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Evaluating Water Management Strategies with the

1. hen Gate Dam Output generated on 03 05 2001 at 11 47 26 Graph Type Scale Data Type Select locations Line Linear ature Upstream end of Copco Res Export C Bar Log Copco Dam mmi C Stacked Ber C Beletive C Acrefeet Cis Upstream end of Iron Gate Res Print Close Statistics Set Axis Iv Exceedence Plot T PlotPoints M Grid T Line Style E Figure 21 Exceedence plot for temperature at Iron Gate Dam To display a water quantity graph select the Water Quantity option from the View menu A default set of flow curves will be displayed Links represent flows in the water quantity model Select those links that you wish to display by clicking on them with the mouse or deselect with another click Flows are displayed in cfs by default Click on the Acre Feet radio button to change to acre feet Figure 22 shows the flows for three links Click on statistics to get a table of curve statistics Figure 23 57 MAX Q Water Years 1992 1994 Water Quantity IGD Control Point Flows xt O e gt y 1 N O O w x ti gt mm z 1 5 a 9 i 6000 S2NDJFMAMJJAS9SNDJFMAMJJAS 9ANDJFMAMJ JAS Month in Water Year 7 Klambelow Scott River Klambel Shasta R fromIG DEM Output generated on 03 05 2001 at 11 44 28 19 Acc Shasta to Scott R 20 Klim above Scott Acc Figure 22 Flow curves for the release from Ir
2. i File Edit View Insert Format Tools Data Window Help lej x OSH e 6ay7 Ses pee GI Arial vi0 Bzru e H s s tstEEB 5 amp k ve M Eg ug 1 2 3 4 Keno Total Phosphorus Site E Keno 8 3000 8 EM 2500 Consituent Total Phosphorus g 2 3 2000 ES 1500 7 1 w Jj 1000 18 E 20 500 21 22 23 24 0 50 100 150 200 250 300 350 400 25 Day of simulation E 27 23 30 Mial Version nutrient database Alternative Chart ADY Canal KS Drain Keno Powerpl 4 OoOo Dg Draw Is AutoShapes Nw HOA gt Z A 2 EMG Ready I D WD EB Figure 66 Chart worksheet in the nutrient loading estimation model The graph displayed is an example of dynamic graphing Using the drop down boxes to the right of the graph locations and constituents to be graphed can be selected The graph changes rapidly once the selections are complete The alternative name or year is not captured on the graph but may be added to the chart title or x axis label manually Note that the model does not estimate simulation periods without representative data from the nutrient database e g days 1 60 October and November and days 336 365 September Periods without representative data may vary from location to location within the model A total yearly loading value is not provided but all the data graphed is in the model on the worksheet tab with the selected location name For example for the a
3. Figure 54 Plot of Reservoir Target Values for Three Hydrologic States Iron Gate 95 STEPS IN USING SIAM 1 Establish Reference Condition a 1 Historical flows and temperatures actual or 2 Historical flows modified and temperatures to represent natural or fully developed system or 3 Time series of flow water quality suitable habitat red flags fish production potential etc b Identify potential limiting conditions what where when how often c Establish agreed upon metrics of potential limiting factors 2 Decide How to Represent the Alternative Conditions to Compare with Reference Alternatives may include a Flow releases from upper basin 1 Reservoir operations 2 Diversions b Flow modifications on represented tributaries c Reservoir storage level targets or capacities d Nutrient input loadings not yet available e Number weight and sex ratio of returning spawners or tributary production 3 Select and Edit Flows and Other Attributes to Mimic Alternative a Historical Flows With modifications necessary to represent existing water use 1f needed b User modified Historical Flows To represent proposed changes in water use 1 Monthly values af or cfs 2 Daily pattern 96 c User created Synthetic Demands at Iron Gate 1 Monthly values af or cfs 2 Daily pattern 96 Meteorology Spawner or tributary addition characteristics as above Nutrient input loadings not yet available Re
4. te che read diit Y Habitat Density related mortality PA Ge d Woran Out reach movers m allocated to Pre smolt mortality by size group A downstream reaches Hatchery supplementation y gt Movement Water temperature Growth rate Imm smolt 4 In movement from upstream ___ by size group mortality Base mortality 7 l Freshet induced movement Water temperature related mortality Habitat induced movement Habitat Density related mortality _ Season induced movement Out reach movers allocated to Imm smolt mortality by size group downstream and upstream reaches Figure 6 SALMOD schematic 29 Usable Habitat Outputs Spawners Maturation growth z o E graduation u o ci o Mortality a base o gt d 5 movement as 5 28 EM Sd E 9 imposition E temperature t o z A 2 Flow SSS Bottleneck S3 Identification Parameters Figure 7 Important inputs and outputs for SALMOD 30 The Ecosystem Health Component Red Flags Unlike the models discussed previously the Ecosystem Health component of SIAM is not an existing stand alone model In fact it is not a model at all Rather the Ecosystem Health component is a summarization tool much like that employed on the Grande Ronde River Lestelle and Mobrand 1995 meant to enable one to get an overview of th
5. Holding Spawning Adults Post spawning mortality by river segment Base mortality Water temperature related mortality Natality Habitat Density related mortality Timing of spawning 4 Water temperature 4 Number and sex ratio of adults Pre spawning adult mortality Fecundity by size group L Spawning habitat capacity In vivo egg mortality Lost eggs a ye Water temperature Maturation rate Eggs and alevins in gravel Base mortality Water temperature related mortality Habitat capacity effective incubation Habitat capcity redd superimposition Eggs and alevins in gravel mortality v m gt Fr Water temperature Growth rate by ar 4 In movement from upstream e dh Base mortality Water temperature related mortality Freshetinduced movement Y Habitat Density related mortality Habitat induced movement Out reach movers allocated to Fry mortality by size group gt downstream reaches Eo Hatchery supplementation v n Pre smolts P Movement Water temperature Growth rate In movement from upstream _ bysize group mortality Base mortality Water temperature related mortality
6. Managing Your Alternatives As you might expect opening an existing alternative one you have already created as we did above is easy SIAM shows recently opened alternatives in the most recent file list found under the File menu Using the File Recent File List feature is the recommended method Otherwise simply use the File Open dialog to select an alternative folder and name previously created Only one alternative is open at a time When you open another alternative SIAM automatically closes the alternative that is currently open Note that the alternative name with an ALT extension and the folder will have the same name Run or make changes and run just as you have above Then you may choose File Save As if you wish to create a new starting point You may save the current alternative as a New alternative or as an Existing alternative Figure 44 Existing Alternative Cancel Figure 44 Save As options For a new alternative enter the new alternative folder name the location folder under which it is to be saved and a description for the new alternative Figure 45 76 New Alternative x Alternative Folder Name Location cAPROJECTSWLAMATH ALTS Browse Description New Alternative 7 omen Figure 45 Dialog for saving as a new alternative Select Existing Alternative to save your current alternative as one that was previously created Enter a new description for the alternative Keep track of you
7. Bovee K D B L Lamb J M Bartholow C B Stalnaker J Taylor and J Henriksen 1998 Stream habitat analysis using the instream flow incremental methodology U S Geological Survey Biological Resources Division Information and Technology Report USGS BRD 1998 0004 Viii 131 pp Available on the Internet at http www fort usgs gov products pubs 3910 3910 asp Cheslak E F and A S Jacobson 1990 Integrating the Instream Flow Incremental Methodology with a population response model Rivers 1 4 264 288 Nehring R B and R M Anderson 1993 Determination of population limiting critical salmonid habitats in Colorado systems using the physical habitat simulation system Rivers 4 1 1 19 121 Appendix 6 Nutrient Loading Estimation Spreadsheet Model Monthly nutrient loading values can be estimated for any one year SIAM simulation generated for the 1961 2001 period of record using an Excel spreadsheet supplied with the distribution The estimates are based on sampling data collected and analyzed as described in Campbell 2001 at various locations in the Klamath River Basin The parameters estimated are total and ortho phosphorus ammonia nitrate total Kjeldahl nitrogen and total nitrogen loading Loading was calculated in kg day using the following convention Load concentration discharge 2 446848 where concentration is mg L of constituent discharge is in cubic feet per second and 2 446848 28 32 L ft 86 400 second
8. Ww Oo o IN IA t A v Fue loo j in Ia A Fw Tu rR Mar 4 Mar 11 CA N r Mar 18 Mar 25 Julian adjusted to begin on a water year boundary but doesn t fully consider months with other than 30 days a nN N Re Re N N O Oo sa o 23 Jr nr N 1 EN EET of ois o on owm o n ow o on Novs 2l Nen o or ETTINENE Novas or des peto os ECTINENE deere 05 Des 3 oo m ee o mua a maj al ms al EN TINENEI oen os ores oos orem os EE marti s Maris o oe Mar2s 6 36 Getting Underway SIAM is organized like most contemporary Windows applications and thus should be familiar to most users This document will not attempt to explain all the nuances of running a Windows application but will highlight information necessary to get the results you want with SIAM Please pay careful attention to the instructions below to enjoy a relatively problem free experience Hardware and Software Requirements Together with the component models and databases SIAM will consume approximately 10 megabytes of hard disk storage an additional 30 megabytes is required for each year of each alternative you choose to create and execute although some of that space is freed upon successful execution of the simulation A Windows 95 or later operating system is required Computer RAM memory is allocated dynamically dependi
9. Because the water quantity model MODSIM is linked to SIAM in a way that provides the user with complete control it is also possible to cause SIAM to crash SIAM has been constructed to deal with MODSIM in a very structured way Altering the number of nodes or links selecting a different set of nodes or links to output or otherwise changing the settings within MODSIM may create a disaster for SIAM from which it may be difficult to recover If you wish to become a MODSIM power user please do so in a completely different folder using completely different input and output files than those supplied with the SIAM installation The same warning applies to HEC 5Q as well After the water quantity model MODSIM completes the water quality model HEC 5Q takes over followed by the fish production model SALMOD Note however that SALMOD is disabled for the No Project network 4 You will see a series of MS DOS windows flash by and also see the programs and their pre and post processor utilities appear and disappear on your Windows Taskbar Depending on the speed of your computer this may take from a few minutes to an hour to run completely Ifit appears that your computer has hung you might check the Close on exit switch on the DOS window as described earlier in the document by right clicking the DOS icon in the upper left portion of the screen and choosing Properties As a footnote you may notice that the DOS MODSIM window lists years that are dif
10. Discharge z Y Discharge Keno Dam 1961 2000 C Absolute Difference z M Difference SelectAlternatives _ am 1961 2000 Seiad Valley Gaune taR1 2nnm C Exceedence C Cyclic Variation Removed Statistics Set Y Axis PlotPoints Grid Line Style Figure 38 Comparison of discharge from Iron Gate Dam with historical data 71 While we are here let s take a moment to work on our Alternative Notes file that we left open in WordPad remember that While a SIAM graph is on the screen press Alt Print Screen then switch tasks to WordPad Position the cursor at the bottom of the document and press the Paste icon This should paste the graph from SIAM directly into your WordPad notes so you can keep track of results as well as your baseline files and working notes Nice huh Generating An Alternative Comparison Report SIAM has the capability to generate detailed comparison reports for two alternatives Comparisons can be made for water quantity model discharge total storage and water surface elevation as well as water quality discharge temperature dissolved oxygen storage water surface elevation and conductivity Differences above specified thresholds are reported for selected locations and time periods To create a comparison report select the Generate Comparison Report from the Run menu Select a comparison alternative from the list of available alternatives similar to comparing alternatives graphically see Figure 39
11. For Windows NT or Windows 2000 place WordPad exe in the WINNT directory 37 Command com Properties 2 x General Program Font Memory Screen Misc MS DOS Prompt LES Cmd line CNWINDOWSNCOMMAND COM Working Batch file Shortcut key None Run Normal window v Close on exit Advanced Change Icon Figure 9 SIAM requires the Close on exit box to be checked in the MS DOS Prompt and Command com properties window Installing SIAM on Your Computer Installation of SIAM is much like that for other Windows programs You may have been supplied with a set of write protected diskettes containing SIAM a CD or you may have a single file downloaded from the Internet You may proceed with installation by double clicking on the disk file d SETUP or typing d SETUP on the Windows Run menu where d is the drive letter or if you have an Internet download simply double click on the application SJAMINST The installation wizard will ask you several questions about where to install SIAM on your hard drive that s up to you but following the defaults is recommended You will be given an opportunity to view any updated information concerning SIAM that is not included in this documentation such as canned alternative data sets that are being distributed with SIAM Assuming that all goes well and that you decide to launch SIAM at the completion of the installation you will be greeted by SIAM s colorful sp
12. Outputs Alt 1 Alt 2 Reference Te e m 1 ua ane 2 a w Iw 3 Nun nlc Constraints Time The Anadromous Fish Production Component SALMOD SALMOD simulates the dynamics of freshwater salmonid populations both anadromous and resident In the context of SIAM SALMOD is useful in identifying habitat bottlenecks the cumulative constraints on an individual fish population caused solely by repeated reductions in habitat capacity through time due to micro or macro habitat limitations The model s premise is that egg and fish mortality are directly related to spatially and temporally variable micro and macrohabitat limitations which themselves are related to the timing and amount of streamflow Habitat quality and capacity are characterized by the hydraulic and thermal properties of individual mesohabitats which we use as spatial computation units in the model The model tracks a population of spatially distinct cohorts that originate as eggs and grow from one life stage to another as a function of local water temperature Individual cohorts either remain in the computational unit in which they emerged or move in whole or in part to nearby units Model processes include spawning with redd superimposition and incubation losses growth including egg maturation mortality and movement freshet induced habitat induced and seasonal Model processes are implemented such that the user modeler has the ab
13. The Water Quantity Component MODSIM sess ener 12 The Water Quality Component HEC 5Q iudei tetur ete trees ciue es rane e o een cuta 16 The Aquatic Habitat Component css sioe sr ero ist sei couse erat sees sonia e vade eni ees 23 The Anadromous Fish Production Component SALMOD sse 26 The Ecosystem Health Component Red Flags seseseeeeenenen 32 Tying the Components Together through Space and Time sss 34 Getting Underway odo ec eda leen ar ARR aide a matis tm 38 Hardware amp Software Requirements io poeseos ce b esce re p put i eos 38 Installing SIAM on Your Computer sess ener enne nnne enne 39 The Basics What s SIAM s Main Screen enne enne nnne 40 Taking SlOfculS s cs ictu qd eei e bna dec ade aea av Un Haec REM Had ud 41 Getting Assistance while You Work ss sessssessessssseessesssssessseeseeseesseesessressessrssees 41 A Guided Tour Your First Evaluation sicssseg dtics caclcseahicvaetiseanseneghaesniaseattonnieas 41 Establishing a Baseline Alternative ue eem tease i etes recte inrer Beas YR HER E ed 41 Making the Necessary C hanges o edem ee det e es 45 Roning SIAM ccena ea deep eate netten eed epep aba aui a ues 54 Lookins at Results osos eam etal clei nasal Nc E EET Sade 55 Making Graphs Convey What You Want sess 56 Comparing Alternatives Graphically essen 70 Generating An Alternative Comparison Rep
14. a graphical user interface GUI to ease river network creation and the water allocation network solver One of the strengths and relatively unique 11 features of MODSIM is its internal solution technique for system priority optimization Fredericks 1993 Labadie 1988 Luckily SIAM users need to understand the solver only enough to try different demand priorities and operations rules explained later MODSIM represents the physical river system as a series of nodes and links Nodes represent both storage and non storage aspects of a river system such as reservoirs demand diversion structures inflow locations and stream gage locations Links represent stream reaches canals tunnels and other methods of water conveyance The basic nodal features of any water resources planning model include reservoirs diversion structures demands and inflow locations A crosswalk between MODSIM s network structure and that of the other models in SIAM for the Klamath River may be found in Table 5 An important assumption inherent in MODSIM s application for the Klamath River is that the time step for the calibrated 1961 to 1999 period is monthly In most cases discharge from Iron Gate Reservoir may be satisfactorily represented by monthly flows for two reasons First the Federal Energy and Regulatory Commission s imposition of minimum flows for Iron Gate adhere to a monthly timetable also reservoir storage levels in Upper Klamath Lake for the endanger
15. lower left corner in Figure 62 and displayed in Figure 63 Additional information about the microhabitat time series can be obtained by using the Export button lower right hand corner in Figure 62 If you Export from the Statistics display the file will contain the values in the table If you Export from the graph the file will contain the values used to generate it Note that if you press the Exceedence Plot option on the graph the values on the graph and in the statistics table will reflect the exceedence values The microhabitat time series output should be examined for major changes occurring both within a water year and major differences between water years to identify potential limiting microhabitat events Another possibility is to test for correlation relationships between microhabitat available and corresponding population indices if available 120 Curve Statistics Fish Production Microhabitat Area m2 1000m created 10 08 2002 Curve units Microhabitat Area m2 1000m Es ters emm Mmm Meter mean d sepsu toe ll 1882 82 82 4480 02 4023 43 388206 47784 74 1994 94 94 1088 84 950 63 894 35 10732 24 Figure 63 Curve statistics for the graph shown in Figure 61 References Cited Bovee K D T J Newcomb and T G Coon 1994 Relations between habitat variability and population dynamics of bass in the Huron River Michigan National Biological Survey Report 21 63 pp
16. option to set the weeks during which fry are present the beginning of February through the end of April Using the spin buttons select the appropriate dates Figure 61 118 Set temporal limits and resolution Temporal Limits A axis units Beginning 19 2 2 4 1982 C Time Steps Dates Ending Ej 4728 1 982 Reset Spatial Limits Upstream 1 0 0 meters wem x metas Cancel Downstream 526 pn 1 6 meters Reset Figure 61 Setting the temporal limits appropriate for a specific life stage At this point the investigator has a choice of how the habitat area is calculated Y Axis Variable upper left hand corner of Figure 62 either as total area in square meters for the study area or area per unit length that is square meters per 1000 meters of stream length The graph can be adjusted to show only the time period when the life stage is actually present For example fry are only present in the study area February through April but the graph would show them as present every week of every year Finally select the life stage appropriate for the dates selected in this case Fry Instream Fish Fry 30 50mm Figure 62 shows the microhabitat output for WY 1982 and WY1994 for the months February through April 119 Fish Production 1982 Water Year 1982 x MUERTE SALMOD OUTPUT COMPARISONS Water Year 1982 Fry 30 50mm Instream Fish Average Weight gm Average Length mm B
17. total ammonia 71 49 mg l pH 7 yellow flag source EPA Anytime anywhere below Iron Gate total ammonia 70 91 mg l pH 9 red flag source EPA Anytime anywhere below Iron Gate total ammonia 76 80 mg l pH 8 red flag source EPA Anytime anywhere below Iron Gate total ammonia 723 0 mg l pH 7 red flag source EPA Phosphorus Anytime anywhere below Iron Gate orthophosphorous gt 50 ug l yellow flag source EPA Anytime anywhere below Iron Gate orthophosphorous gt 1 mg l red flag source EPA 107 Turbidity Anytime anywhere below Iron Gate total suspended solids gt 100 mg l yellow flag source USGS Metals to be refined if values ever get close to acute toxicity levels Anytime anywhere below Keno cadmium gt 0 66 ug l 50 mg l CaCO yellow flag source EPA Anytime anywhere below Keno cadmium gt 1 10 ug l 100 mg l CaCOs yellow flag source EPA Anytime anywhere below Keno cadmium gt 2 00 ug l 200 mg l CaCO yellow flag source EPA Anytime anywhere below Keno copper gt 6 50 ug l 50 mg l CaCO yellow flag source EPA Anytime anywhere below Keno copper gt 12 00 ug l 100 mg l CaCO yellow flag source EPA Anytime anywhere below Keno copper gt 21 00 ug l 200 mg l CaCOs yellow flag source EPA Anytime anywhere below Keno lead gt 1 30 ug l 50 mg l CaCOs yellow flag source EPA Anytime anywhere below Keno lead gt 3 20 ug l 100 mg l CaCOs yellow flag source EPA Anyt
18. 00 m 3 Chinook Sali g 22700 00 22700 00 Chinook Sali M 0 00 22704 00 4 106 Chinook Sali Iv 0 00 22704 00 1500 0 50 Enter upstream and downstream distance in meters Fill Table Enter weight in grams omes Figure 18 The Edit Supplemental Fish dialog after entry of two groups of fish juveniles in May at week 32 and adults for the second year at week 54 Refer to SALMOD documentation for more details Justto see how this works let s add a group cohort of naturally reared chinook pre smolts coming into the mainstem from the Shasta River in early May To do so click on the Week row currently with a 2 in it and press the Insert key This creates a new record The week of May 6 is week 32 of the biological year see Table 6 so type 32 and press the right arrow key Uncheck the Adult check box to indicate juveniles The Shasta River comes into the mainstem approximately 22 7 km downstream from Iron Gate Dam see Table 5 so enter 22700 meters for both the Up and Down Dist entries Let s put 25 000 of the little guys in For juveniles the sex ratio and adult weights don t count so they are shaded out Skip to the rightmost entry by pressing the End key and type 3 6 the approximate weight for a 73 mm pre smolt In our case since we are running three hydrologic years we need to add a third and fourth record to SALMOD s supplemental fish dialog so that spawners will be available for the second
19. 13 U S Fish Wildl Serv Biol Rep 89 17 139 pp Biswas A K 1975 Mathematical modeling and environmental decisionmaking Ecological Modeling 1 31 48 Cunnane C 1978 Unbiased plotting positions A review Journal of Hydrology 37 205 222 Environmental and Social Systems Analysts Ltd 1982 Review and Evaluation of Adaptive Environmental Assessment and Management Environment Canada Vancouver BC 116 pp Flug M and J F Scott 1998 Modeling and Management of Water in the Klamath River Basin Overcoming Politics and Conflicts In ASCE 1998 International Water Resources Engineering Conference Proceedings Water Resources Engineering 98 Abt S R et al Editors American Society of Civil Engineers VA Vol 1 938 943 Flug M J Bartholow and S Campbell 1999 Systems Impact Assessment Model for the Klamath Trinity River In 26th Annual ASCE Water Resources Planning and Management Conference Proceedings June 6 9 1999 Tempe AZ in Erin M Wilson Ed WRPMD 99 CD Proceedings Preparing for the 21St Century July 1 1999 Ford D T and D W Davis 1989 Hardware store rules for systems analysis applications Pages 3 10 in Closing the Gap Between Theory and Practice Baltimore Symposium IAHS Publ No 180 Hanna R B S Campbell M Flug and J Scott 1999 Using Models to Evaluate System Management Flexibility on Water Quantity and Quality Klamath River Manuscript submitted to ASCE July 1999 45 pp
20. A Population Model for Salmonids User s Manual Version 3 USGS FORT Internal Publication 82 pp Available over the Internet at http www fort usgs gov Bartholow J M 1996 Sensitivity of a salmon population model to alternative formulations and initial conditions Ecological Modeling 88 1 3 215 226 Bartholow J M and T J Waddle 1995 The search for an optimum flow regime using a salmon population model Pages 331 339 in WaterPower 95 Proceedings of WaterPower 95 ASCE San Francisco CA July 25 28 1995 Bartholow J M and T J Waddle 1994 A salmon population model for evaluating alternative flow regimes Pages 877 889 in D G Fontane and H N Tuvel Eds Proceedings of the 21st Annual Conference Water Resources Planning and Management Division ASCE Denver CO May 23 26 1994 104 Bartholow J M J L Laake C B Stalnaker and S C Williamson 1993 A salmonid population model with emphasis on habitat limitations Rivers 4 4 265 279 Williamson S C J M Bartholow and C B Stalnaker 1993 Conceptual model for quantifying pre smolt production from flow dependent physical habitat and water temperature Regulated Rivers Research amp Management 8 1 amp 2 15 28 Ecosystem Health Red Flags Environmental Protection Agency U S 1999 1999 Update of ambient water quality criteria for ammonia EPA Office of Water EPA 822 R 99 014 Pages 83 88 Gaffen D J and R J Ross 1998 Increased summertime heat stress in
21. Acc to Confluence w Scott River to Seiad Gage21 Klamath River nr Seiad Valley22 Upstream of Keno R Keno Dam Upstream of JCB Upstream of Copco Copco 1 Dam Upstream of IG IG Dam C0 1 OY G1 0 P2 O o 34 NOTES 1 MODSIM characterizes the flow between known points 2 HEC 5Q characterizes the water quality at specific points With project CP10 is Keno and CP15 is upstream end of JC Boyle res without project CP10 is Link Dam and CP15 is Keno Dam 3 Both HEC 5Q and SALMOD include numerous reaches within the overall longitudinal segmentation HEC 5Q s reaches are for computational accuracy SALMOD s are to match the habitat classification and mapping SYMBOLS V Inflow 6 Diversions 7 Return or accretion Diversion amp return Reservoir Powerplants Gage Demand node Upstream Downstream m m 0 100 100 846 846 13424 13424 22704 22704 30692 30692 47915 47915 61222 61222 70634 70634 78081 Iron Gate Dam to Bogus Creek Bogus to Willow Creek Willow to Cottonwood Creek Cottonwood to Shasta River Shasta to Humbug Creek Humbug to Beaver Creek Beaver to Dona Creek Dona to Horse Creek Horse to Scott River Table 5b Continuation of Table 5a for segments downstream from Seiad California Network 3 to the ocean Note that SALMOD does not extend below the Scott River MODSIM S NODE LINK STRUCTURE HEC 5Q S CONTRO
22. Daily Flows For October Constant Dy Average Wet Defined EE eea e All Months s cC c e E B Edit October C C C c Cc Edit November C C C c c Edit December c cC EL o E Edit January c C o Edit February cC c r LO c Edit March L C C c c Edit April Cc C C c Cc Edit May C P C c c _Edit June C C C c Cc Edit July C C C c c Edit August C C C e c _Edit September E cC c LO s 1 This is a calibration file Recompute Flows m Target Volume Maintain monthly target Monthly Volume acre feet 79955 81 C Update monthly target with new volume Monthly Target acre feet 79955 81 COME NN Figure 46 Iron Gate Daily Flow Variability dialog October s values are displayed in the table Daily flows may be adjusted while maintaining the monthly target specified in the Edit Node Criteria option Here the relative values of the daily flows are preserved while maintaining the specified target volume i e the values you type are not used directly but rather the pattern is maintained If you click on the Update button the table values will be recomputed to show the daily flows that will be used by the HEC 5Q model Even if you do not press the Update button in this mode you are specifying daily flow patterns not specific daily flows If you want to enter and use a specific daily flow check the box fixed column to the right of the flow that was changed This removes it from the update process SIAM maintains the monthly
23. Douglas A J and J G Taylor 1998 Riverine based eco tourism Trinity River non market benefits estimates Int J Sustain Dev World Ecol 5 136 148 105 Appendix 1 Example Red Flag Criteria for SIAM Criteria are proposed for time and space as well as species life stage Time and space in this context refer to the window of application Flags are triggered on the basis of the smallest time step and spatial level representative of the data but are displayed for simplicity on a weekly basis for the flow segments defined by MODSIM That is a weekly flag would be turned on from one or more single day s events and a segment flag for any event within that segment Any criterion may have levels shown here as red versus yellow flags A yellow flag represents chronic or secondary conditions and a red flag represents acute or primary conditions A source who wants this metric or where did it come from should also be given That way multiple interpretations are possible but it is always known to whom the flag belongs Some criteria have values that are yet to be set indicated by and may not be operational in SIAM Hydrology Minimum flows August Iron Gate discharge lt 1000 cfs yellow flag source FERC Long Range Plan September April Iron Gate discharge lt 1300 cfs yellow flag source FERC Long Range Plan May Iron Gate discharge lt 1000 cfs yellow flag source FERC Long Range Plan June July Iron Gate discharge
