SJR DO Depletion Modeling: Model Calibration, Adaptive Management, User Guidance Andy Thuman, P.E. (HydroQual) Laurie De Rosa (HydroQual) SJR Technical Working Group May 16, 2006

2 2 Water Quality Modeling  Adaptive Management Strategy Simulations oDissolved Oxygen Unit Responses oStockton RWCF Ammonia, Algae, Upstream Carbon, SOD oVariable Flows & Stockton RWCF Nitrification oO 2 Injection oMud Slough Flow Reduction  User Guidance oGIS Based Post Processor for Users oWeb Viewer oECOM, RCA Structure

3 3 DO Unit Response, Stockton RWCF Ammonia  Base Model Simulation  RWCF Ammonia Discharge Conc = 0 with base 2001 flow

4 4 DO Unit Response, Stockton RWCF Ammonia  Summer Avg Q=900 cfs in 2000, 600 cfs in 2001  Higher summer ammonia discharge conc in 2001  About 1mg/L difference in DO in 2001

5 5 DO Unit Response, No Algal Processes  Growth, death, grazing, settling = 0  Algal processes provide a net oxygen source of up to 1.0 mg/L

6 6 DO Unit Response, Upstream Non-Algal Carbon  Upstream DOC & NA POC=0 Vs base DOC = 3.0 mg/L, NA POC <1.0 mg/L  Non-Algal Carbon Adds up to 2.5 mg/L DO Deficit in summer

7 7 Summer DO Deficit Contributions  DO Deficit contributions: oNet chl-a -1mg/L oStockton RWCF < 1 mg/L oUS nonalgal carbon 2.5 mg/L oSOD < 1 mg/L

8 8 Simulations for DWSC Flows of 250, 750, 1,250, 1,500 & 1,750 cfs  Five Summer Flow Scenarios were run from June 1 to Sept 30 o250 to 1,250 cfs simulate varying diversions to the Old River based on summer 2001 average 1,400 cfs flow at Vernalis and approx 85% of SJR flow into DWSC at RRI split o1,500 & 1,750 cfs simulations increased flow at Vernalis to 2,100 cfs, adjusted boundary concentrations  Comparative Base Model is Summer 2001 with average flow of 425 cfs June to September  Five Flow Scenarios were run with the Stockton RWCF 2001 flows and concentrations and RWCF ammonia discharge concentrations = 2.0 mg/L

9 9 SJR DWSC Model Base & Five Simulated Flow Scenarios Near Sample location R3

10 Relationship of Summer Chl-a, Carbon & TSS to Flow at Vernalis for 1,500 and 1,750 cfs Scenarios  Chl-a adjusted in proportion to USJR average inflow concentrations  TSS=TSS + 20% TSS  DOC=3.0 mg/L, POC=0.5-Algal C Data: Data Atlas, Dahlgren, 2004, Kratzer, et al., 2004

11 Relationship of Summer Nutrients to Flow at Vernalis for 1,500 and 1,750 cfs Scenarios  Ammonia and DON about the same  Nitrite+Nitrate decrease at higher flows  Changes won’t effect algal growth-still enough nutrients  Phosphorus levels about the same-not shown Data: Data Atlas, Dahlgren, 2004, Kratzer, et al., 2004

12 Variable Flow Scenarios-TSS  As flows increase there is an approximate 28% increase in load to the DWSC for each 500 cfs increase: o Receiving Vol = 4.4MCM o Incremental Load: 1 mg/L*500cfs=1,200kg/d o Conc change for 1 mg/L: 1,200kg/d / 4.4MCM =0.28mg/L-d  TSS moves downstream at higher flows-less time for settling

13 Variable Flow Scenarios-Chl-a  750 & 1,250 cfs: Chl-a increases at R3 due to increased load  1,500 & 1,750 cfs: Chl-a load increase is offset by decreased chl-a at Vernalis and less time for algal processes at higher flows

14 Variable Flow Scenarios-DIN  Peak concentration from Stockton RWCF ammonia is reduced

15 Variable Flow Scenarios-DO  DO at R3 increases with increased flow due to higher USJR DO  Max DO Deficit moves downstream at higher flows  Less DO violations at higher flows

16 Number of DO Violations at Variable Flows  Base Model & 250 cfs-DO violations occur almost daily from June 1 to Sept 30, R3 to R7  As flows increase, # violations decrease, R3 to R6 but increase at R7 & R8  Violations tend to be closer to 5 or 6 mg/L at higher flows

17 Variable Flow Scenarios & Stockton RWCF Nitrification  Ammonia Discharge = 2.0 mg/L  NH 3 reduced from maximums of 0.75 mg/L to 0.1mg/L  Still enough DIN to have no effect on algal growth so DO difference is due to nitrification

18 Variable Flow Scenarios & Stockton RWCF Nitrification  Compared to simulations without nitrification there is little additional improvement in DO except at low flows

19 Number of DO Violations, Variable Flows With & Without Stockton RWCF Nitrification  Number of DO violations are somewhat reduced with Stockton RWCF NH 3 =2 mg/L

20 Impact of 10,000 lb/d O 2 Injection in the DWSC near Rough & Ready Island-June 1 to Sept 30  O 2 Injection greatest benefit is at R5 to R7 at 425 cfs  Greatest benefit might be to maintain flows above 750 cfs coupled with O 2 injection

21 Upstream SJR – Study Area for 1D DSM2 Model SJR at Stevinson, Salt & Mud Sloughs, Merced, Orestimba, Tuolumne & Stanislaus Drains (SLD), diversions, creeks, Modesto WWTP, groundwater & “add-water”

