User`s Manual
Contents
1. Berkeley Madonna User s Guide Version 8 0 University of California Department of Molecular and Cellular Biology Berkeley CA Meselhe E Arceneaux J and Waldon M G 2007 Mass Balance Model Version 1 01 LOXA 07 002 currently available at lt http loxmodel mwaldon com gt University of Louisiana Lafayette in cooperation with the U S Fish and Wildlife Service Lafayette LA Meselhe E A Griborio A G Gautam S Arceneaux J C Chunfang C X 2005 Hydrodynamic And Water Quality Modeling For The A R M Loxahatchee National Wildlife Refuge Phase 1 Preparation Of Data Task 1 Data Acquisition and Processing Report LOXA05 014 University of Louisiana at Lafayette prepared for the Arthur R Marshall Loxahatchee National Wildlife Refuge USFWS Lafayette LA Available online http sofia usgs gov lox_monitor_model advisorypanel data_acq_report html USACE 1994 Environmental Assessment Modification of the Regulation Schedule Water Conservation Area No 1 available at lt http mwaldon com Loxahatchee GrayLiterature USACE 1995 Lox Regulation Schedule pdf gt US Army Corps of Engineers Jacksonville FL USFWS 2000 Arthur R Marshall Loxahatchee National Wildlife Refuge Comprehensive Conservation Plan available at lt http loxahatchee fws gov gt U S Fish and Wildlife Service Boynton Beach Florida Waldon M G Meselhe E A Roth W B Wang H Chen C in prep2. The following equations set variables for precipitation P and evapotranspiration ET to the appropriate imported time series data values P PET day 1 m day ET PET day 2 m day where PET indicates the file of imported data being used day is the integer day of the simulation and the numerical value indicates a column in the imported dataset Once data are successfully imported the file name will appear in the Datasets window on the Madonna desktop Additionally it is important to note that imported data are saved directly in the Madonna model file mmd There is no dynamic link between these data and the parent spreadsheet therefore any changes to the time series data must be made in the parent csv or txt file and then re imported into the Madonna model 3 Comments Constant Values Arrays amp Equations SRSM Version 4 00 User s Manual Comments within the equation window provide model self documentation and are an important part of the SRSM documentation There are two alternative syntaxes for comments in Madonna Any text between left and right curly brackets is treated as a comment and not processed This form of comment can span multiple lines of text On a single line all text following a semi colon is also treated as a comment Additionally in imported text data files all characters on a line following the first non numeric character are ignored This allows comments identifying source or col
3. yt2 Loop End Sub Imported Datasets ol oil Cells z Cells z Cells z Cells z r r F 13 Value 13 14 Value 14 in order to create the spacing and increase the data in the correct order ie row by row in rows skipped by x 2 term Provided below is a list of all imported datasets and their respective variable names used in the SRSM Variable Name File Column Description P PET 1 Area average precipitation m day ET PET 2 Observed evapotranspiration m day 39_out OUTFLOW 1 Observed structure outflow m3 day G94A_out OUTFLOW 2 Observed structure outflow m3 day G94B_out OUTFLOW 3 Observed structure outflow m3 day G94C_out OUTFLOW 4 Observed structure outflow m3 day G300_out OUTFLOW 8 Observed structure outflow m3 day S5AS_out OUTFLOW 9 Observed structure outflow m3 day G301_ out OUTFLOW 11 Observed structure outflow m3 day G338_out OUTFLOW 15 Observed structure outflow m3 day S10E_out OUTFLOW 16 Observed structure outflow m3 day 10D_out OUTFLOW 17 Observed structure outflow m3 day 10C_out OUTFLOW 18 Observed structure outflow m3 day 10A_out OUTFLOW 19 Observed structure outflow m3 day G94A _in INFLOW 2 Observed structure inflow m3 day G94C _in INFLOW 4 Observed structure inflow m3 day G94D _ in INFLOW 5 Observed structure inflow m3 day ACME1 _in INFLOW 6 Observed stru
4. 0 1 1323 0 2 2274 0 3 3188 0 4 2832 0 5 4469 0 6 5901 0 7 7406 0 8 6602 0 9 6356 1 8116 Reduction factor amp Scale up S10 regulatory flows by ratio of total regulatory release S10 convert thousand m3 d to m3 d QoutCale RSQfact 196 7 144 8 1000 QoutCalcS10 The ratio 196 7 144 8 is the historic average annual total Refuge regulatory release volume divided by the average annual S 10 volume 5 Model Execution amp Post processing Berkeley Madonna s user interface for model execution and post processing is very simple in fact they can both be operated from a single location All operations needed for a general simulation run can be performed in the Graph window The provided image designates the pertinent buttons with which the user should be familiar however for explicit explanations on each button the Berkeley Madonna user s guide Macey et al 2000 should be consulted The model may be executed from the Graph window by pressing the Run button otherwise the user may select Run from the Compute menu eine Moin a V Ve Ve Wa TBE ECPI coven Joe Compute Fx Pape Ren gt lal olele fT P ofm oii Paun t 13405 steps in 0 785 seconde v ua n n iail is Figure 2 Graphical Output 13 SRSM Version 4 00 User s Manual Data Table Line Characteristics Overlay Plots Figure 3 Graph Toolbar Lock Graph After pressing the Run button Madonna
