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MOHIDStudioQuickStartGuideforMOHIDWaterImplementationv.2.0
FromActionModulers

Contents
1Preface
1.1Copyright
1.2Warranty
1.3FurtherInformation
2QuickStartTutorialforMOHIDWater
2.1Exploringasampleproject
2.1.1Step1Openingthepredefinedproject
2.1.2Step2Recognizingtheprojectstructureandstudyarea
2.1.3Step3Runningthesimulation
2.1.4Step4ExploringtheResults
2.2CreatingyourownprojectSimulating2DHydrodynamicsforcedwithtide
2.2.1Step1CreatinganewMOHIDWaterSolutionandDomain
2.2.2Step2GeneratetheBathymetry
2.2.3Step3GenerateTide
2.2.4Step4Createanewsimulation
2.2.5Step4Definethesimulation
2.2.5.1Step4.1DefineBathymetryfortheproject
2.2.5.2Step4.2DefinesimulationstartandendinModelfile
2.2.5.3Step4.3DefinegaugestidalcomponentsinTidefile
2.2.5.4Step4.4DefineverticaldiscretizationinGeometryfile
2.2.5.5Step4.4DefinehydrodynamicoptionsinHydrodynamicfile
2.2.5.6Step4.5DefineturbulenceparametersinTurbulencefile
2.2.5.7Step4.6OtherFiles
2.2.5.8Step4.7DefineOutput
2.2.6Step5Runthesimulationandexploreresults
2.3CreatingyourownprojectSimulating3Dhydrodynamicsforcedwithtide,riverdischargeandmeteorology
2.3.1Step1GetMeteorologyandRiverDischarges
2.3.1.1Step1.1GetdataintoMOHIDTimeSeriesformat
2.3.1.2Step1.2Definedischargeslocations
2.3.1.3Step1.3Defineflowandpropertydischarged
2.3.2Step2Createanewsimulation(copyaprevious)
2.3.3Step3Definethesimulation
2.3.3.1Step3.1DefineAtmospherefileandInterfaceWaterAir
2.3.3.2Step3.2DefineDischargesfilewithdischargedflowandproperties
2.3.3.3Step3.3DefineverticaldiscretizationinGeometryfile
2.3.3.4Step3.4DefineHydrodynamicfile
2.3.3.5Step3.5DefineTurbulenceandGOTMfiles
2.3.3.6Step3.5DefineWaterPropertiesfile
2.3.4Step4Runthesimulationandexploreresults
2.4CreatingyourownprojectSimulatingsedimenttransport
2.4.1Step1Createanewsimulation(copyaprevious)
2.4.2Step2Definethesimulation
2.4.2.1Step2.1AddcohesivesedimentpropertyandparametersinInterfaceSedimentWaterfile
2.4.2.2Step2.2DefinecohesivesedimentpropertyverticalvelocityinFreeVerticalMovementfile
2.4.2.3Step2.3AddcohesivesedimentpropertyinDischargesfile
2.4.2.4Step2.4AddcohesivesedimentpropertyinWaterPropertiesfile
2.4.3Step3Runthesimulationandexploreresults
2.5CreatingyourownprojectSimulatingpointdischarges
2.5.1Step1Definethepointdischarges
2.5.1.1Step1.1Definedischargeslocations
2.5.1.2Step1.2Defineflowandproperty
2.5.2Step2Createanewsimulation(copyaprevious)
2.5.3Step3Definethesimulation
2.5.3.1Step3.1DefineDischargesfilewithdischargedflowandproperties
2.5.3.2Step3.2DefineinWaterPropertiesfiledischargedproperties
2.5.3.3Step3.3DefinetheLagrangiandischarge
2.5.4Step4Runthesimulationandexploreresults
2.6CreatingyourownprojectSimulatingnutrienttransportandtransformation(nutrientcycles)
2.6.1Step1Createanewsimulation(copyaprevious)
2.6.2Step2Definethesimulation
2.6.2.1Step2.1AddtoWaterPropertiesfilethepropertiesneededtorunthewaterqualitymodels
2.6.2.2Step2.2AddWaterQualityfilewithdefinedrates
2.6.2.3Step2.3AddtoInterfaceSedimentWaterfilethepropertiesneededtorunthequalitymodels
2.6.2.4Step2.4AddBenthosfilewithdefinedrates
2.6.2.5Step2.6DefineOtherFiles
2.6.3Step3Runthesimulationandexploreresults
3FinalRemarks

Preface
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Copyright
ThisdocumentreferstoMOHIDStudio,proprietarycomputersoftwarewhichisprotectedbycopyright.Allrightsarereserved.Copyingorotherreproductionofthis
documentorrelatedprogramsisprohibitedwithoutpriorwrittenconsentofActionModulers,ConsultoresdeSegurana(ActionModulers).
MOHIDWaterModellingSystemisproprietarysoftwareoftheInstitutoSuperiorTcnicofromUniversityofLisbon.

Warranty
ThewarrantygivenbyActionModulersislimitedasspecifiedinyourSoftwareLicenseAgreement.Pleasenotethatnumericalmodelingsoftwareprogramsarevery
complexsystemsandmaynotbefreeoferrors,soyouareadvisedtovalidateyourwork.ActionModulersshallnotberesponsibleforanydamagearisingoutoftheuseof
thisdocument,MOHIDStudio,MOHIDWaterModellingSystemoranyrelatedprogramordocument.

FurtherInformation
ForfurtherinformationaboutMOHIDStudiopleasecontact:
ActionModulersConsulting&Technology
EstradaPrincipal,n29Paz
2640583Mafra,Portugal
Tel.:+351261813660
Fax:+351261813666
Email:geral@actionmodulers.com
Web:http://www.actionmodulers.com

QuickStartTutorialforMOHIDWater
This"QuickStartTutorialforMOHIDWater"isintendedtohelpfirsttimeuserscreatingtheirfirstprojects,followingasampleproject,animplementationintheTagus
Estuary,nearLisbon,Portugal.
Itissuggestedthattheuserfollowsthetutorial,whichprogresseswithincreasingcomplexity,tryingtoreplicatetheprovidedsampleproject.Afterfinishedexploringall
simulationswiththesamples,itissuggestedthattheuserrevisitsthetutorialapplyingthemodelexamplestohisstudysite.
ThetutorialstartswiththesampleprojectfortheusertogetusedtotheMOHIDStudioenvironment,projectandsimulationstructureandtostartexploringresultswithout
anypreviousknowledgeaboutusingMOHIDWater.
Afterthefirstplayaroundtheuserisinvitedtoindependentlycreateasimpleprojectwith2Dhydrodynamicsforcedwithtide,generatingthebathymetryandtidefiles,
preparetheinputfiles,runthemodelandexploreresultsaspreviously.
Thetutorialthenstartstoincrementcomplexityprovidingastepbysteptoimplementafull3Dsimulationwithriverdischargesandmeteorology,sedimenttransport,point
sources(usingalsoLagrangianapproach)andendinginnutrienttransportandtransformation(fullwaterqualitysimulation),resultinginoneofthemostcomplete
simulation(allprocessesconnected)thatcanberunwithMOHIDWater.
Sincekeywordsandblocksofkeywordsneedtobedefinedintheinputfiles,fortheuserconvenience,theuserisguidedtocopydatafilesfromthesampleproject.
ThisisintendedtobeastepbysteptutorialtoimplementinastraightforwardwayaMOHIDWaterprojectfromsimplertocomplexsimulations.Detaileddescriptionis
notgivenforprocesses,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
ThetutorialstartsbyprovidingasampleprojectsothattheusergetsfamiliarizedtotheMOHIDStudiostructureandisabletogetthesamplesimulationrunningand
producemodelresults.Thiswaythetutorialallowstheusertostraightawayobtainsomemodelresultswithlittleeffortandtheninthefollowingchapterstheintermediate
stepsareexplained(creatingtheprojectandsimulations).
ItisassumedthattheuserhasalreadyinstalledMOHIDStudio(followingMOHIDStudioInstallGuide)andisawareandunderstandsthefunctioningofthedifferent
windows,environmentsandbuttons(followingMOHIDStudioUserGuide).
ThismanualappliestoMOHIDStudioversion1.2.7.
Step1Openingthepredefinedproject
DownloadtheTagusSample.zip(linkbelow)fromActionModulersWebPagetoyourlocaldisk(e.g.toD:\MOHIDStudioProjects).
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http://www.actionmodulers.pt/Biblioteca/Uploads/Downloads/Walkthroughs/TagusSample.zip
Createafolderinyourharddiskfortheproject(e.g.D:\MOHIDStudioProjects\TagusSampleandleaveitempty).
OpenMOHIDStudiowhereitshouldappearthe"WorkspaceManager"windowaskingtocreateanewworkspaceoropenasavedone(Figure1(#label
fig: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).
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Thesolutionwasimportedandnowneedstobeopened.Select"Project"ribbonandin"Solution"group,press"Open"andthe"SolutionManagement"windowappears
nowwiththe"TagusSample"available.Selectitandpress"OK".

