&EPA
United States
Environmental Protection
Agency
Office of Water (4305)
EPA-823-B-05-001
October 2005
AQUATOX (RELEASE 2.1)
MODELING ENVIRONMENTAL FATE
AND ECOLOGICAL EFFECTS IN
AQUATIC ECOSYSTEMS
VOLUME 3: USER'S MANUAL FOR THE
BASINS (VERSION 3.1) EXTENSION TO
AQUATOX RELEASE 2.1
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AQUATOX (RELEASE 2.1)
MODELING ENVIRONMENTAL FATE
AND ECOLOGICAL EFFECTS
IN AQUATIC ECOSYSTEMS
VOLUME 3: User's Manual for the BASINS (Version 3.1)
Extension to AQUATOX Release 2.1
Jonathan S. Clough
OCTOBER 2005
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 an enhanced version of an 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 BASINS Extension to the AQUATOX model has been developed by Dr. Richard A. Park of
Eco Modeling; the AQUATOX-side programming, 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 Arc View 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 ii
ACKNOWLEDGMENTS n
1 INTRODUCTION TO THE BASINS AQUATOX EXTENSION U.
1.1 Overview and Background 1-1
1.2 System Requirements 1-3
2 WINHSPF TO AQUATOX LINKAGE 2J,
2.1 Introduction 2-1
2.2 Selection of Pollutants 2-5
2.3 AQUATOX Linkage 2-6
2.4 Obtain HSPF Watershed Simulation 2-7
2.5 Running AQUATOX from WinHSPF 2-7
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 3-5
4 SWAT TO AQUATOX LINKAGE 4J,
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 5J.
5.1 Introduction 5-1
5.2 Linking to GenScn 5-1
5.3 Using GenScn 5-1
in
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AQUATOX (RELEASE 2.1) 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 2.1) BASINS EXTENSION CHAPTER 1
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)
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 2.1) 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 GIS Layer
^ I \
I
I
AQUATOX
I
I
T
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/Kor more information
about BASINS Hardware and software requirements. Within BASINS, Arc View's Spatial Analyst
extension is required to run the SWAT model and to automatically delineate rivers within the
BASINS modeling system.
1-2
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AQUATOX (RELEASE 2.1) 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, 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. WinHSPF provides an
interactive Windows interface for the HSPF model. WinHSPF assists the user in building UCI files
from GIS data, especially data from the BASINS system. This program can be found under the
BASINS Start menu as shown below.
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
Aquatox
la Basins
Hardware
Microsoft Office Tools
ModelMaker 4
One-Write Plus
Perl
Startup
jsj SYS TAT 10
Microsoft Access
Microsoft Excel
Microsoft FrontPage
Microsoft PowerPoint
Microsoft Publisher
Microsoft Word
GS PhotoWise
Windows NT Explorer
WordPerfect 9
BASINS
Basins Projector
Data Extraction
GenScn
Project Builder
QUAL2E
WDMUtil
I WinHSPFLt
Comma... | ^Microso...|
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 proj ect 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.
2-2
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
WinHSPF - Create Project
Files
BASINS Watershed File |C: \B AS IN S \data\tutorial\H S PF\tutorial. md
Met WDM Files | C:\BASIMS\data\met_data\tutorial.wdm
Project WDM File
C:\BASINS\data\tutorial\HSPF\output2.wdm
Initial Met Station
PA004390:PA JOHNSTOWN 2
PAOQ7229:PA PUTNEYVILLE 2 SE DAM
Model Segmentation
( Grouped
P Individual
OK
Cancel
Start by selecting the tutorial watershed file. Select the "B ASINS\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 BASINS\docs directory).
2-2
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AQUATOX (RELEASE 2.1) 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.
Hydrological Simulation Program - Fortran (HS
File Edit Functions Help
y
Per Imp
Open Project
Look in: _J HSPF
«1base,uei
File name:
Files of type;
tutorial, uci
am-
Open
User Control Input Files (K.uci]
Cancel
2-4
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AQUATOX (RELEASE 2.1) 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, NO2
and NO3, Ortho P, BOD, DO, and Sediment. Click "OK" when finished.