24. Figure 9 SIAM requires the Close on exit box to be checked in the MS DOS Prompt and Command com Properties WIBdOW i5 aiios qoasi paetos arn res ceo go eb ubi tog tax Fuse tabe ud Aa vadis 39 Figure 10 SIAM s main menu showing map toolbar status bar and tool tips 40 Figure 11 The New Alternative dialog with a name typed in and selections being made 42 Figure 12 Selecting the folder in which to store your new alternatives ssessss 43 Figure 13 Completed Pile New 108 idet rete aret rr pe ea dc rere ae 44 Figure 14 The Edit Year dialog with three hydrologic years entered but all use the same meteorologic year Note that the user enters values in the first table only The other tables are for information only and are not editable 45 ertet RR eerie eoe TRE ruo Nune 45 Figure 15 The Edit Node Criteria dialog qe eoe tao et RETO RissE wee pedu re dit 47 Figure 16 Edit Node Priorities dialog showing the relative priority of each storage and demand node Note that the lower the priority the more the water quantity model tries to meet the stated ig em PKT E 49 Figure 17 Edit R servoir Characteristics dialog isses isse eet teta teet inni tesi Paten aed 50 Figure 18 The Edit Supplemental Fish dialog after entry of two groups of fish juveniles in May at week 32 and adults for the second year at week 54 ssssssssssssseeeeeenenes 5 Figure 19 Red Flags dialog after
25. Kimmerer W 1996 The consensus project to create a decision support system for the Central Valley waterscape Phase I Partial Draft Report Natural Heritage Institute 43 pp Majone G and E S Quade eds 1980 Pitfalls of Analysis John Wiley amp Sons New York 213 pp Overton W S 1977 A strategy of model construction Chapter 3 especially pp 50 58 in Ecosystem Modeling in Theory and Practice edited by C A S Hall and J W Day Jr John Wiley amp Sons NY R2 Resource Consultants Inc 1997 Review of prototype System Impact Assessment Model SIAM for the Klamath River Prepared for Karuk Tribe Department of Natural Resources Redmond Washington 23 pages plus figures and tables Schroeder R L and S L Haire 1993 Guidelines for the development of community level habitat evaluation models USDI Fish and Wildlife Service Biological Report 8 Sheer D P 1995 State of the art water resource simulation models Water Resources Management Inc Bay Delta Forum Presentation September 20 1995 24 p handout Scott J F and M Flug 1998 Modeling with MODSIM Klamath River Basin Water Quantity for Protecting Fish and Other Resource Values In First Federal Interagency Hydrologic Modeling 102 Conference Proceedings Subcommittee on Hydrology of the Interagency Advisory Committee on Water Data Las Vegas Nevada April 19 23 1998 Vol 2 8 103 8 110 Water Quantity Model MODSIM Campbell S G Hanna R B M Flug
26. NIS NR Sen uu MS Lower Limit z 15 o M 12UpececocsessaeacsasoccccePeRRHesenrIRo docu ME Sec ono SEDNAE i o 2 lt Graph Type 115 i Line 1992 1993 1994 Ber Water Year Grid Lines Output generated on 03 05 2001 at 11 47 26 I PitPoins Evaluation Period June 1 Sept 30 Location Iron Gate Dam Ocean Statistics SetY Axis I Exceedence Plot Data Type amp Temperature Select starting location Select ending location Dissolved O2 Iron Gate Dam v Ocean v Figure 28 Temperature related macrohabitat ii 63 Longitudinal Profile IGD_Max_Q Water Years 1992 1994 Longitudinal Dissolved Oxygen Profile IGD Max Q Water Years 1992 1994 10 07 aaa eae eau oum peenes A Date i i i i i i l ED j ee ee S MEE Ime E EE OMM MEE MEME QUE Water Year 90T 1 Satis a t 4 memedcduee rc i mene i 993 i i i 8 67 S eer REL ULL Dag CE Iv Grid Lines i i i Plot Points 8 0 i 130 140 150 160 170 180 190 200 Statistics River Miles Set Y Axis Output generated on 05 21 2001 at 10 24 12 Map Evaluation Date June 1 1993 Location Iron Gate Dam RM191 7 Seiad Valley gage RM130 8 Date Type Select starting location C Temperature Graph Type ron Gate Dam RM191 7 xj Export Dissolved O2 Line Select ending location Print C Discharge C Bar Seiad Valley gage RM130 8 v Close Figure 29 Longitudinal profile
27. Oo DN WY oOo Day of Water Year O 0 s rh OO t OR NN NN co o e ct Oo 0 GOD DN O N 00 O ON ere ere ean e Oo DN WO A co DO e c0 OM c5 Figure3a Average measured and simulated mean daily water temperature for Seiad Valley Gage location in the Klamath River from water years 1961 through 1999 Iron Gate Dam 1996 1999 Dissolved Oxygen mg L Simulated Measured anr 417 469 521 1998 n ELT re ix Jr i Day of Simulation 937 989 1041 1093 1145 1197 1249 1999 Fu n me m m 1301 1353 1405 1457 Figure 3b Comparison of simulated and measured mean daily dissolved oxygen concentration at the Iron Gate Dam in the Klamath River from water years 1996 through 1999 Perhaps because the HEC 5Q model was calibrated and validated for wet years 1996 98 the model may simulate temperature in wet years somewhat better than dry years although the RMSE values for the comparisons shown below are very similar The wet years simulated were 1965 and 1971 17 RMSE 1 88 C and the dry years were 1968 and 1977 RMSE 1 94 C Seiad Valley Wet Years 1965 amp 1971 Temperature C Simulated Measured 1 101 201 301 401 501 601 701 Day of Simulation Figure 3c Comparison of measured and simulated mean daily water temperature at the Seiad Valley gage location in the Klamath River for two wet water yea
28. a new red flag has been added sss 53 Figure 20 Available output tables for the water quantity model sees 55 Figure 21 Exceedence plot for temperature at Iron Gate Dam eee 58 Figure 22 Flow curves for the release from Iron Gate Dam the Klamath below the Scott River and the Klamath below the Shasta River ividicssecciosacsane nter toe aede es ee sae inr tas ke vide eodein 59 Figure 23 Water quantity model flow statistics esses 59 Figure 24 Average mean daily temperature at Iron Gate and Keno dams 60 Figure 25 Annual cumulative temperature exposure at Iron Gate Dam sess 62 Figure 26 Exposure periods for Keno Copco and Iron Gate dams sss 63 Figure 27 Area plot of thermal window for Iron Gate Dam at 15 C sss 64 Figure 28 Temperature related macrohabitat cce ok iso deci tei i pa Pblc dec toten 64 Figure 29 Longitudinal profile for dissolved oxygen on June 1 1993 sss 65 Figure 30 Fish production Srapliies s casos beg quA mnm osi E ER 66 Figure 3l Add a Curveuialog c poaae PR ve e bat rs asians dai pie s edm mp dd RE 66 Figure 32 Length frequency distribution for migrating Chinook Salmon pre smolts 67 Figure 33 Mortality partitions for pre smolts sess 68 Figure 34 Select mortality life stage combinations by cl
29. a without project network 2 containing no reservoirs on the mainstem Klamath below Upper Klamath Lake This change also allows us to have the network that simulates from Upper Klamath Lake to the ocean 3 which is available with Version 2 of SIAM Each unique network has data files specific for it particularly the so called XY files for MODSIM Version 1 3 also upgraded the graphics to more correctly handle the output from HEC 5Q and added output in the form of CSV files that are more easily imported into Microsoft Excel Finally error processing is more robust Version 1 2 December 1999 added the ability to run SIAM for up to 50 contiguous years For the Klamath River meteorological data were supplied for WY 1961 to 1997 as well as three synthetic years Hot Cold and Median Fill and Clear buttons were added to the Edit Year dialog to facilitate running such a long data set Note that if more than five years are run in sequence the fish production model SALMOD does not produce a full complement of output Version 1 2 also distributed a more realistic starting set of Red Flag values Version 1 1 October 1999 added many improvements to the prototype release October 1998 Major changes include e SIAM now can run and display up to five years worth of simulation at one time The user has control of which hydrologic and meteorological years to simulate in any order desired 7 e More flexibility in controlling a MODSIM manag
30. could provide very good results for this desired simulation outcome For a one year simulation only management mode could be used in accordance with the instructions given in Example 3 i e setting all three Hydrologic State Targets to identical Monthly Values that correspond to the desired Historical monthly values Alternatively MODSIM can be operated in calibration mode using the complete 92 calibration AXY file except with Historical reservoir storage values replaced by the equivalent values that correspond respectively with monthly Target values for the One Reservoir on which you desire to evaluate some operation flexibility Some adjustment of Priorities might be required in this analysis As described at the end of Example 3 this is a more data intensive modification of an AXYs file when multiple year simulation and analysis is desired the using the management mode for simulation EXAMPLE 6 Adjustment of demands and instream flows Note that this example touches upon some more sophisticated management mode runs that require a thorough understanding of the flow network and some understanding of MODSIM In addition to the reservoir Targets any ofthe other river sections that is MODSIM Alinkz values which may represent either physical constraints or desired flow demands can be modified By proper selection ofriver sections links and redefining the maximum flow through the respective link the model can be made to control the quanti
31. date spin controls The Threshold parameter is an optional bias value subtracted from temperature or dissolved oxygen For example if one were interested in eggs the threshold would typically be zero degrees meaning that SIAM would count a day with a mean water temperature of 5 C as five degree days On the other hand if you were interested in only counting degrees above a stress threshold 16 C for example set the threshold to 16 C This means that a day with mean temperature of 17 C would count as one degree day Note that SIAM counts degrees relative to the default units Celsius or Fahrenheit you have selected in File Preferences Setthe temperature or dissolved oxygen range using the Upper and Lower Limit spin controls Like the other temperature or DO values on this form you may enter whole numbers only This means that values below the Lower Limit will be set to the Lower Limit and values above the Upper Limit will set to the Upper Limit For example the Upper Limit were set to 20 C and the day s temperature were 22 C that day would count no more than a day with 20 The situation is reversed at the low end ofthe scale This may be important if for example one believed that temperatures above or below certain thresholds did not count for a biological process like egg development Tip Most applications will set the Lower Limit equal to the Threshold value Cumulative exposure starts counting at zero on the Start Date of each year an
32. for the evaluation of split month flow schedules An exceedence plot function was added to most of the graphic output for SIAM You can also set the Y axis extents for all graphic output Version 2 2 November 2000 extended the Klamath network downstream from Seiad Valley California to the ocean and upstream to Upper Klamath Lake The user interface has been redesigned to improve ease of use flexibility and utility All new graphics output for water quantity water quality and fish production has been incorporated into SIAM Five new water quality metrics have been added These include annual exposure to temperature and dissolved oxygen exposure period thermal window macrohabitat and longitudinal temperature discharge and dissolved oxygen profiles All output graphics can be exported to files that can be read by MS Excel adding even more flexibility and utility to the software Additional control over MODSIM has been afforded through the ability to specify maximum flows as well as minimum flows Comparison of alternatives may now be made graphically A statistics option has been added to all output graphics providing standard descriptive statistics Finally a preferences dialog has been added to streamline color selection for graphs and facilitate disk file management Version 1 3 January 2000 added the ability to work with different networks For the Klamath in particular the existing with project network 1 was supplemented with
33. four mainstem dams along the Klamath River and losing their associated hydropower production 4 eliminating all harvest of Klamath Trinity fish stocks for a 12 year period including the acquisition of fishing rights from both tribal and commercial marine fishermen and 5 operating all Klamath Trinity fish hatcheries to restore self reproducing stocks In total restoration costs were calculated to be about 5 billion If the assumptions used in this study are valid it is clear that the baseline benefits 20B far outweigh the costs of restoring water quality and the fishery The apparent disparity between restoration benefits and costs for the lower Klamath River may suggest to some that water resources on the Klamath be reallocated to environmentally friendly viii nonmarket uses The economic analysis rests in part on the information made available to the survey designers by the biological hydrologic and water quality data incorporated in The System Impact Assessment Model SIAM It is our hope that SIAM can be used to improve the river s water quality and fishery and strengthen the important regional economy ix Welcome Kick starting SIAM If you are anxious to install SIAM and give it a trial run you may safely skip ahead to the Getting Underway chapter of this document and do just that However if you have a previous version of SIAM installed on your computer please uninstall it completely before installing this version Af
34. if model SIAM may be used also in a planning mode by portraying the simulated effects of actions against a long term historical backdrop Planning models are descriptive fostering the development of robust and non arbitrary policies on which all water users may rely In contrast operational models are prescriptive used primarily to fine tune near future actions We recognize that some components of SIAM may indeed be useful in guiding day to day or month to month operational decisions but that was not its designed purpose SIAM provides the framework for a general purpose modeling environment in the sense of coupling models and data in a manner appropriate for specific applications The keys to a general purpose modeling environment are that 1 the component models and data are independent yet integrated 2 outputs are hierarchical 3 individual components are credible and 4 all parties are quite clear about what the model s will and will not do Independence in this context means that the models are modular and usable on their own Some applications need not employ the full set of capabilities of all models Users from specific disciplines will want to concentrate on specific submodels Being modular also implies that models are portable and can be interchanged when obsolete or in need of refinement Integrated means that the independent models must be harmonized in a relatively transparent manner to form the whole suite In general terms t
35. life stages at different flow levels PHABSIM has two major analytical components stream hydraulics and life stage specific habitat requirements 22 The stream hydraulic component predicts depths and water velocities at specific locations on a cross section of a stream Field measurements of depth velocity substrate material and cover at specific sampling points on a cross section are taken at different flows The sampling points are called verticals and describe conditions for some distance around them judged to be relatively homogeneous Hydraulic measurements such as water surface elevations are also collected during the field inventory These data are used to calibrate the hydraulic models which are used to predict depths and velocities at flows different from those measured It is usually assumed that the substrate material and cover do not change at different flow levels but this assumption is not required The hydraulic models have two major steps The first is to calculate the water surface elevation for a specified flow thus predicting the depth The second is to simulate the velocities across the cross section Each of these two steps can use techniques based on theory or empirical regression techniques depending on the circumstances The empirical techniques require much supporting data the theoretical techniques much less Most applications involve a mix of hydraulic sub models to characterize a variety of hydraulic conditions at va
36. m 0 2 0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Months Figure 52 Plot of Hydrologic State Factors for Upper Klamath Lake Link Dam 89 Reservoir Targets A set of three 3 Targets are given for each of the reservoirs in the MODSIM Network Flow model and for the Ocean Demand Node this is the only Demand Node that has and needs the Targets defined The three Targets correspond with Dry Average and Wet Target Values and are defined for each reservoir for all twelve months Target values for the primary reservoirs because of the relative large size of storage for this Klamath River system are given in Table 9 below These Target values are defined based upon a thorough review of historical storage and project operation practices with due consideration given for below average average and above average water years and more specifically individual months exhibiting extreme hydrologic inflows and therefore requiring increased wet or decreased dry storage in the reservoirs As mentioned previously the Targets should represent and function as Arule curves for water management typically as a guide in reservoir operations under varying meteorologic hydrologic inflows Figures 53 and 54 provide plots of the values respectively for Link Dam and Iron Gate Reservoir Target values are part of the data accessible in MODSIM as one page or table in the data associated with a reservoir the data are accessed by right click
37. may be instructive to mention them as they shed light on the sometimes mysterious world of modeling First we found that MODSIM s method of accounting for evaporation was unexpected Basically the water quantity model subtracts monthly evaporation after all other constraints have been met This meant that although MODSIM accounted for the minimum possible volume as specified in the node characteristics the end of month storage passed to SIAM and therefore HEC 5Q could be lower than that minimum causing problems in the water quality model Second we found that the available reservoir bathymetry estimates for Upper Klamath Lake had problems Depending on the source of the tables both storage elevation and storage area the values may or may not agree This was traced in part to revisions to the bathymetry given new hydrographic surveys and alterations in the benchmark elevations In addition sometimes the units of the table were unclear the values may have been total storage or just active storage 1 e only usable water above the inactive or dead pool Thus the datums for minima and maxima are somewhat fuzzy especially for Upper Klamath Lake We have elected to standardize on the data set inherent in KPOPSIM as downloaded from the Bureau web site http www mp usbr gov kbao A related issue is that the historical reservoir storage volumes reported by the Bureau of Reclamation and PacifiCorp occasionally were either higher or lower than
38. model all important resource impacts and impossible to anticipate all possible water supply situations Discretion and informed guidance will remain a necessary ingredient for appropriate SIAM use We USGS continue to provide training amp support for SIAM in partnership with other users in particular the US Bureau of Reclamation and the US Fish amp Wildlife Service However given the nature of the decision making structure evolving in the Klamath Basin we are looking to all interested parties to help shape SIAM build credibility and lend objectivity through continuous application and monitoring In effect we welcome participation from everyone Please direct comments or questions to U S Geological Survey Fort Collins Science Center 2150 Centre Avenue Bldg C Fort Collins CO 80526 8118 970 226 9319 970 226 9230 fax iii Table of Contents MOT WV AN i LT Vili jiu n 1 Kick starting SIAM ii tinsi essai tette D pss eat aus repa Tae etudes isi agis 1 What is SIAM os eue aded tle etta tases dedue utar edt ca donee wisn Cease co Re av te a 1 SIAM Tor the Klamath River eee aiibi Sen de Open aia DE 2 What s New About SIAM ssssssessessesessseseesesseseessssersessestesesstsressssersessestesesseseestsseesessestesesse 4 Improving SIAM through T Ile usos ise e cre eod hei ecu oec BOR on NE D 8 Acknowledgments o Ce et eve edi ie eie Venet ana RN ido Ret ee M De 8 The Components of SIAM
39. or even make sense depending on the graph being viewed In particular depending on the circumstances the median may be calculated including numerous zero or inapplicable values However on graphs where you can select the time window annual exposure and macrohabitat the statistics are calculated only for that window defined period Graph appearance controls determine the appearance of the graph or the form of the data to be graphed These include graph type scale grid lines line style and plot points The available graph types are line bar stacked bar and area Stacked bar are bar graphs where the bars are stacked vertically instead of displayed side by side The scale control allows you to change the scale on 55 which the graph is plotted Options include linear log or relative The relative scale plots values relative to the maximum value values are 0 to 1 Checking the Grid Lines check box will result in grid lines being displayed on the graph The Plot Points check box controls whether individual points are displayed on the graph If you check the Line Style check box the line style as well as color of each successive curve will be different Up to 20 curves may be displayed on a single graph Additional color control is available through the Fi e Preferences dialog that allows changing each line type s red green blue attributes You can set the extents for the Y axis scale by clicking on the Set Y axis button Enter the minimum
40. small value and then subjecting it to high flow events may seriously violate HEC 5Q s minimum retention time limits reservoir volume max Qin Qou lt 1 day resulting in either unrealistically poor water quality e g water temperatures gt 50 C or complete model failure Luckily these conditions are easy to spot as errors Unfortunately it may also be possible to generate sets of conditions that cause the model to give poor predictions but the user may not know it All we can say is that as you push these models farther from the domain for which they were calibrated you increase the likelihood of encountering problems The complete storage area elevation tables for Upper Klamath Lake Lake Ewauna Keno JC Boyle Copco Lake Copco 2 and Iron Gate have been provided with the SIAM Version 2 7 software In order to provide flexibility for what if simulations the maximum capacities of Upper Klamath Lake Copco Lake and Iron Gate have been increased To achieve this objective the storage area elevation tables have been extrapolated above the previously available maximum reservoir levels as mentioned above These files are named like UKL SAE Table dat with similar names for the other reservoirs are stored in the SIAM install directory and may be easily read Note that Lake Ewauna JC Boyle and Copco 2 are not simulated in HEC 5Q The Klamath to the ocean 61 99 XY and Management All XY files have changed with SIAM Version 2 7 New XY files
41. target by adjusting only those flow values for which the fixed box 1s not checked Click the Update monthly target with new volume radio button to specify fixed flows for all days in the month Fixed boxes are not displayed when this option is selected because they are all exact In this mode the monthly target is automatically updated as changes are made Pressing Cancel will restore the original values without altering anything A Graph function is provided to allow you to better visualize the daily patterns that you are defining You may graph the daily flow values for a selected month or the entire year Figure 47 Click on the Graph button to display a graph of the daily flows Resize the graph window by dragging its corners or move it anywhere on the screen by dragging the title bar The graph window will remain 80 open until you close it or close the daily variability dialog You can continue to edit daily flows with the graph displayed and it will be automatically updated as you make changes You may switch between monthly data and yearly data via the Monthly Data and Whole Year radio buttons Click on the Grid Lines box to add grid lines to the graph Click on the Print button to send a copy of the graph to your printer Daily Discharge For The Year Daily Discharge Of x Daily Discharge For November OND JFM AM J JA SO Month in Water Year 10 20 30 Days in November iti d C Whole Year Pri
42. the Time Series Library Milhous et al 1990 These components collectively relate instream discharge to indices of aquatic habitat availability through time as explained by Bovee et al 1998 Although typically applied on a monthly basis these analysis components are not tied to a fixed time step but instead are more related to the assumptions inherent in relating the time step to relevant biological processes especially limiting factors Though PHABSIM and TSLIB are not actually run like the other models in SIAM understanding what they are about may help understand how they are used as input to the fish production model Some definitions are in order Macrohabitat refers to a longitudinal segment of river within which physical and or chemical conditions influence the suitability of the segment for an aquatic organism water temperature being a prime example Microhabitat refers to the small localized areas within a larger scale habitat type mesohabitat used by an aquatic organism for specific purposes or events typically described by a combination of depth velocity substrate and cover Mesohabitat is a discrete reach of a stream defined by the channel geometry with similar physical characteristics e g slope depth velocity and substrate These mesohabitat areas are commonly termed pools riffles runs etc Finally total habitat is the total available wetted area conditioned by microhabitat and macrohabitat suitability and summed f
43. the US Nature 396 529 530 Lestelle L C and L E Mobrand 1995 Progress report on the application of an ecosystem analysis method to the Grande Ronde Watershed using spring chinook as a diagnostic species In Mobrand L L Lestelle L Gilbertson R Browning D Bryson R Carmichael E Claire B Hadden C Huntington L Kuchenbecker and M Shaw Grande Ronde Model Watershed Ecosystem Diagnosis and Treatment Final Report DOE BP 10331 1 Bonneville Power Administration Portland OR October 1995 v p Ozone Action 2000 Heat waves and hot nights Available on the Internet at www psr org heatsheet html Economic Valuation Douglas A J and R L Johnson 2002 Does the CVM underestimate resource values Further empirical evidence from the Klamath and Trinity Rivers 2002 Annual Meeting of the Western Economic Association Seattle Washington June July 2002 Douglas A J and A Sleeper In Prep Estimating recreation trip related benefits for the Klamath River Basin with TCM and Contingent Use data Douglas A J and J G Taylor 1999a The economic value of Trinity River water International Water Resources Development 15 3 309 322 Douglas A J and J G Taylor 1999b A new model for the travel cost method the total expenses approach Environmental Modelling amp Software 14 81 92 Douglas A J and J G Taylor 1999c Resource management and nonmarket valuation research Intern J Environ Studies 57 1 16
44. the graph data are displayed is the Exceedence option When checked this option displays each item in the series against its probability of being equaled or exceeded Often called a duration curve data displayed in this manner are sorted from high to low and plotted against their cumulative probability calculated by P m n where m is the rank order and n is the total number of events in the series These plots are useful in conceptualizing how much time the system is likely to spend in certain states For example the 5095 value is that value in the series with one half of the values larger and one half smaller The 90 exceedence value has by definition been equaled or exceeded 90 of the time 56 For more information on exceedence plots and their utility please refer to Bovee et al 1998 Note that SIAM employs only the most primitive formulation of exceedence probability for display purposes This has been done because the data are not extreme e g peak flows and the formula is the single most intuitive formulation more analytic formulae for certain purposes are given by Cunnane 1978 Figure 21 shows an exceedence plot for temperature at Iron Gate Dam Water Quality IGD_MAX_Q Water Years 1992 1994 ol x Daily Temperature Exceedence IGD_MAX_Q Water Years 1992 1994 A aa en cc ge Ed Degrees C I eo AR o a o o o o oO o to o ce Li t o Percent Of Time Equaled Or Exceeded
45. the stated maxima or minima implying gauging error large seiching of the reservoir pool or other unspecified problems Since MODSIM was calibrated to the reported storage values it only makes sense that the respective minima and maxima allow for reasonable deviations from the published values We USGS have made what we hope are reasonable compromises in putting in our best understanding of the actual storage elevation area tables as well as good estimates of reservoir storage minima and maxima These limit values were chosen to represent the existing plumbing e g the sill elevation for Upper Klamath Lake and elevations of current reservoir outlets taking MODSIM s evaporation into account and pretty much ensuring that the water quality model is stable for the calibration runs Both MODSIM and HEC 5Q only use a subset of the total number of points on the non linear storage elevation curves therefore the resulting piecewise linear interpolation estimates may contain some discrepancies from the complete tables of curve numbers available In turn SIAM knows these tables curves extrapolated to include storage values both higher and lower than have ever been recorded This is to allow exploration of potentially reasonable water management alternatives like lowering the UKL sill or raising the height of various dams in a what if fashion Providing the freedom to experiment also has its risks For example reducing reservoir storage to a very
46. use SALMOD to calculate a microhabitat time series without conducting a full population level analysis Streamflow and habitat quality as a function of flow are two physical state variables used in SALMOD see Anadromous Fish Production Component SALMOD Using only these variables a microhabitat time series analysis can be conducted using SALMOD The water quality model HEC 5Q is used to conduct the macrohabitat analysis see Water Quality Component While SIAM has the capability to display a microhabitat time series an integration of micro and macrohabitat for a so called total habitat analysis after Bovee et al 1998 is not currently possible How do you do a microhabitat analysis To conduct a microhabitat analysis for fall chinook for the Iron Gate to Scott study area use the 10 input files presently contained in SALMOD To conduct a microhabitat analysis for some other species life stage s such as coho salmon two ofthe SALMOD input files must be modified prior to running SIAM Input files SPECIES DAT Names life stages classes and length limits WUA DAT Flow versus weighted usable area relationships for each life stage and mesohabitat type SALMOD s other files will need to have their species and life stage names modified to match any changes made to these files While the remaining eight SALMOD files are necessary i e must contain the minimum data to run SALMOD they are not directly used in the microhabitat calculatio