Figure4:MOHIDStudioLoadWorkspace.
Thiswillopenthe"TagusSample"solutionin"Explorer"tab.Pressonthetrianglejustlefttothesolutionicontoshowthedomaintree(itwillshow"TagusSample"
domain).Pressonthetrianglejustlefttothedomainicontoshowthedomainfolderstructureandsimulationsavailable.Thereare5simulationsavailablejustthesameas
themainsimulationsofthistutorial.Inthenextsteps,theusermaycopythenecessaryfilesanddoesntneedtocreatethemfromscratch.
Step2Recognizingtheprojectstructureandstudyarea
Withthesolutionopenedanddomaintree,domainfoldersandsimulationstreevisible,theusershouldbeseethesamestructureaspresentedinFigure5(#label
fig:Mw5.png).

Figure5:MOHIDStudioExplorerWindowwithMOHIDWaterSample.
IfhavingsomedoubtsabouttheMOHIDStudiowindowsandstructurepleaserefertotheMOHIDStudioUserGuide.
Whenselectingeachsimulation,the"Modules"sectionontherightpaneisfilledwith"DataFiles"(textfileswithoptionsandinfoneededtoruneachsimulation)andno
filesexistin"HDFFiles"or"TimeSeriesFiles".Thelattercorrespondtomodelresults(mapsandtimeseries,respectively)anddonotexistbecausethesimulationhasnt
runyet.

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Beforerunninganysimulation,checkthestudyareabypressinginthefolderGeneralData\DigitalTerrain(seeFigure5(#labelfig:Mw5.png)),selectingthefile
"TagusBathymetry.dat",andrightclickingitandpressing"AddtoMap"andthenpressing"OK".Selectthe"Map"tabandchecktheTagusEstuarybathymetry.Thisfile
containsdataaboutthecomputationalgridandthebathymetryvalueforeachgridcell.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".Awindowwillappearto
checkiftheuserwantstoruntheselectedsimulation("Sim#1"),press"OK".
Theboxwindowcalled"ModelController"belowthedomainsandsimulationsisfilledshowingtheprogressbarofthesimulation(Figure7(#labelfig:Mw7.png)).To
checkmoredetailsonthesimulationstatuspress"Output"buttontobeabletoseewhatisthecurrentsimulationtime,thecurrentcomputertimeandtheexpectedcomputer
timewhenthesimulationwillend(thecontentofthislogiscontinuouslyupdated).The"Kill"buttononthesameboxwindowexiststoabortthesimulationatanytime.

Figure7:MOHIDStudioModelController.
Whenmodelrunfinishes(getsto100%inprogressbarorcrashed),awindowappears,warningthatthemodelhasfinishedandiftheuserwouldliketoseethelogfile(the
sameasobtainedin"Output"inModelControllerbutnowthefinalfile)Figure8(#labelfig:Mw8.png).

Figure8:MOHIDStudioModelFinished.
Itisalwayssuggestedtowatchthelogtomakesurethatthesimulationendedsuccessfully(browsetilltheendofthefileFigure9(#labelfig:Mw9.png)).Iftheuserdoes
notwanttoseethelogfileorclosesthelogfilethanissentbacktoMOHIDStudioandreadytoexploreresults.Thelogfilecanbeaccessedatanytimerightclickingeach
simulationandselecting"ViewLastLog".

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Figure9:MOHIDStudioLogFilereportingthatsimulationendedwithsuccess.
Step4ExploringtheResults
Duringandafterthesimulationends,theoutputfilesarecreated.Whenselectingthesimulationthatjustfinishedrunning("Sim#1"),the"Modules"sectionontheright
paneisfilledwith"HDFFiles"and"TimeSeriesFiles".HDFfilescontainmodelresultsfortheentirecomputationalgridatdifferenttimeinstantsofthesimulation,similar
toseveralinstantaneoussnapshotsofthestudyareathatcanbeplottedhasmapsandanimatedintime.Timeseriesfilescontainresultsforpredefinedcomputationalgrid
pointswithhighoutputfrequency.Latterinthisdocumentitwillbeexplainedhowtodefinetheoutputlocations.Onbothtypeoffilestheusermaychoosetheoutput
frequency(alsoexplainedlater).
DoubleclickingoneachHDFortimeseries,showsadialogtoselectthepropertiestoplot.MoreinformationonhowtovisualizeandcustomizeHDFresultscanbefound
inchapter4.6of"MOHIDStudioUserGuide"andinchapter5forthetimeseriesresults.
Toviewthetimeseriesresultsforcurrentvelocitymodulusinonepoint,inthe"TimeSeriesFiles"section,doubleclicktoopenthefile"Channel.srh"(locatedinTagus
channelinfrontofLisbon),andselecttheproperty"velocitymodulus"and"OK"toplot(Figure10(#labelfig:Mw10.png)).Thisisthevelocitymodulusvariationintime
intheTagusEstuarychannel.Toseethelocationofthispointandotherpointsthathavebeenselectedtoperformtimeseriesoutputs,in"Map"ribbon,and"VectorData"
grouppress"XML"andopenTimeSeriesLocation.xmlinfolder"GeneralData\TimeSeries"ofthesampleproject,selectastheprojection"Geographic"andpress"OK".
Thetimeseriespointswillbedisplayedon"Map"tab.Toknowthenameofeachpoint,selectthepointslayerandqueryit.PleaserefertoMOHIDStudioUserGuide
chapter4onhowtoquerylayers.
Viewthemapresultsforvelocitymodulusfortheentiredomainbyopening,in"HDFFiles"section,thefile"Hydrodynamic_1.hdf5"andselect"velocitymodulus"in
"Feature"fieldandpress"OK".Goto"Map"tabandpressplayon"Date&Time".Thisisthemapofvelocitymodulusfortheentiredomain(Figure11(#label
fig:Mw11.png))withamapforeachoutputtime.

Figure10:MOHIDStudiotimeseriesofvelocitymodulusforonedayinTagusChannelforSim#1inMOHIDWaterSamples

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Figure11:MOHIDStudioHDFofvelocitymodulusforSim#1inMOHIDWaterSamples.
Toknowmoreonhowtocustomizethetimeserieswindow(axistitles,seriesnamesandcolors,etc.)andmapimages(colorscale,horizontalscale,etc.)followMOHID
StudioUserGuidechapter4and5.

