CAMxUsersGuide_v6.30x CAMx Users Guide V6 30

User Manual:

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March20

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1997–2016



Thispublicationmaybereproducedfor

non‐commercialpurposeswithappropriateattribution.

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ACKNOWLEDGMENTS

RambollEnvironacknowledgesthefollowinggroupsfortheircontributionstothedevelopment

ofCAMx:

 TheTexasCommissiononEnvironmentalQuality(TCEQ),forsponsoringthedevelopment,

testing,andreviewofnumerouscomponentsofthemodel;

 TheLakeMichiganAirDirectorsConsortium(LADCo),forsponsoringthedevelopment,

testingandreviewofnumerouscomponentsofthemodel;

 TheU.S.EnvironmentalProtectionAgency(EPA),forsponsoringthedevelopment,testing,

andreviewofnumerouscomponentsofthemodel,andforco‐sponsoringthe

developmentandtestingoftheMPIparallelprocessingcapability.SpecialthankstoDr.

JonPleimforassistancewithimplementationofACM2;

 TheCoordinatingResearchCouncil(CRC),forsponsoringthedevelopment,testing,and

reviewofnumerouscomponentsofthemodel;

 TheTexasAirQualityResearchProgram(AQRP),forsponsoringthedevelopment,testing,

andreviewofnumerouscomponentsofthemodel;

 Dr.SashaMadronich(NCAR)fordevelopmentoftheTUVradiativetransfermodeland

assistancewithincorporatingthein‐lineTUVtreatmentintoCAMx;

 TheCarnegie‐MellonUniversity,DepartmentofChemicalEngineering,forprovidingfull‐

sciencePMalgorithms,assistanceinincorporatingthemintoCAMx,andtestingthe

implementation;

 TheElectricPowerResearchInstitute(EPRI),forsponsoringthedevelopmentandtesting

oftheVolatilityBasisSet(VBS)organicaerosolalgorithm.

 TheAmericanPetroleumInstitute(API),forsponsoringthedevelopmentandtestingof

improvementstotheverticaladvectionalgorithm;

 TheUtahDepartmentofEnvironmentalQuality(UDEQ),forsponsoringupdatestothe

CB6chemistrymechanism,snow‐covertreatment,andsurfacechemistrymodel;

 TheUniversityofTexas,CenterforEnergyandEnvironmentalResources,forassistancein

developingandtestingtheOpen‐MPmulti‐processorcapability;

 Atmospheric,Meteorological,andEnvironmentalTechnologies(ATMET),forproviding

librariesandimplementationsupportfortheMPIparallelprocessingcapability;

 TheMidwestOzoneGroup(MOG),forco‐sponsoringthedevelopmentandtestingofthe

MPIparallelprocessingcapability;

 AtmosphericandEnvironmentalResearch(AER),fordevelopingthemercurychemistry

algorithm;

 TheSanFranciscoBayAreaAirQualityManagementDistrict(BAAQMD),forsupporting

andtestingthecouplingofSAPRCgas‐phasechemistrytothePMchemistryalgorithm.

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CONTENTS



ACKNOWLEDGMENTS............................................................................................................I

1.OVERVIEW........................................................................................................................1

1.1CAMXFEATURES........................................................................................................2

1.2CAMXEXTENSIONSANDPROBINGTOOLS.................................................................4

1.3NEWFEATURESANDMAJORUPDATESINCAMXVERSION6.3..................................5

2.THECAMXMODELINGSYSTEM.........................................................................................6

2.1CAMXPROGRAMSTRUCTURE...................................................................................7

2.1.1MemoryManagement..........................................................................................8

2.1.2ParallelProcessing.................................................................................................9

2.2COMPILINGCAMX...................................................................................................10

2.2.1ANoteonFortranBinaryInput/OutputFiles......................................................11

2.3RUNNINGCAMX......................................................................................................12

2.3.1ControlFileNamelistInput..................................................................................12

2.3.2UsingScriptstoRunCAMx..................................................................................20

2.4BENCHMARKINGMODELRUNTIMES.......................................................................24

2.5CAMXPRE‐ANDPOST‐PROCESSORS........................................................................24

2.5.1Emissions.............................................................................................................24

2.5.2Meteorology........................................................................................................25

2.5.3PhotolysisRates...................................................................................................26

2.5.4InitialandBoundaryConditions..........................................................................27

2.5.5Landuse................................................................................................................27

2.5.6Post‐processors...................................................................................................28

3.COREMODELINPUT/OUTPUTSTRUCTURES....................................................................29

3.1CAMXCHEMISTRYPARAMETERSFILE......................................................................30

3.2PHOTOLYSISRATESFILE...........................................................................................38

3.3OZONECOLUMNFILE...............................................................................................40

3.4FORTRANBINARYINPUT/OUTPUTFILES..................................................................43

3.4.1WhatisaFortranBinaryFile?.............................................................................43

3.4.2CAMxBinaryFileHeaders...................................................................................44

3.4.3InputFiles............................................................................................................45

3.4.4OutputFiles.........................................................................................................58

4.COREMODELFORMULATION.........................................................................................63

4.1NUMERICALAPPROACH...........................................................................................63

4.2CAMXGRIDCONFIGURATION..................................................................................65

4.2.1GridCellArrangement.........................................................................................65

4.2.2GridNesting.........................................................................................................66

4.2.3Flexi‐Nesting........................................................................................................68

4.3TREATMENTOFEMISSIONS.....................................................................................68

4.3.1GriddedEmissions...............................................................................................69

4.3.2ElevatedPointEmissions.....................................................................................69

4.4THREE‐DIMENSIONALTRANSPORT..........................................................................72

4.4.1ResolvedTransport:Advection............................................................................72

4.4.2Sub‐GridTurbulentTransport:Diffusion.............................................................75

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4.5WETDEPOSITION.....................................................................................................77

4.5.1PrecipitationParameters.....................................................................................78

4.5.2GasScavenging....................................................................................................79

4.5.3AerosolScavenging..............................................................................................82

4.6DRYDEPOSITION.....................................................................................................84

4.6.1TheWesely/SlinnModel.....................................................................................85

4.6.2TheZhangModel.................................................................................................88

4.7SNOWCOVERANDSURFACEALBEDO......................................................................91

4.8SURFACEMODELFORCHEMISTRYANDRE‐EMISSION.............................................93

4.8.1SurfaceModelAlgorithms...................................................................................94

4.8.2RunningCAMxWiththeSurfaceModel..............................................................98

5.CHEMISTRYMECHANISMS............................................................................................101

5.1GAS‐PHASECHEMISTRY.........................................................................................102

5.1.1CarbonBond......................................................................................................102

5.1.2SAPRC2007........................................................................................................109

5.1.3ImplicitGas‐PhaseSpecies................................................................................109

5.1.4PhotolysisRates.................................................................................................109

5.1.5Gas‐PhaseChemistrySolvers............................................................................112

5.2AEROSOLCHEMISTRY............................................................................................114

5.2.1AdditionalGas‐PhaseSpecies............................................................................114

5.2.2AerosolProcesses..............................................................................................114

5.2.3AerosolSectionalApproach..............................................................................122

5.3MERCURYCHEMISTRY...........................................................................................123

5.3.1Gas‐PhaseChemistry.........................................................................................124

5.3.2AdsorptionofHg(II)onPM................................................................................124

5.3.3Aqueous‐PhaseChemistry.................................................................................125

5.3.4ImplementationApproach................................................................................127

5.3.5ChemistryParametersforMercury...................................................................128

5.4SIMPLECHEMISTRYVIAMECHANISM10...............................................................128

6.PLUME‐IN‐GRIDSUBMODEL.........................................................................................130

6.1CAMXPIGFORMULATION.....................................................................................130

6.1.1BasicPuffStructureandDiffusiveGrowth........................................................130

6.1.2PuffTransport....................................................................................................134

6.2GREASDPIG...........................................................................................................136

6.3PARTICULATEMATTERINPIG................................................................................138

6.4IRONPIG................................................................................................................138

6.5PIGFEATURES........................................................................................................139

6.5.1PuffLayerSpanning(IRONandGREASD)..........................................................139

6.5.2PuffOverlapandtheIdeaofVirtualDumping(IRONonly)..............................139

6.5.3MultiplePuffReactors(IRONonly)...................................................................140

6.5.4PuffDumping(IRONandGREASD)....................................................................141

6.5.5PiGRendering(IRONandGREASD)...................................................................141

6.5.6HighResolutionPuffSampling(IRONandGREASD).........................................142

6.6DEPOSITION...........................................................................................................142

6.6.1DryDeposition...................................................................................................142

6.6.2WetDeposition..................................................................................................144

6.7PIGCONFIGURATION.............................................................................................144

6.7.1GuidanceontheUseofCAMxPiG....................................................................145

7.SOURCEAPPORTIONMENT...........................................................................................149

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7.1OZONESOURCEAPPORTIONMENT.........................................................................150

7.1.1OSATFormulation..............................................................................................151

7.1.2OSAT2Formulation...........................................................................................152

7.1.3OSAT3Formulation...........................................................................................153

7.1.4AlternativeOzoneApportionmentUsingAPCA................................................155

7.2PARTICULATESOURCEAPPORTIONMENT...............................................................156

7.3RUNNINGCAMXWITHSA......................................................................................160

7.3.1CAMxControlFile..............................................................................................160

7.3.2SpecifyingEmissionGroups...............................................................................162

7.3.3SourceAreaMapping........................................................................................166

7.3.4ReceptorDefinition...........................................................................................170

7.3.5OutputFileFormats...........................................................................................170

7.3.6Postprocessing....................................................................................................172

7.4STEPSINDEVELOPINGINPUTSANDRUNNINGSA..................................................172

8.DECOUPLEDDIRECTMETHODFORSENSITIVITYANALYSIS............................................176

8.1IMPLEMENTATION.................................................................................................177

8.1.1TrackingSensitivityCoefficientsWithinCAMx..................................................179

8.1.2Flexi‐DDM..........................................................................................................180

8.2RUNNINGCAMXWITHDDMANDHDDM..............................................................180

8.3DDMOUTPUTFILES...............................................................................................185

8.4DDMSENSITIVITYCOEFFICIENTNAMES.................................................................185

8.4.1InitialConditionSensitivityNames....................................................................186

8.5STEPSINDEVELOPINGINPUTSANDRUNNINGDDM..............................................189

9.PROCESSANALYSIS.......................................................................................................191

9.1PROCESSANALYSISINCAMX.................................................................................191

9.1.1IntegratedProcessRateAnalysis......................................................................192

9.1.2IntegratedReactionRateAnalysis.....................................................................193

9.1.3ChemicalProcessAnalysis.................................................................................193

9.2RUNNINGPROCESSANALYSIS................................................................................196

9.2.1SettingCAMxParameters..................................................................................198

9.2.2OutputFileFormats...........................................................................................199

9.3POSTPROCESSING..................................................................................................199

9.3.1IPROutputFiles.................................................................................................199

9.3.2IRROutputFiles.................................................................................................200

9.3.3CPAOutputFiles................................................................................................201

10.REACTIVETRACERS.....................................................................................................202

10.1DESCRIPTIONOFRTRAC.......................................................................................202

10.1.1RTRACGas‐PhaseChemistry...........................................................................204

10.2DESCRIPTIONOFRTCMC......................................................................................206

10.2.1RTCMCGas‐PhaseChemistry..........................................................................206

10.3REACTIVETRACERSINIRONPIG...........................................................................214

10.4RUNNINGCAMXWITHREACTIVETRACERS..........................................................215

10.4.1CAMxControlFile............................................................................................215

10.4.2UserAdjustableParameters............................................................................217

11.REFERENCES................................................................................................................219

APPENDIXA.......................................................................................................................232

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CAMXMECHANISM2:CB6R2GAS‐PHASECHEMISTRY.................................................232

APPENDIXB.......................................................................................................................241

CAMXMECHANISM3:CB6R2WITHHALOGENCHEMISTRY..........................................241

APPENDIXC.......................................................................................................................245

CAMXMECHANISM6:CB05GAS‐PHASECHEMISTRY...................................................245

APPENDIXD.......................................................................................................................251

CAMXMECHANISM5:SAPRC07TCGAS‐PHASECHEMISTRY.........................................251

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TABLES

Table2‐1.ParametersandtheirdefaultsinIncludes/camx.prmusedtostatically

dimensionlocalarraysinlow‐levelsubroutines................................................................8

Table2‐2.CAMxoutputfilesuffixesandtheircorrespondingfiletypes................................................20

Table2‐3.CAMxv6.20speedperformancewithMPIandOMPparallelizationfromthe

LADCotestsdescribedabove.............................................................................................24

Table3‐1.DatarequirementsofCAMx...................................................................................................29

Table3‐2.DescriptionoftheCAMxchemistryparametersfile.Therecordlabelsexistin

columns1‐20,andwheregiven,theinputdataforthatrecordstartin

column21.Theformatdenoted“list”indicatesafree‐formatlistof

numbers(commaorspace‐delimited)...............................................................................31

Table3‐3a.RateconstantexpressiontypessupportedinCAMxandorderofexpression

parametersforthechemistryparametersfile..................................................................39

Table3‐3b.ListofparametersthatmustbeprovidedintheCAMxchemistryparameter

fileforeachoftheseventypesofrateconstantexpressions.Use

ppm/minuteunitsforAandKelvinforEaandTR.ThevariableOisthe

orderofthereaction(1to3).............................................................................................40

Table3‐4.The11WESELY89landusecategories,theirdefaultUVsurfacealbedos,and

theirsurfaceroughnessvalues(m)byseason.Winterisdefinedfor

conditionswherethereissnowpresent;wintermonthswithnosnoware

assignedtotheFallcategory.Roughnessforwateriscalculatedfromthe

function5.26

0102 wz 

 ,wherewissurfacewindspeed(m/s)...................................46

Table3‐5.The26ZHANG03landusecategories,theirUValbedos,defaultannual

minimumandmaximumLAIandsurfaceroughness(m)ranges,and

mappingtotheWeselyscheme(Table3‐4).Roughnessforwateris

calculatedfromthefunction5.26

0102 wz 

 ,wherewissurfacewind

speed(m/s)........................................................................................................................47

Table4‐1.SummaryoftheCAMxmodelsandmethodsforkeyphysicalprocesses..............................63

Table4‐2.Relationshipsbetweenseasonandmonth/latitudeusedintheCAMx

Wesely/Slinndrydepositionmodel.Exception:seasonsforthearea

within50N‐75Nand15W‐15Eareinternallysettothoseoflatitudeband

March2016CAMxUser’sGuideVersion6.3

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35‐50toaccountforregionsofEuropeinwhichtheclimateisinfluenced

bytheGulfStream.............................................................................................................88

Table4‐3.DescriptionofCAMxsurfacemodelvariablesshowninFigure4‐7.......................................95

Table4‐4(a).Weselylandusecategoriesandassociatedannual‐averagedsoil/vegetation

splitfactors,UValbedo,andSWEWc................................................................................96

Table4‐4(b).Zhanglandusecategoriesandassociatedannual‐averagedsoil/vegetation

splitfactors,UValbedo,andSWEWc................................................................................96

Table5‐1.Gas‐phasechemicalmechanismscurrentlyimplementedinCAMxv6.3...............................101

Table5‐2.SpeciesnamesanddescriptionscommontoallCarbonBondMechanismsin

CAMx..................................................................................................................................103

Table5‐3.Defaultdryextinctionefficiencyandsingle‐scatteringalbedoat350nm

(Takemuraetal.,2002)inthedistributedCAMxchemistryparametersfile....................111

Table5‐4.ListofinorganicPMspeciesfortheCAMxCFaerosoloption................................................116

Table5‐5.SOAprecursorreactionsincludedintheCAMxSOAPmodule...............................................117

Table5‐6.PropertiesofCG/SOApairsintheCAMxSOAPmodule.........................................................117

Table5‐7.Molecularpropertiesofthe1.5‐DVBSspecies......................................................................120

Table5‐8.Inputspeciesfor1.5‐DVBSscheme........................................................................................121

Table5‐9.VolatilitydistributionfactorsusedtoallocatePOAemissionsfromfive

differentsourcetypestothefivePAP,PCP,andPFPvolatilitybins..................................121

Table7‐1.Numbersofemissionfilesets(i.e.,griddedfilesandpointsourcefile)needed

fordifferentmodelconfigurations.APCArequiresatleasttwoemission

groups,andthefirstgroupmustbebiogenicemissions...................................................166

Table7‐2.Formatforthereceptordefinitionfile....................................................................................171

Table8‐1.DDMoutputfilesuffixnames.................................................................................................185

Table9‐1.ProcessinformationreportedbytheIPRoption....................................................................193

Table9‐2.ChemicalProcessAnalysis(CPA)variablescalculatedinCAMxfortheCB05

andCB6r2mechanisms.Concentrationsareppb;productionand

destructionareppb/hr;photolysisratesarehr‐1,ratiosareunitless................................194

Table9‐3.ProcessanalysiskeywordsandassociatedCAMxoutputfiles...............................................196

Table10‐1.Keywords,optionsanddefaultvaluesfortheControlsectionoftheIMCfile.....................208

Table10‐2a.RecommendedSCICHEMrateconstantexpressiontypesforuseinCAMx.......................213

Table10‐2b.ParametersrequiredbySCICHEMrateconstantexpressiontypes....................................214

Table10‐3.Determiningthereactionorderandconsequentunitdimensionsforrate

constants............................................................................................................................214

Table10‐4.RTCMCparametersdefaultsettingsintheIncludes/rtcmcchm.inc

includefile..........................................................................................................................218

TableA‐1.ReactionsandrateconstantexpressionsfortheCB6r2mechanism.k298isthe

rateconstantat298Kand1atmosphereusingunitsinmolecules/cm3and

March2016CAMxUser’sGuideVersion6.3

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1/s.Forphotolysisreactionsk298showsthephotolysisrateatasolar

zenithangleof60°andheightof600mMSL/AGL.SeeTable5‐2for

speciesnames.SeeSection3.1ontemperatureandpressure

dependencies.....................................................................................................................232

TableB‐1.ListingoftheCB6r2halogenmechanism(seeTableA‐1foracompletelisting

ofCB6r2).k298istherateconstantat298Kand1atmosphereusingunits

inmolecules/cm3and1/s.Forphotolysisreactionsk298showsthe

photolysisrateatasolarzenithangleof60°andheightof600m

MSL/AGL.SeeTableB‐2forspeciesnames.SeeSection3.1on

temperatureandpressuredependencies.........................................................................241

TableB‐2.ChemicalspeciesincludedinCB6r2h......................................................................................244

TableC‐1.ReactionsandrateconstantexpressionsfortheCB05mechanism.k298isthe

rateconstantat298Kand1atmosphereusingunitsinmolecules/cm3and

1/s.SeeTable5‐2forspeciesnames.SeeSection3.1ontemperature

andpressuredependencies...............................................................................................245

TableD‐1.ReactionsandrateconstantsfortheSAPRC07TCmechanism.k300istherate

constantat300Kand1atmosphereusingunitsinmolecules/cm‐3and

1/s.SeeTableD‐2forspeciesnames.SeeSection3.1ontemperature

andpressuredependencies...............................................................................................251

TableD‐2.ExplicitspeciesintheSAPRC07TCmechanism.......................................................................270



FIGURES

Figure2‐1.SchematicdiagramoftheCAMxmodelingsystem.SeeTable3‐1foradetailed

listofspecificmodelinputrequirementsforthefivemajordataclassesshown

atthetopofthefigure.Certainpre‐andpost‐processorprogramsshownin

thefigurearedescribedinthissection.Third‐partymodels,processors,and

visualizationsoftwarearenotdescribedinthisUser’sGuideandarenot

distributedwithCAMx..........................................................................................................6

Figure2‐2.AsampleCAMxjobscriptthatgeneratesa“CAMx.in”fileandrunsthemodel

withOMPparallelization....................................................................................................21

Figure2‐3.AnexampleofglobalozonecolumnfromtheOzoneMonitoringInstrument

(OMI)platform.Whiteareasdenotemissingdata.From

ftp://toms.gsfc.nasa.gov/pub/omi/data/..........................................................................26

Figure3‐1a.ExampleCAMxchemistryparametersfileforMechanism6(CB05)withCFPM

schemethatincludesthemercuryspeciesHG0,HG2,andHGP.......................................33

Figure3‐1b.Exampleinertchemistryparametersfile(requireschemistryflagtobesetfalse

–seethedescriptionoftheCAMxcontrolfile).................................................................37

Figure3‐2.Exampleofthefirstseveralpanelsoflookupdatainthephotolysisratesinput

file.......................................................................................................................................41

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Figure3‐3.Examplestructureofasingle‐gridozonecolumninputfileshowingpanelsfor

theoptionaltime‐invariantland‐oceanmaskandtime‐varyingozonecolumn

field....................................................................................................................................43

Figure4‐1.AhorizontalrepresentationoftheArakawaCvariableconfigurationusedin

CAMx..................................................................................................................................66

Figure4‐2.Anexampleofhorizontalgridnesting,showingtwotelescopingnestedgrids

withina10×10cellmastergrid.Theouternestcontains10×12cells(including

buffercellstoholdinternallateralboundaryconditions),andtheinnernest

contains6×10cells(includingbuffercells)........................................................................67

Figure4‐3.Schematicrepresentationoftheturbulentexchangeamonglayerswithina

verticalgridcolumnduringconvectiveadjustmentintheACM2(takenfrom

Pleim[2007])......................................................................................................................76

Figure4‐4.ComparisonofmonthlyLAIdataembeddedintheZhangdrydepositionscheme

againstepisode‐specificLAIforJune2005........................................................................90

Figure4‐5.Comparisonofparticledrydepositionvelocitiesasafunctionofsizeandwind

speeds(m/s)forthreemodels:black–Zhangetal.(2001);blue–Slinnand

Slinn(1980);orange–AERMOD(EPA,1998).Resultsareshownforaforest

landusecategoryduringdaytimeneutralstability.Particledensitywassetat

1.5g/cm3............................................................................................................................92

Figure4‐6.Exampleofgrid‐cellalbedoevolutionforahypothetical20‐dayspringtimesnow

event(assumingablationconditions)forlowandtallvegetationgridcellswith

aterrestrial(non‐snow)albedoof0.05.............................................................................93

Figure4‐7.SchematicoftheCAMxsurfacemodel..................................................................................94

Figure4‐8.TheportionsoftheCAMxchemistryparametersfile(highlighted)tosupportthe

surfacemodel.Inthisexample,3gasesaretreated,wherenitricacid(HNO3)

andperoxynitricacid(PNA)reacttoformnitrousacid(HONO).Allthreeare

subjecttodecaybysoilleaching,plantpenetration,andsnowmeltloss.The

valuesshownhereareforillustrativepurposesonlyanddonotrepresentany

knownsurfacechemistrymechanism..............................................................................100

Figure5‐1.Relativehumidityadjustmentfactorappliedtothedryextinctionefficiencyfor

hygroscopicaerosols(FLAG,2000)..................................................................................112

Figure5‐2.SchematicdiagramoftheCAMxVBSmodule.ThemodelVBSspeciesname

consistsof4charactersthatindicatethephase(P–particle;V–vapor),the

source(A–anthropogenic;B–biogenic;C–cooking;F–fire),theformation

(P–primary;S–secondary),andthevolatilitybinnumber.Thesolidand

dashedarrowsrepresentgas‐aerosolpartitioningandchemicalaging,

respectively.ThethickcoloredarrowsrepresentPOAemissionsoroxidation

ofSOAprecursors............................................................................................................119

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Figure6‐1.SchematicrepresentationofCAMxPiGpuffshapeinthehorizontalplane.

Directionalorientationofthepuffisarbitrary,andevolvesaccordingtowind

direction,shearsanddiffusivegrowthalongitstrajectory.............................................131

Figure6‐2.Plan‐viewschematicrepresentationofachainofPiGpuffsemittedfromapoint

sourceintoanevolvinggriddedwindfield.Theredlineconnectedbydots

representspuffcenterlines,withdotsrepresentingleadingandtrailingpoints

ofeachpuff.TheCAMxcomputationalgridisdenotedbythebluelines......................135

Figure6‐3.ExampleofasinglepointsourcePiGplumeasdepictedbyasamplinggridwith

200mresolution(shownbytheextentoftheplot;40kmby32kmtotal

extent).ThissamplinggridwassetwithinaCAMxcomputationalgridwith4‐

kmresolution.Thesourcelocationisarbitraryandisemittinganinerttracer.............143

Figure7‐1.Exampleofthesub‐divisionofaCAMxdomainintoseparateareasfor

geographicsourceapportionment..................................................................................150

Figure7‐2.TheoriginalOSATschemeforozoneapportionment.Informationflowsalong

arrows.Changesincoremodelspeciesareshowninblue,OSATtracersarein

black,thediamondrepresentstheOSATalgorithmthatdeterminesozone

tracerchanges.H2O2/HNO3istheindicatorratiousedtodetermineNOx‐

orVOC‐limitedozoneproduction....................................................................................151

Figure7‐3.DaytimereactionsofozonewithHOx(OHandHO2)showingpotentialfor

reformationofozoneorozonedestructionviaperoxideformation..............................153

Figure7‐4.TheOSAT2schemeforozoneapportionment.Informationflowsalongarrows.

Changesincoremodelspeciesareshowninblue,OSATtracersareinblack,

thediamondrepresentstheOSATalgorithmthatdeterminesozonetracer

producton.H2O2/HNO3istheindicatorratiousedtodetermineNOx‐or

VOC‐limitedozoneproduction........................................................................................153

Figure7‐5.CorrespondencebetweenNOyspeciesinCB6andtracerfamiliesinOSAT3with

conversionsbetweenspecies/tracersshownbyarrows.................................................154

Figure7‐6.TheOSAT3schemeforozoneapportionment.Informationflowsalongarrows.

Changesincoremodelspeciesareshowninblue,OSATtracersareinblack,

thediamondrepresenttheOSATalgorithmsthatdetermineozonetracer

production.H2O2/HNO3istheindicatorratiousedtodetermineNOx‐or

VOC‐limitedozoneproduction.RGNapportionsthenitrogeninNO2whereas

OONandOOVapportiontheodd‐oxygeninNO2............................................................156

Figure7‐7a.AnexampleofSAinputrecordsintheCAMxruncontrolfile.Theoptionsfor

thisOSATrunareasfollows:thisisatwo‐gridrun,masterandnestedgrid

surfaceconcentrationsarewrittentofile,asingletracertypeistobeusedfor

allboundaries,19sourceregions,andoneemissiongroup(i.e.,zero

additionalemissionfilesandnoleftovergroup).Thisisthefirstdayofthe

simulation(i.e.,restartisfalse),sonoOSATrestartfilesaresupplied...........................163

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Figure7‐7b.AsinFigure7‐7a,butinthiscasetherunisacontinuationdayofarunwith

threeemissiongroups.Thethreeemissiongroupsaredefinedbysupplying

extraemissionfilesforpointandareasourcesforeachgrid(emissiongroups1

and2),andsettingthe“Use_Leftover_Group”flagtoTRUEsothatthemodel

calculatesthethirdgroupinternally.Thepointsourcegroup1filenameis

blankbecausegroup1isacategorywithnopointsourceemissions(e.g.,

biogenics).........................................................................................................................164

Figure7‐7c.ThisfigurefollowsfromFigure7‐7b:itisacontinuationdayofa2‐gridrunwith

threeemissiongroups,andallthreeemissiongroupsaredefinedexplicitlyby

supplyingextraemissionfiles;therefore,the“Use_Leftover_Group”flagisset

toFALSE.Thepointsourcegroup1filenameisblankbecausegroup1isa

categorywithnopointsourceemissions(e.g.,biogenics).APCAisusedto

attributeozonesources,sobiogenicemissionsMUSTbepresentasgroup1.

PSATwilltracePMsulfateandnitratespecies................................................................165

Figure7‐8.Exampleoftheoriginalsourceareamapfileforthedomainandsourceareas

showninFigure7‐1.

.........................................................................................................167

Figure7‐9.Examplefractionalareamapfileforasmall(10x10)grid.Thisfileisforsource

category/group#3andincludes2mappanels.Thegridcoverssourceregion

#5and#6andtheseregionsoverlapinthemiddleofthedomain.Panel2

showsjusttheremainingoverlapinformationforregion#6..........................................169

Figure7‐10.Examplereceptorconcentrationfile.Linesendingwith“…”aretruncatedtofit

thepage,andthefilewouldcontinuewithdataforadditionalreceptorsand

hoursinthesameformat.................................................................................................173

Figure8‐1.ExampleofDDMinputsintheCAMxcontrolfile.CAMxisrunwithtwogrids,

andDDMisconfiguredtotrackemissionsfromfoursourceregionsandtwo

sourcegroups.Sensitivitytoozoneinitialandboundaryconditionsare

tracked,whilesensitivitiestoNOxandVOCemissionsaretracked.Sensitivity

forasinglerateconstantgroupwillbecalculatedinvolvingmechanism

reactionnumbers120,121,and122.Threegroupsofsecond‐order

sensitivitiestoanthropogenicNOxandVOCemissions(fromemissionsgroup

2,sourceregion1)willbecomputed(d2/dNOx2,d2/dVOC2andd2/dNOxdVOC).

Nosourceregionmapisprovidedforthenestedgrid(theregionassignments

onthenestaredefinedbythemastergrid).Onlythegroup2pointsources

aretracked(nobiogenicpointsourcesareavailable).....................................................184

Figure8‐2.Exampleconcordanceoflongandshortsensitivitycoefficientnamesfromthe

CAMxdiagnosticoutputfile.............................................................................................186

Figure9‐1.ExamplesectionofaCAMxcontrolfilespecifyingoptionsforProcessAnalysis................198

Figure9‐2.ExampleIPRtimeseriesanalysisforPSO4;lateralboundaryandchemistryterms

arenotaggregated...........................................................................................................200

Figure10‐1.ExampleRTRACchemistryinputfileformodelingspecifictoxicspecies..........................203

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COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS xiwww.camx.com

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Figure10‐2.ExampleRTRACreceptorinputfileidentifyingthegridcellswithlocations

wherehourlydecayrateswillbeoutputforsubgrid‐scalepointsource

modeling(seeformatforSAreceptorfileinTable7‐2)..................................................206

Figure10‐3.Examplefree‐formatRTCMCIMCchemistryinputfile.....................................................207

Figure10‐4.ExampleinputofRTRACoptionsandfilenameswithintheCAMxcontrolfile.................216

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1.Overview

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COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 1www.camx.com

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1.OVERVIEW

TheComprehensiveAirqualityModelwithextensions(CAMx)isanEulerianregional

photochemicaldispersionmodelthatallowsforintegrated“one‐atmosphere”assessmentsof

troposphericairpollution(ozone,particulates,airtoxics)overspatialscalesrangingfrom

neighborhoodstocontinents.Itisa“state‐of‐the‐science”open‐sourcesystemthatis

computationallyefficient,flexible,andpubliclyavailable.Themodel’sFortransourcecodeis

modularandwell‐documented.TheFortranbinaryinput/outputfileformatsarebasedonthe

UrbanAirshedModel(UAM)conventionandarecompatiblewithmanyexistingpre‐andpost‐

processingtools.MeteorologicalfieldsaresuppliedtoCAMxfromseparateweatherprediction

models.Allemissioninputsaresuppliedfromexternalpre‐processingsystems.

CAMxsimulatestheemission,dispersion,chemicalreaction,andremovalofpollutantsby

marchingtheEuleriancontinuityequationforwardintime(t)foreachchemicalspecies(l)ona

systemofnestedthree‐dimensionalgrids.Thecontinuityequationspecificallydescribesthe

timedependencyofvolume‐averagespeciesconcentrationwithineachgridcellasasumofall

physicalandchemicalprocessesoperatingonthatvolume.Thisequationisexpressed

mathematicallyinterrain‐followingheight(z)coordinatesasfollows:



whereclisspeciesconcentration(mass/volume),VHisthehorizontalwindvector,



isthenet

verticaltransportrate,histhelayerinterfaceheight,



isatmosphericdensity,andKisthe

turbulentexchange(diffusion)coefficient.Thefirsttermontheright‐handsiderepresents

horizontaladvection,thesecondtermrepresentsnetresolvedverticaltransportacrossan

arbitraryspace‐andtime‐varyingheightgrid,andthethirdtermrepresentssub‐gridscale

turbulentdiffusion.Chemistryistreatedbysimultaneouslysolvingasetofreactionequations

definedbyspecificchemicalmechanisms.Pollutantremovalincludesbothdrysurfaceuptake

(deposition)andwetscavengingbyprecipitation.

CAMxcanperformsimulationsonfourtypesofCartesianmapprojections:LambertConic

Conformal,PolarStereographic,Mercator,andUniversalTransverseMercator.CAMxalso

offerstheoptionofoperatingonageodeticlatitude/longitudegridsystem.Theverticalgrid

structureisdefinedexternally,solayerinterfaceheightsmaybespecifiedasanyarbitrary

functionofspaceand/ortime.Thisflexibilityindefiningthehorizontalandverticalgrid

structuresallowsCAMxtobeconfiguredtomatchthegridofanymeteorologicalmodelthatis

usedtoprovideenvironmentalinputfields.

 

Removal

Chemistry

Emission

lHH











































March2016CAMxUser’sGuideVersion6.3

1.Overview

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

1.1CAMxFeatures

Two‐WayNestedGridStructure:CAMxcanberunwithvariablegridspacing.Useacoarsegrid

forregionaldomainswherehighspatialresolutionisnotparticularlyneeded,whileinthesame

run,nestfinergridsinspecificareasofinterest.Two‐waynestingpropagatesinformationboth

up‐anddown‐scaleacrossallgrids.Nestsmaypossessdifferentmeshingfactorsfromtheir

parentgrids,aslongastheyarecommondenominatorsofparentresolution.A“Flexi‐Nesting”

featureallowsyoutointroduceand/orremovenestedgridsatanypointduringasimulation.

Youcansupplycompleteinformationfornewgrids(emissions,meteorology,surface

characteristics)orallowCAMxtointerpolateanyoralloftheseinputsfromparentgrids.

MultiplePhotochemicalGasPhaseChemistryMechanisms:CAMxoffersseveralversionsof

CarbonBondchemistry(CB05andCB6variants)andthe2007versionofStatewideAirPollution

ResearchCenterchemistry(SAPRC07TC).ThesemechanismsaresolvedusingtheEuler‐

BackwardIterative(EBI)method,whichisfastandaccurate.CAMxalsoincludesthefully

explicitGear‐typeLivermoreSolverforOrdinaryDifferentialEquations(LSODE),whichweuse

to"benchmark"newmechanismsandevaluatetheperformanceofEBI.Wedonot

recommendLSODEfortypicalapplicationsasthemodelwillrunmuchmoreslowly.

ParticulateMatter(PM)Chemistry:CAMxincludesalgorithmsforinorganicaqueouschemistry

(RADM‐AQ),inorganicgas‐aerosolpartitioning(ISORROPIA),andtwoapproachesfororganic

gas‐aerosolpartitioningandoxidation(VBSorSOAP).Thesealgorithmsuseproductsfromthe

gas‐phasemechanismsfortheproductionofsulfate,nitrate,andcondensableorganicgases.

CAMxprovidestwooptionstorepresenttheparticlesizedistribution:astatictwo‐mode

coarse/fine(CF)scheme,andanevolvingmulti‐section(CMU)scheme.Thehybrid1.5‐

dimensional(1.5‐D)VolatilityBasisSet(VBS)describestheevolutionoforganicsaccordingto

oxidationstateandvolatility,andisimplementedtoprovideaunifiedframeworkforgas‐

aerosolpartitioningandchemicalagingofbothprimaryandsecondaryatmosphericorganic

aerosols.VBSiscompatibleonlywiththeCB05andCB6r2gas‐phasechemistryandthe2‐mode

CFaerosoloption;itisnotcurrentlyenabledforSourceApportionmentorDecoupledDirect

MethodProbingTools.Theoriginalone‐dimensional(overvolatility)SecondaryOrganic

AerosolPartitioning(SOAP)treatmentremainsanoption.SOAPiscompatiblewithCFandCMU

aerosoloptionsandworkswithallProbingTools.

MercuryChemistry:CAMxoptionallytreatsthechemistryoffivemercuryspecies(twogases

andthreeparticulates)viagas‐phaseandaqueouspathways,includingHg(II)adsorptiontoPM.

ThemercurychemistrymodulerequiresPMconcentrations,somercurymustbemodeledwith

the“CF”two‐modePMmechanismbyincludingmercuryspeciesamongthelistofmodeled

species.Alloftherateandequilibriumconstantsforthemercurymechanismarehard‐coded

withinthechemistrymodule.

User‐DefinedChemistryMechanism:“Mechanism10”providesasimplewaytodefineyour

ownchemistrymechanism.Thisoptionisintendedtodefinesimplechemicaldecayor

transformationsbetweengasand/oraerosolspecies.YoumustdevelopyourownMechanism

10subroutineandchemistryparametersfile.

March2016CAMxUser’sGuideVersion6.3

1.Overview

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COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 3www.camx.com

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Plume‐in‐Grid(PiG)Module:PiGtreatsthechemistryanddispersionofpointsourceemission

plumesatsub‐gridscalesusingaLagrangianpuffmodel,untilsuchtimeasthepollutantmass

canbeadequatelyrepresentedwithinthegridmodelframework.Bothgas‐phaseandPM

chemistrycanbetreated.PiGincludesa“samplinggrid”capabilitytopassivelysampleplume

concentrationsatanyresolution,whichisparticularlyusefultovisualizenear‐sourcesub‐grid

scaleimpacts.

HorizontalAdvectionSolverOptions:CAMxoffersthePiecewiseParabolicMethod(PPM)of

ColellaandWoodward(1984),andthearea‐preservingadvectionsolverofBott(1989).Both

possesshigh‐orderaccuracy,littlenumericaldiffusion,andaresufficientlyquickforapplications

onverylargegrids.

VerticalDiffusion(Mixing)Options:Bydefault,CAMxemploysastandard“K‐theory”approach

forverticaldiffusiontoaccountforsub‐gridscalemixinglayer‐to‐layer.Version2ofthe

AsymmetricConvectiveModel(ACM2;Pleim,2007)isavailableasanalternativetotheK‐

theoryapproach.ACM2isahybridoflocalK‐theoryandnon‐localconvectivetransport

betweenthesurfaceandlayersaloft.ACM2canincreaseCAMxruntimeconsiderablyrelative

tothedefaultK‐theory.ACM2doesnotworkwiththeIntegratedProcessRate(IPR)

componentoftheProcessAnalysis(PA)tool.

DryDepositionOptions:CAMxofferstwodrydepositionoptions:anolderapproachbasedon

themodelsofWesely(1989)andSlinnandSlinn(1980);andanupdatedapproachbasedonthe

algorithmsofZhangetal.(2001;2003).TheWesely/Slinnmodelisformulatedfor11landuse

categories,whiletheZhangmodeluses26landusecategories.

SurfaceChemistry/Re‐emissionModel:CAMxincludesasimplesurfacesub‐modelthattreats

sorptionandpenetrationofdepositedpollutantmassintosoilsandvegetation,chemical

degradationandtransformation,andvolatilizationbackintotheair(re‐emission).Thesurface

modeltreatsanysubsetofspecieslistedinthecoremodel’schemicalmechanism.Thesurface

modelcanonlybeusedwiththeWesely(1989)drydepositionoption;itcannotbeusedwith

thePlume‐in‐Gridtreatment.

AdvancedPhotolysisModel:TheTUVradiativetransferandphotolysismodel,developedand

distributedbytheNationalCenterofAtmosphericResearch(NCAR,2011),isusedasaCAMx

preprocessortoprovidetheairqualitymodelwithamulti‐dimensionallookuptableofclear‐sky

photolysisrates.CAMxinternallyadjustsclear‐skyratesforthepresenceofcloudsandaerosols

usingafastin‐lineversionofTUV.

LateralandTopBoundaryConditions:Time‐andspace‐variableboundaryconditionsforthe

mastergridmaybedevelopedfromdown‐scalingthree‐dimensionaloutputfromglobal

chemistrymodelslikeGEOS‐ChemandMOZART.Topboundaryconditionsimprovethe

characterizationofchemicalsenteringverticallyacrossthemodeltop,whichisparticularly

importantforcommonstratosphericconstituentssuchasozoneandnitrogenoxides.Asimpler

topboundarytreatmentremainsavailable,whichisnotreliantonaninputfileandinternally

assumesa“zerogradient”volumemixingratioconditionbetweenthetopmodellayerandthe

environmentabovethemodel.

March2016CAMxUser’sGuideVersion6.3

1.Overview



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 4www.camx.com

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ParallelProcessing:CAMxsupportstwotypesofparallelization:(1)OpenMP(OMP),which

allowsparallelprocessingonshared‐memory(e.g.,multi‐core)computers;and(2)Message

PassingInterface(MPI),whichallowsparallelprocessingacrossdistributedmemory

(networked)computerclusterenvironments.BothOMPandMPIcanbeusedincombination

tomaximizespeedperformance.TouseOMP,yourFortrancompilermustincludelibrariesto

enablein‐codedirectives.TouseMPI,youmusthaveexternalMPIlibrariesinstalledonyour

system.

1.2CAMxExtensionsandProbingTools

OzoneandParticulateSourceApportionmentTechnology(OSAT/PSAT):Sourceapportionment

technologytracksemissioncontributionstopredictedozoneand/orPMspeciesconcentrations

bysourceregionand/orcategory.OSATalsoreportsinformationtodeterminewhethereach

ozonecomponentformedinNOxorVOCsensitiveconditions.OSAT/PSATprovidesozone/PM

attributiontosourceregionsandcategoriesforagivenemissionsmatrix,butdoesnotprovide

quantitativeinformationastohowozone/PMcontributionswouldchangeasemissionsare

alteredbecausechemicalinteractionsarenon‐linear.Sourceapportionmentisavailableonly

forCB05,CB6r2andCB6r3chemicalmechanisms,theCFaerosolschemeandtheSOAPorganic

partitioningalgorithm.

DecoupledDirectMethod(DDM)andHigh‐OrderDDM(HDDM)SourceSensitivity:Thistool

calculatesfirst‐order(DDM)andsecond‐order(HDDM)gasconcentrationsensitivitytochanges

inemissions,initialconditionsandboundaryconditions.PMconcentrationsensitivityislimited

tofirst‐orderDDM.(H)DDMestimateshowpollutantconcentrationsrespondtoregion‐and

category‐specificemissionchanges,butdoesnotprovideinformationonsourceattribution.

(H)DDMcanberunwithanyCBorSAPRCchemicalmechanism,theCFaerosolschemeandthe

SOAPorganicpartitioningalgorithm.

ProcessAnalysis(PA):Thisprobingtoolprovidesin‐depthinformationonthephysicaland

chemicalprocessesoccurringduringaCAMxrun.ThroughPA,onecanmorefullyunderstand

thecomplexinteractionsofthedifferentprocesses,explainsimulationresultswithinthe

contextofmodelformulation,andimprovethedesignofcontrolstrategies.Theintegrated

processrates(IPR)optioncanberunwithanyCBorSAPRCchemicalmechanismandanyPM

aerosoltreatment.Chemicalprocessanalysis(IRRandCPA)isfullyavailableonlyforCB05;a

limitedsetofchemicalprocessratesareavailableforCB6r2.PMratesarenottrackedbyPA.

ReactiveTracers(RTRAC):RTRACprovidesaflexibleadd‐ontosimulatetheemission,

dispersion,chemistry,anddepositionofmultiplegasandparticletracers(suchasspecific

toxics)thatarenotincludedinthemodel’scoregas/PMchemistrymechanisms.Gas‐phase

chemistrymayinvolveuser‐definedlineardecay(photolysisand/oroxidation)byspecies,or

complexnon‐linearsystemssolvedwiththeRTRACChemicalMechanismCompiler(RTCMC).

RTRACcanberunincombinationwithanyCBorSAPRCchemicalmechanismandis

independentfromallaerosoltreatments.

March2016CAMxUser’sGuideVersion6.3

1.Overview



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 5www.camx.com

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1.3NewFeaturesandMajorUpdatesInCAMxVersion6.3

SpeedImprovements:Severalmodificationswereimplementedtoimprovemodelspeed.Our

testswithoutProbingToolsindicatespeedincreasesby15‐50%,dependingoncompiler,

chipsetandmodelconfiguration(gridnumberandsize,PiG,chemistrymechanism,

parallelization).Thesechangeshaveminimalimpactsonconcentrationresults(e.g.,ozone

differences<1ppb).

SourceApportionmentUpdates:OSAThasbeenexpandedtotrackoddoxygenandnitrogen

throughNOychemistrytoaccountforNOxrecyclingofozoneandtoimproveconsistencywith

PSATnitratechemistry.ManymoreOSATtracersarenecessary,andthisaffectsmemory

requirementsandmodelspeed.Expecttoseeslightlymoreozonecontributionsfromlong

rangetransport,andcommensuratelylesscontributionsfromlocalemissions.BothOSATand

PSATcannowuseanewsourceregionmapformatthatsupportsfractional(partial)area

assignmentsforeachgridcell.TheGeographicOzoneAssessmentTechnology(GOAT)option

hasbeenremovedfromOSATasitisconsideredobsolete.

AdditionalMapProjections:CAMxcannowrunonMercatorandPolarprojectionsusingthe

projectionparameters/definitionsfromtheWeatherResearchandForecasting(WRF)model.

SnowandSurfaceChemistryModelUpdates:Surfacealbedoforsnow‐coveredgridcellsisnow

calculatedaccordingtolandcovertypeandnewadditionalinputvariablesforsnowcoverand

age,followingtheapproachusedintheWRF/NOAHlandsurfacemodel.Netsurfacealbedoin

snow‐coveredgridcellscanbesubstantiallydifferentfromtheoriginalconstantvalueof50%,

andthiscanhavealargeimpactonphotochemicalactivity.Thesurfacechemistrymodelhas

beenextendedtoworkwiththeZhangdrydepositionoptionandtoaddsnowcovertothe

originalsoilandvegetationcompartments.Athirdsetofsurfacechemicalsorption,reaction

andlossrateshavebeenimplementedtorepresenttheseprocessesonandwithinthe

snowpack.

UpdatedCB6ChemistryMechanism:CB6“revision3”(CB6r3)isnowavailableaschemistry

mechanism4.CB6r3includesatemperature‐andpressure‐dependentorganicnitrate

branchingratio.Thisupdatewasfoundtobeimportantforphotochemistryincoldand/or

elevatedconditions,suchaswintertimeintheUSinter‐mountainwest.Generally,theeffectof

thischangeistoreduceozoneproductionslightlyrelativetoCB6r2incoldconditions.There

arenoeffectsinwarmconditionsthataremoretypicaloftheozoneseason.

SAPRC07TC:SAPRC07isamorerecentgas‐phasechemistrymechanismthathasreplacedthe

datedSAPRC99mechanism.SAPRC07TCisavariantofSAPRC07thatincludesextramodel

speciesfortoxicsandusesnumericalexpressionsofrateconstantsthatarecompatiblewiththe

currentchemistrymechanismsolver.

Implicit‐ExplicitHybrid(IEH)ChemistrySolver:Thisrarelyusedgas‐phasechemistrysolverwas

removedasitpossessesequivalentaccuracyastheEBIsolver,butrunsmuchmoreslowly.



March2016CAMxUser’sGuideVersion6.3

2.TheCAMxModelingSystem



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 6www.camx.com



2.THECAMXMODELINGSYSTEM

CAMxcomprisesthecorecomponentofanoverallairqualitymodelingsystem,asillustratedin

Figure2‐1.CAMxinputsaredevelopedusingindependentthird‐partymodelsandprocessing

toolsthatcharacterizemeteorology,emissions,andvariousotherenvironmentalconditions

(landcover,radiative/photolysisproperties,andinitial/boundaryconditions).Interface

programsareneededtotranslatetheproductsofeachofthesemodels/processorsintothe

specificinputfieldsandformatsrequiredbyCAMx.Aftertheairqualitysimulationis

completed,additionalprogramsareusedtopost‐processtheconcentrationfields,develop

modelperformancestatisticsandmeasures,manipulateProbingTooloutputintovarious

reportableformats,andfurthertranslaterawresultsintoformsnecessaryforregulatory

purposes.CommonlyavailablegraphicalsoftwarecanbeusedtoviewCAMxoutputfiles;some

likePAVEandVERDIcanreadCAMxfilesdirectly,othersrequirereformattingCAMxfilesto

commondataformatslikeNetCDF.Whilethird‐partyvisualizationsoftware,meteorological

models,andemissionprocessorsarenotdistributedwithCAMx,RambollEnvirondoes

distributemanyofthenecessaryinterfaceprogramsandpost‐processorsontheCAMxwebsite

(www.camx.com).Abriefdescriptionofeachoftheseisprovidedattheendofthissection.



Figure2‐1.SchematicdiagramoftheCAMxmodelingsystem.SeeTable3‐1foradetailedlist

ofspecificmodelinputrequirementsforthefivemajordataclassesshownatthetopofthe

figure.Certainpre‐andpost‐processorprogramsshowninthefigurearedescribedinthis

section.Third‐partymodels,processors,andvisualizationsoftwarearenotdescribedinthis

User’sGuideandarenotdistributedwithCAMx.

SMOKE,

CONCEPT,

EPS3

WRF,

MM5,

RAMS TUV

CAMx

PiGSET,

WINDOW,

MRGUAM

WRFCAMx,

MM5CAMx,

RAMSCAMx,

KVPATCH

Total

Atmospheric

Ozone Column

Landcover

Emission Inventory,

Fire Activity

Analyses,

Observations,

Topography,

Landcover

ICBCPREP

BNDEX

O3MAP

CAMxTRCT,

CAMx2IOAPI,

BIN2ASC

AVGDIF,

CAMxPOST,

EPASTAT

MATS PA Tools,

User-Developed Post-Processors

Land/Ocean Mask

Global Models

(GEOS-CHEM,

MOZART, AM3)

GEOS2CAMx,

MOZART2CAMx

Leaf Area Index

Data

Models &

Pre-Processors

Interfac e

Programs

Core Model

Post-Processors

File Formatting Performance Regulatory Probing Tools

Emissions Meteorology Photolysis Geographic Air Quality

MERGE LULAI

GIS Processin

Bio

enic Models

SEASAL

Vegetative

Cover

March2016CAMxUser’sGuideVersion6.3

2.TheCAMxModelingSystem



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 7www.camx.com



2.1CAMxProgramStructure

ThecoreCAMxmodeliswritteninFortran,butincludessomeutilitieswritteninCtointerface

withMPI.Theprogramishighlymodularandwelldocumentedtoeasecodereview,

modificationsandsubstitutionofalternateroutines.Thesourcecodeisarrangedinseveral

directories,groupedaccordingtofunction.Themainsourcedirectorycontainsversionrelease

notes,theGNUuserlicense,the“Makefile”compileutility,andacontrolfilenamelisttemplate.

Sub‐directoriescontainsourcecodeforthecoremodelandancillaryroutinesaccordingtothe

following:

CAMx/SourcecodeforthemaindriverroutineCAMx.fandcoremodel

routines.

CF_AERO/Sourcecodeforinorganicaerosolchemistry(aqueousand

thermodynamicpartitioning)forthe2‐modeCFscheme.

CMC/ Sourcecodeforthegas‐phasechemicalmechanismroutines.

CMU_AERO/Sourcecodeforinorganicaerosolchemistry(aqueousand

thermodynamicpartitioning)forthemulti‐sectionCMUscheme.

DDM/ Sourcecodeforthe(H)DDMProbingTool,consistingofI/Oandcore

routinesthatareuniqueto(H)DDM.

HG/ Sourcecodeforthemercurychemistryroutines.

Includes/Fortran“include”files,consistingofprogramparametersandmemory

managementcode.

IO_bin/SourcecodeforFortranbinary(unformatted)I/O.

Mod_src/SourcecodeforF90memorymanagementmodules.

MPI/ SourcecodeforroutinesspecifictoMPIparallelization.

OSAT/SourcecodefortheOSAT/PSATProbingTools,consistingofI/Oandcore

routinesthatareuniquetoOSAT/PSAT.

PA/ SourcecodefortheProcessAnalysisProbingTool,consistingofI/Oand

coreroutinesthatareuniquetoPA.

PiG/ SourcecodeforthePlume‐in‐Gridsub‐model,consistingofI/Oandcore

routinesthatareuniquetoPiG.

RTRAC/SourcecodefortheReactiveTracerProbingTool,consistingofI/Oand

coreroutinesthatareuniquetoRTRAC/RTCMC.

SOAP/ Sourcecodeforsecondaryorganicaerosolthermodynamicpartitioning.

March2016CAMxUser’sGuideVersion6.3

2.TheCAMxModelingSystem



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 8www.camx.com



2.1.1MemoryManagement

Allofthemodel’sglobaldatastructuresaredynamicallyallocatedwhenthemodelstarts.The

datanecessarytoallocatememoryspaceforagivenmodelrunarereadfromtheCAMxcontrol

filedevelopedbytheuser(seeSection2.3).However,toalleviatecompilerdependencyon

speedperformance,CAMxutilizessomehard‐codedFortranparameterstostaticallyallocate

localarraysinlow‐levelsubroutines.Alloftheseparametersaredefinedinthe

Includes/camx.prmfile.Thedistributionversionofthis“include”filesetskeyarray

parameterstodefaultvaluesthatshouldbesufficientlylargetoaccommodatemost

applications:seeTable2‐1foradescriptionofparametersandtheirdefaultvalues.However,

youmaywanttocustomizethesevaluestoensurethattheyarelargeenoughtoaccommodate

allofyourmodelconfigurations,ortoexactlymatchyourspecificapplication,thuspreventing

wastedmemory.

Ifanyparameterissettoavaluethatistoosmalltosupportyourapplicationthemodelwill

stop,displayinganinformativeerrormessage.Toconservememory,defaultvaluesof1are

setforProbingTooltracers,PiGsamplinggrids,andsamplinggriddimensions.Thesemustbe

increasedaccordinglyifProbingToolsorsamplinggridsaretobeused.



Table2‐1.ParametersandtheirdefaultsinIncludes/camx.prmusedtostatically

dimensionlocalarraysinlow‐levelsubroutines.

ParameterNameDescription

Default

Value

MXCELLS NumberofcellsinX/Ydirectionforanygrid 200

MXLAYER Numberoflayers 30

MXSPEC Numberofspecies(couldbenumberofradicals,numberofinput

species,ortotalnumberofmodelspecies)133

MXREACT Numberofreactions(dependsonthemechanism;seetheuser's

guideforthevalueforeachmechanism)565

MXGRID Numberofgrids 10

MXPTSRC Numberofpointsources 100000

MXTRSP NumberofProbing Tooltracerspecies 1

MXPIG NumberofPiGpuffs 50000

MXSAMPLE NumberofPiGsamplinggrids 1

MXCOLSMP NumberofPiGsamplinggridcolumns 1

MXROWSMP NumberofPiGsamplinggridrows 1



Alloftheparametersinthetableabovecanbedeterminedbeforestartingasimulationexcept

forMXPIG.Avalueof50,000isusuallysufficientformostapplicationsinwhichPiGisused;set

thisparameterto1ifPiGisnotusedtoconservememory.Ifthisparameterisexceededduring

asimulation,themodelwillstopwithaninformativeerrormessage.Ifthishappens,simply

increaseMXPIG,recompilethemodelexecutable,andrestartthesimulation.Theother

parametersincamx.prmbeyondthoselistedinTable2‐1willnotnormallyneedtobe

changedandarenotdiscussedfurther.

March2016CAMxUser’sGuideVersion6.3

2.TheCAMxModelingSystem



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 9www.camx.com



2.1.2ParallelProcessing

Parallelprocessingreferstodistributingamodelapplicationtomultipleprocessors(CPUs)that

sharethecomputationalload.CAMxsupportstwotypesofparallelization:(1)OpenMP(OMP),

whichallowsparallelprocessingonshared‐memory(e.g.,multi‐core)computers;and(2)

MessagePassingInterface(MPI),whichallowsparallelprocessingacrossdistributedmemory

(networked)computerclusterenvironments.BothOMPandMPIcanbeusedincombination

tomaximizespeedperformance.

TouseOMP,yourFortrancompilermustincludelibrariestoenablethein‐codeparallelization

directives.OMPdistributescalculationsforindividualprocesses,suchaschemistrywithina

singlegridcelloradvection/diffusionalongasinglerowofcells,toanumberofCPUsdefined

bytheuser.OnceeachCPUhascompleteditscalculations,itworksonthenextindividual

processuntilallprocessesovertheentiregridarecompleted.

TouseMPI,youmusthaveanexternalMPIlibraryinstalledonyoursystem.MPICHisaspecific

opensourceMPIlibrarywidelyusedinthenumericalmodelingcommunity;CAMxhasbeen

specificallydevelopedandtestedusingMPICH.WithMPI,eachCAMxgridisdividedintosub‐

domains(“slices”)andeachsliceisassignedtoaCPUontheuser‐definednetwork.EachCPU

operatestheentiremodelonitsassignedsliceandpassescommoninformationneededby

otherCPUsviadata“messages”.

MPIinCAMxisdesignedusinga“master/slave”parallelprocessingapproach.TheCPUon

whichtheprogramislaunchedservesasthemasternodeandwillnotconductanymodel

computationsonanypartofthemodelingdomain.Thisprocesswillperformallofthemodel

setup,thevastmajorityofI/O,andmanagethecommunicationbetweentheslaveorcompute

nodes,whichintegratethemodelforwardforeachgridslice.Sincethemasternodehandles

theimportantI/OitistheonlyCPUthatneedsaccesstothediskvolumecontainingtheinput

filesandthelocationoftheoutputdirectory.Thisapproachallowsforaminimalamountof

networktrafficto/amongthecomputenodesbyeliminatingtheneedforthemtomanageNFS

mounts.ThemasternodemayneedaccesstotheLANfordataaccess,butthecomputenodes

onlyneedaccesstotheinternalclusternetwork.However,thecomputenodeswillneedaccess

toacopyoftheexecutableprogram.Thiscanbeaccomplishedinanumberofways:(1)have

anNFSmountonthemasternodeaccessibletotheinternalclusternetworkandlaunchthe

modelfromthatlocation;or(2)portacopyoftheexecutableprogram,usingrcporscp,to

theuser’shomedirectoryoneachcomputenodeandlaunchthemodelfromtheuser’shome

directoryonthemasternode.

Duringeachmodeltimestep,whengridslicecomputationsareperformedbythecompute

nodes,someinformationiswrittentothediagnosticandmessageoutputfiles.Ratherthanjust

eliminatethisinformationaltogether,wedecidedtocreatenode‐specificversionsofeachof

thesetwofilesandhaveeachcomputenodewritetheinformationtoitsownversion.

However,inordertopreventtheneedtohavetheoutputdirectoryavailabletothecompute

nodeacrossthenetwork,wehavedesignedthemodelsothatthenode‐specificfilesare

createdinthecurrentworkingdirectory.ThismeansthatifthemodelislaunchedfromanNFS‐

mounteddirectory,allofthenode‐specificfileswillallbecreatedinthatlocation.Ontheother

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hand,ifthemodelislaunchedfromauser'shomedirectoryonthecomputenodes,youwill

havetologintothespecificcomputenodetoviewthefiles.