Hydrological Simulation Program - Fortran (HSPF): tutorial
File Edit Functions Help
D
Per Imp
£ Forest Land
rc
La
Agricultural
r_
[E=
WinHSPF - Pollutant Selection
Available:
Land Use
Total
Re
F.COLIFORM
METALS
WATERTEMP
0_K
Selected:
HII3
N02N03
ORTHO P
BOD
SEDIMENT
DO
^|nj_xj
Cancel
f
o.
2-5
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AQUATOX (RELEASE 2.1) 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)
Hydrotoqical Simulation Program - Fortran (HSPF): tutorial
File Edit Functions Help
D
Per Imp
LS Forest Land
I
Agii cultural
Land Use
Total
WinHSPF - Output Manager
Output Type
r
Hydrology Calibration
Flow
AQUATOX Linkage;
bitnei
Output will be generated at each 'AQLIATOX Linkage' output location
for inflow, discharge, surface area, mean depth, water temperature,
suspended sediment, organic chemicals (if available), and inflows of
nutrients, DO, BOD, refractory organic carbon, algae, and sediment.
Output Locations:
Name
| Description
RCHRES 3
STREAM 3
Add | fie
I. X
Total (Acres?
Close
2-6
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
Win HSPF-Add Output
Operation:
RCHRES1 (STREAM 1)
RCHRES2(STREAM2)
RCHRES3 STREAM 3
WDM Location ID: [RCH3~
Base WDM DSN: |
OK
1000
Hourly
Daily
Cancel
The above dialog box appears when you have chosen to add an AQUATOX output location. If
using WinHSPF "build 2.3 revision 1" or higher, when adding AQUATOX output, there will be
options to output time-series on an hourly or a daily basis. AQUATOX release 2.1 allows only
daily time-series to be imported so this feature is not relevant to Release 2.1. If hourly data are
chosen, AQUATOX Release 2.1 will aggregate the hourly data into daily values. Future
versions of AQUATOX will allow the input of hourly time-steps so this feature is provided for
forward compatibility.
2-7
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
2.4 Obtain HSPF Watershed Simulation
Click on the Run HSPF button to obtain a simulation of the watershed.
Executing
Now
Complete
Estimated time left 1G seconds
Pause
Cancel
Output
5 -1 Agricultural
I mm
2.5 Running AQUATOX from WinHSPF
From the Functions menu choose AQUATOX.
Hvdrological Simulation Program - Fortran (HSPF): tutorial
File Edit Functions Help
Land Use
Reaches
Total
1 Implnd
0
(Acres)
0
|perlnd
0
(Acres)
0
| Total
C
(Acres)
.0
D
1
| Met Segs
d Surface
(j
I
i
Reach ]m ,fT\ , NH( H u. jgL r_ _ . £-,
P' Control
1 Pollutant
Point
Fo Edit
(Output
RUN
View
IBMP
Starter
HSPFParm
Land Use 1 Reac
I \ fc. \
RCHRES2 RCHRES1
\,. ^^
^V^ ^^
i S
RCHRES3
aes j Implnd (Acres) [ Perlnd (Acres) Tot-al (Acres)
local 0.0 0.0 0.0 |
2-8
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AQUATOX (RELEASE 2.1) 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 specified. 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.
" WinHSPF - AQUATOX Linkage
| Setec(;| BASINS Wateished File |c:\bagins\dataMutoiial\hsp(MutoiiaLwsd
Select | Pioject WDM File c:\bdsins\ddta\tutofial\hspf\output.wdm
Select RCHRES to Link:
(RCHRESS
SJart AQUATOX Cancel
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 asked 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.
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AQUATOX (RELEASE 2.1) 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 !
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.
Choosing "modify existing simulation" is often useful because the HSPF-AQUATOX linkage
does not pass any information about plants or animals in the system. 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.
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
HSPF-AQUATOX: Select Dates To Import
HSPF simulation has loadings for the following date range:
1/1/1990 to 12/31/1995
(ou may import the entire date range into AQUATOX or import a subset of loadings.
_oading many years of data that you do not plan to simulate in AQUATOX will slow
the linkage procedure and increase AQUATOX's run time.