22 50% Reduction in Mud Slough Flow  Average Mud Sl. Q of 130 cfs is 4% of final average Vernalis Q  Mud Sl. summer NO 3 =15 mg/L, Chl-a=40 ug/L, TSS=55 mg/L  Mass balance US of Merced R. results in 1 mg/L reduction in TSS so no change in algal growth due to light regime change  Model results show no water quality impact at Vernalis DSM2 US of Merced R.DSM2 at Vernalis

23 Adaptive Management Summary  DWSC DO Deficit contributions: US nonalgal carbon 2.5 mg/L, SOD & Stockton RWCF NH 3 < 1mg/L, net chl-a –1 mg/L  Less DO violations at greater than 1,250 cfs DWSC flow  Regulating Old River Barrier to increase flow to the DWSC in the summer could improve DO  As flow increases maximm DO deficit moves downstream  Stockton RWCF nitrification will help DO somewhat  O 2 Injection will increase DO between R4 and R7, less at R3 & R8  50% Reduction of Mud Slough Flow to SJR will not improve SJR water quality at Vernalis

24 Additional Recommendations  Combination of increased DWSC flow and DO Injection would provide best improvement to DO in the DWSC  Lower flow scenarios – need data at lower flows for upstream boundaries  Use new upstream data/model results to drive boundary at Vernalis

25 Viewing RCA Output  Web based viewer can be linked to the SJR DO TMDL Website ohttp://  HydroQual Integrated Modeling System Viewer (HIMSv) for user oStand-alone executable program that displays HydroQual model results in a GIS environment oPlan view, time series & vertical slices with animation

26 3D Model Space (168 rows, 15 cols)

27 Model Folder Structure  HYDRO  Codes/Executable  Inputs – Base & Projections  Outputs – necessary files for RCA (Base Only, to large for all)  QUAL  Codes/Executable  Inputs – Base & Projections for BCs, PSs, parameters/constants, ICs  Outputs-Base only  HIMS-V – GIS Post Processor  RCA Output, shapefile, executable  ECOMSED, RCA, HIMS-V Users Manuals

28 ECOMSED/RCA Modeling Framework Transport Module Processes: Advection Dispersion Products Water Column Conc. Sediment Conc Water Quality Model RCA Processes DO, Algal, Carbon Sediment, TSS, nutrients: Hydrodynamic Model ECOM Processes: Water Movement Physics Temperature/Salinity Conservative Substances Particle Tracking Forcing Functions Tides Winds Rivers Products Water Levels Currents, Mixing Temperature/Salinity Conservative Substances

29  Surface Forcing Wind Stresses (Speed and Direction) Atmospheric Pressure Heat Fluxes  Lateral Boundary Tributary Inflows (Rivers, CSO, WWTP) Temperature and Salinity Sea Surface Levels (Tides, Low Frequency WL) Hydrodynamic Data Requirements

30 Input Files  ECOMSED executable codes o run_data o model_grid  Optional: o init_tands: spatially varying IC* o bfric2d.inp* o restart: for hot start*

31 ECOMSED outputs  For post processing: o gcmprt: standard output (ASCII) o gcmtsr: time series data at selected locations o gcmplt: grid-wide hydrodynamic information  For water quality modeling: o gcm_tran: hydrodynamic info o gcm_geom: geometric info (grid size, depth…) o wet_grid: active grid cell info o gcm_qdiff: CSO/SW/STP flows

32 RCA Model Input Structure  Main input file – contains general information for RCA run o Run/print options o Model systems o Integration type, time step, run length o Names of hydrodynamic transport files o Names of input files  Calls other input files-ECOM, PS, BC, IC, Constants

33 RCA Input Files  ECOMSED files needed o gcm_geom – model segment geometry info (DX, DY, land mask, etc) o wet_grid – water segments in grid o gcm_tran – flow, dispersion, volume info o gcm_qdiff – flow from diffuser inputs  Transport files are developed in 30-day periods for the full 2-yr model calibration /validation period

34 RCA Input Files  rca.inp – main input file  bcinp.a – time-variable BC file  psinp.a – time-variable PS file  pcinp.a – parameters/constants file  icinp.1 – IC file  sedinp.1 – sediment model input file  RCAFIC, RCAFICSED-Initial conditions for hot start

35 RCA Main Input File

36 RCA Main Input File

37 RCA BC input file

38 RCA PS input file

39 RCA PC input file

40 RCA PC input file

41 RCA IC input file

42 RCA Sediment input file

43 Running RCA Model  Models are compiled with Fortran77 to run on any PC  Most input files are created from stand alone Fortran programs that read data and format to RCA input structure  Once created they can be edited with a text editor (Notepad, GVIM) for minor edits or to view inputs

44 Running RCA Model  Create script so that required inputs and executable are linked or copied to run folder  Open DOS or CYGWIN window  Move to run folder  2-year calibr/valid period ~18 hours on mainframe

45 RCA Binary Output Files  RCAF10 – model info & global print times  RCAF11 – global output at all segments  RCAF12 – detailed dump print times  RCAF13 – detailed output at specific segments plus additional model output  RCAF14 – sediment global output  RCAFIC & RCAFICSED – water column & sediment IC (end of run for hotstart)

46 Viewing RCA Output  Takes a little time for output processing  Requires a number of programs: o GDPME – HQI in-house data processing and graphics program (reads RCA binary output files) o Requires Ghostscript and Ghostview for viewing Postscript files created by GDPME  RCA binary output files: RCAF*

47 Viewing RCA Output  HydroQual Integrated Modeling System Viewer (HIMSv) for user oStand-alone executable program that displays HydroQual model resultsint GIS environment oPlan view, time series & vertical slices with animation  Web based viewer can be loaded to the SJR DO TMDL Website ohttp://

48 Questions & Answers Contact info: Andy Thuman Laurie DeRosa HydroQual, Inc. Mahwah, NJ (201) x7184

49 Downstream – Study Area