APPENDIX B1
Contents
1. gt e file El stats 20and 20calculations html 1 1 15 2013 2 09 40 PM APPENDIX A RUN_DATA FILE DOCUMENTATION DATA GROUP Computational and Output Characteristics Comment COM user specified comment for run information Comment Run Options COM header for run options A1 Run Options HYDTYPE INTERNAL use internal ECOM hydrodynamics EXTERNAL use external hydrodynamics input from tran file WAVEDYN NEGLECT no effect of surface waves on bottom friction SMBMODEL include effects of waves bottom friction internal calculation of waves using SMB theory DONMODEL include effects of waves on bottom friction internal calculation of waves using Donelan Theoty EXTERNAL include effects of waves on bottom friction wave parameters input from wave input file external calculation using WAM or HISW A TRACER INCLUDE dissolved tracer transport will be simulated NEGLECT no simulation of dissolved tracer transport SEDTRAN INCLUDE sediment transport will be simulated NEGLECT no simulation of sediment transport CHEMTRAN INCLUDE sediment bound tracer transport will be simulated NEGLECT no simulation of sediment bound transport SEDTYPE BOTH cohesive non cohesive sediment transport MUD cohesive sediment transport only SAND non cohesive sediment transpo2. time control is in number of timesteps If the OPTAVG is in hour and AVGE is not an integer multiple of timestep ECOMSED will stop and ask for another AVGE period IPLTFORM ji PLTZERO OPTAVG C2 Averaging Interval for Skill Assessment GCMTSR File a Comment COM user specified comment b Averaging Interval ISKILL interval in number of time steps for averaging the elevations temperature salinity and currents and cross sectional fluxes for user specified grid elements 0 no element stored in gemtsr for skill assessment NOTE If ISKILL 0 then go to Data Group C6 Computational Results for Water Quality Model C3 Computed Time Series for Elevations Comment COM user specified comment Number of Grid Elements EPTS number of grid elements for which time series of elevations are to be stored in gemtsr NOTE If EPTS 0 then go to Data Group C4 Computed Time Series for Currents Temperature and Salinity Location of Grid Elements INXIE I number of grid element NXJE J number of grid element C4 Computed Time Series for Currents Temperature Salinity and Transport Quantities Comment COM user specified comment for computed time series for temperature salinity and currents Number of Grid Elements VPTS number of grid elements for which time series of temperature salinity and currents are to be stored in gemtsr NOTE If VPTS 0 then go to Data
3. Step 1 9 Input the point source discharges for data group G2 1 Define the number of point source discharges 2 Define the grids and the distribution of the flows over the vertical Input the time series data for each point source flow temperature and salinity by defined grid as block data using the ACCESS database DIRECTPS accdb a This database contains one primary data table Direct PS flows which includes monthly discharges directly to Tampa Bay from Howard F Curren and the City of Clearwater North and Northeast facilities b Final Access table DIRECTPS c Export to DIRECTPS xls i remove header row Row 1 ii set format to 5 decimals iii set column width to 11 in Excel file d Save DIRECTPS prn e Run executable DIRECTPS exe f Creates formatted file for putting into run data DIRECTPS Step 1 10 Input the groundwater inflows for data group G3 1 Define the number of zones in the groundwater map 2 Input the time series data for each zone including flow temperature and salinity using the ACCESS database GROUNDWATER accdb a This database contains one primary data table GW flows which includes the time invariant inflows to 5 bay regions b Final Access table GW c Export to GW xls i remove header row Row 1 ii remove column B iii set format to 6 decimals iv set column width to 10 in Excel file d Convert to GW prn e Run executable G
4. Residuals Min 1Q Median 3Q Max 4 692 0 464 0 007 0 662 2 236 Coefficients Estimate Std Error t value Pr t Intercept 0 1897 0 4271 0 44 0 66 actual 0 9722 0 0176 55 16 lt 2e 16 Signif codes 0 0 001 0 02 0 05 0 1 1 Residual standard error 1 04 on 118 degrees of freedom Multiple R squared 0 963 Adjusted R squared 0 962 F statistic 3 04e403 on 1 and 118 DF p value lt 2e 16 Error EPC47 TB error lt EPC47_TB2 actual EPC47_TB2 interp RMSE and ME functions RMSE lt function EPC47_TB error sqrt mean EPC47 TB error 2 mae function EPC47_TB error 47 error me lt function 7 error mean EPC47 TB2 actual EPC47 TB2 interp Statistics RMSE EPC47 RMSE EPC47 TB error RMSE EPC47 TB round lappl y RMSE EPC47 TB round 1 RMSE EPC47 TB round file El stats 20and 20calculations html 1 1 15 2013 2 09 40 PM Statistics and Calculations R 1 1 1 3 MAE EPC47 TB lt mae EPC47 TB error MAE 47 TB round lapply MAE 47 TB round 1 MAE EPC47 TB round L E11 1 1 1 MESEPCATSTB lt me EPCAT TS en oni ME EPC47 TB round lappl y ME EPC47 TB round 1 ME_EPC47_TB_round 1 1 0 8 R2 EPC47 TB summary EPC47 TB Im r squared R2 47 TB round lapply R2 47 TB round 2 R2 EPC47 TB round 1 1 0 96 lt length EPC47 TB2 1
5. GCMTSR and Wave out GCMPLT GCM TRAN GCM GEOM WATER QUALITY MODEL HYDRODYNAMIC MODEL Calibration Data Analysis Files ECOLOGICAL MODEL OPTICAL MODEL FIGURES epc_plots_Rcode R CUplots_Rcode R TandSBCPlots R Model WL_Plots_rcode R HYDRODYNAMIC MODEL Calibration Observed Data HYDROCALIB accdb STATISTICS Data Analysis Products OBSERVED DATA Calibration Data Analysis Files epc_stats_Rcode R CU_stats R TandSBCstats R WL stats Rcode R Figure 2 Hydrodynamic Output File Structure Post Processing GCMTSR to create txt time series files A program has been provided with the model run files called tsrdat exe This program reads the GCMTSR binary file and creates a series of txt files The txt files each then correspond to associated data files that are used for comparison of the model results to the data files The txt data files and the txt output files from the model base run are provided on the hard drive included with the presentation Tables 1 through 4 below show the one to one correspondence of the txt files from the model with the txt files from the data When the tsrdat exe program is run two files are created these are HeaderData txt and tsrhdr txt These files provide the structure and order of the data within the post processed model files Post Processing Wave out to create txt time series files A program has been provided with the model
6. DATA GROUP Hydrodynamic Characteristics Comment Constants of the Model Problem COM header for Constants of the Model Problem 1 Constants of the Model Problem BFRIC ZOB NU THETA ALPHA TLAG NWAVE BCTYPE minimum bottom friction coefficient non_dimensional If user wants to specify spatially variable 2D bottom friction coefficients specify BFRIC as 6X A4 and provide bfric2d inp file Please refer to Table 10 26 for more details of format specification of bfric2d inp file bottom roughness coefficient in meters coefficient in time filter dimensional 0 1 recommended value weighting factor 0 1 0 explicit and 1 implicit scheme 0 225 recommended value advection time scale for temperature and salinity at the boundary time HOURS over which the boundary values reach their full specified value during the flood cycle from the values exiting at the end of the ebb cycle Caution If the user does not want boundary relaxation V folding specify ALPHA 0 friction time scale Hours for barotropic radiation boundary condition only needed if user selects BCTYPE as PCLAMP number of time steps between each update of bottom friction coefficient only used if WAVEDYN is not NEGLECT This defines the interval in time steps that the wave model is called baratropic radiation boundary condition types CLAMPED clamp boundary conditio