'lease select the date range to load and press OK:
to 12/31,1995
O.K.
If the HSPF simulation is fairly long in duration, 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.
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
HSPF-AQUATOX Linkage: Phosphate Loadings
HSPF includes several forms of phosphorus as listed below. AQUATOX can accept all of
these forms or a subset of these depending on how the check-boxes are set below:
Phosphate Forms to Link
lv> include dissolved oithophosphate
[>7 include adsorbed orthophosphate
IV include organic phosphate
The phosphorus state variable is designated "Total Soluble P." Phosphorus that is not
bioavailable (i.e. immobilized phosphorus/ acid soluble phosphorus) may be specified
using the FracAvail parameter:
Bioavailable Fraction
AQUATOX can model inflow phosphate as Total Soluble P. Alternatively, inflow can be
modeled as Total P by accounting for phosphorus contributed by detrital and
phytoplankton loads and back-calculating the amount available as freely dissolved
nutrients.
Inflow is Total Soluble P
Inflow Represents Total P
O.K.
If using WinHSPF "build 2.3 revision 1" or higher, you will next see the above dialog box
asking for the characterization of phosphate as modeled in HSPF. Total Phosphate in HSPF
includes dissolved orthophosphate, adsorbed orthophosphate, and organic phosphate. These
compartments need to be transformed into bioavailable phosphate within AQUATOX. To do
this, you can choose which of the HSPF forms of phosphate to link, choose a bioavailable
fraction, and also select whether the phosphate being linked best represents Total Soluble P or
Total P. If you don't have any particular information about the bioavailability of the phosphate
you are modeling in HSPF, a reasonable assumption is to pass all phosphate forms and use the
Total P linkage as shown above. Choosing a bioavailable fraction of 1.0, as shown above,
indicates that all phosphate being passed is bioavailable (perhaps through P-solubilizing bacterial
action).
When using earlier versions of WinHSPF, dissolved orthophosphate is the only form of
phosphate that is automatically passed into AQUATOX.
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AQUATOX (RELEASE 2.1) BASINS EXTENSION CHAPTER 2
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
particulate 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 refractory organic 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.
Organic matter loadings must also be broken down into particulate 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.
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
BASINS-AQUATQX Linkage: Please Chaiacterize 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% ofthgBOD is Refractory (90% Labile) unless a different
number using is specified using this screen.
of BOD that is Refractory
Additionally, AQUATOX must characterize incoming loads of organic matter (BOD and
Refractory Organic Carbon) as Dissolved or Particulate in nature.
AQUATOX will assume that the 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).
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
t
File View Library Study Window Help
(modified)
AQUATOX: Study Information
Study Name: [TUTORIAL: STREAM 3
ti- anrl fkriuirm
lAe In Qfi irlv
Model Run Status:
Perturbed Run: No
Control Run: Wo
Data Operations:
Initial Conds.
Basins Linkage Information
Chemical
Site
Setup
Notes
Edit With Wizai
You have linked an HSPF simulation to AQUATOX.
The following categories of data were brought into AQUATOX if they were available:
Simulation Start and End Time
DynamicWaterVolurne Data
Nutrient Time-Series Loadings
Organic Chemical Time-Series Loadings
Site Physical Characteristics
To seethe detailed log of the model linkage, please click the button here> View Log File
You may still wish to specify the following 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 Loadings
Additional Organic Chemicals
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
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AQUATOX (RELEASE 2.1) 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.
BBEB -H->
> Step 1 : Simulation Type
Step 2: Simulation Period
Step 3 Nutrients
Step 4: DetrJus
Step 5: Plants
Step 6 Invertebrates
Step 7- Fish
Step 3: Sle Characteristics
Step 9: Wiser Volume
Step 1 0' Water Temperature
Step 11: Wind Loading
Step 1 2: Light Loading
Step 1 3: Water pH
Step 1 4: Inorganic Solids
Step 1 5: Chemicals
Step 16: Inflow Loadings
Step 1 7: Direct Preciprtation
Step 1 8: Point-source Loadings
Step 1 9: Nonpoint-source Loads
(double click on any step to jump there)
Help | | Hide Progress ]
'
& Edit With Wizard
Simulation Name TUTORIAL: STREAM 3
Simulation Type Stream
Step 1: Simulation Type
Select The Type of System to be Simulated:
Pond
Lake
Stream
r Reservoir
r Lunnocorral
Hide Summary |
Norton System Doctor | f£ WordPerfect 9 - [C:\....\ JjPtogram
«AQUATOX ProfcHi...
