EPA/600/B-15/290
Quantitative Microbial Risk Assessment Tutorial
Pour Point Analysis of Land-applied Microbial Loadings and
Comparison of Simulated and Gaging Station Results
Gene Whelan
Kurt Wolfe
Rajbir Parmar
Michael Galvin
Marirosa Molina
Richard Zepp
U.S. Environmental Protection Agency
Office of Research and Development
National Exposure Research Laboratory
Athens, GA
Keewook Kim
University of Idaho
Idaho National Laboratory
Center for Advanced Energy Studies
Idaho Falls, Idaho
Paul Duda
Mark Gray
AQUA TERRA Consultants, a Division of RESPEC, INC.
Decatur, GA 30030
11/7/15
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Summary
This tutorial demonstrates a pour point analysis
• Initiates execution of the SDMPB.
• Navigates the SDMPB.
• Chooses a pour point within a watershed, delineates the sub-area that contributes to that pour
point, and collects data for it.
• Considers land application of microbes.
• Develops necessary input files to execute HSPF.
• Develops necessary input file to view results from the SDMPB and HSPF.
• Views simulation results for flows and microbial densities with BASINS.
• Retrieves observed daily USGS flows and compares to simulated daily flows at the pour point.
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Pour Point Analysis of Land-applied Microbial Loadings
and Comparison of Simulated and Gaging Station Results
PURPOSE
Automate data acquisition for input data requirements of a confederation of models
OBJECTIVE
Pre-populate input data files of models automatically. Importation of point source data will be
performed in the context of an assessment of microbial fate and transport, within a pour-point
delineated watershed, by capturing contextual data for the watershed model WinHSPF (a.k.a. HSPF) and
pre-populating its input data files to account for:
• Overland runoff;
• Snow accumulation/melt;
• Hourly simulations;
• Remote-sensing NLDAS, coupled with monitoring, meteorological data;
• Land-applied microbial loadings;
• Instream point source microbial loadings; and
• Microbial fate and transport.
DEMONSTRATION
This tutorial reviews screens, icons, and basic functions of the SDMProjectBuilder (SDMPB), performs a
Pour Point simulation for Microbial Fate and Transport using HSPF, and analyzes and visualizes results at
multiple locations in the watershed using BASINS. It demonstrates how to
• Initiate execution of the SDMPB.
• Navigate the SDMPB.
• Choose a pour point within a watershed, delineate the sub-area that contributes to it, and
collect data for it.
• Consider land application of microbes.
• Develop necessary input files to execute HSPF.
• Develop necessary input files to view results from the SDMPB and HSPF.
• View simulation results for flows and microbial densities with BASINS.
• Retrieve observed daily USGS flows and compare to simulated daily flows at the pour point.
SOFTWARE ACCESS, RETRIEVAL, AND DOWNLOAD
Instructions for access, retrieval, and download of the SDMProjectBuilder, HSPF, and BASINS software
products are provided by Whelan et al. (2015a). When installed, three desktop icons appear.
\m
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TUTORIAL - TABLE OF CONTENTS
EXECUTE THE SDMProjectBuilder
• Identify a Project
• Identify a HUC-8 and Watershed of Interest
MODIFY AND IMPORT LOCAL DATA FILES
• Identify and Modify Local Source-term Data
o MonthlyFirstOrderDieOffRateConstants.csv
o WildlifeDensities.csv
• Import Local Data Files
EXEUCUTE THE PROJECT BUILDER
EXECUTE HSPF, SIMULATING FLOW AND MICROBIAL TRANSPORT
VIEW HSPF SIMULATION RESULTS WITH BASINS
• Register Flow and Microbial Densities with BASINS
• View the Discharge Time Series
• View the Microbial Density Time Series
RETRIEVE OBSERVED DAILY USGS FLOWS AND COMPARE THEM TO SIMULATED DAILY FLOWS AT THE
POUR POINT
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EXECUTE THE SDMProjectBuilder
Identify a Project
Whelan et al. (2015b) provide a detailed tutorial for identifying an 8-digit HUC. Whelan et al. (2015c)
extend this tutorial and review screens, icons, and basic functions of how to take output from the
SDMProjectBuilder (SDMPB) and perform a fate and transport analysis of land application of microbes
within a HUC-12. This section follows the instructions of Whelan et al. (2015b, 2015c) without going into
similar detail, describes creation of a working folder, and briefly identifies the HUC-8 and a watershed
based on a pour point.
1. Execute the SDMProjectBuilder (SDMPB) by clicking on the shortcut icon displayed on the computer
screen.
2. Create a folder where you have administrative rights.
3. From the Menu Bar, select "SDMProjectBuilder", then "New SDM Project".
•oje
Legei
H t
Import Local Data Files
Run Project Builder
Options
4. Create a new file within the working folder. A map of the Unites States including Alaska, Hawaii, and
Puerto Rico should appear.
File SDMPmj«tBuiider
.