WhenusingahybridMPI/OMPapproach,thegridswillbedividedintoslicesintheusualwayas

partofMPI,butwhenoperatingonaparticularslice,thehostwillspawnmultipleOMPthreads

toparallelizetheportionsofthecodewhereOMPdirectiveshavebeenincluded.

2.2CompilingCAMx

A“Makefile”scriptisprovidedinthemainsourcedirectory.TheMakefilewillcompileallCAMx

sourcecode,linkwithnecessarylibraries,andbuildanexecutableprogram.Itsupports

platformsrunningLinux(PortlandGroupandIntelcompilers)andMacintoshOSX(Absoft

compiler);itdoesnotcurrentlysupportcompilersonplatformsrunningWindows.

ThechoiceforOMPandMPIparallelization,andthememoryconfigurationforprobingtools,

aresetduringmodelcompilation.AllotherCAMxchoicesforchemicalmechanism,model

algorithms,ProbingTools,andotheroptionsareselectedatruntime.

CAMxiscompiledbyissuingthefollowingcommandatashellpromptwithinthemainsource

directory:

make COMPILER=my_compiler <CONFIG=my_app> <MPI=mpi_option>



wherethetextwithinthebrackets“<>”isoptional.Todisplayaninteractivehelpmessage,

youmaytype

make help



ThemandatoryCOMPILERargumentshouldbesettooneofthefollowing:



pgf orpgfomp(PortlandGroupcompilerforLinux)

ifort orifortomp(IntelcompilerforLinux)

gfortranorgfortranomp(GnucompilerforLinux)

absoftorabsoftomp(AbsoftcompilerforMacintoshOSX)



ThesekeywordsinformtheMakefileofthecompilerbeingusedtocompileandrunthemodel,

sothattheMakefilecaninvokethepropercompiler‐specificcommandsandflags.IfOMPisnot

specifiedaspartofthekeywordthenCAMxwillnotbeabletorunwithOMPparallelization.

TheoptionalCONFIGargumentallowstheCAMxexecutableprogramtobelabeledfora

specificmemoryconfigurationasdefinedwithintheCAMxparametersfile

(Includes/camx.prm)describedabove.Youmaywanttocustomizesomeapplications,for

exampletoconfiguretheProbingToolextensions,anditisconvenienttobeabletodistinguish

betweentheseexecutables.TheMakefilewillsearchforaCAMxparametersfilecalled:

Includes/camx.prm.my_app

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IfCONFIGisnotsetonthemakecommandline,theMakefilewillcompileCAMxusingthe

defaultparametersfile,Includes/camx.prm.v6.30.

TheoptionalMPIargumentwillenableMPIparallelprocessing.Thisrequiresthatthird‐party

MPIlibrarieshavebeenbuiltandinstalledonthemachinethatisrunningthisMakefilescript

andcompilingCAMx.IfMPIisnotsetonthecommandline,theMakefilescriptwillignorethe

MPIlibrariesandCAMxwillnotbeabletorunwithMPIparallelization.TheoptionalMPI

argumentshouldbesettooneofthefollowing:

mpich(MPICHversions1or2)

mpich3(MPICHversion3)

mvapch

openmpi (PGFandIFORTcompilersonly)

Youshouldcheckthatthevariable“MPI_INST”intheCAMxMakefile,andintheMPI

utilitiesMakefile(locatedintheMPI/utilsub‐directory),arecorrectlysettoyoursystem's

MPIinstallationpath.

CAMxsupportstheuseofbothOMPandMPIparallelizationinasinglerunusingPGFandIFORT

compilers.ToutilizeOMPinyourMPIapplication,besuretospecifytheappropriateOMP

compilerkeyword.

TheMakefilewillgenerateaCAMxexecutableprogramnamed

CAMx.my_app.MPI_option.my_compiler

whichwillresideinthemainsourcedirectory.Forexample,adefaultcompilationusingthe

PortlandGroupcompilerwillresultinanexecutablenamed

CAMx.v6.30.noMPI.pgf.

IfyouneedtorebuildCAMxusingdifferentMakefileargumentswerecommendtyping“make

clean”betweenbuilds.Makecleanwilldeleteallexistingobjectfilesandforceacomplete

re‐build.

2.2.1ANoteonFortranBinaryInput/OutputFiles

LargeCAMxinputandoutputdatafieldsarecontainedwithinFortran“unformatted”(binary)

files.Thismeansthatthedataarereadandwrittenasrepresentedinmemory,without

translationbetweenbinaryandASCIIcharactersetsasisperformedfor“text”files.Binaryfiles

reducefilevolumeandimproveprogramread/writespeed,buttheusercannotdirectlyviewor

manuallyeditthem.Therearetwowaystorepresentbinaryinformationinmemory:“big

endian”and“littleendian.”Thedifferencebetweentheseisessentiallytheorderofbitsina

word,andwhichorderisuseddependsonthecomputerchipset.Historically,bigendianhas

beenusedinmanyUnixworkstations(Sun,SGI,HP,andIBM).Thex86processorsonpersonal

computerplatforms(e.g.,IntelandAMD)uselittleendian,whilePowerPCchipsarebigendian.

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CAMxcanbecompiledandrunonmachinesthatuseeitherbigorlittleendianbinary

representations,aslongasthemodelandallofitspre‐andpost‐processorsareconsistently

compiledandrunonthesametypeofplatform.Ifanycomponentofthemodelingsystemis

compiledonadifferentplatformusingtheoppositebinaryrepresentation,I/Ofileswillnotbe

properlyreadandwilllikelyleadtoaprogramcrash.

Atypicalrun‐timeerrormessagefromtryingtoreadthewrongbinaryformatis“inputrecord

toolong,”soifyougetthiserrormessage,checkforbigendian/littleendianconsistency

betweenyourbinaryfilesandFortrancompileroptions.

Compilersforlittleendianmachines(e.g.,x86PCchipsets)providecompile‐timeswitchesthat

allowbinaryfilestobereadandwrittenasbigendian.ThePortlandGroupcompileroptionis

“-byteswapio”,whereastheIntelcompileroptionis“-convert big_endian.”The

CAMxMakefilesetscompilerflagstoconsistentlyusebigendiantomaximizeplatform

portability.Therefore,useoftheCAMxMakefilewillbydefaultresultinthemodelreadingand

writingbigendianbinaryfiles.Inpractice,usersshouldusethedefaultbinaryformatthatis

builtintotheCAMxMakefileandthatisusedfortheCAMxdistributiontestcase.

2.3RunningCAMx

2.3.1ControlFileNamelistInput

CAMxreadsatextruncontrolfilenamed“CAMx.in”thatmustexistlocallyinthedirectory

fromwhichthemodelisrun.ThisfilemustbeintheFortran“namelist”format,andcontains

alluser‐specifiedcontrolparametersforagivensimulation,includingmodelconfiguration,

option‐specificinputs,andI/Ofilenames.Theruncontrolfilemustcontaintheprimary

namelistmodulelabeled“&CAMx_Control”,whichprovidesalloftheinformationto

configurethecoremodel.Additionalnamelistmodulesmaybeprovidedintheruncontrolfile

toconfigurethevariousCAMxProbingToolextensions.Theseoptionalnamelistmodulesare

ignoredifnoProbingToolsareselectedintheprimarynamelist.

EachrecordintheCAMxcontrolfilecontainsavariablenamethatisexplicitlysettoa

numerical,logical,orcharactervalue.Thevariablenamesareusedbytheprogramdirectly,

andthereforecannotbechangedwithoutsourcecodemodifications.Characterstringsmust

beenclosedbysinglequotes,andallvariableassignmentsmustbedelimitedwithcommas.

Theorderoftherecordsmaybearrangedinanyfashionthattheuserprefers.Anynumberof

commentstatementsmaybeincludedanywherewithinthenamelists,providedthattheydo

notinterruptvariableassignments(variable_name = value,).The“!”characteristhe

Fortrannamelistcommentdelimiter.

Certainvariablesaremulti‐dimensionarrays;theusermayprovideacomma‐delimitedlistof

valuestofillthearrayorassignvaluestospecificarrayelements.Certainothervariablesare

optionalorassociatedwithoptionflags;thesedonotneedtoappearinthenamelistiftheir

associatedoptionsarenotinvoked,andtheywillbeignorediftheyremaininthefile.

Iftheuserdoesnotprovidenecessaryinputs,themodelwillstopwithadescriptiveerror

message.

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2.3.1.1CommonErrorsWhenCreatingaNamelist

FortranprogramsingesttheentirecontentsofnamelistmodulesusingasingleREAD

statement.Iftheprogramexperiencesanerrorreadingthenamelist,itechoesasimpleerror

messagelike“errorreadingnamelist”andtheprogramstops.Itisthereforedifficultto

determinethecauseofthereaderror,especiallyifthenamelistislengthyandcontainsa

varietyofdatatypes.WhenexperiencinganerrorreadingtheCAMxcontrolfilenamelist,you

mustcarefullyinspectthefileforanysyntaxerrors.Theseerrorscanbesubtleanddifficultto

spot.Hereareafewofthecommonreasonsanerroroccurswhenreadinganamelist:

 Mistypedvariablename:

Allvariablestobeassignedwithinanamelistmustberecognizedasadeclarednamelist

variablewithinthereadingprogram.Ifavariableismisspelledoranunknownvariable

isassignedavalue,areaderrorwilloccur.

 Incorrectdatatypefortheassignedvariable:

Ifthedatatypeofthevalueassignedtoanamelistvariabledoesnotmatchthe

variable’sdeclareddatatypewithinthereadingprogram,anerrorwilloccur.Some

compilerswillallowrealtypevariablestobeassignedtointegervalues,butnotthe

converse.

 Missingperiodaroundalogicalvalue:

Thelogicalvalues.true.and.false.mustbesurroundedbyaperiod.

 Missingquotesaroundacharactervariable:

Anycharacterdatatypemustbesurroundedbyquotes.

 Overflowwhenassigningvaluestoanarray:

Thevaluesinanarraycanbeassignedusingarrayindexnotation.Iftheindexusedto

assignanarrayvalueexceedsthedeclareddimensionofthearray,areaderroroccurs.

Checkthe“MXNAM”parameterintheIncludes/namelist.incincludefiletosee

ifthisvalueneedstobeincreased.Alternatively,checkyournamelistfiletobesureall

ofyourarrayindicesarecorrect.

 Wrongnumberofdimensionswhenassigningvaluestoamulti‐dimensionalarray:

Whenassigningvaluestoanarrayusingarrayindexnotation,thenumberofsubscripts

intheassignmentmustmatchthedeclareddimensionsofthearray(e.g.,assignments

toanarraydimensionedvar(i,j)mustbereferencedusingtwoindices).

 Missingcommafollowingavariabledefinition:

Acommamustbethelastcharacterinavariableassignment(variable = value,).

Acommentmaybeplacedafterthecomma(delimitedusingthe“!”symbol,seebelow)

onthesamefilerecord.Thisrestrictionontheuseofcommasisignoredonsome

compilers.

 Toomanycommasfollowingascalarvariabledefinition:

Morethanonecommafollowingascalarvariableassignmentwillresultinareaderror.

 Toomanycommasfollowingthevariableassignmentlistforanarray:

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Theentirecontentsofanarraycanbeassignedusingasinglestatementbylistingthe

valuesofeachelementseparatedbycommas.Thereadwillfailiftherearemore

commasthanthedimensionofthearray.

 Commentdoesnotbeginwith!:

Thecharacterthatdelimitsacommentinanamelististheexclamationpoint.

Commentscanappearanywherewithinthenamelist.However,alltextinthenamelist

musteitherbepartofanamelistvariableassignmentorpartofanidentifiedcomment.

WesuggestthatnewCAMxusersstartwiththe“CAMx.namelist.template”thatis

providedwiththesourcecode.

2.3.1.2ThePrimaryNamelistModule

Thissectiondescribestheprimarynamelistmodule;detaileddescriptionsofeachofthe

ProbingToolmodulesareprovidedintheirrespectivesections(Sections7through10).Alisting

ofallnamelistvariablesnecessarytorunthecoremodelispresentedonthefollowingpages.



DescriptionofCAMxRunControlFileVariables



&CAMx_Control  Labelfortheprimarynamelistmodulethatconfiguresthecore

model;itmustbeginincolumn2

&Flagendinganamelistmodule;itmustbeincolumn2

Run_Message60‐charactersimulationmessage,writtentooutputfilestolabel

therun

Theshortsimulation“runmessage”iswrittentoalloutputfilestodescribeandlabeltherun.

ModelClockControl

Time_ZoneIntegertimezone(0=UTC,5=EST,6=CST,7=MST,8=PST)

Restart Logicalmodelrestartflag(TRUE=readrestartfile,FALSE=read

initialconditionsfile)

Start_Date_Hour  Integerarraystarttime(YYYY,MM,DD,HHmm)

End_Date_Hour Integerarrayendtime(YYYY,MM,DD,HHmm)

Maximum_Timestep  Realmaximumallowabletimestep(minutes)

Met_Input_Frequency Realinputfrequencyofenvironmentalfields(minutes)

Ems_Input_Frequency Realinputfrequencyofemissions(minutes)

Output_Frequency  Realoutputfrequency(minutes)

Theuserspecifiesthesimulationstart/endyear,month,day,andhour;themodelusesJulian

datesinternally.Alltimesmustbegiveninmilitaryformat(e.g.,1:30PMmustbegivenas

1330).Thesimulationtimezonemustmatchthetimezoneinwhichtheemissionand

environmentalinputsaredeveloped.

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MapProjectionParameters

Map_Projection  Charactermapprojectionkeyword(LAMBERT,POLAR,RPOLAR,

MERCATOR,UTM,LATLON)

UTM_ZoneIntegerUTMzone

Longitude_Pole  Reallongitudeofprojectionpoleororigin(degrees,west<0)

Latitude_Pole  Reallatitudeofprojectionpoleororigin(degrees,south<0)

True_Latitude1  Realfirsttruelatitudeofprojection(degrees,south<0)

True_Latitude2  Realsecondtruelatitudeofprojection(degrees,south<0)

ThegridprojectionmaybeselectedasCartesian(fixedphysicaldistancecoordinatesonaflat

plane)orcurvi‐lineargeodetic(followingthecurvedsurfaceoftheEarth).TheCartesian

optionsincludeLambertConicConformal(LAMBERT),PolarStereographic(POLAR),Rotated

PolarStereographic(RPOLAR),Mercator(MERCATOR),andUniversalTransverseMercator

(UTM).Thegeodeticoptionperformsthesimulationonalatitude/longitudegrid(LATLON).All

griddedinputfilesmustbedefinedonthegridprojectionspecifiedfortheCAMxsimulation.

TheLAMBERT,POLAR,andMERCATORprojectionsareallequivalenttothedefinitionsusedin

theWRFmeteorologicalmodel,whichassumesasphericalEarthwithradiusof6370km.The

RPOLARprojectionisequivalenttothedefinitionusedintheRAMSmeteorologicalmodel.

WhilethePOLARprojectionofWRFisdefinedtobetangentat(orsecantaround)theNorth

andSouthPoles,theRPOLARprojectionofRAMSisdefinedtobeonlytangenttotheEarth’s

surfaceatanyuser‐definedlatitude/longitude.

IftheLAMBERTprojectionisspecified,theLongitude_PoleandLatitude_Polemust

bespecifiedtodefinetheprojectionorigin(whereLAMBERTcoordinatesaredefinedtobe0,0

km),andTrue_Latitude1andTrue_Latitude2mustbespecifiedtodefinethe

projectiontruelatitudes(theymaybeequal,whichisaprojectiontangetatthatlatitude).

IftheMERCATORprojectionisspecified,theLongitude_PoleandLatitude_Polemust

bespecifiedtodefinetheprojectionorigin(whereMERCATORcoordinatesaredefinedtobe

0,0km),andTrue_Latitude1mustbespecifiedtodefinetheprojectiontruelatitude(it

maybezero,whichisaprojectiontangentattheEquator).

IfthePOLARprojectionisspecified,theLongitude_PoleandLatitude_Polemustbe

specifiedtodefinetheprojectionorigin(wherecoordinatesaredefinedtobe0,0km),and

True_Latitude1mustbespecifiedtodefinetheprojectiontruelatitudeorsecant(itmay

be±90degrees,whichisaprojectiontangentattheNorthorSouthPoles).

IftheRPOLARprojectionisspecified,theLongitude_PoleandLatitude_Polemustbe

specifiedtodefinetheprojectionpole(wherecoordinatesaredefinedtobe0,0km).True

latitudesarenotspecifiedasRPOLARisalwaystangentatthepolepoint.

IftheUTMprojectionisspecified,aUTMzonemustbespecified(1through60).Poleandtrue

latitudevaluesareignoredforUTMandLATLONprojections.

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ParametersForTheMaster(First)Grid

Number_of_Grids  Integernumberofgridsinsimulation

Master_SW_XCoord  Realx‐coordinateofdomainsouthwestcorner(km,ordegrees

forLATLON)

Master_SW_YCoord  Realy‐coordinateofdomainsouthwestcorner(km,ordegrees

forLATLON)

Master_Cell_XSize Realcellsizeinx(km,ordegreesforLATLON)

Master_Cell_Ysize Realcellsizeiny(km,ordegreesforLATLON)

Master_Grid_Columns Integernumberofmastergridcolumns(E‐Wgridcells)

Master_Grid_Rows  Integernumberofmastergridrows(N‐Sgridcells)

Number_of_Layers  Integernumberofgridlayers(appliestoallgrids)

Themastergridisdefinedbyitslocation(southwestcornerofcell[1,1]inthecoordinatesof

thechosenprojectionspace),numberofgridcells(east‐west,north‐south,vertically),and

horizontalresolution.Verticalresolutionisdefinedbythelayerstructurespecifiedintheinput

3Dmeteorologicalfile.

ParametersForTheNestedGrids

Nest_Meshing_Factor Integerarray(bygrid)nestedgridcellsizerelativetomaster

grid

Nest_Beg_I_Index  Integerarray(bygrid)mastergridcolumncontainingwestern

edgeofnest

Nest_End_I_Index  Integerarray(bygrid)mastergridcolumncontainingeastern

edgeofnest

Nest_Beg_J_Index  Integerarray(bygrid)mastergridrowcontainingsouthernedge

ofnest

Nest_End_J_Index  Integerarray(bygrid)mastergridrowcontainingnorthernedge

ofnest

ThedefinitionofnestedgridsisspecifiedintheCAMx.infileintermsoftherangeofmaster

gridcellsthateachnestedgridspans(seeSection4).The“meshingfactor”setstheresolution

orcellsizeofthenestedgridsrelativetothemastergrid.TheCAMxdiagnosticoutputfile

providesinformationonthelocationandsizeofeachnestedgridtohelpensurepropersetup.

ModelOptions

Diagnostic_Error_CheckLogicalmodelstartupdiagnosticflag(TRUE=stopsbeforefirst

timestepindicatingsuccessfulmodelinitialization,

FALSE=continueswithsimulationaftermodelinitialization)

Flexi_NestLogicalflexi‐nestingflag(TRUE=allowsome/allnestedinput

fieldstobeinterpolatedfromtheparentgrid,FALSE=alldata

mustbeprovidedforallnests)

Advection_Solver  Characterhorizontaladvectionsolverkeyword(PPM,BOTT)

Chemistry_Solver  Characterchemistrysolverkeyword(EBI,LSODE)

PiG_Submodel  CharacterPiGsubmodelkeyword(NONE,GREASD,IRON)

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Probing_Tool  CharacterProbingToolkeyword(NONE,SA,DDM,HDDM,PA,

IPR,IRR,RTRAC,RTCMC)

ChemistryLogicalchemistryflag(TRUE=chemistryon,FALSE=chemistry

off)

Drydep_Model Characterdrydepositionmodelkeyword(NONE,WESELY89,

ZHANG03)

Wet_Deposition  Logicalwetdepositionflag(TRUE=depositionon,

FALSE=depositionoff)

ACM2_Diffusion  LogicalACM2verticaldiffusionflag(TRUE=ACM2on,

FALSE=standardK‐theorydiffusion)

Surface_Model  Logicalsurfacemodelflag(TRUE=surfacemodelon,

FALSE=surfacemodeloff)

Super_Stepping  Logicalsuper‐steppingflag(TRUE=usesuper‐steppingfor

horizontaladvectiontomaximizemodelspeed,FALSE=donot

usesuper‐stepping).

Gridded_Emissions Logicalgriddedemissionsflag(TRUE=griddedemissionswillbe

used,FALSE=griddedemissionswillbeignored)

Point_Emissions  Logicalelevatedpointsourceflag(TRUE=pointemissionswillbe

used,FALSE=pointemissionswillbeignored)

Ignore_Emission_Dates Logicaldate‐insensitiveemissionflag(TRUE=datesonemission

fileswillbeignored,FALSE=datesonemissionfileswillbe

checkedagainstsimulationdate)

TheuserhastheoptionofselectingamongtheBottorPiecewiseParabolicMethodhorizontal

advectionsolversbyspecifying“BOTT”or“PPM”askeywordsintheruncontrolfile.Theuser

alsohastheoptiontousetheEBIorLSODEchemistrysolversforgas‐phasechemistryby

specifyingtheserespectivekeywords.ProbingToolsareselectedbyspecifyingoneofthe

allowedkeywords;noProbingToolwillberunifthiskeywordissetto“None”.Thedescription

ofthePiGsubmodelisprovidedinSection6.

Supersteppingmaximizesthemodel’sspeedperformancebysettingthelargestgrid‐specific

drivingtimestepspossible.Thisresultsintheneedforpotentiallymanysub‐stepstobe

appliedinhorizontaladvectiononalayer‐by‐layerbasistomaintainastablesolution.While

supersteppinghaslittleimpactonsurfaceconcentrationsinnon‐MPImode,largerdifferences

areseenusingMPI.A“super‐stepping”flagwasaddedtothecontrolnamelistthatallows

userstospecificallyturnoffsupersteppingwhentheywishtocompareconcentrations

betweenMPIandnon‐MPIrunsinthemostconsistentmannerpossible.Supersteppingcan

reducetheaccuracyoftheverticaltransportsolution,especiallyinhighwindconditionsover

complexterrain.Turningsupersteppingoffwillcausethemodeltorunmuchmoreslowly.

OutputSpecifications

Root_Output_Name  Characterrootoutputpath/filename(seeTable2‐2for

descriptionoffilesuffixes)

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Average_Output_3D Logical3‐Daverageoutputfileflag(TRUE=outputfull3‐D

concentrationfields,FALSE=outputsurfacelayerconcentration

fields)

Output_3D_Grid  Logicalarray(bygrid)3‐Daverageoutputfileflag(TRUE=output

full3‐Dconcentrationfieldsforspecifiedgrid,FALSE=output

surfacelayerconcentrationfields)

Output_Species_Names Characterarray(byoutputspecies)speciesnamestobewritten

toaverageanddepositionoutputfiles,orthesinglename“ALL”

tooutputallstategasandPMspecies(excludingradicals),or

thesinlgename“ALLR”toincluderadicals

PiG_Sampling_GridLogicalsamplinggridflagforIRONPiGoutput(TRUE=sampling

gridsarespecified,FALSE=samplinggridswillnotbegenerated)

Sample_BackgroundLogicalflagtoincludebackgroundconcentrations

(TRUE=backgroundconcentrationsfromthehostcomputational

gridwillbeaddedtopuffincrements,FALSE=onlypuff

incrementswillbeshown)

Number_of_Sampling_GridsIntegernumberofsamplinggrids

SG_Beg_I_IndexIntegerarray(bysamplinggrid)mastergridcolumncontaining

westernedgeofsamplinggrid

SG_End_I_IndexIntegerarray(bysamplinggrid)mastergridcolumncontaining

easternedgeofsamplinggrid

SG_Beg_J_IndexIntegerarray(bysamplinggrid)mastergridrowcontaining

southernedgeofsamplinggrid

SG_End_J_IndexIntegerarray(bysamplinggrid)mastergridrowcontaining

northernedgeofsamplinggrid

SG_Mesh_FactorIntegerarray(bysamplinggrid)cellsizerelativetomastergrid

Theuserspecifiesa“root”pathandfilenamethatwillbeusedforallstandardCAMxcore

modeloutputfiles.Themodelappendssuffixestotheserootnamesaccordingtothefiletype

generated.

ThetypesofCAMxoutputfilesarelistedinTable2‐2.Asubsetofstate(gasorPM)andradical

speciesmaybeoutputtotheaverageconcentrationoutputfiles;seethedescriptionofoutput

fileformatsinSection3.Byspecifyingasingleoutputname“ALL”,themodelwillautomatically

outputfieldsforallstategasandPMspecieslistedintheinputchemistryparametersfile,

excludingradicals(use“ALLR”toincluderadicals).If“ALL”or“ALLR”arespecified,itmustbe

theonlynamelisted;nospeciesnamesmaybelistedbeforeorafter“ALL”.Therearetwoflags

thatcontrolwhether3‐Daverageoutputfilesaregenerated.Thefirst(original)flagwilltoggle

3‐Doutputforallgridsintherun.Thesecondisthe“Output_3D_Grid”flagarray,which

allows3‐Daverageoutputtobesetforspecificgrids.Theoriginalflagsupersedesthegrid‐

specificflag.

PiGsamplinggridsaresetidenticallytothewaynestedgridsarespecifiedforthehostmodel,

withoneexception:therearenoverticallevelstodefine(samplinggridsarecurrentlyonly2‐D

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layer1fields).Thesamerulesthatapplyforthespecificationofnestedgridsholdsforthe

specificationofallsamplinggrids(seeSection4).

InputFiles

Chemistry_Parameters Characterinputchemistryparameterspath/filename

Photolysis_Rates  Characterinputphotolysisratespath/filename(optional

accordingtoChemistryflagandChemistry_Parametersfile)

Ozone_Column  Characterinputozonecolumnpath/filename(ignoredif

Chemistry=FALSE)

Initial_Conditions Characterinputmastergridinitialconditionspath/filename

(ignoredifRestart=TRUE)

Boundary_Conditions Characterinputmastergridlateralboundaryconditions

path/filename

Top_Concentrations Characterinputmastergridtopboundaryconditions

path/filename

Point_Sources  Characterinputelevatedpointsourceemissionspath/filename

(ignoredifPoint_Emissions=FALSE)

Master_Grid_Restart Characterinputmastergridrestartpath/filename(ignoredif

Restart=FALSE)

Nested_Grid_Restart Characterinputnestedgridrestartpath/filename(ignoredif

Restart=FALSEorNumber_of_Grids=1)

PiG_RestartCharacterinputPiGrestartpath/filename(ignoredif

Restart=FALSEorPiG_Submodel=FALSE)

Srfmod_GridCharacterarray(bygrid)inputsurfacemodelrestart

path/filename(ignoredifRestart=FALSEor

Surface_Model=FALSE)

Surface_Grid  Characterarray(bygrid)inputstatic2Dsurfacepath/filename

(optionalfornestedgrids)

Met2D_GridCharacterarray(bygrid)inputtime‐variant2Dsurface

meteorologypath/filename(optionalfornestedgrids)

Met3D_GridCharacterarray(bygrid)inputtime‐variant3Dmeteorology

path/filename(optionalfornestedgrids)

Vdiff_GridCharacterarray(bygrid)inputtime‐variant3Dvertical

diffusivitypath/filename(optionalfornestedgrids)

Cloud_GridCharacterarray(bygrid)inputtime‐variant3Dcloud/rain

path/filename(optionalbutrequiredifWet_Deposition=TRUE,

optionalfornestedgrids)

Emiss_GridCharacterarray(bygrid)inputgriddedemissionspath/filename

(ignoredifGridded_Emissions=FALSE,optionalfornestedgrids)

IfCAMxcannotfindoropenanon‐blankinputfilenameprovidedintheruncontrolfile,the

modelwillstopwithanerror.CAMxwillacceptblankinputfilenamesforonlythosefilesthat

areoptional.

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Table2‐2.CAMxoutputfilesuffixesandtheircorrespondingfiletypes.

SuffixCAMxFileType

.out Textsimulationtrackingfile(CPU,inputfilesread,error/warningmessages)

.diag Textsimulationdiagnosticfile(repeatofruncontrolinputs,PiGdiagnostics,

miscellaneousdiagnosticoutput)

.mass Textmassbudgetfileforsubsequentpostprocessing

.inst Fortranbinarymastergrid3‐Dinstantaneousconcentrationfileattheend

ofthesimulation(usedforrestarts)

.finst Fortranbinarynestedgrid3‐Dinstantaneousconcentrationfileattheend

ofthesimulation(usedforrestarts)

.pig FortranbinaryPiGsub‐modelfile(usedforrestarts)

StandardCAMxOutputOption

.avrg.grdnn Fortranbinaryaverageconcentrationfileforgridnn;optionallycontains2‐D

layer1concentrationfieldorfull3‐Dconcentrationfield

.depn.grdnn Fortranbinary2‐Dsurfacedepositionfileforgridnn

.srf.grdnn Fortranbinary2‐Dsurfacemodelmassfileforgridnn(optional)

.smpnn Fortranbinary2‐Dlayer1averageconcentrationfileforPiGsamplinggrid

nn(optional)



2.3.2UsingScriptstoRunCAMx

Thegenerationoftheruncontrolfileismosteasilyaccomplishedinthejobscriptthatactually

runsthemodel;Figure2‐2showsanexampleofaCAMxjobscriptthatbuildsa“CAMx.in”file

andrunsthemodelforeachdaytobesimulated.Alternatively,theruncontrolfilecouldbe

writtenseparatelywithanamespecifictoagivensimulation,thenlinkedorcopiedtothe

standard“CAMx.in”filenamebeforethemodelisexecutedatacommandlineorinajob

script.



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#!/bin/csh

# CAMx 6.30

setenv OMP_NUM_THREADS 4

setenv MPSTKZ 128M

limit stacksize unlimited

set EXEC = "../../src/CAMx.v6.30.noMPI.pg_linuxomp"

set RUN = "v6.30.midwest.36.12.noMPI"

set INPUT = "../inputs"

set MET = "../inputs/met"

set EMIS = "../emiss"

set PTSRCE = "../ptsrce"

set OUTPUT = "../outputs"

mkdir -p $OUTPUT

# --- set the dates and times ----

set RESTART = "NO"

foreach today (03.154 04.155)

set JUL = $today:e

set CAL = $today:r

set YESTERDAY = `echo ${CAL} | awk '{printf("%2.2d",$1-1)}'`

if( ${RESTART} == "NO" ) then

set RESTART = "false"

else

set RESTART = "true"

endif

# --- Create the input file (always called CAMx.in)

cat << ieof > CAMx.in

&CAMx_Control

Run_Message = 'CAMx 6.30 Test Problem -- Mech6 CF CB05 $RUN',

!--- Model clock control ---

Time_Zone = 0, ! (0=UTC,5=EST,6=CST,7=MST,8=PST)

Restart = .${RESTART}.,

Start_Date_Hour = 2002,06,${CAL},0000, ! (YYYY,MM,DD,HHmm)

End_Date_Hour = 2002,06,${CAL},2400, ! (YYYY,MM,DD,HHmm)

Maximum_Timestep = 15., ! minutes

Met_Input_Frequency = 60., ! minutes

Ems_Input_Frequency = 60., ! minutes

Output_Frequency = 60., ! minutes

Figure2‐2.AsampleCAMxjobscriptthatgeneratesa“CAMx.in”fileandrunsthemodel

withOMPparallelization.

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!--- Map projection parameters ---

Map_Projection = 'LAMBERT', ! (LAMBERT,POLAR,UTM,LATLON)

Longitude_Pole = -97., ! deg (west<0,south<0)

Latitude_Pole = 40., ! deg (west<0,south<0)

True_Latitude1 = 45., ! deg (west<0,south<0)

True_Latitude2 = 33., ! deg (west<0,south<0)

!--- Parameters for the master (first) grid ---

Number_of_Grids = 2,

Master_SW_XCoord = -792., ! km or deg, SW corner of cell(1,1)

Master_SW_YCoord = -1656., ! km or deg, SW corner of cell (1,1)

Master_Cell_XSize = 36., ! km or deg

Master_Cell_YSize = 36., ! km or deg

Master_Grid_Columns = 68,

Master_Grid_Rows = 68,

Number_of_Layers = 16,

!--- Parameters for the second grid ---

Nest_Meshing_Factor(2) = 3, ! Cell size relative to master grid

Nest_Beg_I_Index(2) = 22, ! Relative to master grid

Nest_End_I_Index(2) = 51, ! Relative to master grid

Nest_Beg_J_Index(2) = 22, ! Relative to master grid

Nest_End_J_Index(2) = 58, ! Relative to master grid

!--- Model options ---

Diagnostic_Error_Check = .false., ! True = will stop after 1st timestep

Advection_Solver = 'PPM', ! (PPM,BOTT)

Chemistry_Solver = 'EBI', ! (EBI,LSODE)

PiG_Submodel = 'None', ! (None,GREASD,IRON)

Probing_Tool = 'None', ! (None,SA,DDM,HDDM,PA,IPR,IRR,RTRAC,RTCMC)

Chemistry = .true.,

Drydep_Model = ‘WESELY89’, ! (None, WESELY89, ZHANG03)

Wet_Deposition = .true.,

ACM2_Diffusion = .false.,

Surface_Model = .false.,

Super_Stepping = .true.,

Gridded_Emissions = .true.,

Point_Emissions = .true.,

Ignore_Emission_Dates = .true.,

!--- Output specifications ---

Root_Output_Name = '$OUTPUT/CAMx.$RUN.200206${CAL}',

Average_Output_3D = .false.,

Output_Species_Names(1) = 'NO',

Output_Species_Names(2) = 'NO2',

Output_Species_Names(3) = 'O3',

Output_Species_Names(4) = 'SO2',

Output_Species_Names(5) = 'H2O2',

Output_Species_Names(6) = 'HNO3',

Output_Species_Names(7) = 'NH3',

Output_Species_Names(8) = 'PNO3',

Output_Species_Names(9) = 'PSO4',

Output_Species_Names(10) = 'PNH4',

Output_Species_Names(11) = 'POA',

Figure2‐2(continued).

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Output_Species_Names(12) = 'PEC',

Output_Species_Names(13) = 'FPRM',

Output_Species_Names(14) = 'CPRM',

Output_Species_Names(15) = 'CCRS',

Output_Species_Names(16) = 'FCRS',

Output_Species_Names(17) = 'SOA1',

Output_Species_Names(18) = 'SOA2',

Output_Species_Names(19) = 'SOA3',

Output_Species_Names(20) = 'SOA4',

Output_Species_Names(21) = 'SOA5',

!--- Input files ---

Chemistry_Parameters = '$INPUT/CAMx6.3.chemparam.6_CF',

Photolysis_Rates = '$INPUT/tuv.200206.STL.txt',

Ozone_Column = '$INPUT/o3col.200206.STL_36_68X68_12_92X113.txt',

Initial_Conditions = '$INPUT/IC.vistas_2002gt2a_STL_36_68X68_16L.2002081',

Boundary_Conditions = '$INPUT/BC.vistas_2002gt2a_STL_36_68X68_16L.2002${JUL}',

Top_Concentrations = ' ',

Point_Sources = '$PTSRCE/ptsrce.stl.36km.2002${JUL}.a0.bin',

Master_Grid_Restart = '$OUTPUT/CAMx.$RUN.200206${YESTERDAY}.inst',

Nested_Grid_Restart = '$OUTPUT/CAMx.$RUN.200206${YESTERDAY}.finst',

PiG_Restart = ' ',

Srfmod_Grid(1) = ' ',

Srfmod_Grid(2) = ' ',

Flexi_Nest = .false.

Emiss_Grid(1) = '$EMIS/emiss.stl.36km.200206${CAL}.a1.bin',

Surface_Grid(1) = '$INPUT/met/camx.lu.36k.bin',

Met2D_Grid(1) = '$INPUT/met/camx.2d.200206${CAL}.36k.bin',

Met3D_Grid(1) = '$INPUT/met/camx.3d.200206${CAL}.36k.bin',

Vdiff_Grid(1) = '$INPUT/met/camx.kv.200206${CAL}.36k.bin',

Cloud_Grid(1) = '$INPUT/met/camx.cr.200206${CAL}.36k.bin',

Emiss_Grid(2) = '$EMIS/emiss.stl.12kmsmall.200206${CAL}.a1.bin',

Surface_Grid(2) = '$INPUT/met/camx.lu.12ksmall.bin',

Met2D_Grid(2) = '$INPUT/met/camx.2d.200206${CAL}.12ksmall.bin',

Met3D_Grid(2) = '$INPUT/met/camx.3d.200206${CAL}.12ksmall.bin',

Vdiff_Grid(2) = '$INPUT/met/camx.kv.200206${CAL}.12ksmall.bin',

Cloud_Grid(2) = '$INPUT/met/camx.cr.200206${CAL}.12ksmall.bin',

!-------------------------------------------------------------------------------

ieof

# --- Execute the model ---

if( ! { $EXEC } ) then

exit

endif

end

Figure2‐2(concluded).

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2.4BenchmarkingModelRunTimes

OverallmodelspeedandOMP/MPIscalabilitydependsonseveralfactors,includingthenumber

andsizesofgrids;thechoiceofchemistrymechanism;thenumberofpointsourcestobe

treatedwithPiGandtotalPiGpuffsthataccumulateduringarun;andtheuseofProbingTools.

Parallelizationismostadvantageousforlargerapplicationsinwhichoverheadprocesses(e.g.,

modelsetup,I/O,etc.)areamuchsmallerfractionoftotalmodelruntime.Inotherwords,

CAMxapplicationsonmultipleexpansivegrids,employingPiG,and/orincludingProbingTools

wouldscalemosteffectivelyandthusbenefitmostfromparallelization.

AsetofsystematicruntimetestswererecentlyconductedbytheLakeMichiganAirDirectors

Consortium(LADCo)usingCAMxv6.20withvariouscombinationsofOMPandMPI

parallelization.Notethatmodelspeedhasbeenimprovedsomewhatsincev6.20;however,

resultsfromLADCo’stestareinformative.LADCo’sCAMxconfigurationwasrelativelysimple,

employingasinglelargegridcoveringtheentireUSwith12kmgridspacing(396246,25

layers),andusingCB6r2photochemistrywiththeCFPMtreatment.PiGandProbingTools

werenotactive.CAMxwascompiledusingPortlandGroupv15.7‐0withOMPandMPICH

v3.1.4.CAMxwasrunona2.60GhzIntelXeonchipsetswith12physicalcores(24coreshyper‐

threaded).RuntimeresultsareshowninTable2‐3.



Table2‐3.CAMxv6.20speedperformancewithMPIandOMPparallelizationfromtheLADCo

testsdescribedabove.

OMPThreadsMPISlices TotalCores Hours/SimDay

12 012 4:05:12

12 224 3:30:47

8 324 2:59:08

6 424 2:36:10

4 624 2:35:17

3 824 2:27:34

2 12 24 2:25:25

1 24 24 3:06:57



2.5CAMxPre‐AndPost‐Processors

ThissectiondescribesseveralimportantCAMxpre‐andpost‐processorsthatwemakeavailable

totheusercommunity.LikeCAMxitself,theseprogramsarewritteninFortrananddistributed

asfreesoftwareunderthetermsoftheGNUGeneralPublicLicense.EachcomewithREADME

files,makefiles,andsamplejobscriptsthatdocumenttheirpurposeandusage.Ramboll

Environoccasionallypostsupdatesforcertainwidely‐usedprogramswhennecessary,butdoes

notactivelysupportormaintaineveryone.Userscane‐mailquestions,comments,suggestions

orimprovementstoask‐camx@environ.org.

2.5.1Emissions

Certainemissionmodels(thoseshowninFigure2‐1)canprovidespeciated,temporally‐

allocated,griddedandpointsourceemissioninputfilesintheCAMx‐readyformat.Further

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processingmayberequired,however,toselectpointsourcesforthePiGtreatment,translate

thepointsourcefilesfromacommontextformattoCAMx‐readybinaryfiles,ortorefinethe

domainsize/resolutionforgriddedemissions.

PIGSET:ThisprogramallowstheusertoselectandsetcertainpointsourcesforthePlume‐in‐

Grid(PiG)treatmentinaCAMxsimulation.Italsoconvertstextpointsourcefiles

commonlygeneratedbyemissionmodelssuchasSMOKE,CONCEPT,andEPS3to

CAMx‐readybinaryformat.Seethesourcecodeformoreinformation,andthesample

jobforusage.AlsoseeSection6forguidanceinselectingPiGpointsourcesand

manipulatingday‐specificpointsourcefiles.

WINDOW:Thisprogramisusedto“window”outasub‐sectionofthesurfaceemissionsgridfor

useonasmallerCAMxgrid.Itcanalsobeusedtoaggregateordistributesurface

emissionstocoarserorfinerresolution,respectively.Seethesamplejobforusage.

SEASALT:Thisprogramgeneratesaerosolemissionsofsodiumandchloride,andgaseous

emissionsofchlorineandhalo‐methanecompounds,usingCAMx‐readymeteorological

andlandusefiles.Aseparatemergingprogramisincludedthatallowsseasalt

emissionstobemergedinwithpre‐existingCAMx‐readygriddedemissionfiles.

PREPVBS:Thisprogramconvertstheorganiccompoundemissions(VOCprecursorsandPOA)

preparedfortheCAMxCFaerosolschemetothosecompatiblewiththeVBSschemeso

thattheusercanemploytheVBSschemewithouthavingtodevelopemissioninputsfor

theschemefromscratch.However,thisapproachshouldbeusedwithcautionbecause

significantuncertaintiesexistintheVBSemissionsestimatedbythis.Seethesamplejob

forusage.

REGNMAP:Thisprogramsupportsthedevelopmentofsourceapportionmentfractional

(partial)regionmapswithwhichtoallocategriddedemissionstosourceregions.It

readsSMOKEspatialallocationreportsforaspecificmodelinggridandsourcecategory

(orgroupofcategories),extractsemissionsdatabygridcellandstate/countyFIPScode,

andgeneratesanewCAMxinputfilethatdefinesafractionalregionmapforthatgrid

andsourcecategory/group.

2.5.2Meteorology

TherecommendedapproachtodevelopmeteorologicalinputsforCAMxisthroughtheuseof

prognosticmeteorologicalmodels.RambollEnvirondistributesinterfaceprogramsforthree

specificmodels:WRF,MM5,andRAMS;Thisdoesnotnecessarilyprecludeother

meteorologicalmodelstobeused,butuserswillneedtodevelopinterfaceprogramsontheir

own.

WRFCAMx:ThisprogramgeneratesCAMxv6meteorologicalinputfilesfromWRF(ARWcore)

v3outputfiles.SeetheREADMEinthearchiveforadescriptionoftheprogramand

howitisapplied.YouwillneedNetCDFlibrariestocompileandrunthisprogram.

MM5CAMx:ThisprogramgeneratesCAMxv6meteorologicalinputfilesfromMM5v3output

files.SeetheREADMEinthearchiveforadescriptionoftheprogramandhowitis

applied.

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RAMSCAMx:ThisprogramgeneratesCAMxv6meteorologicalinputfilesfromRAMSv4/5/6

outputfiles.SeetheREADMEinthearchiveforadescriptionoftheprogramandhowit

isapplied.YouwillneedHDF5libariestocompileandrunthisprogram.

METCONVERT:ThisprogramconvertsoldermeteorologicalfilesfromCAMxv4andv5tothe

CAMxformatintroducedwithCAMxv6.

KVPATCH:Thisprogramappliesminimumlimitsonverticaldiffusivity(Kv)withinauser‐defined

surfacelayerdepthbasedonaninputlandusegrid.ItoptionallyallowsKvprofilestobe

extendedintodaytimeboundary‐layercappingconvectionasdefinedbyinput

cloud/rainfiles.Seethesourcecodeformoreinformation.Useofthisprogramto

adjustKvinputsisentirelyoptional.

2.5.3PhotolysisRates

ThedevelopmentofphotolysisrateinputsforCAMxiscrucialforthephotochemical

mechanisms,butisnotneededforinertorsimplechemistry(e.g.,Mechanism10)applications.

Twoprogramsareavailabletoassisttheuserindevelopingphotolysisandozonecolumninput

files.

O3MAP:ThisprogrampreparesozonecolumninputfilesforCAMx,andmustberunpriorto

runningtheTUVmodelasitdefinestheatmosphericozonecolumnintervalsbasedon

inputdata.Ozonecolumndatafiles(http://ozoneaq.gsfc.nasa.gov/data/ozoneor

ftp://toms.gsfc.nasa.gov/pub/omi/data/)inlatitude/longitudetextformatmustbe

suppliedasinput.O3MAPattemptstofilldatagapsinday‐specificozonecolumnfiles

(Figure2‐3)withanaveragedeterminedfromvaliddataprocessedfortheextraction

domain.Alternatively,youmayusemonthly‐averageozonecolumnfiles(nodata

gaps).SeetheReadmefileandjobscriptinthearchiveforusage.



Figure2‐3.AnexampleofglobalozonecolumnfromtheOzoneMonitoringInstrument(OMI)

platform.Whiteareasdenotemissingdata.Fromftp://toms.gsfc.nasa.gov/pub/omi/data/.

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TUV:Thisisaradiativetransfermodelthatdevelopsclear‐skyphotolysisrateinputsforall

CAMxphotochemicalmechanisms.TUVisdevelopedanddistributedbyNCAR(2011).

Theprogramspecifiesdefaultintervalsfor5surfaceUValbedos,3terrainheights,11

altitudesaboveground,10solarzenithangles,and5atmosphericozonecolumn

intervals(fromO3MAP).Seethesamplejobinthearchiveforusage.

2.5.4InitialandBoundaryConditions

RambollEnvironprovidesafewprogramstodevelopinitialandboundaryconditions,butthere

aremanywaystogeneratetheseimportantinputs.Themostcommonapproachinvolves

“down‐scaling”(orextracting)theoutputfromlarger‐scale(e.g.,global)modelstotheCAMx

domain.Userswillneedtodeveloptheirownprogramsiftheychooseanalternative

methodologyorsourceofdatatogenerateinitial/boundaryconditions.

ICBCPREP:ThisprogrampreparessimpleCAMxinitialandlateralboundaryconditionfiles.

Valuesareconstantinspaceandtime,butuniquevaluesmaybespecifiedforeach

chemicalspeciestobemodeled;theyaredefinedinatextfile.Seethesamplejobin

thearchiveforusage.

GEOS2CAMx:ThisprogramgeneratesCAMxinitial,lateralboundary,and(optionally)top

boundaryconditioninputfilesfromGEOS‐Chemglobalmodeloutput.SeetheRelease

Notesandjobscriptsinthearchiveforadescriptionoftheprogramandhowitis

applied.

MOZART2CAMx:ThisprogramgeneratesCAMxandCMAQinitialandlateralboundary

conditioninputfilesfromMOZART4output.ThisprogramwillalsoprocessAM3

datasetsifoutputisfirsttranslatedtoageodetic(latitude/longitude)grid,

concentrationsareprovidedasvolumemixingratio,andallneededstatevariablesare

available.SeetheREADMEinthearchiveforadescriptionoftheprogramandhowitis

applied.YouwillneedI/O‐APIandNetCDFlibrariestocompileandrunthisprogram.

2.5.5Landuse

Approachesfordevelopinglanduse/landcoverinputsforCAMxinclude:(1)translatinggridded

spatialallocationsurrogatesdevelopedduringemissionsprocessingintotheCAMxcategories

describedinSection3;(2)translatingthegriddedlanduse/landcoverfieldsfromthe

meteorologicalmodel;or(3)separatelydevelopinglanduseinputfieldsfromrawdata(suchas

fromUSGS,MODISorNLCD)usingGISorotherprograms.RambollEnvirondistributes

meteorologicalinterfaceprograms(describedabove)thattranslatethemeteorologicalmodel

landuse/landcoverfieldstotheCAMxdefinitionsandgridconfiguration.

MERGE_LULAI:Thisprogrammergesindependently‐developedlanduseand/orLAIfields(for

exampleviaGISprocessingofcommonterrestrialdatasets)withanexistingCAMx2D

surfacefilegeneratedbythemeteorologicalinterfaceprograms.Seethesamplejob

andsourcecodeforadescriptionoftheprogramandhowitisapplied.

March2016CAMxUser’sGuideVersion6.3

2.TheCAMxModelingSystem



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 28www.camx.com



2.5.6Post‐processors

MostoftheCAMxpost‐processorsdistributedbyRambollEnvironprovidesomemannerof

concentrationfilemanipulation,eithertoextractcertaininformationfromtherawoutputfiles,

tore‐formatforuseinotherprogramsandapplications,toconcatenatefiles,etc.Afewothers

aredistributedtoassistinevaluatingProbingTooloutput.RambollEnvirondoesnotadvocate

orsupportanyparticularvisualizationorgraphicssoftware.

AVGDIF:ThisprogramisusedtocomparetwoCAMxformatoutputaveragefilesandprinta

tableofdifferences.ThisisusefulforcheckingdifferencesbetweenCAMxrunson

differentmachinesordifferentcompileoptionsforthetestcase.Seethesamplejobin

thearchiveforusage.

BNDEXTR:Usethisprogramtoextractboundaryconditionsforanestedgridwhenyouapply

CAMxinone‐waynestingmode.One‐waynestingmeansthatCAMxisrunsuccessively

foreachgrid,withBNDEXTRastheinterfacebetweeneachrun.Thisprogramisnot

neededwhenCAMxisruninthemorestandardtwo‐waynestingmode,whereallgrids

areruninasinglesimulation.Seetheexamplejobforusage.

CAMxPOST:Thisisasuiteofpost‐processingutilitiesdesignedtofacilitatetheevaluationof

modelperformance.Itisusedtocombineobservationsandpredictions,calculate

statistics,andplottimeseries.SeetheREADMEfileinthearchiveforusage.

CAMxTRCT:Thisprogramextractsasinglechemicalspeciesforspecifiedgridsfromtheoutput

averageconcentrationanddepositionfiles,andfrominputemissionfiles.Outputfrom

thisprogramcanbewritteninthestandardCAMxformat,oralternativelytoatext

formatinSurfer®“GRD”formatforsubsequentplotting.Italsohasthecapabilityto

convertunitsandcombinespeciestoyieldcertainhard‐codedbulkcompoundslike

NOxandVOC.Seethesamplejobinthearchiveforusage.

CAMx2IOAPI:ThisprogramconvertsCAMxoutputaverageconcentrationanddepositionfiles

toI/O‐APIformat.YouwillneedI/O‐APIandNetCDFlibrariestocompileandrunthis

program.Thisprogramallowsyoutousevariousthird‐partymanipulationand

visualizationsoftwarethathandleI/O‐APIandNetCDFformats.

PA_Tools:Thisisasuiteofpost‐processingutilitiesdesignedtoextractIPR,IRR,andCPAdata

fromCAMxProcessAnalysisoutputfilesandreformatthedatasuitableforsubsequent

analysis(e.g.usingspreadsheets).

XSPCMAP:SimilartoCAMxTRCTyetmoreflexible,thisprogramextractsanynumberofspecific

chemicalspeciesoruser‐definedcombinationsofspeciesforspecifiedgridsfromthe

outputaverageconcentrationanddepositionfiles,andwritesresultstoanewfilein

CAMxformat.Seethesamplejobandspeciesmappingtableinthearchiveforusage.



March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 29www.camx.com

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3.COREMODELINPUT/OUTPUTSTRUCTURES

MostCAMxinput/output(I/O)filesareFortranbinaryandbasedontheUrbanAirshedModel

(UAM)convention.Thisallowstheusertoemploywidelyavailablesoftwaredesigned

specificallyfortheseformatstodeveloptheinputfilesortopost‐processandvisualizethe

outputfiles.

CAMxrequiresinputfilesthatdefinethechemicalmechanismanddescribethephotochemical

conditions,surfacecharacteristics,initial/boundaryconditions,emissionrates,andvarious

meteorologicalfieldsovertheentiremodelingdomain.Table3‐1summarizestheinputdata

requirementsofCAMx.Preparingthisinformationrequiresseveralpreprocessingstepsto

translate“raw”emissions,meteorological,airqualityandotherdataintofinalinputfilesfor

CAMx.Prognosticmeteorologicalmodelsareusedtogeneratealloftherequiredtimevarying

three‐dimensionalmeteorologicalfields.



Table3‐1.DatarequirementsofCAMx.

DataTypesDataFields

Meteorology

SuppliedbyPrognosticMeteorologicalModels



3‐DimensionalGriddedFields:

‐VerticalGridStructure

‐HorizontalWindComponents

‐Temperature

‐Pressure

‐WaterVapor

‐VerticalDiffusivity

‐Clouds/Precipitation(optional)

‐SnowCover(optional)

AirQuality

DevelopedfromOtherModelsorMeasurementData



GriddedInitialConcentrations

 GriddedLateralBoundaryConcentrations

 GriddedTopBoundaryConcentrations(optional)

Emissions

SuppliedbyEmissionsModelsandProcessors



ElevatedPointSources(optional),e.g.:

‐IndustrialFacilities

‐Prescribed,Agricultural,WildFires

‐LightningNOx

 CombinedGriddedSources(optional),e.g.:

‐Low‐LevelPoint

‐On‐RoadandNon‐RoadMobile

‐Area

‐Biogenic

‐Oceanic

Geographic

DevelopedfromTerrain,Landuse/Landcover,and

VegetationDensityDatasets



GriddedSurfaceCharacteristics

‐Landuse/LandCover

‐TerrainElevation(optional)

‐LeafAreaIndex(LAI;optional)

‐Land/OceanMask(optional)

Photolysis

DerivedfromSatelliteMeasurementsandRadiative

TransferModels



AtmosphericRadiativeProperties

‐GriddedOzoneColumnCodes

‐PhotolysisRatesLookupTable

March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 30www.camx.com



CAMxproducesgriddedtime‐averagedconcentrationoutputfiles;theuserselectsthetime

interval(usuallyhourly),thespeciestobeoutput,andwhethertheoutputcontainsjusttwo‐

dimensionalsurfacelayerfieldsorentirethree‐dimensionalfields.Aseparateaverageoutput

fileiswrittenforeachgridemployedinthesimulation.Two‐dimensionalsurfacedeposition

fieldsforthesameuser‐selectedspeciesarealsowrittentooutputfileswiththesamestructure

astheaverageconcentrationfiles.Griddedthree‐dimensionalinstantaneousconcentrationsof

allspeciesonallgridsarewrittenattheendofthesimulationtoallowforamodelrestart.The

CAMxProbingTooloptionsprovidetheirowninformationinseparateoutputfilesinthesame

CAMxoutputformat.Diagnosticoutputfilesincludethreefilesthattrackcomputerresources,

echoinputselections,providemassbudgetanddiagnosticsummaries,andprovide

error/warningmessages.

3.1CAMxChemistryParametersFile

Chemistryparametersareprovidedinatextfilethatspecifiesthechemicalmechanismbeused

andassociateddetailsonspeciespropertiesandreactiontypesandrates.Thechemistry

parametersfileformatisdefinedinTable3‐2,andsamplesaregiveninFigure3‐1.Some

recordsinthisfilearelabeled(columns1‐20)toindicatethetypeofinformationtosupplyon

thatline(startingincolumn21).Forrecordsthatarenotlabeled,datastartincolumn1.Some

chemistryparameterrecordsareoptional,dependinguponthelogicalflagsindicatedforsuch

records,andareshowninTable3‐2byacheckinthethirdcolumn;iftheindicatedoptionisnot

invokedtheserecordsshouldnotappearinthefile.Thefirstrecordofthechemistry

parametersfilemustcontainthestring“VERSION6.3”,whichindicatesthatthefileisspecific

tothisversionofCAMx.

Ifthechemistryflagisset“true”ontheCAMx.infile,CAMxchecksthatcertainpropertiesof

theselectedmechanismareconsistentwithparameterssuppliedontheinputfile(e.g.,number

ofreactions,photolysisreactionsandspecies).Ifanydiscrepanciesarefound,theyare

reportedintheoutputmessagefileandthesimulationishalted.Theusermayalsospecifyan

inertsimulationbysettingthechemistryflagto“false”.Inthiscase,anynumberofarbitrarily

namedspeciesmaybelisted,andchemistryreactionparametersareignored.

Gas‐phasechemistryisselectedbyaMechanismIDassignedtoeachphotochemical

mechanism(seeSection5).Aerosolchemistryisselectedbythekeywords“NONE”,“INERT”,

“CF”or“CMU”.Inthe“INERT”case,theusercandefineanynumberofarbitraryparticulate

namesandsizes.The“CF”and“CMU”optionsinvokeaerosolchemistryandtreataerosolsize

usingeitherstaticcoarseandfinemodes(CF)oranevolvingsizesectionmodel(CMU).BothCF

andCMUoptionsrequireaminimumsetofspecificaerosolnameswithassociatedchemistry.

ThechemistryparametersfilecontrolshowphotolysisratesarecalculatedinCAMx.So‐called

“primary”photolysisratesareinputtoCAMxviathephotolysisratesfile.Theprimary

photolysisreactionsareidentifiedbynumberinthechemistryparametersfileandthe

photolysisratesfilemustmatchthisdeclaration.So‐called“secondary”photolysisratesareset

byscalingfactorstooneoftheprimaryreactions.Useofsecondaryratesrequiresatleastone

primaryphotolysisreaction.

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Table3‐2.DescriptionoftheCAMxchemistryparametersfile.Therecordlabelsexistincolumns1‐20,andwheregiven,the

inputdataforthatrecordstartincolumn21.Theformatdenoted“list”indicatesafree‐formatlistofnumbers(commaorspace‐

delimited).

RecordLabel

(columns1‐20)

Record

OptionalFormatDescription

CAMx version AModelversionkeyword(VERSION6.3)

Mechanism ID list IDnumberofchemicalmechanism(seeTable5‐1)

Aerosol Option AKeywordforaerosolscheme(NONE,INERT,CF,orCMU)1

Description AMessagerecordtodescribethisfile

No of gas species list Numberofradicalandstategasspecies(NGAS≥1)

No of aero species list

Numberofaerosolspecies(NAERO≥0)

Aerosolchemistrytimestep(min)(ifNAERO>0)

Numberofsizebins(NBIN≥1)(ifNAERO>0)2

Aerosoldiameter(m)forNBIN+1cutpoints(ifNAERO>0)

No of reactions list Numberofreactions(NREACT≥0)

Prim photo rxns listNumberofprimaryphotolysisreactions(NPHOT1≥0)

ListofprimaryphotolysisreactionIDnumbers(mustmatchthephotolysisratesinputfile)

No of sec photo rxn list Numberofsecondaryphotolysisreactions(NPHOT2≥0)

ID, prim ID, scale  

list

IfNPHOT2>0,repeatthisrecordforeachsecondaryphotolysisreaction

IDnumberofthesecondaryphotolysisreaction

IDnumberoftheprimaryphotolysisreactionusedforscaling

Secondaryreactionscalefactor

SrfMod #spc, #rxns listNumberofSurfaceModelspeciesandreactions(seeSection4.8)

Setto0,0ifnotusingtheSurfaceModel

Species Records Heading

Gas Spec ... Heading

5X,

A10,

E10.0,

F10.0,

F10.0

F10.0

Repeatthisrecordforeachgasspecies(startincolumn1)

Gasspeciesname(radicalsfirst,followedbystatespecies)

Lowerboundconcentration(ppm)

Henry’slawconstant(M/atm)

Henry’slawtemperaturedependence(K)

Molecularweight(g/mol)

Wesley’sreactivityparameter

Surfaceresistancescalingfactorforstrongacids(0‐1)

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Table3‐2(continued).DescriptionoftheCAMxchemistryparametersfile.Therecordlabelsexistincolumns1‐20,andwhere

given,theinputdataforthatrecordstartincolumn21.Theformatdenoted“list”indicatesafree‐formatlistofnumbers(comma

orspace‐delimited).

