D-Waq NESTWQ User Manual
Contents
1. lt sua aa Mek aka 8 4 Input and output 11 AN apui NESTWOI lt ta ee ea db be ka eee wae ea 11 42 Output NEST L 2 1 bee ee ee dew N 1 ek bk dn E 12 43 MbbutNESTWOR i la salaten 4 Ge ser Fa eee ead 12 44 Output NESTWQ2 gt 2 imu fd KRIS uusia Be hee ik EE 13 5 Tutorial 15 ET NN et a eo m a Pe Hua ana EN as oat VE GR O ORG 17 52 Input and output NESTWQ1 Lokes save mesh son KON KOKO ke 19 Sat TIIG ou uke ee a AS RO Poa vie KN Oe ae AA a 19 522 Diagnoses ie lt lt ss GET lin G ee Pa valtaa 19 523 Administration file sua evas ee eae ee 4 20 5 3 Input and output NESTWQ2 sika kaa ka ka koa NA 21 Sol MAME ee es k Ys ke X a a de Be ow he ag GE 21 S22 Diaogonostitile s saa a 641 10848 ae Di eae te 21 6 Limitations warnings and errors 23 6 1 SIDING lt lt basere ra kb ed he le Ga Cones 23 BE VONDE lt s ee Se GADE EEA ke ha ee eRe eee EG 23 CS FE lt suis eSak Tears ee a cl fe iran 24 7 Description files 27 8 Theoretical background 29 6 1 Boundary segments gt scs date rake dad Bas a d U K GA 0 4 29 8 2 Nest segments and weights ke 29 References 31 Deltares iii D Wag NESTWO User Manual iv Deltares List of Figures List of Figures 2 1 Data flow diagram of D Wag NESTWA e 4 3 1 Title window of Delft3D e 5 3 2 Main window Delft3D MENU e 6 3 3 Selection window for Water Qualityandecology 6 3 4 Select working directory window 2 250055 7 3 5 Select wor2. n S Deltares sustems a AN Enabling Delta Life D Wag NESTWO Offline nesting of water guality models User Manual D Water Ouality Version 1 34 34068 26 May 2014 D Wag NESTWQ User Manual Published and printed by Deltares telephone 31 88 335 82 73 Boussinesqweg 1 fax 31 88 335 85 82 2629 HV Delft e mail info deltares nl P O Box 177 www http www deltares nl 2600 MH Delft The Netherlands For sales contact For support contact telephone 31 88 335 81 88 telephone 31 88 335 81 00 fax 31 8833581 11 fax 31 8833581 11 e mail sales deltaressystems nl e mail support deltaressystems nl www http Awww deltaressystems nl www http www deltaressystems nl Copyright O 2014 Deltares All rights reserved No part of this document may be reproduced in any form by print photo print photo copy microfilm or any other means without written permission from the publisher Deltares Contents Contents 1 Aguide to this manual 1 TI TG lt ved 47 a Wa ew danin a a 1 1 2 Manual version and revisions ss a 1 1 3 Typographical conventions se 1 2 Introduction to D Wag NESTWQ 3 2 1 System name and subsystems e 3 22 Forge lt s s s G bake GE oe ME kote de 208 3 2 3 Overview subsystems sn KL 3 3 Getting started 5 21 Starting DRED lt lt s k YR Aa Sm kokin o Kb EE ke 5 3 2 Getting into D Wag NESTWQ a ve mos e ke va sek ke 6 3 3 Exploring some menu options
3. 5 1 Tutorial Select boundary data file N Data file Filename not provided yet Select I Use selected file instead of the editable boundary data File type Binary file from nesting program C Readable file in Delft3D WAQ format OK Cancel Figure 5 1 Dialog for selecting output from NESTWO2 in D Water Quality GUI tions datagroup and press the Data file button The dialogue that appears allows you to select the output file from NESTWQ2 This will then be included automatically in the input to D Water Ouality The advantage of this method is that the name of this output file becomes part of the scenario and it will be included when you edit the input via the user interface 25 Return to Water quality WAG menu and select Wag 1 and select the adapted lt testd inp gt file 26 Run the detailed model and evaluate the results Introduction The Upgraded WAHMO Model is a fine grid numerical model for the placeHong Kong waters It is based on the shallow water equations in curvilinear co ordinates The spatial resolution is typical 300 1500 m The model was developed in view of the need for a detailed and accurate tidal and water guality model that could be used for accurate computations A further interest was provided by transport and water quality simulations on seasonal and annual scales For this purpose the fine grid water guality model was aggregated The SIU LAM model is a fine grid numerical model f
4. User Manual Configure Processes Library Nesting Return to Delft3D WAQ menu Figure 3 7 Selection window for Additional tools The nesting tools are part of the Additional tools hence Click on Tools The Additional tools window Figure 3 7 contains the supporting programs to configure your own Processes Library and to nest water quality models Click on Nesting to show the various steps in the nesting of water quality models see Figure 3 8 Click on Nest Input 1 The input file for NESTWQ1 is opened see Figure 3 9 Select File Exit to close the input file Select Return to close the Additional tools window Select Return and Return twice again to enter the main window of Delft3D MENU Click Exit The window is closed and the control is returned to the desk top or the command line Exploring some menu options To guide you through some menu options please follow the example in Chapter5 Tutorial 8 Deltares Getting started 7 Nest Input 1 Edit or create input fle for NESTWO1 ae esr dere a Nest Input 2 Edit or create input file for NESTWQ2 sartsa NESTO dot es Edit detailed WAQ inp file for NESTWQ pe oat tols meru Select working directory Figure 3 8 Selection window for Additional tools nesting water quality models com 02d cco com o2d 1ga com d2d cco com d2d 1ga 2d 2d dial 2
