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CLM3.0 UsersGuide

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CommunityClimateSystemModel

NationalCenterforAtmosphericResearch,Boulder,CO

CommunityLandModelVersion3.0

(CLM3.0)User’sGuide

MarianaVertenstein,KeithOleson,SamLevisandForrestHoﬀman

June21,2004

Contents

1Introduction

2ObtainingtheSourceCodeandDatasets

3CreatingandRunningtheExecutable

3.1oﬄinemode:usingjobscript.csh.............

.....................3.1.1Speciﬁcationofscriptenvironmentvariables........................3.1.2SettingtheNamelist.....................................3.1.3Creationofheaderanddirectorysearchpathﬁles.....................3.1.4Buildingthemodel......................................3.1.5Runningtheexecutable...................................3.2cammode...............................................3.3ccsmmode..............................................4NamelistParameters

4.1Rundeﬁnitions............................................4.2Speciﬁcationofmodelinputdatasets................................4.3Speciﬁcationofhistoryandrestartﬁles..............................4.4Speciﬁcationofinputphysicsvariables...............................4.5SpeciﬁcationofRTMRiverrouting.................................4.6Speciﬁcationofcammodenamelist.................................4.7Speciﬁcationofccsmmodenamelist................................

5CLM3.0DataStructures

6CLM3.0SurfaceDatasetFormats7CreatingaSpun-upInitialDataset8HistoryFileFields

9OﬄineModeNamelistExamples

9.1Example1:Oﬄineinitialrun,oneday,global...........................9.2Example2:Restartrun.......................................9.3Example3:Branchrun.......................................9.4Example4:Auxiliaryhistoryﬁles..................................9.5Example5.Generationofregionalgridsurfacedataset......................9.6Example6.Generationofglobalgaussiansurfacedataset

....................

ListofTables

1SourceCodeDirectoryStructure...............................2InputDataDirectoryStructure................................3OﬄineModeSupportedArchitectures...........................4UserModiﬁableScriptVariables...............................5misc.hCPPtokens........................................6preproc.hCPPtokens......................................7Filepath...............................................8NamelistVariablesoverwrittenwithCAMsettings...................9

MasterFieldList-TemperatureandHumidity.

......

...................1

3477810101212121213131519232323242425262732333435353637

56791011112427

10MasterFieldList-SurfaceRadiation...............................10MasterFieldList-SurfaceRadiation...............................11MasterFieldList-SurfaceEnergyFluxes.............................12MasterFieldList-VegetationPhenology.............................13MasterFieldList-CanopyPhysiology..............................14MasterFieldList-Hydrology...................................15MasterFieldList-WaterandEnergyBalanceChecks......................16MasterFieldList-AtmosphericForcing.............................17MasterFieldList-Soil.......................................18MasterFieldList-VolatileOrganicCompounds(onlyincludedifVOCdeﬁned).......19MasterFieldList-DynamicVegetation(onlyincludedifDGVMdeﬁned)...........2

2728292929303031313232

1Introduction

CLM3.0isradicallydiﬀerentfromeitherCLM2.1orCLM2.0,particularlyfromasoftwareengineeringperspective.ThemajordiﬀerenceisthatCLM3.0isnowbothscalarcachefriendlyaswellasvectorfriendlyandcanperformwellonbothtypesofarchitectures.ThesubgridhierarchyintroducedinCLM2.1hasbeenmaintainedinCLM3.0.However,itsimplementationwithinthecodehasbeencompletelymodiﬁedinordertopermitthecodetobehaveacceptablyonvectorarchitecturessuchastheEarthSimulatorortheCrayX1.TheCLM3.0codeisinfacteasiertoreadaswellasbeingmoreaccessibletotheintroductionofnewparameterizationsthaneitherCLM2.1orCLM2.0.

Severalothersoftware-relatedchangeshavealsoaccompaniedthenewCLM3.0datastructures.Abriefdiscussionofthenewdatastructuresaswellastheresultingnewdecompositionalgorithmisgiveninsection5.Inaddition,acompletelynewdecompositionalgorithmhasbeenimplementedformulti-taskedand/ormulti-threadedmodelrunsthatresultinasigniﬁcantimprovementinboththeloadbalancingaswellasscalingnatureofthemodel.Newinterfaceshavebeenimplementedforthespeciﬁcationofhistoryﬁleﬁeldsandinitialdatasetﬁelds.Furthermore,historyoutputforRTMriveroutputisnowontheRTMgridratherthanbeinginterpolatedtothemodelgrid.WereferthereadertotheCLM3.0Developer’sGuideformorecomprehensivedetailsofthecodingimplementations.

CLM3.0containsseveralimprovementstobiogeophysicalparameterizationstocorrectdeﬁcienciesinthecoupledmodelclimateusingCLM2.1.InCLM2.1,the2-mtemperaturefrequentlydroppedbelowtheatmosphericpotentialtemperatureduringdaytimeheatingincertainregions.Stabilitytermswereaddedtotheformulationfor2-mairtemperaturetocorrectthis.InCLM2.1,thereisadiscontinuityintheequationthatrelatesthebulkdensityofnewlyfallensnowtoatmospherictemperature.Theequationwasmodiﬁedtocorrectthisproblem.Aerodynamicresistanceforheat/moisturetransferfromgroundtocanopydoesnotvarywiththedensityofthecanopyinCLM2.1.Thisleadstohighsurfacesoiltemperaturesinregionswithsparsecanopies.AnewformulationwasimplementedinCLM3.0thatprovidesforvariableaerodynamicresistancewithcanopydensity.Theverticaldistributionoflakelayerswasmodiﬁedtoallowformoreaccuratecomputationofgroundheatﬂux.Aﬁxwasimplementedfornegativeround-oﬀlevelsoilicecausedbysublimation.Competitionbetweenplantfunctionaltypes(PFTs)forwater,inwhichallPFTsshareasinglesoilcolumn,isthedefaultmodeofoperationinCLM3.0.CLM2.1acceptseitherrainorsnowfromtheatmosphericmodel.Iftheprecipitationissnow,aformulationbasedonatmospherictemperaturedeterminesthefractionofprecipitationthatisinliquidform.InCLM3.0,theatmosphericmodel(incamandccsmmode)deliversprecipitationexplicitlyinliquidand/orsolidform.Inoﬄinemode(uncoupledfromanatmosphericmodel),theformulationbasedonatmospherictemperatureisstillused.Aﬁxwasimplementedtocorrectroughnesslengthsfornon-vegetatedareas.AfullscientiﬁcdescriptionofCLM3.0isgivenin

TechnicalDescriptionoftheCommunityLandModel(CLM)

Oleson,K.W.,DaiY.,BonanG.,BosilovichM.,DickinsonR.,DirmeyerP.,HoffmanF.,HouserP.,LevisS.,NiuG.-Y.,Thornton,P.,VertensteinM.,YangZ.-L.,ZengX.

NCARTechnicalNote,NCAR/TN-461+STR,2004.

IntheCLM3.0releasewearealsodistributingthedynamicglobalvegetationmodel(CLM-DGVM)andamoduleforsimulatingvolatileorganiccompound(VOC)emissions.TheVOCmoduleisdocumentedintheCLM3.0technicaldescription.AfullscientiﬁcdescriptionoftheCLM-DGVMaswellasanaccompanyinguser’sguideisgivenin

TheCommunityLandModel’sDynamicGlobalVegetationModel(CLM-DGVM):TechnicalDescriptionandUser’sGuide

Levis,S.,Bonan,G.B.,Vertenstein,M.,Oleson,K.W.NCARTechnicalNote,NCAR/TN-459+IA,2004.

Finally,CLM3.0supportsanewability,viatheinputnamelistspeciﬁcation(seesection4),tocreateanduseaslightlydiﬀerentsurface-dataﬁle.Thisnewformatsurfacedataset(”allpfts”)isdiscussedatlengthinsection6.

2ObtainingtheSourceCodeandDatasets

ThesourcecodeanddatasetsrequiredtoruntheCommunityLandModelversion3.0(CLM3.0)inoﬄinemode(uncoupledfromothercomponentsoftheCommunityClimateSystemModelversion3(CCSM3.0))canbeobtainedviathewebfrom:http://www.cgd.ucar.edu/tss/clm.

TheusershouldrefertotheCAM3.0User’sGuideortheCCSM3.0User’sGuideforinstructionsonobtainingcodeanddatasetstorunCLM3.0coupledtootherCCSM3.0components.

Itisassumedthattheuserhasaccesstotheutilitiestar,FreeSoftwareFoundationgunzipandgmake(GNUgmake).

TheCLM3.0distributionconsistsoftwotarﬁles:CLM3.0code.tar.gzand

CLM3.0inputdata.tar.gz.

TheﬁleCLM3.0code.tar.gzcontainscode,documentation,andscripts.Thisﬁlemustﬁrstbeuncom-pressedwiththegunziputilityandthen”untarred”asfollows:gunzip-cCLM3.0code.tar.gz—tarxvf-Theabovecommandbothuncompressesand”untars”thecodeintothefollowingsubdirectoryhierarchycontainingclm3/astheroot:

Table1:SourceCodeDirectoryStructure

DirectoryNamesrc/src/biogeophys/src/biogeochem/src/csmshare/DescriptionDirectoryofFORTRANand”C”sourcecodeBiogeophysicsroutines(e.g.,surfaceﬂuxes)Ecosystemandbiogeochemistryroutines(e.g.,DGVMandVOCs)CodesharedbyallthegeophysicalmodelcomponentsoftheCommunityClimateSystemModel(CCSM).ContainscodeforCCSMmessagepassing,orbitalcalculations,andsystemutilities.Control(driver)routinesRoutinesforgeneratingsurfacedatasetsRiverrouting(RTM)routinesIndependentutilityroutinesEarthSystemModelingFrameworkutilitiesGeneralpurposetiminglibraryDirectoryofbuild,testandrunscriptsScripttobuildandexecutethemodelonvariousplatformsDirectoryoftoolsforinputdatasetmanipulation(thesetoolsareusedin-dependentofrunningthemodel)

Routinesforconvertinguser-generatedasciisurfacedatasetﬁlestonetCDFformatsuitableforusebythemodel

ToolforcreatingnewinitialCLM3.0datasetsfromexistingCLM3.0datasetsatanothermodelresolutionand/orlandmaskToolforcomparingmodelnetCDFhistoryﬁlessrc/main/src/mksrfdata/src/riverroute/src/utils/src/utils/esmf/src/utils/timing/bld/bld/oﬄine/tools/tools/convertascii/tools/interpinictools/newcprnc/TheﬁleCLM3.0inputdata.tar.gzcontainssurfaceandoﬄineatmosphericforcingdatasets.Thisﬁlemustﬁrstbeuncompressedwiththegunziputilityandthen”untarred”asfollows:gunzip-cCLM3.0inputdata.tar.gz—tarxvf-Theabovecommandresultsinadirectoryhierarchycontaininginputdata/lnd/clm2/astheroot.Thisdirectoryhierarchyisoutlinedbelow.

Table2:InputDataDirectoryStructure

DirectoryNameNCEPDATA/SynopsisOneyear’sworthofatmosphericforcingvariablesinmonthlynetCDFfor-matsuitableforrunningthemodelinoﬄinemode(uncoupledfromtheatmosphericmodel)

Plantfunctionaltype(PFT)physiologicalconstantsdataset(asciiformat)”Raw”(highestprovidedresolution)datasets(netCDFformat)(usedbyCLM3.0togeneratesurfacedatasetsatmodelresolution)RiverdirectionmapforRTMinasciiformatDirectorycontainingnetCDFCLM3.0surfaceand”fgrid”datasetsThesurfacedatasetsincludenew-format(”allpfts”)andold-formatdatasetsforrunningCLM3.0inoﬄinemode

NOTEthatsurfacedatasetsusedinanyCAMorCCSMruncanalsobeusedtorunCLM3.0inoﬄinemode

For”fgrid”datasetsseesection4.2andExample6

ModelnetcdfhistoryﬁlesprovidedfortheusertovalidatetheirportofCLM3.0

Thisdatawasgeneratedusingtheﬁle,jobscript.csh(seesection3.1)whichwasrunontheNCARIBMSPfor1yearusingthedataindirectoryNCEPDATA/.

pftdata/rawdata/rtmdata/srfdata/output/NotethatwearecurrentlyprovidingeightsurfacedatasetsforrunningoﬄineCLM3.0.Thesedatasetsarelocatedininputdata/lnd/clm2/srfdata.Abriefsynopsisofeachofthesedatasetsisgivenbelow.ItisimportanttokeepinmindthatanysurfacedatasetusedforaCAMorCCSMruncanalsobeusedforrunningoﬄineCLM.WeareprovidingthesedatasetsasawayfortheusertoquicklybeginusingoﬄineCLM3.0.