47. www fort usgs gov Preface This booklet serves as an introduction to the SIAM a System Impact Assessment Model for riverine ecosystems SIAM is an integrated set of models used to address significant interrelationships among selected physical temperature microhabitat and geomorphic features chemical dissolved oxygen and biological variables young of year salmonid production and stream flow in a river SIAM has been developed for the lower Klamath River from Klamath Falls Oregon to the river s mouth on the California coast using data and models selected to be appropriate for the riverine portion of that study area SIAM is only as good as the data models and its users allow it to be This document highlights the important assumptions and limitations of these data and models so that use may be enlightened as well as productive We have tried to assure the quality of the data and models integral to SIAM for the Klamath River however we stress that common sense may not be left behind in applying SIAM for any specific analysis Users must be vigilant in making sure that the results logically follow from the premises A warranty is neither stated nor implied SIAM represents only a small portion of any true ecosystem analysis and its results must be considered in context with numerous other ecological institutional and political realities SIAM is not meant to be a decision making device but it is rather a decision aid It is infeasible to
48. year in time step 54 the second week of the second year Press the down arrow and enter the new record as shown duplicating entries for week 2 Make sure you go all the way across the table as not all columns may be seen at one time Your screen should now look like Figure 18 When you are through editing press the OK button Note that pressing OK will resort the edit screen by week number if you have entered any records out of numerical order 50 The final editing that you may perform is usually not specific to any alternative but rather applies to the evaluation of the whole set of them the Red Flags Choosing Edit Red Flags or clicking on brings up a seemingly complicated but actually straightforward set of Red Flag Criteria SIAM is supplied with a default set which you may indeed should change to suit your perspective Each flag is tailored to a particular output measure from the various models like flow and water temperature Choosing from the list of possibilities one may add to delete from or create new red or yellow flags The intent ofthe red yellow dichotomy is simply one of degree red flags are meant to convey more severity and stand out visually more than the yellow flags You can be inventive in constructing these flags for your analysis For this alternative let s create a new Red Flag Suppose you have evidence to support the fact that high releases during egg incubation below Iron Gate are detrimental to that bio
49. your computer Note in Figure 12 that the new folder Klamath_Alts has been chosen by double clicking to open it Press the OK button to continue 41 Select a location for the new alternative x Folders c projects klamath_alts m klamath_alts Drives c FY8HJ v Cancel Figure 12 Selecting the folder in which to store your new alternatives Your screen should now look something like that in Figure 11 but with the appropriate folder chosen For our sample tour note that we entered GD Max Q as its name because it relates to setting maximum flows This name becomes both the name of a sub folder in which SIAM stores all relevant files as well as the name of a file in that folder with a ALT suffix but you don t have to worry with all of that SIAM takes care of all those details for you Remember that you will eventually have many more of these alternatives so be creative and specific in your naming SIAM gets indigestion if you use folder names that contain spaces so it will automatically replace spaces with underscores The XY File item required in creating a New alternative identifies the water quantity model data set from which your new alternative is to be derived The water quantity model MODSIM uses the file extension XY as its data set identifier We have supplied one or more data sets in your installation from which to choose Appendix 2 Figure 13 shows what your screen should look like if you have successf
50. 24 Figure 66 Chart worksheet in the nutrient loading estimation model 125 List of Tables Table 1 SLAM s AX BIDU IES cioe n Tod n ete e e tese vgs Ms ede uS REO AL cores 11 Table 2 Differences in MODSIM prediction and gaged flows Adapted from Campbell et al 2001 14 Table 3 Water quality error and correlation statistics 17 Table 4 Example life stage and class structure definition of an anadromous salmonid population along with the model s order of calculation Classes are defined by percent development deposition to emergence for egg stage and by length mm for fry to yearling 29 Table 5a Approximate crosswalk between SIAM component model s spatial representations for the with and without Project network 1 down to Seiad California The without Project network 2 extends the HEC 5Q network upstream to Upper Klamath Lake and differs in the exact location of Control Points 10 and 15 lt u scciessncsessdivacstaguccatcssWeesoasonccdcs BacdessesstasysuacareSdoueens 35 Table 5b Continuation of Table 5a for segments downstream from Seiad California Network 3 to the ocean Note that SALMOD does not extend below the Scott River ssss 36 Table 6 Approximate crosswalk between SIAM component models temporal representations 37 Table 7 Years chosen to represent Iron Gate Dam discharge by month and exceedence level 83 Table 8 Hydrologic sta
51. 7 1982 1979 1983 1990 1984 1968 1983 1979 1975 1961 was actually the 10 year but flows at Iron Gate were still peaking flows in 1961 so the next closest year for mean monthly discharge was chosen X 1975 You can modify the three daily templates supplied with SIAM by selecting the File Daily Pattern Templates option on the SIAM main menu Select the template dry average wet and the month that you wish to modify Enter new relative flow values for the days of the month Absolute flow values are not important here as it is just the pattern that you are defining Use the Graph function to better visualize the pattern Note Changes made to templates affect all projects while daily flow variability patterns are alternative specific It may be comparatively easy to enter a daily pattern that in combination with a specific monthly flow regime produces errors in the water quality simulation For example superimposition of an extreme day to day pattern may cause the resulting flows through reservoirs to violate the residence time criteria imposed by HEC 5Q If flows through any reservoir result in a residence time smaller than the timestep of the simulation the HEC 5Q model may produce erroneous results Since Keno reservoir is the smallest reservoir simulated it has the limiting residence time SIAM checks all flows before running HEC 5Q If possible user 82 requested daily flows are adjusted so that the residence time in Keno is gr
52. Comparison eligibility criteria may be set or relaxed to fit your needs The criteria default to Must have overlapping simulation periods but may be changed by checking or unchecking the boxes provided Click on OK to begin specifying the report parameters Alternatives Available For Comparison x Highlight alternatives for comparison with IGD_MAX_Q NEW NEWS 90 _DAILY2 90 _DAILY WETYEARS Add or delete from the list of available alternatives Maintain List Comparison Eligibility Criteria iv Must have overlapping simulation periods Must have the same simulation length Must have the same starting year Cancel Figure 39 Alternative selection dialog 12 Figure 40 shows the alternative comparison report parameters dialog Enter a descriptive name for the report up to 80 characters This name will be used for selecting reports for viewing Check the boxes for the desired comparison variables Enter values for the difference thresholds corresponding to the comparison variables selected These are values below which differences between alternatives are not reported Enter the number of values exceeding the thresholds that you wish to be reported The maximum time period that can be reported is displayed in the time period edit boxes Use the spin controls to change the starting and ending dates if you want to compare just a subset of these times Select the locations for water quantity dischar
53. Figure 52 are based on an understanding of natural seasonal monthly hydrologic inputs and the historical inflows to and total volume behind Link Dam The normal pattern of a representative hydrograph for water inflow to the basin forms the basis for defining these factors that is expected dry and wet seasons In addition three 3 sets of Target Reservoir Storage Values are provided for each reservoir for each of twelve months for the Dry Average and Wet Targets The FACTORS are accessible through MODSIM by selecting AHydrologic States from the Edit menu Note The actual MODSIM calculated Target values used each month of the simulation for every reservoir are included in the MODSIM output file for reservoirs 1 e file name res and if the res file is imported into a spreadsheet program such as Excel using commas and spaces as delimiters then these values are listed in column L adjacent to 27 Link Dam for the respective year and month The Beginning Ending i e simulated reservoir levels for each month and the Target value used for that month are also included in the res file respectively in columns E F and G if imported into Excel Table 8 Hydrologic state factors 88 HYDROLOGIC STATES Based on Reservoir 27 Link Dam FACTORS WET 0 85 0 80 0 80 0 80 0 85 0 88 0 85 0 93 0 93 0 93 0 93 0 85 Hydrologic States rj E 0 8 o BU x eI ES Dry 04 Wet
54. Flow Variability to display the Daily Flow Variability Dialog Figure 46 This dialog contains controls for specifying the source of variability for each month ofa year editing user defined daily flow values for each month and maintaining monthly target volume or updating monthly targets with a new volume There are five sources or templates for daily patterns available in SIAM The default template is a constant flow for each day of a month That is no daily variability is superimposed on the MODSIM output Other daily pattern templates are provided with SIAM for typical dry average and wet water years Any changes made to these patterns by the user automatically become the fifth template type User Defined Y ou may specify a template for an entire year or pick and choose individual months from all of the sources Click ona radio button in the A Months row to apply a template to the entire year or click on the radio button corresponding to the desired template in the same row for the month to which it is to be applied To edit individual daily flows for a specific month click on the Edit button next to the month desired Edit the daily values by clicking on them in the daily flow table and typing in a new value Values may also be pasted into the table from a spreadsheet program 79 Iron Gate Daily Flow Variability x m Monthly Variability Source User
55. L POINT STRUCTURE Name Link Control Pt Name River Mi Below Indian Ck 65 150 Below Indian Ck 109 Below Elk Ck 64 160 Below Elk Ck 108 Below Clear Ck 63 170 Below Clear Ck 100 Below Salmon R 59 180 Below Salmon R 67 Orleans 58 190 Orleans 59 Below Red Cap Ck 56 200 Below Red Cap Ck 53 Below Bluff Ck 55 210 Below Bluff Ck 50 Below Trinity R 54 220 Below Trinity R 44 Below Blue Ck 52 230 Below Blue Ck 16 Klamath 69 240 Klamath 3 Ocean 67 250 Ocean 0 35 Table 6 Approximate crosswalk between SIAM component models temporal representations Calendar MODSIM HEC 5Q SALMOD Calendar MODSIM HEC 5Q Water Month Julian Day week Month Julian Day year N l Oct 1 Oct 8 N Oct 15 Oct 22 N N 4A Ww Oct 29 N Nov 5 N oo Nov 12 N N Nn N o2 N Nov 19 Nov 26 N o2 No N A oN Dec 3 Dec 10 N Nn w Dec 17 Dec 24 N ON Dec 31 Jan 7 oO N oo ojo In Fr IA J t A N N ta j je A ITN gt o o ON N oo oo Jan 14 ON Jan 21 ww e N No CA Jan 28 N U2 N Feb 4 N No w can No Feb 11 U AR U ion A oU N W Feb 18 Feb 25 AR oo N U Ww CA Nn N N w N oe oN oO gt A A TR TR TB TR TR TR FT BR PTR n TR n n ut n n
56. Ld Klamath Lake j KLAMATH RIVER x 7x Noir CONTROL POINTS permena Ponia I iV Dam ZN repe Dan Tror Gate Dam Cottonwood Ci Copco iniet Sead Valley Beaver Ch Bo Bogus ck a Rowe Ck Witiow Ck forse CR Humbug Chess River cott River S 16 56 15 62 7 15 67 15 78 t 15 78 15 88 15 88 16 00 gt 16 00 C ij 3 3 Set Breakpoints e E 3 1 E 1 d n d Reverse Colors PHO00000000000000088 P e River Miles 2d 0 5 4 1 DL 4 F Ho 1 Uu Li L Uu Uu Uu bits mitaaa biatb tiaba 4 s 6 1 1 1 a T E 5 T Ey 5 j 7 Figure 50 Spatial distribution dialog for temperature on June 1 1993 SIAM gives you the ability to display spatial distribution over time through animation of the river values 1 e colors Click on the Animate button to activate animation Doing so disables the Zoom and Reset buttons and enables the animation controls These controls consist of Play Button Clicking starts an animation sequence Pause Button Clicking suspends the animation Stop Button Clicking stops the animation Step Button Clicking steps through the animation sequence one interval at a time 85 Interval Edit Box Enter the animation interval in days or use the spin control to set the interval at which the animation is updated Starting Edit Boxes Enter the starting day and water year for the animation Ending Edit Boxes Enter the ending day and water year fo
57. Loading Estimation Spreedsheet Model sss 123 List of Figures Figure LS LAM s Components eoe te destino EO muda deos otis Napa dA hava veas ue nin dao i 10 Figure 2 Important inputs and outputs for MODSIM sssesseeeeeeeeneeeenenne enne 15 Figure 3a Average measured and simulated mean daily water temperature for Seiad Valley Gage location in the Klamath River from water years 1961 through 1999 sssssssss 18 Figure 3b Comparison of simulated and measured mean daily dissolved oxygen concentration at the Iron Gate Dam in the Klamath River from water years 1996 through 1999 18 Figure 3c Comparison of measured and simulated mean daily water temperature at the Seiad Valley gage location in the Klamath River for two wet water years 1965 and 1971 19 Figure 3d Comparison of measured and simulated mean daily water temperature at the Seiad Valley gage location in the Klamath River for two dry water years 1968 and 1977 19 Figure 4 Important inputs and outputs for HEC 5Q sese 22 Figure 5 Major components of aquatic habitat analyses sssseeeeeeee 25 Figure 6 SALMOD schematic zo esset ha eed ben SO ER RS I NEN EC POSU 30 Figure 7 Important inputs and outputs for SALMOD ssseeseeeeeeeeen eene nennen 31 Figure 8 Important inputs and outputs for Ecosystem Health component ss 33
58. MAX_Q Water Years 1992 1994 Start Date es S D EN D End Date co e e gg Sept 30 sisi Limit Number Of Series 3 sg C Lower Limit 92 93 94 Water Year H Degrees C B Keno Dam B Copco Dam 3 iron Gate Dam a Consecutive daysinseries Output generated on 03 05 2001 at 11 47 26 Evaluation Period June 1 Sept 30 Consecutive days in series 1 Statistics Set Y Axis T Exceedence Plot Graph Type Select desired locations i J Resolution Data Type Cline Iv Grid Lines ES Export Between Years Temperature G Bar PlotPoints Upstream end of JC Boyle Res Print isi i jw T rond atOnacn Bes z _ Ges Figure 26 Exposure periods for Keno Copco and Iron Gate dams Select the Macrohabitat option of the Water Quality Metrics submenu to compute and display the average number of miles of the river in which the temperature or dissolved oxygen falls within a specified range during a specified period of each year Set the evaluation period using the start date and end date spin controls Set the temperature or dissolved oxygen range using the upper and lower limit spin controls Select the starting and ending location for the evaluation Figure 28 shows the temperature related macrohabitat for the section of the river between Iron Gate Dam and Seiad Valley 62 An additional water quality metric is the longitudinal profile for temperatu
59. ODSIM values and HEC 5Q within the range of 400 to 200 acre ft These small discrepancies are attributed to integer flow values used in MODSIM and passed to HEC 5Q and real number flow values used internally by HEC 5Q Additionally some small discrepancies should also be expected between water surface elevation values from HEC 5Q and those computed using the Storage Area Elevation tables supplied with SIAM These discrepancies are attributed to the subset of nine points used internally by HEC 5Q compared to an even finer mesh of values used by SIAM The most accurate representation of water surface elevations are therefore the values computed by SIAM using the complete Storage Area Elevation curves from the MODSIM storage predictions However the water surface elevations being simulated internally by the water quality model are those available from the water quality output in SIAM New Reservoir Initial Water Quality Conditions Reservoir water quality conditions temperature DO and conductivity for day of any simulation in SIAM are hard coded values These values have been updated to reflect the model predicted average outfall conditions from all October 1 days of the historical simulation These updated hard coded values are the best set of representative October 1 water quality conditions available since they are based on 41 years of simulated hydrologic and meteorologic conditions and serve to eliminate initial values previously used
60. OS version of SALMOD has been replaced with a Windows version and the SALMOD graphics were updated within SIAM SIAM now has the capability to also run the stand alone version of SALMOD The SIAM toolbar has been redesigned and new buttons were added SIAM output additions include an alternative options report and a target matching table Water surface elevation has been added to the red flag criteria Version 2 7 May 2001 Version 2 6 was solely an experimental release allows a much finer prediction of the water surface elevation for each reservoir especially Upper Klamath Lake This version allows one to set minimum and maximum reservoir storage volumes and monthly targets as either water surface elevations feet above mean sea level or volumes acre feet This was accomplished by including a detailed storage elevation surface area table and a revised verification of the water quantity model to reflect the Bureau of Reclamation s current best estimate of Upper Klamath Lake s bathymetry and total storage of the lake rather than just active storage as had been previously modeled Version 2 7 also contains the ability to superimpose a daily release schedule from Iron Gate Reservoir such that the influence of daily variability may be reflected in the water quality and fish production models results Minor changes to river mile designations were made to Version 2 7 In adding the lake level features several potential inconsistencies were identified It
61. Reservoir Demand v Iv Applyta all years Monthly targets demands in cfs Units C Acrefeet CFS Target Type Storage Elevation 1300 31 otal 743009 00 Note Total is always given in acrefeet Figure 15 The Edit Node Criteria dialog As you can see there are 12 monthly flow values available for editing as well as a switch to choose the units you wish you use Note that the Total of the annual values may be found in the last or bottom row and is updated automatically it is always in acre feet For our example we would like to actually reduce and stabilize the October to February spawning rearing flows to 1000 cfs or about 60 000 af so type the new value in for those months Note that you must press the Enter key Tab key down arrow key or click the mouse on another cell to finalize the entry of each number you edit before proceeding This is standard throughout SIAM By default the target values in this table represent minimum values that MODSIM will attempt to achieve Therefore the simulation may result in flows that are higher than the targets entered To force flows to be no greater than the targets click on the corresponding check box in the Maximum column Maximum means that the flow will not be treated as a minimum flow but rather be as its name implies As long as there is enough water the targets will be exactly matched if water is short there may be less You can turn all of the Ma
62. SLIB Bartholow J M and T J Waddle 1986 Introduction to stream network habitat analysis Instream Flow Information Paper 22 U S Fish Wildl Serv Biol Rep 86 8 242 pp Bovee K D B L Lamb J M Bartholow C B Stalnaker J Taylor and J Henriksen 1998 Stream habitat analysis using the instream flow incremental methodology U S Geological Survey Biological Resources Division Information and Technology Report USGS BRD 1998 0004 Viii 131 pp Available on the Internet at http www fort usgs gov products pubs 3910 3910 asp Milhous R T M A Updike and D M Schneider 1989 Physical Habitat Simulation System PHABSIM Instream Flow Information Paper No 11 U S Fish and Wildlife Service FWS OBS 81 13 revised Milhous R T J M Bartholow M A Updike and A R Moos 1990 Reference Manual for Generation and Analysis of Habitat Time Series Version II US Fish Wildl Serv Biol Rep 90 16 249 pp Stalnaker C B L Lamb J Henriksen K Bovee and J Bartholow 1995 The Instream Flow Incremental Methodology A primer for IFIM U S National Biological Service Biological Science Report 29 44 pp U S Geological Survey 2001 PHABSIM for Windows User s Manual and Exercises Midcontinent Ecological Science Center USGS Open File Report 01 340 U S Department of the Interior Anadromous Fish Production Model SALMOD Bartholow J J Heasley J Laake J Sandelin B A K Coughlan and A Moos 2000 SALMOD
63. U S DEPARTMENT OF THE INTERIOR U S GEOLOGICAL SURVEY Evaluating Water Management Strategies with the Systems Impact Assessment Model SIAM Version 3 March 2003 by John Bartholow John Heasley Blair Hanna Jeff Sandelin Marshall Flug Sharon Campbell Jim Henriksen and Aaron Douglas Open File Report 03 82 This report is preliminary and has not been reviewed for conformity with U S Geological Survey editorial standards Any use of trade product or firm names is for descriptive purposes only and does not imply endorsement by the U S Government Although the software referenced by this report has been used by the U S Geological Survey no warranty expressed or implied is made by the USGS as to the accuracy and functioning of the software and related materials nor shall the fact of distribution constitute any such warranty and no responsibility is assumed by the USGS in connection therewith Biological Resource Division Johnson Controls World Services Fort Collins Science Center Fort Collins Colorado Fort Collins Colorado Suggested citation Bartholow J M J Heasley R B Hanna J Sandelin M Flug S Campbell J Henriksen and A Douglas 2003 Evaluating Water Management Strategies with the Systems Impact Assessment Model SIAM Version 3 U S Geological Survey Fort Collins Science Center Open File Report 03 82 Fort Collins Colorado March 2003 127 pp Available on the Internet at http
64. Windows Help if you need assistance in creating a new folder Pick a place that is logical to you For example you might choose to create a location such as C Projects Klamath Alts as an appropriate destination Locating this new folder where you stored SIAM at installation is a reasonable choice but be forewarned that Windows will not be able to fully uninstall SIAM at a later date if you do so you will need to delete that folder manually if you wish a thorough uninstall Once you have created a suitable destination folder choose Fi e New from SIAM s main menu or click on B Note When we say choosing File New we mean highlighting the New option under SIAM s File main menu item This will open a New Alternative dialog see Figure 11 for you to tell SIAM 1 what name you wish to give your new alternative 2 the location in which to store it the same folder you just created with Windows Explorer 3 a brief description to help you 40 remember what you are doing 4 what network configuration to use and 5 where to get the baseline hydrology file XY file to start with Both the baseline file and the network configuration may be selected through pull down menus though only for baseline files distributed with SIAM After selecting a network only those XY files associated with that network are available for selection There are two networks currently installed with SIAM Network 3 and Network 4 Network 3 is with project to the ocea
65. able alternatives All output graphics metrics are available for comparison The graphics screens for the comparisons are identical to the graphics output screens with the addition of a Select Alternatives button In the comparison process SIAM automatically uses the current alternative the one you have opened as the base case You then select one or more other compatible alternatives to compare with the base You must open one base alternative before comparisons can be made Select the Comparison Graphs option from the View menu to compare alternative results Choose the output category Water Quantity Water Quality Fish Production etc in which you wish to compare results The appropriate results will be displayed for the alternative currently open Click on the Select Alternatives button and select those alternatives that you wish to compare Alternatives must be compatible with the alternative currently open in order to be selected That is they must represent the same network the length of the simulation must be the same and in some cases they must start in the same year If a selected alternative is incompatible a message will be displayed and you will not be able to select it Figure 36 illustrates the alternative selection process Click on OK after selecting those alternatives that you wish to appear on the graph with the currently open alternative Select Refresh to plot all of the selected alternatives The functions for controllin
66. and J F Scott 2001 Modeling Klamath River system operations for quantity and quality ASCE Journal of Water Resources Planning and Management September October 2001 284 294 Fredericks J and J Labadie 1995 Decision Support System for Conjunctive Stream Aquifer Management Open File Report No 10 Colorado Water Resources Research Institute Colorado State University Ft Collins Colorado Aug 1995 124 pp plus appendices Labadie J W 1988 Program MODSIM River basin network flow model for the microcomputer Department of Civil Engineering Colorado State University Ft Collins Colorado Additional material may be found on a World Wide Web site maintained at Colorado State University at http modsim engr colostate edu This information may or may not be up to date for the version of MODSIM distributed with SIAM Water Quality Model HEC 5Q Campbell S G 2001 Water Quality and Nutrient Loading in the Klamath River Between Keno Oregon and Seiad Valley California From 1996 1998 USGS Open File Report 01 301 October 2001 55 pp data files Campbell S G 1999 Water Quality and Nutrient Loading in the Klamath River From Keno OR to Seiad Valley CA During 1996 1997 MBS Thesis University of Colorado at Denver Denver CO July 30 1999 109 pp Chapra Steven C 1997 Surface Water Quality Modeling New York McGraw Hill Companies Inc 844 pp Deas M L and G T Orlob 1999 Klamath River Modeling Project Assess
67. and maximum Y axis values or click on Use Defaults to restore the axis to its default values Controls that determine what data are displayed include multiple selection list boxes single selection dropdown lists and spin control edit boxes These control the spatial and temporal extent ofthe data to be displayed There are several ways to interact with a graph once it is displayed to examine data more closely or isolate portions ofthe graph Note that for the zoom options a graphics zoom may not necessarily show axes after the zoom while an axis zoom shows data with the axes However it may not be possible to tell what year of the simulation you are examining To scale a graph 1 Press Ctrl and hold down both mouse buttons or the middle button on a 3 button mouse 2 Move the mouse down to increase the chart size or up to decrease chart size To move a graph 1 Press Shift and hold down both mouse buttons or the middle button on a 3 button mouse 2 Move the mouse to change the positioning of the chart inside the chart area Graphics zoom 1 Press Ctrl and hold down the left mouse button 2 Drag the mouse to select the zoom area and release the mouse button Axis zoom 1 Press Shift and hold down the left mouse button 2 Drag the mouse to select the zoom area and release the mouse button Reset Press the r key to remove all scaling moving and zooming effects The single option currently available that influences how
68. ays running from Copco Dam to Below Horse Ck 5 00 degrees C Figure 19 Red Flags dialog after a new red flag has been added We mentioned earlier that you should keep a set of notes to describe your alternative This is done through the Edit Annotate Alternative option on SIAM s main screen or by clicking Choosing this option brings up Windows WordPad utility and allows you to record whatever you want to fully describe what you have done No one s forcing you to do this it s just good practice We encourage you to be diligent It is awfully easy to forget everything you have changed or even what your rationale was to begin with For now type in a free form description and leave WordPad open on your desktop while returning to SIAM we ll come back to this later If you wish to edit the alternative description select the Edit Alternative Description Option on SIAM s main screen and type in a new description It s about time to Run this simulation don t you think 52 Running SIAM Choose Run Simulation from SIAM s main menu or press the Run icon 8 on the toolbar Assuming that you have made a flow or storage change in the water quantity model the component models will all be run starting with MODSIM Ifyou specifically select Run Water Quantity Expert from the menu you will be given access to the full blown version of MODSIM otherwise you will quickly breeze through MODSIM in a DOS window Warning for expert users
69. cations Line Linear Temperature j C Bar C Log C Stacked Bar C Relative Acrefeet Cts yid nl bed te ose Statistics Set Y Axis Exceedence Plot PlotPoints Grid M Line Style Figure 24 Average mean daily temperature at Iron Gate and Keno dams There are four water quality metrics in SIAM to better assess impacts on fish and other aquatic organisms The Water Quality Metrics option of the View menu has five options Annual Exposure The annual cumulative or daily exposure of aquatic organisms to temperature or dissolved oxygen at different locations during a specified period of the year 59 Exposure Period The number of days in a year in which an aquatic organism is exposed to temperature or dissolved oxygen within a specified range during a specified period of the year Thermal Window The calendar dates when temperature first exceeds a specified temperature and last exceeds that temperature Macrohabitat The average number of river miles experiencing a specified temperature or dissolved oxygen range during a specified period of the year Annual exposure provides a way to look at the cumulative degree days or DO days for an alternative For example you might be interested in how many degree days eggs or fish would be exposed to at a particular location Select the Annual Exposure option from the View Water Quality Metrics submenu Set the evaluation period using the start date and end