5. In version 4 models for stage and constituent concentration were combined into a single Madonna program Use of the Berkeley Madonna commercial numerical differential equation solver package allows greater clarity in coding supports shorter time steps obviating the need for the ad hoc procedures of version 1 and provides a well documented user interface Center for Louisiana Water Studies University of Louisiana at Lafayette gt A R M Loxahatchee National Wildlife Refuge U S Fish and Wildlife Service SRSM Version 4 00 User s Manual 1 1 General Description of Model Structure To calculate water volume the SRSM version 4 00 divides the Refuge into two compartments also termed boxes or cells Canal and Marsh with assumed constant areas of 4 03 million m and 560 02 million m respectively The rate of change of compartment volumes are calculated using the following differential equation which is based on the water budget for each compartment dV A P G ET dt Qnei i i where i denotes compartment marsh or canal V the compartmental volume m t time days Qnet total flow into a compartment m day A compartment surface area m P precipitation m day G loss due to groundwater seepage m day and ET loss due to evapotranspiration m day SRSM version 4 00 simulates the mass and concentration of chloride Cl total phosphorus TP and sulfate SO4 No
6. Observed sulfate concentration mg L S6_S04 S04 12 Observed sulfate concentration mg L G338_SO4 S04 13 Observed sulfate concentration mg L 4 Simulation Option Parameters Variable Name Default Value Explanation CalcQRo Distinguishes between calculated 1 or historic outflow 0 18 SRSM Version 4 00 User s Manual Qinscale 1 Scaling factor for structure inflow Qwsmult 1 Scaling factor for water supply demand RSQfact 1 Scaling factor for regulatory release SCALE_TPLOAD Scaling factor for total phosphorus load SCALE_CLLOAD Scaling factor for chloride load SCALE_SO4LOAD Scaling factor for sulfate load Distinguishes between timeseries data 1 or constant value coristTPConc 0 0 for inflow TP concentration constCLConc 0 Distinguishes tai tied coca constant value constSO4Conc 0 Distinguishes Dein oe value constTP_CONC 0 01 Constant value for TP inflow constCL_CONC 80 Constant value for CL inflow constSO4_CONC 30 Constant value for SO4 inflow SET 1 Distinguishes between initial condition sets for start date 1 1995 2 2004 3 2000 5 Model Parameters Variable Name Value Description Canal_Area 4033485 468 Canal surface area m2 Marsh_Area 560021212 8 Marsh surface area m2 Eo 4 62 Marsh bottom elevation m Eoc 3 24 Canal bottom elevation m Eb 3 5 Water stage ou
7. by http wwwalker net dmsta index htm SRSM Version 4 00 User s Manual dM jx PE qnet gload aload rload where i constituent j compartment number 1 4 k DMSTA calibration set Phosphorus only M mass g t time days qnet net mass flow in surface water g day gload loss to groundwater seepage and evapotranspiration g day aload gain from wet and dry deposition g day and rload loss to storage uptake release TP or reaction SO4 g day Detailed descriptions of the above equations can be found in the companion model manuscript Waldon et al 2009 1 2 Model Platform Berkeley Madonna The SRSM version 4 00 is implemented using the differential equations solver Berkeley Madonna version 8 3 9 Madonna which is a proprietary software developed by Robert I Macey and George F Oster This program is the backdrop for the code of the SRSM and while Madonna has some built in functions all SRSM components and processes are user defined in the Equations window the optional Madonna Flowchart window was not used in SRSM development in terms used in Madonna documentation SRSM is a plain text rather than a visual model Figure 1 shows the general format of the Madonna desktop These windows may be resized or closed by the user Each of these windows is discussed later in this document Madonna also has the capability to perform optimizations c
