MOHID Studio - Quick-Start Guide for MOHID Water Implementation - V.2

7/10/2015 MOHIDStudioQuickStartGuideforMOHIDWaterImplementationv.2.0ActionModulers

http://wiki.actionmodulers.dtdns.net/index.php?title=MOHID_Studio__QuickStart_Guide_for_MOHID_Water_Implementation__v.2.0 1/25

MOHIDStudioQuickStartGuideforMOHIDWaterImplementationv.2.0FromActionModulers

Contents

1Preface1.1Copyright1.2Warranty1.3FurtherInformation

2QuickStartTutorialforMOHIDWater2.1Exploringasampleproject

2.1.1Step1Openingthepredefinedproject2.1.2Step2Recognizingtheprojectstructureandstudyarea2.1.3Step3Runningthesimulation2.1.4Step4ExploringtheResults

2.2CreatingyourownprojectSimulating2DHydrodynamicsforcedwithtide2.2.1Step1CreatinganewMOHIDWaterSolutionandDomain2.2.2Step2GeneratetheBathymetry2.2.3Step3GenerateTide2.2.4Step4Createanewsimulation2.2.5Step4Definethesimulation

2.2.5.1Step4.1DefineBathymetryfortheproject2.2.5.2Step4.2DefinesimulationstartandendinModelfile2.2.5.3Step4.3DefinegaugestidalcomponentsinTidefile2.2.5.4Step4.4DefineverticaldiscretizationinGeometryfile2.2.5.5Step4.4DefinehydrodynamicoptionsinHydrodynamicfile2.2.5.6Step4.5DefineturbulenceparametersinTurbulencefile2.2.5.7Step4.6OtherFiles2.2.5.8Step4.7DefineOutput

2.2.6Step5Runthesimulationandexploreresults2.3CreatingyourownprojectSimulating3Dhydrodynamicsforcedwithtide,riverdischargeandmeteorology

2.3.1Step1GetMeteorologyandRiverDischarges2.3.1.1Step1.1GetdataintoMOHIDTimeSeriesformat2.3.1.2Step1.2Definedischargeslocations2.3.1.3Step1.3Defineflowandpropertydischarged

2.3.2Step2Createanewsimulation(copyaprevious)2.3.3Step3Definethesimulation

2.3.3.1Step3.1DefineAtmospherefileandInterfaceWaterAir2.3.3.2Step3.2DefineDischargesfilewithdischargedflowandproperties2.3.3.3Step3.3DefineverticaldiscretizationinGeometryfile2.3.3.4Step3.4DefineHydrodynamicfile2.3.3.5Step3.5DefineTurbulenceandGOTMfiles2.3.3.6Step3.5DefineWaterPropertiesfile

2.3.4Step4Runthesimulationandexploreresults2.4CreatingyourownprojectSimulatingsedimenttransport


2.4.2.1Step2.1AddcohesivesedimentpropertyandparametersinInterfaceSedimentWaterfile2.4.2.2Step2.2DefinecohesivesedimentpropertyverticalvelocityinFreeVerticalMovementfile2.4.2.3Step2.3AddcohesivesedimentpropertyinDischargesfile2.4.2.4Step2.4AddcohesivesedimentpropertyinWaterPropertiesfile

2.4.3Step3Runthesimulationandexploreresults2.5CreatingyourownprojectSimulatingpointdischarges

2.5.1Step1Definethepointdischarges2.5.1.1Step1.1Definedischargeslocations2.5.1.2Step1.2Defineflowandproperty


2.5.3.1Step3.1DefineDischargesfilewithdischargedflowandproperties2.5.3.2Step3.2DefineinWaterPropertiesfiledischargedproperties2.5.3.3Step3.3DefinetheLagrangiandischarge

2.5.4Step4Runthesimulationandexploreresults2.6CreatingyourownprojectSimulatingnutrienttransportandtransformation(nutrientcycles)


2.6.2.1Step2.1AddtoWaterPropertiesfilethepropertiesneededtorunthewaterqualitymodels2.6.2.2Step2.2AddWaterQualityfilewithdefinedrates2.6.2.3Step2.3AddtoInterfaceSedimentWaterfilethepropertiesneededtorunthequalitymodels2.6.2.4Step2.4AddBenthosfilewithdefinedrates2.6.2.5Step2.6DefineOtherFiles

2.6.3Step3Runthesimulationandexploreresults3FinalRemarks

Preface



Copyright

ThisdocumentreferstoMOHIDStudio,proprietarycomputersoftwarewhichisprotectedbycopyright.Allrightsarereserved.CopyingorotherreproductionofthisdocumentorrelatedprogramsisprohibitedwithoutpriorwrittenconsentofActionModulers,ConsultoresdeSegurana(ActionModulers).

MOHIDWaterModellingSystemisproprietarysoftwareoftheInstitutoSuperiorTcnicofromUniversityofLisbon.

Warranty

ThewarrantygivenbyActionModulersislimitedasspecifiedinyourSoftwareLicenseAgreement.Pleasenotethatnumericalmodelingsoftwareprogramsareverycomplexsystemsandmaynotbefreeoferrors,soyouareadvisedtovalidateyourwork.ActionModulersshallnotberesponsibleforanydamagearisingoutoftheuseofthisdocument,MOHIDStudio,MOHIDWaterModellingSystemoranyrelatedprogramordocument.

FurtherInformation

ForfurtherinformationaboutMOHIDStudiopleasecontact:

ActionModulersConsulting&Technology

EstradaPrincipal,n29Paz

2640583Mafra,Portugal

Tel.:+351261813660

Fax:+351261813666

Email:[email protected]

Web:http://www.actionmodulers.com

QuickStartTutorialforMOHIDWater

This"QuickStartTutorialforMOHIDWater"isintendedtohelpfirsttimeuserscreatingtheirfirstprojects,followingasampleproject,animplementationintheTagusEstuary,nearLisbon,Portugal.