7. Discharges in Loops Location of Grid Elements Vertical Distribution of Intake Outfall Diffuser Discharge IDD inumbet of grid element diffuser enters leaves JDD j number of grid element diffuser enters leaves VDDIST percentage not fraction of total discharge DQDIFF apportioned each model layer from surface to bottom at location IDD JDD d Time of Observation TIME time in hours 0 0 for initial time e Discharge Data QDIFF diffuser discharge in m sec f Temperature Data TDIFF temperature of diffuser discharge in f Salinity Data SDIFF salinity of diffuser discharge in psu 16 G3 Time Variable Offshore Intake Outfall Diffuser Discharges in Loops a Comment COM user specified comment for discharge in loops b Number of Grid Elements NUMDBC2 total number of discharge grid elements If NUMDBC2 0 then go to Data Group G4 Groundwater Data Location of Grid Elements Vertical Distribution of Intake Outfall Diffuser Discharge IDD inumbet of grid element diffuser enters leaves JDD j number of grid element diffuser enters leaves VDDIST percentage not fraction of total discharge DQDIFF apportioned each model layer from surface to bottom at location IDD JDD KBM1 KB 1 d Time of Observation TIME time in hours 0 0 for initial time e Discharge Data DQDIFF diffuser discharge m3 sec Even though DQDIFF N and DQDIFF N 1
8. based on groundwater map file The following outlines the steps for creation of each of the sub groups The USER is referred to Appendix A for details on the specific formats for each group Step 1 1 Define the model controls and the type of model to run using the variables in data group A This includes Run options Run computational characteristics time step etc Run output characteristics Run print characteristics TUUM Step 1 2 Define the model coefficients using the variables in data group B This includes Model coefficients 2 Horizontal mixing coefficients 3 Vertical mixing coefficients Step 1 3 Define the model output using the variables in data group C This includes Model output control for GCMPLT file Output interval for time series in GCMTSR file Model grids for elevation time series into GCMTSR Model grids for velocity salinity and temperature time series in GCMTSR Model grids and directions for flux output to GCMTSR o Eon 6 Model output control for GCM_TRAN file to water quality model Step 1 4 Define the vertical depth levels for calculation of the density gradients that feed into the Hydrodynamic Model Standard Level Declaration for data group D 1 Number of vertical layers 2 Fixed depths for each layer Step 1 5 Define the fixed salinity and temperature initial conditions by Standard Level for data group E 1 Input fixed initial temperature for each layer 2 Input fixed init
9. 0 0 2533 16 51 0 0 25 33 16 51 0 3 0 01042 6 1 91 0 0 2533 16 51 0 0 2533 16 51 0 0 25 33 16 51 0 4 0 01458 6 1 91 0 0 2533 1651 0 0 2533 16 51 0 0 25 33 16 51 0 5 0 01875 6 1 91 0 0 2533 1651 0 0 2533 1651 0 0 25 33 16 51 0 6 0 02292 6 1 91 0 0 2533 16 51 0 0 2533 16 51 0 0 25 33 16 51 0 v4 s4 t4 u5 v5 s5 t5 1 O 2111 13 76 0 0 2111 13 76 2 0 2533 16 51 0 0 2533 1651 3 0 2533 16 51 0 0 2533 16 51 4 0 2533 16 51 0 0 2533 16 51 5 0 2533 16 51 0 0 2533 16 51 6 0 2533 16 51 0 0 2533 16 51 file El epc47example html 1 1 15 2013 10 20 46 AM epc47example R Repeat the above steps to add column names to the epc47 dataset lt TB TM TS SB SM SS Year key TB temperature bottom TM temperature middle TS temperature surface SB salinity bottom SM salinity middle SS salinity surface Year time variable colnames epc47 namesepc head epc47 TB TS SB SM 55 Year 18 6 187 191 26 0 260 258 8843 13 9 137 13 8 273 25 8 25 6 9515 209 214 222 275 273 270 10211 242 242 242 285 285 285 11027 241 242 243 304 303 30 2 11699 290 291 291 320 320 31 9 12539 For plotting purposes need to standardize the time variable in both datasets Create new vector that includes the time variable from velptxx 730121 and add it to the velpt12 dataset velpt12 Time stand velpt12 Time 730121 Use command head to verify column was added head velpt12 Time k dz ul v2 sl tl u2 v2 s2 t2 13 v3 s3 t
10. Data and Wind Data 1 Time of Observation TIME j time in hours 0 0 for initial time ii Met Data Input WDS wind speed in m sec WDD direction of wind in degrees from which the wind blows measured clockwise from north SWOBS observed shortwave radiation in watts m2 AIRTMP air temperaturein C RELHUM relative humidity in percent BAROP barometric pressure in mbar CLD cloud cover fraction 0 0 to 1 0 EXTC extinction coefficient QPREC amount of precipitation in m year QEVAP amount of evaporation in m year 19 APPENDIX MODEL_GRID FILE DOCUMENTATION Data Group A Comment for Grid Information COM user specified comment for grid information Data Group B Vertical Segmentation 1 Comment 2 Number of Sigma Levels IKB number of sigma levels 3 Sigma Levels Z depth of the interface between sigma levels 1 0 lt Z lt 0 0 NOTE Total number IKB Data Group C Horizontal Segmentation 1 Comment COM user specified comment for horizontal segmentation 2 I Index and J Index index inthe 1 direction index in the 2 direction 3 Grid Information I I number of grid element in the lt 1 direction j number of grid element in the lt 2 direction H1 distance in meters in the 1 direction at center of grid element H2 distance in meters in the 2 direction at center of element H average depth of grid element in meters at mean water level MLW tida
11. Group C5 Computed Time Series for Cross Sectional Fluxes Location of Grid Elements I number of grid element INXJV number of grid element C5 Computed Time Series for Cross Sectional Fluxes a Comment user specified comment for computed time series for cross sectional fluxes Number of Cross Sections FPTS number of cross sections for which time series of fluxes are to be stored in gemtst NOTE If FPTS 0 then go to Data Group C 6 Computation Results for Water Quality Model Location of Cross Sections ISFLX I grid element in which cross section begins JSFLX J grid element in which cross section begins DIRFLX direction of cross_section IDIR I direction JDIR J direction NFLXE number of grid elements C6 Computation Results for Water Quality Model a Comment COM user specified comment b Number and Averaging Interval of Computation Result Output Sets JIM number of times all information necessary for the water quality model input is generated NAVE interval in number of time steps for averaging the elevations and currents to be used as input in the water quality model ITRNFORM O user specified time steps for writing the output 1 ECOM will generate the writing block i e section IZERO of time steps to skip before start to writing information IZERO should not be 0 if COLD START If ITRNFORM 0 IZERO wi
12. based on the work of Large and Pond 1982 The local heat flux is determined from local surface temperature use Meteorological Data OPTION 3 Time Variable Surface Heat Flux Parameters Salt Flux Data and Wind Data heat flux sub model based on the work of Rosati and Miyakoda 1988 The local heat flux is determined from local surface temperature use Meteorological Data OPTION 3 Time Variable Surface Heat Flux Parameters Salt Flux Data and Wind Data SYNOPANB SYNOPLNP SYNOPRNM These options allow the user to specify spatially varying wind data along with heat flux sub model options AANDBFLX LANDPFLX and RANDBFLX respectively Latitude in degrees median of modeling domain Longitude in degrees median of modeling domain 0 180 for western hemisphere Fraction of short wave radiation absorbed in surface layer Wind sheltering coefficient default 1 0 Reflection of shortwave radiation at surface 0 0 1 0 0 0 nothing reflected 1 0 complete reflection 0 1 recommended value Option for extinction coefficients If VARI spatially vatying extraction coefficients specified in extc2d inp will be used If OPTEXTC is left in blank or other than VARI the model will use time varying but spatially uniform EXTC specified in OPTION 3 below 18 3 Meteorological Data OPTION 3 Time Variable Surface Heat Flux Parameters Salt Flux