8. more obscure number 3 Madonna does identify constants during compilation and there is apparently no runtime cost associated with this programming style DEFINE ARRAYS REFUGE GEOMETRY ncell 4 total number of cells canal is cell ncell nm ncell 1 number of marsh cells canal ncell cell number for canal there is only 1 canal cell in version 4 00 CONSTITUENTS nconstit 3 cl 1 chloride conservative so4 2 sulfate monod relationship tp 3 tp modeled with DMSTA equations DMSTA CALIBRATION SETS emerg 1 Emergent marsh pew 2 Pre existing wetland SRSM Version 4 00 User s Manual Madonna has a unique notation for array operations Macey et al 2000 Equations imply looping through a range of subscripts through ranges specified on the left hand side of the equation see for examples sections 3 4 5 and 3 4 6 below The variables 1 j and k are reserved in Madonna to refer on the right hand side of the equation to the first second and third array index respectively of the variable on the left This notation replaces loops that are more commonly used in other programming languages 3 1 Runtime Options Madonna offers several numerical methods to solve ODEs The SRSM may be executed accurately and expeditiously using the RK4 fourth order Runge Kutta method The current SRSM is set up to simulate the 13 year period from 1995 to 2007 The user may specify the simulation period with the STARTTIME and STOPTIME funct
9. which allows the user to change values and reset them without directly changing the code Parameters with values modified from those set in the Equations window are flagged by an asterisk in the Parameters window Users are cautioned that if parameter values are changed using the Parameter window the altered values may persist in future model runs until they are reset Additionally the Overlay Plots Figure 3 button can be used to display multiple model runs on the same graph this feature is very helpful when visually assessing parameter alterations Lists of all parameters are given in the appendix of this document 3 3 Processes Model processes are those equations that contribute to state variable calculation e g groundwater seepage corrected evapotranspiration and reaction losses Such equations represent values that can change with each time step The user should consult the referenced material for more in depth discussions and explanations of model processes 3 4 State Variables Berkely Madonna has several ways to code state variables The SRSM uses the d dt option to define differential equations All SRSM differential equations are given below It is necessary to specify an initial value for all state variables using the INIT initializer syntax This version of the SRSM directly calculates the change in volume of the Canal and Marsh compartments as per the 2 compartment structure described by Arceneaux et al 2007 The sta
10. will automatically output several variables from the model in the Graph window To specify which variables to output the user can double click in the window and choose them from a list or select Choose Variables from the Graph menu Once the desired variables are chosen and a model run is complete the user may print the graph directly from Madonna or export the data as csv or txt To export data the table must be displayed in the Graph window by clicking the Data Table button see Figure 3 Then the user can select Export Table from the File menu or use the Copy Table selection under the edit drop down menu 14 SRSM Version 4 00 User s Manual For further information users may contact the authors by email at Dr Ehab Meselhe meselhe louisiana edu Dr Mike Waldon mike mwaldon com or William Roth wbr9736 louisiana edu Citations Arceneaux J 2007 The Arthur R Marshall Loxahatchee National Wildlife Refuge Water Budget and Water Quality Models MS Thesis University of Louisiana Lafayette LA Arceneaux J Meselhe E A Griborio A and Waldon M G 2007 The Arthur R Marshall Loxahatchee National Wildlife Refuge Water Budget and Water Quality Models Report No LOXA 07 004 currently available at lt http loxmodel mwaldon com gt University of Louisiana at Lafayette in cooperation with the U S Fish and Wildlife Service Lafayette Louisiana Macey R Oster G and Zahnley T 2000
11. 4 6 Mass Differential Equations COMPARTMENT 1 d dt mass 1 nconstit 1 emerg pew qload i 1 k qload i 2 k aload i 1 gload i 1 k rload i 1 k COMPARTMENT 2 d dt mass 1 nconstit 2 emerg pew qload i 2 k qload i 3 k aload i 2 gload i 2 k rload i 2 k COMPARTMENT 3 d dt mass 1 nconstit 3 emerg pew qload i 3 k aload i 3 gload i 3 k rload i 3 k COMPARTMENT 4 d dt mass 1 nconstit canal emerg pew sload i j k qload i 1 k aload i canal gload i canal k rload i canal k 3 4 7 Initial Storage Values INIT dmsta_store tp 1 nm emerg pew init_storage i j k g m2 3 4 8 Storage Differential Equations d dt dmsta_store tp 1 nm emerg pew upPrM2 i j k Releaseli j k Buriall i j k arealj 3 5 Volume Stage Relationship SRSM version 4 00 is structured to incorporate a storage stage relationship for both the marsh and canal compartments To maintain consistency with the earlier model version a constant surface area is currently assumed for each compartment resulting in a linear relationship between storage volume and stage Canal Ec and marsh Em stage values in meters are calculated using the GRAPH capability of Madonna Future versions of the SRSM could include a more detailed volume stage relationship However performance of the model is good without the addition of this complexity Stage m NGVD 29 is currently calculated usin