Itissuggestedthattheuserfollowsthetutorial,whichprogresseswithincreasingcomplexity,tryingtoreplicatetheprovidedsampleproject.Afterfinishedexploringallsimulationswiththesamples,itissuggestedthattheuserrevisitsthetutorialapplyingthemodelexamplestohisstudysite.

ThetutorialstartswiththesampleprojectfortheusertogetusedtotheMOHIDStudioenvironment,projectandsimulationstructureandtostartexploringresultswithoutanypreviousknowledgeaboutusingMOHIDWater.

Afterthefirstplayaroundtheuserisinvitedtoindependentlycreateasimpleprojectwith2Dhydrodynamicsforcedwithtide,generatingthebathymetryandtidefiles,preparetheinputfiles,runthemodelandexploreresultsaspreviously.

Thetutorialthenstartstoincrementcomplexityprovidingastepbysteptoimplementafull3Dsimulationwithriverdischargesandmeteorology,sedimenttransport,pointsources(usingalsoLagrangianapproach)andendinginnutrienttransportandtransformation(fullwaterqualitysimulation),resultinginoneofthemostcompletesimulation(allprocessesconnected)thatcanberunwithMOHIDWater.

Sincekeywordsandblocksofkeywordsneedtobedefinedintheinputfiles,fortheuserconvenience,theuserisguidedtocopydatafilesfromthesampleproject.

ThisisintendedtobeastepbysteptutorialtoimplementinastraightforwardwayaMOHIDWaterprojectfromsimplertocomplexsimulations.Detaileddescriptionisnotgivenforprocesses,keywords,modelfunctioning,etc.ForthatintenttheusershouldexploreMOHIDsources:

ActionModulerswebsitehttp://www.actionmodulers.com

MOHIDwebsitehttp://www.mohid.com/

MOHIDwikihttp://wiki.mohid.com/wiki

MOHIDforumhttp://www.mohid.com/forum/

MOHIDcoderepositoryhttp://mohid.codeplex.com/

Exploringasampleproject

ThetutorialstartsbyprovidingasampleprojectsothattheusergetsfamiliarizedtotheMOHIDStudiostructureandisabletogetthesamplesimulationrunningandproducemodelresults.Thiswaythetutorialallowstheusertostraightawayobtainsomemodelresultswithlittleeffortandtheninthefollowingchapterstheintermediatestepsareexplained(creatingtheprojectandsimulations).

ItisassumedthattheuserhasalreadyinstalledMOHIDStudio(followingMOHIDStudioInstallGuide)andisawareandunderstandsthefunctioningofthedifferentwindows,environmentsandbuttons(followingMOHIDStudioUserGuide).

ThismanualappliestoMOHIDStudioversion1.2.7.

Step1Openingthepredefinedproject

DownloadtheTagusSample.zip(linkbelow)fromActionModulersWebPagetoyourlocaldisk(e.g.toD:\MOHIDStudioProjects).
http://www.actionmodulers.com/http://www.actionmodulers.com/http://www.mohid.com/http://wiki.mohid.com/wikihttp://www.mohid.com/forum/http://mohid.codeplex.com/



http://www.actionmodulers.pt/Biblioteca/Uploads/Downloads/Walkthroughs/TagusSample.zip

Createafolderinyourharddiskfortheproject(e.g.D:\MOHIDStudioProjects\TagusSampleandleaveitempty).

OpenMOHIDStudiowhereitshouldappearthe"WorkspaceManager"windowaskingtocreateanewworkspaceoropenasavedone(Figure1(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_02.png)).Select"StartwithanemptyWorkspace"andnameitforinstance"TagusSample".

Figure1:MOHIDStudioWorkspaceManager.

Select"Project"ribbonandin"Solution"group,press"Manage"andthe"SolutionManagement"windowappears(Figure2(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_03.png))showingthelistofsolutionavailable.IfusingMOHIDStudioforthefirsttimethelistwillbeempty.

Figure2:MOHIDStudioSolutionManagement.

Onthesame"SolutionManagement"windowpress"Import"andthe"ImportMOHIDSolutions"windowappears(Figure2(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_03.png))andin"ProjectFileName"browseforthe.zipfiledownloadedearlier(e.g.inD:\MOHIDStudioProjects)andin"DestinationDirectory"choosethedirectorywheretheprojectwillbeplaced(e.g.D:\MOHIDStudioProjects\TagusSample).Thedestinationdirectoryneedstobeempty.

Press"Import"andwaittilltheendoftheprocessandacceptthesuccessfulmessage.

Figure3:MOHIDStudioImportSolution.

NOTE:Ifasolutionwiththesamenameofthesolutiontoimportalreadyexists,thenewlyimportedsolutionisautomaticallyrenamed(example:TagusSample_1).
http://www.actionmodulers.pt/Biblioteca/Uploads/Downloads/Walkthroughs/TagusSample.ziphttp://wiki.actionmodulers.dtdns.net/index.php?title=File%3AMOHID_Studio_-_MOHID_Water_Quick_Start_Guide_v1_02.pnghttp://wiki.actionmodulers.dtdns.net/index.php?title=File%3AMOHID_Studio_-_MOHID_Water_Quick_Start_Guide_v1_03.pnghttp://wiki.actionmodulers.dtdns.net/index.php?title=File%3AMOHID_Studio_-_MOHID_Water_Quick_Start_Guide_v1_04.png



Thesolutionwasimportedandnowneedstobeopened.Select"Project"ribbonandin"Solution"group,press"Open"andthe"SolutionManagement"windowappearsnowwiththe"TagusSample"available.Selectitandpress"OK".

Figure4:MOHIDStudioLoadWorkspace.

Thiswillopenthe"TagusSample"solutionin"Explorer"tab.Pressonthetrianglejustlefttothesolutionicontoshowthedomaintree(itwillshow"TagusSample"domain).Pressonthetrianglejustlefttothedomainicontoshowthedomainfolderstructureandsimulationsavailable.Thereare5simulationsavailablejustthesameasthemainsimulationsofthistutorial.Inthenextsteps,theusermaycopythenecessaryfilesanddoesntneedtocreatethemfromscratch.