•clmsx128USGSc030605.nc:CAMold-formatT42surfacedataset•clmsx128allpftsc040426.nc:CAMnew-formatT42surfacedataset•clms128x256c031031.nc:

CAMold-formatT85surfacedataset•clms128x256allpftsc040426.nc:CAMnew-formatT85surfacedataset

•surface-data.128x0atm.gx1v3ocn.080101.nc:CCSMold-formatT42surfacedataset

•surface-data.128x0atm.gx1v3ocn.allpftsc040426.nc:CCSMnew-formatT42surfacedataset

•surface-data.256x128atm.gx1v3ocn.070903.nc:CCSMold-formatT85surfacedataset

•surface-data.256x128atm.gx1v3ocn.allpftsc040426.nc:CCSMnew-formatT85surfacedataset+

3CreatingandRunningtheExecutable

TheCLM3.0modelcanbebuilttoruninoneofthreemodes.Itcanrunasastandaloneexecutablewhereatmosphericforcingdataisperiodicallyreadin(e.g.,usingthedatainNCEPDATA).Thiswillbereferredtoasoﬄinemode.ItcanalsoberunaspartoftheCommunityAtmosphereModel(CAM)wherecommunicationbetweentheatmosphericandlandmodelsoccursviasubroutinecalls.Thiswillbereferredtoascammode.Finally,itcanberunasacomponentinasystemofgeophysicalmodels(CCSM).Inthismode,theatmosphere,land,oceanandsea-icemodelsarerunasseparateexecutablesthatcommunicatewitheachotherviatheCCSMﬂuxcoupler.Thiswillbereferredtoasccsmmode.

CLM3.0mayberunserially(i.e.,onasingleprocessor),inparallelusingtheMessagePassingInterface(MPI)fordistributedmemorytasks,inparallelusingtheOpenMulti-Processing(OpenMP)directivesforsharedmemorytasks,orﬁnallyinparallelusingbothMPIandOpenMP(hybridparallelism).Asanexample,theIBMSPconsistsofdistributedmemorynodesinterconnectedbyahighperformancenetworkconnection,andeachnodecontainsmultiplesharedmemoryprocessors.WhenrunontheIBMSP,CLM3.0usesOpenMPdirectivesforparallelismonprocessorswithinasharedmemorynodeandMPIroutinesforparallelismacrossdistributedmemorynodestotakefulladvantageofthecapabilitiesofthehardware.ThesupportedarchitecturesandassociatedcompilersforrunningCLM3.0inoﬄinemodeareshowninTable3.NotethatwhenDGVMisdeﬁned(seeTable6),bit-for-bitrestartsarenotsupportedontheCRAYX1whenprocessorconﬁgurationischangedmid-run.

Table3:OﬄineModeSupportedArchitecturesHardwareIBMSPSGIIntelCRAYX1NECSX6NECSX6ArchitectureRS600MIPSIntelX86CrayX1NECSX6NECSX6OSAIXIRIXLinuxUnicos/mpSuper-UXSuper-UXCompilerIBMXLMIPSpgf90,lf95ftnf90sxf90(crosscompiler)ThemethodofbuildingandrunningCLM3.0dependsonboththetargetarchitectureandwhetherthemodelwillberunserially,inpureMPImode(distributedmemory),inpureOpenMPmode(sharedmemory)orinhybridmode.AgeneraldiscussionofthevariousaspectsofbuildingandrunningCLM3.0follows.SeveralcautionarynoteshavetobemadeconcerningLinuxsystems.ForLinuxoperatingsystems,CLM3.0issupportedforbothlf95andpgf90compilers.WehavenotedproblemsinrunningCLM3.0inhybridmodeusingpgf90compilers.Consequently,OpenMPthreadinghasbeenturnedoﬀbydefaultforLinuxsystems.(TheusermayturnitbackonbysettingSMPtoTRUEinjobscript.csh(seebelow).Wehavealsonotedproblemsinboundscheckingwithpgf90whenrunningindebugmode(DEBUG=TRUE).Asaresult,theboundscheckingintheMakeﬁlehasbeentemporarilydisabled.

3.1oﬄinemode:usingjobscript.csh

InordertobuildandrunCLM3.0inoﬄinemode,asamplescript,jobscript.csh,andacorrespondingMakeﬁleareprovidedinthebld/oﬄinedirectory.Inaddition,twoperlscriptsmkDepends(usedtogeneratedependenciesinaformsuitableforinclusionintoaMakeﬁle),andmkSrcﬁles(usedtomakealistofﬁlescontainingsourcecode)arealsoincluded.Theuserneednotworryabouttheseperlscripts.

Thescript,jobscript.csh,createsamodelexecutableatT42modelresolutionwithRTM(rivertransportmodel)activatedandCLM-DGVMandVOCsdeactivated,determinesthenecessaryinputdatasets,con-structstheinputmodelnamelistandrunsthemodelforoneday.Usersmusteditthisscriptappropriatelyinordertobuildandruntheexecutablefortheirparticularrequirementsandintheirparticularenvironment.

ThisscriptisprovidedonlyasanexampletoaidthenoviceuseringettingCLM3.0upandrunningasquicklyaspossible.

Thescriptcanberunwithminimalusermodiﬁcation,assumingtheuserresetsseveralenvironmentvariablesatthetopofthescript.Inparticular,theusermustsetthefollowing:

1.Setbatchqueuedirectivesfortherequiredmachineifwillberunninginbatchmodeasopposedtointeractivemode.Batchmodemeanssubmittingjobscript.cshthroughaqueueingsystem.Interactivemodemeanstypingjobscript.cshatthepromptonyourscreen.2.Setmodelresolution:numberofmodellongitudes(LSMLON)andlatitudes(LSMLAT).

3.SetROOTDIRtopointtothefulldiskpathnameoftherootdirectorycontainingtheuntarredsourcecode.4.SetMODELEXEDIRtopointtothedirectorywheretheuserwantstheexecutabletobebuiltandrun.5.SetCSMDATAtopointtothefulldiskpathnameoftherootdirectorycontainingtheuntarredinputdatasetsubdirectories.6.DetermineifMPIand/orOpenMPwillbeused,andifsodeterminethenumberofMPItasksand/orthenumberofOpenMPthreads(notethatforlinuxsystemsthenumberofmpitasksisdeterminedfromthebatchdirectivesifrunninginbatchmode).7.Setrequiredlibrarypathsandincludepaths.8.Modifythenamelist.

9.Determinewhichmodelcpptokenswillbeenabled.

Thescriptcanbedividedintoﬁvefunctionalsections:1)speciﬁcationofscriptenvironmentvariables;2)creationofthemodelinputnamelist;3)creationoftwoheaderﬁles(misc.handpreproc.h)andadirectorysearchpathﬁle(Filepath)neededtobuildthemodelexecutable;4)creationofthemodelexecutable;and5)executionofthemodel.Jobscript.cshissetupsothattheuserwillnormallyonlyhavetomodifysections1)and2)inordertoobtainamodelexecutableandassociatednamelist.Eachofthesefunctionalsectionsisdiscussedinwhatfollows.3.1.1

Speciﬁcationofscriptenvironmentvariables

Table4liststheusermodiﬁablescriptenvironmentvariables.SomeofthesevariablesareusedbytheMakeﬁletobuildthemodelexecutable.Althoughthescriptprovidestentativesettingsforallthesevariables,theprovidedvalueswillgenerallyhavetobemodiﬁedbytheuser.

Table4:UserModiﬁableScriptVariables

ScriptVariableLSMLONLSMLATROOTDIRMODELEXEDIRCSMDATASMPDescriptionNumberofmodelgridlongitudes.Numberofmodelgridlatitudes.Fullpathnamefortherootsourcecodedirectory.Fullpathnameforthedirectorywherethemodelexecutablewillreside.Objectﬁleswillbebuiltinthedirectory$MODELEXEDIR/obj.Fullpathnameofrootinputdatasetsdirectory.FlagthatturnsonOpenMP(validvaluesareTRUEorFALSE)IfSMPisTRUE,OpenMpisenabledandNTHREADSisthenumberofOpenMPthreads.IfSMPisFALSE,OpenMpisdisabledandNTHREADSisignored.Currently,SMPwillbesettoFALSEforLinuxplatforms.NumberofOpenMPmultitaskingthreads.NTHREADSshouldnotexceedthenumberofphysicalCPUs(ie,proces-sors)onasharedmemorymachineandshouldnotexceedthenumberofCPUsinanodeonadistributedmemorymachine.ThissettingisignoredifSMPissettoFALSE.

FlagthatturnsonMPI(validvaluesareTRUEorFALSE).IfSPMDisTRUE,MPIisenabledandNTASKSisthenumberofMPItasks.IfSPMDisFALSE,MPIisdisabledandNTASKSisignored.NumberofMPItasks.SettingisignoredifSPMDissettoFALSE.NTASKSshouldnotexceedthenumberofphysicalCPUs(ie,processors)onamachine.FullpathnameofdirectorycontainingthenetCDFlibrary.Thesettingdependsonuser’stargetmachine.

FullpathnameofdirectorycontainingnetCDFincludeﬁles.Thesettingdependsonuser’stargetmachine.

FullpathnameofdirectorycontainingtheMPIlibrary.Thesettingdependsonuser’stargetmachine.OnlyneededifSPMDissettoTRUE.NotneededonIBMSP,CrayX1,NECSX6machines,wheretheMPIlibraryandincludeﬁlesareobtaineddirectlyfromthecompilercommand.

FullpathnamefordirectorycontainingtheMPIincludeﬁles.Thesettingdependsonuser’stargetmachine.OnlyneededifSPMDissettoTRUE.NotneededonIBMSP,CrayX1,NECSX6machines.Determineswhichlinuxfortrancompilerisused.Validvaluesarepgf90orlf95.Onlyusedonlinuxplatforms.Nameoflinuxmachine.CurrentlyNCAR-CGDlinuxmachine”anchorage”issupportedinthescripts.Theuserwillneedtotailorthisfortheirownplatform.Onlyusedonlinuxplatforms.

Thefullpathnameofmpiruntouseif$SPMDissettoTRUE.Multiplefortrancompilersoftenexistonasinglelinuxsystem.Eachcom-pilercanhaveauniquepathwherethempichmpirunbinaryisinstalledforthatcompiler.Onlyusedonlinuxplatforms.

Determinesifrunwillbeinbatchorinteractivemode.Onlyusedonlinuxplatforms.

FlagthatturnsondebugginginMakeﬁle.ValidvaluesareTRUEorFALSE.

NTHREADSSPMDNTASKSLIBNETCDFINCNETCDFLIBMPIINCMPIlinuxfortcompilerlinuxmachinelinuxmpiruncmndlinuxbatchDEBUG9

Itisassumedthattheuserhassetuptheenvironmentfortheirparticularcompilerchoice(e.g.LDLIBRARYPATHissetcorrectlyintheuser’senvironment).3.1.2

SettingtheNamelist

Beforebuildingandrunningthemodelwithjobscript.csh,theusermustspecifymodelnamelistvariablesviatheCLM3namelist,clmexp,foundinjobscript.csh.Withoutmodiﬁcation,jobscript.cshgeneratesadefaultnamelistﬁle,lnd.stdin,whichresultsinaonedaymodelrunusingtheprovideddatasets.Namelistvariablescanbedividedintoseveralcategories:rundeﬁnitions,datasets,historyandrestartﬁlesettingsandlandmodelphysicssettings.Afulldiscussionofmodelnamelistvariablesisgiveninsection4.3.1.3

Creationofheaderanddirectorysearchpathﬁles

Theuserwillgenerallynotneedtomodifythesectionofjobscript.cshthatcreatestheheaderanddirectorysearchpathﬁles.Thescriptcreatesthreeﬁlesinthedirectory$MODELEXEDIR/obj:theheaderﬁlesmisc.handpreproc.handthedirectorysearchpathﬁle,Filepath.Tomodifytheseﬁles,theusershouldedittheﬁlecontentsfromwithinthescriptratherthanattempttoedittheﬁlesdirectly,sincethescriptwilloverwritetheﬁlesuponexecution.Theuseoftheseﬁlesbygnumakeisdiscussedbelow.Eachoftheseﬁlesissummarizedbelow.