12. 443495 2 364 443495 2 x 3650 999 0 000093 0 0018 659921 4 443495 2 364 443495 2 x 3651 O 0 0026 435837 3 440314 6 365 440314 6 x 3651 999 O 0 0026 435837 3 440314 6 365 440314 6 x 3652 0 000957 0 0015 450883 9 319501 5 366 319501 5 x 3652 999 0 000957 0 0015 450883 9 319501 5 366 319501 5 x Figure 4 Sample Excel Spreadsheet 2 Data Formatting with VBA Sub LoopRangel have x amp z start at row 2 have y start at row 3 x 2 Z 2 y 3 loop until a blank row is found for the purposes of this we need a column of 7306 in order to separate the input data appropriately note that this is set up for data to be read only in column 2 date column and for the sorted data to be output in columns B C D E F and G 3653 2 values Do While Cells x 1 Value lt gt This will put the values of the 9th column I in the 2nd column B such that data abcd become aabbccdd Cells x 2 Value Cells z 9 Value Cells y 2 Value Cells z 9 Cells x 3 Value Cells z 10 Value Cells y 3 Value Cells z 10 Cells x 4 Value Cells z 11 Value Cells y 4 Value Cells z 11 Cells x 5 Value Cells z 12 Value Cells y 5 Value Cells z 12 16 SRSM Version 4 00 User s Manual Cells x 6 Value Cells y 6 Value Cells x 7 Value Cells y 7 Value increse the value of x by 2 value of z by 1 to read the Y increases by 2 to insert data xt 2 z z4 1
13. A R M Loxahatchee National Wildlife Refuge Water Quality Modeling Rates Constants and Kinetic Formulations Report No LOXA009 003 University of Louisiana at Lafayette in cooperation with the U S Fish and Wildlife Service Lafayette Louisiana 15 Appendix SRSM Version 4 00 User s Manual 1 Example Spreadsheet Format A 68 MMe T FT T wT tT s tT Kk L OM N 0 1 2 3 4 5 6x 1 Orig 2 Orig 3 Orig 4 Orig 5 Orig 6 Orig O 0 000087 0 00169 1838840 7106052 1 7106052 x 0 000087 0 00169 1838840 7106051 836 1 7106051 836 0 999 0 000087 0 00169 1838840 7106052 1 7106052 x O 0 0024 1892298 7237825 712 2 7237825 712 1 O 0 0024 1892298 7237826 2 7237826 x 0 000097 0 0021 2162085 6986682 222 3 6986682 222 1 999 O 0 0024 1892298 7237826 2 7237826 x 0 008411 0 0019 646000 3 6033070 94 4 6033070 94 2 0 000097 0 0021 2162085 6986682 3 6986682 x 0 004089 0 001 2638046 5307923 166 5 307923 166 2 999 0 000097 0 0021 2162085 6986682 3 6986682 x 0 000216 0 002 4257818 555959 474 6 555959 474 3 0 008411 0 0019 646000 3 6033071 4 6033071 x 0 005072 0 0008 1856578 5478255 458 7 478255 458 3 999 0 008411 0 0019 646000 3 6033071 4 6033071 x 0 006708 0 0023 2683455 5464799 158 8 5464799 158 0 001 2638046 5307923 5 5307923 x O 0 0027 3006431 6728223 398 3 6728223 398 928998 5 861937 2 861937 2 x 3549 999 0 000097 0 0014 928998 5 861937 2 363 861937 2 x 3650 0 000093 0 0018 659921 4
14. A R M Loxahatchee National Wildlife Refuge Simple Refuge Screening Model v 4 0 User s Manual Ehab A Meselhe Michael G Waldon William B Roth Prepared for the U S Fish and Wildlife Service under a cooperative agreement with the University of Louisiana Lafayette Report LOXA009 002 April 2009 SRSM Version 4 00 User s Manual A R M Loxahatchee National Wildlife Refuge Simple Refuge Screening Model Version 4 00 Report LOXA009 002 User s Manual Ehab Meselhe Mike Waldon William Roth 1 Introduction As restoration of the Arthur R Marshall Loxahatchee National Wildlife Refuge Refuge continues there is a need for a simple quantitative methodology for predicting impacts of proposed management changes on Refuge stage The Simple Refuge Screening Model SRSM simulates the water budget regulation schedule implementation and constituent dynamics for chloride Cl sulfate SO4 and total phosphorus TP This document presents the model in a format that provides users with an understanding of both the theory and implementation of the SRSM The objective is to give users the ability to accurately simulate various water need scenarios for the Refuge in order to gain a better understanding of this wetlands system and its dynamics This manual assumes that the reader is generally familiar with the location Refuge hydrologic features and with water quality issues relevant to the Refuge For more information users are dire
15. ary CL txt 14 Chloride concentration values mg L INFLOW txt 20 Historic inflow values m3 d OUTFLOW txt 20 Historic outflow values m3 d PET txt 3 Precipitation and Evapotranspiration m d ee 6 ees SO4 txt 14 Sulfate concentration values mg L TP txt 14 TP concentration values mg L Table I SRSM input files Users may create data files for import in any spreadsheet editing program Madonna imports data files in either tab delimited text format or comma separated values CSV format The preloaded input files in the SRSM are primarily derived from data downloaded from the South Florida Water Management District s database DBHYDRO Although these data are readily available and methods of preparation documented Arceneaux 2007 Meselhe et al 2005 it is strongly suggested that the user first run model simulations with the preloaded datasets http www sfwmd gov portal page _pageid 2894 19708232 amp _dad portal amp _schema PORTAL SRSM Version 4 00 User s Manual 2 1 Spreadsheet Formatting The Berkeley Madonna software imports time series data from a 2 dimensional array dataset The first column of the array is the time value in days of the simulation beginning with zero and increasing monotonically to the final simulation day in this case 0 to 4747 Madonna applies linear interpolation between data values In order to avoid interpolation in the time series data the user is encouraged to f