2-16
-------
AQUATOX (RELEASE 2.1) 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 refractory organic carbon data for a
complete set of organic carbon loadings. Therefore, the user should maintain a selection of
"organic matter " in Wizard Step 4.
For a typical stream you should add Diatoms, 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.
Step 1: Simulation Type
Step 2: Simulation Period
Step 3: Nutrients
Step 4: Detritus
-^ Step 5: Plants
Step 6: Invertebrates
Step 7; Pish
Step 8: Site Characteristics
Step 9: Water Volume
Step 10: Water Temperature
Step 11: Wind Loading
Step 12: Light Loading
Step 13: Water pH
Step 14: Inorganic Solids
Step 15: Chemicals
Step 16: Inflow Loadings
Step 17: Direct Precipitation
Step 18: Point-source Loadings
Step 19: Nonpoint-source Loads
(double click on any step to jump there)
Simulation Name: TUTORIAL: STREAM 2
Simulation Type: stream
Help | Hide Progress |
Step 5: Plant Initial Conditions:
Enter initial conditions for each of the plants in this simulation:
Diatoms 1: [Diatoms] J7
mg/L
Greens1: IT"
[Sn"geoclonium,peri.] I
Bl-greeni: [Attached TT~
blue-greens] I
Macrophyiel: Hj
[Myiiopnyllum] I
Edit With Wizard
Plus
itus
Ived detritus
ms]
aclonium, peri.]
-hed blue-greens]
lyriophyllum]
tironomid]
igochaete]
(Baetis)]
od g_m2]
iata]
[Shiner]
[Bluegill]
[Stoneroller]
argemouth Bass, Lg]
Hide Summary |
2-17
-------
AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
Several invertebrates should be chosen, and their initial conditions also set to 1, as shown.
Stepl- Simulation Type
Step 2: Simulation Period
Step 3. Nutrients
Step 4: Detritus
Step 5: Plants
^ Step 6: Invertebrates
Step 7: Fish
Steps. Site Character1
Step 9. Water Volume
Step 10: Water Tempe
Step 11: Wind Lcadini
Step 12: Light Loadira
Step 13; Water pH
Step 14: Inorganic Sol
Step 15: Chemicals
Step 16: Inflow Loadir
Step 17: Direct Precip
Step 18: Point-source
Step 19: Nonpoint-501
(double click on any ste
i
<: Study Information
Version 1.91
n^ Hriirin/H VariaMae In Cti t
Sun' .lalion Name: TUTORIAL: STREAM 3
Simulation Type: stream
Slate Variables in Simulation:
AQUATOX-- Simulation Setup Wizard
Step 6: Invertebrate Initial Conditions:
Enter initial conditions for each of the invertebrates in this simulation:
SeJFeederl:
[CMnnanudl
Grazerl: [Mayfly
(Bactis)]
Snaill: [Gastropod
g_m21
Predbnrtl:[Odonata)
Ammonia
Nitrate
Phosphate
Carbon dioxide
Oxygen
Tot. Susp. Solids
Refrac. sed. detritus
Labile sed. detritus
Susp. and dissolved detritus
BuriedRefrDetr
BuriedLabileDetr
Diatomsl: [Periphyton, Diatoms]
Greensl: [Stigeoclonium, peri.]
Bl-greenl: (Attached blue-greens]
Macrophytel: [Myriophyllum]
SedFeederl: [Chironomid]
SedFeeder2: [Oligochaete]
Grazerl: [Mayfly (Baelis))
Snaill: [Gastropod g_m2]
PredlnvM: (Odanata)
SmForageFishl: [Minnow]
LgForageFishl: [Bluegill]
SrnRottomf isht: (Staneroller|
LgGameFisM: [Largemouth Bass. Lg]
Water Volume
Hide Summary |
Likewise, several fish would usually be chosen. Initial conditions of 0.2 g\m2 are suggested.