Step2Recognizingtheprojectstructureandstudyarea

Withthesolutionopenedanddomaintree,domainfoldersandsimulationstreevisible,theusershouldbeseethesamestructureaspresentedinFigure5(#labelfig:Mw5.png).

Figure5:MOHIDStudioExplorerWindowwithMOHIDWaterSample.

IfhavingsomedoubtsabouttheMOHIDStudiowindowsandstructurepleaserefertotheMOHIDStudioUserGuide.

Whenselectingeachsimulation,the"Modules"sectionontherightpaneisfilledwith"DataFiles"(textfileswithoptionsandinfoneededtoruneachsimulation)andnofilesexistin"HDFFiles"or"TimeSeriesFiles".Thelattercorrespondtomodelresults(mapsandtimeseries,respectively)anddonotexistbecausethesimulationhasntrunyet.
http://wiki.actionmodulers.dtdns.net/index.php?title=File%3AMw4.pnghttp://wiki.actionmodulers.dtdns.net/index.php?title=File%3AMw5.png



Beforerunninganysimulation,checkthestudyareabypressinginthefolderGeneralData\DigitalTerrain(seeFigure5(#labelfig:Mw5.png)),selectingthefile"TagusBathymetry.dat",andrightclickingitandpressing"AddtoMap"andthenpressing"OK".Selectthe"Map"tabandchecktheTagusEstuarybathymetry.Thisfilecontainsdataaboutthecomputationalgridandthebathymetryvalueforeachgridcell.Toplotabackgroundmapasreferencegoto"Map"ribbonandon"Background"grouppress"WebTiles".AcceptthechangeincoordinatesandselectforinstanceGoogleMapsorBingAerialandpress"OK"anditshouldresultsimilartoFigure6(#labelfig:Mw6.png).

Toshowthebathymetryscale,rightclickthebathymetrylayerandpress"Properties"check"Legend"box,writedownthelegendtextin"Text"boxandpress"OK".Unhidethelegendbypressing"Legend"inthebottomrightcornerof"Map"window.

Figure6:MOHIDStudioMapWindowwithprojectsamplebathymetry.

Step3Runningthesimulation

Torunthemodelselectthesimulationtorun(letsstartin"Sim#1"),goto"Project"ribbonandin"ExecuteModels"group,press"RunNow".Awindowwillappeartocheckiftheuserwantstoruntheselectedsimulation("Sim#1"),press"OK".

Theboxwindowcalled"ModelController"belowthedomainsandsimulationsisfilledshowingtheprogressbarofthesimulation(Figure7(#labelfig:Mw7.png)).Tocheckmoredetailsonthesimulationstatuspress"Output"buttontobeabletoseewhatisthecurrentsimulationtime,thecurrentcomputertimeandtheexpectedcomputertimewhenthesimulationwillend(thecontentofthislogiscontinuouslyupdated).The"Kill"buttononthesameboxwindowexiststoabortthesimulationatanytime.

Figure7:MOHIDStudioModelController.

Whenmodelrunfinishes(getsto100%inprogressbarorcrashed),awindowappears,warningthatthemodelhasfinishedandiftheuserwouldliketoseethelogfile(thesameasobtainedin"Output"inModelControllerbutnowthefinalfile)Figure8(#labelfig:Mw8.png).

Figure8:MOHIDStudioModelFinished.

Itisalwayssuggestedtowatchthelogtomakesurethatthesimulationendedsuccessfully(browsetilltheendofthefileFigure9(#labelfig:Mw9.png)).IftheuserdoesnotwanttoseethelogfileorclosesthelogfilethanissentbacktoMOHIDStudioandreadytoexploreresults.Thelogfilecanbeaccessedatanytimerightclickingeachsimulationandselecting"ViewLastLog".
http://wiki.actionmodulers.dtdns.net/index.php?title=File%3AMw6.pnghttp://wiki.actionmodulers.dtdns.net/index.php?title=File%3AMw7.pnghttp://wiki.actionmodulers.dtdns.net/index.php?title=File%3AMw8.png



Figure9:MOHIDStudioLogFilereportingthatsimulationendedwithsuccess.

Step4ExploringtheResults

Duringandafterthesimulationends,theoutputfilesarecreated.Whenselectingthesimulationthatjustfinishedrunning("Sim#1"),the"Modules"sectionontherightpaneisfilledwith"HDFFiles"and"TimeSeriesFiles".HDFfilescontainmodelresultsfortheentirecomputationalgridatdifferenttimeinstantsofthesimulation,similartoseveralinstantaneoussnapshotsofthestudyareathatcanbeplottedhasmapsandanimatedintime.Timeseriesfilescontainresultsforpredefinedcomputationalgridpointswithhighoutputfrequency.Latterinthisdocumentitwillbeexplainedhowtodefinetheoutputlocations.Onbothtypeoffilestheusermaychoosetheoutputfrequency(alsoexplainedlater).

DoubleclickingoneachHDFortimeseries,showsadialogtoselectthepropertiestoplot.MoreinformationonhowtovisualizeandcustomizeHDFresultscanbefoundinchapter4.6of"MOHIDStudioUserGuide"andinchapter5forthetimeseriesresults.

Toviewthetimeseriesresultsforcurrentvelocitymodulusinonepoint,inthe"TimeSeriesFiles"section,doubleclicktoopenthefile"Channel.srh"(locatedinTaguschannelinfrontofLisbon),andselecttheproperty"velocitymodulus"and"OK"toplot(Figure10(#labelfig:Mw10.png)).ThisisthevelocitymodulusvariationintimeintheTagusEstuarychannel.Toseethelocationofthispointandotherpointsthathavebeenselectedtoperformtimeseriesoutputs,in"Map"ribbon,and"VectorData"grouppress"XML"andopenTimeSeriesLocation.xmlinfolder"GeneralData\TimeSeries"ofthesampleproject,selectastheprojection"Geographic"andpress"OK".Thetimeseriespointswillbedisplayedon"Map"tab.Toknowthenameofeachpoint,selectthepointslayerandqueryit.PleaserefertoMOHIDStudioUserGuidechapter4onhowtoquerylayers.