J HUC-8
DN
)t-19667879.41607 Y: 2016625.91599 HUC-8:1 feature selected X:-19667879.41607 ¥: 201662591599 HUC-& 1 feature wteclw)
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Identify a HUC-8 and Watershed of Interest
5. Under "SDMProjectBuilder", select "Nav Helper".
=:-e
Leget
B0
I
SDMProjectBuilder \_ Extensions
New SDMProi ect
QjavHelpep
Import Local Data Files
Run Project Builder
Options
6. Fill out the screen as below, choose "Zoom", then "Get Data".
HUCS: HS3HI
GZ] NHD* Ei HUC12S
7. A screen similar to the following will appear.
[» « U « * 111 O . • • » H 3
0K.U-
i . «_>«ni
8. Choose "Close".
Navigation Helper
County: Manrtowoc County
[7] NHD+ [71 HUC12s
Zoom
Zoom
Zoom
Get Data
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9. In this example, we assess only the four uppermost 12-digit HUCs in the Manitowoc watershed
(highlighted in the following figure). The pour point does not have to coincide with any particular
location or HUC, although in this case it will match four 12-digit HUCs.
10. Using Zoom In,
zoom to this area. Check the "nhdflowline" Map Layer. If it is not at the
top of the listing, move it there to ensure it is the outermost projection and will appear on the map.
11. To see where all ponded waters are located, check the Map Layer titled "nhdwaterbody for
04030101". This provides a picture of all water sources and their locations.
- ,
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12. For this example, you will identify the pour point that includes only the four uppermost HUC-12s, as
designated by the red circle on this map projection.
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MODIFY AND IMPORT LOCAL DATA FILES
This section identifies and modifies local data files, imports local data files to the SDMPB, executes the
project builder, and collects map layers describing environmental characteristics.
Identify and Modify Local Source-term Data
The user can modify certain source-term parameters and influence the degree of resolution of the
watershed through 12 local-data files that are installed when a user begins a new project. They are
located in the "LocalData" folder within the working folder. Descriptions of the local source-term data
are in Whelan et al. (2015d). Whelan et al. (2015c, 2015e) provide additional examples identifying and
modifying the local source-term data example default files. Metadata associated with the parameters
contained within each file, including definitions and units, are summarized in Table 1. Five of the 12 files
denote locations such as the location of point sources, animal locations, septic systems, etc. For this
example problem:
• MonthlyFirstOrderDieOffRateConstants.csv - Different first order die-off rates will be used for
land-applied microbes. They will be changed from 0.36 and 0.51 d"1 to 0.064"1.
• WildlifeDensities.csv - Wildlife densities will be updated to 29 deer/mi2 from 5 deer/mi2 to
more accurately reflect densities in this area (WDNR, 2015).
• AnimalLL.csv, FCProdRates.csv, GrazingDays.csv, ManureApplication.csv, SepticsLL.csv,
SepticsDataWatershed.csv-Animal numbers and locations and septic-system locations will use
default values, since they are applicable to the Manitowoc River basin; no change to these files
is required.
• PointSourceLL.csv, PointSourceData.csv, BoundaryPoints.csv, OutputPoints.csv - There are no
point sources or intermediate points. Since these default locations are outside the watershed,
no modifications to these files are necessary.
The only files that will be modified will be MonthlyFirstOrderDieOffRateConstants.csv and
WildlifeDensities.csv.
MonthlyFirstOrderDieOffRateConstants.csv
13. Using Notepad, the original file includes die-off rate constants by month with units of d"1:
1 MonthlyFirstOr...
File Edit Format View jHelp
Month, Di eof f Ratecontant
January,0.36
February,0.36
March,0. 36
April,0.51
May,0. 51
June,0.51
July.O. 51
August,0.51
September,0.51
October,0.36
November,0.36
December,0.36
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Table 1. Names of default support files and input types to which the user has access for modifications
FILE NAME
INPUT DATA AND DEFINITION
UNITS
Domestic Animals and Wildlife
AnimalLLcsv
FCProdRates.csv
GrazingDays.csv
ManureApplication.csv
MonthlyFirstOrderDieOffRateConstants.csv
WildlifeDensities.csv
Domestic animal locations by Latitude and
Longitude
Domestic animal numbers by type and
location
Production or shedding rate of microbes
from the domestic animal, which equals
the multiple of the 1) Domestic animal
shedding rate in mass of waste (wet
weight) per time and 2) Microbial
concentration based on mass of waste shed
by the domestic animal
Typical microbial production or shedding
rate per wildlife per area
Number of grazing days per domestic
animal per month
Fraction of the number of grazing days that
beef cattle spend in a stream per month
Fraction of manure applied to soil each
month per domestic animal
Fraction of amount of manure shed by the
domestic animal incorporated into soil
First-order microbial inactivation/die-off
rate on the land surface per month
Typical number of wildlife per unit area by
land use type
Degree (by
fraction)
Number
Counts/d/animal
Counts/d/ac
Number
fraction
fraction
fraction
1/d
Number/mi2
Point Sources
PointSourceLLcsv
PointSourceData.csv
Point source locations by Latitude and
Longitude
Annual-average flow for each point source
Annual-average microbial loading rate for
each point source
Annual-average chemical loading rate for
each point source
Degree (by
fraction)
ft3/s
Counts/yr
Lbs/yr
Septic Systems
SepticsLL.csv
SepticsDataWatershed.csv
Septic system locations by Latitude and
Longitude
Number of people per septic unit
Average fraction of septic systems that fail
Average septic overcharge rate per person
Typical microbial density of septic
overcharge reaching the stream
Degree (by
fraction)
Number
fraction
gal/d/person
Counts/L
Intermediate Points
BoundaryPoints.csv
OutputPoints.csv
Boundary point locations by Latitude and
Longitude
Output point locations by Latitude and
Longitude
Degree (by
fraction)
Degree (by
fraction)
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14. Change the rate constants to 0.064 d"1, so the file becomes:
MonthlyFirstOr,.,
File Edit Format View Help
>lonth, Di eof f Ratecontant
January,0.064
February,0.064
March,0.064
April,0.064
May,0.064
June.O.064
July.O.064
August,0.064
September,0.064
October,0.064
November,0.064
December,0.064
15. Save as a csv file, and exit.
WildlifeDensities. csv
16. Using Notepad, the original file includes the following locations:
J WildlifeDensities.csv - Notepad
File Edit Format View Help
Animal ,DensityPerSqMile_Cropland,DensityPerSqMile_Pasture,DensityPersqMile_Forest ,DensityPersqMile_Builtup
Duck,0,0,0,0
Goose,6,0,0,0
Deer,5,5,5,0
Beaver,0,0,0,0
Raccoon,0,0,0,0
other wildlife,0,0,0,0
17. Update the file by changing the "5" to "29" so it looks like the following:
Wi!dlifeDensities.csv - Notepad
File Edit Format View Help
,DensityPerSqMile_Cropl and,DensityPerSqMile_Pasture,DensityPerSqMile_Forest,DensityPerSqMile_Builtup
Duck,0,0,0,0
Goose,0,0,0,0
Deer,29,29,29,0
Beaver,0,0,0,0
Raccoon,0,0,0,0
otherwi 1 dl if e, 0,0,0,0
•
18. Save as a csv file, and exit.
19. Ensure that all revised files have replaced the original files contained in the "LocalData" folder under
the working directory.
Import Local Data Files
After replacing files in the "LocalData" folder within the working folder, these data can be registered
with the SDMProjecBuilder (SDMPB).
10
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20. From the Menu Bar, choose "SDMProjectBuilder", then "Import Local Data Files". AnimaILL,
SepticsLL, and PointSourceLL will be registered using the procedure outlined by Whelan et al.
(2015c, 2015d).
21. To register "AnimaILL", highlight "AnimaILL" and choose "Open File". Wait until the screen changes,
then "Close File."
e Edit Local Data
Loral Data Files
Boundary Points LL
OutputPointsLL
PointSourceLL
SepticsLL
Edit File
Start Adding Points
Delete Selected Point (s) on Map
_, Edit Local Data
Local Data Files
Boundaiy Points LL
OutputPointsLL
PointSourceLL
SepticsLL
1
""
Open File
Edit File
Start Adding Points
Delete Selected Point(s)on Map
22. The map layer for animal locations (typically farms) will appear on the map, like that below:
> O_ » • » • k. B H 4 •{• il
11
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23. To register "SepticsLL", highlight "SepticsLL" and choose "Open File". When the screen changes,
choose "Close File."
Start Adding Points
Delete Selected Point(s)on Map
.AnmalLL
Boundary PointsLL
QutpulPointsLL
Point SourceLL
0
Start Adding Points
Delete Selected Polnt(s) on Map
24. When complete, "Close" the screen.
a-' Edit Local Data
.Animal LL
BoundaryPointsLL
OutputPointsLL
Point SourceLL
A
P
| Start Mding Points "|
Delete Selected Portlslon Map
12
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EXEUCUTE THE PROJECT BUILDER
The project builder delineates the watershed of interest and collects environmental map layers that
support the microbial assessment.
25. From the Menu Bar, choose "SDMProjectBuilder", then "Run Project Builder".
SDM Project E
26. Choose "Pour Point". For "Maximum Upstream", use an upstream distance that reflects the distance
to the upstream divide. Because this HUC-8 is an upstream HUC and has a boundary that is not
totally adjacent to another HUC, a large "Maximum Upstream" distance can be used, such as "200"
km.
EH Build Frames SDM Project
Select Area Of Interest On Map Of Enter Keyfs| Below
Select By: O HUC-8 O HUC-12 O Catchment
Current Map Layer © Pour Point O Bon
Press the button below when ready to select a pour point
Maximum Upstream: 200 | km [ Select Pour Point On Map
Cancel
27. Go back to the map and zoom in on the pour point location, using the Zoom icon
to clearly
see the location which has been highlighted with the red circle and arrow. Zoom in because
identifying the location is crucial to placing the pointer in the next step. If this location is incorrectly
identified, you may inadvertently include more area than is needed for the assessment by getting
too close to the HUC-12 boundary.
13
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28. Click "Select Pour Point On Map".
H Build Frames SDM Project
Select Area 01 Interest On Map Or Enter Key(s] Below
SeleclBji: O HUC-8 O HUC-12 O Catchment Current Map Layer ®PourPoint O Box
Press the button below when ready to select a pour point.