Theﬁle,misc.h,containsresolution-andmodel-independentC-languagepre-processor(cpp)tokens.

Table5:misc.hCPPtokens

misc.hcpptokenSPMDDescriptionIfdeﬁned,enablesdistributedmemory,SPMD(singleprogrammultipledata),implementation.AutomaticallydeﬁnedbyscriptifenvironmentvariableSPMDissettoTRUE.Seesection3.1.1.

Ifdeﬁned,enablesmodiﬁcationsthattestreasonableperturbationerrorgrowth.Notsupportedatthistime.

PERGROTheﬁlepreproc.hcontainsresolution-dependentandmodel-dependentC-languagecpptokens.

Table6:preproc.hCPPtokens

preproc.hcpptokenOFFLINECOUPCSMCOUPCAMSCAMLSMLONLSMLATRTMVOCDGVMNOCOMPETEDescriptionIfdeﬁned,oﬄinemodeisinvokedIfdeﬁned,ccsmmodeisinvokedIfdeﬁned,cammodeisinvokedIfdeﬁned,camsinglecolumnmodeisinvokedThisisonlyapplicableifCOUPCAMisALSOdeﬁnedNumberofmodellongitudesNumberofmodellatitudesIfdeﬁned,RTMriverroutingisinvokedIfdeﬁned,vocemissioniscomputedIfdeﬁned,dynamicvegetationmodelisactivatedIfdeﬁned,competitionforwateristurnedoﬀ(eachpfthasitsowncolumn)Thismodeisnolongeroﬃciallysupported

C-preprocessordirectivesoftheform#include,#ifdeﬁned,etc.,areusedinthemodelsourcecodetoenhancecodeportabilityandallowfortheimplementationofdistinctblocksoffunctionality(suchasincorporationofdiﬀerentmodes)withinasingleﬁle.Headerﬁles,suchasmisc.handpreproc.h,areincludedwith#includestatementswithinthesourcecode.Whengnumakeisinvoked,theCpreprocessorincludesorexcludesblocksofcodedependingonwhichcpptokenshavebeendeﬁned.C-preprocessordirectivesarealsousedtoperformtextualsubstitutionforresolution-speciﬁcparametersinthecode.TheformatofthesetokensfollowsstandardcppprotocolinthattheyarealluppercaseversionsoftheFortranvariables,whichtheydeﬁne.Thus,acodestatementlike

parameter(lsmlon=LSMLON);parameter(lsmlat=LSMLAT)willresultinthefollowingprocessedline(forT42modelresolution):parameter(lsmlon=128);parameter(lsmlat=)

whereLSMLONandLSMLATaresetinpreproc.hviathejobscript.

FilepathcontainsalistofdirectoriesusedbyMakeﬁletoresolvethelocationofsourceﬁlesandtodeterminedependencies.ThesearchbeginsinthecurrentdirectoryandproceedstoeachdirectoryappearinginFilepath,intheorderinwhichtheyarespeciﬁed.Allﬁlesappearinginthesedirectorieswillbeusedunlessduplicateﬁlesarefound.Forthecaseofduplicateﬁles,theﬁrstﬁlefoundwillbeusedbygnumaketocreatetheobjectﬁle.Ifuser-modiﬁedcodeisintroduced,Filepathshouldcontain,astheﬁrstentry,thedirectorycontainingsuchmodiﬁedcode.

Userscanaddnewsearchdirectoriesbyeditingjobscript.cshunder“buildFilepath”.ThedefaultFilepathdirectoryhierarchyforCLM3.0isasfollows:

Table7:Filepath

SourceDirectories$MODELSRCDIR/main$MODELSRCDIR/biogeophys$MODELSRCDIR/biogeochem$MODELSRCDIR/riverroute$MODELSRCDIR/csmshare/shr$MODELSRCDIR/utils/timing$MODELSRCDIR/mksrfdataFunctionalitycontrolroutines(history,restart,etc)biogeophysicsroutinesecosystemandbiogeochemistryroutinesriverroutingroutinescodesharedbyallCCSMgeophysicalmodelcomponentstimingroutinesgenerationofsurfacedatasetroutines11

3.1.4Buildingthemodel

Theuserwillgenerallynotneedtomodifythesectionofjobscript.cshthatbuildsthemodelexe-cutable.Jobscript.cshinvokesgnumaketogeneratethemodelexecutable.Theﬁle,Makeﬁle,locatedinthebld/oﬄinedirectory,containscommandsusedbygnumakeoneachofthesupportedtargetarchitectures.Successfulinvocationofgnumakeresultsinanexecutable,”clm”,alongwithalogﬁle,”compilelog.clm”,documentingthebuildprocedure.Anyproblemsencounteredduringthebuildprocedurewillbedocumentedinthislogﬁle.Aparallelgnumakeisachievedinthescriptbyinvokinggnumakewiththe-joption,whichspeciﬁesthenumberofjobcommandstoruninparallel.3.1.5

Runningtheexecutable

Theuserwillgenerallynotneedtomodifythesectionofjobscript.cshthatrunsthemodelexecutable.Jobscript.cshwillexecutethecommandsrequiredtorunthemodelunderthesupportedtargetarchitectures.MostMPIimplementationsprovideastartupscriptwhichacceptstheMPIexecutableasacommandlineargument.Additionalcommandlineargumentsallowtheusertospecifydetailssuchasthevariousmachinearchitecturesornumberofprocessestousefortherun.OnceMPIhascreatedthespeciﬁednumberofprocesses,modelexecutionwillbegin.Thecollectionofactivetaskswillthencomputelocallyandexchangemessageswitheachothertointegratethemodel.

Uponsuccessfulcompletionofthemodelrun,severalﬁleswillbegeneratedinMODELEXEDIR.Theseincludehistory,restart,andinitializationﬁles(seesection4.3)aswellaslogﬁlesdocumentingthemodelexecution.Theselogﬁleswillhavenamesofclm.log.YYMMDD-HHMMSS,whereYYisthelasttwodigitsofthecurrentmodelyear,MMisthemonth,DDisthedayofthemonth,HHisthehour,MMistheminutes,andSSisthesecondsofthestartofthemodelrun.Timingﬁles,(e.g.“timing.0”),containingmodelperformancestatisticsarealsogeneratedintheexecutabledirectory.

3.2cammode

WhenrunningthemodelaspartoftheCAMexecutable,CAMbuildandrunscriptsmustbeutilized.TheusershouldrefertoUser’sGuide(totheNCARCommunityAtmosphereModel3.0(CAM3.0)atwww.ccsm.ucar.edu/models/ccsm3.0/cam/

forspeciﬁcdetailsonbuildingandrunningtheCAMexecutable.WewillonlydiscusssomeessentialpointsoftheCAMbuildandrunscriptshere.

Theheaderﬁles,preproc.handmisc.h,aswellasthedirectorysearchpathﬁle,Filepath,areneededfortheCAMbuildprocedureinananalogousmannertotheCLM3.0buildprocedure.TheusershouldkeepinmindthattheCLM3.0directoryhierarchyMUSTappearaftertheCAMdirectoryhierarchyinFilepath.CLM3.0containsseveralﬁlesthathavethesamenameasthecorrespondingCAMﬁles(e.g.timemanager.F90).WhenrunninginCAMmode,thecorrespondingCAMﬁlemustbeused.TheCAMbuildandrunscriptsensurethisoccurs.

TheCLM3.0namelist,clmexp,mustalsobespeciﬁed.Bydefault,RTMriverroutingisnotenabledincammode(i.e.thecppvariable,RTM,isnotdeﬁned).Furthermore,CLM3.0doesnotpermittheusertoindependentlysetseveralnamelistvariables(inparticular,thosedealingwithhistoryﬁlelogicandruncontrollogic)whenrunningincammode.CLM3.0willoverrideanyuserinputforthesevariableswiththecorrespondingvaluesusedbytheCAMmodel.Thisisdiscussedinmoredetailinsection4.6.

3.3ccsmmode

CCSM3.0willcontainCLM3.0.InccsmmodeRTMisdeﬁnedbydefault,becausethisprovidesthefreshwaterﬂuxfromthelandtotheoceanmodel.WereferthereadertotheCCSM3.0User’sGuideforfurtherdetailsonrunninginccsmmode.

4NamelistParameters

CLM3.0namelistinputsarepresentedinsections4.1-4.7below.Inwhatfollows,”mode”hasvaluesof”oﬄine”,”ccsm”,”cam”or”all”,correspondingtooﬄinemode,ccsmmode,cammode,orallthemodes.Ifanamelistvariablesettingislistedasrequired,thevaluemustbesetinthenamelistinorderforthemodeltoexecutesuccessfully.Ifasettingisspeciﬁedasrequiredandthemodeisonlygivenasoﬄine,thenthatvariablemustonlybespeciﬁedwhenrunninginoﬄinemode.Fornamelistvariablesettingsnotlistedasrequired,thecodewillprovidedefaultsettingsatinitialization.Inthefollowingvariabledescriptions,werefertoexamplespresentedinsection9.SeeExample1foradescriptionoftheminimumrequirednamelistforasuccessfulrun.

4.1Rundeﬁnitions

Thefollowinglistspeciﬁesnamelistvariablesassociatedwiththedeﬁnitionofruncasenames,runtypes(restart,initialorbranch),modeltimestep,andinitialrundate.

Aninitialrunstartsthemodelfromeitherinitialconditionsthataresetinternallyinthecode(referredtoasarbitraryinitialconditions)orfromaninitialconditionsdataset(seenamelistvariableFINIDAT)thatenablesthemodeltostartfromaspun-upstate.

Arestartrunisanexactcontinuationofaprevioussimulationfromitspointoftermination.Outputfromarestartrunshouldbebit-for-bitthesameasiftheprevioussimulationhadnotstopped.Runcontrolvariablessetinthenamelistmustbethesameasintherunthatisbeingrestarted.

Abranchrunisanewcasethatusesarestartdatasetfromaprevioussimulationtobegintheintegration.Forabranchrun,thelengthofthehistoryintervalandtheoutputhistoryﬁeldsdonothavetobethesameasinthecontrolsimulation.Forexample,thebranchingoptioncanbeusedtooutputselectedﬁeldsmorefrequentlythanwasthecaseintheoriginalrunortoaddnewauxiliaryhistoryﬁlestothemodelrun.

name:description:type:mode:default:

CASEID

Casename(shortidentiﬁerforrun)(seeex.1,2,3).char*256

oﬄine,ccsm(obtainedfromatmincammode)required(mustbechangedforbranchrun

unlessBRNCHRETAINCASENAMEissetto.true.)

name:description:type:mode:default:CTITLE

Casetitleforusewithinhistoryﬁles(longidentiﬁer).char*256

oﬄine,ccsm(obtainedfromatmincammode)blank

name:description:type:mode:default:NSREST

Runtype(0forinitialrun,1forrestart,3forbranch)(seeex.1,2,3).integer

oﬄine,ccsm(obtainedfromatmincammode)required

name:description:DTIME

Modeltimestep(seconds)(seeex.1).

type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:integer

oﬄine,mustagreewithCAMmodelinccsmmode,obtainedfromCAMmodeldirectlyincammode

required(suggestedrange:1200-3600s)

STOPYMDStopdate(YYYYMMDD)integer

oﬄine(obtainedfromCAMincammodeandCCSMcouplerinccsmmode)required(ifNESTEPorNELAPSEnotset)

STOPTODStoptimeofday(seconds).IgnoredifSTOPYMDnotdeﬁnedinteger

oﬄine(obtainedfromCAMincammodeandCCSMcouplerinccsmmode)0

NESTEP

Endingruntimeinmodeltimesteps(positive)ordays(negative)(seeex.1).ValueisignoredifSTOPYMDisspeciﬁed.integer

oﬄine(endingtimeobtainedfromCAMincammodeandCCSMcouplerinccsmmode)

required(ifneitherNELAPSEnorSTOPYMDareset)

NELAPSE

Elapsedruntimeinmodeltimesteps(positive)ordays(negative)(seeex.2).ValueisignoredifeitherSTOPYMDorNELAPSEarespeciﬁed.integer

oﬄine(endingtimeisobtainedfromCAMincammodeandCCSMcouplerinccsmmode)

required(ifneitherNESTEPnorSTOPYMDareset)

STARTYMDStartdateofrun(yyyymmddformat)(seeex.1).integer

oﬄine,ccsm(obtainedfromCAMmodelincammode)required

STARTTODStarttimeofdayofrun(seconds).integer

oﬄine,ccsm(obtainedfromCAMincammode)0

name:description:type:mode:default:

REFYMD

Referencedatefortimecoordinate(yyyymmddformat).integer

oﬄine,ccsm(obtainfromCAMincammode)

nodefaultvaluebutifnotset,thenthemodelreferencedatewillautomaticallybesettoSTARTYMDname:description:type:mode:default:REFTOD

Referencetimeofdayfortimecoordinate(secs).integer

oﬄine,ccsm(obtainfromCAMincammode)0

name:description:type:mode:default:CALENDAR

Calendartouseindatecalculations(”no-leap”or”gregorian”).char*32

oﬄine,ccsm(obtainedfromCAMincammode)no-leap

name:description:type:mode:default:

CLUMPPPROC

Numberof“clumps”perprocess(seesection5).integer

oﬄine,ccsm(obtainedfromCAMincammode)1ifOpenMPisdisabled

numberofOpenMPthreads(speciﬁedintheenvironment)ifOpenMPisenabled.

name:description:

type:mode:default:

BRNCHRETAINCASENAMEFlagtoretaincasenameonabranchrun.Iftrue,thenallowcasenametoremainthesameforbranchrun.Incammode,thisﬂagmustbesetforboththecamandclmnamelists.logical

oﬄine,cam,ccsm.false.