Viewthemapresultsforvelocitymodulusfortheentiredomainbyopening,in"HDFFiles"section,thefile"Hydrodynamic_1.hdf5"andselect"velocitymodulus"in"Feature"fieldandpress"OK".Goto"Map"tabandpressplayon"Date&Time".Thisisthemapofvelocitymodulusfortheentiredomain(Figure11(#labelfig:Mw11.png))withamapforeachoutputtime.

Figure10:MOHIDStudiotimeseriesofvelocitymodulusforonedayinTagusChannelforSim#1inMOHIDWaterSamples



Figure11:MOHIDStudioHDFofvelocitymodulusforSim#1inMOHIDWaterSamples.

Toknowmoreonhowtocustomizethetimeserieswindow(axistitles,seriesnamesandcolors,etc.)andmapimages(colorscale,horizontalscale,etc.)followMOHIDStudioUserGuidechapter4and5.

CreatingyourownprojectSimulating2DHydrodynamicsforcedwithtide

Thissectionwillshowhowtostartanewprojectusingasimpleexampleofa2DtidepropagationintheTagusEstuary(thesameusedinMOHIDWatersamples).Thedescriptioncanneverthelessbeusedtoimplementthemodelinanystudysite.Onegoodexerciseforafirsttimeuseristotrytorepeatthesampleprojectfollowingtheinstructions.

Step1CreatinganewMOHIDWaterSolutionandDomain

CreateanewSolutiongoingto"Project"ribbonandingroup"Solution"pressing"New".Itwillbepromptedtonamethesolutionin"NameoftheSolution".Writedownforinstance"TagusSampleRedone"withoutthequotesifredoingthesampleproject.

Createanewdomaingoingto"Project"ribbonandingroup"Domain"pressing"New".Thefollowingwindowwillappear(Figure12(#labelfig:Mw12.png)).

Figure12:MOHIDStudiocreatenewdomain.

Theinformationprovidedinthe"Creatinganewdomain"windowcharacterizesyourdomain.Thefollowingrestrictionsmustbefulfilled:

thedomainnamemustbeuniquetherootdirectorymustbeempty.

In"DomainName"useyourlocationnameorforinstance"Tagus200m"inthecaseofredoingtheTagussamplecasesincewewillcreateanapplicationwherethecellsizewillbearound200mintheestuary(explainedafter).Sincethedomainislinkedtoahorizontalcomputationalgrid(bathymetry)thisnamingconventionisquitehandywhenhandlingdifferentresolutiongridsforthesamelocation.

Browsefora"RootDirectory"thatisemptyandthatislocatedinyourcomputerharddrive(tip:createinyourcomputerafolderpercomputationalgrid).

Thepathtothebathymetry("DigitalTerrainModel")willnotbespecifiedfornowsinceithasntbeencreatedyet.



PressOKtofinishthedomaincreation.

Moreinformationonhowtomanagesolutionsanddomainscanbefoundin"MOHIDStudioUserGuide"inchapter3.

Step2GeneratetheBathymetry

Inthissectionitisshownhowtogeneratethebathymetryfile.Thisfiledefinesthehorizontaldomain(computationalgridandbathymetryvaluesforeachgridcell)andisthebasicandmostessentialinformationneedtorunthesimulation("Sim#1"2DTide).

Figure13:MOHIDStudiocreatenewdomain.

Tocreateabathymetryfile,thefollowingisneeded:

Ahorizontalgrid.Thiswillbethecomputationalgridforthemodelandthegridforallthegriddedinformationinputtedtothemodel(spatiallydistributed).Digitalterrainelevationdatainpointformat(XYZ)Apolygoncontainingtheareaswherethemodelwillnotcalculateanysolution(e.g.landpoints).

Firstloadabackgroundlayer(BingAerialorGoogleMaps)in"Map"ribbon,"Background"groupandpress"WebTiles".Thislayerwillhelpyoutoidentifythestudysite.

InthecaseofredoingTagussample,zoominintothestudysiteinPortugal,LisbonFigure14(#labelfig:Mw14.png).

Figure14:LisbonandTagusestuaryareausingBingAerialasbackgroundimage.

HorizontalGrid

TheTagussamplewasbuiltwithagridofvariableresolutiontomakeitmoresuitedtodescribeinmoredetailtheareaoftheTaguschannelandsavecells.TobuildthiskindofgridsitismoresuitedtouseaMOHIDtoolcalledGenerateGrid[1]eventhoughitcanbebuiltalsoinMOHIDStudio(theuserhastoprovideallthexandydistances).Tosimplifytheprocedure(variablespacinggridsisforadvancedoptions),theexercisewillbedonewithaconstantspatialspacinggrid.

ToprocessthesameareaastheTagussamplegrid,openthesamplegridforguidancegoingto"Map"ribbonandin"ASCII"grouppress"Grid"andopenthefile"TagusBathymetryGrid.grd"fromthefolder"GeneralData\DigitalTerrain"ofthesampleproject.SeetheTagussamplegrid.

Tocreateaconstanthorizontalgrid(allcellswithsameresolution)goto"Tools"ribbonandin"Grids"group,press"Constant".



Figure15:Tocreateaconstanthorizontalgrid.

The"ConstructConstantSpaceGrid"windowappears.