CreatingyourownprojectSimulating2DHydrodynamicsforcedwithtide
Thissectionwillshowhowtostartanewprojectusingasimpleexampleofa2DtidepropagationintheTagusEstuary(thesameusedinMOHIDWatersamples).The
descriptioncanneverthelessbeusedtoimplementthemodelinanystudysite.Onegoodexerciseforafirsttimeuseristotrytorepeatthesampleprojectfollowingthe
instructions.
Step1CreatinganewMOHIDWaterSolutionandDomain
CreateanewSolutiongoingto"Project"ribbonandingroup"Solution"pressing"New".Itwillbepromptedtonamethesolutionin"NameoftheSolution".Writedown
forinstance"TagusSampleRedone"withoutthequotesifredoingthesampleproject.
Createanewdomaingoingto"Project"ribbonandingroup"Domain"pressing"New".Thefollowingwindowwillappear(Figure12(#labelfig:Mw12.png)).

Figure12:MOHIDStudiocreatenewdomain.
Theinformationprovidedinthe"Creatinganewdomain"windowcharacterizesyourdomain.Thefollowingrestrictionsmustbefulfilled:
thedomainnamemustbeunique
therootdirectorymustbeempty.
In"DomainName"useyourlocationnameorforinstance"Tagus200m"inthecaseofredoingtheTagussamplecasesincewewillcreateanapplicationwherethecellsize
willbearound200mintheestuary(explainedafter).Sincethedomainislinkedtoahorizontalcomputationalgrid(bathymetry)thisnamingconventionisquitehandywhen
handlingdifferentresolutiongridsforthesamelocation.
Browsefora"RootDirectory"thatisemptyandthatislocatedinyourcomputerharddrive(tip:createinyourcomputerafolderpercomputationalgrid).
Thepathtothebathymetry("DigitalTerrainModel")willnotbespecifiedfornowsinceithasntbeencreatedyet.

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PressOKtofinishthedomaincreation.
Moreinformationonhowtomanagesolutionsanddomainscanbefoundin"MOHIDStudioUserGuide"inchapter3.
Step2GeneratetheBathymetry
Inthissectionitisshownhowtogeneratethebathymetryfile.Thisfiledefinesthehorizontaldomain(computationalgridandbathymetryvaluesforeachgridcell)andis
thebasicandmostessentialinformationneedtorunthesimulation("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.Tobuildthis
kindofgridsitismoresuitedtouseaMOHIDtoolcalledGenerateGrid[1]eventhoughitcanbebuiltalsoinMOHIDStudio(theuserhastoprovideallthexandy
distances).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".

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Figure15:Tocreateaconstanthorizontalgrid.
The"ConstructConstantSpaceGrid"windowappears.
Insection"2.Preview"check"AutoUpdate"sothatallthechangesthataredoneareimmediatelyvisible.Leaveuncheckediftheprocessisveryslowinthatcase
youwillneedtopress"Refresh"tovisualizeyourchanges.
Insection"1.GridParameters"theusermaydefine:
Anorigin(lowerleftcornercoordinateofthegrid)byfilling"OriginX"and"OriginY"withgeographiccoordinates,or,simplypressing"Pick"itmayselectinthe
maptheoriginpoint.FortheTagussamplecaseselectanoriginnearthelowerleftoftheprovidedgrid(TagusBathymetryGrid.grd).
Thenumberofcolumnsandrowsorthenumberofcellsinxandydirection.IntheTagussamplecase(variablespacedgrid)145and120wereused,respectively,but
fortheconstantgridaround280and200willbeneeded,respectively[2].
Dxanddyorthecellsize(indegrees).IntheTagussamplecase,avariableresolutionwasusedbutinthiscaseuse0.004inboth(around400mx400mcells).
Theoriginofthegridmaybechangedatanytime.Soifyourgridisnotinthecorrectpositionfeelfreetomoveitaround(press"Pick"andselectanotherorigin)and
checktheresult.
Insection"3.SaveGrid"youmaysavethefileifeverythingisOK,choosingthefolderandfilename(saveitinGeneralData\DigitalTerrainofthenewproject(and
notonsampleproject).Ifdonotwanttosavethegridjustclosethetool.
FortheTagussamplecase,thegridshouldbesimilartotheoneinFigure15(#labelfig:Mw16.png).

Figure16:MOHIDStudioconstantgridtoolfortheTagussample.
FortheTagussamplecase,comparethegridgeneratedwiththeoneusedinTagusEstuary(TagusBathymetryGrid.grd).Theyareverydifferentinresolutionyetthecell
sizeintheTaguschannelissimilar.
DigitalElevationData
Digitalelevationofthebottomoftheseausuallyisnotapublicresourceorifitishascoarseresolution.MOHIDStudiohasalsoaconversiontooltoprocessETOPO[3]1
arcminute(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".Tocompareboth
originsofdataitisbetterifthescalesmatchbyrightclickingthemandpressing"Properties"andon"Style"section,press"Edit"andchangethemaximumandminimumto
bethesame.
Nocomputeareas
Thisoptionisusedtoexcludeareasthatarelandandwherethemodelshouldnotspendtimecomputing.Iftherearenosuchareas(openoceansimulation)thanthisstep
maybeskipped.
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Thelandareascanbeobtainedfromcoastlinesordrawdirectlyinthemap.FortheTagussampleacoastlineisprovided.
Tocreateacoastlinebydrawingoverthemap,goto"Tools"ribbonandin"GeometryLayers"group,press"Polygons".The"ConstructNamedPolygons"windowappears
(seeFigure17(#labelfig:Mw18.png))andinsection"1.DefinePolygonsonMap"press"Draw"andstartpickingpointsthatdefinethelandboundaryandMOHIDStudio
generatesautomaticallythepolygonformedbythepointsdoubleclickatthelastpointtofinishthepolygon.Ifwanttoremovethegeneratedpolygonusethe"Remove"
buttoninsection"2.DefinedPolygons".Insection"3.SavePolygons"press"Save"andselectthefolderandfilenametosavethepolygon(saveitinGeneralData\Digital
Terrainofthenewprojectandnotonthesampleproject).

Figure17:MOHIDStudioPolygonTooltoselectnocomputepointsinTagusestuarygrid(justonepolygonfortheexample,allthelandareawouldneedtobe
comprisedinonepolygonorseveralpolygons.
FortheTagussamplecase,anexistentcoastlinefileisusedsincethelandareasareverycomplex.Asso,goto"Map"ribbon,andin"ASCII"grouppress"Polygon"and
openthefile"CoastLine.xy"infolderGeneralData\DigitalTerrainfromtheTagussampleprojectandselect"Geographic"coordinatesandpress"OK"(Figure18(#label
fig:Mw19.png)).

Figure18:Tagusestuarygridandthelinecoastthatselectslandareasnottocompute.
GeneratingtheBathymetry
FinallythegenerationoftheBathymetryusesalltheabovestepsproducts:thegrid,theelevationpointsandthenocomputeareas.Theelevationinformationinpointswill
beinterpolatedtothegridcells,exceptinthecellsthatareinsidethenocomputepolygon.
Goto"Tools"ribbonandin"GridDataTools"grouppress"FromPoints"(creategriddatafrompoints)and"CreateGridData"windowappears(Figure19(#label
fig:Mw20.png)).Insection"1.SelectGrid"selectthegridthatwasgeneratedabove.Insection"2.NonComputeAreas"checkthepolygondrawnorcoastallineremind
thatseveralpolygonscanbeselected.Insection"3.BaseInformation"check"Tagus_bath_points"and"PortugueseCoast_bath_points"remindthatseveralpointsources
canbeselected.
Insection"4.Options"selectthemethodtocomputetheelevationforeachgridcellfrompointscollection.Whenhavingseveralpointsinsideeachcell(gridiscoarserthan
elevationdata)select"Average"andthecellvaluewillbetheaverageofthepointsinsidethegridcell.Ifthegridhasfinerresolutionthandata(somecellsdonothaveany
rawinformationinside),aninterpolationalgorithmmustbeused.Theusercanselectselect"Triangulation"or"IWD"(inverseweighteddistance).Inthecaseofredoingthe
Tagussamplechoose"Triangulation"sinceintheTaguscoastbathymetricdataissparserthancellresolution.
Insection"5.GenerateGridData"selectthefolderandfilenamefortheDTM(saveitinGeneralData\DigitalTerrainofthenewprojectandnotonthesampleproject).
Pressthe"Process"buttontogeneratethebathymetryandafterawhiletheprocessendsandproducesthebathymetryfile.