4.2Speciﬁcationofmodelinputdatasets

Thefollowinglistspeciﬁesnamelistvariablesassociatedwithmodelinputdatasets.

name:description:type:mode:default:

FSURDAT

Fullpathnameofsurfacedataset(seeex.1,5,6).char*256all

blank(detailsattheendofthissection)

notes:

name:description:type:mode:default:notes:name:description:type:mode:default:notes:name:description:type:mode:default:notes:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:notes:surfacedatasetsprovidedwiththedistributionarein$CSMDATA/srfdata,rawdatasetstogeneratesurfacedatasetsarein$CSMDATA/rawdata

FINIDAT

Fullpathnameofinitialconditionsdataset(seeex.1,2,3).char*256all

blank(detailsattheendofthissection)

noinitialdatasetsareprovided,theuserwillneedtogeneratethese

FPFTCON

Fullpathnameofplantfunctionaltype(PFT)physiologicalconstantsdataset(seeex.1).char*256all

required

datasetprovidedis$CSMDATA/pftdata/pft-physiology

FRIVINPRTM

fullpathnameofRTMinputdataset(seeex.4).char*256oﬄine,ccsm

requiredifcpptokenRTMisdeﬁnedinpreproc.hdatasetprovidedis$CSMDATA/rtmdata/rdirc.05

NREVSN

Fullpathnameofrestartﬁlename(onlyforbranchruns)(seeex.3).char*256all

required(onlyifbranchrun,NSREST=3)

MKSRFALLPFTS

Flagtoturnonnewsurfacedatasetformat.Iftrue,newsurfacedatasetformat(seesection6)isused.logicalall.false.

MKSRFFVEGTYP

Fullpathnameofrawplantfunctionaltypedataset(seeex.5).char*256all

required(ifFSURDATisblank)

datasetprovidedis$CSMDATA/rawdata/mksrfpft.nc16

name:description:type:mode:default:notes:name:description:type:mode:default:notes:name:description:type:mode:default:notes:name:description:type:mode:default:notes:name:description:type:mode:default:notes:name:description:type:mode:default:notes:name:description:MKSRFFSOITEX

fullpathnameofrawsoiltexturedataset(seeex.5).char*256all

required(ifFSURDATisblank)

datasetprovidedis$CSMDATA/rawdata/mksrfsoitex.10level.ncMKSRFFSOICOL

Fullpathnameofrawsoilcolordataset(seeex.5).char*256all

required(ifFSURDATisblank)

datasetprovidedis$CSMDATA/rawdata/mksrfsoicolclm2.nc

MKSRFFLANWAT

Fullpathnameofrawinlandwaterdataset(seeex.5).char*256all

required(ifFSURDATisblank)

datasetprovidedis$CSMDATA/rawdata/mksrflanwat.ncMKSRFFURBAN

fullpathnameofurbandataset(seeex.5).char*256all

required(ifFSURDATisblank)

datasetprovidedis$CSMDATA/rawdata/mksrfurban.ncMKSRFFGLACIER

Fullpathnameofglacierdataset(seeex.5).char*256all

required(ifFSURDATisblank)

datasetprovidedis$CSMDATA/rawdata/mksrfglacier.ncMKSRFFLAI

fullpathnameofleafandstemareaindex,canopytopandbottomheightdataset(seeex.5).char*256all

required(ifFSURDATisblank)

datasetprovidedis$CSMDATA/rawdata/mksrflai.ncMKSRFOFFLINEFNAVYORO

20minnavyorographydatasetusedtogeneratelandmask(seeex.5).

type:mode:default:notes:name:description:type:mode:default:notes:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:notes:char*256oﬄine

required(ifMKSRFOFFLINEFGRIDnotsetandFSURDATisblank)datasetprovidedis$CSMDATA/rawdata/mksrfnavyoro20min.ncMKSRFOFFLINEFGRIDDatasetspecifyinglandgridandmaskatdesiredresolution(seeex.6).char*256oﬄine

blank,required(ifMKSRFOFFLINEFNAVYOROnotsetandFSURDATisblank)

datasetsprovidedin$CSMDATA/srfdata

MKSRFOFFLINEEDGENNorthernedgeoflandgrid(degreesnorth)(seeex.5).realoﬄine90.

MKSRFOFFLINEEDGEEEasternedgeoflandgrid(degreeseast)(seeex.5).realoﬄine180.

MKSRFOFFLINEEDGESSouthernedgeoflandgrid(degreesnorth)(seeex.5).realoﬄine-90.

MKSRFOFFLINEEDGEWWesternedgeofgridland(degreeseast)(seeex.5).realoﬄine-180.

OFFLINEAIRDirectorycontainingatmosphericforcingdatasets(seeex.1).char*256oﬄinerequired

datasetsprovidedareindirectory$CSMDATA/NCEPDATA

Additionaldetails:FSURDATspeciﬁesasurfacedatasetcontainingtime-invariantlandpropertiessuchasplantfunctionaltypesandsoiltexturesandtime-variantpropertiessuchasleafareaindex.IfFSURDATissettotheemptystring,anewsurfacedatasetisgeneratedatruntimeforthespeciﬁedmodelresolution.Thecreationofanewsurfacedatasetrequiresthespeciﬁcationofthefullpathnameofthefollowingrawdatasets:MKSRFFVEGTYP,MKSRFFSOITEX,MKSRFFSOICOL,MKSRFFLANWAT,MKSRFFURBAN,MKSRFFGLACIER,MKSRFFLAI.Thesedatasetsareonlyusedforthegen-erationofamodelsurfacedataset.

Inadditiontorawdatasets,aland/oceanmaskisalsorequiredforthecreationofanewsurfacedataset.Ifthemodelisruninccsmorcammode,thismaskisobtainedfromeithertheccsmﬂuxcouplerorfromthecamatmospheremodelatstartup.Inoﬄinemode,however,theland/oceanmaskcaneitherbecalculatedfromahighresolutionorographydatasetbysettingthenamelistvariableMKSRFOFFLINEFNAVYOROorcanbereadinfromaninputdatasetalreadyatthetargetresolutionviathesettingofthenamelistvariableMKSRFOFFLINEFGRID.

Finally,ifasurfacedatasetistobecreatedatruntime,theusermustspecifyifanew-formatorold-formatdatasetwillbegenerated.Bydefault,old-formatdatasetsarecreated.BysettingthenamelistvariableMKSRFALLPFTSto.true.,anew-formatsurfacedatasetwillbecreated(seesection6).

Subroutinesinvolvedincreatingasurfacedatasetatruntimeresideinthesourcecodedirectorymk-srfdata/.Inmostcasesthecreationofasurfacedatasetinvolvesastraightforwardinterpolationfromtherawdatasetresolutiontothedesiredmodelresolution.Forsoiltexture,however,averagingwouldcreatenewsoiltypes.Consequently,themodeldeterminesthedominantsoiltextureproﬁlepergridcellfromtherawresolutiontothedesiredresolution.

Oncethesurfacedatasetiscreated,theusershoulduseFSURDATtopointtothatdataset,inordertoavoidcreatingthesamedatasetmultipletimes.

TheinputﬁlespeciﬁedbythenamelistvariableFINIDATcontainsvaluesforthetime-dependentvariablesneededtoinitializethemodelfromaspun-upstate.IfFINIDATissettotheemptystring,themodelisinternallyinitializedtononspun-upvalues.Thesettingofthenamelistvariable,HISTCRTINIC(describedinsection4.3)canbeusedtogenerateinitialCLMﬁlesduringamodelrun.Wealsoprovideanewtool,interpinic,whichprovidesuserswiththeabilitytouseanalreadyexistinginitialdatasetatonemodelresolutiontogenerateanewinitialdatasetatanothermodelresolution.Section7providesmoredetailsofthistool.

WhenthecpptokenRTMisdeﬁned,theRTMriverroutingschemewillbeinvokedinrunningthemodel.Inthiscase,FRIVINPRTMmustbesettoariverroutingdataset.

Inoﬄinemode,timedependentatmosphericforcingdatamustbereadinperiodically.ThedirectorycontainingtheseﬁlesisgivenbyOFFLINEAIR.Thisvariableisignoredincamandccsmmode.

4.3Speciﬁcationofhistoryandrestartﬁles

Thefollowingdescribesnamelistvariablesassociatedwithhistory,restart,andinitializationﬁles.Inwhatfollows,maxtapesdenotesthemaximumallowablenumberofdiﬀerenttypesofhistoryﬁles(tapes)thatthemodelcanproduce(currentlysetto6)andmaxﬂdsdenotesthemaximumnumberofhistoryﬁeldsthatmayappearonanygivenhistorytape(currentlysetto1000).

name:description:type:mode:default:name:

HISTCRTINICFrequencywithwhichinitialdatasetswillbegenerated.

Validvaluesare’YEARLY’,’MONTHLY’,’DAILY’,’6-HOURLY’or’NONE’.char*8

oﬄine,ccsm(obtainedfromCAMincammode)’YEARLY’HISTNHTFRQ19

description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:

type:mode:default:

name:description:

type:mode:default:

Historytapeinterval(s)

(+formodeltimesteps,-forhours,0formonthlyave)(seeex.1,3).integerarray(uptomaxtapesvaluesseparatedbycommas)oﬄine,ccsm(obtainedfromCAMincammode)0

HISTMFILTNumberoftimesamplesperhistorytape(s)(seeex.3,4).

integerarray(uptomaxtapesvaluesseparatedbycommas)oﬄine,ccsm(obtainedfromCAMincammode)1whenHISTNHTFRQ=0,else30

HISTNDENSOutputtapeprecision(s).Validvaluesare1(doubleprecision)or2(singlepre-cision).

integerarray(uptomaxtapesvaluesseparatedbycommas)all2

HISTDOV2XYPertapespatialaveragingﬂag.Ifsettotrue,producesgrid-averagehistoryﬁeldsonoutputtape.Ifsettofalse,one-dimensionalﬁeldsareproduced(seeex.4).logicalarray(uptomaxtapesvaluesseparatedbycommas)all.true.

HISTAVGFLAGPERTAPE

Pertapetimeaveragingﬂag.Validvaluesare’A’(averageoverhistoryperiod),’I’(instantaneous),’X’(maximumoverhistoryperiod)or’M’(minimumoverhistoryperiod).

char*1array(uptomaxtapesvaluesseparatedbycommas)all

blank(inthiscaseahardwiredﬂagpervariableisused,foundinhistFldsMod.F90)

HISTTYPE1DPERTAPEPertapeonedimensionaloutputtype.Onlyusedifonedimensionaloutputisselectedforthegiventape(viathesettingofHISTDOV2XY).Validvaluesare’GRID’,’LAND’,’COLS’,’PFTS’.Forexample,ifonedimensionaloutputisselectedfortape3andHISTTYPE1DPERTAPEissetto’COLS’,thenalltheﬁeldswillhave1dcolumnoutput.Ifthespeciﬁedonedimensionaloutputtypeisnotdeﬁnedforagivenﬁeld,outputvalueswillbesetto1.e36forthatﬁeld.char*4array(uptomaxtapesvaluesseparatedbycommas)all

blank(inthiscaseahardwiredtypepervariableisused)

name:description:type:mode:default:name:description:

type:mode:default:

name:description:

type:mode:default:

name:description:

type:mode:default:

name:description:type:mode:default:name:HISTEMPTYHTAPES

Ifsettotrue,allthehistorytapesareemptybydefault.Onlyvariablesexplicitlylistedbytheuserwillbeoutput.logicalall.false.