5. model SEGNR NST 1 4 SEGNR NST 2 4 SEGNR NST 68 20 4 Overall SEGNR 1719 1720 1782 1781 SEGNR 1719 1720 1782 1781 SEGNR 1827 model WEIGHT 0 47127 0 28682 0 09152 0 15038 WEIGHT 0 68195 0 09224 0 02690 0 19890 WEIGHT 0 43793 com o2d com o2d 4774 com d2d com d2d 7400 42 45 cco lga cco lga Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest segment segment segment segment segment segment segment segment segment segment segment segment segment segment segment segment segment weight factors 1782 1718 1779 2896 2957 1655 1714 gt 1651 1712 1649 gt 1709 1770 1707 1830 1828 1889 1826 Deltares 5 3 5 3 1 5 3 2 Tutorial 1889 0 25716 1888 0 11281 1826 0 19211 Input and output NESTWQ2 Input file Input file lt nestwg2 inp gt 2d 2d adm nest segments and weight factors overall model o2d waq map WAQ map file overall model 4 number of active substances for nested model 2d 2d dia2 diagnostics from NESTWQ2 2d2dwaq bcc WAQ boundary conditions for nested model Diagnostic file The diagnostics file lt 2d 2d dia2 gt Deltares NESTWQ2 Version 2 04 00 25853 Jan 18 2013 09 42 44 gt gt Input from nestwq2 inp Nest segments and weight factors overall model 2d 2d a
6. not exist The following error is related to missing nest administration data from NESTWQ1 or D Water Quality map file ERROR xxx non existing file If the format or structure of the input nest administration or D Water Quality map file is incor rect the following errors will be given ERROR while reading nestwq2 inp xxx ERROR xxx premature EOF nestwq2 inp ERROR while reading lt nestwql adm gt xxx ERROR xxx premature EOF lt nestwql adm gt Deltares 25 D Wag NESTWO User Manual ERROR while reading lt d3d waq map gt xxx ERROR premature EOF lt d3d waq map gt The following dimensions may be too small they can be increased in he main program sk ERROR increase MAXVAR to xxxxx xxx ERROR increase MAXSYS to xxxxx xxx ERROR increase MAXBND to xxxxx sk ERROR increase MAXAGR to xxxxx ERROR increase MAXSEG to xxxxx When there is an inconsistency between the files used for NESTWQ1 and the overall map file used in NESTWO2 the error will be ERROR xxx inconsistent number of segments NOSEG from NESTWQ1 xxxxx NOSEG from mapfile XXXXX An inconsistency in the number of layers for 3D models will cause the error ERROR xxx 3D 3D nesting with different number of layers is NOT implemented 26 Deltares 7 Description files The files used by NESTWQ1 and NESTWO2 are described as follows Name lt com ext1 cco gt lt com ext2 cco gt Type binary Acc
7. D Wag NESTWO These windows are grabbed from the PC platform For Linux and UNIX workstations the content of the windows is the same but the colours may be different On the PC platform you can set your preferred colours by using the Display Properties 3D modelling sutte for integral water solutions VP Version 4 01 00 Company Deltares License Valid until 01 feb 2014 Enabting Delte Lite Copyright c Deltares 2007 2013 Figure 3 1 Title window of Delft3D Deltares 5 D Wag NESTWO User Manual E Delft3D 4 01 00 tutorial wag friesian tidal inlet Se Information Information and version numbers Grid Grid and bathymetry Flow Hydrodynamics including morphology Wave Waves standalone Part Particle tracking Far field water quality Utilities Delft3D Utilities N Exit Exit Delft3D menu Select working directory Aggregate and convert hydrodynamic results Select processes Create or edit D WAQ input file Start preprocessor Start WAO simulation View report files Postprocessing with GPP Postprocessing with OUICKPLOT Additional tools Return to Delft3D Water Ouality menu Select working directory Figure 3 3 Selection window for Water Ouality and ecology 3 2 Getting into D Wag NESTWQ To continue restart the menu program as indicat
8. File 57 KB chz File 3 2 MB dat File 26 KB def File 28 KB dps File 520 KB flo File 1KB hyd File 6 KB inp File 115 KB len File Date Modified Si 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 21 03 2013 15 12 34 Files of type Directories z cance Figure 3 5 Select working directory window to set the working directory to lt waglnestwg 2d 20 gt Before continuing with any of the selections of this Water quality WAQ window you must select the directory in which you are going to nest water guality results o Click the Select working directory button Next the Select changing directory window Figure 3 4 is displayed your current directory may differ depending on the location of your Delft3D installation Browse to and enter the lt Tutorial gt sub directory of your Delft3D Home directory Enter the lt wag gt directory Next the lt nestwq gt sub directory Enter the lt 2d 2d gt sub directory and close the Select working directory window by clicking OK see Figure 3 5 Next the Water quality WAQ window is re displayed but now the changed current working directory is displayed in the title bar see Figure 3 6 Deltares 3 3 D Wag NESTWO