70. centage of the EPA criterion for the thirty day average ammonia concentration The equation for this is CCC ___ 0577 s 2 487 x MIN 2 85 1 45 x 10 02805 D 10 0988 pED 10 7 88 PH where pH pH value T water temperature This equation EPA 1999 assumes that early life stages are present Figure 51 shows the set criteria dialog for generating the potential for fish kill data 86 Set criteria for computing potential for fish kill Percent EPA criterion Year Type Potential Category Break point Ez Dry Average Low to Moderate 20 C Wet Moderate to High 100 Cancel Figure 51 Dialog for generating potential for fish kill data After generating the data you have the option of viewing the results temporally longitudinally or as amap Use the Potential For Fish Kill option under the View menu to access these capabilities The Temporal Display option allows you to plot potential for fish kill ammonia concentration or pH over time for a selected location The Longitudinal Display option allows you to plot potential for fish kill ammonia concentration or pH at control points along the river for a selected date You may also compare other alternatives for which potential for fish kill data have been generated The map display capabilities are very similar to those for temperature The spatial distribution of potential for fish kill ammonia concentration or pH are c
71. ces concerning water management alternatives Further we have warned that it may be easy to forget that though calibrated to measured values even the results of the historical water quantity and quality simulations are just that simulations not real measured data Likewise we have mentioned that the program has been developed to shield naive users from the component models underlying complexity At the same time we must acknowledge that it is possible to push these models outside the comfortable domain for which they have been calibrated and tested and venture into a twilight zone of the illogical and unrealistic There are other caveats to convey for the sake of thoroughness For example as a rule SIAM does not display obviously wrong negative flows temperatures or oxygen concentrations Instead almost all graphs are truncated at zero data Exported or reported in the Statistics table also reflect this truncation though values in the more raw simulation model output files report the model s true simulated value How could negative values be generated Frankly the only ones we have seen are water temperature and they reflect the fact that the HEC 5Q model s calibration concentrated on the hot summer season and therefore discounted winter conditions Further the equilibrium temperature sub model within HEC 5Q like most water temperature models is not as accurate at very low lt 4 C temperature conditions those most likely to cause
72. ctual values plotted on the graph for Keno simply click on the Keno tab and scroll through the data for each constituent If you wish to calculate a yearly loading sum compare locations or see how loading varies from year to year then these data can be copied into a blank spreadsheet and manually graphed Our intent was not to develop a complete nutrient loading model for the Klamath Basin but to demonstrate a general potential for water quality modeling that could take advantage of an existing decision support system model to identify the greatest sources of nutrient loading and investigate potential reductions through best management practices in the watershed or operational changes if 124 any that may result in reductions in nutrient loading Because USGS resources were limited this additional module for SIAM is not fully developed but can easily be modified expanded or altered to meet water quality analysis needs of Klamath Basin resource users and managers as desired For further information please contact Sharon Campbell at 970 226 9331 or sharon g campbell usgs gov References Cited Campbell S G 2001 Water Quality and Nutrient Loading in the Klamath River from Keno OR to Seiad Valley CA during 1996 1998 U S Geological Survey Open File Report 01 301 55 pp data files 125
73. d Recall that MODSIM is a monthly model and SALMOD is weekly while HEC 5Q is daily MODSIM s total monthly flow is in acre feet AF though these flows may be specified in SIAM as AF or cubic feet per second cfs If supplied as cfs SIAM converts the value to a monthly AF volume by knowing the number of days in each month February always has 28 days we do not bother with leap years since water years may be run in any arbitrary sequence The monthly volumes are divided evenly into cfs values for HEC 5Q again using the appropriate number of days for each month Note that HEC 5Q simulations run for 360 day years composed of 30 day months regardless of the actual number of days per month for networks 1 and 2 only i e down to Seiad This potentially introduces a small error in the mass balance for some reservoirs in months not having 30 days but we do not consider this to be a significant problem as MODSIM is responsible for system wide mass balance for the duration of the simulation No error accumulates during a multi year simulation since HEC 5Q is reinitialized for each water year Further no error is passed to SALMOD since its flows are aggregated from HEC 5Q s correct daily flows Network 3 files 1 e to the ocean simulate a full 365 days each year in HEC 5Q Network 3 uses real months so this problem does not occur 33 Table 5a Approximate crosswalk between SIAM component model s spatial representations for the with and without P
74. d keeps accumulating throughout the evaluation period Choosing the ndependent option displays daily values instead 1 e showing each day s degree days as defined above Figure 25 shows annual Cumulative temperature exposure above 20 C between June 1 and September 30 at Iron Gate and Seiad Note that some years are warmer at Seiad some at Iron Gate and some are about equal Pressing Advanced for Annual Exposure provides even more flexibility but is only available for the Cumulative counting method and only applies when the new parameters are displayed The Reset parameters are advanced controls that allow you to assess situations where exceeding certain values causes the exposure counter to be reset to zero and begin again For example if you believed that if water temperatures rose above 16 C for one day that developing in vivo eggs would be resorbed you would set the Upper Reset to 16 But if for example it really took seven days above 16 you would set the Days to Reset to seven See Bartholow and Waddle 1986 for more information on the use of this option 60 Using Annual Exposure for dissolved oxygen is a bit more thought provoking since generally we are interested in low DO values instead of high ones For example if we wanted to count DO days when DO dropped below 8 mg l set the Upper Limit to 8 the Lower to zero and the Threshold to 8 Then the number of DO days meeting these criteria will be shown on the graph Annual E
75. d base temperature density habitat and season movement mortalities Click on the Define Partitions button to select the combinations desired see Figure 34 Mortality Partitions IGD_MAX_Q Water Years 1993 1995 x SALMOD MORTALITY PARTITIONS Time Steps 1 to 156 Comp Units 1 to 526 Reduce and stabilize October to February spawning rearing flows to 1000 cfs o A UTERE REN ee ee a ee Oe ee a ee Oe fee 600001 hebheeedeteqeereRededeebeded I coat I d i d dei i d i bei 35000 ie ui pone E a E ute ed le equis 30000 ETE E E Number Of Fish 20000 ED A QU TES 10000 o EEENEEENS HGEEEEEEEEE XE SNDJFMAMJJAS 99AND JF MAM JJA S OND JF MAM JJ AS Month in Water Year BH PreSmols Base E Pre Smolis Temp Pre Smolis Density E Pre Smolis Habitat B Pre Smolts Seas Output generated on 12 31 1969 at 17 00 00 Zoom Press shift and drag mouse Reset Press R Refresh Export Iv Grid Lines Statistics Annual Print Close Select species Advanced Figure 33 Mortality partitions for pre smolts You may configure the X axis as time time steps or dates or space computation units or distance The Advanced button allows you to select the X axis units and set the temporal and spatial extent of the data to be plotted Use the spin controls to set the beginning and ending time step or computation unit The corresponding date and distance are displayed in the edit bo
76. d elements of regulatory certainty while respecting the legal obligations and rights of various parties to existing contracts compacts and decrees and c avoid inappropriate regulations SIAM does not evaluate anything for you 8 Select and Implement Alternative Our goal for the final product is to encourage parties when they are ready to select and implement an alternative with appropriate measurement systems in place to monitor the success or lack of success of that alternative This will serve to improve and expand all parties collective understanding of the ecological system allow for adjustment of the rules for 97 alternative implementation and provide a continuation of monitoring for ecosystem health and restoration of the anadromous fish of the Klamath basin SIAM is not a decision making device it only provides supporting evidence in comparing the extent and frequency of potentially limiting events It is infeasible to model all important resource impacts and impossible to anticipate all possible water supply situations Discretion and informed guidance will remain a necessary ingredient for SIAM use There may be occasions where SIAM suggests operations that seem counterintuitive In such cases additional data collection or monitoring may be in order to confirm the models behavior This is as it should be 98 SIAM Caveats We have mentioned that SIAM is a collection of models meant to reveal a set of consequen
77. data August is the warmest month of the year at the Iron Gate outfall During August the average daily maximum water temperature is 20 7 C while the mean daily temperature is 20 3 C a difference of 0 4 C However at Seiad California water temperatures are more natural Here July is the warmest month with an average daily maximum temperature of 23 3 C while the mean daily temperature is 21 5 C a difference of 1 8 C At the mouth of the Klamath the July difference has declined to 0 8 C Further the fish production model relies on mean weekly thermal exposure to calculate both growth and mortality Therefore given that maximum mean temperature differences are approximately 1 C we do not consider the effort to simulate maximum temperatures worth the added cost to do so especially when there is an alternative Mean daily temperature predictions from SIAM may be used in conjunction with an Excel spreadsheet supplied with the SIAM distribution to generate maximum daily water temperature predictions for locations immediately below Iron Gate Dam River Mile 190 and at the Seiad gage site RM 130 for any with project alternatives during the summer These maximum daily predictions are based on a multiple linear regression analysis using as much measured data for these two locations as was available 72000 data values for each location either from EarthInfo or datasondes deployed in conjunction with our USGS BRD s research program The re
78. de priorities Reservoir characteristics Supplemental fish data Red flag criteria Daily flow variability for Iron Gate Communicating Your Findings with Others We hope that you will on occasion want to share alternatives you create with others To do so is pretty easy Use Windows Explorer to copy the alternative folder from the location where you have chosen to store all of your alternatives to a diskette If it will not fit on a single diskette you may choose to Zip the folder and its contents or copy to a Zip or CD drive Making sure you have your file clean up preferences set to reduce folder size will help reduce the overall size of each alternative folder Clearly label your disk and ship it to whomever On the destination end the recipient may copy or unzip this folder into their SIAM alternatives folder and open it using SIAM to have access to the output That s all there is to it 78 ADVANCED TOPICS Adding Daily Variability To MODSIM Output The water quantity model MODSIM simulates flow on a monthly basis while the water quality model HEC 5Q operates on a daily time step By default SIAM instructs the water quality model to apportion the monthly flow volume evenly among all days of the month However there may be occasions when you might want to pass a daily flow pattern to HEC 5Q SIAM provides a facility for superimposing daily variability on MODSIM s monthly output for flows along the mainstem Klamath Select File Daily
79. destination controls are common to all graphic screens and are located in the lower right corner of the graphic screen These include Refresh Export Print and Close The functions of these buttons are Refresh Displays the graphics based on the current settings of the controls You must press Refresh after making most changes to the display options Export Creates a comma separated value file csv containing the data to be graphed This file can be read easily by MS Excel TIP You can quickly view the values in Excel by pressing the Export button again after the original Export highlighting the file just saved right clicking and choosing Open off of the pop up menu Print Sends the data to be graphed to your printer after an additional dialog Note that the printed graph will not include the control frame but will have footnotes explaining the composition of the graph Long multi year simulations may present challenges to printers with little spare memory In such cases screen captures e g Alt Print Screen may be the best alternative Then paste the graphic into your word processor and print from there Close Closes the window for this graph type An additional button allows you to display a table of statistics for the plotted curves Click on Statistics to display the number of points minimum curve value maximum curve value curve median curve mean standard deviation and total Not all of these values will be useful
80. discharge with historical data Alternatives Available For Comparison x Highlight alternatives for comparison with IGD_MAX_Q Add or delete from the list of available alternatives Maintain List Cancel Figure 36 Comparison alternative selection dialog 70 Water Quality IGD_MAX_Q Water Years 1992 1994 ol x Daily Dissolved Oxygen Comparisons Water Years 1992 1994 Iron Gate Dam Month in Water Year IGD MAX Q 92 94 WETYEARS 82 84 Output generated on 03 05 2001 at 12 55 52 r Graph Type Scale Data Type Select location TT 1 Line Linear Dissolved Oxygen Gne NN RR C f tog SE TE c Sacked Ber Relative pas E Select Alternatives J Statistics Set Y Axis I Exceedence Plot T PlotPoints M Grid I Line Style Figure 37 Comparison of dissolved oxygen for two alternatives Historical Data Comparisons x Evaluation Interval Start Date 1 ct1 End Date 365 Sept 30 Daily Discharge Comparisons Water Years 1993 1995 lron Gate Dam o Total Period Start Date i Oct1 UICIECE ttt ttt 1993 S8NDJFMAMJJAS SNDJFMAMJJAS ISNDJFMAMJJAS End Date Month in Water Year 365 Sept30 End voren 1995 i IGD MAX Q Historical Data Output generated on 01 09 2002 at 12 49 02 d Plot TA 4 Data Type Select location Standard
81. e 112 minimized with further analysis or better estimations of basin wide meteorological data from in basin measured data Second using the 1996 Keno water quality data to approximate the quality including water temperature of all tributary and accretion waters except Big Springs for all simulation years is unrealistic We would like to explore alternatives to adjust tributary and accretion quality through space and time to improve the model s fidelity Statistical examination of HEC 5Q output compared to measured data shows that these air and accretion temperatures are highly correlated and contribute approximately an equal amount to the model error therefore they should both receive equal attention if improvements are to be made It should be emphasized that the HEC 5Q model remains good regardless of these apparent shortcomings see the excellent error statistics i e the error inherent in the model should in no way preclude use of its output for this phase of the Klamath analysis References National Biological Service 1995 Compilation of Phase I Reports for the Klamath River Basin May 1995 River Systems Management Section Midcontinent Ecological Science Center Fort Collins CO v p 113 Appendix 4 Data Files Available for Expert Users The complete storage area elevation tables for Upper Klamath Lake Lake Ewauna Keno JC Boyle Copco Lake Copco 2 and Iron Gate have been provided with the SIAM Version 2 7 and later
82. e entire space time domain at a single glance Each relevant metric that can potentially limit anadromous fish recovery in the Klamath drawn from the output of all the other models may be summarized in this fashion Generally speaking these metrics may be thought of as critical events thresholds or limits to flow quantity or quality or habitat quantity or quality which SIAM terms red flags Some people may prefer to think of ecological health rather than ecosystem health in the sense that ecological refers more to the measurable processes within an ecosystem others may feel that ecosystem components are more important We believe this distinction is artificial and that the health of both the components and their interrelated processes are essential Whichever your leaning SIAM s strength is to enable the user to more quickly scan the often voluminous output from all the models and cull the wheat from the chaff In this way several alternative water management possibilities may be compared and contrasted Because the red flags or yellow flags are so concise this feature of SIAM may be construed as a grossly simplified version of reality Any summary necessarily omits details that have been aggregated It is not our intent to make the Ecosystem Health component stand alone as SIAM s principal output Rather this feature should be used in context with the other tools in the hierarchical sense mentioned earlier The red flags report may s
83. e initial volume of user specified reservoirs In this way one can have a variable rule book for system management Note Although SIAM is currently limited to handling three hydrologic states newer versions of MODSIM can handle up to seven If SIAM encounters a MODSIM management XY file with other than three states SIAM will still function properly but only the expert user can deal with such a file See the MODSIM documentation and the section on Advanced Topics later in this documentation for more information on how to set up and use a management run MODSIM has been calibrated for the Klamath River Results from that calibration are summarized below in Table 2 These figures represent a trivial percentage difference from USGS gaged flows 12 on the order of 2 cfs on average The maximum monthly differences are large but represent one time deviations due to a change in the operation of the upper basin reservoirs not captured by MODSIM Table 2 Differences in MODSIM Prediction and Gaged Flows Adapted from Campbell et al 2001 USGS Gage Average Year Difference m x 10 Maximum Month Difference m x 10 Location Calibration Validation Calibration Validation Keno 1 7 1 9 1 4 146 Iron Gate 1 9 1 7 1 4 143 Seiad Valley 2 3 2 6 3 4 143 13 Outputs dE Alt 1 Alt 2 Reference Simulate hydrologic operation Alt 2 Reference Reser
84. e only in the top left table the tables on the right are for information only You might choose for example to run the same hydrologic year repeatedly with different meteorological conditions For our example we have run 1992 1993 and 1994 each with 1965 s meteorological data If you enter multiple hydrologic years out of a contiguous sequence the small box labeled Begin years at 1 will be checked indicating that SIAM will actually list them in the output as year 1 2 etc This is because none of the component models can deal with multiple out of order years Manually checking or unchecking this box is not available at this time Year IGD MAX Q x Available years 1961 1399 Historic Flow Metrics 1000s of acre feet Hydrologic Meteorologic Year Year Year UKL Inflow AnnualLink Discharge Total Annual AprSep Dam Release To Ocean Diversions 1394 ETS LA Fill Table Clear Table Begin years at1 MetYearData Mean Monthly Air Temperature Degrees F This is a calibration run Cancel Figure 14 The Edit Year dialog with three hydrologic years entered but all use the same meteorologic year Note that the user enters values in the first table only The other tables are for information only and are not editable Alternately you may use Fill Grid to completely populate the Year and MetYear columns with corresponding years suc
85. e week number to view beginning date tti um cwn Sei co Dam ow Ck Cottonwood Ck Humbug Ck se Ck ad Red Flags IGD MAX Q Water Years 1992 1994 x Red Novemberto February Discharge from Iron Gate Dam to Below Shasta R gt 3000 00 cfs nad lt gt Week in Water Year Right click on the week number to view beginning date eno Dam C Boyle Inflow C Boyle Dam Copco Inflow Copco Dam ron Gate Inflow ron Gate Dam ogus Ck t fe s fa s e 2 fa s o vifvel roa oe ve v ve vao Cottonwood Ck hasta R Humbug Ck eaver Ck Horse Ck Figure Right click on a flag cell to view the value 43 SIAM s Red Flag display for the item you added earlier 75 Well you have finished running your first alternative Congratulations There is a lot more to do and learn so carry on with your experimentation How would you compare the run you just completed with the baseline What alternative would you try next For now you may select File Exit on SIAM s main screen You will be asked whether or not you wish to save the changes Answering Yes will save them The next time you start SIAM you will find your saved file under SIAM s File menu Best Wishes
86. eater than one day while still maintaining the monthly water mass balance If even constant monthly flows requested by the user violate this condition these flows are not adjusted but a warning message is issued indicating that the water quality model prediction may be in error A similar message is issued if the daily flows cannot be adjusted and still maintain mass balance and adhere to the residence time criteria Note any adjusted daily flow fractions can be viewed post simulation in the File Daily Flow Variability dialog If the user does not alter these revised flow fractions they will be used by SIAM in subsequent simulation runs It is possible that they may be modified further on subsequent runs under some circumstances Daily Patterns 14000 12000 10000 E th ee em O 6000 Wet 4000 2000 0 o dv c MD OP uS qi qe qe P Ff Day of Water Year Figure 48 Daily patterns constructed from months listed in Table 7 83 lron Gate Daily Flow Pattern Templates x m Monthly Pattern Template Daily Flows For October E Month M Edit October G Dy Edit November La U c Edit December Avarage Edt Janey C Wa Edit February Edit March Edit April Edit May Edit June Edi Edit July Edit August Edit September pi Monthly Volume acre feet 63788 41 cen O om Figure 49 Iron Gate Daily Flow Pattern Template Dia
87. ed sucker adhere to monthly guidelines Thus flows are especially during the low flow portion of the hydrologic year fairly stable Second the nature of the basin s mostly agricultural water demands and system of reservoirs also tends to stabilize the mainstem s flow regime However it is also true that the system wide storage is insufficient in most years to contain large runoff events and the downstream tributaries remain largely unregulated and are therefore subject to peak events much shorter than a month Users of SIAM for the Klamath must remember these limitations but recent upgrades to SIAM allow more creative ways to deal with mid month or daily flow variability For our purposes MODSIM simulates several types of water allocations including direct flow allocations instream flow allocations reservoir storage allocations reservoir system operations exchanges and operational priorities e g augmentation subordination Water is allocated to each of these uses based on a user assigned priority for the link connecting the allocation to the river system Priorities are ranked from low to high with the lower number representing the higher priority i e satisfied first MODSIM can handle multiple sets of priorities in its management mode In this mode the model chooses which set of priorities to use based on a monthly determination of hydrologic state The state is defined in increasingly wet states as dry average or wet based on th
88. el application to that of Deas and Orlob 1999 For the Klamath River HEC 5Q has been calibrated for 1996 and validated for 1997 What may be meaningful to SIAM users is some sense of how well the water quality model simulates temperature and dissolved oxygen compared to actual measurements of these parameters Table 3 indicates the root mean square error RMSE and the correlation coefficients for both temperature and DO For temperature the period of record is 1961 1999 and is based on available data for the entire model domain from Upper Klamath Lake to the ocean Temperature records for the historical period were obtained from the EarthInfo CD s for parts of the 1960 s 70 s and 80 s For DO the period of record is 1996 99 for Iron Gate Dam only as the available data is limited to the measurements collected as part of the overall Klamath River studies Table 3 Water Quality Error and Correlation Statistics Predicted Root Mean Period of Constituent Square Error R Record Temperature 1 9 C 0 94 1961 99 DO 1 8 mg L 0 50 1996 99 Iron Gate Dam location only For the entire period of record the HEC 5Q model generally under predicts measured temperature and over predicts measured dissolved oxygen concentration Figure 3a and 3b illustrate the general trends in simulated and measured temperature and DO concentration 16 Temperature C Seiad Valley 1961 1999 Average Measured Average Simulated oOo o
89. ement style simulation run This allows for different rules to be applied in dry average amp wet months e Consolidated entry of information to create and store New alternatives Improving SIAM through Time It is our intention to continually improve SIAM and it s component models We always have a list of capabilities and data that we d like to add to SIAM In addition there is no way that this version of SIAM is completely bug free Please direct all suggestions for product improvement to the USGS at the address given above Acknowledgments We gratefully acknowledge the feedback provided by R2 Resource Consultants Inc of Redmond Washington in their review 1997 of the prototype SIAM as presented at a workshop in August 1997 R2 s descriptive summary was useful in helping us see SIAM from the perspective of someone not intimately involved in its development In fact we have adapted their summary for some of the introductory material in this manual Their review also helped us understand what to stress or revise to correct some misunderstandings of both fact and interpretation In addition material from other sources was instrumental in shaping the philosophy of SIAM See the citations in the references section for these sources Several individuals from the US Bureau of Reclamation have helped shape SIAM whether they knew it or not Larry Dugan Klamath Basin Area Office generously helped underwrite improvements for Versions 1 2 a
90. emperature on June 1 1993 sss 86 Figure 51 Dialog for generating potential for fish kill data eee 88 Figure 52 Plot of Hydrologic State Factors for Upper Klamath Lake Link Dam 90 Figure 53 Plot of Reservoir Target Values for Three Hydrologic States at Link Dam 95 Figure 54 Plot of Reservoir Target Values for Three Hydrologic States Iron Gate 96 Figure 55 Uninstalling SIAM from your computer sssesesseeeeeneneeneneee nennen 102 Figure 56 Example maximum temperature prediction for Seiad esses 113 Figure 57 Selecting a single hydrologic water year for a STAM run esses 117 Figure 58 Selecting Fish Production Comparative Graphs in the SIAM main window 118 Figure 59 Alternative comparison graph options to compare two or more years 118 Figure 60 Selecting an alternative year for comparison sees 119 Figure 61 Setting the temporal limits appropriate for a specific life stage eects 120 Figure 62 Microhabitat output for fry WY1982 and WY1994 adjusted for time present 121 Figure 63 Curve statistics for the graph shown in Figure 61 sss 122 Figure 64 Excel macro query and selection menu ssssssessseeereneneneennn 123 Figure 65 Alternative worksheet for nutrient loading estimation model 1
91. en Years to view a bar graph of yearly exposure totals and Within Years to observe the dynamics within each year Select the locations of interest Finally set the Consecutive Days in Series If this value is other than one the results reflect multiple day heat waves For example if the number is four it takes four days in a row satisfying the upper and lower limits to count as one series or heat wave To elaborate suppose you wanted to know how many 4 day heat waves over 20 C fall in September Set the lower limit to 20 C and the Consecutive Days in Series to 4 Then if the first 10 days were all above 20 there would be two 4 day series counted This method conforms to that used in similar 61 meteorological studies Ozone Action 2000 Gaffen and Ross 1998 Figure 26 depicts the between year exposure periods for Keno Copco and Iron Gate dams The thermal window depicts the period of time each year when the temperature exceeds a specified value Select the Thermal Window option from the Water Quality Metrics submenu Set the evaluation period using the start date and end date spin controls Set the temperature or dissolved oxygen range using the upper and lower limit spin controls You must simulate at least two years in order to compute the thermal window Figure 27 shows a thermal window for 15 C at Iron Gate Dam using an area plot Exposure Period GD_MAX_Q Water Years 1992 1994 Temperature Range 15 20 degrees C IGD_
92. ent XY file has a number of states defined other than three SIAM will work but not allow user editing These more complicated hydrologic states and all other factors necessary to run MODSIM as a management run must be accomplished by an expert MODSIM user preferably by starting with a management XY file for the baseline in SIAM s NEW alternative creation A calibration run will allow editing only the first column of numbers namely those used as the single node flows For more on the distinction between management and calibration see the section on Advanced Topics later in this documentation 47 Node Priorities IGD_MAX_Q Water Years 1992 1994 This is a calibration run i Node Description 1 JUpper Klamath Lake Link River Dam Storage Note that low A numbers are higher 2 A Canal Diversions Demand ne priority 3 Lake Ewauna Storage 4 Lost River Diversions and Retums Demand 5 North Canal Diversions Demand 6 ADY Canal Diversions Demand Neg Acc UKL to Keno Demand 8 Keno Lake and Dam Storage iS JC Boyle Topsy Lake Storage 10 Copco Lake Storage 111 Copco 2 Forebay Storage 12 Iron Gate Reservoir Storage 13 Instream Flow below Iron Gate Reservoir Demand Figure 16 Edit Node Priorities dialog showing the relative priority of each storage and demand node Note that the lower the priority the more the water quantity model tries to meet t