Maximum Upstream: 200 | km [ Select Pour Point On Map
Cancel
29. On the map, click on the pour point location which should be just downstream of the junction (see
arrow). The location is very sensitive, so zoom in accordingly.
30. Click "Next" on the "Build FRAMES SDM Project" interface.
ffl Build Frames SDM Project
Select Area Of Interest On Map Or Enter Keji(s) Below
Select By: O HUC-3 O HUC-12 O Catchment County n. merit Map Layer © Pour Pcint O Box
Maximum Upstream: 200 I km Select Pour Point On Map
Cancel
Next
14
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31. The aqua square is the pour point and the delineated area is blue in the figure below.
32. When you Zoom Out, I you see the red highlighted area associated with the assessment,
corresponding to the four upstream HUC-12s that comprise the watershed draining through the
pour point.
, •
33. After choosing "Next", complete the "Build FRAMES SDM Project" as shown. Use values included in
this figure. To ensure adequate sizes, define the "Minimum Catchment Size" and "Minimum
Flowline Lengths" as "3" and "3", respectively. Land areas less than 10% of the total have been
factored into other Map Layers, as noted by the "Ignore Landuse Areas Below Fraction" of "0.1".
Check "HSPF"; the "Degree Day" method is chosen for snow accumulation and melt and "Microbes"
for land applied simulation. Output is "Hourly".
Parameters For Mode! Generation
3 Minimum Catchment Siie {square kilometers}
3 Minimum Rowline Length (kilometers)
0 1 Ignore landuse Areas Below Fraction
rf990Simulation Slart Year
2000 Smdabon Bid fear
•/ HSPF Output Interval: Hourly -
Snow: Degree Day —
!_«/] lAcrabes
H Land-Applied Chemical
Q SWAT : WAT 2005 Database |c.Vs
15
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34. Click "Next" and the following screen appears. Change the screen to that below; make no changes to
the "Save Project As" text box unless there is a special folder location:
a^ Build Frames SDM Project
Data Options
Soil
>»' STATSGO
• SSURGO
Elevation
Delineation
Save Project As
| Cancel ~[
Meteorologic
•«• BASINS
, '. NCDC Enter NCDC Token Here
(3 NLDAS Precipitation
NHDPIus Elevation
NHDPIus
C:\Users\gwhdan\iemTechnologies\SDMPB\TESTC\TESTC .mwprj
u/1 Add Layera To Map During Project Creation Previous
= |S|«e«
'
'
CD
Build ~]
35. Now choose "Build" which takes approximately 25 minutes to complete for a pour point with four
HUC-12s, depending on the computer.
36. Some computers may ask several times if the re-project map layer should match the map coordinate
system; choose "Yes" each time.
Projection Mismatch
Reproject map layer to match the map coordinate system? This will not affect the source file.
Yes1 |No
37. When the SDMPB has finished running, choose "Open in BASINS".
Finished Building Project
C:\ProgramFiles\iemTechnrjlogies\SDMProjertBuilder\data\PrjurPointl2175050-3\PourPointl2175050-3.mwpri
[ Ok ] I Open Folder 1 Open in BASINS I
38. BASINS will automatically open with the SDMPB map layers for this assessment:
39. Go to the BASINS menu, choose "File/' then "Save". Choose "File", then "Exit" to close BASINS.
16
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EXECUTE HSPF, SIMULATING FLOW AND MICROBIAL TRANSPORT
40. To open the HSPF project, activate the WinHSPF3.0 icon on the Windows desktop:
41. From the "File" menu, choose "Open", navigate to the UCI file and click "Open".
| Locate UCI file to open
I « SDMPB > TESTS > HSPF
Organise " New folder
MC
TESTA
TESTB
HSPF
HSPF-PEST
huc!2
LocilDiti
met
MHDPIus
NLCD
pcs
SDMPB_061215
a.. M0301010406.uci
^
Filenime M0301010406.ua
- |udfil(a('.ucil
42. The new HSPF project will appear in the HSPF GUI, with the watershed workflow schematic shown
below.
:
. ..
43. To run the HSPF simulation, click the "Run Simulation" icon. Save the HSPF project by clicking "File",
then "Save" on the main menu bar. Leave the HSPF workflow schematic screen open since you may
want to refer to it when operating in the BASINS interface.
• .
[Run Simulation!
17
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VIEW HSPF SIMULATION RESULTS WITH BASINS
Register Flow and Microbial Densities with BASINS
44. If BASINS is not already open, start BASINS with the BASINS 4.1 icon on the desktop. At the
"Welcome" window, open your existing project.
45. Navigate to the project folder (e.g., TESTB) and select the *.mwprj file. Note that the name of the
file reflects your selection. Be certain the file name you assigned to your assessment matches the
*.mwprj extension. An example:
MlOpen
*•-?