9. apter 5 for an example of the diagnostics file Deltares 13 D Wag NESTWO User Manual 14 Deltares 5 Tutorial At this moment no graphical user interface is available to perform the nesting of water guality models In order to perform the nesting correctly the following steps are reguired Edit Create lt nestwg1 inp gt file for NESTWO1 You have to specify the names of the lt x lga gt and lt x cco gt files of the overall and detailed model Specify the administration file On forehand the hydrodynamics of both the overall and nested model must be converted to formats reguired for D Water Ouality Couple menu see D WAQ UM 2013 Create administration file execute NESTWQ1 Within this step a diagnostic file and an administration file is created which is reguired input for the second step of the of the nesting NESTWO2 Edit Create lt nestwg2 inp gt file for NESTWO2 You must specify the name of the administration file created by step 2 the name of the water guality map file of the overall model the number of active substances to nest and the name of the binary boundary output file for the detailed model Create boundary conditions execute NESTWQ2 Within this step a diagnostic file and a boundary file is created which is required input for running the water quality detailed model Examine diagnostic files of NESTWQ1 and NESTWQ2 After executing NESTWQ1 and or NESTWQ2 you can inspect the if the modules have run
10. cco files These files are platform dependent The overall and nested grid have the same co ordinate system The time series boundary conditions for the aggregated nested model are derived from the binary D Water Quality map file from the aggregated overall model The first NOSYS active substances on the map file of the overall model are transferred to the nested model selection of substances is not possible The location of a boundary segment in the nested model is obtained through mirroring from the interior domain The centre of a boundary segment in the nested model before aggregation and the cen tres of the surrounding overall nest segments determine the weight factors The nest procedure transfers 2DH and 3D overall model results to 2DH and 3D boundary conditions for the nested model In case both models are 3D then the number of layers in both models must be equal 2DH overall model results will be transformed to uniform 3D boundary conditions for the nested model 3D overall model results will be transformed to depth averaged boundary conditions if the nested model is 2DH The time series boundary conditions file for the nested model is binary and only suitable for D Water Quality The time span and time interval for the time series boundary conditions of the nested model are determined by the map time span and interval of the map file from the overall model The nesting procedure D Waq NESTWQ does not acc
11. correctly Edit nested WAQ input file In this step you must add the created boundary filename step 4 by editing block 4 of the water quality input file goto block 4 change 7 information in this file to 2 information in binary file write on a new record the name of boundary file between quotes delete all other information in the following records in block 4 until block 5 In order to demonstrate the use of D Wag NESTWO the following tutorial can be applied Available data files lt com d2d dat gt communication file detailed 2D model Siu Lam lt com d2d def gt definition file detailed 2D model lt com o2d dat gt communication file overall 2D model Upgrade 2x2 lt com o2d def gt definition file overall 2D model lt tracer sub gt substance file with CTR1 1 Start Delft3D MENU 2 Select Water Quality from the main menu 3 Select General from the Far field water quality all modules selection window 4 Select Coupling and start COUP GUI by selecting Define input 5 Open in COUP GUI Data Group Hydrodynamics and open lt com 02d dat gt Deltares 15 D Wag NESTWO User Manual N 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 16 Save the input as lt com o2d hyd gt Select File Exit to leave COUP GUI Select Start to execute the coupling A window opens with messages from the coupling Close this window when the coupling is finished Go back by s
12. d 2d adm X Y co ordinates overall model grid table with active cells overall model X Y co ordinates nested model rid table with active cells nested model jagnostics from NESTWO1 nest segments and weight factors overall model Figure 3 9 Input file for NESTWQ1 Deltares 9 D Wag NESTWO User Manual 10 Deltares 4 4 1 Input and output NESTWO1 and NESTWO2 have each their own input file The input files lt nestwg1 inp gt and lt nestwg2 inp gt respectively are free formatted ASCII files Input NESTWQ1 The input file lt nestwg1 inp gt contains the following information lt com ext1 cco gt CHARACTER the overall grid in X Y co ordinates at the depth loca tions lt com ext1 lga gt CHARACTER the table with in active segment numbers of the over all model lt com ext2 cco gt CHARACTER the nested grid in X Y co ordinates at the depth loca tions lt com ext2 lga gt CHARACTER the table with in active segment numbers of the nested model lt nestwq1 dia gt CHARACTER diagnostics from NESTWQ1 and the required nest segments in D Water Quality monitor format lt nestwq1 adm gt CHARACTER per boundary segment the overall nest segments and weight factors required for the nesting procedure in NESTWQ2 The filenames between quotes are free to choose with a maximal length of 128 characters Remarks The required information about the vertical structure of the models is contained in