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Figure19:MOHIDStudioGridDatafrompointsTooltocreateabathymetry.
FortheTaguscase,comparethebathymetrygeneratedwiththeoneusedinTagusestuary(TagusBathymetry.dat)infolderGeneralData\DigitalTerrainofthesample
project.
Step3GenerateTide
Oneofthemaindriversforwatercirculationincoastalareasistideandinthefirstsimulationthatistheonlyforcingagent.
FES(finiteelementsolution)tidemodelisthemostcommonsourceoftidalcomponentsbeingavailablefortheentireworldwhichthemostrecentmodelversionis
FES2012andpreviousversionisFS2004.MOHIDStudioincorporatesatooltoobtaintidalcomponentfromFES2004andinthefuturewillhaveitupdatedforthemost
recentversion.
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:1Define
pointsonmap2Selectedgridpoints3Configtide.

Figure20:TidalToolwindowDrawpoints(start.
Thefirststeptousethistool,istodefinethepointsonMap.Clickonthe"Draw"button(thebuttonwillturnorange)andthenclickonthemaptodrawthepoints(see
Figure20(#labelfig:Mw21.png)).Thepointsshouldbedrawnontheboundariesoftheworkinglayerinzigzag,liketheonesshownontheexampleontheFigure21
(#labelfig:Mw22.png).
Eachtimethemouseispressedanewbluemarkerwillappearonthemapandanewlineisaddedtothetable(seeFigure21(#labelfig:Mw22.png)).Eachlinerepresentsa
singlepoint,withthecoordinatesofeachpointandname(bydefaultthepointnumberisincremented:Point_1,Point_2,andsoon).ThedecimalplacesfortheXandY
coordinatevaluescanbechangedonpanel1(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)and
thereferencelevelvalue(RefLevel).Selectalsothepathandnamefortheoutputfile.ThepathandnameforXYZfileisoptional.Ifthefilenameisempty,theXYZfile
willnotbesaved.
Thereferencelevelisthemeansealevel(measuredfromtheoriginofthebathymetryupwards)obtainedfromtidalgaugesinthearea(inTagusthemeansealevelis2.08m
abovebathymetriczero).TheFEStidesolutionisinGreenwichMeridianTime(GMT)soneedtoadapttoyourareausingtimereference(e.g.Spainis1(+1)andwillbe
negativetroughthewest).
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).

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Figure23:MOHIDStudioNewSimulation.
Step4Definethesimulation
Selectingthejustcreatedsimulationshowsthatthesimulationhasseveralinputfileslistedinthe"Modules"sectionandin"DataFiles".Thesefilesshouldhaveallthe
optionsneededtorunthemodelincludingthetideforcing,themainoptionstorun,etc.
Allthisinfoishardtoconstructfromscratcheverytimeanewprojectisimplementedsoitisrecommendedtoadaptthesettingsfromanalreadyexistingproject.
Sincethereisnoothersimulationtocopyfrom,todoacopyofthesettingsyouneedtoaddtoyoursolutionanotherdomain.Selectyoursolutionandgoto"Project"ribbon
andin"Domain"grouppress"Open".Choosefromthelistthe"TagusSample"orotherprojectifyouhaveonethatyouwanttocopyfrom.Theselectedprojectwillappear
underthesamesolution.
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".Thiswillcopyallthe
settingsfromtheoriginsimulationtothedestination.Nowsomeverificationsneedtooccurtoensurethatyoufillinthedatayoucreated(seenextsteps).
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Afteryouaredonecopyingyoucanremovetheaddeddomainfromthesolution,selectingitandgoingto"Project"ribbon,"Domain"groupandpressing"Remove".This
actiondoesnotdeletethedomainfromthedisk,itjustremovesthedomainfromthesolutionthatisvirtual.InthecaseofredoingTagussampleitsfileswillbeneededin
thenextsimulations,soleaveitfornow.
Step4.1DefineBathymetryfortheproject

Thebathymetryisapropertyofthedomainandremainsthesameforallsimulationssoitsdefinedinthedomainoptions.Editthedomainpropertiesbyselectingit,right
clickingandselecting"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"and
in"DataFiles"section.
Thestartandenddatesareidentifiedwithkeywords"START"and"END"andtheformatisyear,month,day,hour,minuteandsecondintegernumbersseparatedby
spaces.
ThekeywordDTdefinesthemodeltimestep.
Thekeyword"GMTREFERENCE"isthesameasthetimereferenceintide.IfrunningthemodelinaplaceotherthaninGTM+0thanneedtoeditaccordingly(positiveto
eastandnegativetowest).
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(keyword
LAYERTHICKNESS)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"Data
Files"section.
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Theviscosityrepresentsthemixtureordiffusionassociatedtoprocessesnottakenintoaccountincellaveragevelocity(calledturbulence)andsoitdependsonthemesh
usedandunitsarem2/sandrepresentaturbulentvelocity(m/s)multipliedbymixturelength(m).Fora2Dsimulationtheverticalviscosityisnotused(novertical
movement)andtoestimatethehorizontalviscosityuseaturbulentvelocity(usuallyapercentageofaveragevelocity)andmultiplybythecellsize.IntheTaguscasea
representativeaveragevelocityis0.5m/sandiftheturbulentvelocityisaround10%oftheaveragethenitisaround0.05m/s.Forthiscaseofusingagridwitharound
400mcellthentheestimatedviscositywillbe20m2/s(0.05m/s*400m).
Forotherstudycasesestimatethehorizontalviscosityaccordingly.Theobjectivehereistohaveanorderofmagnitudesincesmallvariationsdonotinfluencegreatly
results.
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.This
infoistransversaltoalmostallthedatafiles(allthathaveoutput)andtocreatetimesseriesfollowtheinstructionsinMOHIDStudioUserGuideinchapter6.6.Hint:Save
thetimeseriesfileinGeneralData\TimeSeries(createit).
InthecaseofredoingthesimulationfromTagussincethegridisnotexactlytheoriginaltheprocessneedstoberedoneusingthesamestations.
Openthelocationofthestationsin"Map"ribbonandin"VectorData"grouppress"XML"andopenthefile"TimeSeriesLocation.xml"fromthefolderGeneral
Data\TimeSeriesintheTagussampleprojectanddefine"Geographic"coordinates.
Ifyouwanttomaintainthesametimeseriesnames(somewillbeusedafter)doaqueryonthestation(seeMOHIDStudioUserGuidechapter4onhowtoquery)
andwritedownthenames.
Goto"Tools"ribbonandin"TimeSeries"grouppress"GridLocations".FollowtheinstructionfromMOHIDStudioUserGuideandpickpointsatthesame
locationsastheTagussampleandnamethemthesame.SavethefileinthefolderGeneralData\TimeSeriesonthenewproject(createit).Nameit,forexample,
TimeSeriesLocation.dat.
Thepathtothefilejustcreated(e.g.TimeSeriesLocation.dat)needstobeupdatedineachdatafilethathasoutputwithakeywordTIME_SERIE_LOCATION.Itthis
examplewillbeusedonlyinHydrodynamic_X.datandcheckthatthepathiscorrect.
Thetimeseriesfrequencyisdefinedinsidethecreatedfile(e.g.TimeSeriesLocation.dat)withthekeywordDT_OUTPUT_TIME(inseconds).
TheHDFfrequencyofoutputisgivenintheModulesdatafilesthathaveoutputbythekeywordOUTPUT_TIME(inseconds).InthiscaseonlyinHydrodynamic_X.dat.
Alwaysverifyifthefrequencyofoutputiscorrectgiventhesimulationperiod.Usuallytimeseriesarenotverytimeconsuminganddonotgeneratehugeresultfilesbutfor
HDFoutputs,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,highchangesinbathymetryvaluesmay
occur(usuallyinintertidalareas)thatcancreatenumericalinstabilities.Whenthishappensamessagelike"InstabilityinThomasAlgorithm"canappearinthemodeloutput
window(orlog).Inthiscasecheckwherethevelocityfieldsareinconsistentlyhigh(opentheHDFwithvelocitymodulusthatwillshowresultsuptomodelbecame
unstable)andcheckifthereareinconsistenciesinthebathymetryinthesurroundinggridcells.
Inspectthebathymetrychangingthecolorscaletodefineallthesmallchannelsinintertidalareasandverifythatbigchangesindepthdonotoccurthatcanmakethemodel
unstable.Forsomecases,youcanuseanauxiliaryMOHIDtoolcalledFilterBathymetry[6]thatcansmooththebathymetryandcanbeusefultoautomaticallysolvesomeof
theseproblems.