13. graphics and statistics STEP 1 SETTING UP THE HYDRODYNAMIC MODEL CONTROL AND INPUT FILES In order to run the Hydrodynamic Model application for the Integrated OTB model system four files are needed These are e run data the primary input file for the Hydrodynamic Model includes the model run control model coefficients model output control and boundary conditions e model grid contains the grid geometry data the depths the specification of the vertical layers and the specification of the thin wall dams groundwater map provides information on zoneation of the model grid for the purpose of defining groundwater inflows spatially e ecom3d exe the executable file for the Hydrodynamic Model for this version The time dependant boundary conditions included in the run data file are generated from time series data stored within ACCESS databases provided with the model input files Figure 1 below provides a schematic representation of the ACCESS database structure the specific data sets that feed into the 6 ACCESS database files that contain the boundary condition information and the flow of data from the 6 ACCESS databases to the run data file The specific ACCESS database files which contain the data for each of the boundary conditions listed above are provided within the blue circles in Figure 1 Additionally the specific data input blue box and the individual file names for each input green boxes are shown For each of the s
14. is a coupling intake outfall pair DQDIFF N and DQDIFF N 1 need not be equal f Temperature Data DTDIFF temperature increase decrease of diffuser discharge in C Only effective on diffuser having positive values of DQDIFF This increase decrease of temperature is with respect to the temperature of corresponding intake g Salinity Data DSDIFF salinity increase decrease of diffuser discharge in psu Only effective on diffuser having positive values of DODIFF 17 DATA GROUP 1 Comment OPTMBC ALAT ALON TR WNDSH REFL OPTEXTC Meteorological Data user specified comment for meteorological data Meteorological Data Option AVERAGED _ a single value for each meteorological parameter is used for all grid element at each time _ use Meteorological Data OPTION 1 _ Time Variable Surface Heat Flux Data Salt Flux Data and Wind Data SYNOPTIC _ spatially varying meteorological parameter values are specified for every grid element at each time _ use Meteorological Data OPTION 2 _ Averaged Time Variable Surface Heat Flux Data and Salt Flux Data and Synoptic Time Variable Wind and Atmospheric Pressure Data AANDBFLX heat flux sub model based on the work of Ahsan and Blumberg 1999 The local heat flux is determined from local surface temperature use Meteorological Data OPTION 3 Time Variable Surface Heat Flux Parameters Salt Flux Data and Wind Data LANDPFLX heat flux sub model
15. run files called Waveread exe This program reads the Wave out file and creates a series of txt files for the various output stations identified The txt files each then correspond to time series output from the wave component of the hydrodynamic model The specific variables output in order following the time and I J locations include e Wave Height e Wave Period e Wave Direction e Bottom Shear Stress As there is not direct data for comparison of the wave model results only the model output files are discussed herein Table 1 Correspondence of data txt files with model txt files for water surface elevation Water Level DATA Model Output SPs txt elvpts txt PMs txt elvpts txt tarponcanal txt elvpts txt Table 2 Correspondence of data txt files with model txt files for currents Currents DATA Model Output OPT_CU_TS txt WI CU 3TS txt SS CU TS txt Table 3 Correspondence of data txt files with model txt files for salinity and temperature Salinity and Temperature epc95 txt velpt45 txt epc96 txt velpt46 txt DATA Model Output 14 1 velpt27 txt epc23 bxt epc33 txt epc42 txt epc47 txt epc62 txt velpt17 txt epc70 txt epc44 txt epc8 txt velpt52 txt epc6 txt epc7 txt epc9 txt epc13 txt velpt26 txt epc19 txt epc21 txt epc25 txt velpt39 txt epc28 txt epc32 txt epc36 txt epc38 txt epc40 txt epc41 txt epc50 txt 52 velpt54 txt epc55 t
16. use read table or read csv 3 tell R where the file is 4 how the data are separated 5 and if there are column names header Note R is case sensitive A skeleton example x lt read table C tmpR example txt sep header FALSE Since the file was named the file is now stored in R read table C tmpR example txt sep header FALSE V1 V2 1 1 4 2 A 3 97 8 4 10 10 above command was not named therefore the file will appear the workspace Note R is case sensitive Below is the code used to reproduce the EPC 47 surface salinity figure Figure 3 44 from the hydrodynamic calibration report Data files used model output file velpt12 txt observed data file epc47 txt Both files are text files separated with spaces and no header Code to read the model output file velpt12 txt this will take a few minutes due to the size of the file velpt12 read table C Users john Documents Calibration Report FINAL velpt12 txt sep header FALSE Can use command head to verify the file was read in correctly head velpt12 V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 14 15 1 0 00208 6 1 59 0 02111 13 76 0 0 2111 13 76 0 02111 13 76 2 0 00625 6 1 91 0 0 2533 1651 0 0 2533 16 51 0 0 2533 16 51 3 0 01042 6 1 91 0 0 2533 1651 0 0 2533 16 51 0 0 2533 1651 4 0 01458 6 1 91 0 0 2533 1651 0 0 2533 16 51 0 0 2533 1651 5 0 01875 6 1 91 0 0 2533 1651 0 0 2533 16 51 0 0 2533 16 51 6 0 02292 6 1 91 0 0 2533 1651 0 0 2533 16 51
17. 0 0 2533 1651 file El epc47example html 1 1 15 2013 10 20 46 AM epc47example R V16 V17 18 V19 V20 V21 V22 V23 1 0 0 21 11 13 76 0 0 21 11 13 76 2 0 0 2533 1651 0 0 2533 1651 3 0 0 2533 16 51 0 0 2533 1651 4 0 0 2533 16 51 0 0 2533 16 51 5 0 0 2533 16 51 0 0 2533 1651 6 0 0 2533 16 51 0 0 2533 16 51 Can use the command dim to verify all rows and columns were read correctly dim velpt12 1 963600 23 Code to read the observed data file epc47 txt epc47 read table C Users john Documents Calibration Report FINAL epc47 txt sep header FALSE Verify the data were read in correctly head epc47 VI V2 V3 V4 V5 V6 V7 18 6 18 7 19 1 26 0 26 0 25 8 8843 13 9 13 7 13 8 273 25 8 25 6 9515 209 214 222 275 273 270 10211 242 24 24 2 285 28 5 28 5 11027 24 1 242 243 230 4 303 30 2 11699 29 0 291 291 32 0 32 0 231 9 12539 dim epc47 1 120 7 Add a header to each file Create a vector of the names for example names lt c a b Vector of names for velpt12 namesvelpt c Time k dz u1 v2 51 t1 u2 v2 52 2 s3 t3 u4 s4 u5 v5 55 t5 Use the function colnames to add the vector of column headers created above colnames velpt12 namesvelpt Verify by using the head command head velpt12 Time k dz ul v2 sl tl u2 v2 52 t2 u3 v3 s3 t3 u4 1 0 00208 6 1 59 0 0 2111 13 76 0 0 2111 13 76 0 0 2111 13 76 0 2 0 00625 6 1 91 0 0 2533 16 51