13. dia gt Type ASCII Deltares 27 D Wag NESTWO User Manual Format free formatted Contents the file contains information about subsystem name and version number the names of input and output files used by NESTWQ2 the number of active substances the names of input files used by NESTWQ1 model and run identification of the simulation with the overall model total number of variables on the map file variable names on the map file selected variables to nest warnings and errors occurred while executing NESTWO2 Name lt ext bcc gt Type binary Access transparent Contents for each time step an integer and NOSYS NOBND reals itime CONC isys ibnd isys 1 NOSYS ibnd 1 NOBND 28 Deltares 8 8 1 8 2 Theoretical background Boundary segments Boundary segments are segments with a negative segment number In case of an aggregated grid there may be more than one boundary segment with the same negative number Nor mally when aggregation is done interior grid cells will be aggregated the boundary segments will not be aggregated In the nesting procedure the time series from the nest segments are interpolated to the centre of each individual boundary segment If boundary segments are aggregated these interpo lated time series are then averaged over the boundary segments with the same segment number Nest segments and weights The centre of each boundary segment determines in which
14. dm Map file overall model 02d waq map Number of active substances to nest 4 Diagnostics NESTWQ2 2d 2d dia2 Boundary conditions for nested model 2d2dwaq bcc Deltares NESTWQ1 Version 2 04 02 25853 Jan 18 2013 09 42 45 gt gt Files used to determine nest characteristics X Y co ordinates overall model com o2d cco Grid table with active cells overall model com o2d lga Number of segments overall model per layer 4774 Number of layers overall model 1 X Y co ordinates nested model com d2d cco Grid table with active cells nested model com d2d lga Number of segments nested model per layer E 7400 Number of layers nested model 1 gt gt Delft3D WAO map file characteristics Model and run identification 1 Delft3D WAQ 1 2 Upgrade WAHMO coarse model 2 3 test 3 4 map results to nest SIU LAM 4 Total number of variables 7 Variable names on map file Substance 1 Substance 2 Substance 3 Substance 4 Deltares 21 D Wag NESTWO User Manual Selected variables to nest Total number of segments gt gt Number of warnings gt gt Number of error messages 22 Inactive subst Inactive subst Extra variable Substance Substance Substance Substance 4774 P W N Deltares 6 Limitations warnings and errors 6 1 Limitations The X Y co ordinates of the overall grid and the nested grid are stored in so called binary
15. e If the format or structure of the input lt cco gt or lt Igrid gt files is incorrect the following errors will be given ERROR while reading nestwql inp sok ERROR premature EOF nestwql inp ERROR while reading lt com ext cco gt xxx ERROR xxx premature EOF lt com ext cco gt ERROR while reading lt com ext lga gt ERROR xxx premature EOF lt com ext lga gt The following dimensions may be too small they can be increased in the main program ERROR increase MNMAX to xxxxx ERROR increase MAXBND to xxxxx xxx ERROR increase MAXAGR to xxxxx ERROR increase MAXNST to xxxxx When the lt cco gt or lt x Iga gt file mismatch the errors are 24 Deltares Limitations warnings and errors xxx ERROR inconsistent MMAX MMAX cco xxxxx MMAX lga xxxxx xxx ERROR inconsistent NMAX NMAX cco xxxxx NMAX lga xxxxx xxx ERROR inconsistent LAYT LAYT cco xxxxx LAYT lga xxxxx The next two errors may not occur when they occur your data files were corrupted ERROR xxx increase NMAX in pinpol to xxxx ERROR xxx number of nest segments xxxxx at boundary segment xxx xxx Failures in the determination of the weight factors may cause the errors ERROR Singular points for ichoic x ERROR no convergence newton raphson iteration ichoic xxx Errors from subsystem NESTWO2 can be xxx ERROR The file nestwq2 inp does
16. ed above To access the nesting tool between an overall water guality model and a detailed water guality model select the far field water guality module o Select Water Ouality in the main window see Figure 3 2 The nesting functionality is exactly the same for all water guality modules therefore The selection window for Water quality WAQ is displayed Figure 3 3 in which you can convert and or aggregate hydrodynamic results prepare a substance file using the Process Library Configuration Tool prepare a water quality input file run the pre processor execute a computation inspect the report files with information on the execution visualise the results and access additional tools 6 Deltares Getting started du D Deltares Deift30 4 1 0 jooo HMB F Computer My Compi R mooiman b b b B manuals source tutorial win32 Directory Files of type Directories Ji D Deltares Delft30 4 1 0 tutorial waq nestwa 2d 2d 10900 BB yli My Computer k mooiman Name 2d 2d adm 2d 2d dial 2d 2d dia2 2d2dwag bcc LJ com d2d are LJ com d2d atr com d2d cco LJ com d2d chz LJ com d2d dat B com d2d def _ com d2d dps _ com d2d flo LJ com d2d hyd _ com d2d inp com d2d len ra Size Type 10 KB adm File 13KB dial File 4KB dia2 File 3KB bcc File 520 KB are File 66 bytes atr File 57 KB cco