HISTFINCL1,...,HISTFINCL6Listofﬁeldstoincludeontherespectivehistorytape.Seetables9-18forthelistofdefaultﬁeldsontheprimaryhistorytape.Namelistspeciﬁcationcantakeoneoftwoforms.Theusermaysimplyspecifythenameoftheﬁeldtobeincludedonthehistorytape(inwhichcasethedefaulttimeaveragingforthatﬁeldwillbeused).Forexample,HISTFINCL2=’TV’,willaddtheﬁeldTVtothesecondhistorytapewithwhateverdefaulttimeaveragingwasspeciﬁedforTV.Alternatively,theusermayspecifytheﬁeldname,followedbya”:”followedbythetimeaveragingﬂagdesired(validﬂagsare’I’forinstantaneous,’A’foraverage,’M’forminimum,and’X’formaximum).Forexample,HISTFINCL2=’TV:I”willaddtheﬁeldTVwithinstantaneousoutputtothesecondhistorytape(seeex.3,4).

char*34array(uptomaxﬂdsvaluesseparatedbycommas)allblank

HISTFEXCL1,...,HISTFEXCL6Listofﬁeldstoexcludefromtherespectivehistorytape.TheﬁeldnamemustappearintheMasterFieldListofthedefaulthistorytape(theprimarytape).Seetables9-18formoredetails.

char*32array(uptomaxﬂdsvaluesseparatedbycommas)allblank

MSSIRTMassStoreretentionperiod(days)foroutputdatasets(seeex.4).UsermusthaveMassStoreaccess.ForexampleNCARsupercomputersrecognizeMassStorecommands.integer

oﬄine,ccsm(obtainedfromCAMincammode)

0(i.e.,historyﬁleswillbewrittentolocaldisk,nottheNCARMassStore)

MSSWPASSMassStorewritepasswordforoutputdatasets.char*8allblank

RPNTPATH

description:type:mode:default:name:description:type:mode:default:

Fullunixpathnameofthelocalrestartpointerﬁle.char*256all

Filelnd.CASEID.rpointerplacedinuser’shomedirectoryARCHIVEDIR

MassStoredirectorytoarchiveoutputﬁleschar*256all

/USERNAME/CSM/CASEID

Additionaldetails:Themodelwritesitsownhistory,restartandinitialﬁles.HistoryﬁlesareinnetCDFﬁleformatandcontainmodeldatavalueswrittenatuserspeciﬁedfrequenciesduringamodelrun.Eachﬁeldhasadefaulttimeaveragingﬂagdetermininghowthatﬁeldwillbeaccumulatedintimeoveragivenhistoryinterval.Thechoicesaretorecordaveraged,instantaneous,maximum,orminimumvalues.TheusermayoverwritethisdefaultsettingviathenamelistvariableHISTFINCLtwheretcanequal1to6.Iftheuserwishestoseeaﬁeldwrittenatmorethanoneoutputfrequency(e.g.dailyandhourly),additionalhistoryﬁlesmustbedeclaredcontainingthatﬁeld.Bydefault,CLM3.0producesamonthlyaveragedprimaryhistoryﬁleandallowstheusertodeﬁneuptoﬁveauxiliaryhistoryﬁles.AllﬁlescontaingridaverageddataunlessthenamelistvariableHISTDOV2XYissettofalseforagivenﬁle.Primaryhistoryﬁlescontainthestring’h0’,whereasauxiliaryhistoryﬁlescontainthestring’h1’,’h2’,’h3’,’h4’and’h5’.

ThemodelwillalsocreatenetCDFdatasetscontainingonedimensionalinstantaneousvaluesofinitialdataﬁeldsatthefrequencydeﬁnedbynamelistvariableHISTCRTINIC.Thesedatasetscanbeutilizedas“spun-up”initialconditions.

Restartﬁlesareinbinaryformatandcanbeusedonlyforrestartorbranchrunsfrompreviousmodelsimulations.Wheneverarestartﬁleiswritten,acorrespondinglocaldiskrestartpointerﬁleisoverwritten.Therestartpointerﬁlecontainsthenameofthelatestmodelrestartﬁle.Bydefault,therestartpointerﬁleisplacedintheuser’shomedirectoryunderthename,lnd.CASEID.rpointer.TheusermaymodifythefullpathnameoftherestartpointerﬁleviathesettingofthenamelistvariableRPNTPATH.

Thefollowingtablespeciﬁesthenamingconventionusedforoutputﬁles.Inthistablethestringyyyyreferstothemodelyear,mmreferstothemodelmonth,ddisthemodeldayandssssscorrespondstosecondsintothemodelday.Initialandrestartﬁlesalwayscontainonetimesliceofinstantaneousdata.However,non-monthlyhistoryﬁlesmaycontainmultipletimeslicesoftime-averageddata,soyyyy-mm-dd-ssssscorrespondstotheﬁrsttimesliceofdataontheﬁle.CASEIDisthecaseidentiﬁersetviathenamelistinput.

CASEID.clm2.r.yyyy-mm-dd-sssssrestartﬁlesCASEID.clm2.i.yyyy-mm-dd-sssss.ncinitialﬁles

CASEID.clm2.h[012345.yyyy-mm.nc]monthlyaveragehistoryﬁlesCASEID.clm2.h[012345.yyyy-mm-dd-sssss.nc]non-monthlyhistoryﬁles

History,restartandinitializationﬁlescanbearchivedontheNCARMassStorageSystem(MSS)ifthenamelistvariableMSSIRTissettoavaluegreaterthanzero.History,restartandinitialﬁlesarearchivedasfollows(whereUSERNAMEistheupper-caseequivalentoftheuser’sloginname,i.e.,theuser’srootdirectoryontheMSS):

historyﬁles/USERNAME/csm/CASEID/lnd/histrestartﬁles/USERNAME/csm/CASEID/lnd/restinitialﬁles/USERNAME/csm/CASEID/lnd/init

4.4Speciﬁcationofinputphysicsvariables

name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:name:description:type:mode:default:

IRAD

Frequencyofsolarradiationcalculations(+formodeltimesteps,-forhours).integer

oﬄine,mustbeconsistentwithCAM3.0inccsmmode,obtainedfromCAMincammode-1

CSMDOFLXAVE

Ifsettotrue,ﬂuxaveragingisperformedoverthedurationsetinIRAD.logical

ccsm(mustagreewithCAM3.0settinginatm.setup.csh).true.(.false.notsupported)

WRTDIA

Iftrue,globalaverage2-mtemperaturewrittentostandardout(asciilogﬁleoftherun)(seeex.4).logicalall.false.

PERTLIM

Perturbationlimit(notsupportedatthistime)realall0

4.5SpeciﬁcationofRTMRiverrouting

name:description:type:mode:default:

RTMNSTEPS

FrequencyinnumberoftimestepsatwhichRTMiscalled.integerall

numberoftimestepsin3hours

4.6Speciﬁcationofcammodenamelist

Whenrunningincammode,certainCLM3.0namelistvariablescannotbesetindependently.Inparticu-lar,anyuserspeciﬁcationforthenamelistvariables,CASEID,CTITLE,IRAD,NSREST,HISTCRTINIC,MSSIRT,HISTNHTFRQ,andHISTMFILT(thelasttwoonlyforprimaryhistoryﬁles)willbeover-writtenbyvaluesobtainedfromCAM3.0atstartup.Allothernamelistsettingsmaybesetindependentlybytheuser.

ThefollowingtablespeciﬁesthenamelistvariablesthatareoverwrittenwithvaluesobtainedfromcamandliststheassociatedCAM3.0namelistvariableanditsdefaultvalue.

Table8:NamelistVariablesoverwrittenwithCAMsettings

CLMNamelistCASEIDCTITLENSRESTIRADHISTCRTINICHISTNHTFRQ(1)HISTMFILT(1)MSSIRTCAMnamelistCASEIDCTITLENSRESTIRADSWINITHISTNHTFRQ(1)MFILT(1)MSSIRTCAMdefaultrequiredblank0-1’MONTHLY’0136.7Speciﬁcationofccsmmodenamelist

Whenrunninginccsmmode,theusermustensurethatsettingsofthenamelistvariables,IRAD,DTIMEandCSMDOFLXAVE,haveidenticalvaluestothecorrespondingCAMnamelistvariablesIRADSW,DTIMEandFLXAVEinthescriptcam.buildnmlprestage.csh(seeCCSM3.0User’sGuide).InccsmmodetheRTMinputdatasetmustbespeciﬁedinthenamelistusingvariableFRIVINPRTM,becauseRTMisdeﬁnedbydefault.

Inccsmmode,CAMandCLMrunonthesamegridwhichdependsonthespeciﬁcoceandomainutilized.Consequently,adiﬀerentsurfacedatasetisrequiredforeachatm/ocngridcombination.Currentlyallsupportedccsm-clmsurfacedatasetswillbereleasedwiththeccsmdistribution.NotsupportedonesmaybegeneratedbytheuserbysettingFSURDAT=’’.

Additionally,aCLM3.0spun-upinitialdatasetmaybeprovidedcontainingvaluesforthetime-dependentvariablesneededtoinitializethemodelfromaspun-upstatebysettingthenamelistvariableFINIDAT.ThisﬁleMUSThavethesameatm/ocnresolutionandlandmaskasthemodelrunforwhichitwillbeused.ThevariablesappearingintheFINIDATﬁlewillbeinternallyinitializedtononspun-upvaluesatruntimeifFINIDATisnotset.

Finally,thenamelistvariableCSMDOFLXAVEisspeciﬁctoccsmmodeonly.Ifthisvariableissettotrue(thedefaultsetting),ﬂuxaveragingisperformedoverthetimeintervalspeciﬁedbythenamelistvariable,IRAD(IRADmustbegreaterthan1).Thefalsesettingisnotsupported.

5CLM3.0DataStructures

Inwhatfollows,weprovideabriefsummaryoftheCLM3.0datastructures.Understandingofthesedatastructuresisessentialbeforetheuserattemptstomodifycodeand/oraddnewhistoryoutputﬁeldstothemodel.

ThesubgridhierarchyinCLM3.0iscomposedofgridcells,landunits,columnsandplantfunctionaltypes(pfts).Eachgridcellcanhaveadiﬀerentnumberoflandunits,eachlandunitcanhaveadiﬀerentnumberofcolumnsandeachcolumncanhavemultiplepfts.Thisresultsineﬃcientmemoryallocation,andallowsfortheimplementationofmanydiﬀerenttypesofsubgridrepresentations.

Theﬁrstsubgridlevel,thelandunit,isintendedtocapturethebroadestspatialpatternsofsubgridheterogeneity.Thesebroadpatternsincludephysicallydistinctsurfacetypes(glaciers,lakes,wetlands,andvegetatedareas).IntermsofCLM3.0variables,thecentraldistinguishingcharacteristicofthelandunitisthatthisiswherephysicalsoilpropertiesaredeﬁned:texture,color,depth,pressure-volumerelationships,andthermalconductivity.

Thesecondsubgridlevel,thecolumn,isintendedtocapturepotentialvariabilityinthesoilandsnowstatevariableswithinasinglelandunit.Thecentralcharacteristicofthecolumnisthatthisiswherethestateandﬂuxvariablesforwaterandenergyinthesoilandsnowaredeﬁned.Regardlessofthenumberandtypeofpftsoccupyingspaceonthecolumn,thecolumnphysicsoperateswithasinglesetofupperboundary

ﬂuxes,aswellasasinglesetoftranspirationﬂuxesfrommultiplesoillevels.Theseboundaryﬂuxesareweightedaveragesoverallpfts.

Thethirdandﬁnalsubgridlevelisreferredtoastheplantfunctionaltype(pft),butitalsoincludesthetreatmentforbareground.Itisintendedtocapturethebiophysicalandbiogeochemicaldiﬀerencesbetweenbroadcategoriesofplants,intermsoftheirfunctionalcharacteristics.Allﬂuxestoandfromthesurfacearedeﬁnedatthepftlevel,asarethevegetationstatevariables(e.g.vegetationtemperature,canopywaterstorage,andcarbonfortheleaf,stem,androots).