18. 2SS and epc47 SS epc47 SS file El epc47example html 11 15 2013 10 20 46 AM epc47example R D 4 Station 20 Model Station E 47 Data 47 Dsts 10 1 1 1 I 731000 732000 733000 734000 Time_stand Specify the theme for the plot this theme removes the default gray background and adds the location of the legend epc47_SS_theme lt epc47_SS theme legend title element_blank theme legend justification c 1 1 legend position c 1 1 theme panel border element_rect colour black fill _NA theme axis text element_text colour black size 12 theme panel background element_rect fill NA colour black theme legend key element_rect fill NA Can see the difference epc47_SS_theme file El epc47example html 11 15 2013 10 20 46 epc47example R Model Station EPC47 Data 731000 732000 733000 734000 Time_stand Add the x and y labels epc47_SS_axis lt epc47_SS_theme scale_x_continuous breaks c 730486 00 730852 00 731217 00 731582 00 731947 00 732313 00 732678 00 733043 00 733408 00 733774 00 labels c 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 ylim 0 40 xlab Year ylab Salinity ppt What the figure now looks like epc47_SS_axis file El epc47example html 11 15 2013 10 20 46 epc47example R 40 Model Station EPC47 Dats 30 Salinity ppt
19. 3 u4 1 0 00208 6 1 59 0 0 2111 13 76 0 0 2111 13 76 0 02111 1376 0 2 0 00625 6 1 91 0 0 2533 1651 0 0 2533 1651 0 0 25 33 16 51 0 3 0 01042 6 1 91 0 0 2533 1651 0 0 2533 1651 0 0 25 33 16 51 0 4 0 01458 6 1 91 0 0 2533 16 51 0 0 2533 16 51 0 0 25 33 16 51 0 5 0 01875 6 1 91 0 0 2533 16 51 0 0 2533 16 51 0 0 25 33 16 51 0 6 0 02292 6 1 91 0 0 2533 16 51 0 0 2533 1651 0 0 25 33 16 1 0 v4 s4 t4 u5 v5 5 t5 Time stand 1 0 2111 13 76 0 0 2111 13 76 730121 2 0 25 33 16 51 0 0 2533 16 51 7730121 3 0 2533 16 1 0 0 2533 16 51 730121 4 0 2533 16 51 0 0 2533 16 51 7730121 5 0 2533 16 51 0 0 2533 16 51 730121 0 25 33 16 51 0 0 2533 16 51 730121 Repeat the steps for the epcxx data epc47 Time_stand lt 47 24 730121 head epc47 TB TS SB SM SS Year Time stand 1 186 18 7 19 1 26 0 26 0 258 8843 730489 2 139 13 7 13 8 27 3 25 8 25 6 9515 730517 3 20 9 214 222 275 273 270 10211 730546 4 242 242 242 285 285 285 11027 730580 5 241 242 243 304 303 30 2 11699 730608 6 29 0 29 1 29 1 320 320 310 12539 730643 The velpt12 dataset included data from 1999 so need to subset the data to only included data from 2000 to 2009 use the function subset to do this velpt12 date 2000 subset velpt12 Time_stand gt 730486 file E epc47example html 11 15 2013 10 20 46 AM You now have a new dataset called velpt12_data_2000 that was created from velpt12 and included all data from 2000 to 2009 The data are ready to create the fi
20. 9 10 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 Add title epc47_SS_title lt epc47_SS_axis ggtitle EPC47 Surface Salinity epc47 SS title file El epc47example html 11 15 2013 10 20 46 AM epc47example R EPC47 Surface Salini 40 Model Station EPC47 Data 30 Salinity ppt 10 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 Change the color of the lines and style of the circles epc47_SS_final lt epc47_SS_title scale_colour_manual values c dodgerblue4 scale_shape_manual values 1 The figure is now ready epc47 SS final file El epc47example html 11 15 2013 10 20 46 AM epc47example R EPC47 Surface Salini 40 Model Station EPC47 Data 30 Salinity ppt S 10 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 Year Save the plot as a pdf on the computer using the function ggsave base code name of figure where you want it saved and the name you want the graph to be called size ggsave epc47 SS final filename C Users john Documents oldtampa bay EPC_Plots EPC47SurfaceSalinity pdf height 7 5 width 7 5 file E epcA7example html 11 15 2013 10 20 46 AM Statistics and Calculations R Code for recreating hydrodynamic calibration figures in R Old Tampa Bay Project Hydrodynamic Output R code for statistics EPC statistics sample EPC47 data used model output velptl2 txt observed data epc47 txt See manual on
21. APPENDIX 1 HYDRODYNAMIC MODEL TRAINING MANUAL OTB INTEGRATED MODEL SYSTEM HYDRODYNAMIC MODEL MODEL CALIBRATION MANUAL INTRODUCTION This training manual has been prepared to support the calibration components for the Hydrodynamic Model of the OTB Integrated Model System The objectives of this training manual is as follows e Provide instruction to users on the HYDRODYNAMIC MODEL structure and how to set up and run the model for the OTB Integrated Model System e Provide tools instruction to allow users to produce graphics and statistics using the model calibration graphics and statistics as an example Based upon these objectives this manual provides specific descriptions and instructions for the OTB specific Hydrodynamic Model application and is not meant as a general user s manual The model manual has been provided with the model files and provides more general instruction on the capabilities and options available Additionally this manual provides instructions on how to post process the output to generate the graphics and statistics from the model calibration report Instruction on post processing for assessment of alternate model scenarios will be provided in future training sessions The instructions are presented in three primary steps these are e Step 1 Setting up the Hydrodynamic Model control and input files e Step 2 Running the Hydrodynamic Model e Step 3 Hydrodynamic Model post processing for calibration
22. DATA GROUP E Initial Temperature and Salinity Comment COM user specified comment for temperature and salinity data 1 Initial Temperature and Salinity Data Option OPTTSI FIXED _ initial temperature and salinity data are constant for each standard level DATA _ initial temperature and salinity data vary horizontally and vertically _ data read in from data file init tands If OPTTSI DATA then go to Data Group F Open Boundary Condition Information E2 Initial Temperature Data TSI Initial Salinity Data SSI temperature in C for each standard layer salinity in psu for each standard layer 12 DATA GROUP F Open Boundary Condition Information 1 Elevation Boundary Conditions a Comment COM uset specified comment b Number of Grid Elements and Option NUMEBC total number of elevation boundary grid elements If NUMEBC 0 then go to Data Group Discharge Information OPTEBC DATA use Elevation Boundary Conditions OPTION 1 Time Variable Data TIDAL CONSTITUENT use Elevation Boundary Conditions OPTION 2 _ Computer Generated Data from Tidal Constituents Elevation Boundary Conditions OPTION 1 TIME VARIABLE DATA i Location of Grid Elements I number of grid element where elevation is specified JETA j number of grid element where elevation is specified ICON number of connecting grid element nearest interior bo
23. LTEMP accdb groundwater map SALTEMPBC Temperature HYDRODYNAMIC ecom3d33 exe 4 Figure 1 Hydrodynamic Model Input File Structure The following provides detailed descriptions of all of the variables within the three model input files Additionally detailed instructions are provided for creation of the boundary conditions in the run_data file from the ACCESS databases The run_data file is broken down into 8 separate Data Groups Appendix A presents a detailed discussion of the variables options and input formats for each of the Data Groups The specific Data Groups include Data Group A Computational and Diagnostic Characteristics Data Group B Hydrodynamic Characteristics coefficients Data Group C Result Evaluation Output Data Group D Standard Level Declaration Data Group E Initial Temperature and Salinity Data Group F Open Boundary Conditions Data Group G Inflow Boundary Conditions Data Group H Meteorologic Boundary Conditions Under Data Group F two sub groups of open boundary forcing data exist these are Sub data Group F1 water surface elevation data Sub data Group F2 salinity and temperature data Under Data Group G three sub groups exists these are e Sub data Group G1 tributary inflows and temperatures Sub data Group G2 direct point source discharges and temperatures e Sub data Group G3 groundwater inflows and temperatures by zone