17. electing Return in the Hydrodynamic coupling window Select Define input to start the WAQ GUI Activate in WAQ GUI Data Group Hydrodynamics and select lt com 02d hyd gt file Set dispersion to 10 m s in x and y direction Activate Data Group Substances and select file lt tracer sub gt Set Time Frame to 1 1 2000 3 1 2000 timestep 3 minutes Select Numerical option 5 in Data Group Numerical options Add two discharges at 32 28 and 44 28 and assign a load of 1000 g s of CTR1 to both discharges Data Group Discharges by button Edit data Select Output Option Data Group and set output timers for the map file to 1 1 2000 start 3 1 2000 stop 1 hour time step Save scenario as lt x scn gt file e g lt testo scn gt Exit the WAQ GUI Select Wag 1 in selection window select scenario file e g lt testo scn gt Check report files on errors Select Wag 2 to start the calculation Visualise the results with Delft3D QUICKPLOT or GPP QUICKPLOT 2013 GPP 2013 Repeat the above steps for the detailed model lt com d2d dat gt without step 16 and save the results in e g lt testd scn gt no discharges added Select Tools in the Water quality WAQ menu The following menu will appear 24 1 Edit or create input file for NESTWQ1 You have to specify the names of the lt Iga gt and lt x cco gt files of the overall and detailed model conform the documentation e g lt com o2d gt lt com d2d gt Specify administ
18. ess transparent Contents 1 empty record 2 2 integers 3 reals 2 integers MMAX NMAX XCOR1 YCOR1 0 0 0 LAYT 1 9 records with 0 0 12 NMAX MMAX reals X k k 1 NMAX MMAX 13 NMAX MMAX reals Y k k 1 NMAX MMAX Name lt com ext1 lga gt lt com ext2 lga gt Type binary Access transparent Contents 1 7 integers NMAX MMAX NMNW LAYT NOQ1 NOQ2 NOQ3 2 NMAX MMAX integers LGRID k k 1 NMAX MMAX Name lt nestwg1 dia gt Type ASCII Format free formatted Contents the file contains information about subsystem name and version number the names of the input and output files of NESTWQ1 the required overall segments in D Water Quality monitor for mat warnings and errors occuured while executing NESTWQ1 Name lt nestwq1 adm gt Type ASCII Format free formatted Contents the file contains information about subsystem name and version number the filenames which have been used in the nesting procedure the number of segments per layer in both models the number of layers in both models per boundary segment the required overall nest segments and their weight factors Name lt d3d waq map gt Type binary Access transparent Contents 1 4 character 40 model and run id 2 2 integers NOVAR and NOSEG 3 NOVAR character 20 variable names 4 for each time step an integer and NOVAR NOSEG reals itime CONCf ivar iseg ivar 1 NOVAR iseg 1 NOSEG Name lt nestwg2
19. in the nested model average these boundary conditions in case of aggregated boundary segments in the nested model generate a D Water Quality boundary conditions file for the nested model Overview subsystems Deltares 3 D Wag NESTWO User Manual Data flow NestWQ nestwq1 inp Iga overall Iga detail cco overall cco detail NESTWQ1 Administration Diagnostic adm dia nestwq2 inp map overall nr of substances Diagnostic NESTWQ2 KR dia Boundaries for detail model run detail model bec Figure 2 1 Data flow diagram of D Waq NESTWQ 4 Deltares 3 1 3 Getting started U Starting Delft3D To start Delft3D o On an MS Windows platform select Delft3D in the Applications menu or click on the Delft3D icon on the desktop On Linux and UNIX machines type Delft3D MENU on the command line Next the title window of Delft3D is displayed Figure 3 1 After a short while the main window of the Delft3D MENU appears Figure 3 2 Whether or not you may use specific Delft3D modules and features depends on the license file you have For now only concentrate on exiting Delft3D MENU hence o Select Exit The window will be closed and you are back in the Windows Desk Top screen for PCs or on the command line for Linux and UNIX workstations Remark O In this and the following chapters several windows are shown to illustrate the presen tation of Delft3D MENU and
20. king directory window to set the working directory to lt waq nestwq 2d BY de n dr Bi KIVET a de kr Ge kr dd et AG EE 7 3 6 Current working directory ke L 8 3 7 Selection window for Additional tools 8 3 8 Selection window for Additional tools nesting water quality models 9 3 9 Input file for NESTWQ1 e 9 5 1 Dialog for selecting output from NESTWO2 in D Water Quality GUI 17 5 2 Upgrade and Siu Lam models se 18 5 3 Siu Lam model with 2 open boundaries east and west 18 Deltares v D Wag NESTWO User Manual vi Deltares 1 1 1 2 1 3 A guide to this manual Introduction This User Manual concerns the offline water quality nesting module D Wag NESTWQ of the Delft3D software suite To make this manual more accessible we will briefly describe the contents of each chapter and appendix If this is your first time to start working with D Wag NESTWQ we suggest you to read and practice the getting started of Chapter 3 and the tutorial of Chapter 5 These chapters explain the user input and guide you through the definition of your first nested simulation Chapter 2 Introduction to D Wag NESTWQ provides specifications of D Wag NESTWQ such as the areas of applications the functionality provided and an overview of the system Chapter 3 Getting started explains the use of the overall menu program which gives access to all Delft3D modules and to the pre and post proces