RecordLabel

(columns1‐20)

Record

OptionalFormatDescription

Aero Spec ...  Heading(ifNAERO>

)



5X,

A10,

E10.0,

F10.0

I10

F10.0

I10

IfNAERO>0,repeatthisrecordforeachaerosolspecies(startincolumn1)

Aerosolspeciesname

Lowerboundconcentration(g/m3)

Speciesdensity(g/cm3)

Dryextinctionefficiency(m2/m)

Hygroscopicextinctionadjustment(0=noadjustment,1=RH‐dependent)

Single‐scatteringalbedo

Assignedsizebin(INERTandCFaerosolsonly

–

referencescutpointsinrecord6)

Reaction Records  Heading(ifNREACT>

)

Rxn Typ Param ...  Heading(ifNREACT>

)





list



IfNREACT>0,repeatthisrecordforeachgas‐phasereaction(startincolumn1)

ReactionIDnumber

RateconstantexpressionIDnumber(1‐7,asshowninTable3‐3)

Rateconstantparameters(dependingonexpressiontypeinTable3‐3).Forreactionsidentifiedas

photolysisreactionsabove,therate constantisnotusedandiscustomarilysettozero.

1NONE=gas‐phasechemistryonly;INERT=user‐definedinertPMspecies;CF=Coarse/Fineaerosolchemistryscheme;CMU=multi‐sectionalaerosolchemistryscheme;.

2FortheCFscheme,NBINmustbesetto2,andtheuserspecifiesthecoarse/finesizeranges.



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CAMx Version |VERSION6.3

Mechanism ID |6

Aerosol Option |CF

Description |CB05 plus PM (CF) with Hg: PNA rates set to 0; molecular units

No of gas species |68

#aero, dt, bins |25 15.0 2 0.039 2.5 10.0

No of reactions |156

Prim photo rxns |19 1 8 9 14 15 25 36 51 52 53 62 65 75 76 87 91 102 143 152

No of sec photo rxn|4

ID, prim ID, scale |72 65 1.0

|97 65 0.0

|106 91 1.0

|138 75 9.0

SrfMod #spc, #rxns |0 0

Species Records

Gas Spec lower bnd H-law T-fact Molwt Reactvty Rscale

1 O1D 1.00E-15 1.00E+00 0. 0.0 0.0 0.

2 O 1.00E-15 1.00E+00 0. 0.0 0.0 0.

3 OH 1.00E-15 1.00E+00 0. 0.0 0.0 0.

4 HO2 1.00E-15 1.00E+00 0. 0.0 0.0 0.

5 C2O3 1.00E-15 1.00E+00 0. 0.0 0.0 0.

6 XO2 1.00E-15 1.00E+00 0. 0.0 0.0 0.

7 XO2N 1.00E-15 1.00E+00 0. 0.0 0.0 0.

8 CXO3 1.00E-15 1.00E+00 0. 0.0 0.0 0.

9 MEO2 1.00E-15 1.00E+00 0. 0.0 0.0 0.

10 TO2 1.00E-15 1.00E+00 0. 0.0 0.0 0.

11 ROR 1.00E-15 1.00E+00 0. 0.0 0.0 0.

12 HCO3 1.00E-15 1.00E+00 0. 0.0 0.0 0.

13 CRO 1.00E-15 1.00E+00 0. 0.0 0.0 0.

14 AACD 1.00E-12 5.00E+03 -4000. 60.0 1.0 1.

15 ALD2 1.00E-12 6.30E+03 -6492. 44.0 1.0 1.

16 ALDX 1.00E-12 6.30E+03 -6492. 58.1 1.0 1.

17 CO 1.00E-04 1.00E-10 0. 28.0 0.0 1.

18 CRES 1.00E-12 2.70E+03 -6492. 108.1 1.0 1.

19 ETH 1.00E-12 1.00E-02 -4000. 28.0 0.0 1.

20 ETHA 1.00E-04 1.73E-03 -4000. 30.1 0.0 1.

21 ETOH 1.00E-12 2.20E+02 -4932. 46.1 1.0 1.

22 FACD 1.00E-12 5.68E+03 -6060. 46.0 1.0 1.

23 FORM 1.00E-12 6.30E+03 -6492. 30.0 1.0 1.

24 H2O2 1.00E-12 7.40E+04 -6643. 34.0 1.0 0.

25 HNO3 1.00E-12 2.10E+05 -8707. 63.0 0.0 0.

26 HONO 1.00E-12 5.90E+01 -4781. 47.0 1.0 1.

27 IOLE 1.00E-12 5.00E-03 -4000. 56.1 0.0 1.

28 ISOP 1.00E-12 1.00E-02 -4000. 68.1 0.0 1.

29 ISPD 1.00E-12 6.30E+03 -6492. 70.1 1.0 1.

30 MEOH 1.00E-12 2.20E+02 -4932. 32.0 1.0 1.

31 MEPX 1.00E-12 3.05E+02 -5250. 48.0 0.8 0.

32 MGLY 1.00E-12 2.70E+03 -6492. 72.0 1.0 1.

33 N2O5 1.00E-12 1.00E+05 -4000. 108.0 0.1 0.

34 NO 1.00E-09 1.90E-03 -1480. 30.0 0.0 1.

35 NO2 1.00E-12 1.00E-02 -2516. 46.0 0.8 1.

36 NO3 1.00E-15 1.00E+05 -4000. 62.0 0.1 0.

37 NTR 1.00E-12 9.40E+03 -8706. 119.1 0.0 1.

38 O3 1.00E-12 1.10E-02 -2415. 48.0 1.0 1.

39 OLE 1.00E-12 5.00E-03 -4000. 42.1 0.0 1.

40 OPEN 1.00E-12 2.70E+03 -6492. 84.0 1.0 1.

41 PACD 1.00E-12 5.00E+03 -4000. 76.0 1.0 1.

42 PAN 1.00E-12 3.60E+00 -5910. 121.0 0.6 1.

43 PANX 1.00E-12 3.60E+00 -5910. 135.0 0.6 1.

44 PAR 1.00E-04 1.00E-03 -4000. 72.1 0.0 1.

45 PNA 1.00E-12 2.00E+04 -5910. 79.0 1.0 1.

Figure3‐1a.ExampleCAMxchemistryparametersfileforMechanism6(CB05)withCFPM

schemethatincludesthemercuryspeciesHG0,HG2,andHGP.

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46 ROOH 1.00E-12 1.00E+02 -4000. 90.1 0.8 0.

47 SO2 1.00E-09 1.22E+00 -3156. 64.0 0.0 1.

48 SULF 1.00E-12 1.00E+10 0. 98.0 0.0 0.

49 TERP 1.00E-12 4.90E-02 -4000. 136.2 0.0 1.

50 TOL 1.00E-12 1.20E+00 -4000. 92.1 0.0 1.

51 XYL 1.00E-12 1.40E+00 -4000. 106.2 0.0 1.

52 NH3 1.00E-09 5.76E+01 -4100. 17.0 0.0 0.

53 HCL 1.00E-12 1.00E+05 -4000. 36.5 0.0 0.

54 TOLA 1.00E-12 1.20E+00 -4000. 92.0 0.0 1.

55 XYLA 1.00E-12 1.40E+00 -4000. 106.0 0.0 1.

56 BNZA 1.00E-12 1.80E-01 -4000. 78.0 0.0 1.

57 ISP 1.00E-12 1.00E-02 -4000. 68.0 0.0 1.

58 TRP 1.00E-12 4.90E-02 -4000. 136.0 0.0 1.

59 SQT 1.00E-12 4.90E-02 -4000. 204.0 0.0 1.

60 CG1 1.00E-12 1.00E+05 -4000. 150.0 0.0 1.

61 CG2 1.00E-12 1.00E+05 -4000. 150.0 0.0 1.

62 CG3 1.00E-12 1.00E+05 -4000. 130.0 0.0 1.

63 CG4 1.00E-12 1.00E+05 -4000. 130.0 0.0 1.

64 CG5 1.00E-12 1.00E+05 -4000. 180.0 0.0 1.

65 CG6 1.00E-12 1.00E+05 -4000. 180.0 0.0 1.

66 CG7 1.00E-12 1.00E+05 -4000. 210.0 0.0 1.

67 HG0 1.00E-12 1.11E-01 -4970. 200.6 0.0 1.

68 HG2 1.00E-12 2.00E+05 -4000. 253.1 0.0 0.

Aero Spec lower bnd Density Dry Bext RH Adjust SSA SizeBin

1 PNO3 1.00E-09 1.5 7.0 1 0.99 1

2 PSO4 1.00E-09 1.5 7.0 1 0.99 1

3 PNH4 1.00E-09 1.5 7.0 1 0.99 1

4 POA 1.00E-09 1.0 7.0 0 0.80 1

5 SOA1 1.00E-09 1.0 7.0 0 0.80 1

6 SOA2 1.00E-09 1.0 7.0 0 0.80 1

7 SOA3 1.00E-09 1.0 7.0 0 0.80 1

8 SOA4 1.00E-09 1.0 7.0 0 0.80 1

9 SOA5 1.00E-09 1.0 7.0 0 0.80 1

10 SOA6 1.00E-09 1.0 7.0 0 0.80 1

11 SOA7 1.00E-09 1.0 7.0 0 0.80 1

12 SOAH 1.00E-09 1.0 7.0 0 0.80 1

13 SOPA 1.00E-09 1.0 7.0 0 0.80 1

14 SOPB 1.00E-09 1.0 7.0 0 0.80 1

15 PEC 1.00E-09 2.0 18.0 0 0.25 1

16 FPRM 1.00E-09 3.0 0.4 0 0.70 1

17 FCRS 1.00E-09 3.0 0.4 0 0.70 1

18 CPRM 1.00E-09 3.0 0.4 0 0.70 2

19 CCRS 1.00E-09 3.0 0.4 0 0.70 2

20 NA 1.00E-09 2.0 1.5 1 0.99 1

21 PCL 1.00E-09 2.0 1.5 1 0.99 1

22 PH2O 1.00E-09 1.0 0.0 0 0.99 1

23 HGP 1.00E-15 8.0 0.0 0 0.99 1

24 HGIIP 1.00E-20 8.0 0.0 0 0.99 1

25 HGIIPC 1.00E-20 8.0 0.0 0 0.99 2

Reaction Records

Rxn Typ Order Parameters (1 to 12, depending upon Typ)

1 1 1 0.000E+00

2 3 3 6.000E-34 0.0 -2.40 300.0

3 3 2 3.000E-12 1500.0 0.00 300.0

4 3 2 5.600E-12 -180.0 0.00 300.0

5 4 2 2.500E-31 0.0 -1.80 300.0 2.200E-11 0.0 -

0.70 300.0 0.60 1.00

6 4 2 9.000E-32 0.0 -1.50 300.0 3.000E-11 0.0 0.00

300.0 0.60 1.00

7 3 2 1.200E-13 2450.0 0.00 300.0

8 1 1 0.000E+00

Figure3‐1a(continued).

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9 1 1 0.000E+00

10 3 2 2.100E-11 -102.0 0.00 300.0

11 1 2 2.200E-10

12 3 2 1.700E-12 940.0 0.00 300.0

13 3 2 1.000E-14 490.0 0.00 300.0

14 1 1 0.000E+00

15 1 1 0.000E+00

16 3 2 1.500E-11 -170.0 0.00 300.0

17 3 2 4.500E-14 1260.0 0.00 300.0

18 4 2 2.000E-30 0.0 -4.40 300.0 1.400E-12 0.0 -

0.70 300.0 0.60 1.00

19 1 2 2.500E-22

20 1 3 1.800E-39

21 4 1 1.000E-03 11000.0 -3.50 300.0 9.700E+14 11080.0 0.10

300.0 0.45 1.00

22 3 3 3.300E-39 -530.0 0.00 300.0

23 1 3 5.000E-40

24 4 2 7.000E-31 0.0 -2.60 300.0 3.600E-11 0.0 -

0.10 300.0 0.60 1.00

25 1 1 0.000E+00

26 3 2 1.800E-11 390.0 0.00 300.0

27 1 2 1.000E-20

28 4 2 2.000E-30 0.0 -3.00 300.0 2.500E-11 0.0 0.00

300.0 0.60 1.00

29 6 2 2.400E-14 -460.0 0.00 300.0 2.700E-17 -2199.0 0.00

300.0 6.500E-34 -1335.0 0.00 300.0

30 3 2 3.500E-12 -250.0 0.00 300.0

31 1 2 0.000E+00

32 1 1 0.000E+00

33 1 2 0.000E+00

34 7 2 2.300E-13 -600.0 0.00 300.0 1.700E-33 -1000.0 0.00

300.0

35 7 3 3.220E-34 -2800.0 0.00 300.0 2.380E-54 -3200.0 0.00

300.0

36 1 1 0.000E+00

37 3 2 2.900E-12 160.0 0.00 300.0

38 1 2 1.100E-10

39 3 2 5.500E-12 2000.0 0.00 300.0

40 3 2 2.200E-11 -120.0 0.00 300.0

41 3 2 4.200E-12 240.0 0.00 300.0

42 4 2 6.900E-31 0.0 -1.00 300.0 2.600E-11 0.0 0.00

300.0 0.60 1.00

43 3 2 4.800E-11 -250.0 0.00 300.0

44 3 2 3.000E-11 -200.0 0.00 300.0

45 3 2 1.400E-12 2000.0 0.00 300.0

46 1 2 1.000E-11

47 1 2 2.200E-11

48 1 2 3.500E-12

49 1 2 1.000E-17

50 3 2 8.500E-13 2450.0 0.00 300.0

51 1 1 0.000E+00

52 1 1 0.000E+00

53 1 1 0.000E+00

54 3 2 2.600E-12 -365.0 0.00 300.0

55 3 2 2.600E-12 -365.0 0.00 300.0

56 3 2 7.500E-13 -700.0 0.00 300.0

57 3 2 7.500E-13 -700.0 0.00 300.0

58 1 2 6.800E-14

59 1 2 6.800E-14

60 1 2 6.800E-14

61 3 2 5.900E-13 360.0 0.00 300.0

Figure3‐1a(continued).

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62 1 1 0.000E+00

63 4 2 3.000E-31 0.0 -3.30 300.0 1.500E-12 0.0 0.00

300.0 0.60 1.00

64 3 2 3.010E-12 -190.0 0.00 300.0

65 1 1 0.000E+00

66 7 2 1.440E-13 0.0 0.00 300.0 3.430E-33 0.0 0.00

300.0

67 3 2 2.450E-12 1775.0 0.00 300.0

68 3 2 2.800E-12 -300.0 0.00 300.0

69 3 2 4.100E-13 -750.0 0.00 300.0

70 3 2 9.500E-14 -390.0 0.00 300.0

71 3 2 3.800E-12 -200.0 0.00 300.0

72 1 1 0.000E+00

73 3 2 7.300E-12 620.0 0.00 300.0

74 1 2 9.000E-12

75 1 1 0.000E+00

76 1 1 0.000E+00

77 3 2 3.400E-11 1600.0 0.00 300.0

78 1 2 5.800E-16

79 3 2 9.700E-15 -625.0 0.00 300.0

80 3 1 2.400E+12 7000.0 0.00 300.0

81 1 2 5.600E-12

82 3 2 5.600E-15 -2300.0 0.00 300.0

83 1 2 4.000E-13

84 3 2 1.800E-11 1100.0 0.00 300.0

85 3 2 5.600E-12 -270.0 0.00 300.0

86 3 2 1.400E-12 1900.0 0.00 300.0

87 1 1 0.000E+00

88 3 2 8.100E-12 -270.0 0.00 300.0

89 4 2 2.700E-28 0.0 -7.10 300.0 1.200E-11 0.0 -

0.90 300.0 0.30 1.00

90 4 1 4.900E-03 12100.0 0.00 300.0 5.400E+16 13830.0 0.00

300.0 0.30 1.00

91 1 1 0.000E+00

92 3 2 4.300E-13 -1040.0 0.00 300.0

93 3 2 2.000E-12 -500.0 0.00 300.0

94 3 2 4.400E-13 -1070.0 0.00 300.0

95 3 2 2.900E-12 -500.0 0.00 300.0

96 3 2 4.000E-13 -200.0 0.00 300.0

97 1 1 0.000E+00

98 3 2 4.000E-13 -200.0 0.00 300.0

99 3 2 1.300E-11 870.0 0.00 300.0

100 3 2 5.100E-12 -405.0 0.00 300.0

101 1 2 6.500E-15

102 1 1 0.000E+00

103 3 2 6.700E-12 -340.0 0.00 300.0

104 4 2 2.700E-28 0.0 -7.10 300.0 1.200E-11 0.0 -

0.90 300.0 0.30 1.00

105 4 1 4.900E-03 12100.0 0.00 300.0 5.400E+16 13830.0 0.00

300.0 0.30 1.00

106 1 1 0.000E+00

107 1 2 3.000E-13

108 3 2 4.300E-13 -1040.0 0.00 300.0

109 3 2 2.000E-12 -500.0 0.00 300.0

110 3 2 4.400E-13 -1070.0 0.00 300.0

111 3 2 2.900E-12 -500.0 0.00 300.0

112 3 2 2.900E-12 -500.0 0.00 300.0

113 3 2 8.700E-12 1070.0 0.00 300.0

114 3 2 6.900E-12 230.0 0.00 300.0

115 1 2 8.100E-13

116 3 1 1.000E+15 8000.0 0.00 300.0

Figure3‐1a(continued).

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3.CoreModelInput/OutputStructures

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

117 1 1 1.600E+03

118 1 2 1.500E-11

119 3 2 1.000E-11 280.0 0.00 300.0

120 1 2 3.200E-11

121 3 2 6.500E-15 1900.0 0.00 300.0

122 3 2 7.000E-13 2160.0 0.00 300.0

123 3 2 1.040E-11 792.0 0.00 300.0

124 4 2 1.000E-28 0.0 -0.80 300.0 8.800E-12 0.0 0.00

300.0 0.60 1.00

125 3 2 1.200E-14 2630.0 0.00 300.0

126 3 2 3.300E-12 2880.0 0.00 300.0

127 1 2 2.300E-11

128 3 2 1.000E-11 -550.0 0.00 300.0

129 3 2 8.400E-15 1100.0 0.00 300.0

130 3 2 9.600E-13 270.0 0.00 300.0

131 3 2 1.800E-12 -355.0 0.00 300.0

132 1 2 8.100E-12

133 1 1 4.200E+00

134 1 2 4.100E-11

135 1 2 2.200E-11

136 1 2 1.400E-11

137 1 2 5.500E-12

138 1 1 0.000E+00

139 1 2 3.000E-11

140 3 2 5.400E-17 500.0 0.00 300.0

141 3 2 1.700E-11 -116.0 0.00 300.0

142 1 2 1.700E-11

143 1 1 0.000E+00

144 1 2 3.600E-11

145 3 2 2.540E-11 -407.6 0.00 300.0

146 3 2 7.860E-15 1912.0 0.00 300.0

147 3 2 3.030E-12 448.0 0.00 300.0

148 1 2 1.500E-19

149 1 2 3.360E-11

150 1 2 7.100E-18

151 1 2 1.000E-15

152 1 1 0.000E+00

153 1 2 3.600E-11

154 3 2 1.500E-11 -449.0 0.00 300.0

155 3 2 1.200E-15 821.0 0.00 300.0

156 3 2 3.700E-12 -175.0 0.00 300.0

Figure3‐1a(concluded).



CAMx Version |VERSION6.3

Mechanism ID |0

Aerosol Option |NONE

Description |inert test

No of gas species |1

No of aero species |0

No of reactions |0

Prim photo rxns |0

No of sec photo rxn|0

SrfMod #spc, #rxns |0 0

Species Records

Gas Spec lower bnd H-law T-fact Molwt Reactvty Rscale

1 TRACER 1.00E-09 1.00e-10 0. 1.00 0.0 1.

Figure3‐1b.Exampleinertchemistryparametersfile(requireschemistryflagtobesetfalse–

seethedescriptionoftheCAMxcontrolfile).

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

Thesectionofthefilethatlistsgasspeciesmustincludethenamesofradicalandstatespecies,

accordingtotheselectedchemicalmechanism,alongwitheachspecies’lowerboundvalue,

Henry’sLawsolubilityparameters,molecularweight,andsurfacereactivityandresistance

scalingparametersforuseinthedrydepositioncalculations.Thelowerboundvaluessetthe

minimumconcentration“floor”foranychemicalorphysicalprocessthatreduces

concentrationsto“zero”.Thelowerboundisalsousedtosetinitialand/orboundary

conditionsforspeciesthatareomittedfromtheinitialand/orboundaryconditionfiles.

Thesectionofthefilethatlistsaerosolspeciesnamesmustincludealower‐boundvalue,

particledensity,dryextinctionefficiency,ahygroscopicflag,andsingle‐scatteringalbedo.In

thecaseofINERTorCFoptions,theusermustalsospecifythesizebinassignedtoeachspecies

attheendofeachparticulatespeciesrecord(CMUautomaticallyapplieseachspeciestoallsize

bins).Sincetheeffectofaerosolwateronopticalparametersistakenintoaccountthroughan

internalrelativehumidityadjustment,thedryextinctionefficiencyforparticlespeciesPH2O

mustbesettozero.

CAMxsupportsseveralequationsforspecifyinggas‐phaserateconstants,asshowninTable3‐

3a.Thetypeofequationusedforeachreactionisidentifiedbythesecondparameterspecified

foreachreaction–anumberbetween1and7(Table3‐3a).Thenumberofadditional

parametersrequireddependsupontheexpressiontypeandvariesbetween2and13,asshown

inTable3‐3b.Expressiontype4(Troeexpression)allowsforacompletedescriptionof

dependenciesontemperatureandpressure;backgroundinformationonTroeexpressionsmay

befoundintheNASAandIUPACrateconstantcompilations(NASA,1997;IUPAC,1992).

Rateconstantscanbespecifiedinmolecularunits(e.g.,cm3molecule‐1s‐1)orppmunits(e.g.,

ppm‐1min‐1).Alltherateconstantsmustbeinasingleunitssystem;CAMxwilldetermine

whichunitssystemisbeingusedfromthemagnitudeoftherateconstants.Diagnostic

informationontherateconstantsandunitssystemisoutputbyCAMxatrun‐time.

3.2PhotolysisRatesFile

Theratesfortheprimaryphotolysisreactionsaresuppliedviathephotolysisratesfileinunits

ofminute‐1.Thisfilemustbesuppliedifchemistryisinvoked.Thephotolysisratesfile

comprisesalargelook‐uptableofclear‐skyphotolysisratesspecifictothegas‐phasechemistry

mechanismtorun.Ratesarearrangedinamatrixoffivedimensions,includingvariationsover

10solarzenithangles,5ultraviolet(UV)surfacealbedos,3terrainheights,11altitudesabove

ground,and5totalozonecolumnvalues.Thelook‐uptableisgeneratedusingtheTUV

preprocessor,whichinternallyspecifiestherangesofsolarzenith(0,10,20,30,40,50,60,70,

78,86),surfaceUValbedo(0.04,0.1,0.2,0.5,0.9.),andterrainheights(0,1,3km).Theranges

ofaltitudeabovegroundarecontrolledbytheuser,whiletherangesofozonecolumnare

takenfromtheozonecolumnfile(Section3.3).TUVisrunwithatypicalaerosolprofiledefined

byElterman(1968).



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Table3‐3a.RateconstantexpressiontypessupportedinCAMxandorderofexpression

parametersforthechemistryparametersfile.

Expression

TypeDescriptionExpression

1Constant298

kk 

2UAM(Arrheniusexpression)



















 T

Ekk a

298

exp

298 

3Generaltemperaturedependence























T

Ak a

exp 

4Troe‐typetemperatureandpressure

dependence



kMk

k

















/1 0



























T

Ak a

exp

0



































Ak a

exp 



0/][log





























 n

kMk

G

5Equilibriumwithapreviouslydefined

reaction(kref)

exp





































T

Akk a

ref 

6Lindemann‐HinshelwoodasusedforOH+

HNO323

/][1

][

kMk

kk 

 

7SimplepressuredependenceusedforOH+

CO][

21 Mkkk 





Notes:

Tistemperature(K)

TRisreferencetemperatureof300K

EaisanArrheniusactivationenergy(K)

k0isthelowpressurelimitoftherateconstant

kisthehighpressurelimitoftherateconstant

[M]istheconcentrationofair

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

Table3‐3b.ListofparametersthatmustbeprovidedintheCAMxchemistryparameterfile

foreachoftheseventypesofrateconstantexpressions.Useppm/minuteunitsforAand

KelvinforEaandTR.ThevariableOistheorderofthereaction(1to3).

Expression

Type

Parameters

1234 5 6 7 8 9 101112 13

1Ok298  

2Ok298Ea

3OAEaB TR

4OAEaB TRA’ Ea’B’ TR’ F n

5Okre

AEaB TR

6OAoEa

oBoTR

oA2Ea

2B2TR

2A3Ea

3B3TR

7OA1Ea

1B1TR

1A2Ea

2B2TR

2



Thephotolysisratesfileisareadabletextformatandithasthefollowingstructure:



wherethefirstrecordlabelstheversionofTUVusedtogeneratethefile,andwherevariables

havethefollowingdefinitions:

ozcl  Ozonecolumnvalueforthecurrentinterval(Dobsonunits)

albclUValbedovalueforthecurrentinterval(unitless)

trnclTerrainheightvalueforthecurrentinterval(kmMSL)

height Altitude(kmAGL)

pkPhotolysisrates(min‐1)fornsolsolarzenithangles

Figure3‐2presentsanexampleofaphotolysisratesfileforthefirstseveralpanelsofdata.

3.3OzoneColumnFile

ThisfiledefinestheintervalsoftotalatmosphericozonecolumntobeusedbyTUV,aswellas

itsspatialandtemporaldistributionsforaspecificCAMxdomainandepisode.Thisparameter

isessentialforphotochemicalsimulationsasitdeterminesthespatialandtemporalvariationof

photolysisrates.Therefore,thisfilemustbesuppliedifchemistryisinvoked.Additionally,the

ozonecolumnfilemayalsoprovideanoptionalfielddefiningaland/oceanmask(formercury

chemistry).



TUV4.8CAMx6

Loopfrom1tonoznozonecolumnintervals:

Loopfrom1tonalbUValbedointervals:

Loopfrom1tonthtterrainheightintervals:

ozcl,albcl,trncl (12X,f7.3,8X,f7.3,11X,f7.3)

Loopfrom1tonaltaltitudesaboveground:

height (*)

Loopfrom1tonphotphotolysisreactions:

(pk(n),n=1,nsol) (1X,10F12.0)

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

TUV4.8CAMx6

O3 Column = 0.290 Albedo= 0.040 Terrain = 0.000

0.000 km above surface

4.562E-01 4.526E-01 4.416E-01 4.224E-01 3.934E-01 3.516E-01 2.921E-01 2.065E-01 1.148E-01 3.074E-02

1.670E-03 1.643E-03 1.563E-03 1.427E-03 1.236E-03 9.889E-04 6.936E-04 3.747E-04 1.502E-04 2.570E-05

2.211E-03 2.186E-03 2.107E-03 1.973E-03 1.776E-03 1.506E-03 1.152E-03 7.108E-04 3.352E-04 7.560E-05

2.078E-03 2.007E-03 1.801E-03 1.485E-03 1.097E-03 6.925E-04 3.382E-04 1.034E-04 2.201E-05 2.056E-06

3.131E-04 3.058E-04 2.841E-04 2.491E-04 2.027E-04 1.482E-04 9.100E-05 4.015E-05 1.264E-05 1.517E-06

8.728E-05 8.638E-05 8.364E-05 7.891E-05 7.189E-05 6.212E-05 4.892E-05 3.166E-05 1.580E-05 3.934E-06

0.150 km above surface

4.866E-01 4.830E-01 4.717E-01 4.521E-01 4.223E-01 3.794E-01 3.179E-01 2.284E-01 1.308E-01 3.760E-02

1.855E-03 1.827E-03 1.742E-03 1.598E-03 1.394E-03 1.130E-03 8.102E-04 4.566E-04 1.956E-04 3.701E-05

2.443E-03 2.416E-03 2.334E-03 2.193E-03 1.986E-03 1.701E-03 1.322E-03 8.415E-04 4.159E-04 1.000E-04

2.327E-03 2.249E-03 2.024E-03 1.677E-03 1.250E-03 8.008E-04 4.035E-04 1.337E-04 3.383E-05 4.166E-06

3.489E-04 3.410E-04 3.177E-04 2.799E-04 2.297E-04 1.704E-04 1.075E-04 5.024E-05 1.755E-05 2.556E-06

9.553E-05 9.460E-05 9.176E-05 8.684E-05 7.952E-05 6.928E-05 5.530E-05 3.672E-05 1.910E-05 5.068E-06

0.360 km above surface

5.050E-01 5.013E-01 4.900E-01 4.702E-01 4.402E-01 3.968E-01 3.343E-01 2.426E-01 1.412E-01 4.171E-02

1.974E-03 1.945E-03 1.857E-03 1.708E-03 1.497E-03 1.222E-03 8.862E-04 5.096E-04 2.245E-04 4.415E-05

2.587E-03 2.560E-03 2.477E-03 2.333E-03 2.120E-03 1.826E-03 1.432E-03 9.258E-04 4.673E-04 1.152E-04

2.494E-03 2.411E-03 2.174E-03 1.806E-03 1.353E-03 8.740E-04 4.474E-04 1.536E-04 4.129E-05 5.492E-06

3.722E-04 3.640E-04 3.396E-04 3.002E-04 2.475E-04 1.851E-04 1.183E-04 5.679E-05 2.067E-05 3.210E-06

1.006E-04 9.970E-05 9.681E-05 9.180E-05 8.433E-05 7.382E-05 5.940E-05 3.999E-05 2.122E-05 5.763E-06

0.640 km above surface

5.230E-01 5.193E-01 5.080E-01 4.882E-01 4.581E-01 4.143E-01 3.510E-01 2.574E-01 1.520E-01 4.577E-02

2.092E-03 2.062E-03 1.972E-03 1.819E-03 1.601E-03 1.315E-03 9.632E-04 5.633E-04 2.535E-04 5.126E-05

2.731E-03 2.703E-03 2.618E-03 2.471E-03 2.254E-03 1.951E-03 1.544E-03 1.011E-03 5.191E-04 1.304E-04

2.664E-03 2.577E-03 2.327E-03 1.939E-03 1.459E-03 9.497E-04 4.928E-04 1.738E-04 4.872E-05 6.809E-06

3.958E-04 3.872E-04 3.618E-04 3.207E-04 2.656E-04 2.000E-04 1.294E-04 6.343E-05 2.378E-05 3.860E-06

1.057E-04 1.047E-04 1.018E-04 9.672E-05 8.912E-05 7.839E-05 6.354E-05 4.331E-05 2.336E-05 6.448E-06

0.980 km above surface

5.409E-01 5.373E-01 5.260E-01 5.062E-01 4.760E-01 4.321E-01 3.682E-01 2.727E-01 1.635E-01 4.989E-02

2.210E-03 2.179E-03 2.087E-03 1.930E-03 1.705E-03 1.409E-03 1.041E-03 6.178E-04 2.827E-04 5.837E-05

2.873E-03 2.845E-03 2.758E-03 2.609E-03 2.387E-03 2.077E-03 1.656E-03 1.099E-03 5.718E-04 1.454E-04

2.837E-03 2.746E-03 2.483E-03 2.074E-03 1.567E-03 1.028E-03 5.396E-04 1.944E-04 5.611E-05 8.121E-06

4.195E-04 4.106E-04 3.842E-04 3.414E-04 2.840E-04 2.152E-04 1.407E-04 7.017E-05 2.689E-05 4.509E-06

1.107E-04 1.097E-04 1.068E-04 1.016E-04 9.392E-05 8.299E-05 6.775E-05 4.673E-05 2.556E-05 7.133E-06

1.380 km above surface

5.593E-01 5.556E-01 5.444E-01 5.247E-01 4.947E-01 4.507E-01 3.863E-01 2.892E-01 1.760E-01 5.427E-02

2.329E-03 2.298E-03 2.203E-03 2.042E-03 1.811E-03 1.505E-03 1.122E-03 6.743E-04 3.128E-04 6.563E-05

3.016E-03 2.988E-03 2.900E-03 2.749E-03 2.524E-03 2.207E-03 1.773E-03 1.190E-03 6.270E-04 1.609E-04

3.015E-03 2.920E-03 2.644E-03 2.215E-03 1.681E-03 1.109E-03 5.887E-04 2.158E-04 6.364E-05 9.454E-06

4.437E-04 4.345E-04 4.071E-04 3.627E-04 3.029E-04 2.310E-04 1.524E-04 7.716E-05 3.009E-05 5.169E-06

1.157E-04 1.148E-04 1.118E-04 1.066E-04 9.883E-05 8.772E-05 7.213E-05 5.031E-05 2.789E-05 7.835E-06

1.840 km above surface

5.782E-01 5.746E-01 5.635E-01 5.440E-01 5.141E-01 4.702E-01 4.056E-01 3.069E-01 1.897E-01 5.904E-02

2.451E-03 2.419E-03 2.322E-03 2.157E-03 1.920E-03 1.605E-03 1.206E-03 7.338E-04 3.445E-04 7.312E-05

3.162E-03 3.133E-03 3.045E-03 2.892E-03 2.664E-03 2.341E-03 1.894E-03 1.286E-03 6.856E-04 1.769E-04

3.200E-03 3.101E-03 2.811E-03 2.361E-03 1.799E-03 1.196E-03 6.407E-04 2.385E-04 7.141E-05 1.082E-05

4.685E-04 4.589E-04 4.307E-04 3.846E-04 3.224E-04 2.473E-04 1.647E-04 8.451E-05 3.341E-05 5.848E-06

1.209E-04 1.199E-04 1.169E-04 1.117E-04 1.039E-04 9.263E-05 7.671E-05 5.412E-05 3.039E-05 8.570E-06

2.350 km above surface

5.974E-01 5.939E-01 5.829E-01 5.636E-01 5.340E-01 4.904E-01 4.257E-01 3.258E-01 2.046E-01 6.425E-02

2.572E-03 2.540E-03 2.441E-03 2.273E-03 2.031E-03 1.706E-03 1.292E-03 7.955E-04 3.775E-04 8.077E-05

3.307E-03 3.278E-03 3.190E-03 3.036E-03 2.805E-03 2.477E-03 2.019E-03 1.386E-03 7.476E-04 1.934E-04

3.389E-03 3.285E-03 2.983E-03 2.512E-03 1.922E-03 1.285E-03 6.952E-04 2.622E-04 7.936E-05 1.221E-05

4.934E-04 4.836E-04 4.544E-04 4.068E-04 3.424E-04 2.641E-04 1.774E-04 9.214E-05 3.685E-05 6.538E-06

1.261E-04 1.251E-04 1.221E-04 1.169E-04 1.090E-04 9.763E-05 8.142E-05 5.811E-05 3.305E-05 9.333E-06

2.910 km above surface

6.169E-01 6.134E-01 6.026E-01 5.836E-01 5.543E-01 5.111E-01 4.466E-01 3.458E-01 2.209E-01 7.003E-02

2.694E-03 2.661E-03 2.561E-03 2.390E-03 2.143E-03 1.810E-03 1.382E-03 8.602E-04 4.124E-04 8.867E-05

3.452E-03 3.423E-03 3.335E-03 3.180E-03 2.948E-03 2.615E-03 2.148E-03 1.492E-03 8.140E-04 2.106E-04

3.582E-03 3.474E-03 3.159E-03 2.667E-03 2.049E-03 1.379E-03 7.528E-04 2.874E-04 8.761E-05 1.363E-05

5.187E-04 5.086E-04 4.786E-04 4.294E-04 3.628E-04 2.814E-04 1.906E-04 1.002E-04 4.045E-05 7.246E-06

1.312E-04 1.303E-04 1.273E-04 1.221E-04 1.142E-04 1.027E-04 8.630E-05 6.231E-05 3.593E-05 1.014E-05

3.530 km above surface

6.368E-01 6.334E-01 6.228E-01 6.041E-01 5.754E-01 5.328E-01 4.687E-01 3.673E-01 2.389E-01 7.670E-02

2.818E-03 2.784E-03 2.683E-03 2.510E-03 2.258E-03 1.917E-03 1.476E-03 9.296E-04 4.505E-04 9.704E-05

3.599E-03 3.571E-03 3.482E-03 3.328E-03 3.094E-03 2.759E-03 2.283E-03 1.605E-03 8.871E-04 2.291E-04

3.783E-03 3.670E-03 3.343E-03 2.830E-03 2.184E-03 1.478E-03 8.148E-04 3.147E-04 9.644E-05 1.512E-05

5.446E-04 5.343E-04 5.034E-04 4.528E-04 3.840E-04 2.996E-04 2.046E-04 1.088E-04 4.434E-05 7.989E-06

1.365E-04 1.355E-04 1.326E-04 1.274E-04 1.195E-04 1.080E-04 9.142E-05 6.681E-05 3.911E-05 1.103E-05

4.210 km above surface

6.569E-01 6.536E-01 6.433E-01 6.250E-01 5.969E-01 5.550E-01 4.917E-01 3.902E-01 2.588E-01 8.447E-02

2.943E-03 2.909E-03 2.807E-03 2.632E-03 2.376E-03 2.029E-03 1.574E-03 1.004E-03 4.925E-04 1.060E-04

3.747E-03 3.719E-03 3.631E-03 3.477E-03 3.243E-03 2.906E-03 2.424E-03 1.725E-03 9.679E-04 2.493E-04

3.992E-03 3.875E-03 3.534E-03 3.000E-03 2.325E-03 1.585E-03 8.818E-04 3.447E-04 1.060E-04 1.668E-05

5.711E-04 5.605E-04 5.289E-04 4.769E-04 4.060E-04 3.186E-04 2.195E-04 1.181E-04 4.859E-05 8.775E-06

1.417E-04 1.408E-04 1.379E-04 1.327E-04 1.249E-04 1.135E-04 9.674E-05 7.161E-05 4.262E-05 1.202E-05

O3 Column = 0.290 Albedo= 0.040 Terrain = 1.000

0.000 km above surface

4.655E-01 4.615E-01 4.493E-01 4.279E-01 3.958E-01 3.499E-01 2.855E-01 1.957E-01 1.048E-01 2.871E-02

1.688E-03 1.660E-03 1.576E-03 1.435E-03 1.237E-03 9.833E-04 6.824E-04 3.626E-04 1.414E-04 2.142E-05

2.240E-03 2.212E-03 2.129E-03 1.987E-03 1.780E-03 1.498E-03 1.132E-03 6.858E-04 3.159E-04 6.495E-05

2.098E-03 2.025E-03 1.815E-03 1.492E-03 1.098E-03 6.883E-04 3.334E-04 1.009E-04 2.101E-05 1.716E-06

3.162E-04 3.086E-04 2.863E-04 2.503E-04 2.029E-04 1.473E-04 8.961E-05 3.896E-05 1.193E-05 1.254E-06

8.857E-05 8.761E-05 8.467E-05 7.961E-05 7.213E-05 6.180E-05 4.802E-05 3.042E-05 1.483E-05 3.488E-06

0.150 km above surface

5.004E-01 4.963E-01 4.839E-01 4.623E-01 4.296E-01 3.828E-01 3.163E-01 2.220E-01 1.237E-01 3.1E-02

1.870E-03 1.841E-03 1.752E-03 1.604E-03 1.394E-03 1.123E-03 7.976E-04 4.424E-04 1.847E-04 3.188E-05

2.473E-03 2.445E-03 2.359E-03 2.211E-03 1.994E-03 1.697E-03 1.306E-03 8.179E-04 3.956E-04 8.840E-05

2.338E-03 2.259E-03 2.030E-03 1.677E-03 1.245E-03 7.929E-04 3.960E-04 1.294E-04 3.180E-05 3.572E-06

3.509E-04 3.428E-04 3.189E-04 2.803E-04 2.292E-04 1.690E-04 1.056E-04 4.859E-05 1.651E-05 2.187E-06

9.713E-05 9.614E-05 9.312E-05 8.789E-05 8.013E-05 6.934E-05 5.476E-05 3.574E-05 1.823E-05 4.615E-06

Figure3‐2.Exampleofthefirstseveralpanelsoflookupdatainthephotolysisratesinputfile.

March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures

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Therearetwomandatoryandoneoptionalheaderrecordsintheozonecolumnfile.Thefirst

recordcontainsanarbitraryfilelabel.Thesecondrecorddefinestheintervalsfor5ozone

columnvaluesforthedomainandtemporalperiodtobesimulated.Theseintervalsmust

exactlymatchthosedefinedinpreparingthephotolysisratesfile,sotheozonecolumnfileis

alsoreadbytheTUVpreprocessortodefinethephotolysisrateslookuptable(Section3.2).

Iftheoptionalland/oceanmaskisincluded,thenathirdheaderrecordmustbeaddedto

informCAMxthatthisfieldistoberead.Thetime‐invariantland/oceanmaskisusedfor

mercurychemistrytodefineprofilesofambienthalogens;itissimplyamapof0(landandfresh

waterbodies)and1(ocean)thatmustbelocateddirectlyunderitsheaderrecord.Avalue

mustbesuppliedforeachcellofthemastergridandoptionallyanynestedgrids.

Griddedfieldsoftime‐varyingozonecolumnfollowtheheaderrecordsandoptionalland/ocean

maskdata.Thegriddedfieldsaremapsoftherespective“codes”foreachinterval,asdefined

intheheader.Forexample,5ozonecolumnintervalsarespecifiedinTUVandintheozone

columnheaderrecord,sothemapmustconsistofadistributionofintegersrangingfrom1to5.

Ozonecolumnissuppliedforthemastergridonly;CAMxinternallyassignsmastercellvaluesto

allnestedgridscells.Multiplemapsofthesecodesmaybeprovidedforarbitrarytimeintervals

thatspantheentiresimulationperiod.

Theozonecolumnfileisareadabletextformatandithasthefollowingstructure:



wherethevariablesintheozonecolumnfilehavethefollowingdefinitions:

text  Textidentifyingfileandanymessages

ozname Textstring“OZONECOL”

oznclOzonecolumn(Dobsonunits)foreachofnoznozonevalues

loname Textstring“OCEAN”

igrd  Gridindex(1=mastergrid,2+=nestedgrid,0=endofdata)

nxNumberofgridcolumnsforthisgridindex

ny Numberofgridrowsforthisgridindex

jocn  Gridigrd,rowjland/oceancodesfornxgridcolumns

idt1  Beginningdate(YYJJJ)oftimespan

tim1  Beginninghour(HHMM)oftimespan

idt2  Endingdateoftimespan

text (A)

ozname,(ozncl(n),n=1,nozn) (A10,5F10.0)

loname,igrd,nx,ny (A10,3I10) ‐‐Optional

Loopfromj=nygridrowsto1‐‐Optional

(jocn(i,j),i=1,nx) (999I1) ‐‐Optional

loname,igrd,nx,ny (A10,3I10) ‐‐Optional

ozname,idt1,tim1,idt2,tim2 (A10,I10,F10.0,I10,F10.0)

Loopfromj=nymastergridrowsto1

(jozn(i,j),i=1,nx) (9999I1)

March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures

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tim2  Endinghouroftimespan

jozn  Mastergridrowjozonecolumncodesfornxmastergridcolumns



AnexampleofasmallozonecolumnfileisgiveninFigure3‐3.



Sample ozone column file with optional land ocean mask

OZONE COL 0.285 0.315 0.345 0.375 0.405

OCEAN 1 64 10

0000000000000000000011111111100000000000000000000000000000000000

0000000000000000000000000001111111110000000000000000000000000000

0000000000000000000000001111111111111100000000000000000000000000

0000000000000000000000000001111111111110000000000000000000000000

0000000000000000000000011111111111111100000000000000000000000000

0000000000000000000000111111111111111110000000000000000000000000

0000000000000000000000111111111111111111000000000000000000000000

0000000000000000000001111111000000000111111110000000000000000000

0000000000000000000011111111100000000011111111100000000000000000

0000000000000000000000111111111100000000011111111110000000000000

OCEAN 0 0 0

OZONE COL 05213 0.00 05213 2400.00

3333333333333333333333333333333333333333333333333333333333333333

2222222222222333333333333333333333333333333333333333333333333333

2222222222222223333333333333333333333333333333333333333333333333

2222222222222222222222333333333333333333333333333333333333333333

Figure3‐3.Examplestructureofasingle‐gridozonecolumninputfileshowingpanelsforthe

optionaltime‐invariantland‐oceanmaskandtime‐varyingozonecolumnfield.



3.4FortranBinaryInput/OutputFiles

3.4.1WhatisaFortranBinaryFile?

LargeCAMxinputandoutputdatafieldsarecontainedwithinFortran“unformatted”(binary)

files.Thismeansthatthedataarereadandwrittenasrepresentedinmemory,without

translationbetweenbinaryandASCIIcharactersetsasdonefor“text”files.Binaryfilesreduce

filevolumeandimproveprogramread/writespeed,buttheusercannotdirectlyviewor

manuallyeditthem.Therearetwowaystorepresentbinaryinformationinmemory:“big

endian”and“littleendian.”Thedifferencebetweentheseisessentiallytheorderofbitsina

word,andwhichorderisuseddependsonthecomputerchipset.Historically,bigendianhas

beenusedinmanyUnixworkstations(Sun,SGI,HP,andIBM).Thex86processorsonpersonal

computerplatforms(e.g.,IntelandAMD)uselittleendian,whilePowerPCchipsarebigendian.

CAMxcanbecompiledandrunonmachinesusingtheirnativebigorlittleendianbinary

representations,aslongasthemodelandallofitspre‐andpost‐processorsareconsistently

compiledandrunonthesametypeofplatform.Ifanycomponentofthemodelingsystemis

compiledforadifferentplatformusingtheoppositebinaryrepresentation,I/Ofileswillnotbe

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properlyreadandwilllikelyleadtoaprogramcrash.Atypicalrun‐timeerrormessagefrom

tryingtoreadthewrongbinaryformatis“inputrecordtoolong,”soifyougetthiserror

message,checkforconsistencybetweenyourbinaryfilesandFortrancompileroptions.

Compilersforlittleendianmachinesprovidecompile‐timeswitchesthatallowbinaryfilestobe

readandwrittenasbigendian.The“makefile”compilerscriptthatisdistributedwithCAMx

setscompilerflagstoconsistentlyusebigendiantomaximizeplatformportability.Therefore,

useoftheCAMxMakefilewillbydefaultresultinthemodelreadingandwritingbigendian

binaryfiles.AdditionalinformationonthistopicisprovidedinSection2.

3.4.2CAMxBinaryFileHeaders

TheformatofallbinaryCAMxI/OfilesfollowstheconventionestablishedbytheUrbanAirshed

Model(EPA,1990).CAMxbinaryfilescontainasetoftime‐invariantheaderrecords,followed

byasetofdatarecordsthatcontaintime‐andvariable‐specificfields.Allinputgridded

emissions,initialandtopboundaryconditions,meteorology1,andoutputconcentrationand

depositionfilessharethesamebasicformat.Theinputlateralboundaryconditionandpoint

sourceemissionsfilesaresimilarbutincludeadditionalrecordsspecifictotheirdatastructures.

Theinput3Dmeteorologicalfilemayprovidewindfieldsinastaggeredorun‐staggeredgrid

arrangement.Aflagtoindicatethewindstaggeringisincludedinthesecondheaderrecord

andischeckedonlywhenthe3Dmeteorologicalfileisread.

ThefourheaderrecordswithinallCAMxbinaryfileshavethefollowingstructure:



Theheadervariableshavethefollowingdefinitions:

Record1

name Textstringdescribingfilecontents(character*4(10)array):

AIRQUALITYInitialandtopboundaryconditions

BOUNDARY Boundaryconditions

EMISSIONS Griddedemissions

PTSOURCE Pointsourceemissions

AVERAGE Averageoutputconcentrations/depositionand

inputmeteorology/surfacevariables

INSTANT Instantaneousoutputconcentrations

note Textstringcontainingusernote(character*4(60)array)

itzonIntegertimezone(0=UTC,5=EST,etc.)

nvar Integernumberofvariablesonfile



1NOTE:StartingwithCAMxv6.00,allbinarymeteorologicalfileshavebeenconvertedtotheUAMconvention.

name,note,itzon,nvar,ibdate,btime,iedate,etime

plon,plat,iutm,xorg,yorg,delx,dely,nx,ny,nz,iproj,istag,tlat1,tlat2,rdum

ione,ione,nx,ny

(namvar(l),l=1,nvar)

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ibdateIntegerbeginningdatespanonfile(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedateIntegerendingdatespanonfile(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2

plon Realprojectionpole/originlongitude(degrees;westisnegative)

plat Realprojectionpole/originlatitude(degrees;southisnegative)

iutm IntegerUTMzone(ignoredforotherprojections)

xorg Realx‐coordinateatsouthwestcornerofgrid(mordegreeslongitude)

yorg Realy‐coordinateatsouthwestcornerofgrid(mordegreeslatitude)

delx Realcellsizeinx‐direction(mordegreeslongitude)

dely Realcellsizeiny‐direction(mordegreeslatitude)

nx Integernumberofgridcolumns(east‐west)

ny Integernumberofgridrows(north‐south)

nz Integernumberofverticallayers

iprojIntegerprojectionindex:

0=geodetic(LATLON)

1=UniversalTransverseMercator(UTM)

2=LambertConicConformal(LAMBERT)

3=RotatedPolarStereographic(RPOLAR)

4=PolarStereographic(POLAR)

5=Mercator(MERCATOR)

istagIntegerflagtoindicatewindstaggering(1=staggered,0=notstaggered)

tlat1RealLCPfirsttruelatitude(degrees;southisnegative)

tlat2RealLCPsecondtruelatitude(degrees;southisnegative)

rdum Realdummyvariable

Record3

ione Integerdummyvariable(=1)

nx Integernumberofgridcolumns(east‐west)

ny Integernumberofgridrows(north‐south)

Record4

namvarTextnamesfornvarvariables(character*4(10,nvar)array)

3.4.3InputFiles

TheFortranbinaryinputfilesincludeinitial/boundaryconditions,griddedandelevatedpoint

sourceemissions,andseveralmeteorologicalfiles.Alltimesoninputfilesmustmatchthetime

zonespecifiedintheCAMxcontrolfile(CAMx.in).

Initial/boundaryconditionfilesmayincludeasingletimeintervalcoveringtheentiresimulation

period,ormoredetailedhour‐by‐hour(orotherinterval)variations.Thetimeintervalsare

allowedtobeentirelyarbitrarytomaximizeflexibilityindefiningtheseinputs.Asubsetofthe

pollutantspeciestobesimulatedmaybedefinedintheinitial/boundaryconditionfiles;any

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speciesthataremissingwillbesetto“lowerbound”valuesasdefinedinthechemistry

parametersfile.

Emissioninputsareusuallydevelopedatonehourintervals,butthefilestructuresallowforany

otherintervalaslongasaconsistentintervalisusedthroughoutthefile(allonehour,orall

threehour,butnomixingofthese).Thetimeintervalonallemissionfilesmustmatchthe

emissionupdatefrequencydefinedintheCAMxcontrolfile.Asubsetofspeciestobe

simulatedmaybeincludedintheemissionfiles;zeroemissionrateswillbeappliedforany

speciesthataremissing.

Meteorologicalfieldsareseparatedintotwo‐dimensionalandthree‐dimensionalfields.The

coremeteorologicalfilecontainsthebasicparametersneededformostmodelprocesses,and

includeswindsandbasicthermodynamicproperties.Separateverticaldiffusivityandcloudfiles

allowforeasysubstitutionofalternativeinputswithouttheneedtore‐generateallofthecore

fields.Thetimeintervalonallmeteorologicalfilesmustmatchthemeteorologicalupdate

frequencydefinedintheCAMxcontrolfile.

3.4.3.1InputStatic2‐DSurfaceFile

Thestatic2‐Dsurfacefilecontainstime‐invariantgriddedfieldsoflanduseandtopographic

elevation,andoptionallyleafareaindex(LAI).Thisfilemustbedevelopedforthemastergrid,

andoptionallyanyofthenestedfinegrids.Thefractionaldistributionof26landusecategories,

consistentwiththe“ZHANG03”drydepositionscheme,issuppliedforeachgridcell.Ifthe

“WESELY89”drydepositionoptionisinvoked,CAMxinternallymapsthe26categoriestothe11

Weselycategories.ThelandusecategoriesaredescribedinTables3‐4and3‐5.Landuseisused

todefinesurfaceUValbedo,surfaceresistancesfordrydepositioncalculations,andtoset

seasonaldefaultsurfaceroughnesslengthsandLAIvalues(ifLAIisnotspecifiedinthefile).

Topographicelevationisusedtodefineterrainheightsforphotolysiscalculations.

Table3‐4.The11WESELY89landusecategories,theirdefaultUVsurfacealbedos,andtheir

surfaceroughnessvalues(m)byseason.Winterisdefinedforconditionswherethereissnow

present;wintermonthswithnosnowareassignedtotheFallcategory.Roughnessforwater

iscalculatedfromthefunction5.26

0102 wz 

 ,wherewissurfacewindspeed(m/s).

LandCoverCategorySurfaceRoughness(meters)UV

Albedo

SpringSummerFallWinter

1Urban1.0 1.0 1.0 1.00.08

2Agricultural0.03 0.2 0.05 0.010.05

3Rangeland0.05 0.1 0.01 0.0010.05

4Deciduousforest1.0 1.3 0.8 0.50.05

5Coniferousforest,wetland1.3 1.3 1.3 1.30.05

6Mixedforest*1.15 1.3 1.05 0.90.05

7Waterf(w) f(w) f(w) f(w)0.04

8Barrenland0.002 0.002 0.002 0.0020.08

9Non‐forestedwetlands0.2 0.2 0.2 0.050.05

10Mixedagricultural/range**0.04 0.15 0.03 0.0060.05

11Rocky(withlowshrubs)0.3 0.3 0.3 0.150.05

*Roughnessformixedforestistheaverageofdeciduousandconiferousforest.

*Roughnessformixedag/rangeistheaverageofagriculturalandrangeland.

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Table3‐5.The26ZHANG03landusecategories,theirUValbedos,defaultannualminimum

andmaximumLAIandsurfaceroughness(m)ranges,andmappingtotheWeselyscheme

(Table3‐4).Roughnessforwateriscalculatedfromthefunction5.26

0102 wz 

 ,wherewis

surfacewindspeed(m/s).

LandCoverCategoryWesely

Mapping

Roughness(meters) LAIUV

Albedo

Min Max Min Max

1Water7f(w)f(w)0.0 0.00.04

2Ice80.01 0.01 0.0 0.00.5

3Inlandlake7f(w)f(w)0.0 0.00.04

4Evergreenneedleleaftrees50.9 0.9 5.0 5.00.05

5Evergreenbroadleaftrees52.0 2.0 6.0 6.00.05

6Deciduousneedleleaftrees40.4 0.9 0.1 5.00.05

7Deciduousbroadleaftrees40.4 1.0 0.1 5.00.05

8Tropicalbroadleaftrees52.5 2.5 6.0 6.00.05

9Droughtdeciduoustrees40.6 0.6 4.0 4.00.05

10Evergreenbroadleafshrubs30.2 0.2 3.0 3.00.05

11Deciduousshrubs30.05 0.2 0.5 3.00.05

12Thornshrubs30.2 0.2 3.0 3.00.05

13Shortgrassandforbs30.04 0.04 1.0 1.00.05

14Longgrass10 0.02 0.1 0.5 2.00.05

15Crops20.02 0.1 0.1 4.00.05

16Rice20.02 0.1 0.1 6.00.05

17Sugar20.02 0.1 0.1 5.00.05

18Maize20.02 0.1 0.1 4.00.05

19Cotton20.02 0.2 0.1 5.00.05

20Irrigatedcrops20.05 0.05 1.0 1.00.05

21Urban11.0 1.0 0.1 1.00.08

22Tundra11 0.03 0.03 0.1 2.00.05

23Swamp90.1 0.1 4.0 4.00.05

24Desert80.04 0.04 0.0 0.00.08

25Mixedwoodforest60.9 0.9 3.0 5.00.05

26Transitionalforest60.9 0.9 3.0 5.00.05



Thedatarecordsforthestatic2‐Dsurfacefilehavethefollowingstructure:



Thevariableshavethefollowingdefinitions:

Record1

ibdate Integerbeginningdatespanonfile(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedate Integerendingdatespanonfile(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)



ibdate,btime,iedate,etime

Loopfroml=1tonvarvariables:

ione,namvar(l),((var(i,j),i=1,nx),j=1,ny)



March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures

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Record2throughnvar+1

ione Integerdummyvariable(=1)

namvarTextnamesfornvarvariables(character*4(10,nvar)array):

WATERWaterfraction(Zhang1)

ICE  Icefraction(Zhang2)

LAKE Lakefraction(Zhang3)

ENEEDL Evergreenneedleleafforestfraction(Zhang4)

EBROAD Evergreenbroadleafforestfraction(Zhang5)

DNEEDL Deciduousneedleleafforestfraction(Zhang6)

DBROAD Deciduousbroadleafforestfraction(Zhang7)

TBROAD Tropicalbroadleafforestfraction(Zhang8)

DDECID Droughtdeciduoustreefraction(Zhang9)

ESHRUB Evergreenshrubfraction(Zhang10)

DSHRUB Deciduousshrubfraction(Zhang11)

TSHRUB Thornshrubfraction(Zhang12)

SGRASS Shortgrassfraction(Zhang13)

LGRASS Longgrassfraction(Zhang14)

CROPSCroplandfraction(Zhang15)

RICE Ricecropfraction(Zhang16)

SUGARSugarcropfraction(Zhang17)

MAIZECorncropfraction(Zhang18)

COTTON Cottoncropfraction(Zhang19)

ICROPS Irrigatedcroplandfraction(Zhang20)

URBANUrbanfraction(Zhang21)

TUNDRA Tundrafraction(Zhang22)

SWAMPSwampfraction(Zhang23)

DESERT Desertfraction(Zhang24)

MWOODMixedwoodlandfraction(Zhang25)

TFOREST Transitionalforestfraction(Zhang26)

TOPO_M Topographicelevationabovesealevel(m)

LAI  OptionalLeafAreaIndex

var Realvariablefieldvaluesfornxgridcolumnsandnygridrows

3.4.3.2InputTime‐Variant2‐DSurfaceFile

Thetime‐variant2‐Dsurfacefilecontainsgriddedfieldsofsurfacetemperatureandsnow

cover.Thisfilemustbedevelopedforthemastergrid,andoptionallyanyofthenestedfine

grids.Thesurfacetemperatureisusedfordrydepositioncalculationsandtoestablishsurface‐

layeratmosphericstability.Snowcoverincludessnowdepthandage,whichareusedto

calculatesurfacealbedoforphotochemistry,adjustsurfaceresistancesfordrydeposition,and

definethesnowcompartmentforthesurfacechemistrymodel.