Organize
« SDMPB * TESTB 1 T ., 1 1
New folder
pesU.3 * Name
SARATimeSeriesUtilrty
"sPF-PES,
"'"
-;TA
TESTB |E| jj|*
HSPF
HSPF-PEST
huc!2
Laea3BMi
met , , | „, [
Filename TESTB.mwpij - JMipWinda
[ Ope"
l^-t
TF
e - a •
Dat
LC
!-
;
w
w
1
M Project (*. mwprj) '
^ | Caned ~~[
46. Click "Open" so the SDMPB project will open in BASINS 4.1. The following screen, showing domestic
animal and septic locations, which overlay each other and NLDAS stations,, will appear:
•' • SI. H-3-A-7-X-B
18
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47. Go to the "File", "Manage Data" menu in the BASINS menu bar. With the "Data Sources" window
open, see that no times series data sources are pre-loaded except, possibly, a met.wdm file. Time
series data sources from the HSPF simulation are needed to view the simulation results, so they will
be added.
Annlysi
Help
i • •C:'lUsers1gv/h«l»n\ieinTechiKilo§i«1SDMPB'.TESTOjneR™t.wdm (21)
48. To add time series data source, select "File", then "Open" from the "Data Sources" window. A
selection window appears:
File
Basins Observed WaterQualrty DBF
; QiGen Output
HSPF Sinaiy Output
Integrated Surface Houity Data
i -NASAGDSRIe
; NOM Houriy Predp Data, Archive Format, TD-3240
I NOAA Summary of the Day. Archive Format. TD-3200
: Read Data Wrth Scnpt
i STORE! Water Quality
i SWAT Data Ffes
I -SWATOutput DBF
i SWMM Input
! Timeseries DBF
• Timesenes EXCEL
; Tlmeseries SWHH5 Output
USGS RDB Rle
WRDB Miive
49. Select "WDM Time Series", then "OK". Navigate to the HSPF project folder, and select the file
"SDMProject.wdm". It contains the output time series written from HSPF to WDM. [Note: For the
pour point simulation, the wdm name should be SDMProject. Although an equivalent *.wdm file
name may be there, do not select met.wdm file.]
| Locate UCI file to open
\rctl HSPF f> \
Organize -• New folder $= ~ QJ @
JS TESTB
Ji TESTC
HSPF
HSPF-PEST
ji hud.2
Name [
| a SDMProject.uci 1
LocalData
log
met
NHDPIus
,j)jl NLCD
pcs
Filename SDMProject.uci
v
>
- UCI files (*,uci)
Open Cancel
19
-------
50. With this data source open, the file name appears in the "Data Sources" window.
[Note: Other WDM files may already be registered in the list.]
•I Data Si
File Analysis Help
BWDM
1 ..C:\Usere''8i
:—'-
51. The HSPF Binary file (*.hbn) only exists after executing HSPF; hourly data associated with the "RO"
designation (Reach Outflow) are associated with the *.hbn file. To view results of the Microbial
simulation, the HSPF binary output file must be added to the current BASINS project. From the "Data
Sources" window, choose "File", then "Open". The window below will appear to select a data
source. Select "HSPF Binary Output", then "OK".
Basins Observed Water Quality 0
• CliGen Outpul
Integrated Surface Hourly Data
NASA CDS File
NOAA Hourly Precip Data. Archive Format. TD-3240
NOM Summary of the Day, Archive Format. TD-3200
Read Data With Script
STORE! Water Quality1
SWAT Data Files
SWAT Output DBF
SWMM Input
Timeseries DBF
Timeseries EXCEL
Timeseries SWMMSOutpul
USGS RDG File
WDM Time Series
WRDB Archive
52. Navigate to the HSPF project folder and select the file with the HBN extension. Click "Open".
Because the HBN file may be large, the registration may take time to read.
I Select HSPF Binary Output file to open
Organize *
New folder
TESTE
Ji TESTC
EPA Waters
HSPF
. HSPF-PEST
NHDPIu;
. NLCD
e - a •
! HSPF Binary Output Files C.hbr -.
53. After the file has been read, it appears in the "Data Sources" window. Click "File", then" Exit".
File Analysis Help
g-WDM
• D.\BASINS41*ata'.PoL;rPcirti;Tr5:'=;-; H?F= ;DMP
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View the Discharge Time Series
This sections views discharge time series based on hourly data by graphing the results at multiple
locations. The locations will be Reaches (RCHRES) 11, 19, and 25 since they represent junctions in the
waterbody network. The ID numbering scheme correlates to the site layout in HSPF. Leave HSPF open
with this diagram in the background to allow viewing of the reach locations, numbering scheme, and ID
numbers if you are not using BASINS to number these locations. See Whelan et al. (2015c) for
instructions on how to label the watershed using the BASINS interface.
•
54. Choose "Analysis", then "Graph".
a
DFLOW
,;,,Ph
i
S»n.p«t
Seasonal Attributes
Projection Parameters
CTOP£T Homepage
Water Quialrty Criteria 3
-------
56. Choose "Timeseries" and "Generate".
Choose Graphs to Create
] Timeseries
Row/Duration
Frequency'
Running Sum
Residual (TS2 - TS1) (two datasets needed but 1 datasets sele
Cumulative Difference two datasets needed but 1 datasets se
Scatter (TS2 vs TS1) ftwo datasets needed but 1 datasets self
Multiple WQ Plots
All
None
Cancel
Generate
57. The following graph appears. The discharge is defined as cfs (ft3/s). All three hydrographs are plotted
together.