21. le with active cells nested model 92d 2d dial diagnostics from NESTWQ1 2d 2d adm nest segments and weight factors overall model Diagnostics file Diagnostics file lt 2d 2d dia1 gt Deltares NESTWQ1 Version 2 04 02 25853 Jan 18 2013 09 42 45 gt gt Input from nestwqi inp X Y co ordinates overall model com o2d cco Grid table with active cells overall model com o2d lga X Y co ordinates nested model com d2d cco Grid table with active cells nested model com d2d lga Diagnostics and reguired nest segments 2d 2d diai Nest segments and weight factors overall model 2d 2d adm Weight factors for boundary 1 aggr no 1 1 0 4713E 00 2 0 2868E 00 3 0 9152E 01 4 0 1504E 00 Weight factors for boundary 2 aggr no 1 1 0 6820E 00 2 0 9224E 01 3 0 2690E 01 4 0 1989E 00 WARNING negative 3rd weight for 9 1 WARNING negative 4th weight for 9 1 Weight factors for boundary 68 aggr no 1 1 0 4379E 00 2 0 2572E 00 3 0 1128E 00 4 0 1921E 00 gt gt List of required nest segments in Delft3D WAQ monitor format Deltares 19 5 2 3 D Wag NESTWO User Manual Number of reguired nest segments 1719 1781 2897 1717 1778 2895 1715 1652 2956 1650 1710 1647 1708 1768 1829 1766 1827 Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest segment segment segment segment seg
22. ment segment segment segment segment segment segment segment segment segment segment segment segment 1719 1781 2897 1717 1778 2895 1715 1652 2956 1650 1710 1647 1708 1768 1829 1766 1827 gt gt Number of warnings gt gt Number of error messages Administration file 1720 1780 2959 2958 1716 1654 1653 1713 2894 1711 1648 1771 1769 1706 1767 1890 1888 Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest Nest segment segment segment segment segment segment segment segment segment segment segment segment segment segment segment segment segment 51 1720 1780 2959 2958 1716 1654 1653 1713 2894 1711 1648 1771 1769 1706 1767 1890 1888 1782 1718 1779 2896 2957 1655 1714 1651 1712 1649 1709 1770 1707 1830 1828 1889 1826 Nest administration data file lt 2d 2d adm gt only a part is given Deltares NESTWQ1 Version 2 04 02 25853 Jan 18 2013 09 gt gt Files used to determine nest characteristics X Y co ordinates overall model Grid table with active cells overall model Number of segments overall model per layer Number of layers overall model X Y co ordinates nested model Grid table with active cells nested model Number of segments nested model per layer Number of layers nested model gt gt List of boundary segments reguired nest segments and Nest
23. of the nested model the results from the overall model are reguired as boundary conditions for the nested model The boundary conditions can be water levels currents fluxes or discharges in case of hydrodynamic models and water guality parameters in case of water guality models System name and subsystems The procedure of nesting through concentrations between D Water Quality D WAQ UM 2013 or PART 2013 models is performed by the system NESTWQ In this procedure two steps can be distinguished which are handled by separate subsystems o D Wag NESTWO 1 for the determination of nest segments and nest weights in the overall model The concentrations at these segments are used by the next subsystem o D Wag NESTWQ 2 for the generation of boundary conditions for the boundary segments in the nested model from the results at the nest segments in the overall model Functionality The functionality of the subsystem D Wag NESTWA 1 is determine for each boundary segment in the nested model which nest segments in the overall model are reguired for the nesting of results to these boundary segments determine for each nest segment the weight factors for the interpolation from the surround ing nest segments to the boundary segment in the nested model The functionality of the subsystem D Wag NESTWQ 2 is interpolate the concentration time series from the nest segments in the overall model to boundary conditions for the boundary segments
24. or the waters north of Lantau Island It uses a curvilinear fine grid The hydrodynamic model was developed to investigate the effects of various layouts for a proposed typhoon shelter at Siu Lam As an example to demonstrate the nesting of water guality models a water guality model based upon the hydrodynamic SIU LAM model was set up For the generation of water guality boundary conditions for the WO SIU LAM model the model is nested in a coarse version of the WQ UPGRADE WAHMO model Figure 5 1 shows the coarse grid UPGRADE WAHMO together with the fine grid SIU LAM The locations of the boundary segments of the SIU LAM model are presented in Figure 5 2 In the following application grid cells have not been aggregated in both models Both 3D models have 5 layers Deltares 17 D Wag NESTWO User Manual Select active grid X Y 806512294 821854887 Cartesian 1 domain s selected Figure 5 2 Upgrade and Siu Lam models Fie Edt Opens View Sting Help seoxkpodomelr arr nr Choose menu option X Y 806374 806 822435 561 Figure 5 3 Siu Lam model with 2 open boundaries east and west 18 Deltares 5 2 5 2 1 5 2 2 Tutorial Input and output NESTWQ1 Input file Input file lt nestwg1 inp gt com o2d cco X Y co ordinates overall model com o2d lga grid table with active cells overall model com d2d cco X Y co ordinates nested model com d2d lga grid tab