CreatingyourownprojectSimulating3Dhydrodynamicsforcedwithtide,riverdischargeandmeteorology
Thissimulation,inrelationtothelatter,addsmoreverticallayers,introducesriverdischarges,andaddsmeteorologyandwaterproperties(temperatureandsalinity).
ItwillbereferredtotheMOHIDStudioUserGuidemoreoftensincethissimulationismoreadvancedanditisassumedthattheuserisnowcomfortableinexploring
MOHIDStudio.Ifnotthatcomfortable,pleasetrytoapplythemodeltootherplacesthantheTagusonyourown,usingthelastsimulationdescription.
Step1GetMeteorologyandRiverDischarges
Torunthecompletehydrodynamicssimulationyouneedtodefineriverinputandmeteorologyforcing.MeteorologyandriverinputcanbegivenintimeseriesorHDF
format(butconstantvaluescanalsobeimposed).FortheTagussample,meteorologydataissuppliedintimeseriesformatandriverinputisconstant(shortsimulations).
Step1.1GetdataintoMOHIDTimeSeriesformat

Themeteorologicaldataneededbythemodelcomprisesairtemperature,solarradiation,windvelocityanddirectionandrelativehumidity,thusthesefilesmustbecreated
beforethemodelexecution.
FollowinstructionsinMOHIDStudioUserGuideinchapter10.1tounderstandMOHIDformatfortimeseries[7].
IfredoingtheTaguscasecopytheatmospherefile(AtmophereData.dat)fromthefolderGeneralData\BoundaryConditionsinthesampleprojecttoyourprojectinthe
samelocation.
AfterthetimeseriesfilesarecreatedtheycanbereferredintheAtmosphere_X.dat(seebelow).
Step1.2Definedischargeslocations

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

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Figure27:Locationofthedischargesinthenewgrid.
Inordertodefineinwhichgridcelltheriverdischargewillbeplaced,openthebathymetry("Map"ribbonandin"ASCII"grouppress"GridData"andopenthefilefrom
folderGeneralData\DigitalTerrainfromyourproject).Thenquerythefileandselectthecellswherethedischargeshouldbedone(usingRiverDischargeslocations).Get
the"I"and"J"andwritedowntheinfothatwillbeusedlater.
Step1.3Defineflowandpropertydischarged

Afterthelocation,definetheflowdischargedandpropertiesdischarged(constantortimeseries)fromdataoranyotherassumption.Thewaterpropertiespresentinthe
dischargemustbepresentinthelistofacceptedwaterpropertiesnamesMOHID[8].IfredoingtheTagussampleaconstantflowwillbeusedandthedischargeof
temperatureandsalinitywillbebasedonaverageknownvalues.
Step2Createanewsimulation(copyaprevious)
Assaidbefore,newsimulationsshouldbecopiedfromotherssothatthesettingsarepredefined.Inthiscasecreateanewsimulationasbeforeandintheprocessadd
ModuleDischargesandModuleGOTM(Figure28(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_27.png)).

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Figure28:MOHIDStudioaddnewsimulation.InthiscaseaddedDischargesandGOTM.
Copythefilesfromtheprevioussimulationtothisonesosomeoftheinfoisalreadyfilled.
Step3Definethesimulation
Comparingwiththelastsimulation,themaindifferencesarethattherewillbeamorerealisticatmosphericforcing(usingmeasureddata)andtheriverdischargeswillbe
considered.
Step3.1DefineAtmospherefileandInterfaceWaterAir

CopyonlytheatmospheredatafilefromtheTagussamplefromSim#2sinceitissimilartotheoneneededbecauseithasalltheatmosphericpropertiesblockswithdata
beingreadfromtimeseriesfiles.
Modifythetimeseriesfilepathsforprecipitation,solarradiation,airtemperature,relativehumidityandwindvelocitytotheonesthatwereprepared.Inthecaseofredoing
Tagussamplethisisnotnecessarysincethefileswerealreadycopiedtothesamelocation.
TochangefromdefiningapropertyashavingaconstantvaluetobeingreadfromatimeseriesfileisstraightforwardinMOHIDusingthekeywordFILE_IN_TIME.When
settingthepropertyvaluesasconstant,thekeywordvalueshouldbeNONEandthevalueisreadinkeywordDEFAULTVALUEandkeywordREMAIN_CONSTANT
shouldbe1.Incaseofreadingfromatimeseriesfile,thekeywordFILE_IN_TIMEvalueshouldbeTIMESERIEandkeywordsFILENAMEandDATA_COLUMNneed
tobedefined(thepathtothefileandthedatacolumninsidethefile,respectively).
CopyonlytheInterfaceWaterAirdatafilefromtheTagussamplefromSim#2sinceitissimilartotheneededbecauseithasalltheatmosphericfluxesneeded.This
propertiesdonotneedtobedefined(butcanbe)andinthiscasethemodelwillcomputethem(e.g.theheatfluxestroughthesurfacewater).
Step3.2DefineDischargesfilewithdischargedflowandproperties

CopyonlytheDischargesdatafilefromtheTagussampleinSim#2tothissimulation.Thisexamplehas2dischargeswithtemperatureandsalinity(TagusandSorraia).
Updatethenumberofdischargesyouwanttomakeandchangecelldischargeslocations(keywordsI_CELLandJ_CELL)accordingly.Updatealsodischargesnames
(keywordNAME).
IncaseofredoingtheTaguscaseyouneedtoupdatetheI_CELLandJ_CELLwiththeinfocollectedbecausethegridinthesamplesisdifferentfromthenewlygenerated
grid.
Updatedischargeflowvalues.IfusingconstantflowdefineitinkeywordDEFAULT_FLOW_VALUEineachdischargeandremovekeywordDATA_BASE_FILE.If
usingvariableflowsvalues(readfromatimesseriesfile)usethelatterkeywordtopointtothecorrespondingfileinMOHIDtimeseriesformatandFLOW_COLUMNto
selectwhichcolumntheflowvaluesare.IncaseofredoingtheTagussamplethisisnotneeded.
Adaptthepropertiesblocksandpropertiesdischargeconcentrationsaccordingtoyourdata.
Step3.3DefineverticaldiscretizationinGeometryfile

CopyonlytheGeometrydatafilefromtheTagussampleinSim#2tothissimulation.
Inordertodefinea3Dcomputationaldomainsimplydefinemorethanonelayer(keywordLAYERS)andinordertosetthethicknessofeachverticallayer,usekeyword
LAYERTHICKNESS.SinceaSIGMAtypecoordinateisbeingused,thethicknessisdefinedaspercentageofwatercolumnheightandavalueof1(100%)hastobe
obtainedwhensummingallthelayersthicknesses.

