the SWAT user's manual (swat2000.PDF, located in the BASINS\DOCS\SWAT directory).
Nutrients that can be modeled within SWAT include Ammonia, Nitrate, Phosphate, Oxygen, and
.Biochemical Oxygen Demand. As AQUATOX also models each of these nutrient
compartments, these variables can be linked directly into AQUATOX from SWAT. Total
suspended solids (TSS) may also be linked from SWAT to AQUATOX.
In-stream water-quality processes modeled by SWAT within the sub-basin that is linked to
AQUATOX will not affect the AQUATOX simulation. AQUATOX only reads the inflow
loadings of nutrients within a particular SWAT reach and calculates in-stream water-quality
processes within its own derivatives. However, in-stream water-quality processes that occur
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upstream of the AQUATOX reach will affect the loadings of nutrients into AQUATOX, so the
user may still wish to utilize this option within SWAT.
Important Note: By using a text file editor and editing the SWAT Input Control Code file
(*.COD file) a user may select to limit the number of variables that are output in a SWAT reach
file (*.RCH file). As the SWAT-AQUATOX linkage requires most of the variables from'a
SWAT reach file to be present, the linkage will not work properly when the RCH files are
limited in this manner.
4.3 Loading SWAT data into AQUATOX
To load SWAT data into AQUATOX, a user must first start AQUATOX. This can be done in
two ways. The user can run AQUATOX directly from the BASINS 3.0 menu by selecting
"AQUATOX" from the "Models" menu within the BASINS view:
jsess Delineate Reports Utilities
Window Help
SWAT
ELOAD
Qual2e
Qual2e Visualize
AQUATOX
MSPF
The user will then be asked whether she\he wishes to "Open AQUATOX with Linked BASINS
Stream data."- Selecting "No" indicates to the BASINS interface that the user is not trying to link
CIS data to AQUATOX. AQUATOX will then be started with no attached data.
If a user has already run the SWAT model and does not need to have BASINS open, the user can
run AQUATOX directly from the "Start" menu.
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 4
Basins
Hardware
Microsoft Office Tools
ModelMaker 4
One-Write Plus
Perl
Startup
SYSTAT1D
Microsoft Access
Microsoft Excel
Microsoft FrontPage
Microsoft PowerPoint
Microsoft Publisher
Microsoft Word
PhotoWise
Windows NT Explorer
WordPerfect 9
SUSS C^Eudofa
Once AQUATOX has started, a user can load SWAT data into AQUATOX by clicking on the
"Import Data from SWAT" button in the toolbar.
A
Import Data From SWAT [""
Alternatively, a user may select the "Import Data from SWAT" option from the "File" menu at
the upper left of the screen.
Next, a dialog box appears asking the user to select the completed SWAT simulation from which
to import data. The user must select the "Control InputVOutput File" (File.CIO) that is
associated with the SWAT simulation that is to be linked. This file will be found in the
"txtinout" directory under the directory named after your SWAT project. The full directory
structure will look as follows:
"BASINS\MODELOUT\SWAT\{your project name}\TXTINOUT\FILE.CIO"
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CHAPTER 4
The user will then see the following dialog box:
SWAT Linkage
Please select a sub-basin within the
SWAT simulation you have specified
jSubBasin
! OK
1 d
II Cancel
All sub-basins that are included in the SWAT simulation will be shown within the pull-down
interface. The user should select the relevant sub-basin to be linked to AQUATOX. The
resulting AQUATOX water body will correspond to the main channel within this sub-basin.
4.4 The Linkage Process
As with all BASINS-AQUATOX linkages, a user may choose to link SWAT parameters to a
"blank" AQUATOX simulation or overwrite relevant parameters and loadings in an existing
AQUATOX simulation. See Section 2.5 for more information about this choice.
AQUATOX models organic matter in four compartments:
• Labile Dissolved Organic Matter
• Labile Particulate Organic Matter
• Refractory Dissolved Organic Matter
• Refractory Particulate Organic Matter
Within SWAT, BOD data is not broken down into these compartments. For this reason, a user
must specify the percentage of BOD that is Refractory and the percentage of BOD that is
Particulate organic matter. Default values are provided within the AQUATOX dialog box as
shown, and these values should be used if the user has no additional information about the BOD
loading.
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 4
BASINS-AQUATOX Linkage: Please Characterize Qiganic Carbon Loadings
AQUATOX will import BOD from the SWAT simulation. This must be characterized as
Labile or Refractory organic matter. It is generally assumed that BOD is predominantly
Labile in nature.
AQUATOX will assume that 10% of the BOD is Refractory (90% Labile) unless a different
number using is specified using this screen.
% of BOD that is Refractory
10
Additionally, AQUATOX must characterize incoming loads of BOD as Dissolved or
Particulate in nature.
AQUATOX will assume that the organic loadings are 10% particuiate unless a different
number is specified with this screen:
% of Organic Loadings that are Particulate
[To
O.K.