File Edit View
4.000
3,000
1
a! 2,000
O
1,000
Analysis Coordinate
Help
HOURLY SDMPROJE RO at RCH11
H .I'M • -I'. Ml h J'.i .;(... Ml-.
HOURLY SDMPROJE RO at RCH25
' I [J
i. uiiL>^^ k^ull
u
1990 1991 1992 1993
dkfa^
tiULiktLiJi
U. LijlLl JJjL,
1994 1995 1996 1997 1998 1999 2000
HOURLY
58. Using the editor, as described in Whelan et al. (2015c), the graph can be modified to provide a
better view of the results. See how the discharge changes as one moves downstream to the pour
point of the watershed. Exit by clicking the "X" in the upper right-hand corner.
File Edit View Analysis Coordinates Help
1,000
22
-------
View the Microbial Density Time Series
59. Select "Analysis", then "Graph" again. Under "Constituent", choose "DQAL" which provides
microbial densities in Counts/L at various reaches. Under "Matching Data", choose reaches
corresponding to 11, 19, and 25 (RCH11, RCH19, and RCH25, respectively). After they appear under
"Selected Data", click 'Ok'.
4 Select Data To Graph 1 '~' '^N^
File Attributes Select Help
Select tonbute Values to Filter Available Data
Scenario - ] | Location
COMPUTED 1:102
NLDAS ['202
OBSERVED 1:302
SDMProject 1.502
Ma(chingData(25af4652}
SDMPROJE RCH12
SDMPROJE RCH16
SDMPROJE RCH1B
SOMPROJE RCH7
SDMPROJE RCH20
SDMPROJE RCH21
SDMPROJE RCH14
SeleOed Data (3 of 4652)
SOMPROJE RCH11
SDMPROJE RCH19
SDMPROJE RCH25
Dates to Include
Al I | Common I
Start 1990/01/01 1990/01/01
End 2000/12/31 2000/12/31
|_| Apply month/day range to each year
D Change Time Step To; 1 [Day
- [Consttuert -| [Tme Ltt T
FLOW Month
GAGE
GWtfS
DQAL Hour
DQAL Hour
DQAL Hour
DQAL Hour
DQAL Hour
DQAL Hour
DQAL Hour ~
DQAL Hour
DQAL Hour
DQAL Hour
1990/01/0!
2000/12/31
"H Average/Same » [ Ok j Cancel J
The definitions of
Parameter
Micrcbe-CCdAL-BICCEG
Micrcbe-CCCXAL-GEN
Micrcbe-CCSAL-HYCPCL
Micrcbs-CCSAL-CXIC
M i crobe-DDOAL-P H OTDL
Microbe-DDCtAL-TOT
M i crobe-DDQAL-VDLAT
Microbe-DaAL
Microbe-IDQAL
Microbe-RDElAL
Microbe-RODQAL
Micrabe-RRQAL
Microbe-TIQAL
Microbe-TROCtAL
the microbial pa
Units
counts/time interval
counts/time interval
counts/time interval
counts/time interval
counts/time interval
•counts/time interval
counts/time interval
counts/I
counts/time interval
counts
counts
counts
C C L P t ;
ccurtz
rameters are:
HSPF-12. 2 Manual
(http://water.epa.gov/sc itech/datait/mode!s/basins/b&nidoc5.cfm|
amount c-f parent material decayed by process BICCEG
amount of parent material decayed by process GEN
amount cf parent material decayed by prccess HYCPCL
a rr c urt cf parent material decayed bv prcces; Z-' II:
amount of parent material decayed by process FHCTCL
amount of parent material decayed by process TOT
amount of parent material decayed by prccess K VOLAT
co-ncentration of ''dissolved'^ microbe [i.e., microbe in water)
input of microbe in water column from upstream reach
total storage of microbe in water column
microbial outflow quantity
microbial storage in reach
total inflow of microbes
total outflow of microbes
Time interval' is hourly in this case.
60. Choose "Timeseries", then "Generate".
M| Choose Graphs to Create [•"'[•^•riSM
g| Timeseries
n Row/Duration
F] Frequency
L] Running Sum
L] Residual (TS2 - TS1) Jwo datasets needed but 1 datasets sels
Q Cumulative Difference (two datasets needed but 1 datasets se
L) Scatter (TS2 vs TS1) (two datasets needed but 1 datasets self
ft | | None |
D Multiple WQ Plots
Cancel Generate
23
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61. The following graph is produced with microbial densities of Counts/L:
•1 Tlmeseries Graph I:'1" 1 ^ \l^3mm.
File Edit View
100
90
80
70
0 60
0
0 50
£
I "°
30
20
10
Analysis Coordinates Help
HC
HC
4
URLY SDMPROJE DC
URLY SDMPROJE DC
URLY SDMPROJE DC
1 LltJjffl IlilkiUL
ALatRCHU
ALatRCH25
1
,,]..„„
tnU,,U.I
In ',1
1990 1991 1992 1993 1994 1995 1996 1997 1998
HOURLY
u.,..,.