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The3DdomainpresentedintheTagussampleisonlyforexemplificationandisverysimplewithreducednumberoflayers(only3)thatusuallyisnotenoughfor
describingverticalgradientsincoastalareasorestuaries.ForcoastalcasesitissuggestedtousetwodomainsoneCARTESIANnearthebottomandoneSIGMAnearthe
changingsurfaceandthenumberoflayersdependonthedepthandtheprecisionneededtosimulateforinstancestratification[9].
IfredoingtheTagussampleleavethisfileunchanged.
Step3.4DefineHydrodynamicfile

CopyonlytheHydrodynamicdatafilefromtheTagussampleinSim#2tothissimulation.
AsseenwiththenewoptionsofintroducingdischargesandatmospherethevelocitieswillbeforcedwiththisnewprocessesandsointheHydrodynamic_X.dathasthe
keywordsWINDandWATER_DISCHARGESconnected.
Step3.5DefineTurbulenceandGOTMfiles

CopyonlytheTurbulencedatafilefromtheTagussampleinSim#2tothissimulation.
Inthecaseofa3Dmodeltheverticalturbulenceshouldnotbeconstantbutcomputedsoanewmodeliscalledtocomputeitasseeninthecopiedfile(turbulence_equation
whetherothermethodsmaybeused).ThismodelisGOTM[10]thatiscodedevelopedoutsideMOHIDandthatwasincludedinthepackage.Thismodelhasadatafile
(GOTM.dat)thatshouldbenotchanged.
CopyonlytheGOTMdatafilefromtheTagussampleinSim#2tothissimulationandjustleaveit,itincludesparametersfortheturbulencecomputation.
Step3.5DefineWaterPropertiesfile

CopyonlytheWaterPropertiesdatafilefromtheTagussampleinSim#2tothissimulation.
Thewaterpropertiesfiledefineswhichpropertiesaretobeconsideredandiftheywillbetransported(keywordADVECTION_DIFFUSIONhasvalue1)oriftheywill
havedischargesassociated(keywordDISCHARGEShasvalue1).
IfredoingtheTagussampleleavethefileunchanged.Thepropertiesinthiscaseinsteadofbeinginitializedasconstanteverywhereareinitializedbyboxes(keyword
INITIALIZATION_METHODvalueisnotCONSTANTbutBOXES)meaningthatthecellsbelongingtoeachboxwillhavedifferentvalues.Thiswasdonesincethe
simulationsareveryshorttomaketheinitialconditionsclosertorealitywhereintheupperestuarylowersalinityandhighertemperatureexists.Becauseofthis
initializationandsincethegridoftheredoneprojectisdifferentfromthesample,needtoregeneratetheboxesinthenewgrid:
CopythefolderGeneralData\Boxesinthesampleprojecttothenewproject.Openthepolygonwithboxesgeometryin"Map"ribbonandin"VectorData"group
press"XML"andopenthefileBoxes_reduced.xmlinfolderGeneralData\Boxesofthenewprojecttab.
Openthetooltogenerateboxesfrompolygonin"Tools"ribbonandin"GridDataTools"grouppress"CreateBoxes"andthe"CreateBoxes"windowappears
(Figure29(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_28.png)).
Inthesection"1.SelectGridData"selectthebathymetryinsection"2.SelectPolygons"selecttheBoxes_reducedandonsection"4.GenerateBoxesFile"browse
wheretoplacethefile(placethefileinfolderGeneralData\BoxesofthenewprojectandnameitBoxes.datsothatnochangeisneededintheWaterProperties.dat)
andpress"Process".

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Figure29:MOHIDStudioCreateBoxes.
Ifdoinganotherproject,disconnecttheboxesinitialization(revertINITIALIZATION_METHODtoCONSTANT)orcreateyourownboxes(followtheabovestepswhere
thepolygonfilesdefiningboxeshavetobecreated).
Step4Runthesimulationandexploreresults
Everythingnowispreparedtorunthesimulation.Verifyonelasttimethatallthepathsdefinedinsidethedatafilesexist,thatoutputfrequency(timeseriesandHDF)in
eachfileiscorrectforthesimulationperiodandthatthebathymetrywasdefinedinthedomain.Followthesameinstructionsasintheprevioussimulationtorunandto
exploretheresults.NewresultsareavailableasWaterPropertiesHDFortimeseries(.srw).
Figure30(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_29.png)presentsthetemperaturemapinoneinstantresultofopeningthe
WaterProperties.hdf5andselectingproperty"temperature"toplot.

Figure30:Tagustemperatureatsurfacefor3Dsimulationwithtide,riverdischargeandatmosphericforcing.

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IfthemodelcrasheswitherrorsaboutfloatinginvalidinModuleFunctionsandModuleWaterPropertiesasinFigure31(#labelfig:MOHID_Studio_
_MOHID_Water_Quick_Start_Guide_v1_30.png),thanprobablyexistcellsthatareisolatedwheredischargesareoccurringortheintertidalchannelsarepoorlydefinedand
needtohaveasmootherbathymetry.Followthestepsindicatedintheprevioussimulationtofixthebathymetry.

Figure31:LogmessagewithmodelcrashedwhencomputingdensityinModuleFunctions.Below"PC"referstocodeline(linenumbersmayvarydependingon
executableversion).

CreatingyourownprojectSimulatingsedimenttransport
TosimulatesedimenttransportthepropertycohesivesedimentneedstoexistintheModuleInterfaceSedimentWater(bottommass)andinModuleWaterProperties(water
columnconcentration)andtheparametersassociated(criticalshearforstress,criticalshearfordeposition,erosionrate)needtobedefined.
Step1Createanewsimulation(copyaprevious)
Assaidbeforenewsimulationsshouldbecopiedfromotherssothatthesettingsarepredefined.Inthiscasecreateanewsimulationasbefore,addingtheModule
Discharges,ModuleGOTM,ModuleFreeVerticalMovementandcopythefilesfromtheprevioussimulationtothisonesosomeoftheinfoisalreadyfilled.
Step2Definethesimulation
ThedifferencefromthelastsimulationisthatcohesivesedimentpropertyhastobeaddedinModuleInterfaceSedimentWaterandtoWaterPropertiesandthevertical
velocitycomputationaddingFreeVerticalMovement.Anditwasalsoaddedthecohesivesedimentpropertyintheriverdischarges.
Step2.1AddcohesivesedimentpropertyandparametersinInterfaceSedimentWaterfile

CopyonlytheInterfaceSedimentWaterdatafilefromtheTagussampleinSim#3tothissimulation.Verifythatthedifferencewasthepropertyblockwithcohesive
sedimentthatwasadded.Thisblockdefinestheinitialcohesivesedimentconcentrationeverywhereinthebottominkg/m2(ifanyinthebeginning)inkeyword
DEFAULTVALUE(becausekeywordINITIALIZATION_METHODvalueissettoCONSTANT).Itisalsodefinedthecriticalshearstressforerosion,overwhicherosion
occursinblock"begin_critical_shear_erosion",thecriticalshearstressfordeposition,belowwhichdepositionoccursinblock"begin_critical_shear_deposition",erodibility
inblock"begin_erosion_rate".Alltheseparametersshouldbecalibratedfortheplaceinquestion.
Step2.2DefinecohesivesedimentpropertyverticalvelocityinFreeVerticalMovementfile

CopyonlytheFreeVerticalMovementdatafilefromtheTagussampleinSim#3tothissimulation.VerifythatthatthefallvelocityisdefinedinkeywordWS_VALUE.All
theseparametersshouldbecalibratedfortheplaceinquestion.
Step2.3AddcohesivesedimentpropertyinDischargesfile

CopyonlytheDischargesdatafilefromtheTagussampleinSim#3tothissimulation.Verifythatthatthepropertycohesivesedimentwasaddedtotheriverdischargesto
bedischargedaswellastemperatureandsalinity.
IfredoingtheTaguscaseneedtochangethelocationoftheriverdischarges(I_CELLandJ_CELL)tothenewgridasdoneintheprevioussimulationbecausethenewgrid
isdifferentfromtheTagussample.
Step2.4AddcohesivesedimentpropertyinWaterPropertiesfile

CopyonlytheWaterPropertiesdatafilefromtheTagussampleinSim#3tothissimulation.Verifythatpropertycohesivesedimentwasaddedandinitializedthesameway
astheotherssincethesedimentconcentrationisusuallyhigherintheupperestuary.AlsothekeywordDISCHARGESwasconnectedtoallowtheconcentrationtobe
updatedbydischargesindischargefile(ifanydischargedtheproperty).
Step3Runthesimulationandexploreresults
Everythingnowispreparedtorunthesimulation.Verifyonelasttimethatallthepathsdefinedinsidethedatafilesexist,thatoutputfrequency(timeseriesandHDF)in
eachfileiscorrectforthesimulationperiodandthatthebathymetryfile(digitalterrainmodel)wasdefinedinthedomain.Followthesameinstructionsasintheprevious
simulationtorunandtoexploretheresults.NewresultsofcohesivesedimentareavailableinWaterPropertiesHDForintimeseries(.srw).