Thedatarecordsforthetime‐variant2‐Dsurfacefilehavethefollowingstructureandare

repeatedforeachtimeintervalonfile:

March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures

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Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedateIntegerendingdateoftimeinterval(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2throughnvar+1

ione Integerdummyvariable(=1)

namvarTextnamesfornvarvariables(character*4(10,nvar)array):

TSURF_K Surfacetemperature(K)

SNOWEW_M Snowwaterequivalentdepth(m)

SNOWAGE_HR Snowagesincelastsnowfall(hr)

var Realvariablefieldvaluesfornxgridcolumnsandnygridrows



CAMxtime‐interpolatessurfacetemperaturetoeachmodeltimestepforeachgrid(butholds

snowcoverconstant),andsothemodelrequiresthatdatabeavailableonfileforanadditional

updatetimeattheendofthesimulation.Forexample,inthecaseofhourlyfields,a24‐hour

simulationrequires25inputfieldsonfile.Thetimeintervalofthedatarecordsmustmatchthe

timezoneandinputfrequencyofthemeteorologyasspecifiedintheCAMx.infile.

CAMxisbackward‐compatiblewitholder2‐Dmeteorologicalfilesthatmaycontainthesnow

covervariable(SNOWCOVER),whichisasimplemapof0or1toindicatethepresenceofsnow

ineachgridcell.IftheSNOWCOVERvariableisfound,CAMxarbitrarilyassumesasnowwater

equivalentdepthof0.025m(~25cmsnowdepth)andsnowageof5days.

3.4.3.3InputTime‐Variant3‐DMeteorologicalFile

Thetime‐variant3‐Dmeteorologicalfilecontainsgriddedfieldsofstatemeteorological

parameters.Thisfilemustbedevelopedforthemastergridandoptionallyanyfinegridnest

specifiedforagivensimulation.Thelayerinterfaceheightsdefinetheverticalgridstructurefor

eachgrid.Thenumberofverticallayersandtheverticalgriddefinitionmustbeconsistent

amongallgridsinasimulation;otherwiseCAMxwillstopwithanerrormessageifthis

conditionisnotmet.Thelayerinterfaceheightsmaybespecifiedtovaryinspaceand/ortime

(e.g.,tofollowthelayerstructureofmeteorologicalmodels),ortheymaybesettoaconstant

field.CAMxallowstheusertooptionallysupplywindcomponentsatcellcenter,inwhichcase

themodelwillinterpolatethecomponentstotheirrespectivepositionsoncellinterfaces,or

theusermaysupplythesecomponentsdirectlyonthestaggeredArakawaCconfiguration



ibdate,btime,iedate,etime

Loopfroml=1tonvarvariables:

ione,namvar(l),((var(i,j),i=1,nx),j=1,ny)



March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures

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(recommended).Inanycase,theusermustsupplyafullnx×ny×nzarrayofwindvaluesforeach

component(eventhoughtheCAMxArakawaCconfigurationusesonly(nx‐1)×(ny‐1)valuesin

thehorizontal).Thewindstaggeringflagissetinthesecondheaderrecord.Thepressure,

wind,temperature,andhumidityfieldsareusedfortransport,plumerise,PiG,dryandwet

deposition,andchemistrycalculations.

Thedatarecordsforthetime‐variant3‐Dmeteorologicalfilehavethefollowingstructureand

arerepeatedforeachtimeintervalonfile:



Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedateIntegerendingdateoftimeinterval(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2throughnvar



nz+1

ione Integerdummyvariable(=1)

namvarTextnamesfornvarvariables(character*4(10,nvar)array):

ZGRID_M Layerinterfaceheights(mAGL)

PRESS_MB Pressure(mb)

TEMP_K Temperature(K)

HUMID_PPM Humidityasmixingratio(ppm)

UWIND_MpS U‐component(east‐west)wind(m/s)

VWIND_MpS V‐component(north‐south)wind(m/s)

var Reallayerkvariablefieldvaluesfornxgridcolumnsandnygridrows

CAMxtime‐interpolatesthesemeteorologicalvariablestoeachmodeltimestepforeachgrid,

andsothemodelrequiresthatdatabeavailableonfileforanadditionalupdatetimeattheend

ofthesimulation.Forexample,inthecaseofhourlyfields,a24‐hoursimulationrequires25

inputfieldsonfile.Thetimeintervalofthedatarecordsmustmatchthetimezoneandinput

frequencyofthemeteorologyasspecifiedintheCAMx.infile.

3.4.3.4InputTime‐Variant3‐DVerticalDiffusivityFile

Thetime‐variant3‐Dverticaldiffusivityfilecontainsgriddedfieldsoflayer‐interfacediffusivity

(i.e.,turbulentexchangeordiffusioncoefficients).Thisfilemustbedevelopedforthemaster

grid,andoptionallyanyfinegridnests.Thisfileiskeptseparatefromthemainmeteorological



ibdate,btime,iedate,etime

Loopfroml=1tonvarvariables:

Loopfromk=1tonzlayers:

ione,namvar(l),((var(i,j,k),i=1,nx),j=1,ny)



March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures



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datafiletofacilitatethesubstitutionofalternativeverticalmixingrates.Diffusivityisusedfor

verticaldiffusionandPiGpuffgrowthcalculations.

Thedatarecordsforthetime‐variant3‐Dmeteorologicalfilehavethefollowingstructureand

arerepeatedforeachtimeintervalonfile:



Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedateIntegerendingdateoftimeinterval(YYJJJ)

etime Realendingdecimalhour(e.g.,1:30PM=13.5)

Record2throughnvar



nz+1

ione Integerdummyvariable(=1)

namvarTextnamesfornvarvariables(character*4(10,nvar)array):

KV_M2pS Verticaldiffusivity(m2/s)

var Reallayerkvariablefieldvaluesfornxgridcolumnsandnygridrows

CAMxtime‐interpolatesthediffusivitytoeachmodeltimestepforeachgrid,andsothemodel

requiresthatdatabeavailableonfileforanadditionalupdatetimeattheendofthe

simulation.Forexample,inthecaseofhourlyfields,a24‐hoursimulationrequires25input

fieldsonfile.Thetimeintervalofthedatarecordsmustmatchthetimezoneandinput

frequencyofthemeteorologyasspecifiedintheCAMx.infile.

3.4.3.5InputTime‐Variant3‐DCloud/PrecipitationFile

Thetime‐variant3‐Dcloud/precipitationfilecontainsgriddedfieldsofcloudandprecipitation

parameterstobeusedforphotochemistry,aqueouschemistry,andwet/drydeposition

calculations.Notethatprecipitationrateisnotexplicitlyprovidedtothemodel;instead,itis

internallycalculatedfromthethreeprecipitationwatercontentformsprovidedonthe

cloud/rainfile.Thisfilealsocontainslayer‐specificcloudopticaldepthtoscaledownphotolysis

ratesforlayerswithinorbelowcloudstoaccountforUVattenuation,ortoscaleuptherates

forlayersabovecloudstoaccountforUVreflection.Thisfilemustbedevelopedforthemaster

grid,andoptionallyanyfinegridnests,ifchemistry,dry,and/orwetdepositionareinvoked.

Thedatarecordsforthetime‐variant3‐Dcloud/precipitationfilehavethefollowingstructure

andarerepeatedforeachtimeintervalonfile:



ibdate,btime,iedate,etime

Loopfroml=1tonvarvariables:

Loopfromk=1tonzlayers:

ione,namvar(l),((var(i,j,k),i=1,nx),j=1,ny)



March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures



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

Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedateIntegerendingdateoftimeinterval(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2throughnvar



nz+1

ione Integerdummyvariable(=1)

namvarTextnamesfornvarvariables(character*4(10,nvar)array):

CLODW_GpM3Cloudwatercontent(g/m3)

RAINW_GpM3Rainwatercontent(g/m3)

SNOWW_GpM3Snowwatercontent(g/m3)

GRPLW_GpM3Graupelwatercontent(g/m3)

CLOUDOD Layer‐specificcloudopticaldepth

var Reallayerkvariablefieldvaluesfornxgridcolumnsandnygridrows

TheCAMxcloudfieldsareassumedtobetime‐averaged,sothemodeldoesnotrequirean

additionalupdatetimeattheendofthesimulation.Forexample,inthecaseofhourlyfields,a

24‐hoursimulationrequiresonly24cloudinputfieldsonfile.Thetimeintervalofthedata

recordsmustmatchthetimezoneandinputfrequencyofthemeteorologyasspecifiedinthe

CAMx.infile.

3.4.3.6Input3‐DInitialConditionsFile

Theinput3‐Dinitialconditionsfilecontainsgriddedconcentrationfieldsonthemastergrid.

Initialconcentrationfieldsmaybespecifiedforasub‐setofthetotalnumberofmodeled

species.Aninitialconditionfilemustbedevelopedforthemastergrid,andcontain

concentrationfieldsforatleastonespecies.Forthosespeciesnotontheinitialconditionfile,

CAMxsetsupuniformfieldsusingthe“lowerbound”valuesspecifiedinthechemistry

parametersfile.CAMxtheninterpolatesallmastergridinitialconditionstoeachfinegridnest

atthestartofthesimulation.

Thedatarecordsfortheinitialconditionsfilehavethefollowingstructureandarerepeatedfor

eachtimeintervalonfile:



ibdate,btime,iedate,etime

Loopfroml=1tonvarvariables:

Loopfromk=1tonzlayers:

ione,namvar(l),((var(i,j,k),i=1,nx),j=1,ny)



March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures



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

Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedateIntegerendingdateoftimeinterval(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2throughnspec



nz+1

ione Integerdummyvariable(=1)

namspecTextnamesfornspecspecies(character*4(10,nvar)array):

conc Reallayerkconcentrationfieldvalues(ppmforgases,µg/m3foraerosols)

fornxgridcolumnsandnygridrows

ThetimeintervalofthedatarecordsmustmatchthetimezoneasspecifiedintheCAMx.infile.

3.4.3.7Input3‐DLateralBoundaryConditionsFile

Theinput3‐Dlateralboundaryconditionsfilecontainsgriddedconcentrationfieldsonthe

lateralfacesofthemastergridboundary.Boundaryconcentrationfieldsmaybespecifiedfora

sub‐setofthetotalnumberofmodeledspecies.However,ifaboundaryconcentrationis

specifiedforagivenspecies,itmustbesuppliedforallfourboundaries.Aboundary

concentrationfilemustbedevelopedforthemastergrid,andcontainconcentrationfieldsfor

atleastonespecies.Forthosespeciesnotontheboundaryconditionsfile,CAMxsetsup

uniformfieldsusingthe“lowerbound”valuesspecifiedinthechemistryparametersfile.The

timespanofeachsetofboundarydatarecordsmaybesetarbitrarily;e.g.,asetofboundary

conditionsmaybespecifiedforasixhourspan,followedbyasetspanningjustanhour.

Theboundaryconditionsfileaddsanadditionalsetoffourheaderrecords,resultinginatotal

ofeightheaderrecordsaltogether(notethatfirstfourrecordsareidenticaltotheheader

recordsdescribedabove):



ibdate,btime,iedate,etime

Loopfroml=1tonspecspecies:

Loopfromk=1tonzlayers:

ione,namspec(l),((conc(i,j,k,l),i=1,nx),j=1,ny)



name,note,ione,nspec,ibdate,btime,iedate,etime

plon,plat,iutm,xorg,yorg,delx,dely,nx,ny,nz,iproj,istag,tlat1,tlat2,rdum

ione,ione,nx,ny

(namspec(l),l=1,nspec)

Loopfrom1to4boundaries:

ione,iedge,ncell,(icell(n),idum,idum,idum,n=1,ncell)



March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures



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

Theadditionalheadervariableshavethefollowingdefinitions:

Records5‐8

ione Integerdummyvariable(=1)

iedgeIntegerboundaryedgenumber(1=west,2=east,3=south,4=north)

ncellIntegernumberofrowsorcolumnsonthisedge



icellIntegerindexoffirstcellmodeled(edges1,3),orlastcellmodeled(edges

2,4):if“0”,thisrow/columnisomittedfromthesimulation

idum Integerdummyvariable

Thedatarecordsfortheboundaryconditionsfilehavethefollowingstructure,andare

repeatedforeachtimeintervalonfile:



Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedateIntegerendingdateoftimeinterval(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2throughnspec



4+1

ione Integerdummyvariable(=1)

namspecTextnamesfornspecspecies(character*4(10,nvar)array):

bc Realedgeiedgeboundaryconcentrations(ppmforgases,µg/m3for

aerosols)forncellgridrows/columns,andnzlayers

ThetimeintervalofthedatarecordsmustmatchthetimezoneasspecifiedintheCAMx.infile.

3.4.3.8Input2‐DTopBoundaryConditionsFile

Theinput2‐Dtopboundaryconditionsfilecontainsgriddedconcentrationfieldsabovethetop

ofthemastergridboundary.Boundaryconcentrationfieldsmaybespecifiedforasub‐setof

thetotalnumberofmodeledspecies;thesub‐setofspeciesmaydifferfromthelateral

boundaryconditions.Thetopboundaryconcentrationfileisoptional,butifsupplieditmust

containconcentrationfieldsforatleastonespecies.Forthosespeciesnotontheboundary

conditionsfile,CAMxsetsupuniformfieldsusingthe“lowerbound”valuesspecifiedinthe

chemistryparametersfile.Thetimespanofeachsetoftopboundarydatarecordsmaybeset

arbitrarily;e.g.,asetofboundaryconditionsmaybespecifiedforasixhourspan,followedbya



ibdate,btime,iedate,etime

Loopfroml=1tonspecspecies:

Loopfromiedge=1to4boundaries:

ione,namspec(l),iedge,((bc(i,k,iedge,l),k=1,nz),i=1,ncell)



March2016CAMxUser’sGuideVersion6.3

3.CoreModelInput/OutputStructures



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

setspanningjustanhour.Thetimespanofthetopboundaryconditionsmaydifferfromthe

lateralboundaryconditions.

Ifthetopboundaryconditionfileisnotsupplied,CAMxwilldefaulttointernallyemployingthe

original“zero‐gradient”mixingratioassumption,wherebytheconcentrationsofeachspeciesin

thetopmodellayer(asmolepollutantpermoleair)isassumedtoalsoexistabovethemodel

top.

Thedatarecordsforthetopboundaryconditionsfilehavethefollowingstructureandare

repeatedforeachtimeintervalonfile:



Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedateIntegerendingdateoftimeinterval(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2throughnspec



nz+1

ione Integerdummyvariable(=1)

namspecTextnamesfornspecspecies(character*4(10,nvar)array):

tc Realconcentrationfieldvalues(ppmforgases,µg/m3foraerosols)

fornxgridcolumnsandnygridrows

ThetimeintervalofthedatarecordsmustmatchthetimezoneasspecifiedintheCAMx.infile.

3.4.3.9InputElevatedPointSourceFile

Theinputelevatedpointsourceemissionsfilecontainsstackparametersandemissionratesfor

allelevatedpointsources,andforallemittedspecies,tobemodeled.Ifelevatedpointsources

aretobemodeled,onlyonepointsourceemissionsfilemustbedevelopedfortheentire

modelingdomain.Thepointsourcefilealsoflagstheindividualstackstobetreatedbythe

CAMxPiGsub‐modelbysettingthestackdiameterasanegativevalue.Thefileoffersthe

abilitytooptionallyspecifytheeffectiveplumeheightortheverticalplumedistributionfor

eachpointsourceandtobypasstheinternalplumerisecalculation.

Theelevatedpointsourcefileaddstwoadditionalsetofheaderrecordsthatspecifytime‐

invariantstackparameters,resultinginatotalofsixheaderrecordsaltogether(notethatfirst

fourrecordsareidenticaltotheheaderrecordsdescribedabove):



ibdate,btime,iedate,etime

Loopfroml=1tonspecspecies:

ione,namspec(l),((tc(i,j,l),i=1,nx),j=1,ny)



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Theadditionalheadervariableshavethefollowingdefinitions:

Record5

ione Integerdummyvariable(=1)

nstk Integernumberofelevatedpointsourcestacks

Record6

xstk Realstackx‐coordinate(mordegreeslongitude)

ystk Realstacky‐coordinate(mordegreeslatitude)

hstk Realstackheight(m)

dstk Realstackdiameter(m);negativevalueflagssourceforPiG

tstk Realstackexittemperature(K)

vstk Realstackexitvelocity(m/hr)

Thetime‐variantdatarecordsfortheelevatedpointsourcefilehavethefollowingstructure,

andarerepeatedforeachtimeintervalonfile:



Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedate Integerendingdateoftimeinterval(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2

ione Integerdummyvariable(=1)

nstk Integernumberofelevatedpointsourcestacks



name,note,ione,nspec,ibdate,btime,iedate,etime

plon,plat,iutm,xorg,yorg,delx,dely,nx,ny,nz,iproj,istag,tlat1,tlat2,rdum

ione,ione,nx,ny

(namspec(l),l=1,nspec)

ione,nstk

(xstk(n),ystk(n),hstk(n),dstk(n),tstk(n),vstk(n),n=1,nstk)



ibdate,btime,iedate,etime

ione,nstk

(idum,idum,kcell(n),flow(n),plmht(n),n=1,nstk)

Loopfroml=1tonspecspecies:

ione,namspec(l),(ptems(n,l),n=1,nstk)



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Record3

idum Integerdummyvariable

kcellZeroorpositive:Ignored

Negative:integerflagforOSAT/PSATsourceregionoverride

flow Zero:ignored(plumerisecalculationusestime‐invariantexitvelocity)

Positive:realstackflowrate(m3/hr)forplumerisecalculations

Negative:realplumebottom(m)forverticalplumedistributionoverride

plmhtZeroorpositive:ignored(plumerisecalculationisperformed)

Negative(flow ≥0):realeffectiveplumeriseoverride(m)

Negative(flow <0):realplumetop(m)forverticalplumedistribution

override

Record4throughnspec+4

ione Integerdummyvariable(=1)

namspecTextnamesfornspecspecies(character*4(10,nvar)array):

ptemsRealpointemissionrate(mol/timeperiodforgases,g/timeperiodfor

aerosols)fornstkpointsources

Notethattheemissiontimeinterval(thedenominatorfortheemissionsrate)isnormally,but

notnecessarily,1hour.Thetimeintervaloftheemissionrecordsmustmatchthetimezone

andinputfrequencyoftheemissionsasspecifiedintheCAMx.infile.

3.4.3.10InputGriddedEmissionsFile

Theinputgriddedemissionsfilecontainsgriddedfieldsoflow‐level(i.e.,surface)emissionrates

forallemittedspeciestobemodeled.Ifgriddedemissionsaretobemodeled,agridded

emissionsfilemustbedevelopedforthemastergridandoptionallyanynestedfinegrids.

Thedatarecordsofthegriddedemissionsfilehavethefollowingstructure,andarerepeated

foreachtimeintervalonfile:



Thevariableshavethefollowingdefinitions:

Record1

ibdateIntegerbeginningdateoftimeinterval(YYJJJ)

btimeRealbeginningdecimalhour(e.g.,1:30PM=13.5)

iedate Integerendingdateoftimeinterval(YYJJJ)

etimeRealendingdecimalhour(e.g.,1:30PM=13.5)

Record2throughnspec



nz+1

ione Integerdummyvariable(=1)

namspecTextnamesfornspecspecies(character*4(10,nvar)array):



ibdate,btime,iedate,etime

Loopfroml=1tonspecspecies:

ione,namspec(l),((emiss(i,j,l),i=1,nx),j=1,ny)



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emiss Realgriddedemissionfieldvalues(mol/timeperiodforgases,g/time

periodforaerosols)fornxgridcolumnsandnygridrows

Notethattheemissiontimeinterval(thedenominatorfortheemissionsrate)isnormally,but

notnecessarily,1hour.Thetimeintervaloftheemissionsrecordmustmatchthetimezone

andinputfrequencyoftheemissionsasspecifiedintheCAMx.infile.

3.4.4OutputFiles

Masterandnestedgridinstantaneousfilescontainfullthree‐dimensionalfieldsofallspecies

modeled,whilethegriddedaverageanddepositionfilescontainonlythosespeciesspecifiedin

theruncontrolfile.Forflexibility,CAMxofferstheoptiontowritefullthree‐dimensional

averageconcentrationfields,orjustsurfacelayertwo‐dimensionalfields(seethe“3‐Daverage

file”optionintheCAMxcontrolfile).Itispermissibletochangethenumberofspeciesonthe

averagefile,orchangebetween2‐Dand3‐Daveragefiles,fromoneCAMxsimulationperiodto

thenext(providedtheperiodsareconfiguredasseparateCAMxruns).Astheinstantaneous

concentrationfilesareusedforCAMxrestarts,themodelonlywritesinstantaneousfieldsat

theendofthesimulation.PiGoutputfilespossessauniqueformat,andareusedprimarilyfor

modelrestarts.

3.4.4.1OutputConcentrationFiles

Theoutputaveragefilesforallgrids,andthecoarse(master)gridinstantaneousfile,areall

writtenintheCAMxFortranbinaryformatasdescribedearlier.Therearethreedifferences

betweentheoutputconcentrationfilesandtheinputinitialconcentrationfiles.First,thefile

namegiveninthefiledescriptionheaderrecord(headerrecord#1)is“AVERAGE”forthe

averageoutputfile,“INSTANT”fortheinstantaneousoutputfile,and“AIRQUALITY”forthe

inputinitialconcentrationfile.Second,the“note”inthefiledescriptionheaderrecordofthe

outputconcentrationfilesisthemessagesuppliedinthefirstlineoftheCAMxruncontrolfile,

whereasthe“note”intheairqualityfileissetaspartoftheinputfilepreparation.Third,the

specieslistscanbedifferentamongthefiles:theoutputinstantaneousfilecontainsallspecies

modeled(asspecifiedinthechemistryparametersfile),theaverageoutputfilecontainsonly

thespeciesspecifiedintheruncontrolfile,andtheinputinitialconcentrationfilemaycontain

anysubsetofmodeledspeciesasdeterminedwhenthatfileisprepared.

Twootherdifferencesexistbetweentheaverageandinstantaneousoutputfiles.Asnoted

above,theaveragefilemaycontainonlysurface‐levelfieldsortheentirethree‐dimensional

fields,asselectedbytheuser.Also,gasconcentrationfieldsareoutputasppminaveragefiles,

butasµmol/m3ininstantaneousfiles(aerosolsareinµg/m3inbothfiles).Becauseofthese

differences,andbecauseaveragefilesusuallydonotcontainallmodeledspecies,CAMxdoes

notallowtheaverageoutputconcentrationfiletobeusedforsimulationrestarts.

3.4.4.2OutputDepositionFiles

Theoutputdepositionfileisidenticalinformattothetwo‐dimensionalsurface‐leveloutput

averageconcentrationfile.Thefilenamegivenonthefirstrecordofthedepositionfileis

“AVERAGE”sothatexistingpost‐processingsoftwarewillrecognizetheformat.However,the

outputdepositionfilediffersfromtheoutputaverageconcentrationfileinoneimportantway.

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Thespecieslistisidenticaltothelistontheaverageconcentrationoutputfiles,exceptthatfour

parametersareoutputforeachspecies:

species_DV Real2‐Ddrydepositionvelocityfieldforspecies(m/s)

species_DD Real2‐Ddrydepositedmassfieldforspecies(mol/hafor

gases,g/haforaerosols)

species_WD Real2‐Dwetdepositedmassfieldforspecies(mol/hafor

gases,g/haforaerosols)

species_LC Real2‐Dprecipitationliquidconcentrationforspecies(mol/lfor

gases,g/lforaerosols)

3.4.4.3OutputSurfaceMassFiles

Theoutputsurfacemodelmassfileisidenticalinformattothetwo‐dimensionalsurface‐level

outputaverageconcentrationanddepositionfiles.Thefilenamegivenonthefirstrecordof

thedepositionfileis“AVERAGE”sothatexistingpost‐processingsoftwarewillrecognizethe

format.However,thecontentsofthesurfacemassfiledifferfromtheotherfilesintwoways.

First,thespecieslistisdefinedfromthesectionofthechemistryparametersfilethatexplicitly

liststhespeciestobetrackedbythesurfacemodel(seeSection4.8).Second,twoparameters

areoutputforeachsurfacemodelspecies:

Sspecies Real2‐Ddrymassonsoilorsnowforspecies(mol/ha)

Vspecies Real2‐Ddrymassonvegetationforspecies(mol/ha)

Thisfileisalsousedforrestartstore‐initializethesurfacemodelwithaccumulatedspecies

massonsoil/snowandvegetativesurfacesfromapreviousrun.

3.4.4.4Nested(Fine)GridInstantaneousOutputFile

Thenested(or“fine”)gridFortranbinaryoutputinstantaneousfileisuniqueandcontainsthe

three‐dimensionalconcentrationfieldsforallnestedgridstogether,asopposedtoseparate

filesforeachgrid.Allgriddefinitionparametersgiveninthesefilesarereferencedrelativeto

themastergrid,sospecificabsoluteinformationaboutgridcellsizeorprojectioncoordinates

foreachnestedgridmustbedeterminedfrommastergridparameters.Iftheuserutilizesthe

Flexi‐nestingcapabilityofCAMx,thenthegriddedfieldsoutputtothenestedfinegridfileswill

changeaccordingtohownestsarealtered,added,and/orremovedduringthecourseofa

simulation.

Theheaderportionofthenestedgridoutputfilescontain3+nnestrecordswiththefollowing

structure:

message

nnest,nspec

(mspec(l),l=1,nspec)

Loopfrom1tonnestgridnests

ibeg,jbeg,iend,jend,mesh,ione,nx,ny,nz,iparnt,ilevel

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Thetime‐variantportionofthenestedgridoutputfileshavethefollowingstructure,wherethe

followingrecordsarerepeatedforeachoutputtime:



Thevariablesonthenestedgridoutputconcentrationfileshavethefollowingdefinitions:

message Textstringcontainingfiledescription(character*60)

nnest Numberoffinegridnestsonfile

nspec Numberofspeciesonfile

mspec Speciesnamesfornspecspecies

ibeg Gridnx‐directionstartingindexofgrid(mastergridcell)

jbeg  Gridny‐directionstartingindexofgrid(mastergridcell)

iend Gridnx‐directionendingindexofgrid(mastergridcell)

 jend Gridny‐directionendingindexofgrid(mastergridcell)

mesh  Gridnmeshingfactor(numberofnestedcellspermaster)

ione  Dummyinteger=1

nx Gridnnumberofgridrows

ny Gridnnumberofgridcolumns

nz Gridnnumberoflayers

iparnt Gridn’sparentgrid(gridindexwithinwhichthisfinegridisnested;0=

mastergrid)

 ilevel Gridn’sgridlevel(depthatwhichthisgridisnested;1=mastergridis

parent)

 time  Timeofoutput(HHMM);endinghourforaverageoutput

 idateDateofoutput(YYJJJ)

 conc  Gridn,speciesl,layerkconcentrations(ppmforaveragegases,µg/m3

foraverageaerosols,µmol/m3forinstantaneousgasspecies)fornxgrid

columns,andnygridrows

3.4.4.5PiGRestartFile

WhenthePiGoptionisinvoked,CAMxoutputsallpuffparameterseachhourformodelrestart

capabilities.ThisfileisFortranbinaryandisanalogoustotheinstantaneousgridded

concentrationoutputfilesinthatitrepresentsa“snapshot”ofdataatthetopofeachhour.

Thefileformatisuniqueandcontainsinformationforeachpuff,includingcoordinates,grid

location,sizespecifications,age,andmassofeachofthechemicalspeciescarried.Whilethis

filecontainsPiGinformationfortheentiresimulation,itwouldbeoflimiteduseforcertain

analysessuchasplottingpufftrajectories.Thisisbecausetheinstantaneousnatureofthedata,

time,idate

Loopfrom1tonnestgridnests

Loopfroml=1tonspecspecies:

Loopfromk=1tonzlayers:

((conc(i,j,k,l),i=1,nx),j=1,ny)

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andthedynamicmemoryallocationutilizedinthePiGsubmodel,leadstoinsufficient

informationtoidentifyandtrackindividualpuffshourtohour.

ThePiGrestartfilecontainstworecordswiththefollowingstructure,andthesearerepeated

foreachoutputtime:



ThevariablesonthePiGrestartfilehavethefollowingdefinitions:

idatpig Dateofoutput(YYJJJ)

timpig Timeofoutput(HHMM)

npig NumberofPiGpuffsactiveatthisoutputtime

nreactr Numberofchemicalreactorsineachpuff

ingrd Gridindexfornpigpuffs

idpig Pointsourceindexfornpigpuffs

 xpigf x‐coordinateofpufffront(kmfrommastergridSWcorner)fornpigpuffs

xpigb x‐coordinateofpuffback(kmfrommastergridSWcorner)fornpigpuffs

ypigf y‐coordinateofpufffront(kmfrommastergridSWcorner)fornpigpuffs

ypigb y‐coordinateofpuffback(kmfrommastergridSWcorner)fornpigpuffs

zpig Puffheight(mAGL)fornpigpuffs

 axisy Pufflateralwidth(m)fornpigpuffs

axisz Puffverticaldepth(m)fornpigpuffs

sigy PuffGaussianlateraldimension(m)fornpigpuffs

sigx PuffGaussianlongitudinaldimension(m)fornpigpuffs

sigz PuffGaussianverticaldimension(m)fornpigpuffs

pufftop Pufftopheight(mAGL)fornpigpuffs

puffbot Puffbottomheight(mAGL)fornpigpuffs

htfms Puffhorizontalturbulentfluxmoment,shear(m2/s)

htfmb Puffhorizontalturbulentfluxmoment,buoyancy(m2/s)

 vtfms Puffverticalturbulentfluxmoment,shear(m2/s)

vtfmb Puffverticalturbulentfluxmoment,buoyancy(m2/s)

agepigf Pufffrontagesincerelease(s)fornpigpuffs

agepigb Puffbackagesincerelease(s)fornpigpuffs

fmspig Puffvolumeparameter(unitless)fornpigpuffs

ipufmap PuffOSAT/PSATregionmappointer(unitless)fornpigpuffs

ipufgrp PuffOSAT/PSATgrouppointer(unitless)fornpigpuffs

idatpig,timpig,npig,nreactr

(ingrd(n),idpig(n),xpigf(n),xpigb(n),ypigf(n),ypigb(n),zpig(n),

& axisy(n),axisz(n),sigy(n),sigx(n),sigz(n),pufftop(n),puffbot(n),

& htfms(n),htfmb(n),vtfms(n),vtfmb(n),agepigf(n),agepigb(n),fmspig(n),

& ipufmap(n),ipufgrp(n),

& ((puffrad(i,nr,n),i=1,nrad),nr=1,nreactr),

& ((puffmass(i,nr,n),i=1,nspec),nr=1,nreactr),n=1,npig

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puffrad Puffradicalconcentrations(ppm)fornradspecies,nreactrreactors,and

npigpuffs

puffmassPuffpollutantmass(µmol)fornspecspecies,nreactrreactors,andnpig

puffs

3.4.4.6PiGSampleGridFiles

TheoptionalPiGsamplinggridconcentrationsaretime‐averagedinthesamemannerasthe

outputaverageconcentrationsprovidedonthecomputationalgrids.Thesameuser‐defined

setofoutputspeciesarewrittentothesamplinggridfiles,butonlytwo‐dimensionalsurface

layerconcentrationsarereported.ThesamplinggridfileformatisidenticaltotheCAMx

averageanddepositionfiles,withonefilegeneratedpersamplinggrid,sothattheymaybe

readilyviewedandmanipulatedwithCAMxpost‐processingsoftware.

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4.COREMODELFORMULATION

ThissectionoutlinesthenumericalapproachemployedinthecoreCAMxmodel,anddescribes

thetechnicalformulationoftheemissions,transportandremovalalgorithms.Thespecific

chemicalmechanismsandtheirnumericalsolversarediscussedindetailinSection5.

DescriptionsofPlume‐in‐GridandeachProbingToolareprovidedinSections6through10.

4.1NumericalApproach

Thephysicalrepresentationsandthenumericalmethodsusedforeachtermofthepollutant

continuityequation(describedinSection1)aresummarizedinTable4‐1.CAMxincludespeer‐

acceptedalgorithmsandcomponentformulations,anditsmodularframeworkeasesthe

additionand/orsubstitutionofalternativealgorithmsinthefuture.



Table4‐1.SummaryoftheCAMxmodelsandmethodsforkeyphysicalprocesses.

ProcessPhysicalModels NumericalMethods

HorizontaladvectionEuleriancontinuityequation



Bott(1989)

 PPM(ColellaandWoodward,1984)

HorizontaldiffusionK‐theory1storderclosure Explicitsimultaneous2‐Dsolver

VerticaladvectionEuleriancontinuityequationImplicitbackward‐Euler(time)hybrid

centered/upstream(space)solver

Verticaldiffusion K‐theory1storderclosure

 Non‐localmixing



Implicitbackwards‐Euler(time)

centered(space)solver

 ExplicitACM2non‐local

convection/diffusion(Pleim,2007)

Gas‐PhaseChemistry

 CarbonBond2005(Yarwoodetal.,2005b)

 CarbonBond6(Yarwoodetal.,2010,

2012a,2014;HildebrandtRuizand

Yarwood,2013;Emeryetal.,2015)

 SAPRC07TC(Carter,2010;Hutzelletal.,

2012)

 Inorganic/organicaerosolprecursors

 EBI(Herteletal.,1993)

 LSODE(Hindmarsh,1983)

AerosolChemistry

 Aqueousinorganicchemistry

 Inorganicthermodynamics/partitioning

 Organicthermodynamics/partitioning

 Static2‐modeormulti‐sectionsizemodels



RADM‐AQ(Changetal.,1987)

 ISORROPIA(Nenesetal.,1998)

 SOAP(Straderetal.,1999)or

VBS(Kooetal.,2014)

 Coarse/Fine(CF)2‐modemodel

 CMUsectionalmodel(Pandisetal.,

1993)

Drydeposition

 Resistancemodelforgases(Wesely,1989)

andaerosols(SlinnandSlinn,1980)

 Resistancemodelforgases(Zhangetal.,

2003)andaerosols(Zhangetal.,2001)

Depositionvelocityassurface

boundaryconditioninvertical

diffusionsolver

WetdepositionScavengingmodelforgasesandaerosols

(SeinfeldandPandis,1998)

Exponentialdecayasafunctionof

scavengingcoefficient

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Thecontinuityequationisnumericallymarchedforwardintimeoveraseriesoftimesteps.At

eachstep,thecontinuityequationisintegratedbywayofanoperator‐splittingapproachthat

calculatestheseparatecontributionofeachmajorprocess(emission,advection,diffusion,

chemistry,andremoval)toconcentrationchangewithineachgridcell.Thespecificequations

thataresolvedindividuallyintheoperator‐splittingprocessareshowninorderbelow:



whereclisspeciesconcentration(mol/m3forgasses,g/m3foraerosols),Elisthelocalspecies

emissionrate(mol/sforgasses,g/sforaerosols),tistimesteplength(s),uandvarethe

respectiveeast‐west(x)andnorth‐south(y)horizontalwindcomponents(m/s),AyzandAxzare

cellcross‐sectionalareas(m2)inthey‐zandx‐zplanes,respectively,mistheratioofthe

transformeddistanceonthevariousmapprojectionstotruedistance(m=1forcurvi‐linear

latitude/longitudecoordinates),andΛlisthewetscavengingcoefficient(s‐1).

Amasterdrivingtimestepforthemodelisdynamicallydeterminedduringthesimulationfor

thelargestandcoarsest(master)grid.Timestepstypicallyrangefrom5‐15minutesforgrid

cellsizesof10‐50km,toaminuteorlessforsmallcellsizesof1‐2km.Asaresult,nestedgrids

requiremultipledrivingtimestepspermasterstepdependingontheirgridsizesrelativetothe

mastergridspacing.Furthermore,multipletransportandchemistrytimestepsperdrivingstep

areusedasnecessarytoensureaccuratesolutionsfortheseprocessesonallgrids.



 

equationsreaction specificMechanism





























































































































Chemistry

ScavengingWet

diffusionXY

diffusion

transportZ

lxz

advectionY

lyz

advectionX

Emission

ρ/c

ρK

cvA

cuA

zyx

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Thefirstprocessineachtimestepforagivengridistheinjectionofemissionsfromallsources.

CAMxthenperformshorizontalandverticaladvection,verticaldiffusioncoupledtodry

deposition,horizontaldiffusion,chemistry,andfinallywetscavenging.

Althoughadvectionisperformedseparatelyinthex(east‐west),y(north‐south),andz(vertical)

directions,thenumericallinkagebetweenthesecomponentshasbeendevelopedinamass

consistentfashiontopreservethedensityfieldateachtimestep.Thismaintainstheflexibility

toallowmanytypesofmeteorologicalmodels,andmodelinggridresolutions,projections,and

layerstructures,tocharacterizetransportinCAMx.

Tracegasesandparticlesareremovedfromtheatmosphereviadepositiontotheground.Dry

depositionreferstothedirectsedimentationand/ordiffusionofmaterialtovariousterrestrial

surfacesanduptakeintobiota.Drydepositionvelocitiesforeachspeciesareusedasthe

surfaceboundaryconditionforverticaldiffusion,whichappropriatelycouplessurfaceremoval

ofpollutantsthrougheachcolumnofcellsviatheverticalmixingprocess.Wetdeposition

referstotheuptakeofmaterialintocloudwaterandprecipitation,anditssubsequenttransfer

tothesurface.Theefficiencywithwhichwetanddrydepositionprocessescanremove

pollutantsfromtheairdependsuponthephysicalandchemicalpropertiesofthepollutants,

localmeteorologicalconditions,thetypeofsurfaceonwhichtheyarebeingdeposited,andon

thefrequency,duration,andintensityofprecipitationevents.

4.2CAMXGridConfiguration

4.2.1GridCellArrangement

CAMxcarriespollutantconcentrationsatthecenterofeachgridcellvolume,representingthe

averageconcentrationovertheentirecell.Meteorologicalfieldsaresuppliedtothemodelto

quantifythestateoftheatmosphereineachgridcellforthepurposesofcalculatingtransport,

chemistry,andremoval.CAMxinternallycarriesthesevariablesinanarrangementknownas

an“ArakawaC”gridconfiguration(Figure4‐1).Statevariablessuchastemperature,pressure,

watervapor,andcloudwaterarelocatedatcellcenteralongwithpollutantconcentration,and

representgridcellaverageconditions.Windcomponentsanddiffusioncoefficientsarecarried

atcellinterfacestodescribethetransferofmassinandoutofeachcellface.NoteinFigure4‐

1,forexample,thathorizontalwindcomponentsuandvarestaggeredfromeachother.This

facilitatesthesolvingofthetransportequationsin“fluxform”.

Dependinguponthesourceofmeteorologicaldata,itisrecommendedthattheuserdirectly

providethegriddedhorizontalwindfieldsinthestaggeredArakawaCconfiguration.However,

thisisnotalwaysfeasible,andsoCAMxofferstheoptionfortheusertosupplyall

meteorologicalvariables,includinghorizontalwindcomponents,atcellcenter;inthiscase

CAMxinternallyinterpolatesthewindstocellinterfaces.Notethatthisleadstoaslight

smoothingeffectonthehorizontalwindfields.

Figure4‐1alsodescribesthehorizontalcellindexingconventionusedinCAMx.Eachcellis

definedbytheindexpair(i,j),whereirangesfrom1tonx(thenumberofcellsintheeast‐west

direction),andjrangesfrom1tony(thenumberofcellsinthenorth‐southdirection).The

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Figure4‐1.AhorizontalrepresentationoftheArakawaCvariableconfigurationusedin

CAMx.



easternandnorthernfacesofthecellareindexed(i,j),whilethewesternandsouthernfaces

areindexed(i‐1,j)and(i,j‐1),respectively.

Inthevertical,mostvariablesarecarriedateachlayermidpoint(definedasexactlyhalfway

betweenlayerinterfaces)torepresentlayeraverages.Againtheexceptionsarethosevariables

thatdescribetherateofmasstransportacrossthelayerinterfaces,whichincludethevertical

diffusioncoefficientKVandtheverticaltransportrate



.Thesevariablesarecarriedinthe

centerofeachcellhorizontally,butarelocatedatthetopofthelayer(i.e.,theinterface)

vertically.

4.2.2GridNesting

CAMxincorporatestwo‐waygridnesting,whichmeansthatpollutantconcentration

informationpropagatesintoandoutofallgridnestsduringmodelintegration.Anynumberof

gridnestscanbespecifiedinasinglerun,wherehorizontalgridspacingcanvaryfromonegrid

nesttoanother(notethatverticalgridstructuresmustbeconsistentamongallgrids).The

nestedgridcapabilityofCAMxallowscost‐effectiveapplicationtolargeregionsinwhich

regionaltransportoccurs,yetatthesametimeprovidingfineresolutiontoaddresssmall‐scale

impactsinselectedareas.

Eachgridnestisdefinedoverasubsetofmaster(coarsest)gridcells.Therangeofmastergrid

rowandcolumnindicesthatdefinethecoverageofeachnestedgridmustbespecifiedinthe

runcontrolfile.Anintegernumberofnestedgridcellsmustspanonemastergridcell;this

numberisreferredtoasa“meshingfactor”.“Buffer”cellsareaddedaroundtheperimeterof

eachnestedgridtoholdlateralboundaryconditions.Buffercellsareaddedautomatically

withinCAMxandshouldnotbespecifiedbytheuserintheruncontrolfile.Allnestedgrid

outputfilescontaindatafortheentirearrayofcomputationalandbuffercells;however,buffer

cellconcentrationsareconsideredinvalidandshouldbeignored.Additionally,allnestedgrid

(i, j)

T, p, q, Kv

(i, j)

(i, j-1)

(i-1, j) u, Kx

u, Kx

v, Ky

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Figure4‐2.Anexampleofhorizontalgridnesting,showingtwotelescopingnestedgrids

withina10×10cellmastergrid.Theouternestcontains10×12cells(includingbuffercellsto

holdinternallateralboundaryconditions),andtheinnernestcontains6×10cells(including

buffercells).



inputfilesmustcontaindatafortheentirearrayofcomputationalandbuffercells.Anexample

ofahorizontalnestingarrangementisshowninFigure4‐2.Here,twotelescopingfinegrid

nestsaredefined:onewithameshingfactorof2spanningmastergridcells(5,4)to(8,8),and

onewithameshingfactorof4spanningmastergridcells(6,6)to(6,7).

Restrictionsonspecifyingthesizeandresolutionofallgridnestsincludethefollowing:

1) Theratioofmastergridcellsizetonestedgridcellsizemustbeaninteger(e.g.,a

“meshingfactor”of3meansthat3nestedcellsspanthedistanceof1mastercell,

resultinginanareaof9nestedcellspermastercell);

2) Fortelescopinggrids(anestedgridcontaininganevenfinergrid),thecellsizeofthefinest

gridmustbeacommondenominatorforallparentgridsaboveit(e.g.,a36‐12‐4kmor

36‐12‐2kmarrangementisallowed,buta36‐12‐9kmisnot);

3) Therestrictionin(2)abovedoesnotapplytoparallelnestedgridsofthesamegeneration

(e.g.,4kmand5kmgridscanbelocatedindifferentareasofamastergridprovidedthat

themastercellsizeissomemultipleof20km);

4) Nestedgridscannotoverlap,althoughtheymayshareacommonlateralboundaryor

edge;

Coarse Grid Boundary Cells

Fine Buffer Cells

Boundary of Fine Grid 1

Boundary of Fine Grid 2

1 2 3 4 5 6 7 8 9 10

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5) Nestedgridscannotextendintoalateralboundary,ornon‐modeled,areaofthemaster

grid;

6) CAMxiscurrentlyconfiguredtoallowfour“generations”ofnests(e.g.,fourlevelsof

telescopinggrids);thiscanbeextendedinthecodeifmorethanfourlevelsofnestsare

required;

7) Thetotalverticaldepthofeachnestedgridmustexactlymatchthedepthofthemaster

grid,andnestedgridverticallayerstructuresmustbeconsistentwiththemastergridin

termsofthenumberoflayersandtheirthicknesses;

4.2.3Flexi‐Nesting

ThefollowingFortranbinaryI/Ofilesmustbeprovidedforthemastergrid,andoptionally

providedforeachnestedgrid:

 2‐Dsurfaceemissions;

 2‐Dtime‐invariantsurfacecharacteristics(landuseandLAIdistribution);

 2‐Dtime‐variantsurfacemeteorology(surfacetemperature,snowcover);

 3‐Dtime‐variantstatemeteorology(wind,temperature,pressure,moisture,verticalgrid);

 3‐Dtime‐variantcloudandprecipitationvariables;

 3‐Dtime‐variantverticaldiffusivities

Anyoftheseinputfilesmaybesuppliedforeachnestedgrid,ornoneatall.Ifanyofthesefiles

arenotsuppliedforaparticularnestedgrid,theFlexi‐NestalgorithmwithinCAMxinterpolates

themissingfieldsfromtheparentgrid.Clearlyitisdesirabletoprovidenestedgriddata

wheneverpossible.However,theabilitytointerpolatedataisusefulfortestingsensitivityto

gridconfigurationsorforsituationswhenitisnotpossibletorunameteorologicalmodelforall

gridnests.

TheFlexi‐Nestoptionalsoallowsuserstoredefinethenestedgridconfigurationatanypointin

asimulation.Nestedgridscanbeintroducedorremovedonlyatthetimeofamodelrestart

sinceanewCAMxusercontrolfilemustbeusedtoredefinethegridconfiguration.For

example,theusermaywishto“spin‐up”themodeloverthefirsttwodaysusingjustthemaster

grid.Onthethirdday,theusermightintroduceoneormorenestsformoredetailedanalysis.

Thiswouldrequirethatthemodelberestartedonthethirddaywithanewcontrolfilethat

definesthepositionofthenewnestsand(optionally)providesanyadditionalinputfieldsfor

thesegrids.CAMxwillinternallyreconcilethedifferencesingridstructurebetweentherestart

filesandthenewusercontrolfile,andtheninterpolateanydatafieldsnotsuppliedtoCAMxfor

thenewnestsfromtheparentgrid(s).

4.3TreatmentofEmissions

PollutantemissionsaretreatedintwobasicwayswithinCAMx:low‐level(gridded)emissions

thatarereleasedintothelowest(surface)layerofthemodel;andelevatedstack‐specific

(point)emissionswithbuoyantplumerisethatcanbeemittedintoanymodellayer.Emission

ratesareheldconstant(nottimeinterpolated)betweenreadingintervals(usually1hour)but

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areinjectedateverygrid‐specifictimestepduringthesimulation.Griddedandpointemissions

areprovidedtoCAMxinseparateinputfiles.Externalemissionprocessingsystemsareusedto

developgriddedandpoint,time‐andspace‐resolved,chemically‐speciatedinputfilesforCAMx.

TheseexternalprogramsarenotdiscussedinthisUser’sGuide;seeSection2formore

informationonemissionsystemsthatareusedtosupportCAMxapplications.

4.3.1GriddedEmissions

Two‐dimensionalgriddedlow‐levelemissionsaredefinedbyspace‐andtime‐varyingratesfor

eachindividualgasandPMspeciestobemodeled.Griddedemissionsrepresentsourcesthat

emitnearthesurfaceandthatarenotsufficientlybuoyanttoreachintotheuppermodel

layers.Suchemissioncategoriesinclude:

 Low‐levelstack(point)emissionsthataretoosmalltoresultinplumeriseabovethe

modelsurfacelayer;

 Othernon‐pointindustrialsources(fugitiveleaks,tanks,etc.);

 Mobilesources(cars,trucks,non‐roadvehicles,railroad,marine,aircraft,etc.);

 Residentialsources(heating,cooking,consumerproducts);

 Commercialsources(bakeries,refuelingstations,drycleaners);

 Biogenicsources;

 Naturalsources(smallfires,wind‐blowndust).

Thespatialdistributionofeachindividualsourcewithinthesecategoriesisdefinedbythe

modelinggrid.Informationsuchaspopulationdistribution,housingdensity,roadway

networks,vegetativecover,etc.istypicallyusedasasurrogatetodistributeregionalemission

estimatesforeachsourcetothegridsystem.Processingtoolsareusedtocombineemissions

fromallsourcesintoasingleinputfileforeachgrid(seeSections2and3).

4.3.2ElevatedPointEmissions

Similarlytogriddedemissions,elevatedpointemissionsaredefinedbyspace‐andtime‐varying

ratesforeachindividualgasandPMspeciestobemodeled.Theonlydifferenceisthatthese

sourcesemitfromindividualstackswithbuoyantrisethatmaytakethemintouppermodel

layers.Thesetypesofsourcesarealmostalwaysassociatedwithlargeindustrialprocesses,

suchaselectricgenerators,smelters,refineries,largefactories,etc.butcanalsorepresent

naturalelevatedsourcessuchaswildfiresandlightningNOx.Thespatialdistributionofthese

pointsisspecificallygivenbythecoordinatesofthestacksthemselves(gridlocationsare

determinedwithinCAMx).PlumeriseisdeterminedwithinCAMxasafunctionofstack

parameters(height,diameter,exitvelocityandtemperature)andambientmeteorological

conditions,sothepointsourcefileprovidesspeciatedtime‐resolvedemissionratesandstack

parametersforeachindividualsource.Asinglepointsourcefileprovidesthedefinitionofall

stacksandtheiremissionsovertheentiremodelingdomain(seeSections2and3).

Plumeriseiscalculatedusingthemulti‐layerstability‐dependentalgorithmofTurneretal.

(1986).Thisapproachcalculatesthemomentumandbuoyantplumeriseenergyfromthe

stack,takesthelargerofthesetwovalues,anddeterminesthedissipationofthatenergyvia

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

mixingwithambientairaccordingtothemeteorologicalconditionsthroughthehostmodel

layer.Ifsufficientenergyremainstoreachintothenextmodellayer,thecalculationfor

buoyantriserepeatsforthemeteorologicalconditionsofthatlayer,andsoon,untilalayeris

foundwheretheplumecannotriseanyfarther.Allemissionsfromthissourcearethen

injectedintothegridcelldirectlyabovethestackatthislayerheight.Thisalgorithmwas

adoptedforCAMxbecauseitprovidesamorerealistichandlingofstablelayersaloftthatcan

trapplumerise,whereasthiseffectwouldnotberealizedbasedonmeteorologicalconditions

atstacktopalone.

Underneutral/unstableconditions,momentumriseatthestacktopiscalculatedfrom



whilebuoyancyriseisthelesserof



and



Intheseexpressionsdsisstackdiameter(m),vsisstackexitvelocity(m/s),hsisstackheight(m),

wisambientwindspeed(m/s),andzbisthedistancebetweenthestacktopandthebaseofthe

currentmodellayer.Aminimumwindspeedof1m/sisspecifiedtoavoidunrealisticallylarge

plumerise.Buoyancyfluxfisinitiallycalculatedfromstackparameters,butissettoresidual

fluxenteringthebottomofanyhigherlayer.Theinitialbuoyancyfluxatstacktopisgivenby



wheregisgravitationalacceleration(9.8m2/s),Tsisstackexittemperature(K),andTis

ambienttemperature(K).Theresidualfluxcalculationintothenexthigherlayerdependson

whichneutral/unstablebuoyancyriseequationwasoriginallyusedinthecurrentlayer:



or



whereztisthedistancebetweenstacktopandthetopofthecurrentmodellayer.

Understableconditions,momentumriseatthestacktopiscalculatedfromthelesserofHmu

and

Hss







bbu zwfH  5/3

/30













bsbu zwfhwfH  5/2

5/3

3/200/24















ss T

dvgf 4

3/5

30 











tbu zH



3/2

33 1105.5





















tbu

tbu zH

zHwf

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

whilebuoyancyriseisthelesserof



and



Intheseexpressions,





zisthepotentialtemperaturegradient(ameasureofatmospheric

stability).Herealso,buoyancyfluxisinitiallycalculatedfromstackparameters,butissetto

residualfluxiftheplumeextendsintothenexthigherlayer.Theresidualfluxcalculation

dependsonwhichstablebuoyancyriseequationwasoriginallyused:



or



Whenfinalplumeriseisreachedusingstablebuoyancyrise,itisadjusteddownwardtotwo‐

thirdsoftherisethroughthestabledepth.Afterfinalplumeriseisdetermined,theriseis

furtheradjusteddownwardbystacktipdownwashaccordingtoacriticalFroudenumberand

ambientwindspeed.ThestackFroudenumberisgivenby



ForF<3,nodownwashadjustmentismadetofinalplumerise.Abovethatvalue,thefollowing

downwashfactors(D)areapplieddependingupontheambientwindspeedatstacktop:



CAMxinjectspointsourceemissionsintoallmodellayersspannedbytheplumedepthatfinal

(adjusted)rise.Plumedepthisdeterminedasafunctionofstackdiameter,plume

6/1

3/1

2/1

646.0





























zwT



3/1

8.1































bbs z







56.0 bt zz

ff 









3/83/8

3/1

24.0 bt zz

ff 









TTdg









vwD

vwv

riseplumenowvD













8/3

3/8

3/1

1.4































bbs z



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

temperature,plumevelocity,timeofplumerise,andambientwindandtemperature

conditions.Auniformmassdistributionthroughplumedepthisassumed.Ifthisdepthis

whollycontainedwithinasinglelayer,thatlayerreceivesallemissionmass.Ifthisdepthspans

severallayers,thenfractionsoftheemissionsareinjectedintotheselayersaccordingtothe

fractionofplumedepthspanningthoselayers.Weapplythe“rule‐of‐thumb”thatplumedepth

equalsplumerise(TurnerandSchulze,2007)asamaximumlimitforplumedepth.

Thefollowingequationsareusedtodefinetheplumedepthafterreachingfinalrise.Theseare

basedontheapproachusedintheSCIPUFFmodel(EPRI,2000)andweredevelopedforusein

theCAMxplume‐in‐grid(PiG)submodel.TheplumedepthDpatfinalriseisgivenby







2/1

2223 tKDD sp  



whereDsisstackdiameter,Kisplumediffusivityduringrise,andtisthetimeofrise.Thetime

ofriseisdeterminedbydividingfinalplumerisebythemeanplumerisespeedVp;thelatteris

settohalfthestackexitvelocity.Alowerlimitof1m/sisappliedtotheexitvelocity,sothe

minimumvalueofVpis0.5m/s.Theplumediffusivityisdeterminedbyscalinginitialplume

width(accordingtostackdiameter)bytheturbulentfluxmomentqp2:







215.0 ps qDK 

where





























 22

22 3

4.0

ppp Vv

Vfq 



TheturbulentfluxmomentisafunctionofthemeanplumerisespeedVp,theambientwind

speedvtakenattheleveloffinalrise,andaplumeentrainmentcoefficientfp:

















 2

241

sp VT

gDf 



wheregisthegravitationalconstant(9.8m2/s),Tisambienttemperatureattheleveloffinal

rise,andTpisthemeanplumetemperature,takenasthemeanofthestackexittemperature

andtheambienttemperatureatfinalrise.

4.4Three‐DimensionalTransport

4.4.1ResolvedTransport:Advection

TheCAMxadvectionalgorithmisbothmassconservativeandmassconsistent.Mass

conservationreferstotheabilitytoaccuratelyaccountforallsourcesandsinksofmassinthe

model,withnospuriouslossorgainofmassduringmodelintegration.Tobemass

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conservative,CAMxinternallycarriesconcentrationsofeachspeciesasadensity(µmol/m3for

gases,µg/m3foraerosols),andsolvestheadvectionanddiffusionequationsinfluxform.This

alsoservestosimplifymassbudgetaccounting,whichisusedbythevarioussource

apportionmentandprocessanalysisoptions.Gasconcentrationsareinternallyconvertedto

volumetricmixingratio(partspermillion,orppm)forthechemistrystep,andwhentheyare

writtentotheaverageoutputfiles.

Massconsistencyreferstothemodel’sabilitytotransportpollutantmassexactlyequivalentto

theinputatmosphericmomentumfield.Forexample,amodelthatisperfectlymassconsistent

willpreserveaunitypollutantmixingratiofieldinadivergentmomentumfieldgivenconstant

unityboundaryandinitialconditionsandzerosourcesandsinks.Sourcesofpoormass

consistencyinairqualitymodelsaretypicallyrelatedto(1)supplyingmeteorologythatis

inherentlyinconsistent(e.g.,fromaninterpolativeobjectiveanalysisordiagnosticmodel);(2)

spatiallyinterpolatingoraveragingmeteorologicalmodelfieldstoadifferentairqualitymap

projectionorgridresolution;and(3)employingdifferentnumericaland/orphysicalmethodsin

theairqualityandmeteorologicalmodels.

ItisexpectedthatCAMxuserswillpreparehighquality,massconsistentmeteorologicalfields

usingadvancedprognosticmodelssoastominimizeinconsistenciesintheinputsthemselves.

Thepracticeofdevelopingmeteorologicalinputfieldsusingobjectiveanalysisor“diagnostic”

approachesishighlydiscouraged.

CAMxoperatesonthemapprojectionsandgridsystemsemployedinseveralwidelyused

prognosticmeteorologicalmodels(e.g.,WRF,MM5,andRAMS)sothattranslationof

meteorologicaldatatoCAMxrequiresaslittlemanipulationaspossible.However,CAMx

providesaveryimportantflexibilitythatallowstheairqualitygridtodifferinprojectionand

resolutionfromthesourceofmeteorologicaldata.This,ofcourse,leadstoapotentiallylarge

externalsourceofmassconsistencyerror.TheabilitytodriveCAMxwiththeoutputfromany

prognosticmeteorologicmodelguaranteesadifferenceinnumericalmethodsbetweenthetwo

models,leadingtoaninternalsourceofmassconsistencyerror.Thethreediminensional

advectionalgorithminCAMxisdesignedtocompensateforbothexternalandinternalsources

ofconsistencyerror.

Horizontaladvectionusesinputhorizontalwindsfieldsandissolvedusingtheareapreserving

flux‐formadvectionsolverofBott(1989)orthePiecewiseParabolicMethod(PPM)ofColella

andWoodward(1984)asimplementedbyOdmanandIngram(1993).Thesetwofinite

differenceschemeswereincorporatedintoCAMxbecausetheyprovidehigherorderaccuracy

withminimalnumericaldiffusion,yetareequivalentinexecutionspeedcomparedtoother

simpleradvectionalgorithmswhenoperatingonequivalenttimesteps.InCAMx,theBott

schemeisallowedtotakelargertimestepsthanPPMbecauseBottremainsstableforCourant‐

Friedrichs‐Levy(CFL)numbersupto1(i.e.,theratioofwindspeedtogridspacing).Timesteps

aredeterminedforBottusingaCFLnumberof0.9,whiletimestepsforPPMarerestrainedbya

CFLnumberof0.5.Therefore,theBottoptionresultsinafastersimulationthanthePPM

option,perhapsatthepriceofsomeaccuracy.Werecommendtestingbothforyourspecific

application.