1 -
1999 2000
62. Using the editor described in Whelan et al. (2015c), the graph can be modified to provide a better
view of the results. See how the densities change as one moves downstream to the pour point of
the watershed. As the uncalibrated results indicate, microbial densities are very low in this area, the
headwaters of the Manitowoc River basin. Exit by clicking the "X" in the upper right-hand corner.
File Edrt View Analysis Coordinates Help
Hourly Microbiai Density at Reach 11
Hourly Microbial Density at Reacti 13
Hourly Microbial Density al Reacti 25
24
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RETRIEVE OBSERVED DAILY USGS FLOWS AND COMPARE THEM WITH SIMULATED DAILY FLOWS AT
THE POUR POINT
BASINS can also be used to add data to the project. The objective of this exercise is to retrieve the
Observed Daily USGS Flows at the pour point and compare them to uncalibrated daily discharge
simulations at the pour point, Reach 25.
63. From the main BASINS menu, select "File, then "Download Data".
File
U
*
ft
&
In ^ Models LJ ^ Compute ^
^Jew
Open Project
Save
Save As
^ Archive/Restore Project...
Download Data
Open Data
64. Choose USGS Discharge stations as the data type, and click "Download".
Download Data
Region to Download [ Hydrologic Units •
BASINS
D DEM Shape fj GIRAS Land Use D NED D Census Q Met Stations
Q DEM Grid H Legacy STORE! D NHD D 303
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66. The NWIS Daily Discharge Stations layer will appear on the map. De-select "NHDPIus Catchment"
(red circle in figure below) since these catchments are outside the simulation area; removing them
from the screen will reduce confusion.
BASINS4.1 PouiPointl2175050 •!"
Ffc MfwatershedDelneatlon k4Models ur>Compute mflaunch ^Analysis Laye. View Bookmarts Plug-ins shapeMe Editor Converters Help
it b =. i . a a -H » % !§. !"• |! *?, »& BI» O
: New Open Save Print Settings J: Add Remove dear Syrobotogy Categories Query Properties Table ,: :
Deselect Measure Edentify Label Mover
: P-STi
,* ,-
In Out
/- >
Extent Selected
Previous
Layer ,i Men
•*• «•
shp shp
Add Remove
1 I
Copy Paste
Her^e
Move
Hove vertex
on £2 Port Sowces andvwhdrawals
ED Permit Comptence System
B&1& Otearwed DMJ StationB
^ *
|BS I*«S Daly Discharge Stations
S £7 Westher a«on Sites 2006
•DBKMII
;!CS_>Hydrolo»
B@ Reach File, V1
SO NAftQA Sludy Area Unit Boundaries
E D Accourthg Unft BoundarBs
TI ^ Cataloging Unit Boundaries
rdn _/ Transportation
BD Major Roads
T _/ Soi, Lend UseKover
BD Ecoreojons (Lewi W)
ad Land Use hdex
^^" NhiOPIus CalcnmerO
-i&^Pollbal
En Courrty Boundanes
BD EPA Region Boundaries
tBE) State Boundaries
B0 Area or Interest
B
^ •
^ •
»-
^ D
sj>
i»D
^ -
•& n
^n
^n
^
^D
*D
^n
*
67. Highlight the "NWIS Daily Discharge Stations" (one click), then click on the symbol below this Map
Layer.
- i. s. :: D a X
» » - : I
--'-a-'
26
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68. The size of the symbol for the discharge stations to download data for the correct station is
increased. Change "Size" to 24, "Fore color" to red, select "Apply", then "Ok".
Point style
Preview
..
Rotation
Fore color
[Symbols j j Characters Icons Options
Point shape + Regular
Number of sides 4
Transparency
Side ratio J5
Ok
Cancel
If you can see stations on the map, there is no need to zoom in near the outlet of the study area to
select the nearby USGS station. The USGS flow station nearest the outlet (Reach 25) is identified by the
red circle below.
I. I * fc .• & LZ2 L0 ! G * ** 1* * ^ ^ D it7
New Open Save Print Settings Add Remove Clear Symbolagy Calegone? Query Properties Table Select Dsielert Measure
Editor
e
Identify
Converters Help
+
Label Mover
Legend
Layers Tod
f7]unnamed -I X;610.514.243 Y: J341.814.490 Meters Lit 43.847 Long; -38.369
27
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69. Highlight the "NWIS Daily Discharge Stations" map layer using the BASINS Select button on the tool
bar,
then select the gaging station at the outlet. The symbol will change color (orange in
this case), indicating its selection (see red circle in figure below).
| BASINS 4.1 - TESTC-
Clear Symbology Categories Query Properties Table \ Select
\±-: fe] -^ stip shp ?) J ®
B
;elect Measure Identr
f**j - -''
c*^^- a-a-*•?•#
nnamed - X: 610,222^42 V : Jl-J ta.ilJ MeTer:- LaC 43.927 Long:-86 J6
70. Choose "File", then "Download Data" again, this time specifying download "Daily Discharge"
values.