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Figure32(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_31.png)presentsthecohesivesedimentmapinoneinstantresultofopeningthe
WaterProperties.hdf5andselectingproperty"cohesivesediment"toplot.

Figure32:Taguscohesivesedimentatsurfacefor3Dsimulationwithtide,riverdischargeandatmosphericforcing.

CreatingyourownprojectSimulatingpointdischarges
Simulatingwastewatertreatmentplantspointdischarges(WWTP)isverysimilartosimulatingriverdischargeswherethenewpointscanbeaddedtotheDischargefileas
wellasthecorrespondentflowandconcentrationsvalues.ThenoveltyhereisthatpointsourcesdischargescanalsobesimulatedusingtheLagrangianapproach.This
approachinsteadofusingacomputationalgridtocomputecontaminantconcentrationsusestheconceptofLagrangiantracers,whichconsistsofsimulatingsmall
independentportionsofwateranditsconstituents,whichmoveduetothecurrentvelocitiescomputedontheEuleriangrid.Thisapproachisparticularlyrelevantwhen
simulatingprocesseswherehighconcentrationgradientsexist,whichisthecaseforWWTPdischargesintermsoffecalcontamination.Inthiscase,afirstorderdecayof
fecalcontaminationisalsocomputed(basedontemperature,salinityandradiation).
TheparticlesourceandfateisdefinedintheModuleLagrangianthatneedstobeconnectedandedited.
Step1Definethepointdischarges
Step1.1Definedischargeslocations

Therearetwooptionstodefinethelocation:i)byitscoordinatesorii)bythegridcell.Ifthecoordinatesareknownwritedownthemtobeusedlaterandskiptothenext
step.
Ifthecoordinatesarenotknowntheusermayusethegridcoordinates.Todothat,openthebathymetryfile("Map"ribbonandin"ASCII"grouppress"GridData"and
openthefilefromfolderGeneralData\DigitalTerrain).Thenquerythebathymetryandselectthecellswherethedischargeislocated.Getthe"I"and"J"andwritedown
theinfothatwillbeusedlater.
IfredoingtheTaguscase,getthecellswherethedischargesarelocatedin"Map"ribbonandin"VectorData"group,press"XML"andopenfileWWTPDischarges.xmlin
folderGeneralData\BoundaryConditionsofthesamplecase.ThesouthdischargeisAlcantaraandthenorthoneBeirolas.Querythebathymetryandwritedownthecellfor
thedischarge.
RemindthatthelocationforLagrangiandischargecoordinatefirstisJandthenIandhavetoreduceoneindexintheJandI(seeTagussampleandthedifferencebetween
locationinDischargedatafileandinLagrangiandatafile).

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Figure332.31:LocationoftheWWTPdischargesintheTagussample.
Step1.2Defineflowandproperty

Afterdefiningthedischargelocation,setupthedischargeflowandwaterpropertiesconcentrations(constantorreadfromtimeseries).Thedischargedwaterproperties
namemustbepresentinthelistofacceptednamesinMOHID[11].InthecaseofTagussample,arbitraryconstantvalueswereused.
Step2Createanewsimulation(copyaprevious)
Assaidbefore,newsimulationsshouldbecopiedfromotherssothatthesettingsarepredefined.InthiscasecreateanewsimulationasbeforeandaddModuleDischarges,
ModuleGOTM,ModuleFreeVerticalMovementandModuleLagrangian,
Copythefilesfromtheprevioussimulationtothisone,sosomeoftheinfoisalreadyfilled.
Step3Definethesimulation
Step3.1DefineDischargesfilewithdischargedflowandproperties

CopyonlytheDischargesdatafilefromtheTagussampleinSim#4tothissimulation.Thisexamplehas2newdischargeswithtemperature,salinity,ammonia,inorganic
phosphorusandcohesivesediment.
Updatethenumberofdischargesyouwanttomakeandchangecelldischargeslocations(keywordsI_CELLandJ_CELL)accordingly.Updatealsodischargesnames
(keywordNAME).
IncaseofredoingtheTaguscaseyouneedtoupdatetheI_CELLandJ_CELLwiththeinfocollectedbecausethegridinthesamplesisdifferentfromthenewlygenerated
grid.
Updatedischargeflowvalues.IfusingconstantflowdefineitinkeywordDEFAULT_FLOW_VALUEineachdischargeandremovekeywordDATA_BASE_FILE.If
usingvariableflowsvalues(readfromatimesseriesfile)usethelatterkeywordtopointtothecorrespondingfileinMOHIDtimeseriesformatandFLOW_COLUMNto
selectwhichcolumntheflowvaluesare.IncaseofredoingtheTagussamplethisisnotneeded.
Adaptthepropertiesblocksandpropertiesdischargeconcentrationsaccordingtoyourdata.
IfredoingtheTagussampleyoualsoneedtochangethelocationoftheriverdischarges(I_CELLandJ_CELL)tothenewgridasdoneintheprevioussimulation,because
thenewgridisdifferentfromtheTagussample.
Step3.2DefineinWaterPropertiesfiledischargedproperties

CopyonlytheWaterPropertiesdatafilefromtheTagussampleinSim#4tothissimulation.Verifythattheammoniaandinorganicphosphoruspropertieswereaddedand
havekeywordDISCHARGESsetto1(sothatthedischargeofpropertyisconsidered).IfanypropertyhadtheDISCHARGESsetto0andthepropertyisdischargedthan
onlyflow(dilution)wouldaffectthepropertyconcentrationandthedischargeconcentrationwouldbethesameasbeingzeroforthatproperty.Thesenewpropertiesare
initializedasconstant(keywordINITIALIZATION_METHODissettoCONSTANT).
Step3.3DefinetheLagrangiandischarge

CopyonlytheLagrangiandatafileandtheModeldatafilefromtheTagussampleinSim#4tothissimulation.
CheckthatkeywordLAGRANGIANissetto1inModelinputdatafile,sothattheLagrangianmoduleisactivated.

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TheLagrangiandatafiledefinesthelocationofthesourcesbytwooptionstodefinethelocation:i)byitscoordinateswithkeywordPOSITION_COORDINATESorii)by
thegridcellwithkeywordPOSITION_CELLS.Fillherethelocationofthedischargecollectedinthepreviousstep.RemindthatforthePOSITION_CELLScase,position
isgivenbyJI(andnotIandJasusual)andthatineachcoordinateneedstosubtractonecellinIandinJ.
TheLagrangiandatafilealsodefinesthetypeofsourceinspatial(keywordEMISSION_SPATIAL)andtemporalscales(keywordEMISSION_TEMPORAL)andflow
associated(keywordFLOW)[12].
Foreachpointsourcethedischargedwaterpropertiesarealsodefined.
Step4Runthesimulationandexploreresults
Everythingnowispreparedtorunthesimulation.Verifyonelasttimethatallthepathsdefinedinsidethedatafilesexist,thatoutputfrequency(timeseriesandHDF)in
eachfileiscorrectforthesimulationperiodandthatthebathymetrywasdefinedinthedomain.Followthesameinstructionsasintheprevioussimulationtorunandto
exploretheresults.NewresultsareavailableasLagrangianHDFthatcannotbeopenedwithdoubleclickingbutrightclickingandselecting"AddLagrangian".
Figure34(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_33.png)presentsthefecalcoliformpropertyinLagrangianparticlesmapinoneinstant
resultofopeningtheLagrangian.hdf5andselectingproperty"fecalcoliform"toplot.