24. N 1 120 Output statistics as a csv file Combine RMSE values using rbind function EPC 47 RMSE rbind RMSE EPC47 SS round RMSE EPC47 SB round RMSE EPC47 TS round EPC 47 RMSE 1 1 1 4 2 1 2 3 1 5 4 1 3 Combine MAE values using rbind function 47 lt MAE EPC47 SS round MAE EPC47 SB round MAE EPC47 TS round EPC 47 MAE 1 1 1 1 1 2 1 3 1 3 4 1 1 Combine ME values using rbind function EPC 47 ME rbind ME EPC47 SS round ME EPC47 SB round ME_EPC47_TS_round EPC 47 ME 1 1 0 4 2 0 1 3 1 2 4 0 8 Combine R2 values using rbind function EPC 47 R2 rbind R2 47 SS round R2 EPC47 SB round R2 47 TS round 47 R2 1 1 0 91 2 0 92 3 0 97 4 0 96 file El stats 620and9620calculations html 11 15 2013 2 09 40 PM ME EPC47 TB round R2 EPC47 TB round RMSE EPC47 TB round deparse level 0 MAE EPC47 TB round deparse level 20 deparse level 0 deparse level 20 Statistics and Calculations R Create vector for row names Parameters lt c Salinity Surface Salinity Bottom Temperature Surface Temperature Bottom Bind all values together using function cbind EPC47_STATS lt cbind Parameters EPC 47 RMSE EPC 47 MAE EPC 47 ME EPC 47 R2 Write column names using function colnames names c Paramters RMSE MAE ME R2 col names EPC47 STATS lt names EPC47 STATS Pa
25. OLD START _ all initial conditions are set to zero HOT START _ all initial conditions are input from file restart BAROTROPIC _ 2 D calculation bottom stress calculated in ADVAVE PROGNOSTIC _ 3_D calculation bottom stress calculated in PROFU amp PROFV DIAGNOSTIC _ 3_D calculation with temperature and salinity held fixed TEMP ONLY 3 D prognostic run while initial salinity values are held throughout the simulation SALT ONLY 3 D prognostic run while initial temperature fields are held throughout the simulation LINEAR momentum advection terms NON LINEAR include momentum advection terms SCHEME CENTRAL central finite difference scheme for advection UPWIND upwind finite difference scheme for advection _ finite difference scheme due to Smolarkiewicz and using reclusive formulation for antidiffusive velocities SMOLAR 2 finite difference scheme due to Smolarkiewicz and using two passes for corrections of numerical diffusion Comment Run Print Characteristics COM header to identify Run Print Characteristics A4 Run Print Characteristics ji DEV primary output device for viewing gcmprt SCR for 15 columns across the page suitable for printing on a screen with no wrap around _ for 25 columns across the page suitable for printing on a laser or line printer VSX vertical slice in the x 1 direction of various model quan
26. PC47 55 ME EPC47 SS round lapply ME EPC47 SS round 1 ME EPC47 SS round 11 1 0 4 2 47 SS summary EPC47 SS Im r squared R2 EPC47 SS round lapply R2 47 SS round 2 R2 EPC47 SS round length EPC47 SS2 1 1 120 Repeat above code for bottom salinity change to appropriate columns EPC47 SB data frame actual zinterpl velpt12 Ti me vel pt12 s5 epc47 Ti me stand linear 47 SB2 lt lt data frame interpzEPC47 SB 1 actual zepc47 58B Linear model EPC47 SB Im lt Im interp actual data EPC47_SB2 summary EPC47_SB 1m Call lm formula interp actual data 47 582 Residuals Min 1Q Median 3Q Max 2 594 0 721 0 126 0 974 2 787 Coefficients Estimate Std Error t value Pr gt t Intercept 2 4199 0 6198 3 9 0 00016 actual 0 9066 0 0241 37 6 lt 2e 16 Signif codes 0 0 001 0 01 0 05 0 1 1 Residual standard error 1 14 on 118 degrees of freedom Multiple R squared 0 923 Adjusted R squared 0 922 F statistic 1 41 03 on 1 and 118 DF p value lt 2e 16 Error EPC47_SB error lt 47 SB2 actual EPC47 SB2 interp RMSE MAE and ME functions RMSE lt function EPC47 5 sqrt mean EPC47 SB error 2 mae lt function EPC47_SB error file El stats 20and 20calculations html 1 1 15 2013 2 09 40 PM Statistics and Calculations R mean abs EPC47_SB error me l
27. R figures for details about libraries and reading and formatting data in R See files epc stats Rcode R CU_stats R TandSBCstats R Wl_stats_Rcode R for code for all statistics in the hydrodynamic calibration report vel ptl2 lt read table C Users john Documents Calibration Report FINAL velpt12 txt sepz header FALSE epc47 lt read table C Users john Documents Calibration Report FINAL epc47 txt sep header FALSE Add colnames mess ox viet cc col names vel pt 12 namesvel pt TSS Spe col names epc47 namesepc Standardize epc date epc47 Time_stand lt epc47 Year 24 nterpolation surface salinity Need to install library signal and then code in R for the library to open ibrary signal Loading required package MASS Attaching package signal The following objects are masked from package stats ilter poly nterpolate salinity values at match time stamp values to the observed data using the function interpl EPC47 SS data frame actual zi nterpl velpt12 Ti me vel 12 51 47 me stand linear Create a new data set with the interpolated salinity values and observed salinity values EPC47 552 lt data frame interp EPC47_SS 1 actual zepc47 55 Statistics to compare between salinity values Linear model between the interpolated and observed act
28. Remove header row Row 1 ii Set format to 1 decimal iii Set column width to 8 d Save as SALTEMPBC prn e Run executable SALTEMPBC exe f Creates formatted file for putting into run data SALTEMPBC Step 1 8 Input the river inflows and temperatures for data group G1 1 Define the number of river inflows 2 Define the grids the connecting grids I J and the vertical distribution of the flows for the river inflows 3 Input the time series data for flow temperature and salinity for each defined grid as block data using the ACCESS database RIVERFLOW accdb a This database contains seven primary data tables i Flows_1999 and Flows 2000 2009 contain daily INTB flows by reach including all reaches used to develop port flows ii TCB flows contains monthly flows for Manatee River and Terra Ceia Bay outside the INTB domain from TBEP data Lake Tarpon flows contains daily observed flows for Lake Tarpon iv HR TBC flows contains daily observed flows for Hillsborough River Dam and Tampa Bypass Canal S 160 v Stream Temp contains daily stream temperatures based on monthly observed data for each inflow location b Final ACCESS table RIVERFLOW c Export to RIVERFLOWS xls i Remove header row Row 1 ii Set format to 5 decimals Set column width to 11 d Save as RIVERFLOW prn e Run executable RIVERFLOW exe f Create formatted file for putting into run data RIVERFLOW
29. W exe f Creates formatted file for putting into run data GW Step 1 11 Input the meteorology data for data group H 1 Define the type of met data inputs and basic meteorologic parameters 2 Input the time series data for each zone including wind speed wind direction short wave radiation air temperature relative humidity barometric pressure cloud cover light extinction coefficient precipitation evaporation using the ACCESS database MET accdb a This database contains four primary data tables i DoverET contains daily ET rates in day ii Rainfall contains daily segment specific rainfall in day derived from TBEP rainfall estimates Secchi contains monthly OTB average Secchi disk depth m from EPCHC data iv SP CLW MET contains hourly St Petersburg Clearwater Airport wind speed wind direction air temperature atmospheric pressure cloud cover Dover solar radiation and Dover relative humidity b Final Access table MET c Export to MET xls i Remove header row Row 1 ii Set format to 5 decimals Set column width to 11 d Save as MET prn e Run executable MET exe Creates formatted file for putting into run data MET The OTB model_ grid file has three primary sections these are e Specification of the Sigma Levels e Horizontal Grid Data e Specification of the Locations of Thin Wall Dams Appendix B presents detailed descriptions of the v