March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



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

CAMxinternallycalculatesaninstantaneousverticalvelocityfieldfromgrid‐andtimestep‐

specifichorizontalmomentumfieldsasawaytobalancethelocalatmosphericcontinuity

equation.Tocalculateaverticalvelocityprofileforagivengridcolumn,thedivergent

atmosphericcontinuityequation



islocallyintegratedthroughthedepthofthecolumnbyimposingzeroverticalvelocityatthe

ground:



wherethelocaltime‐ratechangeofatmosphericdensity



/tineachgridcellisknownfrom

theinputmeteorologicalfields.Thehorizontalfluxdivergenceofatmosphericdensityis

calculatedinamannerthatisnumericallyconsistentwiththeprocedureusedtohorizontally

advectpollutants:



andthisequationissolvedusingeithertheBottorPPMadvectionsolvers,asdescribedabove.

Inthisapproach,averticalvelocityprofilew(z)isconstructedthatprovidesabalancebetween

theimposeddensitytendencyandtheresolvedhorizontalmomentumdivergenceineachgrid

cellateachtimestep.Totalthree‐dimensionaladvectionthusincludesresolvedmomentum

convergence/divergenceratesaswellasanyartificialdivergencescausedbythehorizontaland

verticalgridspecifications(e.g.,spatiallyvaryingverticalgridstructure,orsystematic

distortionsassociatedwiththemapprojections).

Thetotalverticaltransportrate



ataparticularlayerinterfaceisdefinedasthecombinationof

resolvedverticalvelocityandthelocaltime‐rateofchangeofthelayerinterfaceheight:



Thetotalverticaltransportrateisusedforsubsequentverticaladvectioncalculationsforall

pollutants.Insimpletestsinwhichauniformpollutantfieldofunitymixingratioistransported

throughoutasingleregionalgridoverseveraldaysusingactualepisodicmeteorologicalinputs,

thisapproachhasbeenshowntoprovidenearlyexact(towithin10‐3‐10‐4%)consistency

betweenthedensityandpollutantfields.

Verticaladvectionissolvedusingaspecificimplicitbackward‐Eulerintegrationscheme

designedspecificallyforCAMx(Emeryetal,2011).Sinceimplicitschemesareabsolutelystable,

onlyonesolutionstepisnecessaryperdrivingtimestep.Explicitapproachesrequire

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

March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



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

potentiallymanysub‐steps(ontheorderof10‐100)tomaintainastablesolution,which

introducesthepotentialforexcessivenumericaldiffusion.

4.4.2Sub‐GridTurbulentTransport:Diffusion

CAMxemploysafirst‐ordereddyviscosity(or“K‐theory”)approachbydefaulttorepresentsub‐

gridturbulentdiffusion(ormixing).Asa“local”closuretechnique,K‐theoryonlytreatsmass

transfercell‐by‐cell(horizontal)orlayer‐by‐layer(vertical),analogouslytothediffusionofheat

throughasolidmedium.WhereasK‐theoryadequatelycharacterizeshorizontaldiffusionand

weakverticalmixingduringneutralandstableconditions,theshortcomingsofK‐theoryare

relatedtoitsinadequatetreatmentofdeepverticalconvectiveboundarylayermixing.In

convectivesituations,buoyantplumesderivingenergyinthesurfacelayerarequicklyand

efficientlymixeddeepintotheatmospherewithineddiesthatareusuallymuchlargerthanthe

individualmodellayers.Therefore,K‐theorymaymixtheconvectiveboundarylayermuchless

efficientlythancommonlyobserved.Thishasbeenshowntohaveveryimportantramifications

forchemistry,especiallyduringtransitionperiodsbetweenstable/neutralandconvective

conditions.CAMxincludestheoptiontouseK‐theoryverticalmixing(default)orthenon‐local

AsymmetricConvectiveModel(ACM2)fromPleim(2007).

4.4.2.1HorizontalDiffusion

AsdiscussedbyYamartino(2000)advectionsolverssuchasBottandPPMreducenumerical

diffusiontothepointwheremodelersneedtobeconcernedaboutincludingappropriatelevels

ofexplicithorizontaldiffusion.Currently,thereisverylittleinformationontheappropriate

levelofhorizontaldiffusionforEuleriangridmodels.ThisissueisnotlimitedtoCAMx.

ExplicithorizontaldiffusioncoefficientsaredeterminedwithinCAMxusingadeformation

approachbasedonthemethodsofSmagorinsky(1963):



Separatediffusivitycomponentsaregeneratedforfluxesinthex‐andy‐directionssinceKXand

KYarecalculatedforseparatecellfacesintheArakawaCgridarrangement.ThevalueofK0is

specifiedaccordingtotheapproachinMM5(AnthesandWarner,1978):



AmaximumvalueofKX/Yissettomaintainnumericalstabilityforthegivengrid‐specific

timestep.Aminimumvalueissetto1m2/s.Horizontaldiffusionisappliedusinganexplicit

simultaneoustwo‐dimensionalflux‐divergencecalculation.

4.4.2.2K‐theoryVerticalDiffusion

Thedefaultverticaldiffusionsolver(K‐theory)usesastandardimplicitbackward‐Euler

integrationscheme.Griddedverticaldiffusioncoefficients(Kv)mustbesuppliedtothemodel

2/1

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4.CoreModelFormulation



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

itislargerthanthelatter.TheCAMximplementationofACM2supportsOMPandMPIparallel

processing.

NotethatACM2increasesCAMxruntimeconsiderably.WhereastheoriginalCAMxK‐theory

solverisimplicitanddoesnotneedtousesmalltimesteps,ACM2anditsK‐theorycounterpart

bothuseexplicitsolvers,whichmustdividethemodeltimestepintomanyverysmallsub‐steps

togenerateastablesolution.Theslow‐downcanbeexacerbatedbyusingthemuchlarger

ACM2verticaldiffusivityvaluesinsteadofthestandarddiffusivityoptionsavailableintheCAMx

meteorologicalpreprocessors.

NOTE:ACM2doesnotworkwiththeDecoupledDirectMethod(DDM)ortheIntegrated

ProcessRate(IPR)componentoftheProcessAnalysis(PA)tool.

4.5WetDeposition

Wetdepositionisthepredominantremovalprocessforfineparticles.Particlesactascloud

condensationnucleiandresultingclouddropletseffiecientlygrowandaccreteinto

precipitation.Particlescanalsobedirectlyscavengedbyprecipitationviaimpaction.Therates

ofnucleationandimpactiondependuponcloudtype(e.g.,prolongedwidespredstratiformvs.

brieflocalizedconvection),precipitationrate,andparticleandcloudwatersizedistribution.

Wetdepositioncanalsobeanimportantremovalprocessforrelativelysolublegasesthrough

thefollowingseriesofsteps:

 Diffusion/absorptionofgasmoleculesintoclouddroplets;

 Scavengingofclouddropletsbyprecipitation;

 Diffusionofambientgasesintofallingprecipitation;

 Possibleaqueous‐phasereactionswithincloudandrainwater.

Eachofthestepsabovemaybereversible,sothattheoverallnetremovalofgasesdependson

theresultsofforwardandbackwardprocessesateachstep.Therateatwhichtheseprocesses

occurdependsoncloudtypeandtheextenttowhicheachpollutantdissolvesinwaterandits

overallreactionrateonceinsolution.Cloudwaterdropletscanabsorbgasesfromtheairup

thelimitoftheirsolubilityinwater.Formanypollutantsthissolubilityfarexceedstheamount

ofpollutantpresentintheairasdeterminedbytheHenry’sLawconstant,whichisdefinedas

theequilibriumratioofpollutantconcentrationsintheliquid‐phasetothegas‐phase.High

valuesfortheHenry’slawconstant(>10,000M/atm)indicateastrongtendencytodissolveinto

waterdroplets,whereaslowvalues(<100M/atm)indicateatendencytoremainintheair

(SeinfeldandPandis,1998).Equilibriumbetweenairandwaterconcentrationisusually

establishedontimescalesofminutes,soequilibriumconditionscangenerallybeassumedto

existintheatmosphere.

ThebasicmodelimplementedinCAMxisascavengingapproachinwhichthelocalrateof

concentrationchangec/



twithinorbelowaprecipitatingclouddependsonascavenging

coefficient



:

March2016CAMxUser’sGuideVersion6.3

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

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

Thescavengingcoefficientisdetermineddifferentlyforgasesandparticles,basedupon

relationshipsdescribedbySeinfeldandPandis(1998).Twocomponentsarecalculatedfor

gases:(1)accretionofclouddropletsthatcontaindissolvedgases,and(2)directdiffusive

uptakeofambientgasesintofallingprecipitation.Twocomponentsarealsodeterminedfor

particles:(1)accretionofclouddropletsthatcontainparticlemassfromthenucleationprocess,

and(2)impactionofambientparticlesintofallingprecipitationwithanefficiencythatis

dependentuponparticleandraindropsize.Eachoftheseprocessesisdescribedbelow.

TheexternalenvironmentalinputstotheCAMxwetdepositionalgorithmincludethethree‐

dimensionalgriddeddistributionofcloudandprecipitationwatercontents,withthe

precipitationcontentsbrokendownintoliquid,snow,andice(“graupel”).Scavengingrate

equationswerederivedintermsofequivalentliquidprecipitationrates,sotheinput

precipitationwatercontentsareinternallytranslatedintothismetric.

ThefollowinggeneralassumptionsaremadeintheCAMxscavengingmodel:

1) Raindrops,snowflakes,andgraupelparticlesareeachseparatelyrepresentedbyasingle

meansize,mass,andfallspeed,whicharedeterminedfromequivalentliquid

precipitationrate;

2) Thereisnomixed‐phasedprecipitationwithinagivengridcell–thedividinglinebetween

liquidrainfallandthetwofrozenformsis273K;

3) Snowisonlyassociatedwithstratiformprecipitation,andgraupelonlywithconvective

precipitation;

4) Liquidcloudwaterisallowedtoexistbelow273K–alinearrampfunctionisappliedto

apportiontotalcloudwaterintoliquidformbetween233‐273K(allcloudwateris

assumedtobeinicecrystalformbelow233K);

5) Allgassescandirectlydiffuseintoorfromliquidrainfall(onlystrongacidscandiffuseinto

frozenprecipitation)atarateaccordingtotheprecipitation’sstateofsaturation,

pollutantdiffusivity,andaerodynamicconsiderations;

6) Allgasescandissolveintoliquidcloudwater,whichcanbescavengedbyallprecipitation

forms–dissolvedgassesareinequilibriumwithambientconcentrationsaccordingto

Henry’sLaw;

7) PMisirreversiblyscavengeddirectlybyallprecipitationformsviaimpaction,andby

uptakeintocloudwater(liquidandice)ascondensationnucleithatisitselfscavengedby

allprecipitationforms;

8) Allin‐cloudPMmassexistsincloudwater(i.e.,no“dry”aerosolsexistintheinterstitialair

betweenclouddroplets)–allPMspeciesandsizesarehygroscopicandinternallymixed.

4.5.1PrecipitationParameters

Themeanraindropdiameterdd(m)andfallspeedvd(m/s)aretakenfromtheempirical

estimatesofScott(1978).ThedropdiameterisrelatedtorainfallrateP(mm/hr),andthefall

cΛ

c



March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



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

speedrelationshiphasbeenmodifiedtobetteragreewithdataprovidedbySeinfeldandPandis

(1998):



TheprecipitationwatercontentLp(g/m3)isrelatedtorainfallrateby



where



wisliquidwaterdensity(g/m3).Thisequationcanbesimplifiedtoadependencyon

justrainfallratewhentheaboverelationsfordropvelocityandsizearesubstituted.The

resultingexpressionforrainfallrateasafunctionofprecipitationwatercontentis



LocatelliandHobbs(1974)developedpowerlawequationsrelatingaveragediameters,fall

speeds,andmassesfor15precipitatingice“habits”.Weconsolidatedtheserelationshipsinto

twoforms,termed“snow”and“graupel”,byfittingnewpowerlawcurvestotheLocatelliand

Hobbsdata.Forsnow,



Andforgraupel,



Notethatintheseequationsforice,ddisinmmandcrystalmassmdisinmg.Byassumingthat

thenumberdensityandmassofsnow/graupelcrystalsareequaltothoseforraindropsgiven

equalprecipitationwatercontents,wecanrelatethemagnitudesoficesizeandfallspeedto

equivalentliquidprecipitationrate.

4.5.2GasScavenging

Wetscavengingofgasesbyprecipitationoccurswithinandbelowprecipitatingclouds.Below

thecloud,thetotalgasconcentrationinagivengridcellisavailableforscavenging.Withina

cloudycellthetotalgasconcentrationmustfirstbepartitionedintoanaqueousfractioncaq

withincloudwaterandtheremaininggaseousfractioncgwithintheinterstitialair.Both

aqueousandinterstitialgasseswithinacloudycellareavailableforscavenging,butare

removedatdifferentratesasdescribedbelow.

21.04

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

March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



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

4.5.2.1ScavengingofGasesinCloudWater

Theaqueousconcentrationinliquidcloudwater(orcloudiceinthecaseofstrongacids)is

determinedbyHenry’sLawtherebyassumingthesolutionexistsinsteady‐stateequilibrium.

TheHenry’sLawconstantforagivengasspeciesk0(M/atm)specifiestheratioofpollutant

massinaqueoussolution(Mormol/lh2o)toitsequilibriumpartialpressure(atm)atstandard

pressureandtemperature.ThisconstantisadjustedfortemperatureTandconvertedtoa

dimensionlessmolarratio:



whereRistheidealgasconstant(8.20610‐2latm/molK),andAisthetemperature

dependencefactor.Dissociationofammonia,nitricacid,andsulfurdioxideasafunctionof

cloudandrainwaterpHisalsoconsideredinthesolubilitycalculation.TheeffectiveHenry’s

LawconstantHthusexpressestheequilibriumratiooftheaqueousconcentrationcaq(massper

volumeofwater)tothegasconcentrationcg(masspervolumeofair),



whicharerelatedtototalconcentrationcby



whereLciscloudliquidwatercontent(g/m3).

Thefractionofgasespresentincloudwatercanberemovedbyprecipitationviaaccretionof

cloudwaterontothefallinghydrometeor(liquidorice).Asthehydrometeorfalls,itsweepsa

cylindricalvolumeperunittimeequalto



wheredcisthesizeofclouddroplets.Thisimpliesthattheambientmotionofclouddropletsis

insignificantcomparedtothehydrometeorfallspeed.Duetoaerodynamicperturbationsofair

flowaroundthefallinghydrometeor,acollectionefficiencyisapplied,i.e.,thefractionofcloud

dropletswithinthecollectionvolumethatarescavengedbyprecipitation.Forlarge

hydrometeorswithsizesgreaterthan0.5mmanddroplets10‐20µm,wetakethisefficiencyto

be0.9(SeinfeldandPandis,1998).Also,wefurtherassertthat(dd+dc)2~dd2.Assumingthen

thatamono‐dispersedistributionofhydrometeorsarefallingthroughamono‐disperse

distributionofcloudwaterdroplets,thescavengingcoefficientforprecipitationcollectingcloud

wateris





dcd vddV 2

4

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dddc NEvdΛ2

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ATRkH 1

298

exp

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aqg

ccc





March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation

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

whereEisthecollectionefficiency(0.9)andNdisthehydrometeornumberdensity.The

numberdensitycanbeexpressedintermsofequivalentrainfallrate,fallvelocity,anddropsize:





SubstitutingtherelationshipbetweenNdandrainfallparameters,then



Thecloudwaterscavengingcoefficientisscaledbytheratioofaqueouspollutantconcentration

tototalgridcellconcentrationtoachievetheaqueous‐phasescavengingcoefficient:



4.5.2.2ScavengingofAmbientGases

Giventherelativelyshortresidencetimesoffallingprecipitationthroughagivengridcell,

aqueousequilibriumbetweenambientgasandprecipitationcannotbeassumedandsothe

transferofambientgasintoliquidrainfall(oriceinthecaseofstrongacids)isexplicitly

calculated.ThemaximumrateoftransferWofagastoafallinghydrometeorcontainingno

pre‐existingpollutantmassis



ThemasstransfercoefficientKccanbedeterminedforafallinghydrometeorwithspeedvdand

diameterddby



whereDgand



arethemoleculardiffusivityofthegasspeciesandair,respectively.



FollowingthemethodologyofSeinfeldandPandis(1998),therateofcaqincreasecanbe

representedbyamassbalancewiththerateoftransporttothehydrometeor:



TheexpressionforWissubstitutedintotheequationabove,rearranged,andexpressedin

termsofrainfallvelocity.Wethenassumethatthroughagivenmodellayertheambientgas

concentrationandhydrometeorpHandsizeisconstant.Multiplyingbythenumberdensityof

fallinghydrometeorsNddescribedaboveyieldsthegas‐phaseconcentrationscavengedbyall

dropsfallingthroughthelayer:

gc cHKW









































3/1

2/1

6.02







Λ7

102.4 



caq

ca c

ΛΛ





108.2

dvd









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

Withincloudylayers,thegas‐phaseandaqueous‐phasescavengingcoefficientsareaddedto

providethetotalin‐cloudscavengingrateforgases,



=



a.Forbelow‐cloudscavenging,



=



g.

4.5.2.3SolubilityLimitsonGasScavenging

Thereisachanceforrainfalltobecomesuper‐saturatedforsparinglysolublegassesasitfalls

throughagridcolumn.Thenetscavengingcoefficientforgasesdescribedaboveprovidesfor

themaximumpotentialuptakerateintocleanrainwater,socarefulconsiderationmustbe

giventoappropriatelydeterminethesignandmagnitudeofambientgridcellconcentration

changeaccordingtothedegreeofrainfallsaturation.Thechangeingasconcentrationis

relaxedtowardthedifferencebetweenthemaximumpossiblegasinsolutionforthegiven

conditionsceq,andtheamountofpre‐existinggasinsolutionfromlayersabovec0,



Hereceqisdeterminedfromthetotalliquidwaterinthecell(rainpluscloudwater)andfrom

Henry’slawequilibriumaccordingtothetotalgasconcentrationinthecell(ambientgrid

concentrationsplustotalgasinpre‐existingsolution).Iftheconcentrationchangeispositive,

massisaddedtotherainwater(c0isaugmented)andremovedfromthegridcell;ifnegative,

massisremovedfromrainwater(c0isdecremented)andaddedtothegridcell.

4.5.3AerosolScavenging

4.5.3.1ScavengingofAqueousAerosols

Allaerosolswithincloudylayersareassumedtoexistwithincloudwater.Therefore,the

scavengingcoefficientforaqueousaerosolsisexactlythesameasforthescavengingofcloud

droplets:



=



c.

4.5.3.2ScavengingofDryParticles

Wetscavengingofdryparticlesonlyoccursbelowprecipitatingclouds.Weusethesame

scavengingcoefficientasderivedforthecollectionofclouddroplets:



Forrainorgraupel,thecollectionefficiencyEisafunctionofparticlesizedp,andisgivenby

SeinfeldandPandis(1998)as:



Λ7

102.4 











tccc eq









exp1)( 0

gvd

Λ6

1067.1 



March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



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

whereµandµwarethekinematicviscosityofair(1.8×10‐5kg/m/s)andwater(10‐3kg/m/s),

respectively,



=dp/ddistheratioofparticlesizetohydrometeorsize,ReistheReynolds

numberforthehydrometeor,ScistheSchmidtnumberforthecollectedparticle,andStisthe

Stokesnumberofthecollectedparticle.TheReynoldsnumberisgivenby



whiletheSchmidtnumberis



whereDpistheparticleBrowniandiffusivity:



Here,kistheBoltzmanconstant(1.38×10‐23J/K)andCistheCunninghamcorrectionfactorfor

smallparticles:



andwhere-isthemeanfreepathofair(6.5×10‐8m).TheStokesnumberisgivenby



where



pistheparticledensity.TheS*parameterisgivenby











2/3

2/1

2/12/13/12/1

3/2

214

16.04.01





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









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







SRSR

cece









R





CTk





























C55.0

exp4.0257.1

ppd

Cdv













S



1ln1

12/1ln2.1

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

Notethatparticlesizedpanddensity



pareaffectedbyaerosolwatercontent,whichis

determinedfromlocalhumidityandPMdeliquescencepropertiesaccordingtotheISORROPIA

model(seeSection5).

Snowpresentsacomplicationfortheefficiencycalculation,sinceitisnotasinglesolidmassbut

ratheracollectionofcrystalsarrangedinamyriadofpossibleshapesthatcanleadtosignificant

aerodynamicdrag.Thisdragaffectsparticlecollectionefficiency.Tosimplifythecalculation,

weusethevalueforEdeterminedforrainandgraupel,butsetalowerlimitforEof110‐3

basedontheworkofSauterandWang(1989).

4.6DryDeposition

Drydepositioncanbeanimportantremovalprocessformanycompounds.Duetothedifficulty

ofmakingdirectmeasurementsofdrydepositionandtheneedforasuitablemodel

parameterization,drydepositionisoftentreatedasafirst‐orderremovalmechanism,where

thefluxofapollutanttothesurfaceistheproductofacharacteristicdepositionvelocityandits

concentrationinthe“surfacelayer”(i.e.,thelowestmodellayer).Depositionvelocitiesare

derivedfrommodelsthataccountforthereactivity,solubility,anddiffusivityofgases,thesizes

ofparticles,localmeteorologicalconditions,andseason‐dependentsurfacecharacteristics.The

factorsaffectingdepositionarediscussedinmoredetailbelow.

Foragivenspecies,particlesize,andgridcell,CAMxdeterminesadepositionvelocityforeach

landusetypepresentinthatcellandthenlinearlycombinesthemaccordingtothefractional

distributionoflanduse.Thedepositionfluxisusedasthelowerboundaryconditioninthe

verticaldiffusionalgorithm.Aerosolsizespectraandspecies‐dependentpropertiesneededfor

thedepositionvelocitycalculationsareexternallysuppliedtoCAMxforallpollutantspeciesvia

thechemistryparametersfile;griddedlanduseissuppliedtothemastergridandoptionallyany

nestedfinegrids;theseasonisdeterminedbythesimulationdateandlocationontheglobe.

Movementofmaterialalongapathfromtheatmosphere,throughanyplantcanopy,andonto

thevariousplantandgroundsurfaceswithinandbelowthecanopyistypicallymodeledby

analogytoanelectricalcircuit.Resistancesinserialandparallelarrangementsareusedto

representtherelativeeasewithwhichmaterialmovesthroughdifferentportionsofthe

depositionpathway.Eachbranchofthecircuitrepresentsadifferentpathbywhichmaterial

maybedeposited.Forexample,gaseouspollutantsmaytransferthroughthelowestlayersof

theatmospherepartiallyintoaplantcanopy,throughthestomatalopeningsonplantleaves

andintotheplantmesophylltissue.Alternatively,thematerialmaytravelallthewaythrough

theplantcanopyanddepositonthegroundsurface.

CAMxofferstwodrydepositionoptions:theoriginalapproachbasedontheworkofWesely

(1989)andSlinnandSlinn(1980);andanupdatedapproachbasedontheworkofZhangetal.

(2001;2003).Bothoftheseoptionsarebrieflydescribedbelow.

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

4.6.1TheWesely/SlinnModel

4.6.1.1DryDepositionofGases

Wesely(1989)developedaresistancemodelthatincorporatesthemajorelementsdescribed

above.Depositionvelocityvdiscalculatedfromthreeprimaryresistancesr(s/m)inseries:

sba

drrr

V

1



Theaerodynamicresistancerarepresentsbulktransportthroughthelowestmodellayerby

turbulentdiffusion,andoperatesequivalentlyforallgasesandsmallparticles.Themagnitude

ofthisresistancedependsontheintensityofturbulentmotion,whichinturndependsonsolar

insolation,windspeed,surfaceroughness,andnear‐surfacetemperaturelapserate.InCAMxit

iscalculatedfrom



whereu*isfrictionvelocity(m/s),kisvonKarman’sconstant,zisthelowestmodellayer

midpointheight(m),z0isthesurfaceroughnesslength(m),and



hisastabilitycorrectionterm.

ThesurfacelayerparameterizationofLouis(1979)isusedtosupplyfrictionvelocityand

stabilitycorrectionasafunctionofinputsurfacemeteorologyandroughnesslength.

Roughnesslengthisinternallyassignedaccordingtoseasonandtheinputgriddeddistribution

of11landusetypesasdescribedinSection3.Ingeneral,aerodynamicresistanceisata

minimumonwarm,sunnydayswithstrongmixingduetosurfaceheatingandmechanical

turbulence,andatamaximumoncool,calmnightswhenturbulentmixingissuppressed.

Thequasi‐laminarsublayer(orboundary)resistancerbrepresentsmoleculardiffusionthrough

thethinlayerofairdirectlyincontactwiththeparticularsurfacetowhichmaterialisbeing

deposited.Itisusuallyassumedtodependonlyonthemoleculardiffusivityofeachpollutant

species,andisgivenby



whereScistheSchmidtnumber,ortheratioofairviscositytospeciesmoleculardiffusivity.

Overland,surfaceresistancersisexpressedasseveralmoreserialandparallelresistancesthat

dependuponthephysicalandchemicalpropertiesofthesurfaceinquestion:



wherethefirstsetofparallelresistancesrepresentsthepathwayintothestomatal(rst)and

mesophyll(rm)portionsofactiveplants,thesecondisthepathwayintotheuppercanopy(ruc),

3/2

b

gsaccldcucmst

rrrrrrr







1111

























h

azuk



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

thethirdisthepathwayintothelowercanopy(rdcandrcl),andthefourthisthepathwaytothe

groundsurface(racandrgs).Manyoftheseresistancesareseason‐andlanduse‐dependent,and

arebuiltintoWesely’smodel;someinturnareadjustedwithinCAMxforsolarinsolationand

surfacewetness(vegetationisassumedtobeunstressed).Afewotherresistanceshavebeen

developedbyWeselyforSO2andozone,andsoarescaledforeachgaseousspeciesbasedon

thefollowingpollutantproperties:

 Moleculardiffusivity(determinedfrommolecularweight,OHg MM 2

/);

 Henry’slawsolubility(H);

 Chemicalreactivitytowardoxidationofbiologicalsubstances(f).

Thisallowstheresistanceapproachtobeusedtoestimatedepositionvelocitiesforawide

rangeofgaseouspollutants.

Thesurfaceresistancesforstrongacids(e.g.,nitric,sulfuric,andhydrochloricacid,peroxides)

aresettozerogiventheirstrongratesofupdatebybiotaandothersurfaces(Huebertand

Robert,1985;WeselyandHicks,2000).Thespeciesforwhichsurfaceresistanceissettozero

aredefinedintheCAMxchemistryparametersfile.

Overwater,thesurfaceresistanceforallgasspeciesotherthanozoneisbasedonsome

improvementsadoptedbyKumaretal.(1996)followingSehmel(1980):



whereTsissurfacetemperature(K).Forozone,thisequationhasbeenupdatedto

parametricallymatchthetendenciesofmeasuredozonefluxesreportedbyHelmigetal.(2012)

fromship‐bornemeasurements:

364

105101

uTH

s 



whereTsisinCratherthanK.Thecubictemperaturedependencefitsthedepositionvelocity

responsetotherangeofseasurfacetemperaturesreportedintheHelmigetal.data.The

additional1×10‐4termsetsanupperlimitonrsandalowerlimitondepositionvelocitysothat

thelatterdoesnotfallmuchbelow0.01cm/s.Alowerlimitof1500s/misplacedonrssuch

thatozonedepositionoverwaterdoesnotexceed6.5cm/s,whichistheupperlimitinthe

measureddata.

4.6.1.2DryDepositionofAerosols

Surfacedepositionofparticlesoccursviadiffusion,impaction,and/orgravitationalsettling.

Particlesizeisthedominantvariablecontrollingtheseprocesses.Theresistanceapproachof

SlinnandSlinn(1980),asimplementedbyKumaretal.(1996),hasbeenadoptedinCAMx.

Particledepositionvelocityforagivenaerosolsizeiscalculatedusingthefollowingresistance

equation:

suTH

103.9







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

wherevsedisthegravitationalsettling(orsedimentation)velocity.Thisvelocityisdependenton

aerosolsizeanddensity:



whereDisthelog‐meanparticlediameter(m)ofagivensizesection,ρpisparticledensity

(g/m3),gisgravitationalacceleration,and



istheviscosityofair.ThefactorCisthe

Cunninghamcorrectionforsmallparticles,asdescribedearlierforwetscavengingofparticles.

Notethatparticlesizeanddensityareaffectedbyaerosolwatercontent,whichisdetermined

fromlocalhumidityandPMdeliquescencepropertiesaccordingtotheISORROPIAmodel(see

Section5).

Aerodynamicresistanceraisidenticaltothevalueusedforgaseousdrydeposition.Resistance

todiffusionthroughthequasi‐laminarsub‐layerlayerdependsonaerosolBrowniandiffusion

andinertialimpaction.Particlesareassumedtoremainonasurfaceoncetheyimpact,so

resuspensioneffectsareignored.Boundaryresistancerbisgivenby



ThestokesnumberStiscalculatedfrom



4.6.1.3SpecificationofSeason

TheWesely(1989)depositionalgorithmspecifiesthevarioussurfaceresistancesbylandcover

typeforfiveseasons:Spring,Summer,Fall,Winter,andWinterwithsnowcover.CAMx

internallydefinesaseasonmaptodeterminefourofthesefiveseasonsbymonthandlatitude

(Table4‐2).Fivelatitudebandsexistineachhemisphere:

 Tropical <20

 Sub‐tropical 20to35

 Temperate35to50

 Cool 50to75

 Polar >75

TheseasonsintheNorthernandSouthernhemispheresareoffsetbysixmonths.Thisoffset

doesnotcauseanydiscontinuityattheequatorbecauseall12monthsaredefinedassummer

inthetropicalbandattheequator.Thisseasonmapisgeneralizedandmaynotbeidealforall

sedbaba

sedd vrrrr

vv 

 1





sed

CgD

v



bSu

r/3

3/2

*10







Ssed





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locations.Theseasonmapiscodedintodatastatementsinthe“CAMx/chmdat.f”

subroutineandcouldbechangedtobettersuitaspecificregion.

TheseasonmapshowninTable4‐2doesnotconsidersnowcoverbecauseitisquitevariablein

spaceandtime.Griddedsnowcoverdataarespecifiedinthetime‐variant2Dsurfaceinputfile

(seeSection3andSection4.7below).SnowcoveredgridcellsareassignedtheWesely(1989)

surfaceresistancesforthecategory“winterwithsnowcover”,regardlessoftheseason.



Table4‐2.Relationshipsbetweenseasonandmonth/latitudeusedintheCAMxWesely/Slinn

drydepositionmodel.Exception:seasonsfortheareawithin50N‐75Nand15W‐15Eare

internallysettothoseoflatitudeband35‐50toaccountforregionsofEuropeinwhichthe

climateisinfluencedbytheGulfStream.

MonthLatitudeBand

Northern

Hemisphere

Southern

Hemisphere

<2020‐3535‐5050‐75>75

Tropical Sub‐tropical Temperate CoolPolar

JanJulSummer Winter Winter WinterWinter

FebAugSummer Spring Winter WinterWinter

MarSepSummer Spring Spring WinterWinter

AprOctSummer Spring Spring SpringWinter

MayNovSummer Summer Spring SpringWinter

JunDecSummer Summer Summer SummerSpring

JulJanSummer Summer Summer SummerSummer

AugFebSummer Summer Summer SummerFall

SepMarSummer Summer Fall FallWinter

OctAprSummer Fall Fall FallWinter

NovMaySummer Fall Fall WinterWinter

DecJunSummer Fall Winter WinterWinter



4.6.2TheZhangModel

EnvironmentCanada’sAURAMSairqualitymodelusesastate‐of‐the‐sciencedeposition

schemethatpossessesanupdatedrepresentationofnon‐stomataldepositionpathways(Zhang

etal.2003;Zhangetal.2008).Theapproachincorporatesthe“leafareaindex”(LAI),whichis

animportantaspectofnewerdrydepositionschemesthatallowsforscalingofpollutant

uptakeintobiotaofvaryingdensities.LAIisdefinedastheratiooftheone‐sidedgreenleaf

areatoaunitareaoftheground.Itismeasuredbysatelliteinstrumentsatfairlyhighspatial

resolution.TheZhangmodelhasbeentestedextensivelythroughitsuseindailyairquality

forecastinginCanada,andhasbeenshowntoreproduceobservedfluxesofozoneandSO2with

reasonableaccuracy.InCAMx,theZhangmodelhastendedtogeneratelowerozone

depositionratesrelativetotheWeselymodel,whichleadstohigherozonepredictionsoverall.

ThiseffectisseasonallydependentandwillvarywiththedefinitionofLAI.Ozoneisless

sensitivetothesourceofLAI(whetherZhangdefaultsorsatellite‐enhanced)thantothechoice

ofdepositionmodel.

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4.CoreModelFormulation



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

4.6.2.1DryDepositionofGases

ThegasresistancemodelofZhangetal.(2003)invokesthesame3‐resistanceequationfor

depositionvelocityastheWesely(1989)model.Theequationsforaerodynamicresistance(ra)

andboundaryresistance(rb)areverysimilartotheWesely(1989)formulations.However,

Zhangetal.(2003)replacethesurfaceresistance(rs)equationwithanewrelationshipforthe

overallcanopyresistance:

gsaccutmst

rrrrr









11

1



whereWstisthefractionofstomatalblockingunderwetconditions,rcutisthecuticleresistance,

andallotherresistanceshavesimilarmeaningtotheWeselymodel.Stomatalresistance(rst)is

calculatedusingasunlit/shade(so‐called“two‐big‐leaf”)stomatalresistancesub‐model.

FollowingWesely(1989),valuesforrgandrcutarecalculatedforSO2andO3andthenscaledfor

othergaseousspecies.Cuticleresistanceisslightlydifferentfromthatdefinedintraditional

big‐leafmodelsinthatitalsoconsiderstheaerodynamicandquasi‐laminarresistancesof

individualleaves.Thisisdonebyparameterizingrcutasafunctionoffrictionvelocity,similarto

theconceptofoverallcuticleuptakeconsideredinamulti‐layermodelframework.

LAIisusedinfunctionsforrac,andrcut,wheretheLAIforanygivendayislinearlyinterpolated

frommonthlydefaultLAIasafunctionoflandusetype.ToaccountforLAIeffectsonsurface

roughness(z0),asimilardailyLAIinterpolationisappliedtothatparameter.Hence,theZhang

modeldoesnotrequirethespecificationofseason,asallresistanceequationsarecontinuous

overeachmonth(notethatCAMxautomaticallyappliesthe6‐monthoffsetforapplicationsin

thesouthernhemisphere).

Forsnowonthegroundandleaves,bothrgsandrcutareadjustedbyasnowcoverfraction,

whichiscalculatedfromsnowdepth,snowage,andlandusetypeasdescribedinSection4.7.

Snowcoverisdefinedthroughtheinput2Dsurfacefile,asdescribedinSection3.Forsurfaces

withoutcanopies,rgsisdefinedastheresistancetoanysurface(e.g.soil,ice,snowandwater),

racissettozero,andverylargevaluesareusedforrst,rmandrcut.

Overwater,theupdatedtemperature‐dependentozonesurfaceresistanceequationdescribed

abovefortheWeselyschemeisalsousedfortheZhangscheme.

TheZhangmodelincludesasetofembeddedannualsurfaceroughnessrangesandmonthlyLAI

specifictoeachofthe26landusecategories.Thecapabilitiesoftheschemewereextendedby

addingtheoptiontouseepisode‐specific(i.e.,satellite‐derived)LAIdata.Satellite‐basedLAI

datafromMODIS(MODerate‐resolutionImagingSpectroradiometer)2canbeprocessedinto

griddedLAIfieldsthatarepassedtoCAMxasanoptionalrecordinthetime‐invariant2D

surfaceinputfile(seeSection3).TheoptionalgriddedLAIfieldsareusedtoscalethedefault

landuse‐specificLAIvalues.Foreachgridcell,alanduse‐weighteddefaultLAIisdetermined



2MODISprovidesLAIat250meterspatialresolutionand16daytemporalresolution.

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March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



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

ThedepositionofaerosolsisbasedonthemodelofSlinn(1982),butusingsimplifiedempirical

parameterizationstoreplacedetailedcanopyinformation.Theaerosoldepositionvelocityis

definedas:

sedd rr

vv 

 1



wherevsedandrahaveidenticalmeaningsastheSlinnandSlinn(1980)definitiondescribed

earlierfortheWesely/Slinndepositionmodel.Notethatinthiscase,thevirtualserial

resistancera



vsedhasbeenremoved,whichresultsinhighervaluesofdepositionvelocity.The

quasi‐laminarboundaryresistanceisgivenby





1*0

REEEu

INIMB

b







wherethevariableEincludesthecollectionefficienciesforBrowniandiffusion,impaction,and

interception,respectively,R1isafactorrepresentingthefractionofparticlesthatsticktothe

surface,and



0isanempiricalconstantthatissettoavalueof3.TheBrowniancollection

efficiencydependsontheSchmidtnumber,whiletheimpactionefficiencyandR1dependon

theStokesnumber.

Thecollectionefficiencybyinterceptionalsoexistsiftheparticlepassesanobstacleata

distanceshorterthanitsphysicaldimensions(e.g.,largeparticlespassingnearhairyleaves).

Zhangetal.(2001)adoptedasimpleequationforthistermthatisafunctionofparticle

diameterandacharacteristicradius,forwhichdefaultvaluesaregivenfordifferentlanduse

andseasonalcategories.

Figure4‐5comparesestimatedparticledepositionvelocitiesfromtheZhangmodel,theSlinn

andSlinn(1980)model,andtheAERMODmodel(EPA,1998).Calculationsweremadefor

daytime,neutrallystableconditionsforarangeofwindspeedsandlandusecategories.Figure

4‐5showsthattheZhangmodelincreasesdepositionvelocitiesoverforestbyroughlyanorder

ofmagnitudeforthe0.1‐1mrange,yetreducesdepositionvelocitiesabove1m.

4.7SnowCoverandSurfaceAlbedo

Surfacealbedoforsnow‐coveredgridcellsiscalculatedaccordingtosnowcover,snowage,and

landcovertype.Theapproachisbasedonliteraturedescribingtheevolutionofsnowalbedoin

theWRF/NOAHlandsurfacemodel(LSM)overthepastdecade(Eketal.,2003;WangandZeng,

2010;Livnehetal.,2010;andBarlageetal.,2010).Fractionalsnowcover(fs)isaccountsforthe

effectsofsurfaceroughnesselements(shrubs,trees,rocksandotherstructures)extending

abovethin/patchysnow:

1exp 



exp

March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 92www.camx.com



Figure4‐5.Comparisonofparticledrydepositionvelocitiesasafunctionofsizeandwind

speeds(m/s)forthreemodels:black–Zhangetal.(2001);blue–SlinnandSlinn(1980);

orange–AERMOD(EPA,1998).Resultsareshownforaforestlandusecategoryduring

daytimeneutralstability.Particledensitywassetat1.5g/cm3.



where



=2.6,Wissnowwaterequivalentdepth(SWE),andWcisthethresholdSWEabove

whichfs=100%.FollowingWangandZeng(2010)andLinvehetal.(2010),Wcissetto0.01m

forbarrenorlowvegetation(grasslands)andto0.2mfortallvegetation(forest),exceptan

intermediatevalueof0.02misassignedtorange,mixedagriculture/range,andshrublands

wherevegetationistypicallyhigherthangrasses(Table4‐4).ThroughoutCAMxweapplya

commonapproximationthatactualsnowdepthis10SWE.

Snowalbedo(as)isallowedtoevolvetoaccountfortheopticaleffectsofmeltingand

accumulationofdirt/soot,followingtheapproachofLinvehetal.(2010):





whereamaxisthemaximumfreshsnowalbedo(0.85;Barlageetal.,2010),tisthenumberof

dayssincethelastsnowfall,A=0.94(0.82)andB=0.58(0.46)duringtheaccumulation

(ablation)phase.Accumulationoccursduringcoldperiodswhensurfacetemperatureisbelow

273K,whereasablationoccursduringmeltingperiodswhensurfacetemperatureisat273K.

Snowalbedoisconstrainedtoalowerboundof0.4.Snowageisrefreshedtozero(andsnow

albedoto0.85)whenSWEaccumulatesbymorethan0.001m/hr(accumulatingsnowdepth>1

cm/hr).

Theresultantgrid‐cellaveragesurfacealbedo(a)isalinearcombinationofsnowalbedo(as)

andterrestrial(non‐snow)albedo(at):



1



Forest

0.01

0.1

100

0.001 0.01 0.1 1 10 100

Particle diameter (m)

(cm s

-1

)

wind = 2

wind = 5

wind = 10

wind = 15

wind = 2

wind = 5

wind = 10

wind = 15

wind = 2

wind = 5

wind = 10

wind = 15

March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 93www.camx.com



whereatisdefinedaccordingtolandusetype(Tables3‐4,3‐5).Incaseadistributionof

multiplelandusetypesexistswithinagivengridcell,alinearweightingschemeisemployedto

accountforvariablesnowcoverfractionsforeachindividuallandusetype:



1







wherethesumisoveralllandusetypes,fnisthefractionalcoverageoflandusen,at(n)isthe

defaultterrestrialalbedoforlandusen,fs(n)isthefractionalsnowcoverforlandusen,andas(n)

isthecalculatedsnowalbedoforlandusen.Figure4‐6showsanexampleofgrid‐cellalbedo

evolutionforahypothetical20‐dayspringtimesnowevent(assumingablationconditions)for

lowandtallvegetationgridcellswithaterrestrial(non‐snow)albedoof0.05.Severalsnow

accumulationeventsarespecifiedtooccuroverthefirst12days,followedbyrapidmeltingto

zerodepthbyday20.Whiletotalalbedoincreasestopeakvaluesof0.85quiterapidlyforlow‐

vegetation,thevaluefortallvegetationlagsandpeaksjustabove0.5atmaximumsnowdepth.

Bothcasesindicateeffectsfromsnowdepth(fractionalsnowcover)andsnowage.



Figure4‐6.Exampleofgrid‐cellalbedoevolutionforahypothetical20‐dayspringtimesnow

event(assumingablationconditions)forlowandtallvegetationgridcellswithaterrestrial

(non‐snow)albedoof0.05.



4.8SurfaceModelforChemistryandRe‐Emission

TheCAMxsurfacemodelisanoptionalcapabilitythattreats:(1)chemicaldegradationand/or

transformationofdepositedpollutantmassonsoil,vegetationandanoverlyingsnowpack;(2)

volatilizationofchemicalproductsbackintotheair(re‐emission);and(3)lossfromleaching

intosoil,penetrationintoplanttissue,anduptakeintosnowmeltwater.Thesurfacemodel

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

01234567891011121314151617181920

Depth(m)

Albedo

DaysofExampleEvent

SnowDepthandAlbedowithAge

LowVegetation

TallVegetation

Depth

March2016CAMxUser’sGuideVersion6.3

4.CoreModelFormulation



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 94www.camx.com



treatsanysubsetofspecieslistedinthecoremodel’schemicalmechanism.Limitationsofthe

currentimplementationinclude:

 ThesurfacemodelcannotbeusedwiththePlume‐in‐Gridtreatment;

 Depositiontowatersurfacesisassumedtobeirreversibleandthusisnottrackedbythe

surfacemodel;

 Wetdepositiondoesnotcontributetosurfacemass,ascompoundsinaqueoussolution

areassumedtobeimmediatelylosttosurfacewaterprocesses(absorption,runoff,etc.).

4.8.1SurfaceModelAlgorithms

Figure4‐7displaysthesurfacemodelprocessesschematicallyandTable4‐3definesparameters

thatarereferredtoinFigure4‐7.Whilecoremodelalgorithmsareusedtodepositcompounds

tothesurfaceandre‐emitthemtotheatmosphere,thesurfacemodeltrackstheaccumulation

ofmassonterrestrialsurfacemedia(soil,vegetationandsnow),subsequentchemical

transformation(bothheterogeneousandphotolysis),re‐emissiontotheatmosphere,and

physicalremoval.



Figure4‐7.SchematicoftheCAMxsurfacemodel.



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Table4‐3.DescriptionofCAMxsurfacemodelvariablesshowninFigure4‐7.

VariableDefinitionUnits

AsAreicmassofcompoundonsoilorsnowmolha‐1

ApAreicmassofcompoundonvegetationmolha‐1

SsoilSoil‐airpartitioningcoefficientunitless

SsnowSnow‐airpartitioningcoefficientunitless

SvegVegetation‐airpartitioningcoefficientunitless

kleachSoilleachingratecoefficientmin‐1

KmeltSnowmeltlossratecoefficientmin‐1

kpenLeafpenetrationratecoefficientmin‐1

JPhotolysischemistryratecoefficientmin‐1

KHeterogeneouschemistryratecoefficientmin‐1

RleachLeachingorsnowmeltlossratemolha‐1min‐1

RpenLeafpenetrationratemolha‐1min‐1

RchemChemistryratemolha‐1min‐1



Afterdepositiontoasnow‐freesurfacegridcelliscalculatedeachtimestep,thenewly

depositedmassincrementsaredividedamongsoilandvegetationcompartmentsandaddedto

totalsurfacemassineachcompartmentaccumulatedduringtherun.Thenetsoil/vegetation

splitforagivengridcellisdeterminedbythecombinationofthefractionalcoverageofeach

landusetypeinthatcellandlanduse‐specificsplitfactors.Thefractionalcoverageof11

(Wesely)or26(Zhang)landusecategoriesineachgridcellisanexternalinputtoCAMx(Section

3).Thesoil/vegetationsplitsassignedtoeachlandusecategoryareinternallydefinedwithin

CAMxandassumedtobeseasonallyconstant.Valuesforsoil/vegetationsplitsareestimated

basedonsimpleconceptualconsiderationsoftheamountofannual‐averagedvegetation(i.e.,

leafareaindex)typicalofeachcategory(Table4‐4).

Snowisactivatedinthesurfacemodelwhensnowdepthissufficientlydeeptocoverexposed

soil.Thelowerlimitonsnowdepthis10cmtobeconsistentwiththeapproachdescribedin

Section4.7inwhicha10cmdepthcompletelycoverslow‐vegetationlanduse.Insuchcases,

thesoil/vegetationsplitisreplacedbythesnowcoverfractionsuchthatthesoilfractionis

entirelysnow‐coveredandthevegetationfractionisprogressivelycoveredwithdeepersnow

depth.Thesoilcompartmenttransitionstoasnowcompartment;sorptioncoefficientsand

ratesforchemistryandlosscoverttothevaluessetforsnow(asdescribedbelow).Withvery

deepsnowexceeding200cm,highvegetationiscompletelycoveredandthesurfacemodel

reducestoasinglecompartmentforsnow.

Thesurfacemodelusespartitioning(equilibrium)coefficientstocalculatetheamountof

accumulatedmaterialsorbedtosoil/snowandvegetation.Thesorbedfractionissubjectto

chemicalreactionsandphysicalremovalassociatedwithsoilleaching,plantpenetration,and

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Table4‐4(a).Weselylandusecategoriesandassociatedannual‐averagedsoil/vegetationsplit

factors,UValbedo,andSWEWc.

Category

NumberLandCoverCategory

SurfaceParameters

Soil

Fraction

UV

Albedo

Snow

c

(mSWE)

1Urban0.70.080.2

2Agricultural0.20.050.01

3Rangeland0.50.050.02

4Deciduousforest0.10.050.2

5Coniferousforest,wetland0.10.050.2

6Mixedforest0.10.050.2

7Watern/a0.04n/a

8Barrenland1.00.080.01

9Non‐forestedwetlands0.20.050.01

10Mixedagricultural/range0.30.050.02

11Rocky(withlowshrubs)0.50.050.01

Table4‐4(b).Zhanglandusecategoriesandassociatedannual‐averagedsoil/vegetationsplit

factors,UValbedo,andSWEWc.

Category

NumberLandCoverCategory

SurfaceParameters

Soil

Fraction

UV

Albedo

Snow

c

(mSWE)

1Watern/a0.04n/a

2Icen/a0.50.01

3Inlandlaken/a0.04n/a

4Evergreenneedleleaftrees0.10.050.2

5Evergreenbroadleaftrees0.10.050.2

6Deciduousneedleleaftrees0.10.050.2

7Deciduousbroadleaftrees0.10.050.2

8Tropicalbroadleaftrees0.10.050.2

9Droughtdeciduoustrees0.10.050.2

10Evergreenbroadleafshrubs0.50.050.03

11Deciduousshrubs0.50.050.02

12Thornshrubs0.50.050.03

13Shortgrassandforbs0.50.050.01

14Longgrass0.30.050.02

15Crops0.20.050.01

16Rice0.20.050.01

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17Sugar0.20.050.01

18Maize0.20.050.01

19Cotton0.20.050.01

20Irrigatedcrops0.20.050.01

21Urban0.70.080.2

22Tundra0.20.050.01

23Swamp0.20.050.01

24Desert1.00.080.01

25Mixedwoodforest0.10.050.2

26Transitionalforest0.10.050.2



snowmelt.Theun‐sorbedfractionisavailableforre‐emission.Separatechemical‐specificsoil‐

air,vegetation‐air,andsnow‐airpartitioningcoefficientsaresetintheCAMxchemistry

parametersfile.Theyrepresenttheequilibriumratioofchemicalonasurfacetochemicalinair

attheair‐surfaceinterface.Forexample,acompoundwithapartitioningcoefficientof10,000

(unitless)hasanequilibriumconcentrationonthesurfacethatis10,000timesmorethanthat

inair.

Chemistrycansimplydecaydepositedmaterialasaremovalprocess,oritcangenerate

productsthatcansubsequentlyre‐emitdependingontheproducts’partitioningcoefficient.All

surfaceremovalprocessesareassumedtobeirreversibleandresultinapermanentremovalof

mass.Chemistry,soilleaching,plantpenetration,andsnowmeltlossaredependenton

chemicalpropertiesofthecompoundsandalsoonnumeroussite‐specificfactorssuchassoil,

vegetation,andsnowproperties,highlytransientmeteorologicalconditions,etc.Oftenthese

factorsareunknownorfallwithinarange.Theratesoftheseprocessesaredefinedasthe

processratecoefficient(k)timesthemassonthesurfacearea,orareicmass(A):

Rprocess=kprocess



Asurface

Whentheactualratecoefficients(orinversely,thehalf‐lives,t½)areunknownforthe

substance,theycanbegeneralizedby5classes:

1.Veryfast:t½=0.04dk=17d‐1=1.2×10‐2min‐1

2.Fast: t½=0.21dk=3.3d‐1=2.3×10‐3min‐1

3.Moderate:t½=1.0dk=0.69d‐1=4.8×10‐4min‐1

4.Slow: t½=5.0dk=0.14d‐1=9.7×10‐5min‐1

5.Veryslow:t½=25dk=0.03d‐1=2.1×10‐5min‐1

A6thclasscanbeaddedbysettingthek‐valuetozeroorademinimisvaluetoeffectively

removetheprocessfromconsideration.Inthismannerchemicalscanbemodeledwithan

estimatedhalf‐lifethatisuniqueforeachprocess.

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Notethatallpartitioningcoefficientsandratesotherthanphotolysisarefixedandignore

dependenceonvariousenvironmentalconditions(e.g.,temperature,pressure,surfacetype,

surfacemoisture,etc.).Photolysisratesarespecifiedbytheusertorepresentpeakdirect‐

exposureclear‐skyvaluesatzerozenith(solarnoon)andareinternallyadjustedforsolarangle,

cloudattenuation(ascalculatedforatmosphericphotolysis),andshadeeffectsusing

multiplicativefactors.Amultiplicative“shadefactor”isdefinedtoreducephotolysisrates

within/belowvegetation.Snowcoverreducesshadingeffectstoaccountforenhanced

reflectionandinternalUVscatteringwithinthesnowpack.

Lossesbysoilleaching,plantpenetration,andsnowmeltarearbitrarilyacceleratedduringrain

events,suchthata1mm/hrrainfallrateresultsinane‐foldinglossofsurfacemassin1hour.

Masslosswithinthesnowpackbymeltingaloneoccursonlywhensurfacetemperatureisat

273K.Snowpacklossalsooccursduringsnowfallsuchthata1cm/hraccumulationresultsin

ane‐foldinglossofsurfacemassin24hoursbysuccessivelyburyingpollutantmassandlimiting

itsabilitytodiffusethroughthesnowpack.Themodelassumesthatnosurfacemassisre‐

introducedassnowdepth/fractiondecreaseduringsublimationormelting(i.e.,irreversibleloss

ofsurfacemassasimplementedforsoilandvegetation).

Theapproachforre‐emissionofvolatilized(un‐sorbed)massisconsistentwiththeCAMxdry

depositionalgorithm.Sincewatersurfacesarenotconsideredbythesurfacemodel,re‐

emissionfluxesfromwaterareignoredinthisimplementation.Drydepositionofmaterialfrom

thelowestmodellayertothesurfaceistreatedasanirreversible(fullysorbed)first‐orderflux

throughtheuseofadrydepositionvelocity.Re‐emissionofvolatilized(un‐sorbed)massisalso

treatedasafirst‐order1‐wayfluxusingan“effective”velocitythatissimilarinformto

deposition:

err

v

1

whereraistheaerodynamicresistancetoturbulenttransferthroughthelowestmodellayer,

andrbistheresistancetomoleculardiffusionthroughthelaminarsub‐layerincontactwith

surfaceelements.Thedepositionsurfaceresistancetermrsismissingsinceonlythepre‐

determinedun‐sorbedfractionofsurfacemassisconsideredforsurface‐to‐airtransfer.Thera

andrbtermsarecalculatedbythesurfacemodelinexactlythesamemannerasthevaluesused

fordrydepositiontoensureconsistency.

4.8.2RunningCAMxWiththeSurfaceModel

TheCAMxsurfacemodelparametersthatneedtobespecifiedforeachcompoundorsurface

reactiontobetrackedareasfollows:

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SsoilSoil‐airpartitioningcoefficientunitless

SvegVegetation‐airpartitioningcoefficientunitless

SsnowSnow‐airpartitioningcoefficientunitless

kleachSoilleachingratecoefficientmin‐1

kpenLeafpenetrationratecoefficientmin‐1

kmeltSnowmeltlossratecoefficientmin‐1

JsoilSoilphotolysisratecoefficientmin‐1

KsoilSoilheterogeneouschemistryratecoefficientmin‐1

JvegVegetationphotolysisratecoefficientmin‐1

KvegVegetationheterogeneouschemistryratecoefficientmin‐1

JsnowSnowphotolysisratecoefficientmin‐1

KsnowSnowheterogeneouschemistryratecoefficientmin‐1



ThesevaluesaresetattheendoftheCAMxchemistryparametersfile;anexampleofthe

chemistryparametersfileformatisshowninFigure4‐8.Acontrolrecordisalsoneededatthe

topofthechemistryparametersfiletodefinethenumberofspeciesandreactionstotrack.

ACAMxnamelistcontrolfilevariablecalled“SURFACE_MODEL”mustbesetto“true”inorder

toinvokethesurfacemodel.Whenthesurfacemodelisinvoked,thesurfacemodelsectionof

thechemistryparametersfileisreadandtherespectiveequilibriumandratevariablesareset

accordingly.

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Figure4‐8.TheportionsoftheCAMxchemistryparametersfile(highlighted)tosupportthe

surfacemodel.Inthisexample,3gasesaretreated,wherenitricacid(HNO3)and

peroxynitricacid(PNA)reacttoformnitrousacid(HONO).Allthreearesubjecttodecayby

soilleaching,plantpenetration,andsnowmeltloss.Thevaluesshownherearefor

illustrativepurposesonlyanddonotrepresentanyknownsurfacechemistrymechanism.

CAMx Version |VERSION6.3

Mechanism ID |2

Aerosol Option |NONE

Description |CB6r2 (r98/30/13 version) + ECH4

No of gas species |75

No of aero species |0

No of reactions |216

Prim photo rxns |23 1 8 9 21 27 28 38 43 47 50 56 88 92 97 98 108 112 114 117

119 128 129 161

No of sec photo rxn|6

ID, prim ID, scale |64 56 1.0

|90 88 1.0

|163 1 0.07

|196 1 0.015

|197 1 0.08

|201 1 0.08

SrfMod #spc, #rxns |3 2

Surface Model

Species SoilSorb SoilLeach VegSorb VegPen SnoSorb SnoMlt

1 HNO3 1.00E+10 1.00E-10 1.00E+10 1.00E-10 1.00E+10 9.70E-05

2 PNA 1.00E+10 1.00E-10 1.00E+10 1.00E-10 1.00E+10 9.70E-05

3 HONO 1.00E+00 1.00E-10 1.00E+00 1.00E-10 1.00E+00 9.70E-05

Rxn Precursor Product Soil K Soil J Veg K Veg J Snow K Snow J

1 HNO3 HONO 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 1.00E-03

2 PNA HONO 0.00E+00 0.00E+00 0.00E+00 0.00E+00 1.00E

01 0.00E+00

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5.CHEMISTRYMECHANISMS

ThephotochemicalmechanismscurrentlysupportedinCAMxarelistedinTable5‐1.Allare

balancedfornitrogenconservationsothatpredictedNOycanbecalculatedasthesumof

nitrogencontainingspecies.Mechanisms2through6canbelinkedtooptionalmodal(CF)and

size‐segregated(CMU)primaryandsecondaryparticulatematter(PM)treatments.CAMx

includesalgorithmsforinorganicaqueouschemistry(RADM‐AQ),inorganicgas‐aerosol

partitioning(ISORROPIA),andorganicgas‐aerosolpartitioningandoxidation(VBSorSOAP).

ThePMtreatmentsrequireadditionalgasspeciesasPMprecursorsanduseproductsfromthe

gas‐phasephotochemistryfortheproductionofsulfate,nitrate,andcondensableorganic

gases.TheCFPMtreatmentalsosupportsseveraloptionalmercuryspecies.Additionally,

thereisaninterfacethatallowsasimpleruser‐definedchemicalmechanismtobeemployedin

themodel(Mechanism10).Alistingofallreactionsandrateexpressionsforsupported

photochemicalmechanismsareprovidedintheappendices.



Table5‐1.Gas‐phasechemicalmechanismscurrentlyimplementedinCAMxv6.3.

MechanismIDDescription

6CB05(Yarwoodetal.,2005b).156reactionsamong 51 species(38 stategases,13radicals).

2CB6“Revision2”(CB6r2;Yarwoodetal.,2010;Yarwoodetal.,2012a;HildebrandtRuizand

Yarwood,2013).216reactionsamong75species(55stategases,20radicals).

3CB6r2withupdatestoincludereactionsinvolvingoceanichalogencompounds(CB6r2h;

Yarwoodetal.,2014).304reactionsamong115species(88stategases,27radicals).

4

CB6“Revision3”(CB6r3) thatincludesupdatestoimproveNO2‐organicnitratebranching

underwinterconditions(Emeryetal.,2015).220reactionsamong77species(55state

gases,22radicals).

5

AversionofSAPRC07thatincludes updatestosupporttoxicsandnumericalexpressionsof

rateconstantstosupportthecurrentchemistrymechanismcompiler(SAPRC07TC;Carter,

2010;Hutzelletal.,2012).565reactionsamong117species(72stategases,45radicals).