Figure34:Tagusfecalcoliformfor3Dsimulationwithtide,riverdischargeatmosphericforcingandWWTPdischarge(arbitrarydischarge,justfor
exemplification).

CreatingyourownprojectSimulatingnutrienttransportandtransformation(nutrientcycles)
ThissimulationrepresentsonethemostcompletesimulationwithnutrientcycleusingthemostoftheModulesinMOHIDWater.
Thesimulationofnutrienttransportwasalreadypresentedintheprevioussimulation.ThenoveltyhereisthenutrientcyclinginthewaterthroughtheuseofModule
WaterQuality(algalactivityincludingassimilation,respiration,mortalityandgrazingandbacterialactivityincludingmineralization,nitrification,denitrification,etc.)and
sedimentbiogeochemicalprocessesusingModuleBenthos[13].
Step1Createanewsimulation(copyaprevious)
Assaidbeforenewsimulationsshouldbecopiedfromotherssothatthesettingsarepredefined.Inthiscase,createanewsimulationasbeforeandaddModuleDischarges,
ModuleGOTM,ModuleFreeVerticalMovement,ModuleLagrangian,ModuleWaterQualityandModuleBenthos.
Copythefilesfromtheprevioussimulationtothisonesosomeoftheinfoisalreadyfilled.
Step2Definethesimulation
Step2.1AddtoWaterPropertiesfilethepropertiesneededtorunthewaterqualitymodels

CopyonlytheWaterPropertiesdatafilefromtheTagussampleinSim#5tothissimulation.Verifythatalotofpropertieswereadded(thepropertiesneededtorunWater
Quality)andthemostparthasthekeywordWATER_QUALITYsetto1sothatthewaterqualitymodelmaychangetheconcentrationduetoalgalandbacterialactivity.
Step2.2AddWaterQualityfilewithdefinedrates

CopyonlytheWaterQualitydatafilefromtheTagussampleinSim#5tothissimulation.Inthisfileyoucanfindthemainoptionstocomputeandthebiogeochemical
processesratesandparameters.Alltheseparametersshouldbecalibratedforyourcasestudy.
Step2.3AddtoInterfaceSedimentWaterfilethepropertiesneededtorunthequalitymodels

CopyonlytheInterfaceSedimentWaterdatafilefromtheTagussampleinSim#5tothissimulation.Verifythatalotofpropertieswereadded(theparticulatedproperties
neededtorunWaterQualityandthedissolvedonesneededtorunBenthos)andsomehavethekeywordBENTHOSsetto1andWATER_FLUXESto1sothatthewater
qualitymodelmaybeinfluencedbyprocessesoccurringonthedepositedsediments.
Step2.4AddBenthosfilewithdefinedrates

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CopyonlytheBenthosdatafilefromtheTagussampleinSim#5tothissimulation.Inthisfilearethemainoptionstocompute(whichspeciestocompute)andthe
maximumrates(withoutlimitations)foreachprocess.Alltheseparametersshouldbecalibratedforyourcasestudy.
Step2.6DefineOtherFiles

CopyonlytheInterfaceWaterAirdatafileandDischargesdatafileandFreeVerticalMovementfromtheTagussampleinSim#5tothissimulation.IntheInterfaceWaterAir
inputfile,theoxygenfluxwasadded,sothatreaerationprocessesarecomputed,andthatintheDischargesinputfileallthewaterpropertiesincludedinthewaterquality
processesarenowdefined.IntheFreeVerticalMovementfile,theparticulatepropertiesaddedtotheWaterPropertiesfilewerealsodefinedhere,alongwiththe
correspondingsettlingvelocity.
IfredoingtheTagussampleyoualsoneedtochangethelocationoftheriverdischargesandWWTPdischarges(I_CELLandJ_CELL)tothenewgridasdoneinthe
previoussimulationbecausethenewgridisdifferentfromtheTagussample.
Step3Runthesimulationandexploreresults
Everythingnowispreparedtorunthesimulation.Verifyonelasttimethatallthefilepathsdefinedinsidethedatafilesexist,thatoutputfrequency(timeseriesandHDF)in
eachfileiscorrectforthesimulationperiodandthatthebathymetrywasdefinedinthedomainproperties.Followthesameinstructionsasintheprevioussimulationtorun
andtoexploretheresults.NewpropertiesexistinthewaterpropertiesHDFandintimeseries(.srw).
Figure35(#labelfig:MOHID_Studio__MOHID_Water_Quick_Start_Guide_v1_34.png)presentsthephytoplanktonpropertyinwaterpropertiesmapinoneinstantresult
ofopeningtheWaterProperties.hdf5andselectingproperty"phytoplankton"toplot.

Figure35:Tagusphytoplanktonfor3Dsimulationwithtide,riverdischargeatmosphericforcingandWWTPdischargeandwaterqualityprocesses.

FinalRemarks
ThisquickstartguidetoimplementMOHIDWaterintendstohelpfirsttimeuserstoquicklygetthemodelrunningbutmayalsobeastartingpointforeverynew
implementation.TheimplementationofMOHIDWaterintheseterms,withincreasingcomplexityandprocessesaddedincumulativeway,givesuserthesensibilitytothe
majorfactorsaffectingcirculationandwaterqualityforeachimplementationsite.
AnydifficultiesorneedformoredevelopedinformationshouldbeaddressedintheMOHIDchannelsmentionedatthestartofthisdocument.
WeappreciateallfeedbackthatyoumaygiveusontheimplementationofMOHIDWaterprojectswithMOHIDStudiosothatthisguidecanimprovewithtime.
1. Downloadthetoolfromwww.mohid.comandfollowinstructionshere:http://wiki.mohid.com/wiki/index.php?title=GenerateGrid
2. Thisistheadvantageofthevariableresolutiongridstosavecellnumber,focusinghigherresolutionontheinterestarea.
3. In"FileConversion"ribbon,"DTMdatasets"an"ETOPO"
4. ToconvertyourdataintoMOHIDpointsformat(XYZ),exploreMOHIDStudioUserGuide,chapter10tounderstandtheformat.
5. Thefileshouldbedownloadedhere:ftp://ftp.legos.obsmip.fr/pub/soa/maree/tide_model/global_solution/fes2004/tide/tide.fes2004.nc
6. Thefilterbathymetrytoolcanbedownloadedinwww.mohid.comandinstructionsinhttp://wiki.mohid.com/wiki/index.php?title=FilterBathymetry
7. Hint:ifyouhavethetimeseriesdatainaspreadsheettogetthetimecolumnindaysjustsubtracteverydatetothereferencedate.
8. SeealistofrecognizedpropertiesinMOHIDinhttp://wiki.mohid.com/wiki/index.php?title=Properties_names.
9. Formoreinformationvisithttp://wiki.mohid.com/wiki/index.php?title=Module_Geometry
10. Formoreinformationvisithttp://wiki.mohid.com/wiki/index.php?title=Module_GOTM
11. SeealistofrecognizedpropertiesinMOHIDinhttp://wiki.mohid.com/wiki/index.php?title=Properties_names.
12. Formoreinfovisithttp://wiki.mohid.com/wiki/index.php?title=Module_Lagrangian
13. Tolearnmoreabouttheseprocessesvisithttp://wiki.mohid.com/wiki/index.php?title=Module_WaterQualityforWaterQuality
http://wiki.mohid.com/wiki/index.php?title=Module_BenthosforBenthos.
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