16. cted to the Refuge Comprehensive Conservation Plan USFWS 2000 This manual describes version 4 00 of the SRSM SRSM version 1 was implemented by Jeanne Arceneaux and others Arceneaux 2007 Arceneaux et al 2007 Meselhe et al 2007 as a daily water budget using Microsoft Excel the results from this model were then used to drive the constituent model The constituents were modeled by WASP a program developed by the United States Environmental Protection Agency Although there were advantages in using a commonly available spreadsheet program paired with a proven robust constituent modeling tool there were also some clear disadvantages The version implementation was complex and did not easily lend itself to modification The workbook file was large and its size grew as more days were simulated Additionally the limitation of using a one day step size required ad hoc procedures to avoid instability of the solution Finally the constituent models in WASP are limited to those provided in the closed source executable from the USEPA These factors and a desire to have a single consistent model platform led to porting the stage and water quality models to the STELLA http www iseesystems com index aspx simulation platform version 2 Version 3 of the models ported the earlier version programs to the Berkeley Madonna http www berkeleymadonna com index html simulation platform In versions 2 and 3 stage and constituent models were separate
17. cture inflow m3 day 362_in INFLOW 7 Observed structure inflow m3 day G300_in INFLOW 8 Observed structure inflow m3 day S5AS in INFLOW 9 Observed structure inflow m3 day S5A_in INFLOW 10 Observed structure inflow m3 day G301_in INFLOW 11 Observed structure inflow m3 day G310_in INFLOW 12 Observed structure inflow m3 day G251_in INFLOW 13 Observed structure inflow m3 day S6_in INFLOW 14 Observed structure inflow m3 day G338_in INFLOW 15 Observed structure inflow m3 day 10A_hurricane Regulation 1 Supplementary emergency water release m3 day 10C_hurricane Regulation 2 Supplementary emergency water release m3 day 17 SRSM Version 4 00 User s Manual 10D_hurricane Regulation 3 Supplementary emergency water release m3 day 39_WS Regulation 4 Supplementary water supply release m3 day G94A_TP TP 1 Observed total phosphorus concentration mg L G94C_TP TP 2 Observed total phosphorus concentration mg L G94D_TP TR 3 Observed total phosphorus concentration mg L ACME1_TP TP 4 Observed total phosphorus concentration mg L 362_TP TP 5 Observed total phosphorus concentration mg L G300_TP TP 6 Observed total phosphorus concentration mg L S5AS_TP We 7 Observed total phosphorus concentration mg L S5A_TP TP 8 Observed total phosphorus concentration mg L G301_TP TP 9 Observed total phosphorus concentration
18. g constant area Vc m3 Ec m Area Canal 4033485 467 m2 Ec GRAPH Vc 13068492 91 0 0 3 24 Canal bottom elevation 27266361 76 10 11 SRSM Version 4 00 User s Manual Vm m3 Em m Area Marsh 560021212 8 m2 Em GRAPH Vm 2587298003 0 0 4 62 Marsh bottom elevation 3012914125 10 4 Regulation Schedule This document assumes that SRSM users are familiar with this WCA 1 Regulation Schedule USACE 1994 as its specifics are not included here A description of the Regulation Schedule is available in the Arthur R Marshall Loxahatchee National Wildlife Refuge Comprehensive Conservation Plan USFWS 2000 The following sub sections present the Regulation Schedule model code which appears in the Madonna Equations window The variables A1FloorFeet and BFloorFeet are the stage in feet NGVD of the bottom of the Al and B Regulation Schedule zones respectively For consistency with the SRSM these variables are converted to meters A1FloorFeet GRAPH DayofYear 0 17 2 132 15 75 188 15 75 267 17 5 334 17 5 366 17 2 Floor of A1 Zone ft BFloorFeet 14 Floor of B Zone ft A1Floor A1FloorFeet 0 3048 A1 Floor m BFloor BFloorFeet 0 3048 B Floor m 4 1 SRSM Regulatory Release A regulatory release is a discharge of water out of the Refuge that occurs as a result of the Refuge stage in relation to the Regulation Schedule Magnitude of outflow during a regulatory release is