93. ers and or fry entering the mainstem for the fish i model SALMOD This is accessed under Edit Supplemental Fish or by clicking Fully understanding the subsequent dialog Figure 18 really requires a more detailed knowledge of SALMOD than we wish to introduce atthis time See the references on Learning More About SALMOD for more information Suffice it to say that you may control the number of returning adults their sex ratio the location in the stream by distance in meters from the most upstream point in the SALMOD study area their weight in grams and the time step ordinal number in the biological year during which they are introduced to the stream Juveniles entering the mainstem from a tributary or hatchery may also be added using this dialog Each new record may be added by pressing the nsert key on your keyboard when positioned at the spreadsheet like entry location or by pressing the down arrow key when positioned at the bottom of the list records may be deleted by pressing Delete Moving through each record with the left and right arrow keys is straightforward If you wish to repeat the last data record for the remaining years click on the Fi Table button The time step will automatically be adjusted to represent the same time step week each year 49 Supplemental Fish IGD MAX Q Water Years 1992 1994 x Species Chinook Salmon Lives species Incun Un Disi Down Dist Number Secreto Mie Female Wt Jim FEE i 22704
94. et 0 25 Sort Values All Storage acre feet fiooo By Magnitude Water Surface Elevation feet AMSL 0 25 C Chronologically Water Quality Storage Locations T Conductivity uS lem fo Upper Klamath Lake All Number of values exceeding thresholds f Save Parameters Cancel Figure 40 Alternative comparison report parameters dialog box Select View Comparison Report to view alternative comparison reports Select the report to be viewed from the report list and click on View Report This will open WordPad with the desired report You may print the report from WordPad The report is paginated at 65 lines and must be printed with all margins set to minimum values in order to fit on the page in portrait mode The 728 default font is assumed to be Courier 10 If you wish to change the name of a report or delete reports select Edit Comparison Report List Select the report that you wish to delete or edit the name for The report name will appear in the edit box below the list of reports Edit the report name in the edit box Click on another report to update the list with the new report name clicking Close will also save your edits Click on Delete to delete the report selected or on Delete All to delete all of the reports listed Figure 41 illustrates editing a report name Alternative Comparison Reports x Select a report Comparison of IGD_Max_Q with a wet years simulation Edit report name repo
95. etimes many kilometers downstream will show its simulated temperature and the gradient is shown between nodes This has minor implications for the calculation of macrohabitat in that summation of acceptable or unacceptable distances may not be 100 accurate On the other hand no one has quantified the true mixing lengths of these junctions which undoubtedly vary depending on relative flows temperatures and channel characteristics 99 Finally we must also remember that though these models are fed by and calibrated to real data those data themselves have problems USGS flow data is probably only good to plus or minus 10 Mean water temperatures are often just simple averages of daily maximum and minimum values not true 24 hour means Dissolved oxygen data are notorious for instrument fouling All records have data gaps and seemingly illogical outliers Etc For all of the reasons listed above it is wise to keep in mind that SIAM does best what it was designed to do look at long term trends under different management strategies and not believe that any single prediction is exactly accurate given the spatial and temporal heterogeneity that exists in the real world River management must admit to uncertainty not only environmental but also political and institutional 100 Uninstalling SIAM from your Computer SIAM may be uninstalled by following the Windows standard of Start Settings Control Panel Add Remove Programs SIAM see Fi
96. ferent than what you asked to simulate This is a quirk in MODSIM s screen display The graphic and tabular output shown in SIAM will be correct Note Expert users of MODSIM may receive a message from SIAM that MODSIM has been run by itself without rerunning a full simulation This message or similar messages means that the date on the runtime XY file is newer than the date on SIAM s simulation results implying that there may be a mismatch between the two Pressing OK will allow display of the results but just be forewarned 53 Looking at Results Whew Simulation Complete shows on the status bar If you ve gotten this far you re over the hump The rest is easy SIAM s View menu will give you access to a variety of tables graphs and the Red Flag display Let s skip most of the tables for the time being They are numerous and a bit cryptic probably of more use to power users who may wish to take the data into a spreadsheet or other program for subsequent analysis and display They may also take a while to load and require changing the Wordpad s word wrap feature to view and print in a useful fashion Power users may prefer using the comma separated values CSV files produced by HEC 5Q as an alternate way to view or analyze results in Excel The target matching table can be very valuable in quickly identifying places and times when targets have not been met Select View Output Tables Water Quantity Choose MODSIM Target Matching ac
97. fication is based primarily on channel structure and slope modified by the general distribution of microhabitat including cover Streamflow water temperature and habitat type are the physical state variables included in this model The stream can be divided into flow and temperature segments either by distance or by computational unit numbers Flow and temperature data are organized by river segments and by time step for each segment Habitat is defined by a flow versus habitat relationship for each habitat type Currently SALMOD only sees a linear stream with no tributaries or branches possible However various options control what happens to fish moving out of the collection of computational units defining the study area either upstream or down In addition tributary contributions of outmigrants may be dumped into the mainstem if estimates of their production and timing are available For more information on how SALMOD s river description relates to the other models in SIAM for the Klamath River please refer to Table 5 Biological Resolution The biological resolution is fairly standard in the sense that we employ a typical categorization of fish life history related to morphology and reproductive potential see Figure 6 Fish in the simulated population are tracked by cohorts within computational units Each cohort is classified by life stages and class within life stages Table 4 Life stages 1 4 are adult life stages defined and
98. for dissolved oxygen on June 1 1993 To display information about fish production select the Fish Production option from the View menu The fish production graphics are a little more complicated than the others You have complete control over what variables are plotted how they are compiled what is plotted on the Y axis and what is plotted on the X axis You must define each curve to be displayed using the facilities provided Once a curve is defined it is added to a list and may simply be selected in the future to display it Upon first entering the fish production module the curve is defaulted to the first one in the list The Y axis variable is numbers of fish and the X axis is time steps Figure 30 illustrates the fish production graphics dialog Select the curves to be plotted from the list or add a new curve To do this click on the Add Curve button The Add a curve dialog will be displayed Figure 31 Enter a legend key up to 20 characters to be used on the graph Enter a longer more detailed description to help you remember what the curve represents Select the data type as instream fish exiters migrating fish or mortality Select a species if more than one species is 64 Fish Production IGD MAX Q Water Years 1993 1995 x E SALMOD OUTPUT Numbers of fish 4 meer Time Steps 1 to 156 Comp Units 1 to 526 Numbers ctfish me HA Reduce and stabilize October to February spawning rearing flows to 1000 cfs Total Weight
99. freezing For this reason SIAM says this water is frozen 0 C when in fact it is likely to still be flowing albeit perhaps super cooled In short the models all contain error usually small and SIAM is set to overlook small errors not likely to be biologically significant Advanced users still have access to the original simulation results so that appropriate reality checks can be made during model testing Additional items are worth mentioning Some comparative graphs show small differences between values recorded for one time step to another or one spatial location to another when those differences simply reflect what we might affectionately call round off error Some of the models automatically round off or truncate fractional parts of values either on the input side the output side or both In particular MODSIM only works in whole acre feet whereas HEC 5Q uses fractional values SIAM always takes the values that it sees and may report minor differences Depending on the graph s scale those differences may appear exaggerated It is up to the user to judge whether any difference is hydrologically limnologically or biologically meaningful Ina slightly different vein note that SIAM s longitudinal plots only record temperatures at selected locations along the river The mixing zones where tributary inflows instantaneously mix with the mainstem are not represented on the graph as instantaneous mixing rather the next downstream value som
100. g Fish Production Comparative Graphs in the SIAM main window Fish Production 1982 Water Year 1982 x SALMOD OUTPUT COMPARISONS Water Year 1982 Adults All Instream Fish Y Axis Variable Numbers of fish m Numbers of fish m2 H4 Total Weight gm Average Weight gm Average Length mm Biomass gm m2 HA Habitat Area m2 Percent Capacity x X Axis 3000 Time C Space Advanced 2000 Scale Linear C Log 1000 C Relative Numbers of fish Graph Type Line 0 C Bar 1982 Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep 1983 Stacked Bar Month in Water Year Iv Grid Lines Plot Points Line Style IT Exceedence Plot Output generated on 10 08 2002 at 13 44 50 Select Alternativ Zoom Press shift and drag mouse Reset Press R Statistics AGUS Select curve to be plotted Ad All Instream Fish Adults All Instream Fish Export Set Y Axis Delete Curve Ad Fem Instream Fish Adult Females Instream Fish TNT Print Ad Fem Mart Adult Female Mortality All Causes Edit Curve Ad Males Mnrtalitz Adult Males Mortality All Causes Close 1982 82 82 Figure 59 Alternative comparison graph options to compare two or more years 117 Alternatives Available For Comparison Figure 60 Selecting an alternative year for comparison Finally referring back to Figure 59 select the Advanced X Axis Time upper right hand corner
101. g the characteristics of the graphic output are the same as those for single alternative output The legend for the comparison graphs consists of the alternative names plus the simulation period Figure 37 shows the comparison of dissolved oxygen for two alternatives The list of alternatives can be created or edited from the Select Alternatives dialog of each graphics screen Click on the Maintain List button to add or delete alternatives from the list Double click on an alternative directory in the directory dialog and on Add to list to add it to the list You may continue to select other alternatives in the same manner To delete alternatives from the list highlight them in the list box Click on Delete from list to remove them from the list Click on Close to stop Any alternatives that were added will automatically be selected for comparison Note SIAM will not let you have alternatives with the same name in the alternative list Each alternative name folder name must be unique even if they are in different locations on your disk directory You may elect to compute maximum differences for longitudinal profile comparisons When the maximum difference box is checked the maximum absolute differences between the base alternative and the compared alternative are calculated for each control point over the time period specified Set the starting and ending date for the time period desired Click on Refresh to display maximum differences for each compa
102. ge water quantity storage water quality variables discharge temperature dissolved oxygen water surface elevation conductivity and water quality storage Use the A buttons to toggle the selections all on or off Difference values may be sorted by magnitude or chronologically Tip It is far better to only choose items of interest choosing A will likely give far more than you will ever want to wade through Click the radio button for the type of sorting desired If you wish to reapply these parameters to other comparisons click on the Save Parameters button The next time you generate a comparison report the values will default to those saved Click on OK to generate the report Alternative comparison report parameters for IGD MAX Q vs WETYEARS Comparison Report Name Comparison of IGD_Max_Q with a wet years simulation m Comparison Variables r Time Period Water Year Water Quantity Discharge Locations Difference thresholds Starting date 1 Water Quantity Rel from Iron Gate Res Iv Discharge cfs 100 a Al i TS Starting year fi 992 Klam above Bogus Crk V Storage acre feet 1000 Ending date pes Water Quantity Storage Locations Iv Water Surface Elevation feet AMSL 0 25 JC Boyle Topsy Lake Sept 30 Ay CLE m Water Quality Ending year 1224 Discharge cfs 100 Iv Temperature Degrees C 0 25 Alternatives do not overlap Iv Dissolved I ponuived Ussoen im
103. gm Average Weight gm Average Length mm 1200 Biomass gm m2 HA Habitat Area m2 Percent Capacity gt 100011 80011 X Axis Time C Space Advanced Scale Linear wien 200 C Relative Numbers of fish o e Graph Type 1 0 i Line S3NDJFMAMJJAS SANDJFMAMJJASSENDJFMAMJJAS C Bar Month in Water Year C Stacked Bar Frequency Distribution _ Ad All Instream Fish Martality Partions Output generated on 07 23 2002 at 08 54 18 Zoom Press shift and drag mouse Reset Press R E Eu THRICE Select curves to be plotted All Curves PARU Ad All Instream Fish Adults All Instream Fish E Export T Line Style Delete Curve Ad Fern Instrearn Fish Adult Fernales Instream Fish 7 TET 3 Ad Fem Mart Adult Females Mortality All Causes _Annual_ Pin _ Statistics Edit Curve Ad Males Mortality Adult Males Mortality All Causes z Close Figure 30 Fish production graphics Add a curve definition x Enter a legend key Total Mortality Up to 20 characters Enter a curve description Mortality for all fish from all causes Up to 70 characters Data Type C Instream Fish C Exiters Mortality Select species Selectlife stages Select classes Select mortality causes Chinook Salmon All Stages All Classes OK Figure 31 Add a curve dialog 65 available the life stages desired and any specific classes within life stages if all are not wa
104. gressions are based on the same complement of mean daily meteorological data used by HEC 5Q the model s mean daily water temperature prediction for the two locations and mean daily discharge Predictions are not possible for no project alternatives because the regression models unlike the physically based HEC 5Q were constructed from data measured with the influence of mainstem reservoirs below Upper Klamath Lake Without those intervening reservoirs the regression models are no longer valid especially for the Iron Gate site Further the regressions are only applicable for the summer period 1 June through 30 Oct The spreadsheet may be accessed through the task bar by Start Programs Siam Max Temp Model anytime after a SIAM simulation is run After opening the spreadsheet in Excel and enabling the macros you will be asked to supply the paths for the SIAM installation e g C SIAM and the alternative to be evaluated e g C SIAM ALTERNATIVES ALT1 Then pressing the large button will import all necessary data from the SIAM predictions and historical meteorology data Tables and charts for both Iron Gate and Seiad e g Figure 56 will then be available on worksheet tabs shown near the bottom of the Excel window An example graph is shown below 111 Predicted Temperatures at Seiad Valles 30 25 Daily Average Temperature C Maximum Daily Temperature C Temperature deg C m 0 616 636 656 676 696 716 736 756 Day
105. gure 55 Removing alternatives you have created is simply a matter of dragging any folders you no longer want to the Recycle Bin If you have stored alternatives under the SIAM installation folder the results of an Uninstall are unpredictable as Uninstall can only remove items from your computer that nstall itself put there Also if you have created a shortcut to SIAM on your desktop you must manually delete the icon E Control Panel Eile Edit View Go Favorites Help oop foe ux Back Forward Up Copy Paste m E S mu B A 32bit ODBC 3Com Accessibility AddNew Add Remove Date Time Desktop Dynamiccc Options Hardware Programs Themes Add Remove Programs Properties z Al uy Install Urinstall Windows Setup Startup Disk e Mail To install a new program from a floppy disk or CD ROM drive click Install 3f Install Power Management Ihe following software can be automatically removed by Windows To remove a program or to modify its installed Ed components select it from the list and click Telephony Microsoft Expedia Streets 98 Microsoft IntelliPoint Microsoft Small Business Financial Manager 98 Microsoft Word 97 Figure 55 Uninstalling SIAM from your computer 101 To Learn More about SIAM Please refer to the following to learn more about SIAM s philosophy and design SIAM Bartholow J M 1989 Stream temperature investigations field and analytic methods Instream Flow Information Paper No
106. h that the full period of record 41 years in this case is to be simulated Note that a 41 year simulation is quite lengthy both in computer time and space Such a run will require up to one hour on a moderately fast 400 mhz computer and consume over 1 gigabyte of 44 disk storage Clear Grid does what you might imagine namely erases the contents of the table containing the years to run so you can start over Selecting the value for any year and pressing the Delete key will completely remove that row from the table Pressing the nsert key will insert a row prior to the one you are pointing to You may also cut and paste values from any compatible application In addition to the meteorological data for individual years we have supplied synthetic meteorologic years hot cool and median The years 1964 1979 and 1992 correspond to cold median and hot meteorological years based on April through September air temperatures and you may type those names Cold Median Hot instead of the year numbers Though not supplied as such wet median and dry were also categorized The total Upper Klamath Lake inflow for April through September of each year and other metrics were tallied and used in the hydrologic categorization The years 1983 1986 and 1992 correspond to the Max Median and Min hydrological year types respectively You may also type the names Max Median Min instead of the year numbers The actual years will be substituted for the na
107. he drop down menu at the top of SIAM s control panel However as you become more skilled in operating SIAM you may find some Toolbar buttons found below the menu items see Figure 10 to be useful shortcuts for your work Moving the mouse over each button in turn will show you what it does in small tool tips Figure 10 and in the status bar at the bottom of the screen Don t be shy Note that menu options that are unavailable will be grayed out on the SIAM screen Getting Assistance while You Work SIAM has built in not context sensitive Help screens Pressing the F7 key or choosing Help Help Topics will bring up the Help system It works like any Windows Help system with tabs for Contents Index and Find There is also a show me Help button on the toolbar A Guided Tour X Your First Evaluation Establishing a Baseline Alternative Giving you a guided tour through SIAM will teach you just about everything you need to know to become proficient In this tour the first thing that you will do with SIAM is to create your own alternative revising the minimum flow schedule below Iron Gate Dam by selecting a baseline or calibrated water quantity model data file from which to work SIAM automatically creates a folder called c siam alternatives to house all of your alternatives If you wish to use a different folder or want a different name use the Windows Explorer to create a new folder or rename the one created by SIAM Please see your
108. he stated target Other elements from the water quantity model may be edited as well like maximum and minimum reservoir capacities Figure 17 We will not edit this screen on your first guided tour but feel free to have a look by choosing Edit Reservoir Characteristics Also remember that the basin hydrology is all interrelated For example changing irrigation demands likely implies a change in the timing and delivery of irrigation return flows This subtle relationship is beyond the scope of SIAM and is not a functional relationship within the water quantity model Expert judgement is required Please refer to our report on System Operational Flexibility Campbell et al 2001 for more on the considerations necessary to realistically define a water management alternative and some guidelines or rules of thumb we have found helpful SIAM provides great power to experiment with alternatives but the user must be aware of the full suite of implications and consequences If you become a MODSIM power user you will have even greater flexibility to edit system wide attributes 48 Reservoir Characteristics IGD MAX Q Water Years 1993 19 x Upper Klamath Lake Link River Dam Acre Feet Minimum Storage Type Storage Maximum Storage 1665610 Elevation Cancel Figure 17 Edit Reservoir Characteristics dialog Other values currently available for defining a unique alternative in SIAM include the number of spawn
109. he water quantity model is the fundamental driver the entr e for all subsequent models and serves as a shared resource and core database the integrator In another sense however integrated also means the user interface which is the front end this is SIAM Hierarchical outputs means three things It means that the user can look at output 1 at a single location or aggregated through space and 2 at a single time or aggregated through time It also means that there are enough detailed outputs that the user can trace a high level output back through the simulation results that comprise that aggregate For example if a user is interested in the number of outmigrating fish she or he can see why that number changed in one scenario versus another i e trace the result back to water quality then to temperature then to streamflow then to the meteorology of a hot day Hierarchical output also facilitates dealing with hierarchical users That is users with a policy focus can deal with aggregated responses while technical users can deal with the more detailed elements Credible means several things It means that the component models are testable that they are scientifically up to snuff 1f not state of the art and that they are peer reviewed Credible means that the components are detailed enough to give the spatial and temporal resolution required to meet the objectives satisfactorily but simple enough to understand and satisfy the goa
110. ical total storage 87 levels inflows and releases Hydrologic States Three 3 states are chosen Dry Average and Wet Every month a determination is made based upon the month s Beginning Storage for Link Dam i e Reservoir 27 in the MODSIM Network plus the Unregulated Inflow historical unregulated inflow values that flow into Link Dam Note These unregulated inflow values are part of the Link Dam database accessible through MODSIM and represent water accretions that enter the river system above Link Dam that were defined to help maintain mass balance with respect to historical data sets of flows and total storage These are relatively small flow values The determination of whether a Dry Average or Wet Target Reservoir value is used for that month is based on the following inequality calculation computed for each and every month R Beginning Storage Unregulated Inflow W Maximum Storage for Link Dam only 540700 Ac ft Dry Target Values are used when R lt month s Dry Factor W Wet Target Values are used when R gt month s Wet Factor W Average Target Values are used when R is between or equal to the Lower Dry and Upper Wet bounds i e Lower Dry storage volume R Upper Wet storage volume Therefore a two row set of factors 1 e total of 24 factors is included in the management AXY file that corresponds to the Dry and Wet Factors for each of twelve months The set of factors given in Table 8 and
111. icking on the check boxes 69 Figure 35 Dialog for setting temporal limits and units essere 69 Figure 36 Comparison alternative selection dialog sse 71 Figure 37 Comparison of dissolved oxygen for two alternatives esee 72 Figure 38 Comparison of discharge from Iron Gate Dam with historical data 72 Figure 39 Alternative selection dialog eee doa save cite atr e ER ROM E dede us 73 Figure 40 Alternative comparison report parameters dialog box ssssssssseees 74 Figure 41 Dialog for editing a report name or deleting reports sse 75 Figure 42 Red Flag results for week s maximum temperatures greater than 16 C 76 Figure 43 SIAM s Red Flag display for the item you added earlier sssssss 76 Figure 44 Save AS ODIO ceto Rp ae eese E alates ates ale TI Figure 45 Dialog for saving as a new alternative 0 0 ec eeeeseceecsceeeceeeeeeecesecaecaceeaeeeneeeecneeeaee 78 Figure 46 Iron Gate Daily Flow Variability dialog eere 81 Figure 47 Yearly and monthly graphs of daily flows sese 82 Figure 48 Daily patterns constructed from months listed in Table 7 00 0 eeceseeceeseeereeeeeeeeeeee 84 Figure 49 Iron Gate Daily Flow Pattern Template Dialog eee 85 vi Figure 50 Spatial distribution dialog for t
112. iewed by repeated testing MMMM Table 1 SIAM s Attributes LIMITATIONS Each component model has inherent uncertainty Fall chinook only no hatchery component Not all features of the final product are available In particular geomorphology and refugia are not yet represented Evaluation of results is left to the user The methodology governs the kinds of questions that are asked 1 e SIAM leaves out non habitat biological issues e g exotics disease genetics which may be important STRENGTHS ntegrates physical chemical and biotic components of ecosystem using sophisticated yet modular routines Provides quick insight into what is and is not possible for resource management Handles all units conversion and file formatting to interweave models Insulates the casual user from component model complexity and terminology ASSUMPTIONS A model is an abstraction and simplification of reality Reasonably represents the major limiting habitat factors whose modification is necessary to recover natural reared anadromous salmonids in the mainstem Klamath All of the component models especially fish production have fundamental assumptions Assumes that actual operations can closely mimic simulated operations Assumes a caretaker to update the model and become an expert user Assumes that errors do not escalate from one model to another WEAKNESSES Makes it so simple to run that some users may no
113. ility to more or less program the model on the fly to create the dynamics thought to animate the population SALMOD then tabulates the various causes of mortality SALMOD is best explained by describing its fundamental structure in terms of temporal spatial and biological resolution These three components are not independent the size of any computational unit spatial resolution has a direct bearing on the distance a fish of a given size biological resolution might need to move within one time step temporal resolution The scale of resolution also affects the way model processes are envisioned and implemented their assumptions and their limitations Temporal Resolution We employ a weekly time step for one or more biological years Biological years typically but not mandatorily start with the onset of spawning All rate parameters e g growth and mortality are weekly values unless otherwise stated Physical state variables e g streamflow and water temperature are represented by weekly averages For more information on how SALMOD s time step relates to the other models in SIAM for the Klamath River please refer to Table 6 25 Spatial Resolution Spatial resolution in SALMOD is consistent with the mesohabitat inventory approach in which the study area is classified and mapped as discrete mesohabitat types intermediate between micro and macrohabitat that tend to behave similarly in response to discharge fluctuations Classi
114. ime anywhere below Keno lead gt 7 70 ug l 200 mg l CaCOs yellow flag source EPA Anytime anywhere below Keno mercury gt 0 12 ug l yellow flag source EPA Anytime anywhere below Keno selenium gt 35 0 ug l yellow flag source EPA Anytime anywhere below Keno zinc gt 47 ug l 50 mg CaCOs yellow flag source EPA Microhabitat Thermal Refugia Anytime anywhere maximum daily water temperatures are above 22 C if mainstem flows are above long term median discharge yellow flag source USGS Spawning Habitat September October for entire study area amount of fall chinook spawning habitat lt sq ft yellow flag September January for entire study area redds stranded needs definition ditto previous two for other races species 108 Rearing Habitat December April entire study area amount of fall chinook fry habitat lt sq ft yellow flag source USGS March June entire study area amount of fall chinook pre smolt habitat lt sq ft yellow flag source USGS Fish Production Year class strength Any year for which the number of outmigrants is below the floor of individuals Outmigrant Timing Any year for which peak of outmigration lt April 1 or gt June 15 Channel Morphology To Be Determined 109 Appendix 2 Baseline Files Supplied with SIAM The following MODSIM XY files have been supplied with SIAM Version 2 7 Esa_Fp1 This file contains the Utah State University Phase I re