25. ount for drying in the overall model If there are missing boundary segment numbers gaps in the numbering they will get the value 0 0 as concentration in the boundary conditions file 6 2 Warnings Warnings from subsystem NESTWQ1 can be x WARNING centre of boundary segment xxxxx M N xxx xxx not inside a nest segment the nearest nest segment will be taken When the centre of a boundary segment is not inside the polygon spanned by the centres of the nest segments extrapolation takes place This may cause one or more negative weight factors Consequently this may lead to negative concentrations To avoid this NESTWQ2 will reset negative concentrations to 0 0 The following four warnings may occur WARNING negative ist weight for XXX xxx WARNING negative 2nd weight for XXX xxx sk WARNING negative 3rd weight for XXX xxx WARNING negative 4th weight for XXX xxx Deltares 23 6 3 D Wag NESTWO User Manual When the seguence of boundary segment numbers is interrupted the following warning is issued In the time series file for the nested model a missing boundary segment will have zero concentrations WARNING xxx boundary segment xxx is missing NESTWO2 gives no warnings Errors Errors from subsystem NESTWQ1 can be xxx ERROR The file nestwql inp does not exist The following error is related to missing grid or segment numbers files ERROR xxx non existing fil
26. overall nest segment the centre is located Depending on the guadrant within this nest segment maximal three other adjacent nest segments are determined It may be possible that 3 2 1 or no other nest segments can be specified For instance when the first nest segment is at the edge of the overall grid only 1 additional nest segment may be identified When the centre of a boundary segment is not included in any overall segment then the nearest overall segment is taken as the only nest segment The criterion for the nearest segment is that segment with the shortest distance between its centre and the centre of the boundary segment The centres of the nest segments and the centre of the boundary segment determine the weights for each nest segment The options are linear 2 and 3 nest segments and bi linear 4 nest segments interpolation Deltares 29 D Wag NESTWO User Manual 30 Deltares References D WAQ UM 2013 D Water Quality User Manual Deltares 4 02 ed 3 15 GPP 2013 Delft3D GPP User Manual Deltares 2 14 ed 16 N PART 2013 DelftsD PART User Manual Deltares 2 13 ed 3 OUICKPLOT 2013 Delft3D QUICKPLOT User Manual Deltares 2 14 ed 16 Deltares 31 D Wag NESTWO User Manual 32 Deltares Deltares sustems PO Box 177 31 0 88 335 81 88 2600 MH Delft sales deltaressystems nl Rotterdamseweg 185 www deltaressystems nl 2629 HD Delft The Netherlands Photo by Mathilde Matthij
27. ration file e g lt 2d 2d adm gt 24 2 Start NESTWQ1 Within this step a diagnostic file and an administration file is created which is re quired input for the second step of the of the nesting NESTWQ2 24 3 Editor create input file for NESTWQ2 You must specify the name of the adminis tration file created by step 2 the name of the water quality map file of the overall model e g lt testo map gt the number of active substances to nest and the name of the binary boundary output file for the detailed model e g lt 2d 2d bcc gt 24 4 Start NESTWQ2 Within this step a diagnostic file and an boundary file is created which is required input for running the water quality detailed model 24 5 Examine diagnostic files of NESTWQ1 and NESTWQ2 24 6 Edit nested WAQ input file In this step you must add the created boundary file name step 4 by editing block 4 of the water quality input file e g lt testd inp gt goto block 4 replace the block of lines starting with ITEM right after the Thatcher Harleman timelags for each boundary segment up to but not including the line 5 delimiter for the fifth block by the single line 2 information in binary file write on a new record the boundary filename between quotes e g 2d 2d bcc delete all other information in the following records in block 4 until block 5 Note You can also use the D Water Quality user interface select the Boundary Condi Deltares