19. ge is then calculated from the volume It must be noted that the area of the compartments is constant i e it does not change with stage The calculated value for the exchange flow canal to marsh flow is used to drive the volume differential equations for the 4 compartment constituent model 3 4 1 Initial Volume Values 2 compartment Model INIT vol_canal Ecinit Eoc Canal_Area Initial Canal Volume m3 INIT vol_marsh Eminit Eo Marsh_Area Initial Marsh Volume m3 3 4 2 Volume Differential Equations 2 compartment Model d dt vol_canal NetInFlow Exchange_Flow P Gc ETc Canal_Area d dt vol_marsh Exchange_Flow P Gm ETm Marsh_Area 3 4 3 Initial Volume Values 4 compartment Model INIT vol 1 nm Eminit Eo areali INIT vol canal Ecinit Eoc area canal 3 4 4 Volume Differential Equations 4 compartment Model 10 SRSM Version 4 00 User s Manual d dt vol canal d dt vol 1 nm Qin Qout Exchange_Flow P ETc Gc area canal P ETm Gm area i Exchange_Flow qmcfactor i In addition to volume state variables the SRSM calculates storage and constituent mass similarly 3 4 5 Initial Mass Values Chloride Only INIT mass cl 1 emerg pew D_MO area 1 INIT_Concfi j k INIT mass cl 2 emerg pew D_MO area 2 INIT_Concli j k INIT mass cl 3 emerg pew D_MO area 3 INIT_Concli j k INIT mass cl canal emerg pew D_CO area canal INIT_Conc i j k 3
20. ial rate 1 yr K3 pew 0 6631 Phosphorus Pre existing Wetland burial rate 1 yr mindepth 0 05 Minimum water depth m 20
21. ions Model coding for the runtime parameters is given below 3 1 1 Code METHOD RK4 STARTTIME 0 JAN95 3287 JAN04 1826 JANOO STOPTIME 4747 DEC07 3652 DEC04 4382 DEC06 DT 0 005 DTOUT 1 By default Madonna saves model output every calculation time step which can become costly as model size and complexity increases The built in variable DTOUT defines the time period that elapses between data storage for a simulation run Setting DTOUT can reduce memory requirements Here SRSM output is stored every one time unit i e one day If the user desires to store all output data then DTOUT should be set equal to zero or alternatively the DTOUT statement can be removed 3 2 Parameters These values fall into two categories for the SRSM code simulation option parameters and model parameters The simulation option parameters are given at the beginning of the model code found in the Equations window These allow some flexibility with model calculations input data and initial conditions The user can choose outflow type scale flow and constituent load choose time series or constant values for boundary concentration and choose different initial condition sets The remaining parameters are calibrated and calculated values needed for an accurate base simulation of the SRSM SRSM Version 4 00 User s Manual All model parameters constant values that are not arrayed can also be viewed in the Parameters window
22. mg L G310_TP TP 10 Observed total phosphorus concentration mg L G251_TP TP 11 Observed total phosphorus concentration mg L S6_TP TP 12 Observed total phosphorus concentration mg L G338_TP TP 13 Observed total phosphorus concentration mg L G94A CI CL 1 Observed chloride concentration mg L G94C_Cl CL 2 Observed chloride concentration mg L G94D_Cl CL 3 Observed chloride concentration mg L ACME1 Cl CL 4 Observed chloride concentration mg L 362_Cl CL 5 Observed chloride concentration mg L G300_Cl CL 6 Observed chloride concentration mg L S5AS Cl CL 7 Observed chloride concentration mg L S5A_Cl CL 8 Observed chloride concentration mg L G301_Cl CL 9 Observed chloride concentration mg L G310_Cl CL 10 Observed chloride concentration mg L G251_Cl CL 11 Observed chloride concentration mg L S6_Cl CL 12 Observed chloride concentration mg L G338_Cl CL 13 Observed chloride concentration mg L G94A_SO4 S04 1 Observed sulfate concentration mg L G94C_S04 S04 2 Observed sulfate concentration mg L G94D_S04 S04 3 Observed sulfate concentration mg L ACME1_S04 S04 4 Observed sulfate concentration mg L S362_S04 S04 5 Observed sulfate concentration mg L G300_S04 S04 6 Observed sulfate concentration mg L S5AS_S04 S04 7 Observed sulfate concentration mg L S5A_S04 S04 8 Observed sulfate concentration mg L G301_S04 S04 9 Observed sulfate concentration mg L G310_S04 S04 10 Observed sulfate concentration mg L G251_S04 S04 11
23. nna SRSM users are strongly urged to consult the user s guide before attempting to run or manipulate any of the model components All parameter values represent those used to accurately validate and calibrate this model discretion should be used when altering these values This model is set up to simulate a 13 year 1995 2007 period All time series data needed to successfully run the model are stored within the model file This manual provides the user with the background and understanding needed to revise this model simulation for other user selected time periods or scenarios Should the user want to simulate another time period or alternative conditions the proper data must be obtained properly formatted and imported into the model SRSM Version 4 00 User s Manual 1 4 4 Because of the level of spatial aggregation in the SRSM the SRSM is not appropriate for applications that involve site specific events All results should be considered as spatial average values for the area of study 1 4 5 This document offers a brief summary of model theory and equations Users should consult the referenced documentation the model code and the companion manuscript for more in depth descriptions of equations and calibration parameter values 2 Data Preparation This section describes how to import the necessary time series text files The 7 separate data input files are outlined in Table 1 pen Data Vectors Summ