115. imply be a convenient place for some to start Additional limitations of the Ecosystem health component are that those standard metrics of ecosystem health such as primary production or species diversity are not included and that synergistic impacts are not addressed Our response is Show us the models and how you wish to summarize the results and we ll do it 31 E Example Example Inputs E Outputs Red Flags rate eR C Start Identification o P thresholds emp E 5 Se FS 2 iteri AS ii E CriteriaA g Examine V simulation 2 Sediment o outputs flushing 8 for ED 9 criteria encroachment F amp S on agreed ke a QS t 7 Z OQ AS S 5 Criteria B ee 2 upon Where and how often 8 g standards 5 Passage T 5 9 frequency g d 5 duration iv OS AN k magnitude gt ax X oa Rearing habitat bottleneck o o ue Criteria N Se Figure 8 Important inputs and outputs for Ecosystem Health component 32 Tying the Components Together through Space and Time It is a good idea to look at all of SIAM s components across both space and time Tables 5 and 6 attempt to do just that and are well worth your while to scrutinize Each of the models portrays space and time just a bit differently One of SIAM s strengths is interweaving them as seamlessly as possible An explanatory note about mixed time steps may be needed in how SIAM for the Klamath River was assemble
116. imulation it was designed for However the easiest way to get the desired result in this case is to run the model in management mode but use a modified management AX Y file as follows To fix the Targets regardless of computed hydrologic states define all three sets of Target Values to the same desired specific value for each month the same value is not required each month but rather the same monthly value is needed for all three states i e Dry Average and Wet This will ensure that the MODSIM simulations use the specified and desired monthly target values each year in the simulation period Note The easiest way to define these desired specific target values is to simply edit the existing AXY file in MODSIM and then save the edited file under a new name Then use the new file in a SIAM alternative or conduct a MODSIM simulation run Alternatively an option to edit these values through the SIAM interface is available Additional Note A similar set of results can be obtained by performing a calibration mode simulation however this would require a greater effort in preparing the data set to replace historical reservoir storage values for each month in every year unless only a one year simulation is desired EXAMPLE 4 Determine the tradeoff between Targets Storage Values on One Reservoir as compared to Another Reservoir This is similar to the base case for the management mode of operation and makes very good use of the Targets and Prior
117. ing on the reservoir node or by use of the SIAM interface Table 9 Primary reservoir targets RESERVOIR TARGET VALUES Acre feet Reservoir and MODSIM oomen ko care tay comoTs AvG Wer pry avaj WET DRv Avo wer Oct Lor rin sn 3500 sezo 57300 3rinn 1520 44500 Nov 388000 383000 523000 s5500 STOOO 57500 42400 43200 44500 Dec 349000 72000 533000 55700 57700 _58000 32400 43200 44500 Jas 423000 483000 56900 56200 s8000 S amp a0o 42400 43200 44500 Fob 8000 502000 5 000 s6s0o 5820058700 42400 43200 44500 Mar 23000 873000 643000 S700 8800 39200 42400 43200 24500 Apr 72000 603000 683000 56500 58700 59500 42400 43200 44500 May 23000 623000 ses000 56700 58200 S9700 42400 43200 44500 Jun 888000 622000 673000 s7000 58000 59400 42400 43200 44500 Jui 523000 623000 663000 56500 7500 39300 42400 43200 24500 Aug 43000 23000 633000 55700 5T200 58700 42400 43200 24500 Sep 353000 403000 583000 54700 56700 58000 42400 43200 44500 The remaining Reservoir targets as well as The Ocean Demand node targets were set at only one value 1 e the maximum reservoir storage the same for every month and for each Hydrologic State i e Dry Average and Wet Note All of these reservoirs are relatively small and have historically been operated at near constant storage volume and are not used for carry over storage from mo
118. iomass gm m2 HA 50007 Habitat Area m2 s i i i i i i i Percent Capaci T i i i i EEA v 8 4000 4 aE Beer eee pe aera eee fo esse seey X Axis S l l i Time H i i i i C Space w 3000 S Pais eae ee ee qe eae eg 2 i i i i i i i Advanced lt i i eE E 1 t 3 t 1 3 Scale E 2000 Linear E 1 C Log o 1000 i Zssiese5sed i ne en AEE E C Relative B i 1 i 1 i 1 zx i i i i i i i Graph Type d i H i H i Line 0 C Bar 1982 Nov Dec Jan Feb Mar Apr Stacked Bar Month in Water Year Grid Lines I Plot Points 1982 82 82 1994 94 94 Line Style I Exceedence Plot Output generated on 06 05 2002 at 15 28 12 Select Altematives zoom Press shift and drag mouse Reset Press R Stoisics Eure Select curve to be plotted f JW Fry Instream Fish Fry 30 50mm Instream Fish Export Set Y Axis Delete Curve Fry Mort All Causes Fry 30 50mm Mortality All Causes Fry Temp Mort Fry 30 50mm Temperature Mortality _Annual_ o Print EdiCuve Im Sm Hahitat Mort Immature Smolts Rfl 2fifimm Hahitat Induced Mnrtalite Close Figure 62 Microhabitat output for fry WY1982 and WY1994 adjusted for time present Curve statistics for this graph can be viewed by selecting Statistics as shown with the arrow
119. ion model What s New About SIAM Version 3 0 January 2002 added target matching tables to the water quantity output tables The SIAM Help was replaced by extensive context sensitive help A new splash screen was added for version 3 0 along with numerous other minor enhancements Version 3 4 contains bug fixes to several items especially Red Flags and adds fish mortality partitions to the graphing options and a Delete Alternative feature to the File menu Importantly SIAM now supports only two networks Upper Klamath Lake to the ocean either with or without project By project we mean the series of reservoirs below Upper Klamath Lake that are managed by PacifiCorps Though you will find reference to other networks in this documentation these references were retained for historical purposes only There were also minor changes to MODSIM s data files Version 3 6 added the capability to compute potential for fish kill based on ammonia concentrations pH and temperature We also added two more years 2000 and 2001 to the historical database and added a nutrient loading spreadsheet model supplement Appendix 6 Version 2 9 November 2001 added a spatial display module to SIAM This module shows the spatial distribution of temperature dissolved oxygen and discharge over the length of the Klamath River This display can be animated over time The capability to display temperature in Fahrenheit degrees was added to SIAM s graphic displays The D
120. ities for a given set of Hydrologic State Factors as identified Multiple runs might need to be performed one with equal Priorities for both reservoirs in question another run with a higher priority i e lower numeric value in MODSIM for the reservoir expected to be the first to meet or come closest to the defined Target Values other runs with additional adjustment of Priorities between Reservoirs and quite possibly other Demand Nodes Again these types of analysis and model runs are what the management mode of MODSIM is designed for EXAMPLE 5 Desire to evaluate Targets Storage Values on One Reservoir while trying to maintain Historical or some other set of defined values on Another Reservoir This is similar to Example 3 described above but includes other elements also mentioned in Example 4 Unfortunately the management mode AX Y has replaced and therefore lost the first three years of historical reservoir storage values 1 e the first three years of the file are made up of identical data to the Dry Average and wet Storage Target Values In addition management mode simulations utilize Reservoir Storage Targets for ALL Reservoirs in the network not a combination of Target Values and Historical values Therefore an exact model simulation desired in this example for multiple year analysis is not possible with management mode However smart use of Target definitions and Priorities in accordance with the methods described in Example 4
121. ity x Allows generation of monthly flow alternatives throughout the network Calibrated for 1961 1997 period Flows in acre feet per month Tracks reservoir storage and capacities Application user and peer reviewed under FWS contract Water Quality Model HEC 5Q X Developed by US Army Corps of Engineers x Calculates longitudinal water temperature and other water quality parameters from daily flows and meteorology X Includes in reservoir water quality effects X Calibrated for 1996 validated for 1997 Aquatic Habitat Models As Input to Other Models x Developed by USGS formerly FWS x Estimates quantity and quality of habitat x Requires channel geometry and more x Peer and user review has been extensive Anadromous Fish Production Model SALMOD x Developed by USGS formerly FWS x Estimates outmigrating young of year fall chinook from weekly flows temperatures aquatic habitat and life history data x Published in refereed scientific literature Ecosystem Health Component Red Flags 2 Internal to SIAM x Highlights when user defined criteria have been exceeded through space and time Linkages CrossTalk X Internal to SIAM Converts monthly flows into daily and weekly patterns x Will use daily accretions from Phase I analysis x Sets up input files for communication between models in terms of data units and format x Presents limited model input for editing and displays limited model output for analysis x To be rev
122. l of parsimony If too complex models consume precious resources and computing power Credible means that the simulations operate with a level of realism agreement with intuitive or testable perceptions and precision close enough agreement with measurements to be persuasive Credible also means that assumptions and limitations of the components are clearly stated and that care is taken to prevent misuse beyond their inherent regions of predictive extrapolation SIAM for the Klamath River If SIAM remained merely a concept it would serve no useful purpose This version of SIAM is targeted for a portion of the mainstem Klamath River from Upper Klamath Lake Oregon to the Pacific ocean Important metrics for this evaluation include water quantity water quality fish habitat fish production and other measures of ecosystem health Consequently models and data dealing with these elements and focused on the Klamath River form the core elements for SIAM SIAM starts with a water quantity model MODSIM Fredericks and Labadie 1995 to predict river flows and track reservoir volumes in the Klamath River system including the U S Bureau of Reclamation s Klamath Project and downstream through the reservoir complex managed by PacifiCorp MODSIM employs a prioritization scheme to model flows throughout this system under different water management alternatives consisting of reservoir operating rules and constraints instream flow requirements agricult
123. lash screen followed by SIAM s main menu 38 The Basics X What s on SIAM s Main Screen After the splash screen you will first see SIAM s main menu Like most other Windows programs it is exercised by clicking on the items across the top ofthe screen The main window displays a E map ofthe Klamath River area and the control points used in SIAM Use the CR Zoom and Reset toolbar buttons or the keys Z and R to change the extent ofthe map window To zoom in on an area of the map select Zoom and then drag the mouse across the screen to form a box representing the new window Select Zoom and click the right mouse button anywhere in the window to zoom out by 20 percent Click on the Reset button or press R to reset the window to its original extent W SIAM 3 40 1971 New Alternative olx File Edit Run View Help Ta z bine 7A WA 3 29 BO TE wa x e il Upper Fi Klamath 1 Lake LRL Reef KLAMATH RIVER A VOX CR LetePvutae JC Boyle li CONTROL POINTS KOC cuspis a note Keno Oregon Dan Jo a Califomia Fron Gate Dany apco Inlet attorwood Ck Bopus Ck Y Seica Vapi Benner CE Witiow CX a Indian Ch fy Morse Citiumiup Ck taste River EIR CR cott Raver Clear CK a Saimon River sae Orleans w Red Cap Ck Trinity River Select the active years NUM 7 Figure 10 SIAM s main menu showing map toolbar status bar and tool tips Taking Shortcuts 39 This document will discuss menu options from t
124. log October values are displayed in the table A final note on daily variability You may get very unexpected results if you mix daily pattern types with hydrologic types What we mean by this may be explained by the following example Suppose that one month s target release for Iron Gate is the FERC minimum let s say June but you have chosen to apply the wet daily pattern for June As you might expect the wet monthly pattern has quite a lot of daily variability since it arose in a month with rainstorm events when flows were quite high SIAM apportions the low FERC flow across the days using the daily pattern resulting in some days that are higher than the FERC flow and some much lower This may not be what you intended Viewing Spatial Distribution of Temperature in SIAM SIAM has the capability to display the spatial distribution of temperature dissolved oxygen or discharge within the mainstem of the Klamath River The river is displayed as a series of river segments on a map of the Klamath River area Each segment represents the average temperature dissolved oxygen or discharge between each of the control points implemented in SIAM These segments are color coded according to value breakpoints set up by the user The colors range from dark blue through green yellow to red There is also a bar scale that depicts values by river mile This spatial distribution dialog is accessed via the Map button on the Longitudinal Profile dialog You must
125. logical year s fall chinook production Highlight the following items Severity red Category discharge Operator gt Value 3000 Time Period November to February Location Iron Gate Dam to Shasta Then click Add followed by Close That s all there is to it See Figure 19 for what your screen should look like 51 Red Flags IGD_MAX_Q Water Years 1992 1994 E xj Severity Category Operator Value Discharge cfs 3000 e Pen Reservoir volume af lt C Yellow Water Surface Elevation ft AMSL Mean daily water temperature degrees C Maximum seven daws running denrees Ci z Time Period Location Month Upstream Downstream Upstream end of Iron Ge 4 Begin Octobe Below Cottonwood Ck a Iron Gate Dam Below Shasta R End February Below Bogus Ck v Below Humbug Ck Flag List Yellow August Discharge at Copco Dam 1000 00 cfs Yellow September to April Discharge at Copco Dam lt 1300 00 cfs Yellow May Discharge at Copco Dam lt 1000 00 cfs Yellow June to July Discharge at Copco Dam lt 710 00 cfs Yellow Anytime Reservoir volume at lt 43339 00 af Red Anytime Reservoir volume at lt 12724 00 af Red Anytime Water Surface Elevation at gt 22 00 ft AMSL Yellow Anytime Mean daily water temperature from Copco Dam to Below Horse Ck 16 00 degrees C Yellow Anytime Maximum seven days running from Copco Dam to Below Horse Ck 7 00 degrees C Red Anytime Maximum seven d
126. lt 710 cfs yellow flag source FERC Long Range Plan Ramping rate Needs thought Reservoir Operations Anytime Iron Gate reservoir lt 43 339 af yellow flag source IG hatchery upper outlet elevation Anytime Iron Gate reservoir lt 12 724 af red flag source IG hatchery lower outlet elevation Anytime Boyle reservoir lt af red flag Anytime Keno reservoir af red flag Electrical Generation need some criteria 106 Water Quality Temperature Anytime anywhere below Iron Gate mean daily water temperature gt 16 C for 7 consecutive days yellow flag source USGS Anytime anywhere below Iron Gate mean daily water temperature gt 22 C for a single day red flag source USGS October January anywhere below Iron Gate mean of maximum of 7 consecutive days gt 12 8 C red flag source Oregon DEQ for salmonid spawning egg incubation and fry emergence DO Anytime anywhere below Iron Gate dissolved oxygen 7mg l yellow flag source EPA Anytime anywhere below Iron Gate dissolved oxygen 5mg l red flag source EPA pH Anytime anywhere below Iron Gate pH lt 6 5 or gt 9 0 red flag source EPA Alkalinity Anytime anywhere below Iron Gate alkalinity CaCO gt 75 mg l yellow flag Ammonia nitrogen Anytime anywhere below Iron Gate total ammonia 70 13 mg l pH 9 yellow flag source EPA Anytime anywhere below Iron Gate total ammonia 71 00 mg l pH 8 yellow flag source EPA Anytime anywhere below Iron Gate
127. ly daily or monthly time interval The model has a long history of supported use and is in the public domain HEC 5Q is one of a very few models that have been used for simulating both rivers and reservoirs For the Klamath only selected features of HEC 5Q have been implemented None of HEC 5Q s water quantity capabilities have been used SIAM uses MODSIM for these The water quality portion of the model has been set up for mean daily simulation from Upper Klamath Lake downstream using flow demands and reservoir storage imposed by the water quantity model MODSIM The quantity model s mean monthly flow pattern is disaggregated into 30 days or 28 or 31 as necessary of equal daily average flow Note that you may provide daily flow patterns for SIAM if desired In addition to Upper Klamath Lake Keno Copco and Iron Gate reservoirs are modeled along with all major tributary creeks and rivers e g the Shasta and Scott Small tributaries and undistributed inflows are also modeled solely as accretions JC Boyle was simplified due to model constraints In addition to water temperature conductivity was chosen as a conservative constituent to improve the estimation of unknown boundary conditions Dissolved oxygen is simulated using HEC 5Q s simplified computation of DO which includes BOD SOD and reaeration only due to the difficulty of fully implementing the more sophisticated oxygen nutrient phytoplankton option in the model Because of the daily
128. ly qualified directory name of the alternative to analyze NN O O Representative nutrient sampling data to use ADY Canal KS Drain 2000 z pun 1998 Powerplant Iron Gate Shasta R Scott R Seiad Salmon R Trinity R Youngs Bar 1999 E i4 YIN Alternative Chat f ADV Canal Z Keno f Power EIC Figure 65 Alternative worksheet for nutrient loading estimation model In Figure 65 an example of a directory folder and simulation file name is shown in blue in the upper left corner Using the drop down boxes to the right of the sampling locations you can select representative years of measured data for loading computations You can either match actual years for the period 1996 2000 or select representative years such as a wet year 1996 an average year 1998 or a dry year 2001 Although 2001 data is not yet available for the database we hope to add this in the near future Once you have identified a SIAM alternative and selected the representative years of measured nutrient concentrations to use to estimate nutrient loading press the Compute Nutrient Loading button In a short time nutrient loading for all the constituents listed above will be computed The results can be viewed by clicking on the Chart tab The Chart worksheet page is displayed in Figure 66 123 E Microsoft Excel nutrient_loading_model xls BE x
129. ly to all years You have also probably noticed the two grayed out columns on this table They apply to the so called management simulations that you will learn about as we go to the next dialog you will use So you have entered the flows you want to see below Iron Gate but how do you control who gets the water You do this by editing the node by node priorities for water allocation within the water quantity model Access the appropriate screen by choosing Edit Node Priorities or clicking on see Figure 16 The lower the priority shown on this screen the more MODSIM will try to meet that flow or storage target In fact the best way to think about the priorities as we have implemented them in the water quantity model is to think sequence That is water is allocated to the reach with the lowest priority first then the next lowest priority and so on In the case ofa tie in general the model will allocate water to the most upstream reach first In this example the instream flow demand node below Iron Gate Dam has a default priority of 30 higher than that for the upstream diversions For our purposes here change the value 30 to 5 so that priority will be given to meeting the specific targets we imposed earlier This screen will also inform you whether you are using a calibration run or a management run for MODSIM Ifit isa management run SIAM will support user editing of three hydrologic states dry average amp wet If the managem
130. ment of alternatives for flow and water quality control in the Klamath River below Iron Gate Dam Center for Environmental and Water Resources Engineering University of California Davis Report No 99 04 236 pp plus appendix Hanna R B S G Campbell and J M Bartholow 2000 Water Quality Modeling HEC 5Q and Systems Impact Assessment Modeling SIAM for U S Bureau of Reclamation Klamath Project Operations in FY2000 Interim Contract Completion Report for the US Bureau of Reclamation Klamath Basin Office Version 2 0 January 11 2000 Hanna R B 1997a Water quality modeling in the System Impact Assessment Model Case study Klamath Basin US Geological Survey Denver Colorado September 15 1997 57 pp Hanna R B 1997b Analysis of water quality scenario results for the Klamath Basin US Geological Survey Denver Colorado October 2 1997 19 pp Hanna R B 1998 Water Quality Modeling in the Systems Impact Assessment Model Case Study Klamath Basin Addendum to Final Report US Geological Survey Fort Collins Colorado 32 103 pp Hanna R B and S G Campbell 1999 Water Quality Modeling in the Systems Impact Assessment Model for the Klamath Basin Keno Oregon to Seiad Valley California USGS Open File Report 99 113 82 pp US Army Corps of Engineers 1986 HEC 5 Simulation of Flood Control and Conservation Systems Appendix on Water Quality Analysis CPD 5Q Davis California Aquatic Habitat Models PHABSIM and T
131. mes in the table the next time you edit the years Note For a multi year simulation the initial reservoir volume fora MODSIM calibration run is derived from the previous month end storage target For example if you chose water year 1992 as your first hydrologic year the reservoir storage target for September 1991 would be used to initialize the simulation If you choose the very first year in the database to simulate 1961 SIAM will use MODSIM s starting reservoir volume set by an expert user only This starting reservoir volume is also the value used for a MODSIM management run Initial reservoir water quality is handled in much the same way Fora single year or the first year of a multi year run the initial conditions are derived from representative field data collected in 1996 Initial conditions in subsequent years of a multi year run are derived from the previous month s outflow water quality under the assumption that the reservoirs are at or near their annual fully mixed condition For our example we are interested in revising the flow schedule below Iron Gate Dam Under the Edit menu choose Node Targets or click on Then select Klamath River Below Iron Gate Demand from the drop down menu provided Nodes are listed in geographic order Your screen should look something like Figure 15 below 45 Node Targets IGD MAX OQ Water Years 1993 1995 This is a calibration run Node Description Instream Flow below Iron Gate
132. n and Network 4 is without project to the ocean Any XY files you subsequently save or create through MODSIM may be selected using the Advanced button Note that in doing so it is possible to select a baseline file that does not match the chosen network This will result in an error when running SIAM s models so be sure you choose files compatible with the desired network Also note that SALMOD is disabled when using the without project network It is disabled because we do not know what fish dynamics were like pre project and have not described the habitat upstream from Iron Gate New Alternative Ed Altemative Folder Name IGD Mex Location c projects klamath_alts Browse Description Reduce and stablizie October to February spawning rearing flows to 1000 cfs a El Network Upper Klamath Lake to the ocean with project XY File Files Mi modsim Klamath_to_th cean_61 99 C xy Advanced Program Files A 9 C CAProgram Files USGS SIAM modsim Klamath to theo ocean yir 89 xy C Program Files USGS SIAM modsim ManagementAll xy C Program Files USGS SIAM modsim Klamath_to_the_ocean_61 99 B C Program Files USGS SIAM modsim ManagementAll B Figure 11 The New Alternative dialog with a Name typed in and selections being made If need be use the Browse button for Location Figure 11 to tell SIAM where to store your alternative Doing so will bring up another dialog Figure 12 allowing you to step through the folders on
133. nd 1 3 Leon Basdekas in the same office and now with Utah State University along with Matt Combes asked critical questions helping to improve SIAM s interface with other models such as KPOPSIM Nancy Parker Ken Mangelson and Ron Sutton Denver Regional Office helped with product development and suggestions for application improvements In addition staff from the US Fish and Wildlife Service have been instrumental in testing and shaping SIAM Tom Shaw Charlie Chamberlain Paul Zedonis and George Gullien have made significant contributions to SIAM Other members of the USGS Klamath River study team including Clair Stalnaker and Sam Williamson all served as extensive advisors in the construction of SIAM Jeff Sandelin artfully engineered the first versions of the SIAM user interface John Scott Steve Witter and Catherine Cat Shrier have made MODSIM a great tool for the Klamath Mark Baldo helped with MODSIM technical issues Graphics assistance was provided by Jennifer Shoemaker and her staff Figure 1 SIAM s Components Data Requirements VA J E Flow ie d Data A gt Location n Years Location 1 n A o FE Meteorology A gt Years Basinwide os Water gt 88 Quality TT Data A gt Location n Location 1 Years 2 Habitat e Data gt Location n Flow Location 1 and more Functional Models and Routines Water Quantity Model MODSIM x Developed at Colorado State Univers
134. ng on the software s needs This makes knowing the exact requirements tricky and perhaps dependent on other applications you may be running simultaneously You may be able to squeak by with 8 megabytes of RAM if you are running Windows 95 but 16MB will be dramatically better and 32MB highly desirable An NT based system may require 64MB to 128MB Note that some users have experienced difficulty on NT systems Minimum screen resolution is 800 by 600 pixels SIAM is always in memory even when the various components and their pre and post processors are running within a child MS DOS or Windows foreground process To properly support these child processes you must check the Close on exit setting on your MS DOS Prompt or Command com Properties Program tab See the Figure 9 as an example note that your other settings may be different from what is shown If you do not do this SIAM may seem to simply halt after running a child process in a DOS window If this happens to you wait for a while to see if it is just slow on your computer If it continues to hang right click the small icon in the upper left corner of the DOS prompt window to access the MS DOS Properties page see below Call us if you have problems SIAM uses the Windows WordPad utility It expects WordPad to be found in the C Program Files Accessories folder If you do not have WordPad in this directory please put a copy or a shortcut to it there or place it in the Windows directory
135. ns You should develop a life stage periodicity chart so the microhabitat output graphs can be properly plotted interpreted to reflect the time ofthe year when the life stage is actually present in theriver Recall that SALMOD uses weekly flow data and therefore the habitat time series is done using a weekly time step 115 Identifying microhabitat bottlenecks The preferred approach Once SALMOD is run either as a stand alone program or as part of SIAM there are several ways to display the microhabitat time series output One method we do not recommend is to run SIAM for a multi year simulation The problem is that these graphs do not allow direct comparison between two or more years because the years are plotted in sequence The preferred approach is to run each year of interest separately i e run SIAM with a New alternative several times once for each year To accomplish this start by using SIAM s Edit drop down menu and select Year then enter one year in the dialog Figure 57 shows 1982 Year 1982 x Available years 1961 1939 Historic Flow Metrics 1000s of acre feet Hydrologic Meteorologic year UKLInflow Annual Link Discharge Total Annual Year Year Apr Sep Dam Release To Ocean Diversions 1982 4 Co n2 Fill Table Clear Table I Begin years at1 Met Year Data Mean Monthly Air Temperature Degrees C This is a calibrati
136. nt Grid Lines Print I Grid Lines Figure 47 Yearly and monthly graphs of daily flows You might wonder where the water year type daily pattern templates came from that are supplied by SIAM Those for the Klamath River were selected from a database of USGS recorded daily values at Iron Gate Dam USGS gage 11516530 for water years 1961 1993 The 90 50 and 10 exceedence levels for the total monthly flow for each month were selected as representative of dry average and wet conditions respectively and the daily values for those months became the template values The months selected are shown in Table 7 and their corresponding daily values are shown in Figure 48 Note daily releases are passed downstream from Upper Klamath Lake through the mainstem Klamath and affect all nodes to the ocean This daily pattern is not however applied to any tributaries Only constant daily values for the month are applied in all these other cases meaning that SIAM is only approximating daily flow effects Daily patterns are not applied for simulations greater than one year Also note that SIAM and MODSIM and HEC 5Q do not properly handle travel time along the mainstem A daily pattern is superimposed all the way downstream even though daily flow changes would actually dampen in the downstream direction 81 Table 7 Years chosen to represent Iron Gate Dam discharge by month and exceedence level 1986 1984 1986 1971 1986 1970 1987 1986 1979 1986 196
137. nted All classes within a life stage are automatically selected whenever a life stage is selected Unselect those not wanted If mortality was selected select the causes of interest The All Stages All Classes and All Causes buttons select or unselect all items in the respective category For example if you wanted a curve of adult mortality due to temperature and density select Adult Females Spawning Females Adult Males and Spawning Males from the life stage list and Temperature Related and Density Related from the mortality causes list The new curve will be added to the list of available curves The procedure for editing curves is the same as for adding a new curve Select Delete Curve if you want to remove a curve from the list Choose the curve to be deleted from the displayed list Note Both Lost Eggs and Invivo Eggs mortality are associated with the first egg size class The Frequency Distribution button allows you to plot the frequency distribution of fish weight or length for a specified life stage and time period Figure 32 shows the length frequency distribution Frequency Distribution Length Frequency Distribution For Exiters Pre Smolts CompuUnits 1 to 526 Dates May 1 1994 Sept 28 1996 Reduce and stabilize October to February spawning rearing flows to 1000 cfs Start Date 121 EX 10000 May 1 5 Start Year 8000 5 o 5 4000 End Date 3 271 aa 2000 Sept 28 End Year 0 rM o