2-18
-------
AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
Step 1: Simulation Type
Step 2 Simulation Period
Step 3: Nutrients
Step4:Detrlus
Step 5: Plants
Step 6: Invertebrates
> Step 7 Fish
Step 6: Site Characteristics
Step 9: Water Volume
Step 10: Water Temperature
Step 11: Wind Loading
Step 12: Light Loading
Step 13 Water pH
Step 14, Inorganic Solids
Step 15: Chemicals
Step 16: Inflow Loadings
Step 17. Di-ect Preciplation
Step 1B Point-source Loadings
Step 19. Nonpoint-source Loads
(double click on any step to jump there)
Help | Hide Progress |
|£i]i{Jfiij^^ljjJJ{ll££]|:f£4LiU^X^I
Step
7: Fish Initial Conditions:
Enter initial conditions for these fish in this simulation:
°1skLr] °'2 *****
LgForageFishl: ^ «
[Bluegill|
Sm&ottmnHshl: rt -
.. _. , U.2 g.'sujfi
[Stoneivller]
[L^S,FB "s; °-2 i*****
ftus
(us
lued detritus
ihyton. Diatoms)
iclonium, peri.]
:hed blue-greens]
lyriophylliirn]
lironomid]
igoehaete]
>dsjr,21
iat.|
[Shiner]
[Bluegilll
: IStoneroller]
arqemouth Bass, Lg|
Hide Summary j
_
d
Edit With Wizard
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.
2-19
-------
AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 2
Step 1 Simulation Type
Step 2. Simulation Period
Step 3: Nutrients
Step 4: Detrius
Step 5: Plants
Step 6: Invertebrates
Step 7: Fish
Step 6: Site Character^
* Step 9: Water Volume
Step 10: Water Tempi
Step 11: Wind Loadint
Step 12: Light Loadint
Step 13: Water pH
Step 14: Inorganic Sol
Step 1 5- Chemicals
Step 16: Inflow Loadir
Step 1 7: DTect Precip
Step 16: Point-source
Step 19: Nonpoint-soi
(double click on any ste
C: Study Information
Version 1.91
nrf Rriuirtn
AQIIATOX- Simulation Setup WiHard
Edit With V
Step 9: Water Volume Data
AQUATOX can simulate the water volume in several different ways:
- The water volume can be kept constant given an inflow volume.
- The water flow can vary dynamically given an inflow and a discharge.
- The volume can be set to known values given an inflow of water.
- For a stream, Manning's Equation can be used to calculate the water volume.
Select a method for modeling water volume:
c Keep Volume Constant
" Vary Given Inflow and Outflow
<~ Set to Known Values
f Use Mannings Equation
Simulation Name: TUTORIAL: STREAM 3
Simulation Type: stream
Slate Variables in Emulation:
Ammonia
Nitrate
Phosphate
Carbon dioxide
Oxygen
Tot. Susp. Solids
Refrac. sed. detritus
Labile sed. detritus
Susp. and dissolved detritus
BuriedRefrDetr
BuriedLabileDetr
Diatoms'!: [Periphyton, Diatoms]
Greensl: [Stigeoclonium, peri.]
-greenl: (Attached blue-greens]
Macrophytel: [Myriophyflum]
SedFeederl: [Chironomid]
SedFeederZ: [Oligochaete]
Grazer1:[MaynV(Baetis>]
MI mi: [Gastropod g_m2|
Predlnvtl: |0donata]
SmForageFishl: [Minnow]
LgForageFishl: [Bluegill]
SmBottomFishl; [Stoneroller]
LgGameFishl: [Largemouth Bass, Lg]
Water Volume
Hide Summary |
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 not 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 appropriate.)
2-20
-------
AQUATOX (RELEASE 2.1) 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.