Insection"2.Preview"check"AutoUpdate"sothatallthechangesthataredoneareimmediatelyvisible.Leaveuncheckediftheprocessisveryslowinthatcaseyouwillneedtopress"Refresh"tovisualizeyourchanges.Insection"1.GridParameters"theusermaydefine:Anorigin(lowerleftcornercoordinateofthegrid)byfilling"OriginX"and"OriginY"withgeographiccoordinates,or,simplypressing"Pick"itmayselectinthemaptheoriginpoint.FortheTagussamplecaseselectanoriginnearthelowerleftoftheprovidedgrid(TagusBathymetryGrid.grd).Thenumberofcolumnsandrowsorthenumberofcellsinxandydirection.IntheTagussamplecase(variablespacedgrid)145and120wereused,respectively,butfortheconstantgridaround280and200willbeneeded,respectively[2].Dxanddyorthecellsize(indegrees).IntheTagussamplecase,avariableresolutionwasusedbutinthiscaseuse0.004inboth(around400mx400mcells).Theoriginofthegridmaybechangedatanytime.Soifyourgridisnotinthecorrectpositionfeelfreetomoveitaround(press"Pick"andselectanotherorigin)andchecktheresult.Insection"3.SaveGrid"youmaysavethefileifeverythingisOK,choosingthefolderandfilename(saveitinGeneralData\DigitalTerrainofthenewproject(andnotonsampleproject).Ifdonotwanttosavethegridjustclosethetool.

FortheTagussamplecase,thegridshouldbesimilartotheoneinFigure15(#labelfig:Mw16.png).

Figure16:MOHIDStudioconstantgridtoolfortheTagussample.

FortheTagussamplecase,comparethegridgeneratedwiththeoneusedinTagusEstuary(TagusBathymetryGrid.grd).TheyareverydifferentinresolutionyetthecellsizeintheTaguschannelissimilar.

DigitalElevationData

Digitalelevationofthebottomoftheseausuallyisnotapublicresourceorifitishascoarseresolution.MOHIDStudiohasalsoaconversiontooltoprocessETOPO[3]1arcminute(around1kminTagus)elevationdatathatincludesbathymetricdatabutthisresolutionisnotsuitablefortheselectedhorizontalgridresolution.

Asso,ortheuserisintendingtosimulateawideareawithcoarseresolutionandmayuseETOPObathymetryorneedstogetelevationdataforitsownstudysite[4].

FortheTaguscasethisdataisprovidedinthesampleproject.Goto"Map"ribbon,"ASCII"groupandpressin"XYZPoints"andopenthefile"Tagus_bath_points.xyz"and"PortugueseCoast_bath_points.xyz"infolderGeneralData\DigitalTerrainofthesampleprojectandselect"Geographic"coordinatesandpress"OK".Tocomparebothoriginsofdataitisbetterifthescalesmatchbyrightclickingthemandpressing"Properties"andon"Style"section,press"Edit"andchangethemaximumandminimumtobethesame.

Nocomputeareas

Thisoptionisusedtoexcludeareasthatarelandandwherethemodelshouldnotspendtimecomputing.Iftherearenosuchareas(openoceansimulation)thanthisstepmaybeskipped.



Thelandareascanbeobtainedfromcoastlinesordrawdirectlyinthemap.FortheTagussampleacoastlineisprovided.

Tocreateacoastlinebydrawingoverthemap,goto"Tools"ribbonandin"GeometryLayers"group,press"Polygons".The"ConstructNamedPolygons"windowappears(seeFigure17(#labelfig:Mw18.png))andinsection"1.DefinePolygonsonMap"press"Draw"andstartpickingpointsthatdefinethelandboundaryandMOHIDStudiogeneratesautomaticallythepolygonformedbythepointsdoubleclickatthelastpointtofinishthepolygon.Ifwanttoremovethegeneratedpolygonusethe"Remove"buttoninsection"2.DefinedPolygons".Insection"3.SavePolygons"press"Save"andselectthefolderandfilenametosavethepolygon(saveitinGeneralData\DigitalTerrainofthenewprojectandnotonthesampleproject).

Figure17:MOHIDStudioPolygonTooltoselectnocomputepointsinTagusestuarygrid(justonepolygonfortheexample,allthelandareawouldneedtobecomprisedinonepolygonorseveralpolygons.

FortheTagussamplecase,anexistentcoastlinefileisusedsincethelandareasareverycomplex.Asso,goto"Map"ribbon,andin"ASCII"grouppress"Polygon"andopenthefile"CoastLine.xy"infolderGeneralData\DigitalTerrainfromtheTagussampleprojectandselect"Geographic"coordinatesandpress"OK"(Figure18(#labelfig:Mw19.png)).

Figure18:Tagusestuarygridandthelinecoastthatselectslandareasnottocompute.

GeneratingtheBathymetry

FinallythegenerationoftheBathymetryusesalltheabovestepsproducts:thegrid,theelevationpointsandthenocomputeareas.Theelevationinformationinpointswillbeinterpolatedtothegridcells,exceptinthecellsthatareinsidethenocomputepolygon.

Goto"Tools"ribbonandin"GridDataTools"grouppress"FromPoints"(creategriddatafrompoints)and"CreateGridData"windowappears(Figure19(#labelfig:Mw20.png)).Insection"1.SelectGrid"selectthegridthatwasgeneratedabove.Insection"2.NonComputeAreas"checkthepolygondrawnorcoastallineremindthatseveralpolygonscanbeselected.Insection"3.BaseInformation"check"Tagus_bath_points"and"PortugueseCoast_bath_points"remindthatseveralpointsourcescanbeselected.

Insection"4.Options"selectthemethodtocomputetheelevationforeachgridcellfrompointscollection.Whenhavingseveralpointsinsideeachcell(gridiscoarserthanelevationdata)select"Average"andthecellvaluewillbetheaverageofthepointsinsidethegridcell.Ifthegridhasfinerresolutionthandata(somecellsdonothaveanyrawinformationinside),aninterpolationalgorithmmustbeused.Theusercanselectselect"Triangulation"or"IWD"(inverseweighteddistance).InthecaseofredoingtheTagussamplechoose"Triangulation"sinceintheTaguscoastbathymetricdataissparserthancellresolution.