10

Auser‐definedsimplechemistrymechanismcanbedevelopedforanygasand/or

particulatespecies,whichisdefinedbya“Mechanism10”parametersfileandsolvedwithin

auser‐suppliedsubroutinecalled“chem10.f.”





TheselectionofwhichmechanismtoemployinagivenCAMxapplicationisdeterminedbythe

“chemistryparameter”inputfile.Thisfiledefinesthemechanismnumber,thenumberofgas

andaerosolspecies,andthenumberofreactionsforthemechanism,liststhespeciesbyname

withassociatedphysical‐chemicalproperties,liststhereactionrateconstantsandtemperature

dependenciesforeachreaction,anddefineswhichreactionsarephotolytic.Chemistry

parameterinputfilesfortheavailablemechanismsareprovidedwithCAMxandshouldnotbe

modifiedbyusers.SeeSection3foradditionalinformationontheformatandusageofthese

files.ChemistryparametersfilesarespecifictoversionsofCAMx.Alwaysusechemistry

parametersfileswiththerightCAMxversionnumber,donotattempttousefilesforanother

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5.1Gas‐PhaseChemistry

5.1.1CarbonBond

TheCarbonBondIV(CB4)mechanismwasfirstdevelopedbyGeryetal.(1989),andwas

subsequentlyupdatedinthe1990’stoincluderevisedPANchemistry,additionalradical‐radical

terminationreactionsandupdatedisoprenechemistry(Carter1996;Whittenetal.,1996).

AdditionalCB4updateswerethenmadetoexpandozonemodelingfromurbanto

regional/ruralenvironmentsandtosupportsecondaryaerosolchemistry,mercuryandtoxics

(Yarwoodetal.,2005a).

SeveralnewerCarbonBondversionsareavailableinCAMxasdescribedbelow.Table5‐2lists

chemicalspeciesnamesandpropertiescommontoallCAMxCarbonBondmechanisms.

5.1.1.1CarbonBond2005

Mechanism6isthe2005versionofCarbonBond(CB05)developedforEPAatmospheric

modelingstudies(Yarwoodetal.,2005b).UpdatesinCB05include:

 Updatedrateconstantsbasedon2003–2005IUPACandNASAevaluations.

 Anextendedinorganicreactionsetforurbantoremotetroposphericconditions.

 NOxrecyclingreactionstorepresentthefateofNOxovermultipledays.

 Explicitorganicchemistryformethaneandethane.

 Explicitmethylperoxyradical,methylhydroperoxideandformicacid.

 Lumpedhigherorganicperoxides,organicacidsandperacids.

 Internalolefin(R‐HC=CH‐R)speciescalledIOLE.

 HigheraldehydespeciesALDXmakingALD2explicitlyacetaldehyde.

 HigherperoxyacylnitratespeciesfromALDXcalledPANX.

 LumpedterpenespeciescalledTERP.

CB05wasevaluatedagainstsmogchamberdatafromtheUniversitiesofNorthCarolinaand

CaliforniaatRiverside.Thenewhigheraldehydeandinternalolefinspeciesimprove

mechanismperformanceforthesespeciesandproduceoxidantsmorerapidlyatlowVOC/NOx

ratios.ThenewterpenespeciesimprovessimulationofoxidantsandPMfrombiogenic

emissions.Severalneworganicperoxidespeciesimprovethesimulationofoxidantsthatare

involvedinPMsulfateformation.Theadditionofexplicitmethylperoxyradicalimprovesthe

simulationofhydrogenperoxideunderlowNOxconditions.

5.1.1.2CarbonBondVersion6

CarbonBondversion6(CB6)wasdevelopedbyYarwoodetal.(2010).Sincethen,CB6has

undergone2majorupdates,asdescribedbelow.Mechanism2isCB6revision2(CB6r2;

HildebrandtRuizandYarwood,2013).

Severalorganiccompoundsthatarelong‐livedandrelativelyabundant,namelypropane,

acetone,benzeneandethyne(acetylene),wereaddedexplicitlyinCB6toimproveoxidant

formationfromthesecompoundsastheyareoxidizedslowlyattheregionalscale.Alpha‐

dicarbonylcompounds(glyoxalandanalogs),whichcanfromsecondaryorganicaerosol(SOA)

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Table5‐2.SpeciesnamesanddescriptionscommontoallCarbonBondMechanismsinCAMx.

Species DescriptionCarbon#CHOMol.Wt.

BZO2PeroxyradicalfromOHadditiontobenzene6 675159.1

C2O3Acetylperoxyradical2 23375.0

CROAlkoxyradicalfromcresol7 771107.1

CXO3C3andhigheracylperoxyradicals3 35389.0

EPX2PeroxyradicalfromEPOXreactionwithOH 5 595149.1

HCO3AdductfromHO2plusformaldehyde 1 13363.0

HO2Hydroperoxyradical1 1128.0

ISO2PeroxyradicalfromOHadditiontoisoprene5 593117.1

MEO2Methylperoxyradical1 13247.0

NO3Nitrateradical362.0

OOxygenatomintheO3(P)electronicstate 116.0

O1DOxygenatomintheO1(D)electronicstate 116.0

OHHydroxylradical1117.0

OPO3PeroxyacylradicalfromOPEN4 434115.0

RO2Operatortoapproximatetotalperoxyradicalconcentration 47287.1

RORSecondaryalkoxyradical1 47171.1

TO2PeroxyradicalfromOHadditiontoTOL7 795173.1

XLO2PeroxyradicalfromOHadditiontoXYL8 8115187.1

XO2NOtoNO2conversionfromalkylperoxy(RO2)radical 47287.1

XO2HNOtoNO2conversion(XO2)accompaniedbyHO2production 47287.1

XO2NNOtoorganicnitrateconversionfromalkylperoxy(RO2)radical 47287.1

AACDAceticacid2 24260.0

ACE

Acetone3 36158.1

ALD2Acetaldehyde2 24144.0

ALDXPropionaldehydeandhigheraldehydes 3 36158.1

BENZBenzene6 6678.1

CAT1Methyl‐catechols7 782124.1

COCarbonmonoxide1 1128.0

CH4Methane1 1416.0

CRESCresols7 781108.1

CRONNitro‐cresols7 773153.1

EPOXEpoxideformedfromISPXreactionwithOH 5 5103118.1

ETHEthene2 2428.0

ETHAEthane2 2630.1

ETHYEthyne2 2226.0

ETOHEthanol2 26146.1

FACDFormicacid1 12246.0

FORMFormaldehyde1 12130.0

GLYGlyoxal2 22258.0

GLYDGlycolaldehyde2 24260.0

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Species DescriptionCarbon#CHOMol.Wt.

H2O2Hydrogenperoxide2234.0

HNO3Nitricacid1363.0

HONONitrousacid1247.0

HPLDhydroperoxyaldehyde5 583116.1

INTROrganicnitratesfromISO2reactionwithNO 5 594147.1

IOLEInternalolefincarbonbond(R‐C=C‐R) 4 4856.1

ISOPIsoprene5 5868.1

ISPD

Isopreneproduct(lumpedmethacrolein,methylvinylketone,

etc.)4 46170.1

ISPXHydroperoxidesfromISO2reactionwithHO2 5 5103118.1

Ketonecarbonbond(C=O)4 48172.1

MEOHMethanol1 14132.0

MEPXMethylhydroperoxide1 14248.0

MGLYMethylglyoxal3 34272.0

N2O5Dinitrogenpentoxide5108.0

NONitricoxide130.0

NO2Nitrogendioxide246.0

NTROrganicnitrates4 493119.1

O3Ozone348.0

OLETerminalolefincarbonbond(R‐C=C) 3 3642.1

OPANPeroxyacylnitrate(PANcompound)fromOPO3 4 436161.0

OPENAromaticringopeningproduct(unsaturateddicarbonyl) 4 44284.0

PACDPeroxyaceticandhigherperoxycarboxylicacids 2 24376.0

PANPeroxyacetylNitrate2 235121.0

PANXC3andhigherperoxyacylnitrate 3 355135.0

PARParaffincarbonbond(C‐C)1 51272.1

PNAPeroxynitricacid1479.0

PRPAPropane3 3844.1

ROOHHigherorganicperoxide410290.1

SO2Sulfurdioxide264.0

SULFSulfuricacid(gaseous)2498.0

TERPMonoterpenes 10 1016136.2

TOLTolueneandothermonoalkylaromatics 7 7892.1

XOPNAromaticringopeningproduct(unsaturateddicarbonyl) 5 56298.1

XYLXyleneandotherpolyalkylaromatics 8 810106.2

NTR1Simpleorganicnitrates493119.1

NTR2Multi‐functionalorganicnitrates 494135.1

ECH4Emittedmethane(toenabletrackingseperatefromCH4) 1 1416.0

XPRPOperatorfororganicnitratesfromPRPA 3 37289.1

XPAROperatorfororganicnitratesfromPAR 1 5112117.1

CRNONitro‐cresoloxyradical7 763152.1

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Species DescriptionCarbon#CHOMol.Wt.

CRN2Nitro‐cresolperoxyradical7 764168.1

CRPXNitro‐cresolhydroperoxide7 774169.1

CAO2Ring‐openingproductfrommethylcatechol 7 795173.1



viaaqueous‐phasereactions(Carltonetal.,2007),wereaddedinCB6toimprovesupportfor

SOAmodeling.Precursorstoalpha‐dicarbonylsinCB6arearomatics,alkenesandethyne.CB6

includedseveralupdatestoperoxyradicalchemistrythatimprovedformationofhydrogen

peroxide(H2O2)andthereforesulfateaerosolformation.Thegas‐phasereactionofdinitrogen

pentoxide(N2O5)withwatervaporisslowerinCB6thanCB05,whichreducednighttime

formationofnitricacid,althoughheterogeneousreactionsonaerosolsurfacesmaydominate

nitricacidformationatnight(Brownetal,2006).CB6includedthecalculationofthe

heterogeneousN2O5hydrolysisrateasafunctionofnitrate,chloride,andwaterconcentrations

inparticles(BertramandThornton,2009)whenPMisexplicitlysimulated;ifnoPMchemistryis

included,CAMxsetstheheterogeneousratetotheIUPAC(2015)N2O5hydrolysisrate.

ThecoreinorganicchemistrymechanismforCB6wasbasedonevaluateddatafromtheIUPAC

troposphericchemistrypanelasofJanuary,2010(Atkinsonetal.,2010).IUPACalsowasthe

primarysourceforphotolysisdatainCB6withsomedatafromthe2006NASA/JPLdata

evaluation(Sanderetal.,2006)orothersourcesforphotolysisofsomeorganiccompounds.

Therewerechangestotheorganicchemistryforalkanes,alkenes,aromaticsandoxygenates.

Themostextensivechangeswereforaromaticsandisoprene.Chemistryupdatesforaromatics

werebasedontheupdatedtoluenemechanism(CB05‐TU)developedbyWhittenetal.(2010)

extendedtobenzeneandxylenes.Theisoprenemechanismwasrevisedbasedonseveral

recentlypublishedstudies(Paulotetal.,2009a,b;Peetersetal.,2009).

CB6wasevaluatedusing339experimentsfromseveralchambersattheUniversityofCalifornia

atRiversideandtheTennesseeValleyAuthority.TheperformanceofCB6andCB05insimulating

chamberstudieswascomparableforalkanes,alkenes,alcoholsandaldehydeswithbothCB6and

CB05performingwellandexhibiting20%orlessbiasformaximumozone.Forspeciesthatwere

explicitlyaddedinCB6(ethyne,benzeneandketones),CB6performedmuchbetterthanCB05.For

aromatics,CB6improveduponCB05byreducingunderpredictionbiasinmaximumozonetoabout

10%forbenzene,tolueneandxylene.Forisoprene,bothCB05andCB6showlittlebiasfor

maximumozone(lessthan5%)butCB6tendedtoformozonetooslowly.CB6improvedupon

CB05forsimulatingmixturesofVOCs.Formixtureswithoutaromatics,bothCB05andCB6showed

minimalbiasformaximumozone.Formixturesincludingaromatics,bothCB05andCB6under

predictedmaximumozonebutbiaswasreducedfromabout30%forCB05toabout20%forCB6.

CB6revision1(CB6r1)includedrevisedchemistryforisopreneandaromatichydrocarbonsand

moreNOx‐recyclingfromthedegradationoforganicnitrates(Yarwoodetal.,2012a).Revision

2(CB6r2)increaseddetailintheformationandfateoforganicnitrates(ON),includingorganic

nitratedestructionbyreactionsinaerosols(HildebrandtRuizandYarwood,2013).ONsare

formedwhenVOCsdegradeinthepresenceofNOxandareimportantintheatmosphere

becausetheysequesterNOxandcancontributetoorganicaerosol(OA).NO2isreleasedwhen

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ONsdegradebyphotolysisinthegas‐phase,returningNOxtotheatmospherewhereitmay

contributetoozoneproduction.CB6r2differentiatesorganicnitratesbetweensimplealkyl

nitratesthatremaininthegas‐phaseandmulti‐functionalONsthatcanpartitionintoOA

(HildebrandtRuizandYarwood,2013).ONspresentinaerosolsarethenassumedtoundergo

hydrolysistonitricacidwithalifetimeofapproximately6hoursbasedonlaboratory

experimentsandambientdata.Thesechangestendtoreduceregionalconcentrationsofozone

andONs,andincreasenitricacid.RegionalmodelingsimulationsusingCAMxwithCB6r2show

thataccountingforONhydrolysisinaerosolsimproveperformanceforozoneandinsimulating

thepartitioningofNOybetweenONsandnitricacid.

5.1.1.3CarbonBondVersion6withHalogenChemistry

Mechanism3isanextensionofCB6r2chemistrythataddsreactionsinvolvingocean‐bornehalogen

compounds(CB6r2h;Yarwoodetal.,2014).Brominereactionswereintegratedwithpreviously

developedreactionsforiodine(Yarwoodetal.,2012b)andchlorine(Tanakaetal.,2003;Kooetal.,

2012)withrateconstantsupdatedtocurrentlyacceptedvalues(IUPAC,2014aandb)and

mechanismrevisionstopromoteconsistency.Theadditoinalhalogencompoundsandreactions

addedtoCB6r2arelistedinAppendixB.

Thechlorine(Cl)reactionmechanismisbasedonKooetal.(2012)withthefollowingupdates:

 ReactionrateconstantsupdatedtoIUPAC(2014aandb)asnecessary;

 Cl‐atomswithorganiccompoundsarelimitedtoalkanesandisoprene

 AddedClOradicalreactionswithBrOandIO

 AddedClNO3hydrolysistoHOClonaerosols

 Cl‐atomreactionswithorganiccompoundslimitedtoalkanesandisoprene

ReactionsofCl‐atomswithorganiccompoundsarelimitedtoalkanesandisoprene.Cl‐atom

productionfromthephotolysisofchloromethanesisincludedonlyforthosehalomethanesthat

areincludedassourcesofBrfromseawater.Degradationofanthropogenicchlorocarbons(e.g.,

HCFCs)isnotincludedinthemechanism.ThedominantsourceofatmosphericClisexpected

tobeseasaltemissions.Hydrochloricacid(HCl)isdisplacedintothegasphasewhenseasalt

aerosolsareacidifiedbynitricandsulfuricacids.TheHClformedfromseasaltcanreactwith

dinitrogenpentoxide(N2O5)onaerosolsurfacestoproducenitrylchloride(ClNO2)which

photolyzestoproducesCl‐atoms.WhenPMisexplicitlymodeled,theheterogeneousreaction

rateforN2O5+HCliscalculatedusingtheparameterizationdevelopedbyBertramand

Thornton(2009).

Thebromine(Br)reactionmechanismissimilartothemechanismsofYangetal.(2005),

SmoydzinandvonGlasow(2009)andParrellaetal.(2012)andismorecompactthanthe

mechanismsofVogtetal.(1999),WhittenandYarwood(2008)andOrdóñezetal.(2012).

ReactionrateconstantsfortheBrmechanismarefromIUPAC(2014aandb).Hydrolysisof

BrNO3isincludedaspseudogas‐phasereactionwitharateconstantcomparabletohydrolysis

ofN2O5.ThelargestsourceofatmosphericBrisseasaltaerosol(Yangetal.,2005)althoughthe

mechanismbywhichseasaltBrentersthegas‐phasediffersfromthatforCldepletionunder

acidconditions(discussedabove)andthiscanalsooccuratneutralpH.Othersourcesof

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atmosphericBrincludedinthemechanismaredecompositionofthehalomethanesCHBr3,

CH2Br2,CH2BrCl,CHBr2ClandCHBrCl2.

Theiodine(I)reactionmechanismisbasedonYarwoodetal.(2012b)withthefollowing

updates:

 ReactionrateconstantsupdatedtoIUPAC(2014aandb)asnecessary

 AddedIOradicalreactionswithClOandBrO

 AddedINO3hydrolysistoHOIonaerosols

 RemovedINOandrelatedreactions

ReactionsofINOwereremovedbecauseINOconcentrationswerefoundtobesmall(Yarwood

etal.,2012b).HydrolysisofINO3isincludedaspseudogas‐phasereactionwitharateconstant

comparabletohydrolysisofN2O5.

Emissionsfromoceansarethemajorsourceofatmosphericiodine(Carpenter,2003),including

methyliodide(CH3I),otheriodo‐methanes(CH2I2,CH2ICl,CH2IBr),largeralkyiodides,andmolecular

iodine(I2).Iodineemissionsresultbothfrombiologicalandphotochemicalprocessesinocean

water(MooreandTokarczyk,1993;MooreandZafirou,1994).Photochemicalprocessesthatcause

iodineemissionsarelinkedtoreactionsofdissolvedozoneandtherebytoenhancedozone

depositiontooceanicwaters(Ganzeveldetal.,2009;Helmigetal.,2012).

ReactionsamongtheradicalsClO,BrO,andIOareincludedtointerconnectthemechanismsfor

differenthalogens.AtmosphericreactionsofCl‐atoms,Br‐atomsandI‐atomscanproduceor

destroytroposphericozonethroughaseriesofcatalyticcycles,whereeachhalogenatomis

regeneratedinthereactionsandthereforeoneatomcanpotentiallydestroymanyO3

molecules.CatalyticdestructionofO3byClandBristerminatedonlywhendepositionremoves

reservoirspecies,e.g.,bydryorwetdepositionofHClandHBr.TheatmosphericreactionsofI‐

atomsdifferfromBrandClinseveralways:

 I‐atomsdonotabstractHfromorganiccompoundsincontrasttoBrandCl‐atoms;

 FormationofoxidesismoreextensiveforI(IO,OIO,I2O2,IxOy)thanforBr(BrO)orCl

(ClO);

 Largeriodineoxides(IxOy)formaerosolswhereasClandBroxidesremaininthegas

phase.

AerosolformationbylargeriodineoxidesisasinkforreactiveIthatcanterminateO3

destructionbyreactiveI.

5.1.1.4CarbonBondVersion6,Revision3

Mechanism4isCB6revision3(CB6r3),whichincludesupdatestoimproveNO2‐alkylnitrate

branchingincoldconditions(Emeryetal.,2015).Alkylnitrateformationcaninfluenceozone

productionbecausebothNOandradicalsareterminatedbyalkylnitrateformation.However,

temperaturedependenceofNO2‐alkylnitratebranchingisomittedfromcurrentphotochemical

modelmechanisms,i.e.,CB05‐TU(Whittenetal.,2010),CB6(HildebrandtRuizandYarwood,

2013),SAPRC11(CarterandHeo,2013)andRACM2(Goliffetal.,2013)andalsofromthe

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explicitMasterChemicalMechanism(http://mcm.leeds.ac.uk/MCM/).Leeetal.(2014)

consideredhowcoldwinterconditionsaffectalkylnitratebranchingandconcludedthat

omittingthetemperaturedependencemaycausea15%highbiasinozoneformation.

WehavedevelopedtheCB6r3chemicalmechanismfromCB6r2toextendapplicabilityto

winterandsummerconditions.Thetemperatureandpressuredependentformationofalkyl

nitratesincludesreactionsinvolvingpropane(CB6species“PRPA”)andotheralkanes(CB6

species“PAR”).CB6r3wasdesignedtoproducethesamealkylnitrateyieldsasCB6r2atroom

temperatureandpressure(298Kand1atm).SeeAppendixDforacompletelistingof

reactions,rateexpressions,andVOCproperties.

Alkylnitrates(RONO2)areformedwhenalkanesareoxidizedintheatmosphereinthepresence

ofnitricoxide(NO).Alkanesarecompoundsofhydrogenandcarbonwithonlysinglebonds

connectingtheatoms,e.g.,methane(CH4),ethane(C2H6),propane(C4H8),etc.Analysesofair

samplescollectedinwesternUSoilandgasdevelopmentbasinsduringwintertimeozone

eventsshowthatalkanesdominatetheorganicgasespresentintheair.Theformationofalkyl

nitratesfromalkanescanbedescribedbythefollowingreactionsinwhichanalkane(RH)reacts

withhydroxylradical(HO•)3andoxygen(O2)toformanalkylperoxyradical(RO2•)thathastwo

potentialreactionpathwayswithNO•:

1)HO•+RH R•+H2O

2)R•+O2 RO2•

3a)RO2•+NO• RONO2

3b)  RO•+NO2•

Perringetal.(2013)havereviewedtheatmosphericimpactsofalkylnitrateformation.The

yieldofalkylnitrateisdeterminedbythebranchingratioamongreactions3aand3b,which

dependsonbothtemperatureandpressure(Atkinsonetal.,1983).Theassociationreactionof

RO2withNOinreaction3aisfavoredoverreaction3batlowertemperaturesandhigher

pressures.

Emeryetal.(2015)confirmedthedirectionalityoftheozoneeffecthypothesizedbyLeeetal.

(2014)whenthemostrecenttemperature/pressureequationsofAreyetal.(2001)foralkyl

nitratebranchingwereincorporatedintoCB6r3,representingthealkanemixofahighwinter

ozoneepisodeintheUintahBasinofUtah.RecentexperimentaldataofYehandZiemann

(2014)confirmtheexpressionofAreyetal.(2001)forn‐alkanescontaining3to14carbon

atoms.WeightingmeasuredorganicgasconcentrationsbytheirOHreactivityindicateswhich

speciesaremostlikelytoparticipateinozoneformation.Consideringthealkanesrepresented

byCBspecies“PAR”measuredintheUintahBasin,thosewith4to7carbonatomsdominate

OHreactivityandindicatethatthetemperature/pressuredependenceforpentane(with5

carbons)maybeconsideredrepresentativeforalkanesintheUintaBasin.WhileCB6r3is

suitableforrepresentingthealkanemixturereactingintheUintaBasin,thederivationofCB6r3

doesnotrelyuponthisparticularmixtureofalkanes.



3Thedotsignifiesthathydroxyl(HO)isaradical,i.e.,hasoneunpairedelectron.NotethatNOandNO2alsoare

radicals.O2isadi‐radical.

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5.1.2SAPRC2007

The2007updatetotheSAPRCchemistrymechanism,calledSAPRC07(Carter,2010),replaced

thedatedSAPRC99mechanism.TheversionimplementedinCAMxisSAPRC07TC,which

includesadditionalmodelspeciestoexplicitlyrepresentselectedtoxicsandreactiveorganic

compoundsandusesnumericalexpressionsofrateconstantsthatarecompatiblewiththe

currentchemistrymechanismsolver(Hutzelletal.,2012).Chlorinechemistryisnotincludedin

theCAMximplementation.SeeAppendixEforacompletelistingofreactions,rateexpressions,

speciesdefinitions,andVOCproperties.

5.1.3ImplicitGas‐PhaseSpecies

AllphotochemicalmechanismsinCAMxemployfixedconcentrationsformolecularoxygen(O2),

molecularhydrogen(H2),andmethane(CH4).Concentrationsforthesecompoundsaresetto

thefollowingconstantmixingratios(i.e.,theyarenotimpactedbythechemicalsolution):

[O2] =2.095×105ppm

[H2]=0.60ppm

[CH4]=1.75ppm

Mechanisms2and3(CB6r2)includesaspeciesnamedECH4torepresentemittedmethane

overandabovetheglobalbackgroundof1.75ppm.

5.1.4PhotolysisRates

Theratesofatmosphericphotolysisreactionsdependuponsolarirradianceandthereforeare

sensitivetotheamountofsolarradiationtransmittedthroughtheatmosphereaswellas

reflectedfromtheearth’ssurface(albedo).Photolysisratesareexternallyderivedassuming

clear‐skyconditionsasafunctionoffiveparameters:solarzenithangle,altitudeaboveground,

totalozonecolumn,surfacealbedo,andterrainheight.TheratesareprovidedtoCAMxasa

largelookuptablethatspanstherangeofconditionsforeachofthefivedimensions.The

lookuptableisdevelopedusingaCAMxpre‐processorthatincorporatestheTropospheric

UltravioletandVisible(TUV)radiativetransfermodel(NCAR,2011).TUVemploysastandard

atmospheredensityprofileforRayleighscatteringandotherabsorberssuchasoxygen.User‐

specifiedozonecolumnvaluesareusedtoscaleatypicalverticalozoneprofilewithinTUV.A

defaultaerosolprofilefromElterman(1968)iscombinedwithtypicalaerosolopticalproperties

withinTUVtoaccountforhaze.

TheCAMxversionofTUVismodifiedtooutputphotolysisrateinformationinaformatdirectly

compatiblewithallCAMxphotochemicalmechanisms.SeeSections2and3formore

informationondevelopingphotolysisinputs.

AsCAMxruns,thelookupratesareinterpolatedtothespecificconditionsineachgridcell.

Theyarethenadjustedforanylocalcloudcoverandlocalaerosolattenuation(ifPMis

simulated).Additionally,solarangle‐dependenttemperatureandpressureadjustmentsare

appliedtofivekeyphotolysisreactions(NO2,O3,acetaldehyde,andtwoformaldehyde

reactions).

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5.1.4.1CloudandAerosolAdjustments

Photochemistryisstronglyinfluencedbythepresenceofclouds,whichcanbothattenuateand

enhancetheactinicfluxofultraviolet(UV)andvisibleradiationresponsibleforphotolysis.

Theirspecificradiativeimpactsdependonmanyfactors,includingheight,depthandfractional

skycover;watercontent;andwaterphase(i.e.,liquiddropletsoricecrystals).Aerosolsalso

influencephotochemistryaccordingtotheiropticalpropertiesandmassloadingasafunction

ofaltitudeanddepth.CAMxincludesafastin‐lineversionofTUV(Emeryetal.,2010)to

calculatephotolysisadjustmentprofilesthrougheachcloudy,aerosol‐ladengridcolumn.

Thein‐lineTUVisruntwiceforeachgridcolumn:firstfornon‐cloudyconditionswiththesame

Elterman(1968)aerosolprofileusedinthefull‐scienceTUVpre‐processor,andsecondwith

cloudsandsimulatedaerosolstoderiveaverticalprofileofthecloudy:clearactinicfluxratio(in

thecasethataerosolsarenotruninCAMx,theEltermanprofileisusedconsistently).Thisratio

isthenappliedasamultiplicativefactortotheclear‐skyvalueineachgridcell.Thisapproach

maintainsaccuracyinthecalculationofclear‐skyphotolysisrates,whileallowingcloudsand

aerosolstobedirectlyinvolvedinradiativetransfercalculationsthrougheachgridcolumn.

TUVincludesacalculationofintegratedatmosphericdensityabovetheCAMxdomain,based

ontheU.S.standardatmosphere,sothatatmosphericattenuationoftheUVstreamisproperly

calculatedenteringthemodeltop.Otheraspectsofthein‐lineTUVmodelweresubstantially

streamlinedtominimizeruntimes.First,radiativecalculationsareperformedforonlyasingle

representativewavelength(350nm).Second,sinceabsorptionbygasesoccursinrather

narrowUVbandsrelativetothebroad‐bandinfluenceofclouds,theabsorptionfromoxygen,

ozone,nitrogendioxideandsulfurdioxidewereremoved.Third,theextraterrestrialfluxwas

notneededasitcancelsoutinthecalculationofthecloudy:clearratio.Finally,theplane‐

parallelversionofthedelta‐Eddingtonapproachwasusedinlieuofthemorecomplexand

expensivepseudo‐sphericalgeometry.Preliminarytestsagainstthefull‐scienceTUVshowed

thatthestreamlinedversionresultedinlessthan1%differencesinactinicfluxratioforarange

ofcloudyconditions(Emeryetal.,2010).

Opticaldepth



expressesthereductionofincidentlightI0throughalightattenuatingmedium

ofdepth



zaccordingto





eII 0



Thein‐lineTUVadjustmentschemeutilizescloudopticaldepthfieldsprovidedbytheCAMx

cloud/rainfile,andaerosolopticaldepthscalculatedfromthePMmassconcentrations

simulatedbyCAMx.

TheCAMxmeteorologicalinterfacepre‐processorsgeneratecloudwaterandopticaldepth

fieldsfromthevariablefieldspresentintherawmeteorologicaloutputfiles.Cloudoptical

depthiscalculatedineachmodelgridcellaccordingtotheapproachofDelGenioetal.(1996)

andVoulgarakisetal.(2009),whichsatisfactorilyapproximatestheeffectsofrandomcloud

overlapaccordingto

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

2/3











whereLiscloudliquidwatercontent(g/m3),



zisthecelldepthcontainingcloudwater,



wis

thedensityofliquidwater(106g/m3),andFcisfractionalcloudcover.Themeanclouddroplet

radiusrdisnotdependentonwaterphase,andisassumedtobeatypicaltroposphericvalueof

1.510‐5mforliquidcloudwater.TUVassumesconstantMiescatteringparametersforclouds:

asinglescatteringalbedoof0.99,andanasymmetryfactorof0.85.

WhenCAMxisrunwithPM,verticalhazeopacityprofilesarecalculatedfromsimulatedaerosol

concentrationfields.WhenCAMxisrunwithonlygas‐phasechemistrywithoutaerosols,

photolysisratesareonlyadjustedforclouds.Aerosolopticalparametersarebestdetermined

fromMietheory,butintheinterestofminimizingimpactstomodelspeedandconsideringthe

degreeofuncertaintyinthesimulatedaerosolconcentrationsthemselves,asimplermethod

wasadopted.Aerosolsareassumedtoexistasanexternalmixtureoftheircomponent

chemicalspecies.Aerosollightextinction(scatteringandabsorption)isafunctionofeach

species’concentration,extinctionefficiency,andaffinityforhygroscopicgrowth.Totalaerosol

opticaldepthisdeterminedbysummingextinctionoverallspeciesandmultiplyingbylayer

depth.

Dryextinctionefficienciesandsingle‐scatteringalbedosforeachaerosolspecies,validat350

nm,areexternallydefinedintheCAMxchemistryparametersfile.Whilethesecanbealtered

bytheuser,thechemistryparametersfilesthatareprovidedwiththeCAMxdistribution

includedefaultvaluesaccordingtoTakemuraetal.(2002),asshowninTable5‐3.



Table5‐3.Defaultdryextinctionefficiencyandsingle‐scatteringalbedoat350nm(Takemura

etal.,2002)inthedistributedCAMxchemistryparametersfile.

Species

DryExtinctionEfficiency

(m2/g)

Single‐Scattering

Albedo

Sulfate7



10‐60.99

Nitrate7



10‐60.99

Ammonium7



10‐60.99

Organics7



10‐60.80

ElementalCarbon18



10‐60.25

Crustal(Fine+Coarse)0.4



10‐60.70

Seasalt(Na+Cl)1.5



10‐60.99



Takemuraetal.(2002)provideextinctionefficienciesandsingle‐scatteringalbedosforsulfate,

organics,soot,totaldust,andseasalt;wehaveextendedthesulfatevaluestonitrateand

ammonium.Theasymmetryfactorisinternallysettoadefaultvalueof0.61regardlessofthe

compositionoftheaerosols.

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Hygroscopicaerosolsarealsoflaggedinthechemistryparametersfile.Foreachflagged

species,aninternalgrowthfactorisappliedtothedryextinctionefficienciesaccordingtothe

relativehumidityconditionsineachgridcell.ThegrowthcurveistakenfromthePhaseIreport

oftheFederalLandManagers’AirQualityRelatedValuesWorkgroup(FLAG,2000).Bydefault,

therelativehumiditygrowthfactorisflaggedforsulfate,nitrate,ammoniumandseasalt;a

singlegrowthfactorisappliedforallhygroscopicspecies(Figure5‐1).Minimumandmaximum

limitsonrelativehumidityaresetat1%and95%,respectively.



Figure5‐1.Relativehumidityadjustmentfactorappliedtothedryextinctionefficiencyfor

hygroscopicaerosols(FLAG,2000).



5.1.4.2EffectsofSurfaceAlbedoandSnowCover

PhotolysisratesdependontheamountofsolarradiationreflectedfromtheEarth’ssurface

(albedo).UValbedoisassignedwithinCAMxaccordingtothedistributionofgriddedlanduse

providedbythetime‐invariant2Dsurfacefile(Tables3‐4and3‐5).Snow‐freeUValbedosfallin

therange0.04to0.08andareconstantintime.AnalysesofreflectedUVradiationrecordedin

satellitedata(HermanandCelarier,1997)reportsimilarUValbedovaluesintherange0.02‐

0.08fortypicalterrestrialandwatersurfaces.Snowismuchmorereflectivethanothertypes

ofsurfacesandsoitisimportanttocharacterizetheeffectofsnowcoveronphotolysisrates.

TheCAMxphotolysisrateinputfileisgeneratedforfivesurfacealbedos,twoofwhich

representthenon‐snowrange(0.04–0.10)andfourthatrepresentthesnowrange(0.1–0.2–

0.5–0.9).CAMxdeterminesthelanduse‐andsnow‐weightedaveragesurfacealbedoineach

gridcell(Section4.7)andinterpolatesphotolysisratesbetweenthefivealbedos.

5.1.5Gas‐PhaseChemistrySolvers

Solvingthetimeevolutionofgas‐phasechemistryrequiresnumericallyintegratingasetof

ordinarydifferentialequations(ODEs)andisamongthemostcomputationallyexpensive

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95

F(RH)

RelativeHumidity(%)

ExtinctionAdjustment,f(RH)

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operationsperformedinaphotochemicalgridmodel.OnereasonforthisisthattheODEs

describingtroposphericchemistryare“stiff”–meaningthatthechemicalspeciesinvolvedhave

widelyvaryingproductionand/ordecaytimes.Thecomputationalefficiencyofthegas‐phase

chemistrysolverstronglyinfluencestheoverallefficiencyofagridmodel.CAMxincludestwo

chemistrysolversthatoffertrade‐offsbetweenaccuracyandefficiency.

ThemostaccuratesolutionmethodsavailableforstiffODEsare“Gear”typeimplicitsolvers

(Gear,1971)suchasLSODE(Hindmarsh,1983).Gearsolversarestablewhenappliedto“stiff”

problems,suchasgas‐phasechemistry,butaregenerallytooslowforroutineuseingridmodel

applications.Herteletal.(1993)developedanimplementationoftheEulerBackwardIterative

(EBI)methodthatisveryefficientandalsoaccuratebecauseitutilizesexplicitalgebraic

formulaetosolveseveralimportantgroupsofspecies(HOx,NOx,etc.).

5.1.5.1LSODE

CAMxincludesthedoubleprecisionversionoftheLivermoreSolverforOrdinaryDifferential

Equations(LSODE;Hindmarsh,1983)distributedbytheNetlibrepositoryofnumerical

algorithms(http://www.netlib.org/).LSODEistooslowforeverydayusebutvaluableasa

referencemethodwithinCAMx.LSODEisbasedonGear’smethodwithnumericalrefinements

toimproveefficiencyandeaseofuse(RadhakrishnanandHindmarsh,1993).Gearmethods

(Gear,1971)areimplicitandemploybackwards‐differentiationformulaetostepforwardin

timebytakingmultiplesteps.Theconvergedsolutionsateachsteparesavedinahistory

matrixandusedtopredictthenextsolution.Thus,LSODEmustinitiallytakeshorttimestepsto

buildthehistorymatrixandmaythentakeprogressivelylongersteps.LSODEismostefficient

forlongintegrationtimes(andinefficientforshortintegrationtimes)andthereforeleast

burdensomeforcoarsegridmodelapplicationsthathaverelativelylongcouplingtimes

betweengas‐phasechemistryandotherprocesses,e.g.,advection.

User‐suppliedinformationrequiredbyLSODEisessentiallytheerrorcontrolparametersand

thefunctionsdefiningthesystemofODEs,f(y,t),whereyisthevectorofspeciesconcentrations

andtistime.Supplyingasubroutinetoevaluatethetimederivativesofspeciesconcentrations

(f=dy/dt)ismandatory.SupplyingafunctiontoevaluatetheJacobianmatrix(J=df/dy)is

optionalsince,ifnotsupplied,LSODEcanderiveanumericalJacobianbyfinitedifference

betweenrepeatedevaluationsoff.SupplyinganalgebraicJacobianensuresaccuracy,although

anumericalJacobianmaybeequallyaccurateifadequateprecision(e.g.,doubleprecision)is

employed.SupplyinganalgebraicJacobianismoreefficientwhenJissparse,butfor

condensedmechanismssuchasCB05JisnotsparseandthenumericalJacobianmethodis

faster.CAMxusesthenumericalJacobianmethodwitharelativeerrortoleranceof10‐7andan

absoluteerrortoleranceof10‐10.

5.1.5.2EBISolver

ThebackwardEulermethodsolvesconcentrations(y)asy(t+h)=y(t)+hf,wherefisthetime

derivativeofspeciesconcentrations(f=dy/dt)evaluatedatt+h.Themethodmustbeiterated

toconvergenceiny(t+h)becausespeciesconcentrationsareinterdependent.ThebasicEBI

methodisnotefficientforstiffproblemssuchastroposphericchemistrybecauseconvergence

isslowandthestepsize(h)mustbeshort.Herteletal.(1993)greatlyimprovedtheefficiency

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andaccuracyofthemethodbydevelopinganalyticalsolutionstotheEBIequationforgroupsof

speciesthatarestronglycoupled(e.g.HOxandNOx/O3).Timestepsofupto3minutesare

takenbytheHertelEBIsolverinCAMx.

5.2AerosolChemistry

Thegas‐phasechemistryisrunalone(noaerosols)bysupplyingCAMxwithachemistry

parametersfilewiththeaerosoloptionkeywordsetto“NONE”,thenumberofaerosolspecies

settozero,andtheentirelistofaerosolspeciesparametersomitted(seeSection3).Aerosols

aretreatedbysupplyingCAMxwithachemistryparametersfilewiththeaerosolkeywordset

to“INERT”,“CF”,“CF_VBS”or“CMU”.Inallsuchcases,thenumberofaerosolspecies,the

numberofsizesectionsandtheirsizeranges,andvariousaerosolparametersarespecified.

Theaerosolkeyword“INERT”allowstheusertodefineanynumberofarbitrarily‐namedinert

particulatespeciestobecarriedbythemodelduringaphotochemicalsimulation(e.g.,

modelingthedispersionofonlywind‐blowndust).

Aerosolchemistryprocessescanberuntogetherwithgas‐phasechemistryusingtwooptions

fortreatingaerosolsizedistributions:theCFschemeandCMUscheme.TheCFschemedivides

thesizedistributionintotwostaticmodes(coarseandfine).Primaryspeciescanbemodeled

asfineand/orcoarseparticles,whileallsecondary(chemically‐formed)speciesaremodeledas

fineparticlesonly.TheCMUschemeemploysasectionalapproachthatdynamicallymodels

thesizeevolutionofeachprimaryandsecondaryaerosolconstituentacrossanumberoffixed

sizesections.TheCFandCMUoptionsrequireaminimumsetofspecificaerosolspecieswith

associatedchemistry.AerosolwaterisexplicitlytreatedinbothCFandCMUoptions,which

affectsaerosolsizeanddensity.

5.2.1AdditionalGas‐PhaseSpecies

WheneithertheCForCMUaerosoloptionisselected,thefollowinggas‐phasespeciesare

addedtomodelgas‐aerosolinteractions:

1) Ammonia(NH3)asaprecursorforinorganicaerosol.

2) Gaseoussulfuricacid(SULF)asaprecursortosulfateaerosol.

3) Sodium(Na)andhydrogenchloride(HCL)asproductsofacidifiedseasaltaerosol.

4) Separately‐trackedemitted(“primary”)VOCsthatformintermediateorganiccondensable

gas(CG)speciesviaoxidationreactions:toluene,xylene,monoterpenes,sesquiterpenes,

andisoprene.

5) SeveralintermediateCGspeciesthatmaycondensetosecondaryorganicaerosol(SOA)or

areproductsofSOAvolatilization.

5.2.2AerosolProcesses

Aerosolchemicalandthermodynamicprocessesincludethefollowing:

1) AqueoussulfateandnitrateformationinresolvedcloudwaterusingtheRADMaqueous

chemistryalgorithm(Changetal.,1987).

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2) Partitioningofinorganicaerosolconstituents(sulfate,nitrate,ammonium,andnatural

minerals)betweenthegasandaerosolphasesusingtheISORROPIAthermodynamic

module(Nenesetal.,1998,1999);uptakeofnitricacidbycalciuminsoildustparticlesis

calculatedexternaltoISORROPIA.

3) Organicaerosol‐gaspartitioningandoxidationchemistryusingtwooptions:

a. Asemi‐volatileequilibriumschemecalledSOAP(Straderetal.,1999)thatformsa

condensed“organicsolutionphase”;

b. Ahybrid1.5‐dimensionvolatilitybasisset(1.5‐DVBS)approach(Kooetal.,2014)

providingaunifiedframeworkforgas‐aerosolpartitioningandchemicalagingofboth

primaryandsecondaryorganicaerosols.

Organicaerosoltreatmentsaredescribedinmoredetailinseparatesub‐sectionsbelow.

Aqueouschemistryisnotexplicitlyappliedtosub‐gridclouds;cloudsareassumedtoeither

occupytheentiretyofagridcellvolume,orbecompletelyabsentfromit.Thecell‐averaged

effectofsub‐gridcloudsistreatedintheCAMxmeteorologicalpreprocessorsthatgenerate

three‐dimensionalgriddedcloudinputfields.Cloudygridcellsaredeterminedbycloudliquid

watercontentsaboveathresholdof0.05g/m3.Aqueouschemistryiscalculatedforeachcloud

gridcellateachmodeltimestep.

Incloudygridcellsundergoingaqueouschemistry,theISORROPIAequilibriumalgorithmis

calledeverytimesteptoensurethatrapidlyevolvingsulfate,nitrateandneutralizingcations

areinbalancewiththelocalenvironment.Incloud‐freegridcells,ISORROPIAiscalledona

uniqueaerosol“coupling”timestepthatisdefinedwithinthechemistryparametersfile.By

default,theaerosolcouplingtimestepis15minutes,andthisisusedforallmasterandnested

gridsinasimulationregardlessofthegrid‐specificdrivingtimestep.

Uptakeofnitricacidonmineraldustparticlesisoneofthepathwaysofparticlenitrate

formation.Forexample,calciuminsoildustparticlesreactswithnitricacidtoformcalcium

nitrate.BasedonSaharanduststudy(Astithaetal.,2009),weestimateabout6%massfraction

ofcalciumcarbonate(CaCO3)infinedustparticles(FCRS),andhalfofitisassumedtobe

replacedbycalciumnitrate.SincethecurrentISORROPIAimplementationinCAMxdoesnot

considermineralcationsotherthansodium,nitrateuptakebycalciuminsoildustiscalculated

externaltoISORROPIA.CAMxoutputstotalparticulatenitrate,i.e.,thesumofparticlenitrate

determinedbyISORROPIAandcalciumnitrate.

Table5‐4showstheinorganicaerosolspeciesthatcanbeincludedwiththeCFscheme.Some

speciesmustbepresentforthisscheme(“MandatorySpecies”)toestablishlinkagesbetween

gasandaerosolphasechemistry.Otherspeciesareoptional(meaningthattheycanbe

removedfromthechemistryparametersinputfile),exceptthatsodiumandchloridemust

alwaysbepresentorabsenttogether(i.e.,onecannotbepresentwithouttheother).Ifsodium

andchloridearenotmodeledthendefaultbackgroundvaluesareusedwithinCAMx.

IntheCMUscheme,CRSTisusedtoidentifyallprimaryinertmaterial,whichreplacestheCF

speciesofFPRM,FCRS,CPRM,andCCRSinTable5‐4.Individualaerosolspeciesnamesspecify

boththeconstituentandthesizesectionusingasetnamingconvention,e.g.,PSO4_1refersto

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Table5‐4.ListofinorganicPMspeciesfortheCAMxCFaerosoloption.

InternalLabelName MandatorySpecies

PSO4SulfateX

PNO3ParticulateNitrate X

PNH4ParticulateAmmonium X

PH2OAerosolWaterContent X

NASodium

PCLParticulateChloride 

PECPrimaryElementalCarbon 

FPRMFineOtherPrimary(diameter



2.5µm)

FCRSFineCrustal(diameter



2.5µm)

CPRMCoarseOtherPrimary 

CCRSCoarseCrustal



particlesulfateinsizesection1.TheCMUschemerequiresthatthecompletelistofallaerosol

speciesbepresentinthechemistryparametersfile(i.e.,noaerosolspeciesareoptional).

5.2.2.1SOAP

SOAPisthedefaultSOAchemistry/partitioningmodulewhentheaerosolkeywordissetto“CF”

or“CMU”inthechemistryparametersinputfile.Directlyemitted(primary)organicaerosolis

treatedbySOAPasasinglenon‐volatilespeciescalledPOAthatdoesnotchemicalevolve.

However,POAdoesinfluencetheevolutionofSOA.SOAspeciesexistinequilibriumwith

condensablegasses(CG)thatcanbeproducedbyVOCoxidation:



VOC+oxidant→CG↔SOA



CGformationfromVOCoxidationreactions(Table5‐5)ishandledwithintheSOAPmodule

ratherthanthemaingas‐phasechemistry,asdescribedbelow.Thisapproachhasthefollowing

advantages:(1)separatestheVOCprecursorsandlumpingschemesforoxidantchemistryand

SOAformation(e.g.,foraromatics,differentlumpingschemesmaybeappropriateforoxidant

andSOAformation);(2)allowsthesameSOAmechanismtobeusedwithdifferentoxidant

mechanisms;(3)allowsinclusionofSOAprecursorswithoutexplicitlydefiningoxidantreactions

(e.g.,sesquiterpenesareexplicitintheSOAmodulebuttheiroxidantformationmaybe

representedbysurrogatespecies).

EmissionsofSOAprecursorsmustbeprovidedseparatelyfromtheemissionsofoxidant

precursors,e.g.,isopreneemissionsmustbespeciatedbothasISOPforoxidantchemistryand

ISPforSOAchemistry.This“doublecounting”ofemissionsiscorrectbecausethespecies(e.g.,

ISOPandISP)servedifferentpurposes.Ideally,emissionsprocessorswilldevelopVOC

speciationschemesthatsuitbothoxidantandSOAmodeling.Intheabsenceofmorerefined

information,emissionsofSOAprecursorsmaybesetequaltoemissionsofoxidantprecursors

asfollows:ISP=ISOP;TRP=TERP;BNZA=BENZ;TOLA=TOLorARO1;XYLA=XYLorARO2.

SomeemittedVOCsaresemi‐volatile(SVOCs)andcancondensedirectlytoSOA,e.g.,biogenic

emissionsofoxygenatedVOCs.SOAformationfromSVOCemissionsmaybeaccountedforby

includingtheSVOCintheCAMxemissionsasoneoftheCGslistedinTable5‐6.ChooseaCG

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Table5‐5.SOAprecursorreactionsincludedintheCAMxSOAPmodule.

PrecursorReactionCGProducts1k298

Anthropogenic

ToluenesTOLA+OHTO2 5.63E‐12

TO2+NO0.036CG1+0.069CG2 9.04E‐12

TO2+HO20.22SOAH31.49E‐11

XylenesXYLA+OHXLO2 1.85E‐11

XLO2+NO0.022CG1+0.064CG2 9.04E‐12

XLO2+HO20.21SOAH31.49E‐11

BenzeneBNZA+OHBZO2 1.22E‐12

BZO2+NO0.037CG1+0.46CG2 9.04E‐12

BZO2+HO20.19SOAH31.49E‐11

Biogenic

IsopreneISP+OH0.015CG3+0.12CG4 9.99E‐11

ISP+O3none 1.27E‐17

ISP+NO3none 6.74E‐13

TerpenesTRP+O0.065CG5+0.29CG6 3.60E‐11

TRP+OH0.065CG5+0.29CG6 6.77E‐11

TRP+O30.065CG5+0.29CG6 7.63E‐17

TRP+NO30.065CG5+0.29CG6 6.66E‐12

SesquiterpenesSQT+OH0.85CG7 1.97E‐10

SQT+O30.85CG7 1.16E‐14

SQT+NO30.85CG7 1.90E‐11

Notes:

1Yieldvaluesareinppm/ppm.

2Rateconstantsareshownfor298Kand1atmosphereinmolecules/cm‐3and1/s.

3SOAHrepresentsnon‐volatileoxidationproducts.



Table5‐6.PropertiesofCG/SOApairsintheCAMxSOAPmodule.

Species

Molecular

Weight

(gmole‐1)

Saturation

Concentration

(µgm‐3at298K)

Heatof

vaporization

(kJmole‐1)

CG1/SOA1150 1.15 19.9

CG2/SOA2150 81.6 18.0

CG3/SOA3130 0.726 42.0

CG4/SOA4130 136 42.0

CG5/SOA5180 3.92 75.5

CG6/SOA6180 55.8 75.5

CG7/SOA7210 0

–



SOAH150 0

–



SOPA220 0

–



SOPB220 0

–



thathasappropriatevolatilityproperties,andaccountforanymolecularweightdifference

betweentheSVOCandsurrogateCG(molesCGemitted=molesSVOCxMWSVOC/MWCG).

TheSOAPmoduleconsistsoftwoparts:gas‐phaseoxidationchemistrythatformsCG,and

equilibriumpartitioningbetweengasandaerosolphasesforeachCG/SOApair.Thephysical

propertiesofCG/SOApairsareshowninTable5‐6.TheCGyieldsareexpressedasppmofCG

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formedperppmofVOCreactedsothatCGconcentrationsfollowtheCAMxconventionfor

gasesandareinppm.TheSOAsformedfromtheCGsareinunitsofµg/m3asareallother

aerosolspecies.

Polymerizationreactionsinorganicaerosolphaseswillincreasethemolecularweightofthe

condensedaerosolandreducethevolatility.Detaileddescriptionsofpolymerizationdepend

uponthechemicalcompositionoftheorganicandinorganicaerosolphases(e.g.,aerosol

acidity).SOAPassumesthatSOAispolymerizedtoanon‐volatileform(i.e.,moved

permanentlytotheaerosolphase)withalifetimeofabout1day(Kalbereretal.,2004).

PolymerizationslowlyformsorganicaerosolpolymerscalledSOPA(anthropogenic)andSOPB

(biogenic).

TotalSOAisthesumofSOA1‐7plusSOAH,SOPAandSOPB.Totalorganicaerosolisthesumof

totalSOAandthesinglePOAspecies.

5.2.2.21.5‐DVBS

TheVBSorganicaerosol(OA)chemistry/partitioningmoduleisselectedwhentheaerosol

keywordissetto“CF_VBS”inthechemistryparametersinputfile.VBSworkswiththe2‐mode

CFsizeoptionbutisnotcurrentlycompatiblewiththeCMUsectionalsizeoption.

TheVBSapproach(Donahueetal.,2006;Robinsonetal.,2007)providesaunifiedframework

forgas‐aerosolpartitioningandchemicalagingofbothPOAandSOA.Itusesasetofsemi‐

volatileOAspecieswithvolatilityequallyspacedinalogarithmicscale(thebasisset).VBS

memberspeciesareallowedtoreactfurtherintheatmosphere(chemicalaging)todescribe

volatilitychanges(i.e.,shiftingbetweenvolatilitybins).FirstgenerationVBSmodelsuseone‐

dimensionalbasissets(1‐DVBS)whereinorganiccompoundsaregroupedonlybyvolatilityand

thusareunabletodescribevaryingdegreesofoxidationobservedinatmosphericOAofsimilar

volatility.Toovercomethisshortcoming,atwodimensionalVBS(2‐DVBS)wasdeveloped

whereorganiccompoundsaregroupedbyoxidationstateaswellasvolatility(Donahueetal.,

2011,2012).However,useof2‐DVBSina3‐DPGMhasbeenlimitedduetohigh

computationalcost.

AhybridVBSapproachisimplementedinCAMx,called1.5‐DVBS,whichcombinesthe

simplicityofthe1‐DVBSwiththeabilitytodescribeevolutionofOAinthe2‐Dspaceof

oxidationstateandvolatility(Kooetal.,2014).Figure5‐2showsaschematicdiagramofthe

1.5‐DVBSschemecurrentlyimplementedinCAMx.Thisschemeusesfivebasissetstodescribe

varyingdegreesofoxidationinambientOA:twobasissetsforchemicallyagedoxygenatedOA

(OOA;anthropogenicandbiogenic)andthreeforfreshlyemittedOA(hydrocarbon‐likeOA

[HOA]frommeat‐cookingandotheranthropogenicsourcesandbiomassburningOA[BBOA]).

Eachbasissethasfivevolatilitybinsrangingfrom10‐1to103µgm‐3insaturationconcentration

(C*),whichroughlycoversthevolatilityrangeofsemi‐volatileorganiccompounds(SVOCs).An

effectiveheatofvaporization(H)valueof35kJmole‐1isusedforallSOAspecies.ForPOA,H

isestimatedusingthefollowingempiricalformulas:



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∆H4

C298K

*85kJmole‐1 (Forbiomassburning;Mayetal.,2013c)

∆H 11C298K

*85kJmole‐1(Forotherprimary;Ranjanetal.,2012)

Table5‐7liststhemodelOAcompoundsassignedtothevolatilitybins.Theirmolecular

structuresweredeterminedbyplacingthemonthe2‐DvolatilityspacedefinedbyDonahueet

al.(2011,2012).The1.5‐DVBSschemeadjustsoxidationstateaswellasvolatilityinresponse

tochemicalagingbysimplifyingthe2‐DVBSmodel.ChemicalagingofSOAandoxygenated

POAismodeledbyshiftingOAmassalongapre‐definedpathwayoftheOOAbasisset,which

reducesvolatilitywhileincreasingoxidationstate.POAaging,whichwouldrequiredifferent

pathwaysfromtheHOA(orBBOA)basissettotheOOAbasisset,issimplifiedinthis1.5‐DVBS

schemewhereoxidationproductsofPOAarerepresentedasamixtureofPOAandOPOAinthe

nextlowervolatilitybins.Thegas‐phaseOHreactionratesforPOAandanthropogenicSOAare

assumedtobe4x10‐11and2x10‐11cm3molecule‐1s‐1,respectively.AgingofbiogenicSOAis

disabledinourimplementationbasedonpreviousmodelingstudiesthatfoundagingbiogenic

SOAledtoasignificantover‐predictionofOAinruralareas(Laneetal.,2008;Murphyand

Pandis,2009).Additionaldetailsonthe1.5‐DVBSmodelcanbefoundelsewhere(Kooetal.,

2014;HildebrandtRuizetal.,2015).TotalOAisthesumofallOAinthefivevolatilitybinsfrom

primaryformation(PAP+PCP+PFP)andfromsecondaryformation(PAS+PBS).



Table5‐7.Molecularpropertiesofthe1.5‐DVBSspecies.

BasisSetModelSpecies

Namea

C*b

(µgm‐3)

OSC

cC#O#MW

(gmole‐1)

OA/OC



OOA

PAS0&PBS00d0.102 74.90 1722.05

PAS1&PBS11‐0.188 7.25 4.38 1671.92

PAS2&PBS210‐0.463 7.5 3.84 1631.81

PAS3&PBS3100‐0.724 7.75 3.30 1581.70

PAS4&PBS41000‐0.973 82.74 1531.59



HOA

PAP0&PCP00d‐1.52 17 2.69 2781.36

PAP1&PCP11‐1.65 17.5 2.02 2751.31

PAP2&PCP210‐1.78 18 1.34 2721.26

PAP3&PCP3100‐1.90 18.5 0.632 2681.21

PAP4&PCP41000‐2.00 19 0.0 2661.17



BBOA

PFP00d‐0.704 10 4.32 2051.71

PFP11‐1.02 11 3.60 2081.58

PFP210‐1.29 12 2.85 2111.47

PFP3100‐1.52 13 2.08 2131.37

PFP41000‐1.73 14 1.27 2151.28

a:SeeFigure5‐2forthemodelspeciesnamingconvention.

b:Effectivesaturationconcentration.

c:Averageoxidationstateofcarbon.

d:PropertiesofthelowestvolatilitybinswereestimatedassumingC*=0.1µgm‐3,buttheyactuallyrepresentallOAwithC*≤

0.1µgm‐3,andaretreatedasnon‐volatileinthemodel.

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Table5‐8listsinputemissionspeciesusersneedtoprepareforthe1.5‐DVBSOAscheme.

AnthropogenicandbiogenicVOCprecursorsaresimplycopiedfromtherespectiveemissions

fortheCBgas‐phasemechanisms(TOL,XYL,BENZ,ISOP,TERP)totheir“A”and“B”

counterparts.Sesquiterene(SQT)isentirelybiogenicandidenticaltothatusedbySOAP.The

CAMxVBSschemeallocatesPOAemissionsfromfivesourcetypestothePAP,PCP,andPFP

speciesbasedonemissionfactors(Table5‐9)determinedfromlaboratoryexperiments.VBS

usessource‐specificvolatilitydistributionfactorsforgasolinevehicles(POA_GV),dieselvehicles

(POA_DV),meatcooking(POA_MC),andbiomassburning(POA_BB)basedonrecentchamber

studies(Mayetal.,2013a,b,c;Woodyetal.,2015).ForotherPOAemissions(POA_OP),VBS

appliesdistributionfactorsestimatedbyRobinsonetal.(2007).



Table5‐8.Inputspeciesfor1.5‐DVBSscheme.

SpeciesDescriptionNotes

TOLAToluene(anthropogenic)

AnthropogenicVOCprecursors

XYLAXylene(anthropogenic)

BNZABenzene(anthropogenic)

ISPAIsoprene(anthropogenic)

TRPAMonoterpenes(anthropogenic)

TOLBToluene(biogenic)

BiogenicVOCprecursors

XYLBXylene(biogenic)

BNZBBenzene(biogenic)

ISPBIsoprene(biogenic)

TRPBMonoterpenes(biogenic)

SQTSesquiterpenes(biogenic)

IVOGIVOCfromgasolineengines

IVOCprecursors

IVODIVOCfromdieselengines

IVOAIVOCfromotheranthropogenic sources

IVOBIVOCfrombiomassburning

POA_GVPOAfromgasolinevehicles

POAprecursoremissionsassignedtoPAPand

PFPmodeledspecies

POA_DVPOAfromdieselvehicles

POA_MCPOAfrommeatcooking

POA_OPPOAfromotheranthropogenicsources

POA_BBPOAfrombiomassburning



Table5‐9.VolatilitydistributionfactorsusedtoallocatePOAemissionsfromfivedifferent

sourcetypestothefivePAP,PCP,andPFPvolatilitybins.