Inadditiontostateandﬂuxvariabledatastructuresforconservedquantities(energy,water,carbon,etc.),eachsubgridlevelalsohasaphysicalstatedatastructureforhandlingquantitiesthatarenotinvolvedinconservationchecks(diagnosticvariables).Forexample,soiltextureisdeﬁnedthroughphysicalstatevariablesatthelandunitlevel,thenumberofsnowlayersandtheroughnesslengthsaredeﬁnedasphysicalstatevariablesatthecolumnlevel,andtheleafareaindexandthefractionofcanopythatiswetaredeﬁnedasphysicalstatevariablesatthepftlevel.

Thehierarchicalsubgriddatastructuresareimplementedinthecodethroughthemodulesclmtype.F90,clmtypeInitMod.F90,decompMod.F90andinitGridCellsMod.F90.Theseroutinesareallinthe/src/main/subdirectory.ThenewcodemakesextensiveuseoftheFortran90implementationofthederiveddatatype.Thispermitstheusertodeﬁnenewdatatypesthatcanconsistofmultiplestandarddatatypes(integers,doubles,strings)aswellasotherderiveddatatypes.

ThissubgridhierarchyisimplementedinCLM3.0asasetofnestedderivedtypes.Theentiredeﬁnitioniscontainedinmoduleclmtype.F90.Extensiveuseismadeofpointers,bothfordynamicmemoryallocationandforsimpliﬁcationofthederivedtypereferencingwithinsubroutines.Theuseofpointersfordynamicmemoryallocationensuresthatthenumberofsubgridelementsateachlevelinthehierarchyisﬂexibleandresolvedatruntime,therebyeliminatingtheneedtostaticallydeclarearraysofﬁxeddimensionsthatmightendupbeingsparselypopulated.Theuseofpointersforreferencingmembersofthederiveddatatypewithinthesubroutinesprovidesacoherenttreatmentofthelogicalrelationshipsbetweenvariables(e.g.,theusercannotinadvertentlychangeapft-levelvariablewithinasubroutinethatissupposedtooperateonthecolumnstatesandﬂuxes),andamoretransparentrepresentationofthecorealgorithms(itiseasytotellwhenthecodeisinacolumnorpftloop).

Themodule,clmtype.F90,isorganizedsuchthatderivedtypeswhicharemembersofotherderivedtypesaredeﬁnedﬁrst(aFortran90compilerrequirement).Inparticular,theenergyandmassconservationdatatypesaredeﬁnedﬁrst,followedbydatatypesconstitutingthepftlevel,columnlevel,landunitlevel,gridcelllevelandthemodeldomainlevel.Finally,thehierarchicalorganizationofthesetypesisdeﬁned,startingwiththemodeldomainlevel,whichconsistsinpartofapointertoanarrayofgridcells,eachofwhichconsistsinpartofapointertoanarrayoflandunits,eachofwhichhasapointertoanarrayofcolumns,whicheachhaveapointertoanarrayofpfts.

ModelinitializationoccursinmoduleinitializeMod.F90.AbriefsummaryoftheCLM3.0initializationisprovided.Foramoredetaileddiscussion,theuserisreferredtotheCLM3.0Developer’sGuide.TheﬁrststepinCLM3.0initializationistodetermineprocessorandthreaddecomposition(i.e.“clump”layout).ThisisdoneviaacalltosubroutineinitDecompinmoduledecompMod.F90.Subsequently,memoryisallocatedfortheclmdatastructuresinsubroutineinitClmtypeinmoduleclmtypeInitMod.F90.Oncememoryallocationhasoccurred,thehierarchyofthedatastructures(e.g.assignmentofpftstocolumns,etc.)isdeterminedinsubroutineinitGridCellsinmoduleinitGridCellsMod.F90.Useismadeofinputgriddeddatasetsdeﬁningthespatialdistributionofpftsandothersurfacetypes(glacier,lake,etc.).Finally,thenecessarymodelﬁlters(e.g.isolatingsoilpoints,lakepoints,etc)aredeterminedinroutineinitFiltersinmoduleﬁlterMod.F90.

6CLM3.0SurfaceDatasetFormats

Asmentionedinsection4.2,CLM3.0nowsupportstwosurface-dataformats.Thenewformatdiﬀersfromtheoldformatinonlytwovariables:

•PFT-removedfromthenewformatsurface-dataﬁle.

•PCTPFT-percentofthelandgridcellcoveredbyeachpft,includingpftswithzeropercentcover(notpercentofthevegetatedportioncoveredbythefourdominantpfts).Thenewformatsurfacedatasetwillbecreatedifthefollowingnamelistvariableisset:

mksrf_all_pfts=.true.

Theoriginalformatsurfacedatasetwillbecreatedbydefault,orif

mksrf_all_pfts=.false.

Thesurfacedatainitsnewformatprovidesmoreﬂexibilitythanintheoriginalformatbyallowingtheusertodecidethenumberofdominantpftspergridcellfortheirsimulationwithoutcreatinganewsurface-dataﬁleeachtimethisnumberchanges.Thisispossiblebecauseallpftsfoundintherawdataareincludedinthenewformatsurfacedatasetintheorderthattheyarelistedinthepft-physiologyﬁleFPFTCON.Usingthenewformatsurface-dataﬁleasinput,themodelselectsatrun-timethe4dominantnaturalpftsandplacesthemonanaturalvegetationlandunit,whileitplacescropsseparatelyonacroplandunit.

Theusermaychangeatcompiletimethemodelparameterthatspeciﬁesthenumberofdominantpftsusedinthemodel.Theparameter,maxpatchpftinmoduleclmvarpar.F90inthesrc/maindirectorydeterminesthemaximumnumberofvegetatedpftsinthenaturallyvegetatedlandunit.Currentlythisissetto4.Iftheuserweretoincreasethisvalueto6andrecompilethecode,thenthemodelwouldselectthe6dominantnaturalpftsandplacethemonthenaturalvegetationlandunit.Intheoriginalformat,afterrecompilingthecode,anewsurfacedatasetwouldneedtobecreated,whichwouldcontainthe6dominantpfts(bothnaturalandcrop).

Similartomaxpatchpft,theparametermaxpatchcftspeciﬁesthemaximumnumberofcroppftsinthecroplandunitinthenewformat.Currentlythisnumberissetto2andcorrespondstocornandwheatvegetationtypes.InCLM3.0,thesevegetationtypesforcornandwheatarecurrentlyhard-wiredtovaluesof15and16,respectively,whichareidenticalintermsoftheirphysiologicalproperties.Thishard-wiringofvalueswillberemovedinfuturereleases.

Thenewformatsurface-dataﬁlewillfacilitatechangingthelandcoverinthemiddleofasimulation.Itisimportanttonote,however,thatsuchacapabilitywillrequireadditionalcodedevelopmentwhichisnotcurrentlyintheCLM3.0release.Thepresenceofdistinctnaturalandcroplandunitswillalsoallowtheseparatetreatmentoftheselandunitsusingdiﬀerentmodules.Forexample,thedynamicvegetationmodel(DGVM)inCLM3.0maybeusedforthenaturallandunit,whileacropmodelcouldbeusedforthecroplandunit.AlthoughnocropmodelisincludedyetandonlynaturalvegetationispermittedwhenDGVMisactiveintheCLM3.0release,thenewsurfacedatasetformwillfacilitatetheintroductionofthesechangesinthecode.

Thenewsurface-dataformatandtheseparatevegetationlandunitsleadtosmallchangesinCLM’ssimulatedﬂuxestotheatmosphere.Asaresult,onewillseesmallchangesinthesimulatedclimateinCAMorCCSMmode.Usersshoulddecidetoworkwithoneofthesurface-dataformatsandnotswitchbetweensuchformatsinthemiddleofastudy.However,ifauserdesirestodosurfacedatasetdevelopment,theyarestronglyencouragedtousethenewsurfacedatasetformat.

7CreatingaSpun-upInitialDataset

Oftenitmaytakeseveralsimulatedyearsto“spinup”themodel.Forexample,inCCSMmodeitmaytakenumerousdecadestospinupthedeepsoilliquidwater.Asaresult,ithasbecomenecessarytoprovideuserswiththetooltocreateanewinitialdatasetusingaspunupinitialdatasetatanotherresolutionorlandmask.InCLM3.0weareprovidingsuchatool,interpinic,inthedirectorytools/interpinic.Theonlyconstraintisthattheusermusthavealreadycreateda“template”initialdatasetatthenewresolutionbeforethistoolisused.ThiscanbedonebyrunningthemodelforonedayasinExample1butwithanadditionalnamelistsetting:

hist_crtinic=’DAILY’

Anewinitialdatasetwillbecreatedasaresultofthisrun.Thetoolinterpinicwillthenoverwritethenonspun-upvaluesofCLM3.0variablesinthisinitialdatasetwithspun-upvaluesfromthespun-upinitialdataset.

8HistoryFileFields

ThefollowingsectionsdiscussboththeﬁeldsthatmaycurrentlybeoutputtoCLM3.0historytapesaswellascodemodiﬁcationsthattheusermustmaketoaddnewﬁeldstothehistorytapes.

Tables9-18listtheﬁeldsthatcurrentlymaybeoutputtoaCLM3.0historytape.Bydefault,theseﬁeldsappearontheprimaryhistorytape.Thedimensionsofeachﬁeldmayinclude’time’(dayssincethebeginningofthesimulation),’levsoi’(numberofsoillayers,levsoi=10),’levlak’(numberoflakelayers,levlak=10),and’lat’and’lon’(numberoflatitudeandlongitudepoints,e.g.,lat=,lon=128foraT42simulation)forgridaveragedtwodimensionaloutput,and’gridcell’,’landunit’,’column’or’pft’foronedimensionaloutput.ThedimensionsoftheRTMﬁelds,QCHOCNRandQCHANR,include’lonrof’and’latrof’,thenumberoflatitudeandlongitudepointsontheRTMgrid.ThetwoRTMﬁeldsarealwaysoutputonthe0.5degreeRTMgridregardlessoftheresolutionofthemodelrun.Notethatthe1ddimensiontypeappearinginthedimensionsentryspeciﬁesonlythedefault1doutputtype.Forexample,’TSA’willbeoutputbydefaultinpft1doutput.However,thatdefaulttypemaybechangedforagivenhistorytapeviathesettingofthenamelistvariableHISTTYPE1DPERTAPE.Ahistoryﬁeldmayappearassingle-level(SL)ormulti-level(ML).Finally,unlessexplicitlyspeciﬁedinthedescription,allﬁeldsaretimeaveragedovertherequestedhistoryinterval.

Table9:MasterFieldList-TemperatureandHumidity

NameTSATVTGTSOITLAKETSNOWTREFMNAVTREFMXAVQ2MDescription2-mairtemperaturevegetationtemperaturegroundtemperaturesoiltemperaturelaketemperaturesnowtemperaturedailyminimumofhourly-averaged2-mtemperature

dailymaximumofhourly-averaged2-mtemperature

2-mspeciﬁchumidityUnitsKKKKKKKKkg/kg1dOutputpftpftcolumncolumncolumncolumnpftpftpftLevelSLSLSLMLMLSLSLSLSLSpatialValid-ityglobalglobalgloballakesexcludedonlylakesin-cluded

lakesexcludedglobalglobalglobalTable10:MasterFieldList-SurfaceRadiation

NameFSASABGSABVFSRFSRVDDescriptionabsorbedsolarradiationsolarradiationabsorbedbygroundsolarradiationabsorbedbyvegetationreﬂectedsolarradiationdirectvisiblereﬂectedsolarradiation27

UnitsW/m2W/m2W/m2W/m2W/m21dOutputpftpftpftpftpftLevelSLSLSLSLSLSpatialValid-ityglobalglobalglobalglobalglobalTable10:MasterFieldList-SurfaceRadiation

FSRNDFSRVDLNFSRNDLNFSRVIFSRNIFIRAFIREdirectnear-infraredreﬂectedsolarra-diation

directvisiblereﬂectedsolarradiationatlocalnoon

directnear-infraredreﬂectedsolarra-diationatlocalnoon

diﬀusevisiblereﬂectedsolarradiationdiﬀusenear-infraredreﬂectedsolarra-diation

netinfrared(longwave)radiationemittedinfrared(longwave)radiationW/m2W/m2W/m2W/m2W/m2W/m2W/m2pftpftpftpftpftpftpftSLSLSLSLSLSLSLglobalglobalglobalglobalglobalglobalglobal28