30. alue lt 2e 16 EET OE EPC47 5 lt EPC47 TS2 actual EPC47 TS2 interp RMSE MAE and ME functions RMSE lt function EPC47 5 sqrt mean EPC47 TS error 2 mae function EPC47_TS error mean abs EPC47 TS error lt function EPCAT TS i mean EPC47 TS2 actual EPC47 TS2 i nterp file El stats 20and 20calculations html 1 1 15 2013 2 09 40 PM Statistics and Calculations R Statistics 15 lt 5 5 er ron RMSE EPC47 TS round lappl y RMSE EPC47 TS round 1 RMSE_EPC47_TS_round 1 235 MAE EPC47 TS lt mae EPC47 TS error MAE EPC47 TS round lapply MAE 47 TS round 1 MAE EPC47 TS round L E11 1 1 3 ME EPC47 TS me EPC47 TS error ME EPC47 TS round lappl y ME EPC47 TS round 1 ME EPC47 TS round 111 1 1 2 R2 EPC47 5 lt summary EPC47 TS Im r squared R2 EPC47 TS round lapply R2 47 5 round 2 R2 EPC47 TS round 111 1 0 97 lt length EPC47 TS2 1 1 120 Repeat above code for bottom temperature change to appropriate columns EPC47 TB data frame actualzinterpl velptl12 Ti vel pt12 t5 epc47 Ti me stand linear 47 TB2 lt data frame interpzEPC47 TB 1 actual zepc47 TB Linear model EPC47 TB Im lt Im interp actual data EPC47_TB2 summary EPC47 Call formula interp actual data 47 TB2
31. ariables within the model_grid file and the input formats The OTB groundwater map file defines what grid cells are located within 5 different zones within the model grid domain A total of 5 zones are defined and the groundwater map file simply provides for the I J grid numbers and what zone 1 to 5 that cell resides in Within the run data file in Section G under the Diffuser GW the constant flow values for each of the 5 segments are read in at time 0 0 and the same value for time 99999 0 which sets these values to the constants for the full simulation STEP 2 RUNNING THE MODEL Prior to running the OTB Hydrodynamic Model it is recommended that the user set up a base directory for the runs an example might be as follows OTBhydro gt baserun Under the baserun sub directory set up two directories model_input model_output Put the three model inputs run_data model_grid and groundwater map the model executable ecom3d33 exe and the batch file discussed below in the model_input directory Subsequent runs could then be identified by other names i e baserun_1 and set up under their own sub directory A batch file lt file gt bat is set up in the same directory as the executable and the model input files The batch file has the structure as shown below set ncpus 4 set OMP_NUM_THREADS 4 ecom3d33 exe pause The first two lines of code in the batch file are common methods for setting the number of threads on the computer
32. being utilized The specification of the number if threads is critically important to model run time command line window will then appear The window will provide a count on the number of days the model has run JHIST lt number gt provides the count by days that the model has run The number of processors in the computer running the model its processor speed and other factors will define how long the model will run STEP 3 MODEL POST PROCESSING FOR CALIBRATION GRAPHICS AND STATISTICS Figure 2 provides a flow chart showing the output file structure from ECOMSED and what each will be utilized for ECOMSED outputs 4 primary files for use in post processing data These are GCMTSR GCM_TRAN GCM_GEOM GCMPLT Wave out The GCMTSR file provides high temporal resolution time series results at specified grid cells based upon the control variables defined in Data Group C In data group C specific cells for the GCMTSR output are specified for elevations as a group currents temperature and salinity as a group and fluxes as a group The GCM TRAN and GCM GEOM files provide the hydrodynamic input to the RCA water quality model The GCMPLT file provides output for the full grid for all variables at specified intervals The Wave out file contains the time series of information from the wave model For the purposes of the calibration manual only the GCMTSR and Wave out results are discussed HYDRODYNAMIC MODEL HYDRODYNAMIC MODEL
33. evel 14 DATA GROUPG Discharge Information G1 Time Variable Tributary Inflow a Comment COM user specified comment for discharge b Number of Grid Elements NUMQBC total number of discharge boundary grid elements If NUMQBC 0 then go to Data Group G 2 Time Variable Offshore Intake Outfall Diffuser Discharges 6 Location of Grid Elements Vertical Distribution of flow IQD inumber of grid element discharge enters leaves JQD j number of grid element discharge enters leaves IQC inumber of connecting exterior boundary grid element jQC jnumber of connecting exterior boundary grid element VODIST percentage not fraction of total discharge QDIS apportioned to each model layer from surface to bottom at location IQD JOD d Time of Observation TIME tme in hours 0 0 for initial time Discharge Data QDIS discharge flow m3 sec gt 0 0 positive for flow into the model domain river outfall lt 0 0 negative for flow out of the model domain intake f Temperature Data TDIS temperature of discharge in C g Salinity Data SDIS salinity of discharge in psu 15 G2 Time Variable Offshore Intake Outfall Diffuser Discharges a Comment COM user specified comment for discharge b Number of Grid Elements NUMDBC1 total number of discharge grid elements If 0 then go to Data Group G3 Time Variable Offshore Intake Outfall Diffuser
34. gure from the hydrodynamic calibration report Note verify you opened up the library ggplot2 from the above steps if not do it now library ggplot2 Skelton of the ggplot2 function name plot lt ggplot name of data set aes xaxis what column yaxis what column geom line or geom point etc this command specifys what kind of plot wanted scale x continuous breaks c usethis command if you want specific breaks in the x axis continuous scale aesthetics xmin xend xintercept scale name position palette identity breaks 1 expand expand guide none Naming the plot allows you to add additional layers Note the plot will not appear in the R window when named unless you specifically tell R to open it First layer velpt12 date 200025 a line velpt12SS ggplot velpt12 date 2000 aes x Time stand y s1 colour Model Station geom line shape line See plotin R velpt12SS file El epc47example html 1 1 15 2013 10 20 46 AM epc47example R 30 20 7 Model Station Model Station 10 I 1 1 I 731000 732000 733000 734000 Time stand Add the observed epc47 data as points he observed EPC data as a point plot note when adding a second layer need to specify data outside of the aes line shape size and color epc47 SS velpt12SS geom point aes x Time stand y SS shape EPC47 Data data epc47 size 3 colour black The above plot now as both layers velpt1
35. ial salinity for each layer Step 1 6 Input the water surface elevation forcing function for data group F1 1 Define the number of cells over which the water surface elevation forcing is applied 2 Define the grids and the connecting grids 1 for the water surface elevation forcing 3 Input the time series data for each defined grid as block data using the ACCESS database ELEVATION accdb a This database contains one primary data table Elevation BC which includes time and elevation data at 6 minute intervals b Export four BC files i ELEVATIONBC1 xls Hour 0 24999 976 ii ELEVATIONBCA xIs Hour 25000 076 49999 976 ELEVATIONBC3 xls Hour 50000 076 74999 976 iv ELEVATIONBCA xIs Hour 75000 076 96430 176 Remove header row Row 1 from each file Set format to 5 decimals Set column width to 11 Save as ELEVATIONBCH1 prn ELEVATIONBC2 prn ELEVATIONBCS3 prn ELEVATIONBCA prn Run executable elevationoc exe Creates formatted file for putting into run data ELEVATIONBC moop ae Step 1 7 Input the salinity and temperature forcing function for data group F2 1 Input the time series data for each defined grid as block data using the ACCESS database SALTEMP accdb a This database contains one primary data table SalTemp which includes monthly water column EPCHC salinity and temperature data at Station 94 b Final ACCESS table SALTEMPBC Export to SALTEMPBC xls i