24. not specified within the Regulation Schedule It is therefore necessary to make assumptions related to water management in order to model regulatory releases The prior version of the SRSM modeled regulatory releases based on historic discharges 4 2 Regulatory Release Calculations This section describes calculations used in the Regulation Schedule Outflow is calculated when the CalcQRo value in the simulation option parameters section is set to a value of 1 conversely a value of O uses historical outflow in the model simulation The calculated outflow only represents regulatory releases from certain structures SIOACDE and S39 therefore historic outflows from other structures in the Refuge must be imported to supplement the calculated outflow Qout IF CalcQRo 0 THEN QoutHistoric ELSE QoutCalc QWaterSupply Qout_HistStruct Qout_hurricane Qout_HistStruct G94A_out G94B_out G94C_out G300_out S5AS_out G301_ out G338_out Structures in the north and east involved with water supply 12 SRSM Version 4 00 User s Manual Regulatory release thousand m3 d as a function of difference between stage and A1 zone floor ft This is based on historic S10 flow 1 1 1995 8 31 2007 initially copied from file CA1 elevations xls QoutCalcS10 GRAPH Ec A1Floor 0 3048 1 3 0 1 2 32 1 1 113 1 64 0 9 94 0 8 148 0 7 311 0 6 238 0 5 175 0 4 328 0 3 288 0 2 450 0 1 765 0 957
25. ormat the time series such that there are two values the same value for each time period e g t1 000 5 656 and ti 999 5 656 thus the imported data become similar to a step function To minimize the effort a data organization subroutine may be written into a Visual Basic for Applications VBA module in Microsoft Excel Additionally the user must note that text and other non numerical symbols will not be imported into Madonna in fact the importing process will cease if Madonna encounters such a symbol As a reference an abbreviated example spreadsheet along with its VBA data organization subroutine is provided in the Appendix of this document 2 2 Importing Data Once a dataset has been created it may be imported into Madonna by choosing Import Dataset from the File menu The user is then prompted to specify the dataset type and filename in this case all datasets are entered as 2D and given a specified filename per Table 1 the file extension should not be included Madonna syntax requires that the name of the input file be preceded by a pound sign Typically for 2 dimensional datasets a timing variable must be given this variable tells Madonna at which times to read imported data A simple solution is to use the build in function named TIME In Madonna the syntax TIME represents a linear function that counts from the specified start time STARTTIME value to the specified stop time STOPTIME value based upon the time step DT
26. sses Exchange_Flow Comt HGJ ECEm Flow ftom canal to marsh m3 day Const BIOT WRadias Constant used in the Power Law flow equation 1 mday Ge Iseep ECEb Canal seepage loss myday Gm reeep Em Eb Marsh seepage loss m day This run compares the Sa ECPBase scenano run with SRSM cakutated stages The onty parameters changed in the SRSM for thes ron are related to the calculated outflow fo regulatory releases n an mutial run parameter AIF chpnged to Oytich results in no regulatory releases below the canal At door stage The paramet na Curve Ft camganng SRSM calculated canal stage Ec to ti ti ISFVMM The current version allows regulatory release fows to be cakulated using the GRAPH fe ction Re Regulatory roleares may be based on the ECPBASE run or on average values historic discharges theough ut Ow pear dararia Water supply may be scaled to historic values the leve in the ECPBASE model un This is Smyk adjusted by commenting out appropnato lines appopnate Figure I Madonna model desktop 1 3 User s Manual Objectives This manual presents the pertinent information required for users to understand the components of SRSM i e imported data SRSM equation format and post processing methods Ultimately users should use this document as a companion for the model to assure accurate execution and interpretation 1 4 Caveats 1 4 1 1 4 2 1 4 3 If unfamiliar with Berkeley Mado