Insection"5.GenerateGridData"selectthefolderandfilenamefortheDTM(saveitinGeneralData\DigitalTerrainofthenewprojectandnotonthesampleproject).Pressthe"Process"buttontogeneratethebathymetryandafterawhiletheprocessendsandproducesthebathymetryfile.



Figure19:MOHIDStudioGridDatafrompointsTooltocreateabathymetry.

FortheTaguscase,comparethebathymetrygeneratedwiththeoneusedinTagusestuary(TagusBathymetry.dat)infolderGeneralData\DigitalTerrainofthesampleproject.

Step3GenerateTide

Oneofthemaindriversforwatercirculationincoastalareasistideandinthefirstsimulationthatistheonlyforcingagent.

FES(finiteelementsolution)tidemodelisthemostcommonsourceoftidalcomponentsbeingavailablefortheentireworldwhichthemostrecentmodelversionisFES2012andpreviousversionisFS2004.MOHIDStudioincorporatesatooltoobtaintidalcomponentfromFES2004andinthefuturewillhaveitupdatedforthemostrecentversion.

PleasenotethatforMOHIDStudioversion1.2.7theTidalToolisinstalledexternalasexternalplugin.Pleasefollowthelinkbelowtoinstallthisplugin.

http://www.actionmodulers.pt/default.aspx?canal=95

FortheTagussampleonlyatidalgaugewillbeused(extractedfromFES2004)sincetheobjectiveistoexplainthemainprocessesandtheusermayskipthisstep.However,theusershoulddotheirimplementationsalwaysusingthetoolwhichstepsaredescribednext.

BeforestartusingtheTidalTool,theusershouldloadthebathymetryforinstanceifnotalreadyloaded(previousstep).

Goto"Tools"ribbonandpress"TidalTool"andtheTidalToolwindowwillappear(seeFigure20(#labelfig:Mw21.png)).Thistoolisdividedunder3sections:1Definepointsonmap2Selectedgridpoints3Configtide.

Figure20:TidalToolwindowDrawpoints(start.

Thefirststeptousethistool,istodefinethepointsonMap.Clickonthe"Draw"button(thebuttonwillturnorange)andthenclickonthemaptodrawthepoints(seeFigure20(#labelfig:Mw21.png)).Thepointsshouldbedrawnontheboundariesoftheworkinglayerinzigzag,liketheonesshownontheexampleontheFigure21(#labelfig:Mw22.png).

Eachtimethemouseispressedanewbluemarkerwillappearonthemapandanewlineisaddedtothetable(seeFigure21(#labelfig:Mw22.png)).Eachlinerepresentsasinglepoint,withthecoordinatesofeachpointandname(bydefaultthepointnumberisincremented:Point_1,Point_2,andsoon).ThedecimalplacesfortheXandYcoordinatevaluescanbechangedonpanel1(bydefaultthedecimalplacesare4).
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Figure21:TidalToolpluginDrawingpoints(end.

Figure22:TidalToolConfigurations.

Theusercanremoveasinglepoint,byselectingasinglelineandpressingthe"Remove"button.The"ClearList"buttonwilleraseallpointsfromthetable.

Thepanel3isforthetideconfigurations(seeFigure22(#labelfig:Mw23.png)).Firstselectthepathtothe"tide.nc"file[5].Selectthetimereferencevalue(TimeRef)andthereferencelevelvalue(RefLevel).Selectalsothepathandnamefortheoutputfile.ThepathandnameforXYZfileisoptional.Ifthefilenameisempty,theXYZfilewillnotbesaved.

Thereferencelevelisthemeansealevel(measuredfromtheoriginofthebathymetryupwards)obtainedfromtidalgaugesinthearea(inTagusthemeansealevelis2.08mabovebathymetriczero).TheFEStidesolutionisinGreenwichMeridianTime(GMT)soneedtoadapttoyourareausingtimereference(e.g.Spainis1(+1)andwillbenegativetroughthewest).

Togeneratethetidefile(theoutputfile)justpressthebutton"Process".

Step4Createanewsimulation

Thelattersteps(createthebathymetryandtide)arethemostbasicstepstoimplementacoastalproject.Sonowthefirstsimulationcanbecreated,a2Dmodelwithtide,redoingthe"Sim#1"fromTagussample.

On"Explorer"tab,selecttheDomainnameandgoto"Project"ribbonandin"Simulation"grouppress"New".Nameyoursimulation(e.g.Sim#12DTide),andPress"OK"whenfinishedtohavethenewsimulationreadyFigure23(#labelfig:Mw24.png).



Figure23:MOHIDStudioNewSimulation.

Step4Definethesimulation

Selectingthejustcreatedsimulationshowsthatthesimulationhasseveralinputfileslistedinthe"Modules"sectionandin"DataFiles".Thesefilesshouldhavealltheoptionsneededtorunthemodelincludingthetideforcing,themainoptionstorun,etc.

Allthisinfoishardtoconstructfromscratcheverytimeanewprojectisimplementedsoitisrecommendedtoadaptthesettingsfromanalreadyexistingproject.

Sincethereisnoothersimulationtocopyfrom,todoacopyofthesettingsyouneedtoaddtoyoursolutionanotherdomain.Selectyoursolutionandgoto"Project"ribbonandin"Domain"grouppress"Open".Choosefromthelistthe"TagusSample"orotherprojectifyouhaveonethatyouwanttocopyfrom.Theselectedprojectwillappearunderthesamesolution.

Tocopythesimulationfiles,selectthesimulationtocopyfrom(ifthedomainjustaddedisTagussampleselectthe"Sim#12DTide")andgoto"Project"ribbonandin"Simulation"group,press"Copy".Thecopywindowappearsandletsyouchoosewhichfilesfromtheoriginsimulationtocopyandselectthedestinationsimulation(Figure24(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_23.png)).

Figure24:MOHIDStudiocopysimulationsbetweendomains.