36. ical turbulent mixing based on Kent and Pritchard 1959 and Offcer 1976 constant or background mixing in m sec 1 0E_06 recommended value if VERTMIX CLOSURE or EMPIRICAL If user wants to specify spatially variable 2D UMOL specify UMOL as VARI 6X A4 and provide umol2d inp file Please refer to table 10 27 for more details of format specification of umol2d inp file vertical Prandtl number _ ratio of vertical viscosity to vertical diffusivity momentum mixing diffusive mixing for VERTMIX CONSTANT If VERTMIX EMPIRICAL VPRNU acts as coefficient V in the empirical mixing equation 8 9a DATA GROUP Result Evaluation Comment Computational History Output for Plotting COM user specified comment C1 Number and Averaging Interval of Computational History Output Sets JHM number of times all information necessary for plotting will be written in gemplt and part location i PARTICLE INCLUDE AVGE interval in number of time steps or hours for averaging the elevations temperature salinity and currents for all grid elements USER or left in blank spaces user specifies the ocmplt output intervals AUTO output interval will be generated by ECOMSED based on the values of PLTZERO AVGE and JHM The beginning timestep or hour of gcmplt output TZERO indicating the units of AVGE and PLTZERO HOUR time control is in hour
37. ix boundary conditions a single ACCESS database file is created which merges all of the data within the circle The final output files are shown attached to the circle feeding into the run_data file The 6 ACCESS files are as follows ELEVATION accdb Time series of water levels applied uniformly to the Hydrodynamic Model offshore boundary e SALTEMP accdb Time series of salinity and temperature applied uniformly to the OTB hydrodynamic model grid offshore cells e RIVERFLOW accdb Time series of tributary inflows and temperatures input at specific model grid locations DIRECTPS accdb Time series of direct point source inflows and temperatures input at specific model grid locations e GROUNDWATER accdb Constant groundwater inflows and temperatures applied throughout the OTB hydrodynamic model e MET accdb Time series of meteorologic data applied throughout the hydrodynamic model RIVERFLOW accdb Mite Y WATERSHED MODEL Extinction Coefficients Point Source Stream Non iNTB Flows Flows Temperature STP cua cua DoverET Rainfall OTB_Secchi 5 1999 MR TCB flows Lake Tarpon flows PS flows Stream_Temp MET Data Flows_2000_2009 HR_TBC_flows RIVERFLOW ELEVATION accdb Model Control DIRECTPS accdb And 2 Boundary Coefficients Direct Point es Source Flows DIRECT PS ELEVATIONBC Direct_PS_flows run_data model_grid GROUNDWATER accdb SA
38. l amplitude ANG angle in degrees between east and 1 direction measured in a countet clockwise direction YGRID latitude of grid center in degrees positive for northern hemisphere to compute the Coriolis parameter XGRID longitude of grid center in degrees Note model does not use this Only used for postprocessing purposes DATUM datum of grid element in meters above some reference elevation NOTE Total number of wet grid total number of grid elements Grid information need be specified for wet points only and it is not necessary to specify grid information for other grid elements H must be sufficiently large in order to remain wet at low tide Data Group D Specification of Thin Dams 1 Comment COM user specified comment for thin dams 2 Number of Thin Dams NUMTDAM Number of thin dams NOTE If there is no thin dam specified in the model domain user can either specify NUMTDAM 0 or skip Data Group D 3 Location of Thin Dams ISTDAM N I number of grid element in which thin dam begins JSTDAMWN j number of grid element in which thin dam begins DIRTDAM N direction of thin dam cross section IDIR cross section is in the gt direction JDIR cross section is in the gt gt direction NTDAM N number of grid elements in the thin dam cross section
39. ll be ignored IWET 0 entire grid output 1 wet grid only output If JTM 0 then go to Data Group D Standard Level Declaration Time in Number of Time Steps for Writing the Output IF ITRANFORM 0 IF ITRANFORM 1 skip this block ITRAC time in number of time steps at which the information will be output necessary for water quality model input NOTE ITRAC relative to start of run independent of RESTART option specified 10 DATA GROUP D Comment COM Standard Level Declaration user specified comment about the standard levels D1 Number of Standard Levels IKSL NOTE D2 Standard Levels DPTHSL NOTE number of standard levels lt 50 To reduce the amount of computer storage required keep the number of standard levels IKSL at a minimum 1 IKSL lt 50 depth of standard level in meters with respect to surface water level It is not necessary to include the surface level although it may be included If not constituent values associated with the first level below the surface will be applied to the depth between the surface and the first standard level Extrapolation to the surface may cause incorrect representation of the vertical profile To ensure proper interpolation of data from standard level to sigma level each bottom_most sigma level must be bracketed by two standard levels These standard levels must contain data 11
40. n no radiation PCLAMP partially clamped Note if user selects PCLAMP type B C user must provide TLAG in Hours optimized clamp which is same as RANDB except 8t is non unity RANDP Reid and Bodine type boundary condition IRANDP inverted Reid and Bodine type boundary condition 8 1 Comment Horizontal Mixing Characteristics COM header for horizontal mixing characteristics B2 Horizontal Mixing Characteristics HORZMIX HORCON HPRNU j CONSTANT _ value given for HORCON is scaled in each grid element relative to the smallest grid element CLOSURE _ value given for HORCON is used in Smagorinsky s formula for mixing value used as a constant or in Smagorinsky s formula based on HORZMIX non dimensional If user wants to specify spatially variable 2D HORCON specify HORCON as VARI 6X A4 and provide horcon2d inp file Please refer to Table 10 25 for more details of format specification of horcon2d inp file horizontal Prandtl number _ ratio of horizontal viscosity to horizontal diffusivity momentum mixing dispersive mixing 1 0 recommended value Comment Vertical Mixing Characteristics COM header for vertical mixing characteristics B3 Vertical Mixing Characteristics VERTMIX UMOL VPRNU CONSTANT _ value given for UMOL applies everywhere CLOSURE value given to UMOL is background mixing EMPIRICAL empirical vert
41. ramters RMSE MAE ME R2 1 Salinity Surface 1 4 1 1 0 4 0 91 2 Salinity Bottom 1 2 1 0 1 0 92 3 Temperature Surface 1 5 1 3 1 2 0 97 4 Temperature Bottom 1 3 1 1 0 8 0 96 Export as an write csv EPC47_STATS C Users john Documents old tampa bay EPC stats output HB TEMP STATS csv row names FALSE Calculations on current data Sunshine Skyway NOAA 702010 velptl lt read table C Users john Documents Cali bration Report FINAL velptl txt sep header FALSE namesvel pt lt c dz ul v1 si t1 u2 v2 s2 t2 uz v3 53 t3 u4 v4 s4 t4 us y5 55 gge col names vel pt 1 namesvel pt Square the columns lt data frame lapply velpti c 4 5 function z z 2 Sum across the row v Sum lt rowSums v Square root the sum v sqrtsum lt v Sum 5 Repeat for the other two columns v2 lt data frame lapply velpti c 8 9 function z z 2 v Sum2 lt rowSums v2 v sqrtsum2 lt v Sum2 5 Add the calculated square root values together v Sum3 lt v sqrtsumtv sqrtsum2 Divide the sume by 2 v divide lt v Sum3 2 Multiply by 100 v magn v divi de 100 Make a new data set with the calculated magnitude v ti me data frame velpt1 Ti me v magn v names c Ti me Magnitude col names v time v names head v ti me Time Magnitude 00208 00625 01042 01458 01875 02292