138. nth to month The Ocean value is very large but also uses the lowest priority this 90 MODSIM modeling ploy ensures that the model moves any unaccounted water down the river system Therefore only one value is provided in the following table however MODSIM and the AXY file DOES include full sets of these respective values for each month and Hydrologic State As with the previous primary reservoir target values all reservoir target values can be edited modified or adjusted by the model user on a monthly basis Table 10 Secondary smaller reservoir targets DRY AVERAGE amp WET TARGET VALUES Ac ft Reservoir and MODSIM Keno 31 JC Boyle 6 Copco 2 30 18500 3377 74 Lake Ewauna 2 1000 Ocean 40 50000000 Some Guidance on when to use MODSIM Management Mode or Calibration Mode EXAMPLE 1 Duplicate historical flow operations This is the base case for the Calibration mode of operation and utilizes the historical data sets for reservoir storage levels In fact the three sets of Target values do not even need to be defined nor do the hydrologic state and the definition of Factors This is truly a calibration run in that the results can be analyzed to determine if the model actually reproduced matched the historical time series of reservoir storage river flows as compared to gaged or otherwise recorded streamflow and deliveries to any or all of the demand nodes In simplest terms thi
139. o 1996 iD ire Starting CU 8 5 2 pa a Length Category mm Ending CU 526 Output generated on 01 09 2002 at 12 49 10 Grid Lines Select species Select stage s fe Pe piu eed Category Mode ChinookSelmon Spawning Males Export C Instream fish Length S Auto s z F Print Exiters C Weight C Manual SetC J immatura Cmnlte Figure 32 Length frequency distribution for migrating Chinook Salmon pre smolts for migrating Chinook Salmon pre smolts Select the type of fish instream or exiters data type length or weight the species and life stage s Enter the date for instream fish or the starting and ending date for exiters If fish of the selected life stage exist for the time specified a frequency distribution bar graph will be displayed Categories can be automatically or manually determined 66 Set the number of categories up to 20 for the auto mode using the spin control in the Category Mode group Click on the Manual radio button and then the Set Categories button to manually set each category range Enter the minimum and maximum values for each category on the categories dialog Up to 20 categories may be defined for length and weight Use the Mortality Partitions button to display the relative contributions of selected mortality causes for selected life stages You can display up to 20 mortality life stage combinations at a time Figure 33 shows the mortality partitions for pre smolts an
140. of simulation Figure 56 Example maximum temperature prediction for Seiad Note the gap in predictions that result from HEC 5Q s not simulating days 361 365 for each water year Because of the nature of the two models it is possible for the regression equation to predict a maximum daily temperature that is less than the mean daily prediction from HEC 5Q This is especially true at Iron Gate where the daily maximums are not markedly different from the daily means due to the buffering capacity of all upstream reservoirs We elected to keep the regression model as is since both models are doing their best job at their respective predictions even if seemingly illogical conditions may arise In such cases it is probable that one or both of the HEC 5Q daily average and the maximum daily predictions are in error with no a priori indication of which is the most suspect This should simply reinforce the message that there is indeed error in both models as reflected in their goodness of fit statistics given elsewhere for HEC 5Q and in the spreadsheet itself for the regression model During our work we identified two areas for improvement in the HEC 5Q model s input data that we believe would ultimately improve its predictive power First the translocation of Medford Oregon air temperature data to Montague Yreka to represent the Klamath Basin introduced some errors These appear as systematic errors in equilibrium temperature estimation that could likely b
141. olor coded as river reaches on the map This can be displayed for a single day or animated for the whole year Making Management Runs with MODSIM A MODSIM AXY 2 file the network and all needed input data is provided in SIAM which is pre set to run in a management mode and utilize Target values for water storage each month on every reservoir A management mode type of simulation allows the computer model to operate water allocation in the Klamath Basin according to the defined demands and constraints but also allows the model to manage reservoir storage in accordance with these Targets Therefore the Targets take the place of historical monthly water storage values 1 e equivalent to reservoir or lake elevations The general concept is to provide a set of Targets that in a water resources context means reservoir rule curves The use of target levels is what an experienced operator would strive for given their sense of water stored throughout the system and the expected monthly inflow based on hydrologic meteorologic conditions anticipated at the beginning of each month Anticipation of water conditions leads to the concept of Hydrologic States a variable input used when MODSIM is run in a management mode Note The provided management mode AXYz file is named Management All XY or later version The Calibration mode AXY file is named Klamath to the ocean 61 99 XY or later version and by definition includes all data that are the histor
142. on Gate Dam the Klamath below the Scott River and the Klamath below the Shasta River Flow created 03 05 2001 Curve Statistics Water Quantity i i 80168 25 Figure 23 Water quantity model flow statistics 58 You may also plot storage and target matching difference between simulated and historical or target data by selecting them from the Data Type dropdown list Again select those curves to be plotted from the accompanying list box Select the Water Quality option from the View menu to display graphs of water quality output The graphics default to a graph of mean daily temperature at Iron Gate Dam Select any additional locations that you wish to display from the locations list box Simply click on the desired locations Figure 24 depicts the temperature at Iron Gate and Keno dams Other available water quality variables include discharge conductivity storage in feet above mean sea level and storage in acre feet Water Quality IGD MAX Q Water Years 1992 1994 jo x Daily Temperature IGD MAX Q Water Years 1992 1994 25 20 15 Degrees C 10 0 E E 4 2NDJFMAMJJAS 9SSNDJFMAMJJ A S SQNDJFM AM J JA S 95 Month in Water Year Keno Dam Iron Gate Dam Output generated on 03 05 2001 at 11 47 26 m Graph Type Scale Data Type Select lo
143. on results is the user interface for SIAM which tracks the options that the user wants to simulate passes data and simulation results as necessary to the appropriate models and summarizes the output for convenient display We have termed this overall component Cross Talk for convenience even though there is no software with this specific name for SIAM Cross Talk is responsible for the almost endless bookkeeping that is required to link models together that may have different spatial and temporal scales months days weeks different input and output units feet meters and different computer file formats no small task We will have more to say about each of the major subcomponents in the remainder of this document For the present it is necessary simply to introduce a few modeling terms that may be useful in understanding SIAM Calibration means using measured or observed input and output information to adjust or estimate parameters so the model s predications match empirical observations Reference or Baseline Condition refers to those conditions occurring during the reference time frame usually referring to water supply habitat values or population status The reference condition is often an actual recent historical condition but may also represent 1 the same climatological meteorological conditions but with present level water development and operations 2 the same climatological meteorological conditions but with both current and pro
144. on run 1961 27 00 10 72 18 78 20 89 22 00 14 00 a 1962 24 50 9 89 15 61 19 72 18 50 16 61 1963 25 06 9 00 15 33 17 39 19 44 19 72 Cancel 1964 25 89 11 44 15 61 19 61 18 83 14 17 1965 25 61 11 33 16 33 21 00 19 33 14 72 h Figure 57 Selecting a single hydrologic water year for a SIAM run Repeat this process for each additional year of interest and run each one separately For this example years 1984 and 1994 were run To plot a graph comparing 1982 and 1994 select View Comparative Graphs Fish Production from the SIAM main window as shown in Figure 58 Next use the Select Alternatives option on the SALMOD window lower left hand corner in Figure 59 to select an additional year s for comparison see Figure 60 116 A SIAM 3 10 WY96 99 Multiyear SALMOD comparision File Edit Run View Help ERES Output Tables gt MICA S a Bo DIEZ Output Graphs ries Gi 2 i Water Quantity Red Flags Water Quality Comparison Repart Water Quality Metrics gt Alternative Options Longitudinal Profile Toolbar Fish Production Historical Data Status Bar CONTROL POINTS Ts j JC Boyle inte tt JC Boyle Dem Ea Inlet Keno Dam Oregon Fon Gah ad n Tur dron Gate Dam Inlet pus Ck 5 j low Ck d Compare fish production alternatives NUM ifiStart James A BiWindows Appendix BJ Exploring fl SIAM 3 BS MOU 9 22AM Figure 58 Selectin
145. oncentrations at saturation and adjustment for elevation Chapra 1997 have been used with water temperature regression results to develop the tributary DO data available for use by SIAM HEC 5Q simulations The description of basin wide accretion water quality and temperatures of the Big Springs remains unchanged One dataset for water temperature and DO concentration measured at Keno during water year 1996 has been used for the small tributaries distributed throughout the mainstem Klamath basin This data is used to describe the water quality of ungaged accretion water around reservoirs and along river reaches Another dataset measured upstream of the powerhouse below JC Boyle dam describes the constant 100 cfs Big Springs inflow below JC Boyle 20 Inputs Outputs e a b o jae o E Q 5 g r Time e Simulate 2 Alt 2 gt thermo amp S Reference zz DB ererence s Q chemo Sl Time 2 S dynamics e vertically 5 2 Storage E n 2393 amp reservoirs 9 T constituent a and 5 profiles D itudi 3 longitudinally Time 9 in rivers 2 C 9 e o g o S F Time amp Parameters Figure 4 Important inputs and outputs for HEC 5Q 21 The Aquatic Habitat Component The aquatic habitat portion of SIAM is currently composed of features related to two sets of models commonly used in conjunction with an instream flow analysis PHABSIM Milhous et al 1989 USGS 2001 and
146. or all relevant river segments i e the area of a stream with suitable macro and microhabitat A time series is a record of events flow habitat or other through time and usually describes those events for a regular averaging interval such as hours days weeks months or years A time series analysis is the analysis of the pattern frequency duration magnitude and timing of time varying events such as habitat area temperature power etc In SIAM the aquatic habitat component is largely accessible through the advanced use of SALMOD Run Fish Production Ultimately we wish to add appropriate metrics relevant to the Klamath fishery to the Red Flags component to be able to examine the consequences of specific water management alternatives on aquatic habitat metrics Please refer to the section on Ecosystem Health for more information and appropriate examples It is beyond the scope of this reference to delve into the murky depths of aquatic habitat analysis However the following introductory material covering PHABSIM adapted from our Primer Stalnaker et al 1995 may be of some use For additional information see the references cited in the bibliography Many people confuse IFIM with the Physical HABitat SIMulation System PHABSIM Whereas IFIM is a general problem solving approach employing systems analysis techniques PHABSIM isa specific model designed to calculate an index to the amount of microhabitat available for different
147. ordered as Male Adult Male Spawner Female Adult and Female Spawner Adult life stages cannot be further divided Juvenile life stages can be divided into classes Life stage 5 is reserved for egg life stages and is classified by percent development deposition to emergence Life stages six through twelve are non adult life stages classified by size Table 4 The number of size classes and their definition can vary but at least 1 size class must be used to describe each non adult life stage As a cohort grows its life stage and size class attributes are modified when it graduates or matures to the next size class or life stage The various rate parameters e g growth and mortality can depend on life stage and class Non adult cohorts are tracked individually within a computational unit but any given cohort s identity may be lost when part or the entire cohort moves into a different computational unit 26 Several variables are tracked for each cohort throughout the model including e Number of eggs or fish e Average weight and length of fish e Percent egg development deposition to emergence e Number of redds composing an egg cohort e Number of in vivo eggs per ripe spawning female e Life stage and class of the cohort Variables are defined only for appropriate cohorts e g the in vivo eggs variable only applies to spawning females Individual measurements such as weight length and number of in vivo eggs represent the a
148. ort essen 73 Viewing Red Flag Results ene peii tet aee t o e Ret Ebo dieu 75 Managing Your Alternatives o esee epa tos Ea ro eco een trn esc oars YE Generating An Alternative Options Report sssssssssseee eene 78 Communicating Your Findings with Others esses 79 iv Table of Contents continued Advanced TOPICS 5o aaro deci dsl ah cede a a needa heeded 80 Adding Daily Variability to MODSIM Output eee 80 Viewing Spatial Distribution of Temperature in SIAM eene 85 Computing The Potential For Fish Kill In SIAM nee 87 Making Management Runs with MODSIM eere 88 Steps ad Using SIAM S ode esee dc aute eue had soie Pun ce oat 97 SISNECAVEBS e e Cig e rr ede tue db uno Mid Ea A a ae 100 Uninstalling SIAM uoo oia TRE nr E uie en LUI T Ed vus 102 To Learn More about SEA M ies de sestertia dnte ene qe ei PD R ve beu Ded dU E e Re Rede 103 Appendix 1 Example Red Flag Criteria for SIAM 0 0 0 0 cecesssssccseecsseeecesseeseeeeeseeceesceseeeeeseees 107 Appendix 2 Baseline Files Supplied with SIAM sse 111 Appendix 3 Summer Maximum Daily Water Temperature Prediction sssss 112 Appendix 4 Data Files Available for Expert Users eeeeeeeeeeneeneennnenn 115 Appendix 5 Conducting a Microhabitat Time Series Analysis Using SIAM 116 Appendix 6 Nutrient
149. ough appropriate input data preparation For SIAM on the Klamath River MODSIM has been applied using a monthly time step For more on how MODSIM s time step relates to that of the other models in SIAM please refer to Table 6 the ability to incorporate complex institutional and legal structures governing water allocation in a basin including complex exchanges and operating policies relies on user input data not a priori defined operating policies to describe system features and operational requirements separate from the network modeling algorithmic structure capable of modeling looped and bifurcating water system features and is not limited to branching or treelike network structures accurate calculation of system losses as a function of averaged flows and storage such as evaporation loss channel loss reservoir seepage and losses in water application a graphical user interface GUI for drawing and editing system features as well as a spreadsheet style data editing capability emulating a data centered information system hydrologic streamflow routing capabilities for daily simulation utilization of a network flow optimization algorithm based on Lagrangian relaxation accurate calculation of hydropower generation capacity and energy production based on power plant efficiencies which can vary with flow head and load factor calculates peak vs non peak and firm vs secondary energy production MODSIM is split into two functional pieces
150. port recommended minimum instream flows at Iron Gate Dam scenario This is a calibration type run Ferc_esa FERC release schedule at Iron Gate Dam scenario This is a calibration type run KLA97_6C Original USGS historical validation run This is a calibration type run KLA F Example of a MODSIM management type run No_proj The without dam or irrigation project river flow scenario This is a calibration type run Klamath_to_the_ocean_61 99 Historical run for Upper Klamath Lake to the ocean This is a calibration run Management All Full management file from ULK to the ocean 1961 1999 Klamath_to_the_ocean_61 99 C Historical run for Upper Klamath Lake to the ocean that reflects the extrapolated Upper Klamath Lake Copco and Iron Gate storage elevation area values Management All C Full management file from ULK to the ocean that reflects the extrapolated Upper Klamath Lake Copco and Iron Gate storage elevation area values 110 Appendix 3 Summer Maximum Daily Water Temperature Prediction Many people intuitively object to characterizing mean daily temperature preferring the maximum instead However NBS 1995 has shown that in the Klamath River differences between the daily maximum and daily mean water temperatures are typically small particularly in the segment immediately below Iron Gate Dam For example based on older 1963 1980 depending on the site USGS daily max min gage
151. posed future development on line and or 3 some estimate of virgin or pre development conditions Validation means determining how accurately the model can predict conditions different from what was used to develop and calibrate the model Contrast this with verification by which we mean only assuring that a computer program functions or makes its calculations as intended SIAM for the Klamath is a medium resolution model through time and space That is river flows and related elements range from monthly to daily in the temporal domain and are rarely truly continuous through space It is anticipated that SIAM will not fully answer all detailed questions if the spatial or temporal scales necessary are finer than this Other models could of course be added to SIAM as discussed previously However in many or most cases a better strategy may be to have SIAM help focus a more intensive analysis For example diurnal dissolved oxygen swings are thought to be important in the Klamath However it is likely that only certain times of the year are critical SIAM may be used to identify those critical times of the year or river segments under a variety of water management scenarios to be examined in more detail with techniques appropriate to the questions being asked For dissolved oxygen this may involve a more detailed hydrodynamic model such as is being applied by the University of California Davis Deas and Orlob 1999 ora relatively sophisticated regress
152. r changes in the A ternative Notes area and create new baselines frequently so you can try new options to see what effect they have You may delete alternatives from within SIAM or via Windows Explorer To delete an alternative from within SIAM you must have the alternative to be deleted open Click on File Delete and the Yes button to verify that you really want to delete it A DOS window will pop up asking you to enter y to verify that you wish to delete the whole directory The alternative folder and all of its files will then be deleted As noted previously the full set of simulation output files may consume large amounts of disk space up to one gigabyte or more for 40 year simulations However a new feature of SIAM allows more streamlined permanent storage by deleting unnecessary files at the conclusion of each simulation Deleting these files is the default condition If you need to change this for more hands on work with output files including maximum temperatures see the File Preferences dialog Generating An Alternative Options Report Suppose you forget exactly how you created an alternative How do you find out what you have Click on View Alternative Options to get a listing of the parameters used for the alternative and their current values Options contained in the report include Network used Baseline XY file XY file type Number of years simulated Hydrologic and meteorologic years selected 77 Target values No
153. r the animation Speed Slider Use this control to set the animation speed from as fast as your computer will allow to as slow as one interval per second Loop Checkbox Check this box to enable the play option to automatically restart the animation after reaching the end As the animation sequence plays the colors representing each river section will change with the temperature dissolved oxygen or discharge output from the simulation Colors will change on both the map and distance bar river miles The date being displayed at the end of each animation interval is shown in the dialog s title bar Computing The Potential For Fish Kill In SIAM SIAM has the capability of estimating the potential for fish kill based on ammonia concentrations pH and temperature at points along the river Potential for fish kill is categorized as low moderate or high based on EPA s criterion for thirty day ammonia concentrations Data files for ammonia concentration and pH were compiled for dry average and wet years This capability can only be used with single year simulations It will only be active after a simulation has been run Once a simulation has been run you must generate the potential for fish kill data using the option under the Run menu Here you select the type of year dry average or wet to be represented and specify the break points for the low to moderate and moderate to high categories for potential for fish kill These are entered as a per
154. re discharge or dissolved oxygen Select the Longitudinal Profile option from the View menu Set the date for which you wish to generate the longitudinal profile using the date spin control For multiple year simulations select the year Specify the starting and ending location for the profile Figure 29 shows the longitudinal profile for dissolved oxygen on June 1 1993 between Iron Gate Dam and Seiad Valley Annual Thermal Window IGD MAX Q Water Years 1992 1994 ol x Thermal Window for Iron Gate Dam at 15 C IGD MAX Q Water Years 1992 1994 Jan Calendar Date 1993 1994 Calendar Year Bl Date When Temperature Last Exceeds Reference S Date When Temperature First Exceeds Reference Output data generated on 03 05 2001 at 11 47 26 _ Statistics Graph Type RENE Reference Temperature C fis C Line T Grid Lines Select desired location Export C Bar Iv Plot Points fronGeteDem H Print Area F Line Style Close Figure 27 Area plot of thermal window for Iron Gate Dam at 15 C Macrohabitat IGD_MAX_Q Water Years 1992 1994 ol x EE Temperature Related Macrohabitat Range 15 20 eu xz IGD MAX Q Water Years 1992 1994 June 1 14r rere RRRru heu Iu eene nSpere soc dene ouPe ne a esse eteeesSEi End Date o Ses E Sept30 Bl aaa E a cl CELL EL MEUS Upper Limit on O 190p euer a a yea snccaassccriskesccssess ro 0 2 aaa lhe ciate im THEN
155. re ft cfs from the list of available tables see Figure 20 Because simulations may produce numbers very slightly different from the target values we have chosen SIAM expects that you only really care if there is a significant difference Enter a percent deviation from target criterion like 5 A table of targets that exceed the criterion will be displayed in WordPad Note Only negative deviations are reported 1 e values below the targets If you wish to print this table make sure your printer is set to landscape mode Tables IGD_MAX_Q Water Years 1992 1994 xi Select a table to view MODSIM Reservoir total storage levels MODSIM Flows MODSIM Target Matching acre ft cfs MODSIM Target Matching water surface elevation Enter the target matching tolerance percent deviation from target 5 View Table Close Figure 20 Available output tables for the water quantity model 54 Making Graphs Convey What You Want Graphic output is provided for water quantity water quality and fish production model results The user interface for each graphics type is very similar with some differences specific to each one The controls on each graphic screen can be divided into four categories those that control the geographic location or time of year of the displayed data those that control what data are displayed those that control the appearance of the graph those that control how the data are displayed Data
156. refresh the graph after making any parameter changes date starting and ending location data type etc before pressing the Map button Figure 50 shows the spatial distribution dialog for temperature on June 1 1993 The zoom and reset functions are similar to those on SIAM s main screen Click on Zoom and drag the mouse across the map window to form a box around the new window Click on Zoom and click the right mouse button on the map window to zoom out by 20 percent Click on Reset to reset the 84 map window to its original extent The key to color codes is located on the right side of the dialog You may specify up to 18 intervals for the key Click on Set Breakpoints to customize the color coding for the river values Enter the low value high value and the number of intervals in the resulting dialog SIAM will automatically compute the value ranges You may reverse the color scheme by clicking on the Reverse Colors button Spatial Distribution of Temperature For June 1 1993 Slow Interval Start 5 mE End Zoom Reset FIRE ee E ET Days H Oct1 Efe Sep 30 Pi ep Wo oes Water 186 Water Year 1994 Year D 14 00 C 14 00 14 11 C 1411 1422 C 14 22 14 33 C 14 33 14 44 C 14 44 14 56 C 14 56 14 67 C 14 67 14 78 C 14 78 14 88 C 14 89 15 00 C 15 00 15 11 C Ashes e 15 22 15 33 C 15 33 15 44 C 15 44 15 56 C C C C C j E Upper 14
157. rious simulated flows and may involve two dimensional stream modeling in addition to one dimensional modeling The habitat component weights each stream cell using indices that assign a relative value between 0 and 1 for each habitat attribute depth velocity substrate material cover indicating how suitable that attribute is for the life stage under consideration These attribute indices are usually termed habitat suitability indices and are developed using direct observations of the attributes used most often by a life stage by expert opinion about what the life requisites are or by a combination Various approaches are taken to factor assorted biases out of suitability data but they remain indices that are used as weights of suitability In the last step of the habitat component the hydraulic estimates of depth and velocity at different flow levels are combined with the suitability values for those attributes to weight the area of each cell at the simulated flows The weighted values for all cells are summed thus the term weighted usable area WUA There are many variations on the basic approach outlined above with specific analyses tailored for different water management phenomena such as hydropeaking and unique spawning habitat needs or for special habitat needs However the fundamentals of hydraulic and habitat modeling remain the same resulting in a WUA versus discharge relationship This relation is combined with water availabilit
158. rison 69 You may also compare alternatives with historical data for temperature dissolved oxygen and discharge Select Historical Data from the Comparison Graphs option of the View menu A graph for the base alternative and any historical data for the same time period will be displayed for the data type temperature dissolved oxygen or discharge and location selected Locations with measured data along with the years included are listed in a location list box Gaps in the historical data curve indicate missing data You may set the total period to be considered for comparison as well as restrict the time period each year that the results are compared using the spin controls on the left side of the dialog Five types of graphs can be displayed Standard actual values Absolute Difference absolute difference between an alternative and historical data Difference actual difference between an alternative and historical data Exceedence exceedence plots or Cyclic Variation Removed mean value for each date is subtracted from the actual values Simple statistics can be calculated for each curve as well as R and mean square error for each comparison with the historical data Additional alternatives may be also compared to the historical data by selecting them from your comparison alternative list Only those alternatives with the same start date and simulation length as the base alternative may be compared Figure 38 compares the base alternative
159. roject network 1 down to Seiad California The without Project network 2 extends the HEC 5Q network upstream to Upper Klamath Lake and differs in the exact location of Control Points 10 and 15 MODSIM S NODE LINK STRUCTURE HEC 5Q S CONTROL POINT STRUCTURE SALMOD S SEGMENT STRUCTURE V 6 gt yuw 6 7 6 V gt E 7 gt 7 E E 7 gt gt E 7 gt E 7 7 7 7 7 7 7 7 7 7 3 Inflow Into Upper Klamath Lake Control IE Accagal Drversions 5 UKL Reef Klamath F Upper Klamath Lake Link River Dam West and East Side Powerplants Link River at Klamath Falls Lake Ewauna Lost River Diversions and Returns North Canal Diversions lamath Straights Drain ADY Canal Diversions Klamath River Above Keno eno Lake and Dam eno Gage eno to JC Boyle JC Boyle Topsy Lake JCB Dam Large Springs JC Boyle Power Plant lamath River below JC Boyle JC Boyle to Copco Copco Lake Copco Power Plant 1 Copco 2 Forebay Copco Power Plant 2 Blw Bogus Creek to Iron Gate PER SA Blw Willow Creek Iron Gate Reservoir Blw Cottonwood Creek Iron Gate Power Plant Blw Shasta River Klamath River Below Iron Gate Blw Humbug Creek Demand Below Iron Gate Bogus E SRRA i dd Ww Bogus Creek Reach Bie oed ARN Willow Creek Reach Blw Scott River Cottonwood Creek Reach Seiad Valley Gage Shasta River near Yreka Humbug Creek Reach Beaver Creek Reach Dona Creek Reach Horse Creek Reach 9 ott River and
160. rs 1965 and 1971 Seiad Valley Dry Years 1968 amp 1977 Temperature C Simulated Measured 1 101 201 301 401 501 601 701 Day of Simulation Figure 3d Comparison of measured and simulated mean daily water temperature at the Seiad Valley gage location in the Klamath River for two dry water years 1968 and 1977 18 Water Quality Model Enhancements for SIAM Version 2 7 Updated Reservoir Storage Area Elevation Curve Data The Storage Area Elevation relationships have been updated in the HEC 5Q model file for Upper Klamath Lake Copco Lake and Iron Gate for Network 3 Nine data points are used within the HEC 5Q model to describe each reservoir These descriptions are more finely represented than in previous versions of SIAM and allow for more accurate computation of water surface elevations by the HEC 5Q model and replace the three data points previously used The points describe or allow the physical size of each reservoir to be larger than the current design The larger reservoir descriptions offer flexibility for user what if alternatives that may involve the simulation of enlarged reservoirs throughout the basin Flow and storage values simulated by MODSIM control the volume of water in each reservoir in HEC 5Q simulations This enhancement provides a much better correlation of simulated storage conditions between the MODSIM and HEC 5Q models However some small discrepancies should be expected between month end M