Leavetheoriginunchangedbutselectthedestinationsimulation(insideyournewdomainselectthecorrectsimulation).Press"Copy"andafter"OK".Thiswillcopyallthesettingsfromtheoriginsimulationtothedestination.Nowsomeverificationsneedtooccurtoensurethatyoufillinthedatayoucreated(seenextsteps).
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Afteryouaredonecopyingyoucanremovetheaddeddomainfromthesolution,selectingitandgoingto"Project"ribbon,"Domain"groupandpressing"Remove".Thisactiondoesnotdeletethedomainfromthedisk,itjustremovesthedomainfromthesolutionthatisvirtual.InthecaseofredoingTagussampleitsfileswillbeneededinthenextsimulations,soleaveitfornow.

Step4.1DefineBathymetryfortheproject

Thebathymetryisapropertyofthedomainandremainsthesameforallsimulationssoitsdefinedinthedomainoptions.Editthedomainpropertiesbyselectingit,rightclickingandselecting"Properties".InThe"DigitalTerrainModel"browseforthebathymetryfilecreatedinthepreviousstepsFigure25(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_24.png)(thisimageisforTagussamplebutissimilartoanyproject).

Figure25:MOHIDStudioDomainPropertieswherebathymetryisdefined.

Step4.2DefinesimulationstartandendinModelfile

Thesimulationstart,endandtimesteprelatedinfoisinputtedinfileModel_X.datwhereisXisthesimulationnumber.Thisfileison"Explorer"tab,under"Modules"andin"DataFiles"section.

Thestartandenddatesareidentifiedwithkeywords"START"and"END"andtheformatisyear,month,day,hour,minuteandsecondintegernumbersseparatedbyspaces.

ThekeywordDTdefinesthemodeltimestep.

Thekeyword"GMTREFERENCE"isthesameasthetimereferenceintide.IfrunningthemodelinaplaceotherthaninGTM+0thanneedtoeditaccordingly(positivetoeastandnegativetowest).

AllthesekeywordscanbeeditedbutifredoingthesimulationfromTagusleaveitasis.

Step4.3DefinegaugestidalcomponentsinTidefile

TheinformationonthetidalcomponentswithinfoseparatedbygaugesisinputtedinfileTide_X.datwhereisXisthesimulationnumber.Thisfileison"Explorer"tab,under"Modules"andin"DataFiles"section.

Thetidefilecanbetakendirectlyfromtidetool(justcopytheoutputofthetidetooltothisfile).

IfredoingtheTagussample,onlyonegaugeisusedandcanbeleftasis.

Step4.4DefineverticaldiscretizationinGeometryfile

ThedefinitionofverticallayersisinputtedinfileGeometry_X.datwhereisXisthesimulationnumber.Thisfileison"Explorer"tab,under"Modules"andin"DataFiles"section.

IfredoingtheTagussampleorany2Dsimulationonlyonedomainandonelayerexists(keywordLAYERSis1)andsinceitisatypeSIGMAthethickness(keywordLAYERTHICKNESS)isdefinedinpercentageofdepthandvalueis1(100%).LeavethisfileunchangedfortheTaguscase.

Step4.4DefinehydrodynamicoptionsinHydrodynamicfile

Thehydrodynamicoptionstorun(whichforcingtoconsider)isinputtedinfileTurbulence_X.datwhereisXisthesimulationnumber.Thisfileison"Explorer"tab,under"Modules"andin"DataFiles"section.

SincethissimulationisforconsideringonlytidethanthekeywordTIDEisconnected(1)andwaterdischargesorwindwillnotbeaccountedforcomputingvelocity.

Step4.5DefineturbulenceparametersinTurbulencefile

ThehorizontalandverticalviscosityisinputtedinfileTurbulence_X.datwhereisXisthesimulationnumber.Thisfileison"Explorer"tab,under"Modules"andin"DataFiles"section.
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Theviscosityrepresentsthemixtureordiffusionassociatedtoprocessesnottakenintoaccountincellaveragevelocity(calledturbulence)andsoitdependsonthemeshusedandunitsarem2/sandrepresentaturbulentvelocity(m/s)multipliedbymixturelength(m).Fora2Dsimulationtheverticalviscosityisnotused(noverticalmovement)andtoestimatethehorizontalviscosityuseaturbulentvelocity(usuallyapercentageofaveragevelocity)andmultiplybythecellsize.IntheTaguscasearepresentativeaveragevelocityis0.5m/sandiftheturbulentvelocityisaround10%oftheaveragethenitisaround0.05m/s.Forthiscaseofusingagridwitharound400mcellthentheestimatedviscositywillbe20m2/s(0.05m/s*400m).

Forotherstudycasesestimatethehorizontalviscosityaccordingly.Theobjectivehereistohaveanorderofmagnitudesincesmallvariationsdonotinfluencegreatlyresults.

Step4.6OtherFiles

OtherfilesasAtmosphere_X.dat,InterfaceWaterAir_X.datandWaterProperties_X.datareemptybecausearenotusedinthissimulation.Thesefilesareon"Explorer"tab,under"Modules"andin"DataFiles"section.

FileInterfaceSedimentWater_X.dattakesintoaccountthebottomofthedomainandarugosityisdefinedtocomputeshear.

Thesefilesdonotneedtobechanged.

Step4.7DefineOutput

ThelastthingtotakeintoaccountbeforerunningthesimulationiswheretoplacetimeseriesoutputanditsfrequencyandwhatshouldbetheHDFmapsfrequency.Thisinfoistransversaltoalmostallthedatafiles(allthathaveoutput)andtocreatetimesseriesfollowtheinstructionsinMOHIDStudioUserGuideinchapter6.6.Hint:SavethetimeseriesfileinGeneralData\TimeSeries(createit).

InthecaseofredoingthesimulationfromTagussincethegridisnotexactlytheoriginaltheprocessneedstoberedoneusingthesamestations.