Table11:MasterFieldList-SurfaceEnergyFluxes

NameFCTRFCEVFGEVFSHFSHGFSHVFGRFSMTAUXTAUYDescriptioncanopytranspirationevaporationofcanopy-interceptedwa-ter

groundevaporationsensibleheatﬂuxsensibleheatfromgroundsensibleheatfromvegetationheatﬂuxintosnow/soil(includessnowmelt)

snowmeltheatﬂuxzonalsurfacestressmeridionalsurfacestressUnitsW/m2W/m2W/m2W/m2W/m2W/m2W/m2W/m2kg/m/s2kg/m/s21dOutputpftpftpftpftpftpftpftcolumnpftpftLevelSLSLSLSLSLSLSLSLSLSLSpatialValid-ityglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalTable12:MasterFieldList-VegetationPhenology

NameELAIESAIDescriptionexposedone-sidedleafareaindexexposedone-sidedstemareaindexUnitsm2/m2m2/m21dOutputpftpftLevelSLSLSpatialValid-ityglobalglobalTable13:MasterFieldList-CanopyPhysiology

NameRSSUNRSSHABTRANFPSNDescriptionsunlitleafstomatalresistance(mini-mumovertimeinterval)

shadedleafstomatalresistance(mini-mumovertimeinterval)

transpirationbetafactor(soilmois-turelimitation)photosynthesisUnitss/ms/munitlessunitless1dOutputpftpftpftpftLevelSLSLSLSLSpatialValid-ity

lakesexcludedlakesexcludedlakesexcludedglobal29

Table14:MasterFieldList-Hydrology

NameH2OSOIH2OSNOFSNOH2OCANSOILLIQSOILICESNOWLIQSNOWICESNOWDPSNOWAGEQINFLQOVERQRGWLQDRAIQINTRQDRIPQMELTQSOILQVEGEQVEGTQCHOCNRQCHANRDescriptionvolumetricsoilwater(ratioofwatertototalsoilvolume)

snowdepth(liquidwaterequivalent)fractionofsoilcoveredbysnowwateronthecanopysoilliquidwatersoilicesnowliquidwatersnowicesnowheightsnowagewaterinﬁltrationinsoilsurfacerunoﬀsurfacerunoﬀatglaciers,wetlands,andlakes

sub-surfacedrainagecanopyinterceptionofprecipitationthroughfallsnowmeltgroundevaporationevaporationofcanopy-interceptedwa-ter

canopytranspirationRTMriverdischargeintoocean(in-cludedifRTMdeﬁned)

RTMriverﬂow(includedifRTMde-ﬁned)

Unitsmm3/mm3mmunitlessmmkg/m2kg/m2kg/m2kg/m2munitlessmm/smm/smm/smm/smm/smm/smm/smm/smm/smm/sm3/sm3/s1dOutputcolumncolumncolumnpftcolumncolumncolumncolumncolumncolumncolumncolumncolumncolumnpftpftcolumnpftpftpft2-Donly2-DonlyLevelMLSLSLSLMLMLSLSLSLSLSLSLSLSLSLSLSLSLSLSLSLSLSpatialValid-ity

lakesexcludedglobalglobalgloballakesexcludedlakesexcludedlakesexcludedlakesexcludedglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalTable15:MasterFieldList-WaterandEnergyBalanceChecks

NameERRSOIERRSEBERRSOLERRH2ODescriptionsoil/lakeenergyconservationerrorsurfaceenergyconservationerrorsolarradiationconservationerrortotalwaterconservationerrorUnitsW/m2W/m2W/m2mm1dOutputcolumnpftpftcolumnLevelSLSLSLSLSpatialValid-ityglobalglobalglobalglobal30

Table16:MasterFieldList-AtmosphericForcing

NameRAINSNOWTBOTWINDTHBOTQBOTZBOTFLDSFSDSFSDSVDFSDSNDFSDSVDLNFSDSNDLNFSDSVIFSDSNIDescriptionrainsnowatmosphericairtemperatureatmosphericwindvelocitymagnitudeatmosphericairpotentialtemperatureatmosphericspeciﬁchumidityatmosphericreferenceheightincidentlongwaveradiationincidentsolarradiationdirectvisibleincidentsolarradiationdirectnear-infraredincidentsolarra-diation

directvisibleincidentsolarradiationatlocalnoon

directnear-infraredincidentsolarra-diationatlocalnoon

diﬀusevisibleincidentsolarradiationdiﬀusenear-infraredincidentsolarra-diation

Unitsmm/smm/sKm/sKkg/kgmW/m2W/m2W/m2W/m2W/m2W/m2W/m2W/m21dOutputgridcellgridcellgridcellgridcellgridcellgridcellgridcellgridcellgridcellpftpftpftpftpftpftLevelSLSLSLSLSLSLSLSLSLSLSLSLSLSLSLSpatialValid-ityglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalTable17:MasterFieldList-Soil

NameZSOIDZSOIWATSATDescriptionsoillayernodedepthsoillayerthicknessvolumetricsoilwateratsaturation(equaltotheporosity)saturatedsoilmatricpotentialUnitsmmmm3/mm31dOutputcolumncolumncolumnLevelMLMLMLSpatialValid-ity

lakesexcludedlakesexcludedglaciers,wet-lands,lakesexcludedglaciers,wet-lands,lakesexcludedglaciers,wet-lands,lakesexcluded

SUCSATmmcolumnMLBSWslopeofsoilwaterretentioncurveunitlesscolumnML31

Table18:MasterFieldList-VolatileOrganicCompounds(onlyincludedifVOCdeﬁned)

NameBIOGENCOISOPRENEMONOTERPORVOCOVOCVOCFLXTDescriptionbiogenicCOﬂuxisopreneﬂuxmonterpeneﬂuxotherreactiveVOCﬂuxotherVOCﬂuxtotalVOCﬂuxintoatmosphereUnitsµg/m2/hµg/m2/hµg/m2/hµg/m2/hµg/m2/hµg/m2/h1dOutputpftpftpftpftpftpftLevelSLSLSLSLSLSLSpatialValid-ityglobalglobalglobalglobalglobalglobalTable19:MasterFieldList-DynamicVegetation(onlyincludedifDGVMdeﬁned)

NameFMICRFRMSFRMRFRMFFRGFCO2DMIHTOPHBOTTLAITSAITDAT10AGDD0AGDD5DescriptionmicrobialrespirationstemmaintenancerespirationrootmaintenancerespirationfoliagemaintenancerespirationgrowthrespirationnetCO2ﬂuxnetprimaryproductionheightoftopofcanopyheightofbottomofcanopytotalone-sidedleafareaindextotalone-sidedstemareaindexdailyaverage2-mtemperature10-dayrunningmeanof2-mtempera-ture

growingdegree-daysbase0degreesCgrowingdegree-daysbase5degreesCUnitsµmol/m2/sµmol/m2/sµmol/m2/sµmol/m2/sµmol/m2/sµmol/m2/sµmol/m2/smmm2/m2m2/m2KKdegree-daysdegree-days1dOutputpftpftpftpftpftpftpftpftpftpftpftpftpftpftpftLevelSLSLSLSLSLSLSLSLSLSLSLSLSLSLSLSpatialValid-ityglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalglobalNotethatforsnowrelatedﬁelds(e.g.SNOWLIQ),horizontalaveragingisdoneonlyusingcolumnsthathavesnow.Inthishorizontalaveraging,lakesubgridpointsareexcluded.Furthermore,forsnowrelatedﬁelds,verticalaveragingisdonebysumming(e.g.,SNOWLIQ)oraveraging(e.g.,TSNOW)onlyovervalidsnowlayers.

AlsonotethatadditionalhistoryﬁeldsappearintheprimaryhistoryﬁlewhenDGVMisdeﬁned.Inaddition,aseparatehistoryﬁleisproducedonceperyearwhenDGVMisdeﬁned.ThisﬁleisdescribedintheCLM-DGVMuser’sguide.

9OﬄineModeNamelistExamples

ThefollowingexamplesillustratediﬀerentnamelistoptionsthatcanbeusedtorunCLM3.0inoﬄinemode.

9.1Example1:Oﬄineinitialrun,oneday,global

Whenthemodelisruninoﬄinemodeusingapre-existingsurfacedataset,theminimumnamelistparame-tersare:CASEID,NSREST,NESTEPorNELAPSE,FSURDAT,FPFTCON,OFFLINEAIR,STARTYMD,andDTIME.IfFSURDATisblank,asurfacedatasetwillbegeneratedatruntimeandadditionalvariablesneedtobespeciﬁed(seesection4.2andExamples5and6).Namelistparametersnotspeciﬁedwillbesettodefaultvalues.Thefollowinggivesanexampleofasimplenamelist.&clmexpCASEIDNSRESTNESTEPFSURDATFINIDATFPFTCON

FRIVINP_RTMOFFLINE_AIRSTART_YMDDTIME

HIST_NHTFRQ/

===========

’test01’0-1

’$CSMDATA/srfdata/clms_x128_USGS_c030605.nc’’’

’$CSMDATA/pftdata/pft-physiology’’$CSMDATA/rtmdata/rdirc.05’’$CSMDATA/NCEPDATA’199712311800-24

CASEID=’test01’

Caseidentiﬁerwhichdistinguishesthisparticularsimulationfromanother.ThestringinCASEIDshowsupinthenamesofhistory,restart,andinitialﬁles,intherestartpointerﬁlename(seeExample2)andintheMassStorepathnamewherehistory,restart,andinitialﬁlesareplacediftheMassStoreisused.NSREST=0

Requestsaninitialrun,asopposedtoarestartorabranchrun.Aninitialrundoesnotrequiretheuseofaninitialinputdataﬁle(FINIDAT).Ifnoneisprovided,themodelusesnonspun-upinitializationprovidedinthecode(seesrc/main/iniTimeVar.F90).

NESTEP=-1

Speciﬁestherun’sendingtimetobeattheendofday1.

FSURDAT=’$CSMDATA/srfdata/clmsx128USGSc030605.nc’

Speciﬁesthenameofthesurfacedatainputﬁle.ThisparticularT42surfacedatasetcanbeusedbothincamandoﬄinemode.Themodelresolution(i.e.parametersLSMLONandLSMLAT)mustbecompatiblewiththeresolutionofFSURDAT.Iftheﬁlenameappearedwithoutapathspecifyingitsexactlocation,theﬁlewouldbeexpectedintheexecutabledirectory,deﬁnedbytheenvironmentvariable$MODELEXEDIR.FINIDAT=’’

Speciﬁestheinitialﬁletobeusedtoprescribeinitialvaluesfortime-dependentvariables.Sincenoﬁleisspeciﬁedinthiscase,themodelwillbeinternallyinitializedtononspun-upvalues(arbitraryinitialization).FPFTCON=’$CSMDATA/pftdata/pft-physiology’

SpeciﬁesaﬁlewithPFT(PlantFunctionalType)parameters.

FRIVINPRTM=’$CSMDATA/rtmdata/rdirc.05’

SpeciﬁestheinputﬁlerequiredfortheoperationofRTM(RiverTransportModel).Bydefault,RTMwilloperateathalfdegreehorizontalresolutionandwillbeinvokedevery3hours,wheretheﬂuxesinputtoRTM(i.e.,runoﬀ)areaveragedoverthe3hourperiod.IftheuserwantstheRTMschemetooperateatadiﬀerentfrequencythanonceevery3hours,RTMNSTEPSshouldbesettothedesiredvalueoftimesteps.UseofRTMisactivatedinthejobscript.cshwiththeCpre-processor(cpp)directive#deﬁneRTMintheheaderﬁlepreproc.h(seesection3.1.3).

OFFLINEAIR=’$CSMDATA/NCEPDATA’

Speciﬁesthelocationoftheatmosphericdriverdataset.Suchadatasetisrequiredforthemodeltoruninoﬄinemode.

STARTYMD=19971231

Speciﬁesthebasedateofthesimulationandmustbecompatiblewiththeatmosphericinputdata.Forexample,STARTYMD=19971231willusetheatmosphericinputﬁle1997-12.nc.Inarestartorbranchrun,STARTYMDneednotbechanged,aslongasitreferstoadateearlierthanthedateofrestartorbranch.

DTIME=1800

Speciﬁesthesimulation’stimestepinseconds.Inoﬄinemode,themodelcanhandleatimestepofupto3600seconds.

HISTNHTFRQ=-24

Primaryhistoryﬁlesandrestartﬁleswillbeproducedintheexecutabledirectoryandwillbewrittenevery24hours.