POAspecies

EmissionFractionforvolatilitybinwithC*of

01101001000

POA_GV0.270.15 0.26 0.150.17

POA_DV0.030.25 0.37 0.240.11

POA_MC0.350.35 0.1 0.10.1

POA_OP0.090.09 0.14 0.180.5

POA_BB0.20.1 0.1 0.20.4

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Emissionsofintermediate‐volatilityorganiccompounds(IVOCs;104≤C*≤106)makeimportant

contributionstoOAintheatmospherebutgenerallyaremissingfromemissioninventories

becauseneitherVOCnorPOAemissionfactorsaccountforIVOCs.Apre‐processor(PREPVBS)

canbeusedtomapsource‐specificPOAemissionstothefivedistinctPOAemissionspeciesfor

VBS,andtoscaleIVOCemissionsfromtotalnon‐methaneorganiccompound(NMOC)

emissionsbasedonsmogchamberdata(Jatharetal.,2014).

5.2.3AerosolSectionalApproach

UnliketheCFscheme,whereeachspeciesisrepresentedbyasingleparticlesize,theCMU

schemeinstitutesanadditionalsteptodistributethebulkaerosolconcentrationsfromthe

aqueous/aerosolchemistrymodulesintoeachsizebin.Forinorganicaerosolspecies,

ISORROPIAyieldsthebulkaerosolcompositionatequilibrium.Theaerosolsizedistributionis

thendeterminedbydistributingthechangeinaerosolmassduringthetimestepintoeachsize

binusingaweightingfactor(Pandisetal.,1993).Thefractionfi,koftotalfluxofspeciesi

betweengasandaerosolphasesthatcondensesontoorevaporatesfromanaerosolsize

sectionkisgivenby,

















iiikk

ki ccDdN

ccDdN

f12



,



whereNkanddkarethenumberandmeandiameterofparticlesinthesectionk,respectively,

Di,ci,andcieqarethediffusivity,bulkgas‐phaseconcentration,andequilibriumconcentrationat

theparticlesurfaceofspeciesi,respectively,



k=2

/adk,

isthemeanfreepathofair,andais

theaccommodationcoefficient(Pandisetal.,1993).Assumingthatcieqisindependentof

particlesize,thefractionisreducedto,









kkk

ki f

f



1



.



Theaboveweightingfactorthendependsonthesurfaceareaonly.



Fororganicaerosols,SOAPcalculatesthebulkequilibriumcomposition.Usingthepseudo‐ideal

solutionassumption(Straderetal.,1999),theeffectofchemicalcompositionoftheparticlecan

beincorporatedintotheweightingfactor:



















kikiikk

ki cxcdN

cxcdN



.



wherexi,kisthemolefractionofspeciesiinthesectionkandci*istheeffectivesaturation

concentrationofspeciesi.Sincethefractiondeterminesthecompositionofeachsizesection,

theaboveequationshouldbesolvediterativelyateachtimestep.Assumingthatthechemical

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compositionchangesslowlyduringatimestep,however,themolefractionscanbe

approximatedwiththosefromtheprevioustimestep(Kooetal.,2003).

Forcloud/fogdroplets,RADMisusedtocalculatesulfateandnitrateformationinthebulk

aqueousphase.Theaddedmassisthendistributedintoeachsizebinbyaweightingfactor

whichisbasedonthesize‐resolvedaqueouschemistrymodelsimulationresults(Faheyand

Pandis,2001).

Inaddition,mathematicaldescriptionsofnucleationandcoagulationhavebeenaddedtothe

CMUscheme.Thenucleationmodelemploysthenucleationrateparameterizationproposed

byRusselletal.(1994).Themodelassumesalinearsulfuricacidvaporconcentrationvariation

forthegiventimestepoftheaerosolmodulebasedontheinitiallyavailablesulfuricacidand

assignsallthenucleatedmasstothefirstsectionofthedistribution.Thecoagulationrateof

theaerosolparticlesismodeledaccordingtoSeinfeldandPandis(1998).Ahigh‐resolution

distributionisusedforthecoagulationcalculationsbysubdividingeachsectionoftheoriginal

distributioninto3additionalsections.

5.3MercuryChemistry

Mercuryexistsintheatmosphereaselementalmercury,Hg(0),andoxidizedmercury,Hg(II)

(SchroederandMunthe,1998).Hg(II)canbeinorganic(e.g.,mercuricchloride,HgCl2)or

organic(e.g.,methylmercury,MeHg).Itcanalsobepresentasparticulatemercury(e.g.,

mercuricoxide,HgO,ormercurysulfide,HgS).Intheglobalatmosphere,Hg(0)isthedominant

form.Hg(II)typicallyconstitutesafewpercentoftotalmercuryandispredominantlyinthegas

phase.MeHgconcentrationsintheatmospherearenegligible,aboutafactorof10to30lower

thanHg(II)concentrations,basedonanalysisofprecipitationsamplesconductedbyFrontier

Geosciences,Inc.(e.g.,Seigneuretal.,1998).However,Hg(II)becomesmethylatedinwater

bodies,whereitcanbioaccumulateinthefoodchain.Hg(0)issparinglysolubleandisnot

removedsignificantlybywetdeposition;itsdrydepositionvelocityisalsobelievedtobelow.

Asaresult,Hg(0)hasalongatmosphericlifetime,ontheorderofseveralmonths,thatis

governedbyitsoxidationtoHg(II).Ontheotherhand,Hg(II)isquitesoluble;itisconsequently

removedrapidlybywetanddrydepositionprocesses.Particulatemercury,Hg(p),ismostly

presentinthefinefractionofparticulatematter(PM2.5),althoughsomeHg(p)maybepresent

incoarsePM(e.g.,LandisandKeeler,2002).

Knowntransformationsamonginorganicmercuryspeciesincludethegas‐phaseoxidationof

Hg(0)toHg(II),theaqueous‐phaseoxidationofHg(0)toHg(II),theaqueous‐phasereductionof

Hg(II)toHg(0),variousaqueous‐phaseequilibriaofHg(II)species,andtheadsorptionofHg(II)

toPMinboththegas‐phaseandaqueous‐phase.Theinorganicmercurychemistrymodules

implementedinCAMxarebasedonourcurrentknowledgeofthesetransformations.However,

itshouldbenotedthatourknowledgeofmercurychemistrycontinuestoevolveasnew

laboratorydatabecomeavailable,andtheHgchemicalkineticmechanismsinCAMxandother

modelsthattreattheatmosphericfateofmercurywillneedtoberevisedaccordingly.

Below,weprovideadditionaldetailsonthegas‐andaqueous‐phasemercurychemistry

mechanismsimplementedinCAMx,andtheimplementationapproach.

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5.3.1Gas‐PhaseChemistry

Thegas‐phasetransformationsincludetheoxidationofHg(0)toHg(II)byozone(O3)(Hall,

1995),hydrogenperoxide(H2O2)(Tokosetal.,1998)hydroxylradicals(OH)(Sommaretal.,

2001;PalandAriya,2003;2004),bromine(Br)(Ariyaetal.,2002),andhypobromite(BrO)

(RaofieandAriya,2003).TheoxidationofHg(0)byO3,H2O2,andOHaregivenbythefollowing

threereactions:

-1-13-20

3smolec cm 103 = (g), Hg(II)(g) O + (g) Hg(0)  k

-1-13-19

222 smolec cm 108.5 = (g), Hg(OH)(g) OH + (g) Hg(0)  k

-1-13-14

2smolec cm 108 = (g), Hg(OH)(g) OH + (g) Hg(0)  k,

whileoxidationbyBromineisbasedonasequenceof5reactions(SeigneurandLohman,2008):

1-1-3

-1.86

13-

1smolec cm

298

103.6 = (g),HgBr (g)Br + (g) Hg(0) 











 T

Pk 

1-9

8537

exp 103.9 = (g), Hg(0)(g)HgBr 











 T

k

1-1-3

-0.57

10-

32 smolec cm

298

102.5 = (g), HgBr(g)Br + (g)HgBr 











 T

k

1-1-3

-0.57

10-

4smolec cm

298

102.5 = (g), HgBrOH(g) OH + (g)HgBr 











 T

k

-1-13-15

5smolec cm 101 = (g), Hg(II)(g) BrO + (g) Hg(0)  k

Thereactionrateconstantsprovidedabovearefortemperaturesintherangeof20to25oC;no

temperaturedependenceinformationisavailable.Forthebrominereactions,Tisthe

temperatureindegreesKelvin,andPisthepressureinatmospheres.Thefivereactionsare

treatedasasinglereaction,withaneffectiveHg(0)first‐orderrateconstantthatisafunctionof

theindividualreactionratesandtheconcentrationsofBr,BrOandOHbasedontheassumption

thatBr,BrOandOHconcentrationsdon’tchangebytheirreactionswithmercury.This

treatmentissimilartothatofHolmesetal.(2006),whoconsideredtheoxidationofHg(0)by

bromineatomswithasetofthreereactions.Theeffectivefirst‐orderrateconstantiscalculated

bythefollowingexpression:















   

432

431 s BrOk

OHkBrkk

OHkBrkBrk

keff 









5.3.2AdsorptionofHg(II)onPM

InthefirstimplementationofmercuryinCAMx,Hg(II)adsorptiononPMwasconsideredonlyin

theaqueousphase(seebelow),usinganadsorptioncoefficientderivedfromavailable

experimentaldata(Seigneuretal.,1998;Ryaboshapkoetal.,2002).Itisessentialtoalso

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considertheadsorptionofgaseousHgspeciestoPMbecausegas/particleconversionalso

affectsHgdeposition(Lindbergetal.,2007).RutterandSchauer(2007a)reportedresultsof

laboratoryworkmeasuringtheadsorptionofreactivegaseousmercury(RGM)toatmospheric

andsyntheticparticlesasafunctionoftemperature.Theirexperimentalresultssuggestthat

surfacearearatherthanPMmasscontrolsthepartitioningprocess.Theyreportedthree

surface‐areaadsorptioncoefficientsforurbanPM(collectedinMilwaukee,WI,andRiverside,

CA),ammoniumsulfateandadipicacid,respectively.Theyexpressedthesurface‐area

adsorptioncoefficient(Ksa)asfollows:





PMARGMHgK spadspsa





,

whereKsaisinm3m‐2,Hgp,adsandRGMareinpgm‐3,Aspisthespecificsurfaceareaofambient

PMinm2μg‐1andPMistheambienturbanPMconcentrationinμgm‐3.Here,Hgp,adsrefersonly

totheadsorbedRGM,i.e.,itdoesnotincludenon‐volatileprimaryparticulatemercury.Rutter

andSchauer(2007a)alsofoundthattheKsaobtainedforurbanPMfallsbetweenthatof

ammoniumsulfate(moreRGMadsorption)andadipicacid(lessRGMadsorption).Their

laboratoryexperimentsleadtothefollowingvalueforKsaasafunctionoftemperature(inK)for

adsorptiontourbanPM:





10/4250

10 

T

K (1)

RutterandSchauer’s(2007b)experimentalresultsalsoshowaten‐foldincreaseinadsorption

ofRGMtosodiumchloridecomparedtoammoniumsulfateandorganicparticulatecompounds

(alargerincreasewasobservedforsodiumnitrate).Thus,theadsorptioncoefficientforRGM

adsorptiontosea‐saltisabout10timesthatforurbanPM:





9/4250

10 

T

K (2)

FollowingtheapproachusedinVijayaraghavanetal.(2008),wetreatallnon‐sea‐saltPMas

urbanPMforsimplicityanduseEquation(1)tosimulateRGMadsorptiontoallnon‐sea‐salt

PM.Theadsorptiontosea‐saltPMiscalculatedusingEquation(2).Thus,theeffective

adsorptioncoefficientforeachaerosolsizesectioniscalculatedas:











effsa FFK   11010 10/42509/4250

,

whereFssisthefractionofsea‐saltinthatsizesection.IntheCAMximplementation,we

assumethatRGMisadsorbedonprimaryfineandcoarsePM.

5.3.3Aqueous‐PhaseChemistry

Theaqueous‐phasechemistryincludesthereductionofHg(II)toHg(0)viareactionwith

hydroperoxyradicals(HO2)andbytheformationofthesulfitecomplexes(atlowHCl

concentrations),HgSO3andHg(SO3)22‐,aswellastheoxidationofHg(0)toHg(II)bydissolved

O3,OH,andCl2.AdsorptionofHg(II)speciesonatmosphericparticulatematter(PM)is

simulatedusinganadsorptioncoefficient(K=34Lg‐1)recommendedbySeigneuretal.(1998).

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Therelevantreactionsarelistedbelow.Notethatthegas‐liquidequilibriaandionicequilibria

ofthenon‐mercuryspecies(e.g.,SO2,O3)involvedinthemercuryaqueous‐phasechemistryare

notshownhere,sincetheyareidenticaltothoseintheotherCAMxmechanisms.

5.3.2.1Gas‐liquidEquilibria



-1

atm M0.11 = (aq), Hg(0) (g) Hg(0) K(Sanemasa,1975;Cleveretal.,1985)

-16

22 atm M 101.4 = (aq),HgCl (g)HgCl  K(LindqvistandRodhe,1985)

-14

22 atm M 101.2 = (aq),Hg(OH) (g)Hg(OH)  K(LindqvistandRodhe,1985)



TheHenry'sLawconstantslistedabovearefortemperaturesintherangeof20to25oC.

TemperaturedependenceinformationisavailablefortheHg(0)Henry'sLawconstantbutthe

validityofthisinformationfortemperaturesbelow0oCisnotestablished.

5.3.2.2Aqueous‐phaseEquilibria



2-14-+2

2M 10 = ,2Cl + Hg (aq) HgCl K(SillenandMartel,1964)

2-22-+2

2M 10 = ,2OH + Hg (aq) Hg(OH) K(SillenandMartel,1964)

-113

-2

+2 M 102.1 = ,HgSO SO + Hg  K(vanLoonetal.,2001)

-110-2

-2

33 M 101 = ,)Hg(SO SO + HgSO  K(vanLoonetal.,2001)



5.3.2.3AdsorptionofHg(II)onPMintheAqueousPhase



-1

g L 34 = (p), H(II) (aq) Hg(II) K(Seigneuretal.,1998)



5.3.2.4Aqueous‐phaseKinetics



-1-17+2

3sM 104.7 =,Hg(aq) O + (aq) Hg(0)  k(Munthe,1992)

-1-19+2 sM 102 =,Hg(aq) OH + (aq) Hg(0)  k(LinandPehkonen,1997)

-1

3s 0.0106 =(aq), Hg(0)(aq) HgSO k(vanLoonetal.,2000)

-1-14

2sM 101.7 =(aq), Hg(0)(aq) HO + (aq) Hg(II)  k(PehkonenandLin,1998)

-1-16+2 sM 102.09 =,Hg(aq) HOCl + (aq) Hg(0)  k(LinandPehkonen,1998)

-1-16+2- sM 101.99 =,HgOCl + (aq) Hg(0)  k(LinandPehkonen,1998)

Inthelasttworeactionslistedabove,HOClandOCl‐comefromthedissolutionandsubsequent

dissociationofmolecularchlorine(Cl2).NotethatHg(II)(aq)referstoalldivalentHgspeciesin

solution(i.e.,Hg2++HgCl2(aq)+Hg(OH)2(aq)+HgSO3+Hg(SO3)22‐).Therateconstantslistedfor

theaqueous‐phasekineticsarefortemperaturesintherangeof20to25oC.Temperature

dependenceinformationisavailablefortheHgSO3reductionreaction.

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Asmentionedpreviously,thegas‐andaqueous‐phaseHgtransformationspresentedabove

representthestateofthesciencefromadecadeago(Ryaboshapkoetal.,2002;Seigneuretal.,

2001a,2004)andourknowledgeofmercurychemistrycontinuestoevolve.Forexample,

GardfeldtandJohnson(2003)challengedtheaqueous‐phasereductionofHg(II)toHg(0)by

dissolvedHO2,suggestingthatthispathwayisunimportant.Therealsoseemstobesome

circumstantialevidenceofreductionofHg(II)toHg(0)inpowerplantplumesfromvarious

experimentalstudiesthatisnotaccountedforincurrenttreatmentsofHgchemistry(e.g.,

Edgertonetal.,2001;Seigneuretal.,2001b).Additionaldetailsareprovidedinascopingstudy

formercurydepositionconductedfortheMidwestRegionalPlanningOrganizationbySeigneur

etal.(2003).

5.3.4ImplementationApproach

Theapproachusedtoimplementthemercurytransformationpathways,discussedabove,into

CAMxisbasedontheassumptionthatthemercuryspeciesconcentrationsaremuchsmaller

thanthoseofthespecieswithwhichtheyreact.Thus,theconcentrationsofthenon‐mercury

speciescanbeassumedtobeconstantduringthemercurychemistrycalculationsandanalytical

solutionsareavailableforboththegas‐phaseandaqueous‐phaseconversions.

Themercurychemistrydiscussedintheprevioussectionsrequirestheconcentrationsofthe

followingnon‐mercuryspecies:O3,H2O2,OH,SO2,HO2,Cl2,HCl,Br,BrOandatmospheric

particulatematter(PM).TheconcentrationsofmostofthesespeciesareavailablefromCAMx.

However,thehalogencompoundsCl2,Br,andBrOareonlyincludedforonespecificgas‐phase

mechanism(CB6r2h,Mechanism3)andotherwisenotexplicitlysimulated.Sincethemercury

chemistryiscurrentlynotlinkedtoanyhalogensthatmightbeavailablefromthegas‐phase

chemistry,wespecifytypicalverticalprofilesofCl2,Br,andBrOconcentrations.TheCl2

concentrationsareprescribedtobenon‐zerooveroceansandzeroelsewhere.Also,daytime

Cl2concentrationsarelowerthannighttimevaluestoaccountforthefactthatCl2isphotolyzed

duringtheday.Thezenithangleisusedforthedeterminationofnight/day.A2‐Darrayof

integervalues(1ifocean,0ifnot)isusedtodetermineifthegridcolumnispredominantlyover

ocean.Thisarrayisinitializedatthebeginningofthesimulationfromaninputfileandis

specificforthemodelingdomainandgrid.ForBrandBrO,verticalprofilesoverlandandocean

areprescribed,withhighervaluesoveroceanthanoverland.Duringthenight,the

concentrationsofthesespeciesareassumedtobezero,sincethephotolysisofBr2isthe

primarysourcefortheseradicals.

Themercuryaqueous‐phasechemistrymodulealsorequiresthespecificationofcloudliquid

watercontent(LWC)andcloudwaterpH.BoththesevariablesareavailablefromCAMx–the

mercuryaqueous‐phasechemistrymoduleisinvokedaftertheCAMxPMaqueous‐phase

chemistrycalculationsareperformed,sothecloudwaterpHhasalreadybeencalculated.Note

thatthePMaqueous‐phasemodule(basedontheRADMaqueous‐phasechemistrymodule

thatisalsousedinModels‐3/CMAQ)doesnotexplicitlysimulatethecloudchemistryofOHand

HO2radicals.Theconcentrationsoftheseradicalscanbereducedbytheirheterogeneous

chemistrywithinclouds(e.g.,Jacob,2000;Jaegleetal.,2001).IntheCAMximplementation,

weaccountforthisbyreducingtheconcentrationsofOHandHO2radicalsbyfactorsof2and

10,respectively.

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5.3.5ChemistryParametersforMercury

ThemercurychemistrymodulerequirestotalPMconcentrations,somercurycanonlybe

modeledinconjunctionwithPMchemistry.Mercurychemistryisselectedbyincluding

mercuryspeciesamongthelistofmodeledspecies.TheCAMxmercuryspeciesnamesare:

HG0–elementalgaseousmercury,orHg(0)

HG2–reactivegaseousmercury,orHg(II)

HGP–primaryparticulatemercury,orHg(P)

HGIIP–reactivegaseousmercury,orHg(II)adsorbedontofinePM

HGIIPC–reactivegaseousmercury,orHg(II)adsorbedontocoarsePM



CAMxrequiresthatallfiveornoneofthesespeciesbeincludedinasimulation.Therefore,

mercurychemistryisnotrequiredforPMmodeling,butifmercurychemistryisselectedthen

allfivemercuryspeciesmustbemodeled.Alloftherateconstantsandequilibriumconstants

forthemercurychemistrymodulearehard‐codedandsonomercuryreactionratedataare

includedinthechemistryparametersinputfile(seeSection3).ThisissimilartotheRADM

aqueouschemistryandISORROPIAinorganicaerosolequilibriummodules.

Severalphysicalpropertiesofthemercuryspeciesmustbespecifiedonthechemistry

parametersfile(seeFigure3‐3a).Thephysicalpropertiesspecifiedforthegasspecies(Henry’s

Law,molecularweight,surfacereactivity)influencethedepositioncharacteristics.TheHenry

constantforHG2isassumedtobesimilartothatofHNO3becausethesetwogaseshavesimilar

solubility.TheHG2speciesrepresentsHgCl2andHg(OH)2;theHenryconstantfortheformeris

1.4106Matm‐1andforthelatteritis1.2104Matm‐1.Thesurfaceresistancefactorissetto

zeroforstrongacids,suchasHNO3,thathaveastrongtendencytosticktosurfaces–this

forcesthesurfaceresistancecalculatedinthedrydepositionalgorithmstozero.Thereactivity

parameterforHG2issetto0,asforHNO3.

ThedrydepositionofHG0issettozerobychoosingaverylowHenryconstant(similartoCO).

ThisisbasedontheassumptionthatnaturalemissionsanddrydepositionofHG0balanceeach

otheroverthemodelingdomain.Thisassumptionisjustifiedbythefactthattheatmospheric

lifetimeofHG0(about1year)greatlyexceedsitsresidencetime(daystoweeks)withina

regionalmodelingdomain.IfnaturalemissionsofHG0arenotincludedinthemercury

emissionsinventory,thedryandwetdepositionofHG0shouldbezerobysettingaHenry

constantofsmallerthan110‐8Matm‐1.However,ifnaturalemissionsofHg(0)areusedinthe

CAMxsimulation,theHenryconstantshouldbesetto0.111withatemperaturefactorof‐4970

K(Cleveretal.,1985).

5.4SimpleChemistryViaMechanism10

ThechemicalmechanismsinCAMxrequiresignificantefforttoprepareemissionsdataandcan

resultinextensiveruntimes.Therearemanycaseswhenairpollutionproblemscouldbe

investigatedwithamuchsimplerchemistryscheme.Anexampleofthiswouldinclude

modelingSO2fromafewspecificsourcesoverarelativelysmallregion,andtreatingconversion

tosulfatebyassumingarepresentativedecayrate.CAMxprovidesanoptiontoconfigurea

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simpleandflexibleschemethatcanbeusedformodelingchemicalreactionsotherthanthe

ozoneorsecondaryPMreactionstreatedbythefull‐sciencemechanisms.

Thesimplechemistryschemeisselectedbyspecifying10forthemechanismIDinthechemistry

parametersinputfile.Theusermustdevelopspecificchemicalreactionsandcodetheminto

thesubroutineCAMx/chem10.f;anexamplesubroutineisavailableinthesourcecode

directory.Followtheguidelinesinthatsubroutinetoimplementyourspecificsetofreactions.

Thisapproachrequiressomeknowledgefromtheuser,butalsoprovidescompleteflexibility.



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6.PLUME‐IN‐GRIDSUBMODEL

Photochemistryisahighlynon‐linearproblembecausechemicalreactionratesamongmost

compoundsdependupontheirambientconcentrations.InEulerianairqualitymodels,ambient

concentrationsdependonhowwellthemodelinggridresolvesemissions,transport,and

chemicalhistory.Thus,gridresolutionplaysavitalroleintheabilityofthemodeltoproperly

characterizephotochemicalconditions.Increasingresolutionshouldintheoryleadtoabetter

modelasthetime/spacediscretizationtendstowardacontinuum.However,practicaland

theoreticalconsiderationssuggestthatthelowerlimitonhorizontalgridspacingisabout1000

metersforEulerianairqualitymodelssuchasCAMx.Nevertheless,evenhigherresolutionis

oftennecessarytoadequatelysimulatechemistrywithinconcentratedpointsourceplumes.

Plume‐in‐gridtreatmentshavebeendevelopedtotrackindividualplumesegments(orpuffs)in

aLagrangiansense,accountingforplume‐scaledispersionandchemicalevolutionuntilsuch

timeaspuffmasscanbeadequatelyrepresentedwithinthelargergridmodelframework.

Thenthepuffmassisaddedtothegridsystemasavirtualsource,andthatmassis

subsequentlycarriedbythegridmodelprocesses.Itisimportanttounderstandthatthe

inclusionofaLagrangianpuffmodelwithinanEuleriangridmodelisaforcedconstruct.The

formulationsamongthevariousmodelingapproachesarefundamentallydifferentandthereis

notheoretically“correct”methodology.

TheCAMxPlume‐in‐Grid(PiG)sub‐modeladdressesthesizeandchemicalevolutionofpoint

sourceplumes.TwoPiGoptionsareavailablethatvaryintheirchemicalcomplexity.Both

approachessharecommondesignfeaturesforpuffinitialization,puffstructure,transport,and

growth.Theydeviateinhowtheytreatchemistryandwhentheytransfermassfrompuffsto

gridcells.Thissectiondetailsthestructureandfunctionalityofbothoptions.

1) GREASDPiG:TheGreatlyReducedExecutionandSimplifiedDynamicsPiGoptionis

aimedattreatingtheearlychemicalevolutionoflargeNOxplumeswhenmostly

inorganicgas‐phasereactionsareoperative.GREASDPiGworkswithOSAT/PSAT

becauseofthesimplifiedapproachemployedandbecausecompatibilitywithsource

apportionmentwasanexplicitdesignobjective.

2) IRONPiG:ThetheIncrementalReactionsforOrganicsandNOxPiGoptiontreatsthe

fullsuiteofgas‐phasephotochemistryforalltypesofpointsources.Gas‐phase

chemistryissimulatedwithineachplumesegmentusingan“incrementalchemistry”

approach(EPRI,2000),wherebypuffscarrytheincrementalcontributionsofthepuff

relativetothegridconcentrations.IRONPiGsupportstheReactiveTracer(RTRAC)

ProbingTool,butitdoesnotworkwithotherProbingToolsanditdoesnottreatPM.

6.1CAMxPiGFormulation

6.1.1BasicPuffStructureandDiffusiveGrowth

BothGREASDandIRONPiGsub‐modelsshareacommonphysicalstructureandgrowth

algorithm.Astreamofplumesegments(puffs)isreleasedfromadesignatedpointsource.

Eachpuffpossessesalongitudinallengthanddirectionalorientationdefinedbytheseparation

ofaleadingandatrailingpoint.Initialseparationofthesepointsisdeterminedbythewind

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vectoratfinalplumerise.Eachpointisthensubsequentlyandindependentlytransported

throughthegriddedwindfields,whichdirectlyaccountsforpuffstretchingandchangesto

centerlineorientationduetodeformingshears.The"position"ofeachpuffisdefinedatthe

centerpointofeachpuffbetweentheendpoints,andisusedtoidentifythegridcellinwhich

thepuffresidesforthecalculationofdiffusivegrowthandchemistry.

Likeotherpuffmodels,theshapeofeachpuffischaracterizedbyaspreadtensor,whichis

definedfromasetofGaussianstandarddeviations()alongthethreespatialaxes(



x,



y,



z).

Diffusivegrowthisdescribedbytheevolutionofthesevalues.Thetotalcross‐sectionalwidth

extends±1.5



yfrompuffcenterline.Similarly,thetotalcross‐sectionaldepthextends±1.5



z

frompuffcenterline(withlimitsplacedondepthbythegroundandbycappingstablelayers

aloft).Thetotallongitudinallengthisthedistancebetweenthepuffendpointswithan

additional±1.5



xaddedineachdirection.Horizontalareaandtotalvolumearecalculated

usingtheformulaeforanellipse.Figure6‐1presentsaschematicrepresentationofeachpuff

inhorizontalcross‐section.

Figure6‐1.SchematicrepresentationofCAMxPiGpuffshapeinthehorizontalplane.

Directionalorientationofthepuffisarbitrary,andevolvesaccordingtowinddirection,

shearsanddiffusivegrowthalongitstrajectory.



PiGpuffgrowthisbasedonSCICHEMtheoryandconcepts(EPRI,2000),butincludessome

simplifications.SCICHEMsolvespredictivespatialmomentequationswithsecond‐order

closurethatrelatetheevolutionofthepuffspreadtensor(



ij=





j)toresolvedmeanshears

andturbulentvelocitystatistics.TheReynolds‐averagedsecond‐momenttransportequationis

givenas



P (lead)

P (trail)

1.5

cux

dijji

ij 



















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whereuisthemeanwindvectorcomponent,theprimedvaluesrepresentturbulent

fluctuationsfromthemean,andtheanglebracketsdenoteintegralsoverspace.TheReynolds

averagingprocessalwaysintroduceshigher‐orderfluctuationcorrelations,andthisisgivenby

theturbulentfluxmomentscux  ,wherecu  representstheturbulentfluxof

concentration.ItistheselasttwodiffusiontermsthatSCICHEMsolvesinitssecond‐order

closurescheme.

Forsub‐puffscaleturbulence,SCICHEMemploystherestrictionthattheonlyactiveoff‐diagonal

componentofcux  isthesymmetrichorizontalterm(i=x,j=y),butitisappliedonlyforthe

large‐scale(mesotosynoptic)contributiontopuffdeformationwhenpuffscalesreachsuch

dimensions.InCAMx,weignorethisoff‐diagonalfluxmomenttermaltogethersincepuffsare

ultimatelyterminatedwhenpuffscalesapproachmuchsmallergridscales(typically<50km).

SCICHEMalsomakestheassumptionthatthehorizontalturbulenceisisotropic,

cvycux 



 .Thisresultsinasinglediffusivityequationforbothxandydirections,anda

singlediffusivityforthezdirection:

cvy

KK yx



 

cwz





TheSCICHEMsecond‐ordertendencyequationsareusedtomodelthetime‐evolutionofPiG

puffturbulentfluxmoments(representedbydiffusivitiesKx=KyandKz)andtheircontributionto

theevolutionofpuffspread(representedbythediagonalcomponentsofthepuffspread

tensor,



x2,



y2and



z2).Puffspreadisdefinedforpuffdepth(



z),puffwidth(



y),andpuff

length(



x).Weaccountfortheeffectsofgrid‐resolvedshearsofhorizontalwindinthe

evolutionoflateralandlongitudinalspread.Butweassumethattheevolutionofvertical

spreadissolelytheresultofturbulentfluxes,whichareordersofmagnitudelargerthangrid‐

resolvedshearsofverticalwind.

TheresultingReynolds‐averagedsecond‐momenttransportequationsforCAMxPiGare:



xyzyy

yKSD

d222 2











xxzxx

xKSD

d222 2

2





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

whereDistotalexplicit(grid‐resolved)horizontalshearofhorizontalwind(i.e.,“deformation”,

seeSection4.4).Sistheexplicitverticalshearofhorizontalwind,whichisbrokendowninto

puff‐relativelateral(y)andlongitudinal(x)components:



Thedifferencebetween



and



representstherelativeanglebetweenthepuff’slongitudinal

orientationandthedirectionofverticalshear,respectively;across‐puffshearresultsinmore

lateralspreadwhilealong‐puffshearresultsinmorelongitudinalspread.Theexplicitshear

termscontainingDandSmaybetoggledbytheuser:(1)sheareffectsarealwaysappliedto

puffgrowthrates;(2)sheareffectsareappliedonlywithintheboundarylayerbutneverabove;

or(3)sheareffectsareneverapplied.

TheSCICHEMtendencyequationforthehorizontalturbulentfluxmomentis



whereA=0.75,q2=vv  ,andisthehorizontalturbulentlengthscale.Separateequations

aregivenfortwodifferentboundarylayerturbulencescales(shear‐andbuoyancy‐produced),

suchthat



Withinthesurface‐basedboundarylayer,thehorizontalvelocityvarianceisgivenby



whereu*isthefrictionvelocity,w*istheconvectivevelocityscale,zisheightabovethe

surface,andziistheheightofthesurface‐basedboundarylayer.Thehorizontalturbulent

lengthscaleisgivenby



cvy

AQqcvy

d





 2

buoyancyshear cvycvycvy 













ishear zzuq /15.2 2

2









ibuoyancy zzwq /exp5.1113.0 2

2



222 65.0

3.0

zzi

shear





ibuoyancy z3.0







2/1

cos 











 dz





2/1

sin 











 dz



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

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

Inthestableboundarylayer,onlytheshearcomponentsofq2andareapplied.Abovethe

boundarylayer,SCICHEMappliesroughapproximationsforthevelocityvarianceandturbulent

lengthscale.InCAMxwehavesetthesevaluestoq2=0.1m2/s2,and=300m.

TheSCICHEMtendencyequationfortheverticalturbulentfluxmomentis



whereqv2=ww  ,vistheverticalturbulentlengthscale,andKzeqistheequilibriumdiffusivity.

WhereasaspecificequationforKzeqisformulatedforSCICHEM,wehavechosentospecifythe

valueofthisparameterfromthegriddedfieldsofverticaldiffusivityinCAMx.AgainSCICHEM

givesseparateequationsforshear‐andbuoyancy‐producedturbulencescales.

Withinthesurface‐basedboundarylayer,theverticalvelocityvarianceisgivenby



Theverticalturbulentlengthscaleforbothshearandbuoyancyisequaltosheargivenabove

forhorizontallengthscale.Abovetheboundarylayer,SCICHEMappliesroughapproximations

forthevelocityvarianceandturbulentlengthscaleandwehaveadoptedtheseforCAMx:qv2=

0.01m2/s2,andv=10m.

TheexternalvariablesneededbyPiGtocompletethedispersioncalculationsincludezi,u*and

w*.AlloftheseareavailablefromaninternalmoduleinCAMxthatcalculatestheseboundary

layersimilaritytheoryparameters.Thus,noadditionalparametersareneededtobeinputto

themodel.

6.1.2PuffTransport

AfreshsetofnewpuffsarereleasedfromallPiGpointsourceswithinthemodelingdomainfor

thedurationofthesmallesttimestepamongthemasterandallnestedgrids.Thelengthof

eachpuffisdeterminedbythecombinationofthemeantotalwindspeedattheheightoffinal

plumeriseandtimestep.Limitsareplacedonmaximumextrudedlengthbasedonhalfthe

finestresolutioninthegivensimulation.Ifwindsandtime‐stepsaresuchthatthemaximum

allowedlengthisviolated,thenseveralpuffsareautomaticallyemittedfromagivenstackper

timestep.Theusercanalsosetamaximumtimeintervalofreleaseifmorepuffs(betterplume

resolution)aredesiredoverthedefaultautomatedreleaseinterval.Theorientationofthepuff

lengthisalongthetotalwindvector.Totalpuffvolumeisdeterminedbystackvolumetricflow

rateinconjunctionwithgrowthduetoturbulententrainmentfollowingtheSCICHEMapproach.

Initially,



x=



yand



zvaluesareexplicitlycalculatedfromthisentrainmentcalculation.





cwzQK

Acwz

deq

v













shear

vzzuq /15.1 2

2









buoyancy

vzzzzwq /05.1/1.1 3/2

2

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Theeffectsofresolvedwindshearonplumedeformation(i.e.,atplumescaleslargerthan

individualpuffscales)aretreatedusinga“chainedpuff”approach(Figure6‐2).Pointsatthe

leadingandtrailingedgesofthepuffcenterlineareindividuallytransportedthroughthe

griddedwindfields,whichdirectlyaccountsforpuffstretchingandchangestocenterline

orientationduetodeformingshears.Sincepuffscanextendovermultiplelayers,layerdensity‐

weightedaveragewindcomponentsaredeterminedforeachendpointbasedonthevertical

coverageofthepuff.The“chain”aspectmeansthatatleastinitially(aspuffsareemittedfrom

thestack)thetrailingpointofapuffemittedattimetwillbetheleadingpointofapuffemitted

attimet+dt.However,asthepuffsareadvecteddownstream,theleadingpointofonepuffwill

deviatefromthetrailingpointthepuffbehinditduetoevolvingpuffdepthandwindfields.

The“position”ofeachpuffisdefinedbyitscenterpointbetweentheendpoints.Thisposition

definesthegriddomainandgridcellinwhichthepuffresidesforthecalculationofdiffusive

growthandchemistry.Thisdefinitionholdsevenifthepuffissufficientlylongthatthe

endpointsareindifferentgridcells(orevendifferentnestedgridsifnearanestboundary).

Withourdefinitionforterminationwhenhorizontalareaapproachesgridcellarea,thepuff

lengthshouldnotextendacrossmorethantwogridcells.



Figure6‐2.Plan‐viewschematicrepresentationofachainofPiGpuffsemittedfromapoint

sourceintoanevolvinggriddedwindfield.Theredlineconnectedbydotsrepresentspuff

centerlines,withdotsrepresentingleadingandtrailingpointsofeachpuff.TheCAMx

computationalgridisdenotedbythebluelines.



Stack

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6.2GREASDPiG

TheGREASDPiGisdesignedforlargeNOxpointsources,whereonlyinorganicchemistryis

operativeduringearlyplumeevolution.TheintentionofGREASDPiGistomoreproperlyage

emittedNOxwithintheconfinedplumevolumetomitigatetheartificiallyrapidchemical

processingoffreshNOtoNO2toozonethatwouldotherwiseoccurifimmediatelyreleasedinto

alargegridvolume.AcondensedinorganicchemicalmechanismisemployedinGREASDPiG

thatincludes23reactionsinvolvingoxidationofNOxandSOx.Therefore,GREASDPiGshould

notbeusedforVOCsources.ChemicallimitationsappliedwithinGREASDPiGcausepuffsto

transfertheirmasstothegridbeforeoxidantproductionfromVOCsisnolongersuppressed;

thiscanoccurbeforepuffsreachasizethresholddeterminedbythegridspacing.

ThechemicalevolutionoflargeNOxpointsourceplumescanbecharacterizedinthreestages

(EPRI,2000),asdescribedbelow:

 Stage1:EarlyplumeconditionswhereNOxconcentrationsareveryhighandradical

concentrationsarenegligible–simpleNO/NO2/O3photostationarystateappliesalong

withtheNO‐NOselfreaction;

 Stage2:Mid‐rangeplumeconditionswhereradicalconcentrationsaresufficientlylarge

togeneratesecondaryinorganicacidslikenitrateandsulfate;

 Stage3:Long‐rangeplumeconditionswheresufficientmixingwiththeambientairleads

tothefullrangeofgas‐phasereactionsinvolvingVOCoxidationandozoneformation.

TheobjectiveforGREASDPiGistotransfermasstothegridataboutthetimewhenradical

productionviaorganicchemistrystartstobecomeimportant,soGREASDPiGtreatsplume

chemistryduringStages1and2.WedefinetheonsetofStage3chemistrywhenthefollowing

criterionismet:



AtthispointGREASDpuffstransferalloftheirmasstothegridbeforetheonsetofStage3.

Thisspecificdesignconstraintisalsocompatiblewiththerequirementsofthesource

apportionmentProbingTools.

KumarandRussell(1996)andKaramchandanietal.(1998)foundthatPiGmodelswith

simplifiedinorganicchemistryproducedresultsthatwereverysimilartofullchemistry.The

chemicalmechanismforGREASDPiGincludes23reactionslistedinTable6‐1thatwere

selectedasfollows:

 ReactionsfortheNO‐NO2‐O3photo‐stationarystateestablishedinsunlight(1‐3)

 Self‐reactionofNOimportantonlyatveryhighNOconcentrations(4)

 ProductionofOHbyphotolysisofO3andHONOinsunlight(5‐9)

 Productionofnitricacidinsunlight(10)

 FormationofNO3andN2O5atnight(11‐17)









2



NOk

SOkCOk

OHOH

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Table6‐1.Listof23reactionsforGREASDPiGincludingcorrespondencetoCAMxreaction

numbersintheCB05,CB6andSAPRC07TCmechanisms.



ChemicalMechanismforGREASDPIG

CorrespondingReaction

NumberforGridChemistry

Number ReactionCB05CB6S07

1NO2=NO+O111

2O+O2+M=O3+M222

3O3+NO=NO2337

4NO+NO+O2=2NO2222410

51NO+NO2+H2O=2HONO2341N/A

6O3=O1D9918

7O1D+M=O+M101021

8O1D+H2O=2OH111120

9HONO=NO+OH254323

10NO2+OH=HNO3284525

11NO2+O3=NO37268

12NO3=NO2+O142717

13NO3=NO152816

14NO3+NO=2NO216299

15NO3+NO2=NO+NO2173015

16NO3+NO2=N2O5183611

17N2O5=NO3+NO2213712

182N2O5+H2O=2HNO3193913

19SO2+OH=SULF+HO2635244

20OH+CO=HO26612329

21FORM=2HO2+CO7597204

22FORM=CO7698205

23HO2+NO=OH+NO2302531

1. RateforGREASDPiGreaction5issettozerowhenusedwithSAPRC07TC.

2. RateforGREASDPiGreaction18maybeenhancedbyreactiononaerosol.



 Productionofnitricacidatnight(18)

 Productionofsulfuricacidinsunlight(19)

 RemovalofOHbyCO(20)

 ProductionofOHbyphotolysisofformaldehyde(21‐22)

 ConversiontoOHofanyHO2formedin20‐22(23)

Thesereactionsdominategas‐phasechemistryinplumesfrommajorNOxemittersduring

stages1and2.Table6‐1alsoshowsthecorrespondencebetweenGREASDPiGreactionsand

thecompletegas‐phasechemicalmechanismsimplementedinCAMx.Thismappingisusedin

CAMxtosettherateconstantsandphotolysisratesforGREASDPiGreactionsfrom

correspondingreactionsinthegridchemicalmechanisms.Thisimplementationensures

consistencywiththesechemicalmechanisms.TheGREASDPiGperformsgas‐phasechemistry

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foronlythosechemicalspeciesemitteddirectlyintotheplume,anddoesnotincludethe

influencefromanybackgroundcompoundsonthegridexceptforozone,carbonmonoxide,and

formaldehyde.Assumingzerobackgroundforgasspeciesisreasonablefortheearlystagesof

NOxplumesbecausepuffconcentrationsareordersofmagnitudelargerthanambient

concentrations.Ontheotherhand,backgroundozone,carbonmonoxide,andformaldehyde

aretheprimarysourcesofoxidantsinthecondensedmechanismthatdriveinorganic

processingofplumeNOxtootherformsofoxidizednitrogen(NOz),sothesearehandledas

“incremental”speciesasdescribedbelowforIRONPiG.TheLivermoreSolverforOrdinary

DifferentialEquations(LSODE)isusedtosolvethecondensedmechanismindouble‐precision.

6.3ParticulateMatterInPiG

Non‐lineareffectsanderrorsingas‐phasechemistryaretransmittedto(andpotentially

amplifiedby)thePMaqueouschemistryandpartitioningalgorithms.Theimplementationof

PMandPSATinPiGpromptedtheneedtolimittheimpactofsuchissuessimilarlytothe

constraintsimposedbyOSATforgas‐phasechemistry.Therefore,PMandPSATcanonlyberun

usingtheGREASDPiGoption.Asforgas‐phasechemistry,onlyinorganicPMchemistryis

treatedbyGREASDPiG.NotealsothatthePiGPMtreatmentwasdesignedspecificallyforthe

static2‐modePMchemistryonly(CF),andwillnotoperateforthemulti‐sectionPMchemistry

(CMU).

TheGREASDPiGgas‐phasechemistryoxidizesNOxandSOxemissionstonitricandsulfuric

acids,whicharePMprecursors.Tomaintainconsistencywiththegridchemistry,aqueousPM

chemistry(RADM‐AQ)isthenperformedateverytimestepifthepuffresidesinacloudygrid

cell.However,inorganicgas/PMpartitioning(performedbyISORROPIA)amongsulfate,nitrate

andammoniaisnotperformedbyGREASDPiG,butisdelayeduntilthemassesofthese

compoundsaredumpedtothegrid.Additionally,chemistryandpartitioningforsecondary

organicaerosolsisnotperformed.

6.4IRONPiG

TheIRONPiGmodelincorporatesacompletetreatmentofgas‐phasechemistryinpointsource

pollutantplumes,whilesecondarilyaddingadditionalfeaturescentralfortreatingtoxic

pollutantsnotnormallycarriedbythestandardCAMxchemicalmechanisms.Thereforethe

IRONPiGcantreatawidevarietyofpointsourceemissions,includingVOCsources.

IRONPiGadoptsthe“incrementalchemistry”conceptfromtheSCICHEMmodel(EPRI,2000),

wherebyeachpuffcarriesconcentrationsrelativetoambientbackground.Thisresultsinthe

possibilityofbothpositiveandnegativepuffconcentrationsdependingonhowthechemistry

evolves.Thefullgas‐phasechemistrymechanismchosenforagivenrunissolvedtwicefor

eachpuffateachtimestep:firstforthevertically‐averagedbackgroundconcentrationsfrom

thegridcellsverticallyspannedbythepuff;andsecondforthesumofpuffandbackground

concentrations.TheLSODEsolverisusedtosolvebothchemistrysteps.Afterbothstepsare

completed,theupdatedbackgroundconcentrationsaresubtractedfromtheupdated

puff+backgroundconcentrations,yieldingthenewpuffincrementalconcentrations.Notethat

theupdatedbackgroundconcentrationsareusedforreferenceonlyinthepuffincremental

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chemistryalgorithm;theactualgridconcentrationsarenotaffectedandareseparatelysolved

bythegridchemistryroutine.

6.5PiGFeatures

ThissectiondescribesspecificfeaturesofthePiGsubmodel;certainfeaturesarealwaysactive

whileotherscanbeoptionallyinvokedforaparticularCAMxrun.TheIRONPiGsub‐model

includestwoconstructsdesignedspecificallytofacilitatetheincrementalchemistryapproach:

 Theconceptof“virtualdumping”tohandlethechemicalimpactsoflargepuffsthatcan

overlapotherpuffswithinagivengridcolumn;

 Theconceptofmultiplepuff“reactor”cellstoaccountforthechemicaleffectsof

concentrationdistributionswithineachpuff.

Eachoftheseisdescribedbelow.

6.5.1PuffLayerSpanning(IRONandGREASD)

ThePiGisdesignedtochemicallyprocesspointsourceplumemasswithinstreamsofpuffsuntil

suchtimethateachpuffcanbeadequatelyresolvedonthehorizontalgrid.Puffsareallowed

toverticallyspanmultiplegridmodellayersbeforetheyreachhorizontalgridscales.This

introducestechnicalimplicationsfordefining“background”concentrationsandambient

conditionsforpuffchemistry,aswellasfortransferringplumeincrementalmasstothegrid.

Thesolutionemployedisto:

1) Assumethattheverticaldistributionofpuffconcentrationisalwaysuniform;

2) Distributepuffmasstransfer(via“leaking”and“dumping”)tothegridaccordingtothe

pufffractionalcoverageacrosseachmodellayerandbydensity‐weighting;and

3) Determinemeanbackgroundconcentrationsandotherambientconditions(e.g.,

temperature,humidity,etc.)overthepuffverticalspanviasimilarfractionallayer‐density

weighting.

Horizontally,themeanbackgroundconcentrationandambientconditionsaretakenfromthe

singlehostgridcolumncontainingeachpuffcenterpoint,evenifthepuffislargeand/orspans

ahorizontalcellinterface.Asdescribedearlier,puffsareconsideredtobeellipticalinthe

horizontal,withtheminoraxisspanningthecross‐windpuffwidth(definedas1.5



y),andthe

majoraxisspanningthealong‐windpufflength(definedaslength1.5



yoneachend).

However,giventhecomplicationsassociatedwithmultiplelayersspanningandmass‐weighting

ofambientinputsanddumpedmass,puffsarerectangularanduniforminthevertical,with

totalpuffdepthdefinedas1.5z.

6.5.2PuffOverlapandtheIdeaofVirtualDumping(IRONonly)

ThechemicaleffectsofpuffoverlapwereconsideredtobeanimportantattributeofIRONPiG.

However,wewishedtomaintainarelativelysimpleapproach,whileappropriatelyaccounting

forthelargestprobableeffects.Weassumethatthelargesteffectistheconditioninwhich

olderexpansivepuffsspansignificantfractionsoftheirhostgridcell,therebypotentially

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overlappingallotherpuffscontainedwithinthesamecell.Insteadofgeometrically

determiningfractionaloverlappuff‐by‐puff,weinsteadintroduceaprocessthatwerefertoas

“virtualdumping.”

Foragivengridcolumn,themassfromallpuffsdeterminedtobe“sufficiently”largeare

temporarilydumpedtothecolumn,distributedaccordingtoeachpuff’sverticallayerspan,and

addedtogetheralongwiththepre‐existinggridconcentrations.Thisprocessisreferredtoasa

“virtualdump”ofpuffmasstothegridcolumn.Thecriteriatodeterminea“sufficiently”large

puffisthesamethatinitiatespuffmassleakingtothegrid(asdescribedbelow).Inthis

approach,alllargepuffscontributetothebackgroundchemistrystepforotherpuffsoccupying

thesamegridcolumn.Double‐countingisavoidedbynotincludingapuff’scontributiontothe

backgroundwhileitsspecificbackgroundandincrementalchemicalcalculationsareperformed.

6.5.3MultiplePuffReactors(IRONonly)

Accountingforfullchemistrypotentiallyintroducessignificantnon‐lineareffectsthatarehighly

dependentuponthedistributionofpollutantmasswithineachpuff.Especiallyforozone,

aircraftflightsthroughpowerplantplumeshaveoftenrecordedwideconcentrationvariations

relativetoambientconditions:withintheplumecorewhereNOxremainsconcentrated,ozone

isoftendepressedandfollowsNO‐NO2‐ozoneequilibrium,whereasonplumefringeswhere

NOxisdiluteandmixeswithambientVOC,ozoneconcentrationscanexhibitconcentration

maxima.Pastmodelshaveaccountedforcross‐plumechemistryvariationsthroughtheuseof

reactors,withapproachesrangingfrommultiplerectangularslabstoconcentricshells.

Theusermayselectmultiplereactorsaswelltosub‐dividethepuff.Anynumberofreactors

maybechosen(thedefaultis1).Multiplereactorssimplydividethetotalpuffvolumeevenly,

andtheinitialmassassignmentsfornewlyemittedpuffsaremadeusingthestandarderror

functionthatresultsinaninitialGaussian‐likemass/concentrationdistributionamongthe

reactors.Thisprovidesamechanismforsimulatingthedifferingchemicalprocessingthattakes

placeinvariousconcentrationregimes.Asthepurposeofthereactorsismerelytorepresent

therangeofphotochemicalconditionsthatarelikelytooccuratvariouslocationswithinthe

puffasitundergoesdifferentialshearingandmixing,thereisnoparticularphysicalorientation

assignedtothesereactorswithrespecttoeachotherortothepuffasawhole.Thus,thereis

nocommunication(i.e.,diffusionalmassexchange)betweenthereactors.Thesame

backgroundconcentrationchemistryappliestoallreactorsofagivenpuff.Whenpuffmassis

leakedordumped,allreactorsshedthesamerelativefractionofmass.

Insummary,chemistryissolvedforeachpuff“reactor”inthreesteps:

1) Thelayer‐meanbackground(grid+overlappingpuff)concentrationsandenvironmental

conditionsoverthevolumeoccupiedbythepuffarestoredandthenchemicallyupdated

viatheLSODEgas‐phasechemistrymechanism;

2) Thepre‐updatedmeanbackgroundconcentrationsareaddedtothepuffincrementsand

thetotalconcentrationsarechemicallyupdated;and

3) Theupdatedresultsfromstep1aresubtractedfromtheupdatedresultsofstep2to

providetheupdatedincrementalconcentrations.

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6.5.4PuffDumping(IRONandGREASD)

Masstransferfrompufftogridcanhappenintwoways:slowly,termed“leaking”,orsuddenly,

termed“dumping.”Asdescribedearlier,allmassistransferredtotheverticalgridstructurein

adensity‐weightedfashionaccordingtoeachpuff’sfractionallayercoverage.Theprocessof

leakingensuresthatpuffmassistransferredtothegridcontinuously,ratherthanindiscrete

lumpsofpollutantswithverydifferentconcentrationsthanthoseinthegrid.Suddendumping

cancauseunphysicalnumericalshocksinthegridandcanleadtounrealisticgridded

concentrationpatternsthatappearas“bulls‐eyes”.Theideabehindpuffleakageistoaccount

forturbulentshearingofmassfromthemainplumeanditssubsequentdispersiontothegrid

scale.Thisrateoftransfershouldbedirectlyproportionaltothepuffsizerelativetothegrid

scale.

Puffleakageiscontrolledbycomparingthehorizontalareaofapufftoaspecifiedleakage

parameter,definedasafractionofhorizontalgridcellarea.Whenapuffisfirstemittedthere

isnoleakage.Asthepuffgrowsinvolumetheconcentrationswithinthereactorsarereduced

accordinglybydilution.Whenthepuffareaexceedstheleakageonsetparameter,afractionof

themassineachpuffreactoristransferredtothegrid.Thisfractionisdeterminedbythe

relativeexceedanceoftheleakageparameter;initialleakageisslowastheexceedanceis

relativelysmall,butleakageratesgrowasthepuffcontinuestogrowbeyondtheleakage

parameter.

Thereducedmassfromleakageiscompensatedbyareducedeffectivevolume,sothat

concentrationsarenotartificiallydilutedbyleakage(anessentialchemicalimperative).Thus,

twodistinctvolumesaretracked:theactualvolume(definedbythepuffspread)andthe

effectivevolume.Whiletheseareidenticalbeforeleakage,theydeviateafterleakageis

initiated,andthereaftertherelativedeformationoftheactualpuffvolume(viadiffusion,

shearing,etc.)isusedtoscalethedeformationofeffectivepuffvolume.

Eventuallythehorizontalspanofthepuffwillexceedthegridcellarea,andtheremainingmass

isthendumpedallatoncetothegrid.However,becauseofthecombinationofphotochemical

processingandleakage,bythetimeapuffdumpsthepotentialforproducingnumericalshocks

ismuchreduced.Furthermore,ifthepuffexceedsauser‐definedmaximumage,puffmassis

transferredtothegridattherateof10%pertimestep.

6.5.5PiGRendering(IRONandGREASD)

Whilethemassconfinedtothepuffsatanygiventimehasnotyetaffectedthegrid

concentrations,itwilleventually,soitcanbesomewhatmisleadingtosequesterthismassfrom

visualizationsofamodelsimulation.Thepuffmasscanbeoptionallyincorporatedintothe

modelaverageoutputfilesforvisualizationpurposes(referredtoas“PiGrendering”).

Renderingemploysa“virtualdump”ofthepuffmassesintotheaverageoutputconcentration

arrayeachtimestep.Asdescribedforchemistry,virtualpuffmassisaddedasanincrement

overtheentiregridcolumnaccordingtofractionallayer‐densityweightingoverpuffdepth,

thusdilutingit’sconcentrationsrelativetothatwithinthepuff.Theactualpuffmassremains

withineachpuffoverthecourseofitslifetime,andtheactualgridmassinunaffecteduntil

puffsarekilledandtheirmassestrulydumpedintothegrid.Thisvisualizationisavailablefor

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either2‐Dsurfaceor3‐Daverageoutputfiles,andcanproducesomeratherstartlingeffectsin

outputdisplays,includingverynarrowvirtualplumes,orstreaks,representingmassmoving

throughthegridinsub‐gridpuffs,butnotsubjecttogrid‐scaleeddydiffusion.

6.5.6HighResolutionPuffSampling(IRONandGREASD)

PiGoptionallyemployssurface‐layerpuffsamplingonauser‐definedgridofarbitraryhorizontal

resolution,similarlytothewaynestedgridsaredefined.Samplinggridsareentirelypassive,

andintendedtoprovideadisplayoftheplumeconcentrationsatscalesmuchsmallerthan

typicallyusedforthefinestcomputationalgrids(i.e.,<1km),primarilyaroundanddownwind

ofasourcecomplex.SampledPiGconcentrationsaretime‐averagedliketheoutput

concentrationsprovidedonthecomputationalgrids,andarewrittentofileswithsimilarformat

sothattheymaybereadilyviewedandmanipulatedwithCAMxpost‐processingsoftware.

AdditionalinformationonconfiguringandusingPiGsamplinggridsisprovidedinSections2and

4.

Giventhatthepuffsconstantlyevolveviadiffusivegrowthandreshapingduetodeforming

shears,thesamplingprocedureincludestrigonometriccalculationstodefinewhichsampling

pointsareinfluencedbyeachpuff.Thisinfluenceisdeterminedaccordingtothepuffs’two‐

dimensionalhorizontalGaussianshapeshowninFigure6‐1.Toincludeasufficientlylarge

percentageofmassacrosseachpuffforsampling,limitsof±3



x/yinbothhorizontaldimensions

areusedtodefinethepuffs’totalellipticalareacoverage.Puffsareonlysamplediftheyextend

verticallywithin10moftheground.

SamplinggridsaredefinedintheCAMxcontrolfile(seeSection2),andarraydimensionsmust

besetsufficientlylargeintheCAMxFortranparametersfilein./Includes/camx.prm(see

Section2).Anexampleofthetypeofplumedetailthatcanbevisualizedusingasamplinggrid

isprovidedinFigure6‐3.Inthiscase,averyfine200msamplinggridissetwithina4‐km

computationalgrid.

6.6Deposition

TheCAMxPiGtreatstheremovalofgasandPMspeciesfromeachpuffviadeposition

processes.Bothdryandwetdepositioncalculationspresenteduniqueimplementationissues

forpuffs.Themostdifficultissueforbothformsofdepositionwashowtomanagedeposition

exchangebetweenpuffsandthegroundinthecaseofnegativepuffconcentrationincrements.

6.6.1DryDeposition

Drydepositionneedstoconsiderthefollowing:(1)thepointatwhichpuffsbegintodepositto

thesurface;(2)howtohandledepositionthroughpotentiallydeeppuffsthatmaystraddle

severallayersofvaryingstabilitysincethepuffsdonotthemselvesresolvethesestratifications

orverticalconcentrationdistributions;(3)managingdepositionfluxesofnegative

concentrationincrements.Oursolutiontoissue(1)wastoignoredrydepositionwithinpuffs

untiltheydiffusivelygrowtotheground,althoughinrealitydepositionoccursonroughness

elementsthatextendsomedistanceabovetheground(trees,buildings,etc.).We

implementedacriterionthatthebottomofthepuffmustextendtoorbelowthemidpointof

thesurfacelayer,orbelow10m(whicheverislarger),inorderfordrydepositiontobeactive.

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Figure6‐3.ExampleofasinglepointsourcePiGplumeasdepictedbyasamplinggridwith

200mresolution(shownbytheextentoftheplot;40kmby32kmtotalextent).This

samplinggridwassetwithinaCAMxcomputationalgridwith4‐kmresolution.Thesource

locationisarbitraryandisemittinganinerttracer.



Issue(2)canbehandledinavarietyofwaysandcomplexity.Thecurrentimplementation

institutesasimplersolutionandwewillconsidermorecomplicatedimprovementsforfuture

developmentsifevidencesuggeststhattheywouldbenecessary.PiGutilizespre‐computed

species‐dependentdepositionvelocitiesderivedforthegrids.Eachpuffinaparticulargridcell

isprovidedthehostcell’sdepositionvelocitiesforeachspecies,andtheseareusedto

determinethefluxofmassthroughthefractionofpuffdepthoccupyingthemodel’ssurface

layer.