AQUATOX- Simulation Setup Wizard
Step 16: Inflow Loadings
The below list shows the modeled components of the water directly flowing into the
simulation. You can specify constant or dynamic loadings for each of these
components. To do so, select a component from the list and enter the loading below:
F" Ignore ALL Loadings for this State Variable
'" Use Constant Loading of
Inflow Loadings in Simulation:
Inflow NH4
Inflow NO3
InflowF04
Inflow CO2
I
(" Use Dynamic Loadings
Inflow Susp and Diss Detr
Inflow Diatoms
Inflow loadings serve two purposes: they can be realistic time-series predicted by HSPF, or they
can be "seed" values to account for colonization and recruitment. The recommendation is to use
loadings of 0.00001 for plants, fish, and invertebrates other than insects. A value of 0.0001 is
suggested for insects to account for drift and eggs from free-flying adults.
2-21
-------
AQUATOX (RELEASE 2.1) 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; Detritus
Step 5: Plants
Step 6: Invertebrates
Step 7: Fish
Step 8: Site Characteristics
Step 9: Water Volume
Step 10: Water Temperature
Step 11: Wind Loading
Step 12: Light Loading
Step 13; Water pH
Step 14: Inorganic Solids
Step 15: Chemicals
-^ Step 16: Inflow Loadings
Step 17: Direct Precipitation
Step 13; Point-source Loadings
Step 13: Monpoint-source Loads
(double click on any step to jump there)
Simulation Name: TUTORIAL: STREAM 1
Simulation Type: stream
State Variables in Simulation:
Ammonia as H
Nitrate as H
AQUATOX- Simulation Setup Wizard
Help | Hide Progress |
Step 16: Inflow Loadings
The below list shows the modeled components of the water directly flowing into the
simulation. You can specify constant or dynamic loadings for each of these
components. To do so. select a component from the list and enter the loading below:
Inflow Loadings in Simulation:
Inflow NH4
Inflow NO3
Inflow PO4
Inflow C02
Inflow Oxygen
Inflow Snsp and Piss Deo
Inflow Stigeocloniiun,
Inflow Attachedblue-
Inflow Myriophyllum
Inflow Chirononud
Inflow Oligochaete
Inflow Mayfly (Baetis
Inflow Gastropod s m.2
Tnflnw Odniinia
Use Constant Loading of
|iT~ ~ mg/L
' Use Dynamic Loadings
Date
I2.'27/1995
12/28/1995
12/29/1995
12/30/1995
> 12/31/1995
Loading _^L
0.0000
0.0000
0.0000
0.0000
OJOOOO
mg/L
I Import |
About Dynamic Data
Ived detritus
ms]
iiiurn, peri.]
hed blue-greens]
iophyllum]
itronomid]
igochaete]
]
od g_m2]
iata]
[Shiner]
[Bluegill]
[Stoneroller]
gemouth Bass, Lg]
Hide Summary
2-22
-------
AQUATOX (RELEASE 2.1) 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).
File Vtew Ibrary Window Help
I
AQUATOX: Study Information
\forcinn 1 Q1
Perturbed Simulation Control Simulation | Perturbed Graph; Control Graph | Difference Graph Uncei <
Graph Setup | Change Variables | Copy | Prim Setup | Print Graph | Help
Data 0
TUTORIAL: STREAM 3 (PERTURBED) 101(2002 9:16:59 AM
-------
AQUATOX (RELEASE 2.1) 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\
2-24
-------
AQUATOX (RELEASE 2.1) 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
Arc View 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:
5-1
-------
AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 3
Open a BASINS project by selecting BASINS from the "Programs" menu as shown.
H aid ware
Microsoft Of'ice Tools
MocclMahei 4
Dne-WlitePlus
Pal
Starrup
EYSTAT 10
Microsoft ACCOSJ
Microsoft [HOC!
Microsoft Pcwcrjont
MicrosdtPiii
Microsoft Wsrd
.. tkl'r
| i^^J
Windows MT
Vcitf-'errec'
Basins Projector
BA5IN5
Data Extraction
Gen5cn
Project Builder
QUAL2E
Uninstall BASINS Pate
WDMUtil
WinHSPF
WinHSPFLt
Comrra... | [^Mcroso...|
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.