9.2Example2:Restartrun

ThefollowingnamelistgeneratesarestartrunwhichcontinuestheruninExample1.&clmexpCASEIDNSRESTNELAPSEFSURDATFINIDATFPFTCON

FRIVINP_RTMOFFLINE_AIRSTART_YMDDTIME

HIST_NHTFRQ/

===========

’test01’1-1

’$CSMDATA/srfdata/clms_x128_USGS_c030605.nc’’’

’$CSMDATA/pftdata/pft-physiology’’$CSMDATA/rtmdata/rdirc.05’’$CSMDATA/NCEPDATA’199712311800-24

NSREST=1

Requestsarestartrun.Arestartrunﬁndsthenameoftheappropriaterestartﬁleautomaticallybyreadingtheﬁle,lnd.CASEID.rpointerfoundbydefaultintheuser’shomedirectory.Inthisexample,thepointerﬁlewillbelnd.test01.rpointer.Restartrunsaremeanttobe’seamless’,producingthesameoutputasrunswhichcontinuedwithoutarestart.

NELAPSE=-1

Speciﬁestherun’sendingtimetobeonedayafterthepointofrestart.ThisisequivalenttoenteringNESTEP=-2,sincethepreviousrunstoppedattheendofday1.IfNESTEPwereusedinthisnamelist,itwouldoverridethevaluegiventoNELAPSE.

Allothernamelistvariablesremainthesametoensurea’seamless’restart(forinformation,seeexample1).Also,foraseamlessrestart,theusershouldgenerallyexecutethecodewiththesameexecutableusedintheinitialrun(ie,withoutcompilingthecodeagain).Thejobscriptwillnotrecompilethecodeunlesstheuserhasmadechangestothecodeorﬁleshavebeenremovedfromtheblddirectory.

9.3Example3:Branchrun

ThefollowingnamelistgeneratesabranchrunstartingfromrestartﬁlesgeneratedbyExample1.Theusermaybrancharunwiththesameexecutableusedintheinitialrun(i.e.,withoutrecompilingthecode)unlessbranchingisusedtotestchangesinthecode(fordebuggingorsensitivitypurposes).&clmexpCASEIDNSRESTNREVSNNELAPSEFSURDATFINIDATFPFTCON

FRIVINP_RTMOFFLINE_AIRSTART_YMDDTIME

HIST_FINCL2HIST_NHTFRQHIST_MFILT/

==============

’branch_run’3

’test01.clm2.r.1998-01-01-00000’-1

’$CSMDATA/srfdata/clms_x128_USGS_c030605.nc’’’

’$CSMDATA/pftdata/pft-physiology’’$CSMDATA/rtmdata/rdirc.05’’$CSMDATA/NCEPDATA’199712311800’TV:I’-3,52,3

SeeExample1forexplanationsofnamelistvariableswhichremainunchanged.NSREST=3

Requestsabranchrun.

NREVSN=’test01.clm2.r.1998-01-01-00000’

Suppliesthenameoftherestartﬁlewhichwillinitializethisrun.(ThisﬁlecanbeproducedbyrunningExample1above).

NELAPSE=-1

Speciﬁestherun’sendingtimetobeonedayafterthepointofbranching.HISTFINCL2=’TV:I’

Addanauxiliaryhistoryﬁlewiththeﬁeld“TV”thatisoutputinstantaneously.

HISTNHTFRQ=-3,5

Changesthefrequencyofprimaryhistorywritestoevery3hours.Thewritefrequencyoftheauxiliaryﬁleisevery5timesteps.Thisisanexampleofachangewhichausermaywishtotestinabranchrun.HISTMFILT=2,3

Theprimaryhistoryﬁlewillhave2timesamplesoneverytape.Theauxiliaryhistoryﬁlewillhave3timesamplesoneverytape.

9.4Example4:Auxiliaryhistoryﬁles

Thisexamplecoverstheadditionofanauxiliaryhistoryﬁle,theremovalofaﬁeldfromtheprimaryhistoryﬁleandthechangeofﬁeldtypeinahistoryﬁle.Avarietyofothernamelistoptionsarealsoillustrated.&CLMEXPCASEIDNSRESTNESTEP

=’rtm_run’=0=-31

FSURDATFINIDATFPFTCON

FRIVINP_RTMOFFLINE_AIRSTART_YMDDTIME

HIST_FEXCL1HIST_FINCL2HIST_DOV2XYHIST_NHTFRQHIST_MFILTMSS_IRTWRTDIA/

==============’$CSMDATA/srfdata/clms_x128_USGS_c030605.nc’’’

’$CSMDATA/pftdata/pft-physiology’’$CSMDATA/rtmdata/rdirc.05’’$CSMDATA/NCEPDATA’199801011800’TSNOW’

’TV’,’TG:I’.true.,.false.-24,-124,2365.true.

Fornamelistvariableswhicharerepeated,refertoExamples1,2,and3.HISTFEXCL1=’TSNOW’

Theﬁeld’TSNOW’willbeexcludedfromtheprimarytape.

HISTFINCL2=’TV’,’TG:I’

Speciﬁesthetwoﬁeldstobeaddedtotheauxiliaryhistoryoutput.Theﬁrstﬁeld,’TV’,willhavethedefaulttimeaveragingdone,whereasthesecondﬁeld,’TG’,willhaveinstantaneousoutput.

HISTDOV2XY=.true.,.false.

Historyoutputwillappearingriddedtwo-dimensionalformatfortheprimaryﬁleandinone-dimensionalsubgridformatfortheauxiliaryﬁle.

HISTNHTFRQ=-24,-12

Historyoutputwillbedirectedtotheprimaryhistoryﬁleevery24modelhoursandtotheauxiliaryhistoryﬁleevery12hours.

HISTMFILT=4,2

Eachprimaryhistoryﬁlewillcontain4timeslicesofoutput,whileeachauxiliaryhistoryﬁlewillcontain2timeslicesofoutput.

MSSIRT=365

OutputﬁleswillbearchivedontheNCARMassStorageSystemwitharetentiontimeof365days.WRTDIA=.true.

Aglobalaverageoflandsurfaceairtemperatureasdiagnosticwillappearinthestandardoutputﬁleofthesimulation.

9.5Example5.Generationofregionalgridsurfacedataset

Aregulargridsurfacedatasetcanbegeneratedatruntimeforasinglegridcellorforgridcellscomprisingare-gionalorglobaldomain.Inallcases,thecpptokensLSMLONandLSMLATmustbesettothedesiredres-olution(e.g.,LSMLON=1,LSMLAT=1forasinglegridcellsimulationorLSMLON=120,LSMLAT=60fora3degreeby3degreeglobalsimulation).Togenerateasurfacedatasetforaregionalrun,thevari-ablesMKSRFOFFLINEEDGES,MKSRFOFFLINEEDGEN,MKSRFOFFLINEEDGEE,andMKSRFOFFLINEEDGEWandtheirvaluesneedtobeaddedtothenamelist.Asurfacedatasetwillbecreatedwiththenamesurface-data.LSMLONxLSMLAT.nc(e.g.,forasinglepointsimulationthe

ﬁlenamewillbesurface-data.001x001.nc).ThemodelcanthenberunbyfollowingExample1whereFSURDATpointstothenewsurfacedataset.

Inthefollowingexample,aregionalgridiscreatedovertheAmazonbasin.LSMLONandLSMLATshouldbesetto15and11,respectively,for3degreeby3degreehorizontalresolution.&clmexpCASEIDNSRESTNESTEPSTART_YMDDTIMEFSURDAT

FRIVINP_RTMFPFTCON

OFFLINE_AIR

MKSRF_OFFLINE_FNAVYOROMKSRF_FVEGTYPMKSRF_FSOITEXMKSRF_FSOICOLMKSRF_FLANWATMKSRF_FGLACIERMKSRF_FURBANMKSRF_FLAI

MKSRF_OFFLINE_EDGENMKSRF_OFFLINE_EDGESMKSRF_OFFLINE_EDGEEMKSRF_OFFLINE_EDGEW/

=====================

’create_regional_surfdat’02

199712311800’’

’$CSMDATA/rtmdata/rdirc.05’

’$CSMDATA/pftdata/pft-physiology’’$CSMDATA/NCEPDATA’

’$CSMDATA/rawdata/mksrf_navyoro_20min.nc’’$CSMDATA/rawdata/mksrf_pft.nc’

’$CSMDATA/rawdata/mksrf_soitex.10level.nc’’$CSMDATA/rawdata/mksrf_soicol_clm2.nc’’$CSMDATA/rawdata/mksrf_lanwat.nc’’$CSMDATA/rawdata/mksrf_glacier.nc’’$CSMDATA/rawdata/mksrf_urban.nc’’$CSMDATA/rawdata/mksrf_lai.nc’12-21-36-81

FSURDAT=’’

Asurfacedatasetnamedsurface-data.LSMLONxLSMLAT.ncwillbecreatedinthemodelexecutabledirec-tory.LSMLONandLSMLATaredeﬁnedinjobscript.csh(seesection3.1.3).

MKSRFOFFLINEFNAVYORO=’$CSMDATA/rawdata/mksrfnavyoro20min.nc’

Pointstotheorographydatasetusedtoderivethemodel’slandmaskinoﬄinemode.Theenvironmentvariable$CSMDATAisexplainedin3.1.1.

MKSRFFVEGTYP,MKSRFFSOITEX,MKSRFFSOICOL,MKSRFFLANWAT,MKSRFFGLACIER,MKSRFFURBAN,andMKSRFFLAISpecifytheraw(usuallyhighresolution)inputdatasetsusedtocreatethemodelsurfacedataset.

MKSRFOFFLINEEDGES,MKSRFOFFLINEEDGEN,MKSRFOFFLINEEDGEE,andMK-SRFOFFLINEEDGEW

Mustbedeﬁnedforthedesiredmodelregionaldomainbecausethedefaultvaluesassumeaglobaldomain.TheunitsaredegreesnorthforEDGESandEDGENanddegreeseastforEDGEEandEDGEW.

9.6Example6.Generationofglobalgaussiansurfacedataset

Onlyglobalsurfacedatasetscanbecreatedonanon-regulargrid,suchasagaussiangrid.Togenerateasurfacedatasetonagaussiangrid,thecpptokensLSMLONandLSMLATmustbesettothedesiredresolution(e.g.,LSMLON=128,LSMLAT=foraT42grid),andMKSRFOFFLINEFGRIDmustbesettotheappropriatedatasetin$CSMDATA/srfdataspecifyingthemodelgrid,landmaskand

landfractionforthemodelgrid.AtT42resolution,asurfacedataset,“surface-data.128x0.nc”,willbecreatedinthemodelexecutabledirectory.Thisdatasetmayberenamedbytheusertobemoreself-explanatory.Forexample,thesurfacedatasetcreatedusingthisexamplewasclmsx128USGSc030605.ncin$CSMDATA/srfdata.AndwiththeadditionofMKSRFALLPFTS=.true.tothisnamelist,wecreatedclmsx128allpftsc040426.nc.Thefollowingnamelistwillresultinthegenerationofasurfacedatasetonaglobalgaussiangrid.&clmexpCASEIDNSRESTNESTEPSTART_YMDDTIMEFSURDAT

FRIVINP_RTMFPFTCON

OFFLINE_AIR

MKSRF_OFFLINE_FGRIDMKSRF_FVEGTYPMKSRF_FSOITEXMKSRF_FSOICOLMKSRF_FLANWATMKSRF_FGLACIERMKSRF_FURBANMKSRF_FLAI/

=================

’create_global_surfdat’02

199712311800’’

’$CSMDATA/rtmdata/rdirc.05’

’$CSMDATA/pftdata/pft-physiology’’$CSMDATA/NCEPDATA’

’$CSMDATA/srfdata/fgrid.clms_x128_USGS_c030605.nc’’$CSMDATA/rawdata/mksrf_pft.nc’

FSURDAT=’’

Asurfacedatasetnamedsurface-data.128x0.ncwillbecreatedatruntimeinthemodelexecutabledirec-tory.

MKSRFOFFLINEFGRID=’$CSMDATA/srfdata/fgrid.clmsx128USGSc030605.nc’

Pointstothedatasetcontainingthemodelgrid,landmaskandfractionallandforthesurfacedataset.

MKSRFFVEGTYP,MKSRFFSOITEX,MKSRFFSOICOL,MKSRFFLANWAT,MKSRFFGLACIER,MKSRFFURBAN,andMKSRFFLAISameasExample5.

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