The user will then be prompted as to whether a pesticide is tracked within the SWAT reach. If
the user selects "yes," the loadings of the "Routing Pesticide" specified above will be linked into
the AQUATOX simulation. To model an organic toxicant within AQUATOX, parameters are
required about the chemical properties and toxicity of the substance. After selecting to model
the routing pesticide, the user will be prompted to load these chemical parameters from a
database of organic toxicants. Alternatively, the user can press "cancel" and enter these
chemical parameters later, within the AQUATOX "chemical underlying data" interface.
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 4
Select Chemical Parameter Data to Load into Pesticide:
Entry Name:
Aldicarb
Anthracene
Atrazlne
Azlnphos
Bromacil
Bromoxynil
Butyl ate
Carbaryi
Carbofuran
Chlordane
Chlorpyrifos
Chrysene
Cyanazine
DDT
Dia^lnnn
Default File! C Other File
Default File-- Chemical.CDB
From the SWAT linkage, AQUATOX will load data about channel geometry, nutrient and
pesticide loadings, simulation period, water.flow, and organic and inorganic sediment loadings.
In each case when a parameter value or time-series is loaded, AQUATOX writes the source and
result of the linkage into the log file. The log file can be viewed by pressing the "View Log
File" button from the screen shown below.
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AQUATOX (RELEASE 2) BASINS EXTENSION
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Basins Linkage Information
A new AQUATOX simulation has been created using the SWAT data you selected
The following categories of data were brought into AQUATOX if they were available:
-Simulation Startand EndTime
Inflow and Outflow of Water
Nutrients and BOD Time-Series Loadings
Pesticide Time-Series Loadings
Site Physical Characteristics
Time Varying TSS Concentrations
To see the detailed log ot the model linkage, please click the button here->
View Log File
You may still wish to specify1 the following categories of data which are unavailable from the linkage'
Nutrient Initial Conditions WaterTernperature
Organic Matter in the Sediment Bed Additional Organic Chemicals
Additional Plants and or Animals
Wind and Light Loadings
Additional Model Characteristics may be specified using the AQUATOX Simulation-
Setup Wizard which is designed for user-friendly input of model parameters
Bypass Wizard
Continue to Wizard
From this screen, the user may continue to the AQUATOX Wizard to complete setting up the
new AQUATOX simulation or may bypass this step and work with AQUATOX through the
main AQUATOX interface.
The data required to finish specifying a SWAT simulation are almost identical to those required
after an HSPF to AQUATOX linkage. The only difference is that water temperature is available
from an HSPF simulation but must be specified after a SWAT to AQUATOX linkage. For more
information about finishing the specification of the AQUATOX simulation, please see sections
2.7 and 2.8 ("Specification of Additional State Variables and Loadings" and "Run AQUATOX
and Plot Results") in the "WINHSPF to AQUATOX Linkage"chapter .
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 5
5 AQUATOX TO GENSCN LINKAGE
5.1 Introduction
After an AQUATOX simulation has been run, a user may view output data using AQUATOX's
output screens, a user may export the data to several database and spreadsheet formats, or the
user may choose to send the output data to GenScn, the post-processor within BASINS. GenScn
offers several statistical functions that are not available through the AQUATOX output screen
such as comparison of predicted and observed time-series and duration analysis.
5.2 Linking to GenScn
There are three ways to link to GenScn from within AQUATOX.
1. Select "Export to GenScn" from the "File" menu.
":. Click the Export to GenScn button in the toolbar as shown here;
3. Click the "Export All Results to GenScn" button on the Export Results Dialog.
All three of these options are enabled when AQUATOX has run a simulation and has results in
memory. These options are not enabled if GenScn has not been installed on a user's computer.
When AQUATOX exports data to GenScn, a set of two files are written to the AQUATOX
"OUTPUT" directory. (This is the "OUTPUT" sub-directory within the directory in which
AQUATOX was installed). A file with an"RDB" extension is written that contains all of the
AQUATOX time-series results (control and perturbed), and a file with an "STA" extension is
written that tells GenScn the format and location of the RDB file.
5.3 Using GenScn
The AQUATOX linkage produces a set of GenScn data within a single "Location" (the
AQUATOX river reach). There are up to two "Scenarios" produced, "Control" and "Perturbed,"
depending on which types of AQUATOX runs have been executed. (The "OBSERVED"
scenario that appears within GenScn is empty and should be ignored.) Finally, each AQUATOX
output variable is available under the GenScn "constituent" menu.
To produce a graph, a user can select the location, scenario, and constituent to graph and then
press the plus button at the top of the "Time Series" list. The constituent will appear as a new
item on the "Time Series" list. With this item selected, the user can then click on the "Generate
Graphs" button at the bottom of the screen and a graph generation dialog is created.
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AQUATOX (RELEASE 2) BASINS EXTENSION
CHAPTER 5
For more information about how to use GenScn see GenScn.pdf located in the
BASINS\DOCS\GENSCN directory.
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