28. s the reguired information about the vertical structure of each model See Chapter 5 for an example of these files 4 3 Input NESTWO2 The input file lt nestwg2 inp gt contains the following information lt nestwq1 adm gt CHARACTER the nest administration file with per boundary seg ment the overall nest segments and weight factors required for the nesting procedure in NESTWQ2 lt d3d waq map gt CHARACTER the map file with results from the overall model nosys INTEGER the number of active substances to be nested lt nestwq2 dia gt CHARACTER diagnostics from NESTWQ2 lt ext bcc gt CHARACTER the boundary conditions at the aggregated bound ary segments of the nested model The filenames between quotes are free to choose with a maximal length of 128 characters O Remark o The first nosys active substances will be transferred as boundary conditions for the nested model Example input file lt nestwg2 inp gt gt Jnestwqi v20V3d 3d adm nest segments and weight factors overall model 03d waq map map file overall model 4 number of active substances to nest 3d 3d dia diagnostics from NESTWQ2 3d3dwaq bcc boundary conditions for nested model we we we 42 Deltares Input and output 4 4 Output NESTWO2 The output files of NESTWO2 are lt nestwg2 dia gt the diagnostics from NESTWO2 lt ext bcc gt the boundary conditions at the aggregated boundary segments of the nested model See Ch
29. sing tools D Wag NESTWQ being one of them as part of the WAQ module Chapter 4 Input and output provides detailed information on the parameters in the input file and the output files from D Wag NESTWO Chapter 5 Tutorial emphasis at giving you some first hands on experience in using the D Waq NESTWQ tool Chapter 6 Limitations warnings and errors discusses the underlying assumptions and warnings and errors that might occur Chapter 7 Description files explains in detail the contents of input and output files Chapter 8 Theoretical background provides information about boundary segments nest segments and weights References provides a list of related Delft3D modules and background information Manual version and revisions A manual applies to a certain release of the related numerical program This manual applies to D Wag NESTWQ 1 version 2 00 02 and D Wag NESTWQ 2 version 2 00 03 Typographical conventions Throughout this manual the following conventions in text formats help you to distinguish be tween different types of text elements Deltares 1 D Wag NESTWO User Manual Example Description Waves Title of a window or sub window Boundaries Sub windows are displayed in the Module window and cannot be moved Windows can be moved independently from the Mod ule window such as the Visualisation Area window Save Item from a menu title of a push button or the name of a user interface inpu
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31. t field Upon selecting this item click or in some cases double click with the left mouse button on it a related action will be executed in most cases it will result in displaying some other sub window In case of an input field you are supposed to enter input data of the reguired format and in the reguired domain lt tutorial wave swan curvi gt lt siu mdw gt Directory names filenames and path names are ex pressed between angle brackets lt gt For the Linux and UNIX environment a forward slash is used in stead of the backward slash for PCs 27 08 1999 Data to be typed by you into the input fields are dis played between double quotes Selections of menu items option boxes etc are de scribed as such for instance select Save and go to the next window delft3d menu Commands to be typed by you are given in the font Courier New 10 points gt User actions are indicated with this arrow m s Units are given between sguare brackets when used next to the formulae Leaving them out might result in misinterpretation 2 Deltares 2 2 1 2 2 2 3 Introduction to D Wag NESTWQ The transfer of data from an encompassing or overall numerical model to an embedded or nested numerical model is called nesting In general the overall model has a coarse resolution of grid cells whereas the nested model has a higher resolution At the boundary locations
32. the grid files If the overall model is 2DH and the nested model is 3D NESTWQ2 will generate a uniform 3D profile for the nested model If the overall model is 3D and the nested model is 2DH NESTWQ2 will generate depth averaged boundary conditions for the nested model If both models are 3D then the number of layers in each model must be equal Example input file lt nestwq1 inp gt gt nkers 3d com 03d cco gt hkcrs 3d com 03d 1lga gt siulam 3d com d3d cco gt siulam 3d com d3d 1lga 3d 3d dia 3d 3d adm Deltares X Y co ordinates overall model grid table with active cells overall model X Y co ordinates nested model grid table with active cells nested model diagnostics from NESTWQ1 nest segments and weight factors overall model 11 D Wag NESTWO User Manual 4 2 Output NESTWQ1 The output files of NESTWQ1 are lt nestwg1 dia gt the diagnostics from NESTWO1 and the reguired nest segments in D Water Ouality monitor format lt nestwq1 adm gt per boundary segment the overall nest segments and weight factors required for the nesting procedure in NESTWQ2 O Remarks It is not necessary to include the required nest segments in the simulation with the overall model as the nesting is performed with the results in the map file The map file contains the concentrations at every grid point thus including the reguired nest segments o The administration file contain
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