3-1
-------
AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 3
BASINS Extension Manager
Select an Extension Category:
| Models
BASINS Extensions:
HSPF
PLOAD
SWAT
AGWA
OK
Cancel
Load All Extensions
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
-------
AQUATOX (RELEASE 2.1) 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)
Edit i/iew Iheme Analysis Surface firaphics Data Assess Delineate Reports Utilities Models Window Help ASCII Tool
A/
SoilClass
| | PA022
PA033
PA044
PA051
PA052
PA063
|| PA054
| | PA055
| | PAOS6
| | TXW
SwiatLandUseClass
BAGRL
FRSD
||FRSE
i HFRST
| | UCOM
| | UIDLI
i~| URLD
| | IJRMD
HUTRN
WATR
Outlets
Linking stream added Liuil
Permit Compliance Systen
Subbasins
Opening AQUATOX
Open AQUATOX with Linked BASINS Stream data?
i Yes I
No
Cancel
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
5-L
-------
AQUATOX (RELEASE 2.1) 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 following categories of data were brought into AQUATOX if they were available:
Site Name
Site Physical Characteristics
To seethe 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 2.1) 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.
5-6
-------
AQUATOX (RELEASE 2.1) 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 BASINSVDOCS
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 2.1) 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:
|*2 Set Up and Run SWAT model simulation Q|
n _i [ I L-
Starting date
| January ^ 1 |l
Month Day
| Daily rain /CN / Daily ^_
_ . ,. _,
("Not active (T >
<~ Active C
\ II
<~ Daily
( Monthly
<~ Yearly
_d 1 1993 ^J
Year
n ( n _r L -i_ L-
(" Skewed normal
*" I.Mixed.exponentiai]
water routing method: Channel
Variable Storage ^ No
vluskingum ' '
n i- -j
|Weed-B-Gon ^J
Help E
Ending date
| December _^J 1 31 ^J |1995 _d
Month Day Year
(* Priestley-Taylor method
(" Penman-Monteith method
<" Hargreaves method
f Read in
Quality Processes: Quality Processes:
Active
<~ Not Active C Not Active
ive
<" Active (* Active
. . , .
Basin Input File: Bsn
General Water Quality Input File: Wwq
Chek,nput Ranges
:it Setup SWAT Run
Run SWAT
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.
4-2
-------
AQUATOX (RELEASE 2.1) 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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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 4
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:
BASINS 3.1
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Window Help
BASINS View
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 4
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
GIS 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.
Basins
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Once AQUATOX has started, a user can load SWAT data into AQUATOX by clicking on the
"Import Data from SWAT" button in the toolbar.
ImportDataFromSWATp
Alternatively, a user may select the "Import Data from SWAT" option from the "File" menu at
the upper left of the screen.
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 4
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 Input\Output 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_proj ect_name}\TXTINOUT\FILE.CIO"
The user will then see the following dialog box:
SWAT Linkage
Please select a sub-basin within the
SWAT simulation you have specified
SubBasin 1
OK
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
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AQUATOX (RELEASE 2.1) BASINS EXTENSION
CHAPTER 4
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.
BASINS-AQUATOX Linkage: Please Characterize Organic 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
fTF
Additionally, AQUATOX must characterize incoming loads of BOD as Dissolved or
Particulate in nature.
AQUATOX will assume that the organic loadings are 10% particulate 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 2.1) BASINS EXTENSION
CHAPTER 4
Default File; r Other File
Aldicarb
Anthracene
Atrazine
Azinphos
Bromacil
Bromoxynil
Butyl ate
Carbaryl
Carbofuran
Chlordane
Chlorpyrifos
Chrysene
Cyanazine
DDT
Defau t F e-- Chem ca .CDS
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 2.1) BASINS EXTENSION
CHAPTER 4
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 Start and End Time
Inflow and Outflow of Water
Nutrients and BOD Time-Series Loadings
Pesticide Time-Series Loadings
Site Physical Characteristics
Time Varying TSS Concentrations
To seethe detailed log of the model linkage, please click the button here-> i Vle':'".t;°9f.i!?.
You may still wish to specify the following categories of data which are unavailable from the linkage:
Nutrient Initial Conditions Water Temperature
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 2.1) 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.
1
2. 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
AQUATOXwas 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.
5-1
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AQUATOX (RELEASE 2.1) 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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