161. rt 1 Close Delete All Figure 41 Dialog for editing a report name or deleting reports Viewing Red Flag Results Last but not least the Red Flag report is ready for your perusal Figure 42 43 On this screen accessed by View Red Flags you can view each of the Red Flag items one at a time by choosing them from the drop down list or by the forward gt or backward lt buttons On this display model output is summarized on a week by week basis across the screen while the different spatial locations are displayed down the screen obviously not to scale If there is a violation of your Red Flag criteria within any week it will be highlighted in red or yellow if appropriate if there is no violation the shading will be blue During times the criterion does not apply the boxes will be colorless Did your alternative have any red flags Note that you may have to scroll left or right to examine the whole simulation period Right clicking the number of the week on the top row of the Red Flag display will tell you what the calendar date is for the start of that week Right clicking on a violation will tell you what the value of that week s metric is Displaying Red Flags for a long simulation may take a while 74 Red Flags IGD MAX Q Water Years 1992 1994 x Yellow Anytime Maximum seven days running from Iron Gate Dam to Seiad Valley gage gt 16 00 degrees C x lt gt Week in Water Year Right click on th
162. s Calibration uses the historical data sets and just duplicates or verifies that the model can simulate what historically occurred This is simple and accurate as long as the data sets are truly representative and mass balanced Otherwise some corrections to the data sets unregulated inflows or evaporation or storage or flow releases and adjustment of priorities might be required EXAMPLE 2 Allow the model the greatest flexibility to simulate operation of the system of reservoirs according to the defined network flow system using the defined target values priorities and other constraints This is the base case for the management mode of operation and makes best use of the Targets and Hydrologic State Factors identified in the above description Such a model run is fully designed to simulate the expected operation and water allocation of an experienced reservoir system operator responding to real time hydrologic meteorologic variability The use can generate even more flexibility by performing multiple model runs utilizing modified sets of Targets Priorities and possibly re defining the Hydrologic State Factors 91 EXAMPLE 3 Simulation of reservoir operations according to a very specific Target To remove any decision about what the reservoir target values will be for a given month that is the model will not make decisions based on a hydrologic state for each month then the management mode should not be used with all the flexibility and s
163. s day 1 kg 1 000 000 mg The nutrient loading estimation spreadsheet model may be accessed through the task bar by StartPrograms SiamWNut Load Model anytime after a one year SIAM simulation is run or as a stand alone model by selecting the Nutrient Loading Model from the SIAM program listing if you wish to analyze previously generated SIAM simulations When the nutrient loading model is initialized Excel will bring up a message regarding macros used in the spreadsheet Figure 64 Microsoft Excel C Piles KLAMATH nutrient loading putrient_loading_model xis contains macros Macros may contain viruses It is always safe to disable macros but if the macros are legitimate you might tose some functionality Coben Enable aces weno Figure 64 Excel macro query and selection menu Next press the Enable Macros button The spreadsheet may be entered on any worksheet page The various worksheet pages are shown as tabs across the bottom of the window as in Figure 65 The Alternatives worksheet tab is active in this figure and asks for the location where the one year SIAM simulation file may be found representative nutrient values can be selected and nutrient loading computed The first step is to enter the alternative name of the SIAM simulation for nutrient loading computation 122 4 Microsoft Excel nutrient loading model xls Ci D gcEE GS eX BEBO orc rw ao o emu SOME STET fF Us ess Ea Enter ful
164. servoir characteristics as above Red Flags nn r 0590 96 4 Run Linked Model s a MODSIM b HEC 5Q c SALMOD 6 View Summary Results a Verify that you got what you wanted to get i e if you changed the flow make sure the model s output confirm that change b Red Flags see attached sample list c Flows through space and time 1 Monthly af 2 Weekly cfs 3 Daily cfs d Reservoir volumes through time Habitat metrics f Water quality through space and time 1 Temperature C 2 Dissolved oxygen ppm g Salmon production responses 1 Outmigrant numbers and size mm 2 Mortality summary 3 Life stages in system through space and time number h Hydropower production agricultural deliveries etc not yet available e 7 Evaluate Results of Simulation Compared to Reference Condition SIAM adds nothing to assist in evaluating alternatives beyond comparison graphs and summary statistics We expect that users will approach the evaluation with the ideas of effectiveness efficiency reliability equity and cost of alternatives in mind incorporating a broad range of information on ecosystem health indicators fish habitat and life cycle needs as well as legal and institutional regulations regarding water allocations in the Basin It is our hope that such a process created with a buy in from all water users will a help formulate objective science based realistically attainable alternatives b add neede
165. software In order to provide flexibility for what if simulations the maximum capacities of Upper Klamath Lake Copco Lake and Iron Gate have been increased To achieve this objective the storage area elevation tables have been extrapolated above the previously available maximum reservoir levels These files are named like UKL SAE Table dat with similar names for the other reservoirs are stored in the SIAM install directory and may be easily read Note Do not change the number of header records lines or SIAM will not read them correctly 114 Appendix 5 Conducting a Microhabitat Time Series Analysis Using SIAM Why do a habitat time series The purpose of a microhabitat time series analysis is simply to quantify physical habitat over time The output can be used in two ways 1 to identify episodes of limited habitat that potentially affect the abundance growth and survival of a life stage habitat bottlenecks see Cheslak 1990 Nehring 1993 and Bovee 1994 and or 2 to quantify habitat losses and gains for individual life stages by comparing a baseline flow regime to an alternative flow regime A user of SIAM may find it helpful to conduct a habitat time series analysis to aid in the interpretation of SALMOD output or it may be necessary if a population analysis is not possible because the rate parameters e g growth and morality required for calibrating SALMOD are unavailable e g for coho salmon In other words you can
166. t fully realize inherent limitations Not all features of component models are available for editing within SIAM Documentation is always incomplete Data for validation of component models are limited HEC 5Q is calibrated for only two years and SALMOD has not yet been fully calibrated for the Klamath River The Water Quantity Component MODSIM SIAM s water quantity model called MODSIM was developed at Colorado State University MODSIM is a network based water allocation planning model which means that its specialty is the analysis of water systems with numerous diversions returns and reservoirs in an interconnected and managed system Careful applications generate useful information about which when and how fully water allocations are satisfied or not satisfied under a variety of water supply and system operation policies for river basins In short MODSIM allocates water in a manner consistent with the hydrological physical and institutional aspects of a river basin MODSIM simulates several types of water allocations including Direct flow allocations including conditional allocations Instream flow allocations Reservoir storage allocations Reservoir system operations Exchanges and operational priorities e g augmentation subordination MODSIM offers a number of unique features though SIAM does not make use of them all at this time They include the ability to operate in monthly weekly or daily time steps thr
167. te factors iacere rode eit nde die ar b d c ib d cent 90 Table 9 PrifdtioreSetVOIb tance Siri aie qo ronis quPa d epa t Pon hago Pa doct ia E a oua 9 Table 10 Secondary smaller reservoir targets sess 92 vii Forward Water from many of California s coastal rivers has been used for a wide variety of development ventures including major agricultural diversions hydropower generation and contaminant assimilation from industry agriculture and logging Anthropogenic impacts often degrade water quality and decrease the quantity and quality of aquatic habitat Reallocating streamflow away from uses that degrade water quality to uses that foster higher water quality is a critical step in restoring riverine habitat and the anadromous fish that rely on that habitat for a portion of their life cycle Reallocation always brings with it the need to examine the economic efficiency of the proposed changes Ifthe dollar benefits of improving water quality are greater than the costs the criterion of improving economic efficiency is satisfied a fact that can be highly persuasive to decision makers contemplating reallocation Previous related studies have examined nonmarket benefits of the Trinity River in northern California Douglas and Taylor 1998 Douglas and Taylor 1999abc but nothing of this kind had been done on the Klamath River another system with numerous uses for and competition over water in times of drought An economic surve
168. ter installation it would be wise to re run any alternatives you wish to retain Then do come back to review the background and components of SIAM as they are important in any informed use of this software and its models to do otherwise would be negligent What is SIAM The System Impact Assessment Model SIAM is an integrated set of models and data assembled to evaluate and compare the potential impacts of water management alternatives from an ecological perspective SIAM s goal is to further the process of reaching a decisive consensus on management of water resources in order to stabilize and restore riverine ecosystems and is meant to be used in the context of the Instream Flow Incremental Methodology IFIM as summarized by Stalnaker et al 1995 To achieve this goal SIAM must help quantify consequences of water management alternatives in terms of the major physical chemical and biological indicators known or strongly believed to be intimately related to the success of anadromous fish restoration For our purposes water management may be defined as direct or indirect control of the quality magnitude duration frequency timing or rate of change in river flows under man s influence SIAM is primarily intended for planning and management as opposed to research SIAM is not meant to supply the answer Management models integrate the best available knowledge to provide managers with the predicted results of potential actions i e a what
169. that were based on one year of data This update only impacts the first day of the SIAM simulation As with previous SIAM versions the first day of subsequent years in a multi year simulation uses the end of year water quality conditions from the previous year s simulation as initial conditions Note that this includes setting the reservoirs 1 October temperatures isothermally to 30 September outfall temperatures meaning that approximately the first two weeks of October may show reservoir thermal profiles that are incorrect Given that the reservoirs are generally close to isothermal shortly after this period this has not been viewed as much of a problem but it is an admitted deviation from reality 19 New Tributary Inflow Water Quality Data Temperature estimates for the Shasta Scott Salmon and Trinity Rivers have been available in earlier versions of SIAM A complete set of estimated daily inflow water temperature and DO values for the water years 1961 1999 period are now available for all major tributaries in the HEC 5Q model These water temperature estimates were created using linear regression on historical data sets for tributary water temperature and local air temperature data Estimated values for historical tributary DO conditions have been developed using these temperature data files It has been assumed that DO conditions are saturated with respect to water temperature and elevation for all the major tributaries Equations for DO c
170. time step and the simplified DO option only mean daily values are computed by HEC 5Q Though diurnal values for water temperature and dissolved oxygen would be useful biological indicators for the Klamath daily values can provide a useful benchmark with which to compare alternative management strategies As with all of the major component models within SIAM we must refer the reader to the complete users manual for HEC 5Q to more fully explore the program s formulation capabilities limitations specific data requirements and implementation USACOE 1986 SIAM uses a plain vanilla version of HEC 5Q that is unmodified from the original maintained by the USACOE This version executes in a DOS window provided by SIAM with SIAM taking the responsibility of providing appropriate files as input and reading the required files containing output to pass back to SIAM The most important consideration is that SIAM only knows how to exercise HEC 5Q for the existing plumbing of the Klamath system with the exception ofthe no project network That is though the model is capable of exploring a multilevel outlet for example this feature would need to be 15 accomplished using HEC 5Q in a standalone manner For more information on the implementation of HEC 5Q for the Klamath including data sources calibration and model validation details please refer to Hanna 1997a amp b and Hanna and Campbell 1999 It may also be instructive to compare the HEC 5Q mod
171. ty of water delivered to various points nodes downstream MODSIM is designed to respect maximum flow values in a link as a Atight constraint and thus will never distribute allocate more than the maximum defined flow volume for a given month to that link This can create a simulation if the maximum values are low volume constraints in which larger quantities of water will need to be stored in upstream reservoirs or spilled through some other unconstrained demand node upstream remember that downstream flow is strictly limited to the maximum defined link volume for each month Once again right clicking on the link object within MODSIM accesses the data tables containing these link values In addition to adjusting the monthly flow volumes it may be necessary to adjust the priorities at several locations within the flow network to achieve the desired or expected simulation result 93 LINK DAM TARGETS 800000 700000 iu 600000 LL U w 500000 g DRY hj 400000 AVG WET amp 300000 p k 200000 100000 0 gt O c Ke gt c Oo es 0285222232524 MONTHS Figure 53 Plot of Reservoir Target Values for Three Hydrologic States at Link Dam 94 IRON GATE TARGETS 61000 60000 59000 58000 e DRY 57000 56000 AVG 55000 a WET 54000 53000 52000 STORAGE AC FT O M OA S d S S fou qe S 9 Nd yS we S SS SP ce MONTHS
172. ully completed this step If you get confused you can just delete everything with Windows Explorer and start over 42 New Alternative IGD_Max_Q cAProjectsXKlamath alts Reduce and stabliize October to February spawning rearing flows to 1000 cfs Upper Klamath Lake to the ocean with project C Program Files USGS SIAM modsim Klamath_to_the_ocean_61 99 x EE ERI cms Figure 13 Completed File New dialog 43 Making the Necessary Changes Now you have a baseline alternative as supplied in MODSIM s calibration data set Klamath_to_the_ocean_61 99C_XY a starting point from which to experiment SIAM s main screen will show your alternative name and the alternative description on the top line of its window Choosing the Edit Year menu item or clicking on C brings up a new dialog as shown in Figure 14 Next you may choose any combination of available hydrologic years and meteorologic years to run in SIAM A table of historical flows is provided as an aid in selecting hydrologic years Your choice of hydrologic years is listed in the top table and your choice of meteorologic years is listed in the bottom table which also shows selected attributes of that data so you can make an informed choice You may sort the values in the information tables on the right side of the dialog ascending or descending by right clicking on the column you wish to sort and selecting ascending or descending order from the popup menu Your entry is mad
173. ural demands and water allocations MODSIM can also track power generation at reservoir power plants though SIAM does not make these results available at present Flows simulated by MODSIM are next passed to a Corps of Engineers developed water quality model HEC 5Q USACOE 1986 to predict selected water quality constituents throughout the river For the Klamath River the constituents simulated are water temperature dissolved oxygen and conductivity Aquatic habitat is a general term that refers to any part of a stream where an aquatic organism lives Aquatic habitat is dependent on both water quantity and quality the determinants of micro and macro habitat combined to give total habitat Aquatic habitat has been characterized in SIAM using elements from the Physical Habitat Simulation System PHABSIM Milhous et al 1989 USGS 2001 and from the Time Series Library TSLIB as described Milhous et al 1990 Important habitat elements include water depth velocity substrate and cover In addition channel morphology sediment budget and thermal refugia are relevant macrohabitat features but not adequately addressed in SIAM at present Quantification metrics include duration frequency magnitude and rate of change of integrated measures of total habitat Strictly speaking PHABSIM is not a functional component of SIAM in the same way as the other models This is because it has been run independently to generate a portion of the data made a
174. vailable to SIAM these data are used primarily in a fish production submodel SALMOD Fish production is dependent on the time series of micro and macro aquatic habitat as well as the number of adult spawners present SIAM employs a fish production model SALMOD Williamson et al 1993 Bartholow et al 1993 to track the relative number and weight of juvenile chinook salmon successfully exiting the study area It also identifies the relative magnitude of various sources of mortality including water temperature movement and nesting superimposition throughout the early life history of the species under consideration All mortality sources are ultimately traceable back to water quantity and quality variations over time Collectively all of SIAM s output metrics are used to characterize ecosystem health Though not represented by a single numeric quantity ecosystem health in the context of SIAM is embodied in the output by the number of occurrences of various metrics falling outside of user prescribed bounds and the physical extent of those deviations For example dissolved oxygen falling below 5 0 mg l on a daily basis would be flagged as unacceptable In fact SIAM s presentation for ecosystem health is a set of so called Red Flag displays that capture the encroachment of standards through time and space These Red Flags are supplemented by a set of powerful water quality metrics such as degree days Binding the models data and simulati
175. verage value for the cohort Fish growth is computed in weight length is determined from a weight length relationship with the exception that a loss in weight does not result in a loss of length Fish must regain lost weight prior to new growth in length Biomass of each cohort is defined for non egg cohorts as the number in the cohort times the average weight of individuals in the cohort Biomass of each life stage is the sum over all cohorts in that life stage In short SALMOD provides an important link between the physical habitat models and anadromous fish production For more information on SALMOD its concepts applications and implementation please refer to Williamson et al 1993 Bartholow et al 1993 and Bartholow et al 2000 27 Table 4 Example life stage and class structure definition of an anadromous salmonid population along with the model s order of calculation Classes are defined by percent development deposition to emergence for egg stage and by length mm for fry to yearling Calculation Class Class definition Life stage name order Spawner Adult Egg Alevin Fry Pre smolt Immature smolt Sf Sm Af Am F1 F2 P1 P2 P3 il i2 28 Spawning Female Non Spawners Female Male 0 0 33 3 66 6 34 mm 38 mm 50 mm 60 mm 70 mm 80 mm 90 mm to to to to to to to 33 3 66 7 100 0 38 mm 50 mm 60 mm 70 mm 80 mm 90 mm 110 mm
176. voir Volumes Diversions amp Returns B of river o reservoir d system to E achieve E t mass balance e A E and ZE Reference 5 e optimize DE amp deliveries R a based on priority system Reservoir Power Production Parameters Figure 2 Important inputs and outputs for MODSIM The user is referred to the complete on line help for MODSIM for more information on using its standalone features that are not incorporated into SIAM 14 The Water Quality Component HEC 5Q The water quality portion of SIAM for the Klamath River is filled by HEC 5Q This model was developed by the U S Army Corps of Engineers at the Hydrologic Engineering Center at Davis California USACOE 1986 HEC 5Q simulates the sequential operation of a reservoir system to evaluate the operational rules for flood control and conservation i e instream flow purposes Water quality analyses include water temperature three conservative and three non conservative constituents and a dissolved oxygen nutrient phytoplankton option Reservoir releases may be computed to satisfy multiple control point node criteria using a philosophy of minimizing violations of control point water quality requirements HEC 5Q has some capability to simulate multilevel reservoir withdrawal to accomplish downstream water quality objectives Twenty reservoirs forty control points and almost any length of study period can be simulated on an hour
177. with a C XY suffix have been included that reflect the extrapolated Upper Klamath Lake Copco and Iron Gate storage elevation area values If the user wishes to simulate larger reservoirs for what if alternatives the C XY files should be used Version 2 7 also adds the capability to generate alternative comparison reports Differences above specified thresholds for water quantity model discharge and storage and water quality model discharge temperature dissolved oxygen storage water surface elevation and conductivity can be reported Version 2 5 March 2001 added a matrix of historical flows to aid in the selection of comparable years to evaluate SIAM can now set reservoir storage targets in terms of water surface elevations as well as volumes This is important for consideration of lake levels mandated for endangered lake sucker protection Some of the MODSIM data files have been updated with more accurate data or parameter values As always numerous small bugs were found and corrected NOTE it would be best to rerun any previous versions of SIAM alternatives since this new software may not be able to process previous results correctly in all circumstances Versions 2 3 and 2 4 January 2001 added the capability to superimpose daily flow variability on the monthly output from the MODSIM model downstream from Iron Gate dam This should provide more realistic estimates of the variability of downstream water quality results and allow
178. x to the right of the spin control Figure 35 shows the dialog for setting advanced features for the X axis as time 67 Define Partitions Exi Select partitions up to 20 Reset Adult Spawning Adult Spawning Eggsi lev Fry Pre Smolts Immature Females Females Males Males Smolts Base L L L TC E L L DL Temperature r E r E E r r Density L a L L LI E L a L Catastrophic r r L L E T L L Habitat LI a E a E E L Freshet E E L a E LI L L Seasonal a E E E E E L L Dying Spawners r r Lost Eggs m Invivo Egg m Incubation B Superimposition m Cancel Figure 34 Select mortality life stage combinations by clicking on the check boxes Set temporal limits and resolution Temporal Limits Beginning n i f 0 1 1992 Ending f 56 H 9 30 1995 Reset Spatial Limits Unstream 1 0 0 meters P og EN Cancel Downstream 526 E rn 1 6 meters x axis units C Time Steps Dates Figure 35 Dialog for setting temporal limits and units 68 Comparing Alternatives Graphically An important feature of SIAM is the capability to graphically compare alternative results This is done in a manner very similar to graphing results for a single alternative The only differences are that you can only select a single curve i e location MODSIM node link etc or other graph and you must select the alternatives to be compared from a list of avail
179. ximum boxes on or off by clicking on the Total Maximum box Note that Maximum has no implication for the decision priorities covered later in this document You may paste data from a spreadsheet into the target table by right clicking on the single cell that you wish to begin the paste operation and then selecting Paste from the pop up menu 46 How will you adjust the other months so that the total annual value remains the same Or should you Or is that important These are important issues to consider Press OK when you are satisfied TIP Though SIAM lets you easily switch between acre feet and cfs it is good to keep the conversion in mind To convert from cubic feet per second cfs to acre feet per month multiply the cfs by 59 5 or roughly 60 for an assumed 30 day month Note that SIAM displays values for reservoirs only in acre feet and in these cases they define the end of month total storage values There are a few other things you need to know about the Edit Year dialog even though we will not use them at this time If you choose a reservoir node from the drop down box the storage targets may also be edited as water surface elevations in feet above mean sea level Select elevation as the target type The Apply to all years check box will use the values you enter for each year of a multi year simulation By default the values would only apply to the first year for storage nodes except for Iron Gate releases that always app
180. xposure COMPARISON_91 95 Water Years 1991 1995 Oy x Start Date n2 E Em COMPARISON 91 95 Water Years 1991 1995 en e Sept 30 Upper Limit m sla e m O x a q 1 T 1 1 1 1 1 1 1 1 1 e QJ Lower Limit z ege en e 2 n e ate Cumulative Degree Days a4 e ma Q a e 20 1991 1992 1994 1995 1996 re Water Year Iron Gate Dam Seiad Valley gage Output generated on 02 14 2002 at 12 39 28 Evaluation Period June 1 Sept 30 Temperature Range 20 30 degrees C Zoom Press shift and drag mouse Reset Press A Statistics Sev Asis Advanced Graph Type 7 Grid Li Select desired locations Reset Type p Data Type 9 ac Below Horse Ck Cumulative k Temperature C Bat x ds Eni Below Scott R C n ine Style C Independent Dissolved 02 Stacked Bar reru Indian Ck Figure 25 Annual cumulative temperature exposure at Iron Gate Dam Exposure period provides the number of days in a year in which an aquatic organism is exposed to temperature or dissolved oxygen within a specified range during a specified period ofthe year To view a graph of exposure period select Exposure Period from the Water Quality Metrics submenu Set the evaluation period using the start date and end date spin controls Set the temperature or dissolved oxygen range using the upper and lower limit spin controls Select Betwe
181. y is nearing completion for the lower Klamath River including the Scott Shasta and Salmon Rivers but excluding the Trinity This survey provides valuable insights about the magnitude of the benefits and nature of the costs of reallocating water from market uses to instream flows that improve water quality and assist in the recovery of Klamath River fish stocks Preliminary survey results Douglas and Johnson 2002 Douglas and Sleeper In Prep indicate that about 234 000 California Oregon and Nevada households made recreation trips to the lower Klamath River Basin 1997 1998 and that these users spent about 780 million on trip related expenditures Clearly the prosperity of the region is closely linked to the demand for Lower Klamath River Basin recreation trips Further respondents indicated that they would make roughly 36 more recreational trips per annum to the Klamath ifthe water quality and the fishery were restored to an unspoiled condition Using two distinct types of survey data these additional trips would yield benefits with a present value of approximately 20 billion at a discount rate of 7 5 Calculating costs to restore the fishery and raise water quality involved five major hypothetical restoration activities 1 purchasing Klamath project farmland and environmentally sensitive forest lands 2 allocating more water down the Trinity River to enhance the quantity and quality of Klamath flows below the confluence 3 removing
182. y to develop an idea of what life stages are impacted by a loss or gain of available habitat at what time ofthe year Time series analysis also factors in physical and institutional constraints on water management so that alternatives can be evaluated Milhous et al 1990 Several things must be remembered about PHABSIM First it provides an index to microhabitat availability it is not a measure of the habitat actually used by aquatic organisms It can only be used if the species under consideration exhibit documented preferences for depth velocity substrate material cover or other predictable microhabitat attributes in a specific environment of competition and predation The typical application of PHABSIM assumes relatively steady flow conditions such that depths and velocities are comparably stable for the chosen time step PHABSIM does not predict the effects of flow on channel change 23 Aquatic Habitat Inputs ES w ae S Velocity 5 8 9 Depth m a l Substrate o kae Eg O Cover ag 2 Refuges ot 2 Quantification of physical habitat availability to calculate total habitat duration frequency magnitude rate macro usable micro usable surface area Morphology Sediment Potential Physical Macro Habitat Flow Regime a Habitat Suitability 0 Temporal and Spatial Loop Figure 5 Major components of aquatic habitat analyses 24

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