42. rt only PARTICLE INCLUDE particle tracking will be simulated NEGLECT no simulation of particle tracking Comment _ Run Computational Characteristics COM header to identify run computational characteristics A2 Run Computational Characteristics DTI SPLIT IRAMP IYR IMO IDA IHR NHYD SGW WETEPS WETMIN time step in seconds of the internal mode the maximum allowable time step in seconds can be found in ecmprt number of time steps between the internal and external modes Please refer to Section 8 1 for more details number of time steps over which all model forcing functions are ramped from zero to their full values linearly year month day hour of model start time and should be a 4 digit number number of time steps between each hydrodynamic transport field input from hqi tran only used if HYDTYPE EXTERNAL semi prognostic coefficient based on Sheng Greatbatch and Wang 2001 Please see Section 8 4 for details If SGW 1 and TOR PROGNOSTIC the model will be in full prognostic mode Default 1 0 Drying Depth Minimum Depth for Wetting Comment Run Output Characteristics COM header for Run Output characteristics Run Output Characteristics NSTEPS IPRINT IPRTSTART RESTART TOR ADVECT HM I ji number of time steps in the model run print interval in number of time steps time in number of time steps at which printing will begin C
43. t function EPC47_SB error mean EPC47_SB2 actual EPC47_SB2 interp Statistics RMSE EPC47 SB lt RMSE EPC47_SB error RMSE EPC47 SB round lappl y RMSE_EPC47_SB round 1 RMSE_EPC47_SB_round Pe MAE EPC47 SB lt 7 SB error MAE EPC47 SB round lapply MAE EPC47 SB mound 1 MAE EPC47 SB round eo Pe ME EPC47 SB lt mef EPC47_SB error ME EPC47 SB round lapply ME EPC47 SB round 1 ME EPC47 SB round 11 1 0 1 R2 EPC47 SB summary EPC47 SB Im r squared R2 EPC47 SB round lapply R2 47 SB round 2 R2 EPC47 SB round length EPC47 SB2 1 1 120 Repeat above code for surface temperature change to appropriate columns 47 TS data frame actual zi nterpl velpt12 Ti me vel pt 12 t1 epc47 Ti me stand linear EPC47 TS2 lt data frame interp EPC47_TS 1 actual zepc47 TS Linear mode EPC47 TS im Im interp actual 47 TS2 summary EPC47 5 1 Calls formula interp actual data 47 752 Residuals Min 1Q Median 3Q Max 3 928 0 519 0 076 0 592 2 070 Coefficients Estimate Std Error t value Pr gt t Intercept 0 2719 0 3725 0 73 0 47 actual 0 9621 0 0153 63 00 lt 2e 16 Signife codes 0 0 001 0 02 0 05 0 1 1 Residual standard error 0 912 on 118 degrees of freedom Multiple R squared 0 971 Adjusted R squared 0 971 F statistic 3 97e403 on 1 and 118 DF p v
44. tities included in the gcmprt file Y _ vertical slices no vertical slices JROW jnumber at which the vertical slice in the x 1 direction will be taken 0 for VSX N VSY vertical slice in the y 2 direction of various model quantities included in the ecmprt file Y vertical slices _ no vertical slices ICOL I number at which the vertical slice in the y 2 direction will be taken 0 for VSY N velocity included in gemprt Y include omit V velocity included in gcmprt Y _ include omit W velocity included in Y _ include N _ omit horizontal mixing included in Y include _ omit PTS salinity and conservative tracer included in ji PTU 11 ji PTV ji ji ji PTW ji ji PTAM j PRHO PTQ2 PTL PTKM PTKH ji 11 ji Y _ include _ omit temperature included in gcmprt Y include _ omit density included in gcmprt Y include _ omit turbulent kinetic energy included gcmprt for closure vertical mixing Y include _ omit mixing length included in gcmprt for closure vertical mixing Y include _ omit mixing KM included in gemprt for closure vertical mixing Y include N omit mixing KH included in gcmprt for closure vertical mixing Y include _ omit
45. ual values EPC47 SS Im Im interp actual datazEPC47 SS2 summary EPC47 55 Call formula interp actual data 47 552 Residuals Mi n 10 Median 3Q Max 2 674 0 720 0 091 0 858 3 315 Coefficients Estimate Std Error t value Pr t Intercept 3 1965 0 6363 5 02 1 8 06 actual 0 8891 0 0253 35 20 lt 2e 16 Signif codes 0 0 001 0 01 0 05 0 1 1 Residual standard error 1 25 on 118 degrees of freedom Multiple R squared 0 913 Adjusted R squared 0 912 F statistic 1 24e403 on 1 and 118 DF p value lt 2e 16 Calculate error between the interpolated and observed actual values EPC47 SS error lt EPC47_SS2 actual EPC47_SS2 interp Functions to calculate RMSE MAE and ME RMSE lt function EPC47 55 sqrt mean EPC47 SS error 2 lt function EPC47_SS file El stats 20and 20calculations html 1 1 15 2013 2 09 40 Statistics and Calculations R mean abs EPC47_SS error me function EPC47_SS error mean EPC47 SS2 actual EPC47 SS2 interp Use the above functions to calculate the statistics RMSE EPC47 SS lt RMSE EPC47_SS error Round value RMSE EPC47 SS round lappl y RMSE_EPC47_SS round 1 RMSE EPC47 SS round eo j gt MAE EPC47 SS lt mae EPC47 SS error MAE EPC47 SS round lapply MAE EPC47 SS round 1 MAE EPC47 SS round 47 SS lt me E
46. undary grid element JCON jnumber of connecting grid element nearest interior boundary element NOTE Every boundary element should have a connecting interior grid element ii Time of Observation TIME time in hours 0 0 for initial time NOTE TIME is absolute time measured from beginning of COLD START run and incremented with each subsequent HOT START run 13 iii Elevation Data EBDRY boundary elevation data in meters at time TIME NOTE Sequence TIME EBDRY repeated for each observation Final TIME must be greater than NSTEPS DTI 3600 the duration of the run for COLD START runs and greater than IEND NSTEPS x 3600 for HOT START runs F2 Time Variable Temperature and Salinity Boundary Conditions a Comment COM uset specified comment b Temperature and Salinity Boundary Conditions 1 Time of Observation TIME time in hours 0 0 for initial time NOTE TIME is absolute time measured from beginning of COLD START run and incremented with each subsequent HOT START run Location of Grid Elements Temperature and Salinity Data ITAS inumber of grid element where temperature and salinity are specified JTAS j number of grid element where temperature and salinity are specified TBDRYSL temperature in C at time TIME for each standard level not sigma level SBDRYSL salinity in psu at time TIME for each standard level not sigma l
47. xt epc61 txt epc63 txt epc65 txt epc66 txt epc67 txt epc68 txt epc73 txt velpt58 txt epc80 txt epc81 txt epc84 txt velpt35 txt epc90 txt epc91 txt epc92 txt 94 velpt44 txt _ velptas txt velpt txt Table 4 Correspondence of data txt files with model txt files for flux through CCC Flux DATA Model Output East032312 txt West032312 txt East041712 txt West041712 txt R CODE FOR POST PROCESSING epc47example R Code for recreating hydrodynamic calibration figures in R R Manual for Hydrodynamic Model Calibration Objective Create hydrodynamic calibration figures and statistics using an open resource data analysis package Below is an example of how to import data get data ready for use and create figures using ggplot2 in R General information R stores functions as libraries We will be using the library ggplot2 for all of the graphics The first time you use ggplot2 you must download the library 1 select the cran mirror choose USA CA2 and then select install package S choose ggplot2 all of this is under the Packages drop down menu afterwards you then need to tell R to open the library by using the following command library ggplot2 Data Import The primary functions to read data into R are read table for text files and read csv for csv files To read in a data file 1 name the file if you do not name the file then R will open up the data in the workspace 2 tell R what function to
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