data
Region to Download I Hydrologic Units j^^^^^^^^^^^^^^^^^^^^^^M
BASINS
D DEM Shape 0 GIRAS Land Use d NED d Census d Met Stations
D DEM Grid " Legacy STORE! CH NHD O 303
-------
71. Click "Download". A prompt will ask where the data should be saved. Click "Ok".
m
[HI
Daily Discharge Processing Options
•
l^a™
After downloading Row data,
'_' Addindividualfiles(oneperstation}toproject
o Add data to new WDM file: C:\Users\gwhelan\iemTechnologies\SDMPB\TESTC\nwis\flow.wdm Bra*
Add data to existing WDM file: Brai
Do not add data to project
C
ree...
use...
k
72. When the download is complete, this message appears. Click "OK":
1 WDM Data sets added
73. When the following screen appears, click "OK".
Data Download
Downloaded Data file:
C:\Users\gwhelan\iemTechnologieE\SDMPB\TESTCVnwis\flow.wdm
OK
74. The "Data Sources" window appears, indicating NWIS data have been added to the project. Choose
"file", then "Exit". In the main BASINS menu, choose "File", then "Save".
File Analysis Help
I -C:\Users-lgA-helan\iemTechnologies1|,SDMPBi.TESTC''.met\met.wclm[21)
|-C:\Users\g(vhelmn\iernTechnologies\SDMPE;iTESTC\HSPF\SDMProject.wdm[162)
i C:\LJsers'gwhelan'',ierr,Technologies'l,SDMPB[.TESTC'',nwis'',fl
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75. To generate a graph of the observed and simulated discharge time series, go to the main BASINS
screen, select "Analysis", then "Graph" on the tool bar. Make the following choices [Note: The
lower-case "observed", if available, refers to observed instantaneous discharge data that were
added and that are not part of this tutorial.]:
File Attributes Seiect Help
Select Attribute Values to filter Available Dala
••• Consthient
-_ DEWP
U DEWTMP
DQAL
SDMProject
Matching Data {3 of 4653)
Selected Data (2 of 4653)
SDMPROJE
OBSERVED
RCH25
040S5395
FLOW
FLOW
Dates to Include
( All I Common ]
Start 1990/01/01 1993/07/01 " 1990/01/01
End 2005/09/30 2000/12/31 2005/09/3tT
Apply month/day range to each year
Q Change Time Step To. 1 f]
T, | Average/Same
a I
Day
Day
Day
76. Select "Timeseries", then "Generate".
Timeseries
| Flow/Duration
Frequency
] Running Sunn
Residual (TS2 - TS1] (two datasets needed but 1 datasets self
Cumulative Difference (two datasets needed but 1 datasets se
Scatter (TS2 vs TS1] (two datasets needed but 1 datasets sell
D Multiple WQ Plots
Cancel
Generate
77. The following graph appears.
2.000
500
30
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78. Using the editor described in Whelan et al. (2015c), the graph can be modified to provide a better
view of the results. The daily average observed discharge at Chilton (Reach 25) is in red and the daily
average simulated discharge is in blue. The simulated results are uncalibrated and appear to
overestimate base flow. The trends are captured well.
400
I
C,
§> 300
5
£
2 200
DISCLAIMER
This document has been reviewed in accordance with U.S. Environmental Protection Agency policy and
approved for publication.
REFERENCES
WDNR (Wisconsin Department of Natural Resources). 2015. Deer abundance and densities in Wisconsin
deer management units, (Last accessed 23.09.15).
Whelan, G., K. Kim, K. Wolfe, R. Parmar, M. Galvin. 2015a. Quantitative Microbial Risk Assessment
Tutorial: Installation of Software for Watershed Modeling in Support of QMRA. EPA/600/B-15/276. U.S.
Environmental Protection Agency, National Exposure Research Laboratory, Athens, GA.
Whelan, G., K. Kim, K. Wolfe, R. Parmar, M. Galvin, M. Molina, R. Zepp. 2015b. Navigate the SDMPB and
Identify an 8-Digit HUC of Interest. EPA/600/B-15/273. U.S. Environmental Protection Agency, Athens,
GA.
Whelan, G., K. Kim, R. Parmar, K. Wolfe, M. Galvin, M. Gray, P. Duda, M. Molina, R. Zepp. 2015c.
Quantitative Microbial Risk Assessment Tutorial: Land-applied Microbial Loadings within a 12-Digit HUC.
EPA/600/B-15/298. U.S. Environmental Protection Agency, Athens, GA.
Whelan, G., R. Parmar, K. Wolfe, M. Galvin, P. Duda, M. Gray. 2015d. Quantitative Microbial Risk
Assessment Tutorial-SDMProjectBuilder: Import Local Data Files to Identify and Modify Contamination
Sources and Input Parameters. EPA/600/B-15/316. U.S. Environmental Protection Agency, Athens, GA.
Whelan, G., K. Wolfe, R. Parmar, M. Galvin, M. Molina, R. Zepp, P. Duda, M. Gray. 2015e. Quantitative
Microbial Risk Assessment Tutorial: Point Source and Land-applied Microbial Loadings within a 12-Digit
HUC. U.S. Environmental Protection Agency, Athens, GA.
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