Openthelocationofthestationsin"Map"ribbonandin"VectorData"grouppress"XML"andopenthefile"TimeSeriesLocation.xml"fromthefolderGeneralData\TimeSeriesintheTagussampleprojectanddefine"Geographic"coordinates.Ifyouwanttomaintainthesametimeseriesnames(somewillbeusedafter)doaqueryonthestation(seeMOHIDStudioUserGuidechapter4onhowtoquery)andwritedownthenames.Goto"Tools"ribbonandin"TimeSeries"grouppress"GridLocations".FollowtheinstructionfromMOHIDStudioUserGuideandpickpointsatthesamelocationsastheTagussampleandnamethemthesame.SavethefileinthefolderGeneralData\TimeSeriesonthenewproject(createit).Nameit,forexample,TimeSeriesLocation.dat.

Thepathtothefilejustcreated(e.g.TimeSeriesLocation.dat)needstobeupdatedineachdatafilethathasoutputwithakeywordTIME_SERIE_LOCATION.ItthisexamplewillbeusedonlyinHydrodynamic_X.datandcheckthatthepathiscorrect.

Thetimeseriesfrequencyisdefinedinsidethecreatedfile(e.g.TimeSeriesLocation.dat)withthekeywordDT_OUTPUT_TIME(inseconds).

TheHDFfrequencyofoutputisgivenintheModulesdatafilesthathaveoutputbythekeywordOUTPUT_TIME(inseconds).InthiscaseonlyinHydrodynamic_X.dat.

Alwaysverifyifthefrequencyofoutputiscorrectgiventhesimulationperiod.UsuallytimeseriesarenotverytimeconsuminganddonotgeneratehugeresultfilesbutforHDFoutputs,ifthefrequencyistoohigh,itmaymakethemodelrunslowerandgeneratehugefilesthataredifficulttomanage.

Step5Runthesimulationandexploreresults

Everythingnowispreparedtorunthesimulation.VerifyonelasttimethatallthepathsdefinedinsidethedatafilesexistandthattheDTMwasdefinedinthedomain.Followthesameinstructionsasintheprevioussimulationtorunandtoexploretheresults.

Ifthesimulationdoesnotendsuccessfullyandtheoutputwindowsaysthatisolatedhorizontalgridcellsoccurredandanewbathymetrywascreated(usuallyappended"_v01"tothefilename)thenreplacethebathymetryoftheprojectwiththenewoneandrerunthemodel.

TheresultsofthissimulationshouldbeverysimilartotheTagussamplesimulation#1(Figure26(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_25.png))despitethegridisnotthesame.

Figure26:Tagus2Dvelocitymodulusinredonesimulation.

RetouchingtheBathymetry
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Thisisanadvancedprocessingoptionthatwillnotbeneededinthesamplecase.However,incoarsehorizontalgridsorcoarsedata,highchangesinbathymetryvaluesmayoccur(usuallyinintertidalareas)thatcancreatenumericalinstabilities.Whenthishappensamessagelike"InstabilityinThomasAlgorithm"canappearinthemodeloutputwindow(orlog).Inthiscasecheckwherethevelocityfieldsareinconsistentlyhigh(opentheHDFwithvelocitymodulusthatwillshowresultsuptomodelbecameunstable)andcheckifthereareinconsistenciesinthebathymetryinthesurroundinggridcells.

Inspectthebathymetrychangingthecolorscaletodefineallthesmallchannelsinintertidalareasandverifythatbigchangesindepthdonotoccurthatcanmakethemodelunstable.Forsomecases,youcanuseanauxiliaryMOHIDtoolcalledFilterBathymetry[6]thatcansmooththebathymetryandcanbeusefultoautomaticallysolvesomeoftheseproblems.

CreatingyourownprojectSimulating3Dhydrodynamicsforcedwithtide,riverdischargeandmeteorology

Thissimulation,inrelationtothelatter,addsmoreverticallayers,introducesriverdischarges,andaddsmeteorologyandwaterproperties(temperatureandsalinity).

ItwillbereferredtotheMOHIDStudioUserGuidemoreoftensincethissimulationismoreadvancedanditisassumedthattheuserisnowcomfortableinexploringMOHIDStudio.Ifnotthatcomfortable,pleasetrytoapplythemodeltootherplacesthantheTagusonyourown,usingthelastsimulationdescription.

Step1GetMeteorologyandRiverDischarges

Torunthecompletehydrodynamicssimulationyouneedtodefineriverinputandmeteorologyforcing.MeteorologyandriverinputcanbegivenintimeseriesorHDFformat(butconstantvaluescanalsobeimposed).FortheTagussample,meteorologydataissuppliedintimeseriesformatandriverinputisconstant(shortsimulations).

Step1.1GetdataintoMOHIDTimeSeriesformat

Themeteorologicaldataneededbythemodelcomprisesairtemperature,solarradiation,windvelocityanddirectionandrelativehumidity,thusthesefilesmustbecreatedbeforethemodelexecution.

FollowinstructionsinMOHIDStudioUserGuideinchapter10.1tounderstandMOHIDformatfortimeseries[7].

IfredoingtheTaguscasecopytheatmospherefile(AtmophereData.dat)fromthefolderGeneralData\BoundaryConditionsinthesampleprojecttoyourprojectinthesamelocation.

AfterthetimeseriesfilesarecreatedtheycanbereferredintheAtmosphere_X.dat(seebelow).

Step1.2Definedischargeslocations

Sincethissimulationdoesnothavethesamecomputationalgridasthesample,thedischargeslocationneedstobechanged.Therewillbetwodischargeswithreferencetothetwomainrivers(TagusonnorthandSorraiaeast)presentedinFigure27(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_26.png)(in"Map"ribbonandin"VectorData"group,press"XML"andopenfileRiverDischarges.xmlinfolderGeneralData\BoundaryConditionsofthesamplecase).NoticethattheSorraiadischargeappearstobeinsidetheestuarybecausethecomputationalgridattheSorraiaentranceisnotsowelldefined.

Documents

MOHID Studio - Quick-Start Guide for MOHID Water Implementation - V.2