27. te that TP mass is measured as phosphorus not phosphate and SO4 mass is measured as sulfate not sulfur The compartmental design for these calculations differs from the water balance simulation Here a concentric arrangement of 4 compartments is used to represent the Refuge Compartments 1 3 disaggregate the water budget marsh compartment compartment 4 represents the canal Exchange flow is calculated in the marsh based on compartment surface area ratios Calculation of flow between marsh cells 1 2 and 2 3 is made using a flat pool assumption and is analogous to a tidal prism flow calculation All constituents are simulated based on a mass balance equation The loading terms of the mass budget gnet gload and aload are similar in all three constituents However the reactive load term rload is uniquely structured for each constituent Chloride is modeled as a conservative constituent with zero reactive load Its mass is lost or gained solely through the transport of water into or out of the system therefore the rload term in the following equation should be ignored when chloride is considered Total Phosphorus TP dynamics are approximated with equations adapted from those presented in the Dynamic Model for Stormwater Treatment Areas DMSTA developed by Walker and Kadlec Finally sulfate SO4 dynamics are simulated using a Monod relationship Thus a general equation for the rate of change of constituent mass in a compartment is given
28. tside Refuge m Iseep 0 042 Canal seepage constant 1 day rseep 0 000349076 Marsh seepage constant 1 day B 30 Transport coefficient 1 m day Radius 13000 Average marsh radius m Ww 81500 Average marsh width m ETMin 0 2 ET reduction factor HET 0 25 ET depth reduction boundary m area 1 89359148 07 Surface area of compartment 1 m2 area 2 224100185 Surface area of compartment 2 m2 area 3 246561879 8 Surface area of compartment 3 m2 19 SRSM Version 4 00 User s Manual area canal 4033485 467 Surface area of compartment 4 m2 evap 0 65 Fraction of ET that is evaporation transp 0 35 Fraction of ET that is transpiration WetDep cl 2 Chloride concentration in rainfall mg L DD cl 1136 Chloride dry deposition mg m2 yr WetDep so4eco 1 Sulfate concentration in rainfall mg L DD so4eco 138 2 Sulfate dry deposition mg m2 yr WetDep dmsta_constit 0 01 Phosphorus concentration in rainfall mg L DD dmsta_constit 10 Phosphorus dry deposition mg m2 yr khalfSO4 1 Sulfate half saturation constant g m3 MaxSO4Removal 14 4 Maximum sulfate removal g m2 yr benthic 0 Internal loading rate for the canal g m2 day K1 emerg 0 1064 Phosphorus ae maximum uptake K1 pew 0 221 Phosphorus Sane Baty maximum uptake K2 emerg 0 002 Phosphorus Emergent nee recycle rate m2 mg K2 pew 0 0042 Phosphorus Sine tie recycle rate K3 emerg 0 3192 Phosphorus Emergent Wetland bur
29. umn names to be included within these files Equation syntax in Berkeley Madonna is similar to that in other programming languages such as Basic or FORTRAN The value calculated on the right hand side of an equals sign is assigned to the variable on the left hand side Unlike common programming languages but similar to spreadsheets Berkeley Madonna is non procedural meaning the ordering of the equations is not significant Berkeley Madonna effectively sorts the equations in order to calculate the value of variables before they are used in subsequent calculations the program recognizes circular references if such a sorting can not be accomplished Macey et al 2000 Many of the SRSM equations have been consolidated by using arrays Such equations are set up by using the square brackets for the values to be arrayed There are 3 sets of arrayed variables constituents compartment and DMSTA calibration sets For all equations displayed in sections labeled 3 4 3 8 the user can see examples of arrayed initial conditions and differential equations Labels for each of the arrayed variables are given below Arrays are used extensively in SRSM to express equations that are repeated for a range of cells or constituents Many of the array index values have been programmed as constants to enhance clarity of the code For example the equation tp 3 defines a constant named tp that can be used as an array index subscript in place of simply the
30. urve fitting and sensitivity analyses For a comprehensive description of all pre programmed functions users of the SRSM are encouraged to download the Madonna user s guide from www berkeleymadonna com Additionally users may download a demo version of this software from the Berkeley Madonna web site and run this version of the SRSM version 4 00 However while the demo version of the Madonna program allows users to modify and run models the demo version does not allow the user to save model files or output of any kind Available for download at http loxmodel mwaldon com SRSM Version 4 00 User s Manual ana Stage Model Fie bk Piht Mode Opte Gah Parameters Widow mi Osa gt e St Option 2 Regulatory cebease housed m3 day as function of diference between stage and Al rane foor t Thes is based on reduced ECPBASE VMM 510 flow QowCakS Ec A1 FlooryO 3048 10 0 BO 52 45 3 14 2 11 amp 1 14 0 1255 1 1155 351 48382 5 12015 6 1 Reduction ior sa thousand OotCak foor 8 Option 3 Regutat e QI i mAd at a fonction of diference between stage and Al zone Thes is based on elevations 1s CoutCaicS10 08 148 OTIM 0623 aes WAL os DEEI e VI rs 7 Ta eye 95 SS atts Reduction factor amp Scale up S10 regulatory Sows by ratio of total regulatory release S10 convert thousand md to me QoutCaic RSOtact 196 7 144 87100 OowCake S10 svenan Proce
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