Issue(3)isuniquetotheincrementalchemistryconceptintroducedwithIRONPiG.Thefluxof

materialdepositingtothegroundisgivenby d

vcF





,wherebythenormaldefinitiona

positivedepositionvelocityvdleadstoapositivedepositionfluxtotheground.Ifthepuff

incrementcisnegative,thenanegativefluxiscalculated(fluxfromgroundtopuff).Thisis

appropriateifweconsiderthefollowingargument.Drydepositionappliedtoagridcell

removessomepollutantmassfromtheentirevolume.Ifthereisapuffexistinginthatcellwith

anegativeconcentrationincrement,thentheamountofmassremovedfromthecellwasover

estimatedifweconsiderthepuff’scontributiontototalcellmass.Thenegativedepositionflux

calculatedforthispuffleadstotheadditionofmasstothepuffincrement.Addingmasstoa

negativeincrementreducesthemagnitudeoftheincrement,asexpectedforadeposition

process.Thismassistakenfromthegridcell’saccumulateddepositedmasstomaintain

accuratemassaccountingwithinthemodel.

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6.6.2WetDeposition

Wetdepositionneedstoconsiderthefollowing:(1)howtohandlescavengingofpollutants

throughpotentiallydeeppuffsthatmaystraddleseverallayersofvaryingcloudandrainwater

contentsbutthatdonotthemselvesresolveverticalconcentrationdistributions;(2)managing

depositionfluxesofnegativeconcentrationincrementsincombinationwiththepotentialfor

masstomoveinandoutofrainwaterasitfalls(e.g.,forslightlysolublegasses);(3)accounting

fortheinitialpollutantconcentrationsinrainwaterastheyenterthetopofeachpuff.

Itwasimportanttomaintainconsistencybetweenthetreatmentofwetdepositionandthe

approachforpuffchemistry.Thechemistryreliesontheassumptionofverticallywell‐mixed

puffreactorsthatcanspanmultiplelayers,andthisiswhylayer‐densityweightedaverage

ambientconditionsarepassedtothechemistryroutines.Tomaintainthisassumptionforwet

deposition,asinglescavengingrateisappliedthroughtheentirepuffdepthaseffectivelya

singlelayerofpollutant.Thiswasfoundtobethesimplestimplementationapproach.This

singlescavengingrateiscalculatedaccordingtolayer‐densityweightedaverageambientcloud

andrainwatercontents.

Wetscavengingisperformedthroughouttheentiredepthofthepufftodeterminetheamount

offluxinoroutofrainwater.Totalconcentrations(puff+background)areusedtodetermine

species‐dependentscavengingratesusingtheidenticalalgorithmasforgridremoval.Therates

areusedtoderiveremovalfractions,andthesefractionsarethenapplieddirectlytothepuff

incrementalmassforeachspecies.Removalfractionsareconsideredpositiveforthestandard

caseofmassmovingfrompufftorain.

Wefurtherassumethatthetopboundaryconditionforrainwaterenteringthetopofeachpuff

iszero.Thismeansthattheremovalfractionisalwayspositive(frompufftorain)inthesingle‐

layerpuff.Incontrast,forgriddedconcentrationsthelayer‐by‐layerbuildupofslightlysoluble

speciescanleadtoareversaloffluxes(fromraintogrid)ifsupersaturationisdiagnosedina

particularlayer.

Notethatnegativepuffmassincrementsincombinationwithapositiveremovalfractionlead

toareversalofthefluxdirection(raintopuff),butthatisnotallowedandinsuchcaseswet

scavengingissettozero.Weaccountforimpactsonthemassbudgetappropriatelybyadding

tothewetdepositionmassarrayaccordingtothenetfluxesintorainwater.

6.7PiGConfiguration

SelectingtheindividualelevatedpointsourcestoreceivethePiGtreatmentisaccomplishedby

settingtheirstackdiametersnegativewithintheheader(time‐invariantpointlist)sectionofthe

CAMxinputpointsourcefile.CAMxwillruncorrectlywiththesenegativediametersevenifthe

PiGalgorithmisnotinvoked.CAMxpreprocessorsexisttoeasetheprocedureofranking

elevatedpointsourcesbyemissionrateandflaggingthesourcesthattheuserwishestotreat.

InvokingtheCAMxPiGsub‐modeliscontrolledbykeywordsintheCAMxcontrolfile

(CAMx.in),asdescribedinSection2.Thechoicesare:

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PiG_Submodel = 'NONE',

PiG_Submodel = 'GREASD',

PiG_Submodel = 'IRON',

NotethatthesinglechoicebetweenGREASDandIRONappliestoallflaggedpointsources.Itis

notpossibletomakeasingleCAMxrunwithIRONPiGappliedtoacertaingroupofsources,

andGREASDPiGappliedtoanothergroup.AlsonotethatGREASDmustbeselectedtorunPiG

withOSAT,PMandPSAT;IRONmustbeselectedtorunPiGwiththeRTRACProbingTool.

SeveraladditionalparametersareusedtoconfigurethePiG.ItisimportanttonotethatallPiG

configurationparametersexistintheCAMxFortranparametersfile

(./Includes/camx.prm),asdescribedinSection2.PiGparametersaregroupedtogether

andbrieflydescribedattheendofthatfile.ByconfiguringthePiGsubmodelinthecode,the

defaultPiGconfiguration(asrecommendedbythemodeldevelopers)ispresetwithinthe

modeldistributionandalleviatestheneedforuserstoselectsettingsontheirown.

Thedefaultvaluesareshownbelow:

parameter ( MXPIG = 50000 )

parameter ( MXRECTR = 1 )

parameter ( FLEAK = .25 )

parameter ( LEAKON = .FALSE. )

parameter ( LVISPIG = .FALSE. )

parameter ( OVERLAP = .FALSE. )

parameter ( DXYMAX = -10000. )

parameter ( AGEMAX = 18.*3600. )

parameter ( PIGMXDT = 300. )

parameter ( SHRFLG = 1 )

Usersshouldexercisethoughtfulconsiderationwhenalteringthesedefaultvalues.A

descriptionofeachoftheremainingparametersisprovidedbelow,alongwithguidancein

settingvalues.

6.7.1GuidanceontheUseofCAMxPiG

6.7.1.1PiGKeyword

ThePiGkeywordcontrolswhetherthePiGoptionistobeinvokedinaCAMxsimulation,and

whethertheemissionsaretreatedwiththeGREASDorIRONoptions.Thiskeywordcanbe

switchedfromNONEtoGREASDorIRONonamodelrestarttoinvokethePiGtreatmentatany

pointduringamulti‐daysimulation.Toallowforthis,itisnotmandatorytoprovideCAMxwith

apre‐existingPiGoutputfileuponamodelrestart–CAMxwillnotstopifthisfileismissing.It

isrecommendedthatthisfilebeprovidedonallsubsequentrestartssincethePiGoutputfileis

neededtoreinitializethePiGmodule,otherwiseallmasscontainedinpuffsattheendofthe

previousrunwillbelost.IfthePiGkeywordisswitchedtoNONEonamodelrestart,CAMxwill

continuethesimulationwithoutPiG,butallmasscontainedinpuffsattheendoftheprevious

runwillbelost.

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6.Plume‐in‐GridSubmodel

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 Guidance:

- InvokeGREASDorIRONPiGatanypointduringamulti‐daysimulation,ornoneatall.

OncePiGisstarted,provideCAMxwiththePiGoutputfilefromthepreviousrunfor

allsubsequentmodelrestartssothatnopointsourcemassislost.

- GREASDPiGshouldbeinvokedforlargeNOxpointsourcesonly,sinceitdoesnot

provideanyorganicchemistry.GREASDPiGsupportsPMchemistry(CFbutnotCMU).

ItcanberuninconjunctionwiththeOSAT/PSAT.ItdoesnotsupportDDM,PA,or

RTRAC.

- IRONPiGcanbeinvokedforanypointsourcetotreatgas‐phasechemicalevolution

usinganyoftheCAMxphotochemicalmechanisms.IRONPiGdoesnottreat

particulatechemistry.ItcanberuninconjunctionwiththeRTRACProbingTool.It

doesnotsupportOSAT/PSAT,DDM,orPA.

BothGREASDandIRONoptionsusetheLSODEchemistrysolverexclusively,souserswillnotice

animpactonruntime,particularlyifmany(thousands)puffsaretobetracked,andIRONPiGis

invoked(2solutionsoffullphotochemistryforeachpuff),andIRONpuffsareconfiguredwith

manypuffreactorcells(fullphotochemistrysolutionseach).SinceGREASDchemistryissimpler

andthelifetimeofGREASDpuffsaremuchshorterthantheirIRONcounterparts,GREASDPiG

willrunfasterthanIRONPiGforthesamenumberofflaggedsources.PiGchemistryis

internallyparallelizedusingOMPtomaximizePiGspeedperformance.

6.7.1.2NumberofPiGPuffs

MXPIGsetsthemaximumnumberofPiGpuffstobeexpectedduringasimulation.Itisusedto

staticallyallocatememoryarraysforthePiGsub‐model.Avalueof10,000isusuallysufficient

formostapplicationsinwhichPiGisused;setthisparameterto1ifPiGisnotusedtoconserve

memory.Ifthisparameterisexceededduringasimulation,themodelwillhalt.Ifthishappens,

simplyincreaseMXPIG,recompilethemodelexecutable,andrestartthesimulation.

 Guidance:Usethedefaultvalueformostsimulations,orsetto1ifPiGisnottobeused.

IfthemodelstopsbecauseMXPIGisexceeded,increaseitsvalue,recompile,andrestart

themodel.

6.7.1.3NumberofPiGReactors(IRONonly)

MXRECTRsetsthenumberofpuffreactors;whengreaterthan1,eachpuffisseparatedinto

thatnumberofreactorcellsandprimaryemissionsareapportionedamongthemusinga

Gaussiandistribution.Sincechemistryisperformedforeachindividualreactorcell(both

backgroundandpuff+background),thisparametercanaffectthespeedofchemical

computationsinthePiG.Wehavenotseenasignificantsensitivitytovaluesgreaterthan1,but

testingforeachapplicationiswarranted.

 Guidance:Usethedefaultof1forinitialsimulations,buttestthesensitivitytothis

parameterforeachuniqueapplication.

 Reactorsgreaterthan1arenotallowedforGREASDPiG.

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6.7.1.4LeakageParameters

FLEAK,LEAKON,andDXYMAXtogethercontrolpuffleakagetothecomputationalgridand

ultimatelypufftermination.WhenLEAKONistrue,FLEAKandDXYMAXcontrolwhenpuffs

begintoleakportionsofreactormasstothegridalongtheirtrajectory.WhenLEAKONisfalse,

noleakingisperformedandpuffsmaintainalloftheirmassuntiltheyreachsizesfor

termination,atwhichpointallmassisdirectlyintroducedtothegridatthatpoint.DXYMAX

setsthemaximumdimensionthatpuffsizewillbecomparedtoforleakingandtermination:

whenitiszero,puffsizewillbecomparedtogridareaonly;whenitispositive,puffsizewillbe

comparedtothevalueofDXYMAXregardlessofgridresolution;whenitisnegative,puffsize

willbecomparedtoDXYMAXorgridresolution,whicheverissmaller.FLEAKistherelative

fractionofhorizontalpuffareatocellarea(orDXYMAX)abovewhichleakingwillbeginand

continueuntilsufficientmassisshedandthepuffisterminated.Intheexampleabove,puffs

willbegintoleakmasswhentheyreach25%ofthehostgridcell’sarea.

 Guidance:IfLEAKONissettotrue,maintainFLEAKatthedefaultvalueof0.25.Thentest

modelsensitivitytodifferentvaluesofFLEAKand/orDXYMAX.

 Guidance:WesuggestleavingDXYMAX=‐10000,meaningpuffswillbeterminatedwhen

theyreachthegridscaleor10km,whicheverissmaller.Puffsexceedingthissizeare

usuallywell‐agedandgobeyondreasonableassumptionsofpuffcoherence(alsosee

AGEMAXparameterbelow).

 LeakingisnotallowedwhenPiGisrunwithPM.

6.7.1.5OverlapFlag(IRONonly)

OVERLAPcontrolswhetherpuffoverlapistobetreatedinthebackgroundchemistrystep.As

statedearlier,puffsonlyoverlapiftheymeetthesizecriteriaforleaking;allpuffssmallerthan

thissizedonotoverlapanyotherpuffsinthesamegridcell.

 Guidance:WerecommendthattheOVERLAPflagremainsettothedefaultvalueof

“false”.

 OverlapisnotallowedforGREASDPiG.

6.7.1.6VirtualPuffRendering

LVISPIGisaflagthatturnsonpuff“rendering”tothecomputationalgridaverage

concentrations.Whenitisfalse,thechemicaleffectsofpuffmassarenotseenontheoutput

averagefilesuntiltheyeitherbegintoleakmasstothegridand/ortheyareterminatedand

theirmassisentirelyintroducedtothecomputationgrid.However,whentheflagistrue,all

puffmassthatresidesineachgridcolumnissummed,apportionedverticallytoeachgridcell

accordingtopuffverticalextent(viadensityandlayer‐depthweighting),convertedto

concentrations,andaddedtotheaveragegriddedconcentrationsforoutput.Thisprocessis

referredtoasrenderingsincetheeffectsofallpuffmasscanbereadilyvisualizedintheCAMx

output.

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 Guidance:ThisoptionhasnoimpactontheactualCAMxchemicalsolution.However,

outputaverageconcentrationfileswillbeaffectedbypuffrendering,andthereforecould

impactgraphicsofCAMxresultsandmodelperformancemeasures.

 VirtualdumpsarenotallowedwhenPiGisrunwithPM.

6.7.1.7MaximumPuffAge

AGEMAXistheagelimitforallPiGpuffs(IRONandGREASD).Whenpuffsreachthisagelimit,

theyareterminatedandalloftheirmassistransferredtothehostgrid.Theassumptionofa

streamofcoherentpuffsbecomeslessvalidwithtimeashorizontalandverticalwindshears

increaseplumespread.Atsomepointtheplumemassisbetterresolvedonthegridthan

withinpuffs.Themaximumpuffageprovidesasafetychecktoensurethatpuffsdonotpersist

forunrealistictimesinstableenvironments.Themaximumpuffageshouldbesetlongenough

toallowpuffstopersistovernight,butalifetimeoflongerthanadayisprobablynotrealistic.

 Guidance:limitpuffageto12‐24hours–wefindthat18hoursworksbestsinceitwill

allowpuffsemittedinthelateafternoontolastthroughthenightandintothefollowing

morning.Twelvehoursisseentobetooshortinthisregard;puffsusuallydonotreach24

hoursofagebeforebeingterminatedbygridconstraints.

6.7.1.8MaximumPuffReleaseInterval

PIGMXDTsetsthemaximumfrequencyofreleaseandbydefaultissetto300seconds(5

minutes).Thisvalueshouldbeadequateformostapplications.However,iftheuserwishesto

improveplumeresolutionbyincreasingthenumberofpuffs,thefrequencyofreleasecanbe

increasedbyreducingthevalueofPIGMXDT.Thisvaluesupersedestheautomatedpuffrelease

ratethatisdeterminedbywindspeedandgridsize.

 Guidance:Maintainthedefaultvalueof300sandallowPiGtousetheautomatedPiG

releasefrequency.Settoalowervalueifbetterplumeresolutionisdesired;notethat

morepuffswillbereleasedandthiscouldslowthemodelmarkedly.

6.7.1.9EffectsofWindShearonPuffGrowthRates

SHRFLGsetstheapproachbywhichtoapplytheeffectsofexplicitlyresolved(gridscale)wind

shearonpuffgrowthrates.Therearethreeoptionsavailabletotheuser:

0=shearisneverapplied;

1=shearisappliedonlywithintheboundarylayer;

2=shearisalwaysapplied.

 Guidance:Theapplicationofwindshearcanleadtolargegrowthrates,especiallyabove

theboundarylayerwherestabilitysquelchesturbulentgrowth,andthismayover‐dilute

puffconcentrations,leadtoearlytransferofpuffmasstothegrid,andhavemarkedly

reducedimpactsdownwind.Shearhaslessrelativeimpactongrowthratesinneutral/

unstableconditionsbecauseturbulentgrowthonitsownleadstorapidplumedilution.

Forthesereasons,thedefaultistoignoretheeffectsofshearwhenpuffsareabovethe

boundarylayer.

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7.SOURCEAPPORTIONMENT

Photochemicalgridmodelsareoftenusedtodevelopemissionreductionstrategiestoattainair

qualityobjectives.Traditionalmethodsinvolverunningnumerousiterativereductionor“zero‐

out”simulations(i.e.,“bruteforce”methods)toidentifythecontributionsfromspecific

pollutants,sourcecategoriesandsourceregions.Thisprocessquicklybecomesimpractical,but

thelackofsuchinformationmightleadtoimplicatingsourcesthatcontributelittletohigh

pollutantlevelsor,conversely,notproperlyidentifyingsourcesthatdocontribute.

CAMxincludesasourceapportionment(SA)orattributioncapabilitythatestimatesthe

contributionsfrommultiplesourceareas,categories,andpollutanttypestothespatialand

temporaldistributionofozoneandPMinasinglemodelrun.Themainchallengesin

implementingamethodologytotracktherelationshipsbetweenseparategroupsofprecursor

emissionsandsubsequentnon‐linearformationoftargetpollutantsinclude:

 Accountingnotonlyforthepresenceofprecursorsfromagivensourceregionatagiven

receptorlocation,butalsoaccuratelyestimatingtheircumulativecontributiontotarget

pollutantswhiletheywereen‐routetothereceptor;

 Ensuringcompatibilitywiththeunderlyingairqualitymodelformulationsothatderived

source‐receptorrelationshipsareconsistentwithmodelresultsfortotalconcentrations;

 Providingsufficientspatialandtemporalresolutionwhilemanaging,withinpractical

constraints,thecomputerresourcesrequiredtorunthesourceapportionmenttool.

SAusessetsoftracerspeciestotrackthefateofprecursoremissionsandtheozoneandPM

compoundsformedfromtheseemissions.Thetracersoperateas“spectators”tothenormal

CAMxcalculationssothattheunderlyingrelationshipsbetweentotalemissionsand

concentrationsarenotperturbed.SAtracersarenot“passive”:rathertheytracktheeffectsof

chemicalreaction,transport,diffusion,emissionsanddepositionwithinaCAMxsimulationand

arethusreferredtoas“reactiontracers.”Asourcecanbedefinedintermsofgeographical

area(orregion)and/oremissioncategory(orgroup).Figure7‐1providesanexampleofthe

wayaCAMxdomaincanbesub‐dividedintomultiplesourceareas–40inthisexample.Also,

theemissioninventorycouldbesub‐dividedintoseveralsourcecategories;forexample,three

emissioncategories(mobile,industrial,biogenic)over40sourceregionswouldproduce120

separatesetsoftracers.Allsourcesofprecursors,ozone,PMmustbeaccountedfor,soCAMx

intialandboundaryconditionsarealsotrackedasseparatesourcegroups.Themethodologyis

designedsuchthatallozone,PMandprecursorconcentrationsareattributedamongthe

selectedsourceregions/groupsatalltimesandthroughoutallgrids.Themethodologyalso

estimatesthefractionsofozoneformeden‐routeunderVOC‐orNOX‐limitedconditions,

indicatingwhetherozoneataparticulartimeandlocationswillrespondtoreductionsinVOCor

NOXprecursoremissions.

AnimportantfeatureofthereactiontracerapproachisthatthenormalCAMxcalculationsare

notperturbed;thus,SAestimatesthesametotalozone,PMandprecursorconcentrationsas

CAMx.Further,sincethesameinputsareusedformeteorology,emissionsetc.,andthesame

numericalmethodsareemployedthroughoutthemodel,thesource‐receptorrelationships

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Figure7‐1.Exampleofthesub‐divisionofaCAMxdomainintoseparateareasforgeographic

sourceapportionment.



developedbySAinherentlyhaveahighdegreeofconsistencywiththosegeneratedbyCAMx.

Thebiggestlimitationofthis(oranyother)sourceapportionmentapproachrelatestonon‐

linearchemicalinteractionsbetweenemissionsfromdifferentsources,whichbyextension

meansthatanyperturbationtotheemissioninventorychangessource‐receptorrelationships

andattributioninanon‐linearway.Thus,forpollutantslikeozoneandsomePM,SAresults

onlyapplytoaparticularemissionsscenario,andcannotbeusedtoextrapolateeffects

resultingfromemissionchangesamongthetrackedsourceregions/groups.

7.1OzoneSourceApportionment

Yarwoodetal(1996a,b)developedanozonesourceattributionapproachthathasbecome

knownasthe“OzoneSourceApportionmentTechnology”(OSAT).Thismethodwasoriginally

implementedintheUrbanAirshedModel(UAM)andwasbuiltintothefirstversionofCAMx.

Thesecondversion(OSAT2–althoughthistermwasnotwidelyused)wasreleasedwithCAMx

v4.20in2005alongwiththeadditionofParticulateSourceApportionmentTechnology(PSAT).

TheOSAT2updateaccountedforsimultaneousproductionanddestructionofozoneby

photochemistryandtendedtoallocatelessozonetolong‐rangetransport(becauseof

destructionduringtransport)andmoretolocalproduction.Thethirdversion(OSAT3)was

releasedwithCAMxv6.30in2016,andincludesanimprovedapproachtohandleNOxrecycling

(YarwoodandKoo,2015).TheOSAT3updatetendstoallocatemoreozonetolong‐range

transport(duetocontributionsfromNOxduringdownwindtransport)andlesstolocal

production.

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7.1.1OSATFormulation

TheoriginalOSATusesfourtracerspersourceregion/grouptoaccountforcontributionsto

ozoneformation.OzoneformationinvolvesbothNOxandVOC,andOSATusestwotracer

families(NiandVi)toapportionNOxandVOCbysourceregion/groupi.Theozoneformation

processiscontrolledbytherelativeavailabilityofNOxandVOC,andsoozoneformationis

describedeitherasNOx‐limitedorVOC‐limited,respectively.Theratiooftheproductionrates

ofhydrogenperoxide(H2O2)andnitricacid(HNO3)istheindicatorusedtoclassifyozone

formationasbeinginstantaneouslylimitedbyNOxorVOC.Ozoneformationisclassifiedas

beingNOx‐limitedwhenP(H2O2)/P(HNO3)<0.35(Sillman,1995).Whenozoneproductionata

givenlocationandtimeisNOx‐limited,itmakessensetoattributethatproductiontosource

region/groupsbasedontheircontributionstothelocalNOx,andsimilarlytoattribute

productionbasedonVOCcontributionswhenozoneformationisVOC‐limited.Consequently,

separateozonetracerfamilies(O3NiandO3Vi)areusedtotrackozoneformedunderNOxand

VOC‐limitedconditions.

TheOSATtracersbysourceregion/groupiare:

NiNitricoxide(NO)andnitrogendioxide(NO2)emissions

ViVOCemissions

O3NiOzoneformedunderNOx‐limitedconditionsfromNi

O3ViOzoneformedunderVOC‐limitedconditionsfromVi

TheoriginalOSATtracerschemeisillustratedinFigure7‐2.Netozonechangeduetochemistry

(ΔO3)istrackedbythetracerfamiliesO3NandO3V.Ozonedestruction(ΔO3<0)reducesall

O3NandO3Vproportionately.Ozoneproduction(ΔO3>0)isclassifiedeitherasNOx‐limitedor

VOC‐limitedusingtheindicatorH2O2/HNO3andassignedeithertoO3NorO3V,respectively,

inproportiontotheprecursortracerspresent,respectivelyNorV.TheprecursortracersNand

Vareremovedbychemicaldecay.



Figure7‐2.TheoriginalOSATschemeforozoneapportionment.Informationflowsalong

arrows.Changesincoremodelspeciesareshowninblue,OSATtracersareinblack,the

diamondrepresentstheOSATalgorithmthatdeterminesozonetracerchanges.

H2O2/HNO3istheindicatorratiousedtodetermineNOx‐orVOC‐limitedozoneproduction.



ΔO

O3V O3N

ΔH2O2/ΔHNO3

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7.1.2OSAT2Formulation

TheoriginalOSATalgorithmallocatedthenetozonechange(ΔO3)totracersO3Nand/orO3V.

However,ozoneproductionanddestructionreactionsoperatesimultaneouslyandsothenet

ozonechangeisthebalanceofproductionanddestruction.Forexample,VOCoxidationcan

causephotochemicalozoneproductionatthesametimethatO3+VOCreactionsdirectly

consumeozone,andtheseprocessesmayleadtoanetozoneincreaseordecreasedepending

mainlyuponavailabilityofNOxandsunlight.

OSAT2accountsforthefollowingozonedestructionmechanisms:

1) O3+VOCreactionssincetheseremoveozone;

2) O(3P)+VOCreactionssincetheseeffectivelyremoveozone;

3) O(1D)+H2Oreactionsincethiseffectivelyremovesozone;

4) HOx+O3reactionsthatdonotre‐formozone.

Ozonedestructioniscalculatedasthesmaller(i.e.,morenegative)ofthesumofthesefour

mechanismsorΔO3.OzoneproductionisthencalculatedasthedifferencebetweenΔO3and

theozonedestruction.TheO3VandO3Ntracersareadjustedfirstforozonedestruction

(appliedtoalltracers)andsecondforozoneproduction(appliedusingtheOSATrules).

Theamountofozonedestructioniscalculatedfromthetime‐integratedratesofthefour

chemicalprocesseslistedabove.Itiseasytoaccountforprocesses1‐3sincetheozone

destroyedissimplythetime‐integralofthereactionsinvolved.Process4islesseasyto

quantifybecauseozonecanbere‐formed.Forexample:

O3+OH→HO2

HO2+NO→OH+NO2

NO2+hν→NO+O

O+O2→O3

However,process4isanimportantozonedestructionmechanisminlowNOx(e.g.,rural)

environments.Therefore,accountingforprocess4isimportanttounderstandinglong‐range

ozonetransport.ThemainreactionpathwaysbetweenozoneandHOx(OHandHO2)are

showninFigure7‐3.

TheozonedestructionrateduetoO3+HOxreactionsiscomputedfrom:



TheOSAT2tracersarethesameastheoriginalOSAT.TheOSAT2schemeforozone

apportionmentisillustratedinFigure7‐4.Ozoneproductionanddestructionaretreated

separatelyandcanoccursimultaneously.Ozonedestruction(−ΔO3)reducesallO3NandO3V

proportionately.Ozoneproduction(+ΔO3)isclassifiedeitherasNOx‐limitedorVOC‐limited

 





















termHONOHO

termHO

HOxO

3RateRate

Rate

RatenDestructioO3

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Figure7‐3.DaytimereactionsofozonewithHOx(OHandHO2)showingpotentialfor

reformationofozoneorozonedestructionviaperoxideformation.



Figure7‐4.TheOSAT2schemeforozoneapportionment.Informationflowsalongarrows.

Changesincoremodelspeciesareshowninblue,OSATtracersareinblack,thediamond

representstheOSATalgorithmthatdeterminesozonetracerproducton.H2O2/HNO3isthe

indicatorratiousedtodetermineNOx‐orVOC‐limitedozoneproduction.



usingtheindicatorH2O2/HNO3andassignedeithertoO3NorO3V,respectively,in

proportiontotheprecursortracerspresent,respectivelyNorV.TheprecursortracersVandN

areremovedbychemicaldecay.

7.1.3OSAT3Formulation

OSAT3improvestheaccuracyoftheOSATmethodsbykeepingtrackofthesource(s)ofozone

removedbyreactionwithNOtoformNO2andsubsequentlyreturnedasozonewhenNO2is

destroyedbyphotolysis.Accomplishingthisobjectiverequiresmaintainingsourceattribution

ofodd‐oxygenthroughthechemicalreactionsthatlinkozone,NOandNO2.Thisisillustratedin

thefollowingchemicalreactionswhereozoneiswrittenasOOO,NO2iswrittenasONO,and

thesourceattributedodd‐oxygenisshowninred:

HO2

OH HO2

NO Peroxides

NO2

HOx

Radical

Pool

HO2,

RO2

+ΔO

O3V O3N

ΔH

/ΔHNO

−ΔO

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NO+OOO→ONO

ONO+hv→NO+O

O+OO→OOO

Sourceattributionoftheodd‐oxygencontentofNO2isperformedbytracerfamiliesOONand

OOVthatareintroducedinOSAT3.Twotracerfamiliesareneededinordertokeeptrackofthe

sourceprofileofozoneconsumed,whichwasrepresentedbyO3VandO3N.

SourceattributionofthenitrogeninNOandNO2mustalsobeperformedinordertoapplythe

apportionmentalgorithmsthattrackozoneproductionusingO3NandO3V.Accordingly,

OSAT3simultaneouslyattributesboththeNandodd‐oxygeninNO2tosources,andthesource

signaturesofthesetwoapportionmentswillalmostalwaysdiffer.Thisisillustratedbelow,

wherechemicalsourceattributionisshowninbluefornitrogenandredforodd‐oxygen:

NO+OOO→ONO

ONO+hν→NO+O

O+OO→OOO

Thechemicalconversionpathwaysbetweenoxidizednitrogenspecies(NOy)inCB6are

summarizedinFigure7‐5.Arrowsshowthedirectionofconversion,whichisbi‐directionalin

somecases.OtherchemicalmechanismshavesimilarNOyconversionpathwaystoCB6.Also

showninFigure7‐5aretheOSAT3tracerfamilies.Colorcodingshowsthecorrespondence

betweenOSAT3tracerfamiliesandtheNOyspeciesthattheyrepresent(notethatthepurpose

forcolorcodinginFigure7‐5isdifferentfromcolorsusedinthechemicalreactionsabove).



Figure7‐5.CorrespondencebetweenNOyspeciesinCB6andtracerfamiliesinOSAT3with

conversionsbetweenspecies/tracersshownbyarrows.



HONO

HNO

RNO

PAN

PNA

NIT

RGN

HN3

NTR

TPN

CB6 OSAT3

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TrackingsourceattributionofnitrogenthroughallformsofNOyenablesOSAT3toaccountfor

NOxrecyclingwhenNOxisconvertedtoanotherformofNOy(e.g.,PANorHNO3)andlater

convertedbacktoNOx.OSAT3usesthefollowing10tracersbysourceregion/groupi:

ViVOCemissions

NITiNitricoxide(NO)andnitrousacid(HONO)emissions

RGNiNitrogendioxide(NO2),nitrateradical(NO3)anddinitrogenpentoxide(N2O5)

TPNiPeroxylacetylnitrate(PAN),analoguesofPANandperoxynitricacid(PNA)

NTRiOrganicnitrates(RNO3)

HN3iGaseousnitricacid(HNO3)

O3NiOzoneformedunderNOx‐limitedconditionsfromNi

O3ViOzoneformedunderVOC‐limitedconditionsfromVi

OONiOdd‐oxygeninNO2formedfromO3Ni

OOViOdd‐oxygeninNO2formedfromO3Vi

TheOSAT3schemeforozoneapportionmentisillustratedinFigure7‐6.TheVOCprecursor

tracerfamilyVisunchangedinOSAT3andremovedbychemicaldecay,whilethetracerNis

replacedwithNIT.ThefateofNOxemissionsistrackedbythenitrogentracerfamiliesNIT,

RGN,TPN,NTRandHN3.Ozoneproductionanddestructionaretreatedseparatelyandcan

occursimultaneously(asinOSAT2).Ozoneproduction(+ΔO3)isclassifiedeitherasNOx‐limited

orVOC‐limitedusingtheindicatorH2O2/HNO3andassignedeithertoO3NorO3V,

respectively,inproportiontotheprecursortracerspresent,respectivelyNITorV.Ozone

destruction(−ΔO3)reducesallO3NandO3Vproportionately.Whenozonedestructionresults

fromreactionwithNOtoformNO2,theamountsofO3NandO3Vremovedaretransferredto

therespectiveodd‐oxygentracersOONandOOV.WhenNO2isremovedbyphotolysistoform

ozone,theamountsofOONandOOVremovedaretransferredtotherespectivetracersO3N

andO3V.

7.1.4AlternativeOzoneApportionmentUsingAPCA

AnalternativeozoneapportionmenttechniquecalledAnthropogenicPrecursorCulpability

Assessment(APCA)differsfromOSATinrecognizingthatcertainemissioncategoriesarenot

controllable(e.g.,biogenicemissions)andthatapportioningozoneproductiontothese

categoriesdoesnotprovideinformationthatisrelevanttodevelopmentofcontrolstrategies.

Toaddressthis,insituationswhereOSATwouldattributeozoneproductiontonon‐controllable

emissions,APCAre‐allocatesthatozoneproductiontothecontrollableprecursorsthat

participatedinozoneformationwiththenon‐controllableprecursor.Forexample,whenozone

formationisduetobiogenicVOCandanthropogenicNOxunderVOC‐limitedconditions(a

situationwhereOSATwouldattributeozoneproductiontobiogenicVOC),APCAattributes

ozoneproductiontotheanthropogenicNOxpresent.UsingAPCAinsteadofOSATresultsin

moreozoneformationattributedtoanthropogenicNOxsourcesandlessozoneformation

attributedtobiogenicVOCsources.

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Figure7‐6.TheOSAT3schemeforozoneapportionment.Informationflowsalongarrows.

Changesincoremodelspeciesareshowninblue,OSATtracersareinblack,thediamond

representtheOSATalgorithmsthatdetermineozonetracerproduction.H2O2/HNO3isthe

indicatorratiousedtodetermineNOx‐orVOC‐limitedozoneproduction.RGNapportions

thenitrogeninNO2whereasOONandOOVapportiontheodd‐oxygeninNO2.



TheonlydifferencebetweenAPCAandOSATisthealgorithmusedtoallocateozoneproduction

underVOCorNOx‐limitedconditions.TheOSAT3updatedoesnotrevisetheallocationof

ozoneproductionunderVOCorNOx‐limitedconditionsandthereforetheAPCAalgorithm

workswiththeOSAT3update.

7.2ParticulateSourceApportionment

ParticulateSourceApportionment(PSAT)usesmultipletracerfamiliestotrackthefateof

primaryandsecondaryPM(Yarwoodetal.,2004).PSATisdesignedtoapportionthefollowing

classesofCAMxPMspecies(CFmodeonly):

 Sulfate(PSO4)

 Particulatenitrate(PNO3)

 Ammonium(PNH4)

 Secondaryorganicaerosol(SOA)

 Particulatemercury(HgP)

 SixcategoriesofprimaryPM:

- Elementalcarbon(PEC)

- Primaryorganicaerosol(POA)

- Crustalfine(FCRS)

+ΔO

O3V O3N

ΔH

/ΔHNO

−ΔO

NIT

OOV−OON−RGN

NTR

TPNHN3

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- Otherfine(FPRM)

- Crustalcoarse(CCRS)

- Othercoarse(CPRM)

AsingletracerfamilycanapportionprimaryPMspecieswhereassecondaryPMspeciesrequire

severaltracerfamiliestotracktherelationshipbetweengaseousprecursorsandtheresulting

PM.PNO3andSOAarethemostcomplexPMcategoriestoapportionbecausetheemitted

precursorgases(NO,VOC)areseveralstepsremovedfromtheresultingPMspecies(PNO3,

SOA).

ThePSAT“reactivetracers”foreachtypeofPMbysourceregion/groupiaredescribedbelow.

PSATtracernamesforparticulatespeciesbeginwiththeletter“P.”

Sulfur

SO2iPrimarySO2emissions

PS4iParticulatesulfatefromprimaryemissionsplussecondarilyformedsulfate

Nitrogen

NITiNitricoxide(NO)andnitrousacid(HONO)

RGNiNitrogendioxide(NO2),nitrateradical(NO3),anddinitrogenpentoxide(N2O5)

TPNiPeroxylacetylnitrate(PAN),analoguesofPANandperoxynitricacid(PNA)

NTRiOrganicnitrates(RNO3)

HN3iNitricacid(HNO3)

PN3iParticulatenitratefromprimaryemissionsplussecondarilyformednitrate

NH3iAmmonia(NH3)

PN4iParticulateammonium(NH4)

SecondaryOrganics

AROiAromatic(benzene,tolueneandxylene)secondaryorganicaerosolprecursors

ISPiIsoprenesecondaryorganicaerosolprecursors

TRPiTerpenesecondaryorganicaerosolprecursors

SQTSesquiterpenesecondaryorganicaerosolprecursors

CG1iCondensablegasesfromaromatics(lowvolatilityproducts)

CG2iCondensablegasesfromaromatics(highvolatilityproducts)

CG3iCondensablegasesfromisoprene(lowvolatilityproducts)

CG4iCondensablegasesfromisoprene(highvolatilityproducts)

CG5iCondensablegasesfromterpenes(lowvolatilityproducts)

CG6iCondensablegasesfromterpenes(highvolatilityproducts)

CG7iCondensablegasesfromsesqiterpenes

PO1iParticulateorganicaerosolassociatedwithCG1

PO2iParticulateorganicaerosolassociatedwithCG2

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PO3iParticulateorganicaerosolassociatedwithCG3

PO4iParticulateorganicaerosolassociatedwithCG4

PO5iParticulateorganicaerosolassociatedwithCG5

PO6iParticulateorganicaerosolassociatedwithCG6

PO7iParticulateorganicaerosolassociatedwithCG7

POHiParticulatenon‐volatileorganicaerosolfromaromaticprecursors

PPAiAnthropogenicorganicaerosolpolymers(SOPA)

PPBiBiogenicorganicaerosolpolymers(SOPB)

Mercury

HG0iElementalMercuryvapor

HG2iReactivegaseousMercuryvapor

PHGiParticulateMercury

PrimaryParticulates

PECiPrimaryElementalCarbon

POAiPrimaryOrganicAerosol

PFCiFineCrustalPM

PFNiOtherFineParticulate

PCCiCoarseCrustalPM

PCSiOtherCoarseParticulate

BothozoneandPNO3areassociatedwithNOxemissions.Theoxidizednitrogentracerfamilies

forOSAT3andPSATareequivalentwiththeonlydifferencebeingtheadditionaltracerfor

particulatespeciesinPSAT.Therefore,PSATusesthesameOSAT3tracerfamilyforoxidized

nitrogen.

PSATincludesatotalof40tracersforeachsourceregion/groupifappliedtoallPMtypes.

Sincesourceapportionmentmaynotalwaysbeneededforallspecies,thePSAT

implementationisflexibleandallowssourceapportionmentforanyorallofthechemical

classesineachCAMxsimulation(i.e.thePSO4,PNO3,PNH4,SOA,HgPandprimaryPMclasses

listedabove).Forexample,sourceapportionmentforsulfate,nitrateandammoniumrequires

just10tracerspersourceregion/group.

AfundamentalassumptioninPSATisthatPMshouldbeapportionedtotheprimaryprecursor

foreachtypeofPM.Forexample,PSO4isapportionedtoSOxemissions,PNO3isapportioned

toNOxemissions,PNH4isapportionedtoNH3emissions,etc.Asasourceapportionment

method,PSATmustaccountforallmodeledsourcesofaPMspecies.Considertwomodel

speciesAandBthatareapportionedbyreactivetracersaiandbi,respectively.Reactivetracers

mustbeincludedforallsourcesofAandBincludingemissions,initialandboundaryconditions

sothatcompletesourceapportionmentisobtained,i.e.,A=aiandB=bi.

InPSAT,thegeneralapproachtomodelingchangeoveramodeltimestep



tisillustratedfora

chemicalreactionA



B.Thegeneralequationforspeciesdestructionis:

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Here,therelativeapportionmentofAispreservedasthetotalamountchanges.Thisequation

appliestochemicalremovalofAandalsotophysicalremovalofAbyprocessessuchas

depositionortransportoutofaspecificgridcell.

Thegeneralequationforspeciesproduction(e.g.,chemicalproductionbythechemicalreaction



B)is:

Here,productionofBinheritstheapportionmentoftheprecursorA.Thesameequation

appliesfor“production”ofBinaspecificgridcellduetoemissionsortransport.Forthecase

whereBincreasesduetoemissions,aiistheapportionmentoftheemissionsinventory.For

thecasewhereBincreasesduetotransport,aiistheapportionmentoftheupwindgridcell.

Insomecases,sourcecategoryspecificweightingfactors(wi)mustbeaddedtotheequation

forspeciesdestruction:

AnexampleischemicaldecayofthearomaticVOCtracers(ARO),whichmustbeweightedby

theaverageOHrateconstantofeachAROi.AROtracersfordifferentsourcegroupshave

differentaverageVOCreactivitiesbecausetherelativeamountsofbenzene,toluenesand

xylenesdifferbetweensourcecategories.

Insomecases,sourcecategoryspecificweightingfactors(wi)mustbeaddedtotheequation

forspeciesproduction:



Anexampleischemicalproductionofcondensablegases(CG1orCG2)fromaromaticVOC

tracers,whichmustbeweightedbyaerosolyieldweightingfactors.Theaerosolyieldweighting

factorsdependupontherelativeamountsofbenzene,toluenesandxylenesineachsource

group.

Severalaerosolreactionsaretreatedasequilibria,A



B.IfAandBreachequilibriumateach

timestep,itfollowsthattheirsourceapportionmentsalsoreachequilibrium:

 

ii a

Atatta 



 

ii a

Btbttb 



 

ii aw

Atatta 



 

ii aw

Btbttb 



   

   



































tbtattb

tbtatta

iii

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Examplesaretheequilibriumbetweengasphasenitricacidandaerosolnitrate,gasphase

ammoniumandaerosolammonium,andcondensableorganicgases(CG)andsecondary

organicaerosols(SOA).

7.3RunningCAMxWithSA

7.3.1CAMxControlFile

SourceapportionmentisinvokedsimilarlytotheotherProbingToolswithintheCAMxcontrol

file.Inthe&CAMx_Controlnamelistmodule,thevariableProbing_Toolmustbesetto

“SA”ifOSAT,APCAorPSATaretoberun.Anadditionalnamelistmodulecalled

&SA_Control mustthenbeprovidedinthecontrolfiletoconfiguretheSAportionofthe

model.Theadditionalnamelistmoduleisdescribedbelow.Theorderofthevariablesfollows

thetemplateavailablewiththesourcecode.SeveralexamplesoftheSAportionoftheCAMx

runcontrolfileareshowninFigures7‐7a‐c.

DescriptionofSAControlintheCAMxRunControlFile



&SA_Control   LabelfortheProbingToolnamelistmodulethatconfiguresthe

SAoption;itmustbeginincolumn2



&Flagendinganamelistmodule;itmustbeincolumn2



SA_Summary_Output Logicalflagusedtolimitthespecieswrittentothetracer

concentrationfiletoasubsetoftheSAtracers.Ifsettotrue,

theoutputwillberestrictedtoO3NandO3VforOSAT/APCA,

andthefollowingspeciesforPSAT:PS4,PN3,PN4,PO1,PO2,

PO3,PO4,PO5,PO6,PO7,POH,PPA,PPB,PEC,POA,PFC,PFN,

PCC,PCS,HG0,HG2,PHG



SA_Treat_SULFATE_Class Logicalflagtoturnonthesulfateclassoftracerspecies

SA_Treat_NITRATE_Class Logicalflagtoturnonthenitrateclassoftracerspecies

SA_Treat_SOA_Class LogicalflagtoturnontheSOAclassoftracerspecies

SA_Treat_PRIMARY_Class LogicalflagtoturnontheprimaryPMclassoftracerspecies

SA_Treat_MERCURY_Class Logicalflagtoturnonthemercuryclassoftracerspecies

SA_Treat_OZONE_Class Logicalflagtoturnontheozoneclassoftracerspecies(uses

OSATattributionbydefault)

SA_Use_APCA LogicalflagtouseAPCAattributionratherthanOSAT

(SA_Treat_OZONE_ClassmustbesettoTRUE)



SA_File_Root  Characterrootoutputpath/filename

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SA_Master_Sfc_OutputLogicalflagformastergridsurfaceoutput(TRUE=SA

concentrationfilewillbeoutput,FALSE=SAconcentrationfile

willnotbeoutput)



SA_Nested_Sfc_OutputLogicalflagfornestedgridsurfaceoutput(TRUE=SA

concentrationfilewillbeoutput,FALSE=SAconcentrationfile

willnotbeoutput)



SA_Stratify_BoundaryLogicalflagtostratifyboundarytypes(TRUE=separatetracer

typeswillbeusedfortheNorth,South,East,WestandTop

boundaries,FALSE=asingletracertypewillbeusedforall5

boundaries)

SA_Deposition_OutputLogicalflagtooutputdepositedtracermasstoafile

(TRUE=outputdepositedtracermass,FALSE=donotgeneratea

tracerdepositionoutputfile)



SA_Number_of_Source_Regions Integernumberofsourceregionsforthisrun.Thismustbe

thesameasthenumberofsourceareasdefinedinthe

SA_Source_Area_Mapfile



SA_Number_of_Source_GroupsIntegernumberofemissiongroups(categories)forthisrun.

TogetherwiththeUse_Leftover_Groupflag,this

determinesthenumberofpairedgriddedandpointemission

filesthatmustbesupplied(additionaldetailsbelow)



Use_Leftover_GroupLogicalflagtodefinea“leftover”emissionsgroup(TRUE=

calculatea“leftover”emissionsgroupfromthedifference

betweenthesumoftheemissiongroupfilesandtheregular

CAMxemissionfiles,FALSE=donotcalculatea“leftover”

emissionsgroup)



SA_Receptor_DefinitionsCharacterinputSAreceptordefinitionpath/filename.(Thisisan

optionalfile)



SA_Source_Area_MapCharacterarray(byCAMxgrid)inputSAoriginalsourcearea

definitionpath/filenameuniquelyassigningeachgridcelltoa

singlesourceregion(requiredformastergrid,optionalfor

nestedgrids)



SA_Use_Partial_SourceMapLogicalflagforfractional(orpartial)sourceregion(orarea)

maps(TRUE=usefractionalmaps,FALSE=useoriginalsource

areadefinitiononly)



Partial_Source_Area_MapCharacterarray(bySAemissionsgroupandCAMxgrid)inputSA

fractionalsourceareadefinitionpath/filenameassigningeach

gridcelltomultiplesourceregionsbyemissiongroup(optional)

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SA_PT_OverrideLogicalflagtoallowpointsourceoverride(TRUE=lookforand

usethepointsourceoverrideflagsinsector‐specificpoint

sourcefiles,FALSE=ignorepointsourceoverrideflags)

SA_Master_RestartCharacterinputmastergridSArestartpath/filename(ignoredif

Restart=FALSE)



SA_Nested_RestartCharacterinputnestedgridSArestartpath/filename(ignoredif

Restart=FALSEorNumber_of_Grids=1)



SA_Points_GroupCharacterarray(bysourcegroup)inputSAelevatedpoint

sourceemissionspath/filename(optional,ignoredif

Point_Emissions=FALSE)



SA_Emiss_Group_GridCharacterarray(bysourcegroup,byCAMxgrid)inputSA

griddedemissionspath/filename(optional,ignoredif

Gridded_Emissions=FALSE)



Eachpartialsourceareamaptobeusedintherunmustbelistedbysourcegroupandgrid:e.g.,

Partial_Source_Area_Map(3,2)referstoSAemissionsgroup3andgrid2.Thesemapfilesmust

belistedinthesameorderasthegroupemissioninputfiles(i.e.,themapassignedtocategory

1mustbeconsistentwiththeemissionsassignedtocategory1).

7.3.2SpecifyingEmissionGroups

SAcanapportionozone,PMandprecursorconcentrationsamongseveralemissioncategories

(or“groups”).Toachievethis,theemissionsforeachgroupmustbesuppliedinseparate

emissionfiles,bothforlowlevel(gridded)emissionsforthemasterandeachnestedgrid,and

forelevatedpointsources.TheadditionalemissionfilesmustbeintheCAMxgriddedand

pointemissionfileformats,asdescribedinSection3.Ifacategorydoesnotincludepoint

sources(e.g.biogenics),thepointsourcefilenameforthegroupcanbeleftblank.Ifacategory

hasnogriddedemissions,thegriddedfilenameforthegroupcanbeleftblankforallgrids.

APCArequiresatleasttwoemissiongroups,andthefirstgroupmustbebiogenicemissions.

Forexample,inthecasewhereemissionsaretrackedbythreegroups,threesetsofemission

filesshouldbesuppliedthatwhensummedequalthetotalemissionsintheregularCAMx

emissionfilessuppliedtothecoremodel.CAMxalsoallowsforanalternativeoption:twosets

offilescouldbesuppliedandthethirdgroupcanbecalculatedfromthe“leftover”emissions

(i.e.,thedifferencebetweentheregularCAMxemissionsandthetwospecifiedemission

groups).Theleftoveroptionissetaccordingtotheinputflag“Use_Leftover_Group”.If

theleftoveroptionisselected,themodelverifiesthattheleftovergroupisnottoosmallto

calculatewithinthenumericalprecisionofthecomputer(thisalsotrapscaseswheretheflag

wassetinerror).Iftheleftoveroptionisnotselected,themodelverifiesthatthetotal

emissionsforthegroupssuppliedareequaltotheregularmodelemissions,i.e.,thataleftover

groupisnotneeded.Inbothcases,ifappropriateconditionsarenotmet,themodelstopswith

adescriptiveerrormessage.

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&SA_Control

SA_File_Root = './OSAT_output/CAMx.OSAT.020603',

SA_Master_Sfc_Output = .true.,

SA_Nested_Sfc_Output = .true.,

SA_Summary_Output = .true.,

SA_Stratify_Boundary = .false.,

SA_Deposition_Output = .false.,

SA_Number_of_Source_Regions = 19,

SA_Number_of_Source_Groups = 1,

Use_Leftover_Group = .false.,

SA_Treat_SULFATE_Class = .false.,

SA_Treat_NITRATE_Class = .false.,

SA_Treat_SOA_Class = .false.,

SA_Treat_PRIMARY_Class = .false.,

SA_Treat_MERCURY_Class = .false.,

SA_Treat_OZONE_Class = .true.,

SA_Use_APCA = .false.,

SA_Receptor_Definitions = './OSAT_input/receptor.cities ',

SA_Source_Area_Map(1) = './OSAT_input/OSAT.source.area.map',

SA_Source_Area_Map(2) = ' ',

SA_Use_Partial_SourceMap = .false.,

Partial_Source_Area_Map(1,1) = ' ', ! Map for SA group 1, grid 1

Partial_Source_Area_Map(1,2) = ' ', ! Map for SA group 1, grid 2

SA_PT_Override = .false.,

SA_Master_Restart = ' ',

SA_Nested_Restart = ' ',

SA_Points_Group(1) = ' ',

SA_Emiss_Group_Grid(1,1) = ' ',

SA_Emiss_Group_Grid(1,2) = ' ',



Figure7‐7a.AnexampleofSAinputrecordsintheCAMxruncontrolfile.Theoptionsforthis

OSATrunareasfollows:thisisatwo‐gridrun,masterandnestedgridsurfaceconcentrations

arewrittentofile,asingletracertypeistobeusedforallboundaries,19sourceregions,and

oneemissiongroup(i.e.,zeroadditionalemissionfilesandnoleftovergroup).Thisisthefirst

dayofthesimulation(i.e.,restartisfalse),sonoOSATrestartfilesaresupplied.

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&SA_Control

SA_File_Root = './OSAT_output/CAMx.OSAT.020604',

SA_Master_Sfc_Output = .true.,

SA_Nested_Sfc_Output = .true.,

SA_Summary_Output = .true.,

SA_Stratify_Boundary = .false.,

SA_Deposition_Output = .false.,

SA_Number_of_Source_Regions = 19,

SA_Number_of_Source_Groups = 3,

Use_Leftover_Group = .true.,

SA_Treat_SULFATE_Class = .false.,

SA_Treat_NITRATE_Class = .false.,

SA_Treat_SOA_Class = .false.,

SA_Treat_PRIMARY_Class = .false.,

SA_Treat_MERCURY_Class = .false.,

SA_Treat_OZONE_Class = .true.,

SA_Use_APCA = .false.,

SA_Receptor_Definitions = './OSAT_input/receptor.cities ',

SA_Source_Area_Map(1) = './OSAT_input/OSAT.source.area.map',

SA_Source_Area_Map(2) = ' ',

SA_Use_Partial_SourceMap = .false.,

Partial_Source_Area_Map(1,1) = ' ', ! Map for SA group 1, grid 1

Partial_Source_Area_Map(1,2) = ' ', ! Map for SA group 1, grid 2

SA_PT_Override = .false.,

SA_Master_Restart = './OSAT_output/CAMx.OSAT.020603.sa.inst',

SA_Nested_Restart = './OSAT_output/CAMx.OSAT.020603.sa.finst',

SA_Points_Group(1) = ' ',

SA_Points_Group(2) = './OSAT_input/utils.020604',

SA_Emiss_Group_Grid(1,1) = './OSAT_input/bio.grd1.020604',

SA_Emiss_Group_Grid(1,2) = './OSAT_input/bio.grd2.020604',

SA_Emiss_Group_Grid(2,1) = './OSAT_input/util.grd1.020604',

SA_Emiss_Group_Grid(2,2) = './OSAT_input/util.grd2.020604',



Figure7‐7b.AsinFigure7‐7a,butinthiscasetherunisacontinuationdayofarunwith

threeemissiongroups.Thethreeemissiongroupsaredefinedbysupplyingextraemission

filesforpointandareasourcesforeachgrid(emissiongroups1and2),andsettingthe

“Use_Leftover_Group”flagtoTRUEsothatthemodelcalculatesthethirdgroupinternally.

Thepointsourcegroup1filenameisblankbecausegroup1isacategorywithnopointsource

emissions(e.g.,biogenics).

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&SA_Control

SA_File_Root = './OSAT_output/CAMx.APCA.020604',

SA_Master_Sfc_Output = .true.,

SA_Nested_Sfc_Output = .true.,

SA_Summary_Output = .true.,

SA_Stratify_Boundary = .false.,

SA_Deposition_Output = .false.,

SA_Number_of_Source_Regions = 19,

SA_Number_of_Source_Groups = 3,

Use_Leftover_Group = .false.,

SA_Treat_SULFATE_Class = .true.,

SA_Treat_NITRATE_Class = .true.,

SA_Treat_SOA_Class = .false.,

SA_Treat_PRIMARY_Class = .false.,

SA_Treat_MERCURY_Class = .false.,

SA_Treat_OZONE_Class = .true.,

SA_Use_APCA = .true.,

SA_Receptor_Definitions = './OSAT_input/receptor.cities ',

SA_Source_Area_Map(1) = './OSAT_input/OSAT.source.area.map',

SA_Source_Area_Map(2) = ' ',

SA_Use_Partial_SourceMap = .false.,

Partial_Source_Area_Map(1,1) = ' ', ! Map for SA group 1, grid 1

Partial_Source_Area_Map(1,2) = ' ', ! Map for SA group 1, grid 2

SA_PT_Override = .false.,

SA_Master_Restart = './OSAT_output/CAMx.APCA.020603.sa.inst',

SA_Nested_Restart = './OSAT_output/CAMx.APCA.020603.sa.finst',

SA_Points_Group(1) = ' ',

SA_Points_Group(2) = './OSAT_input/utils.020604',

SA_Points_Group(2) = './OSAT_input/other.020604',

SA_Emiss_Group_Grid(1,1) = './OSAT_input/bio.grd1.020604',

SA_Emiss_Group_Grid(1,2) = './OSAT_input/bio.grd2.020604',

SA_Emiss_Group_Grid(2,1) = './OSAT_input/util.grd1.020604',

SA_Emiss_Group_Grid(2,2) = './OSAT_input/util.grd2.020604',

SA_Emiss_Group_Grid(3,1) = './OSAT_input/othr.grd1.020604',

SA_Emiss_Group_Grid(3,2) = './OSAT_input/othr.grd2.020604',

Figure7‐7c.ThisfigurefollowsfromFigure7‐7b:itisacontinuationdayofa2‐gridrunwith

threeemissiongroups,andallthreeemissiongroupsaredefinedexplicitlybysupplyingextra

emissionfiles;therefore,the“Use_Leftover_Group”flagissettoFALSE.Thepointsource

group1filenameisblankbecausegroup1isacategorywithnopointsourceemissions(e.g.,

biogenics).APCAisusedtoattributeozonesources,sobiogenicemissionsMUSTbepresent

asgroup1.PSATwilltracePMsulfateandnitratespecies.

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Thenumberofemissionfilesthatneedtobesuppliedfordifferentmodelconfigurationsis

summarizedinTable7‐1;thetablealsoshowshowtheemissionsgroupsarenumbered,which

isreflectedinthetracerspeciesnames(definedbelow).



Table7‐1.Numbersofemissionfilesets(i.e.,griddedfilesandpointsourcefile)neededfor

differentmodelconfigurations.APCArequiresatleasttwoemissiongroups,andthefirst

groupmustbebiogenicemissions.

Numberof

EmissionGroups

Use

LeftoverGroup

NumberofEmission

FileSetsNeeded

NumberingofEmissionGroups

andTracerSpecies

n=1NotApplicable 0 0

n>1Falsen1,2,3,...n

n>1Truen‐11,2,3,...n



Whenspecifyingpointsourcefilestoresolvesourcecategories,thelistofpointsourcesoneach

filemustbeidentical(i.e.,samenumberofsources,sameorder)totheregularmodelpoint

sourcefile.Thisformalrestrictionisnecessarytoensurethatpointsourcesarecorrectlycross‐

referencedwithinCAMx.Thus,apointsourcefileforaspecificsourcegroupmayneedto

containrecordsforsourcesthatarenotinthegroup:theserecordsshouldhavezero

emissions.

7.3.3SourceAreaMapping

SAcanapportionozone,PMandprecursorconcentrationsamongseveralgeographicregions

withinthemodelingdomain,asshowninFigure7‐1.SArequiresadigitalmapofthemodeling

gridthatdefineshowtracersareallocatedspatially–this“sourceareamap”fileassignseach

gridcelltooneormoregeographicsourceregions.Asourceareamapmustbedefinedforthe

mastergridandoptionallyanynestedgrids.Thesourceareamapformatsareidenticalamong

allgrids,butmapsfornestedgridsmustincludetheboundary(“buffer”)rowsandcolumns.

Thesourceregionsdefinedoneachnesttakeprecedenceoverthosedefinedforthemaster

grid.Ifasourceareamapisnotprovidedforaspecificnestthenthesourceregiondefinition

willbedefinedbythesourceareamapfortheparentgrid.

Therearetwowaystodefinesourceareamaps.Thefirst(original)approachistouniquely

assigntheentiretyofeachgridcelltoasinglegeographicregionwithwhichtoapportionall

sourcecategoriespresentinthatgridcell.Thesecondoptionallowsforthefractional

allocationofeachgridcelltomultipleregions,forexample,incaseswhereseveralgeopolitical

boundariesintersectwithinasinglecell.Furthermore,separatefractionalareamapsmaybe

developedthatuniquelydefinesourceregiondistributionsforeachemissioncategorytobe

trackedbySA.TheoriginalsourceareamapsarerequiredtorunSA,butcanbesupercededby

theoptionalfractionalsourceareamaps.TheoriginalmapsprovidethedefaultSAregion

definitionincaseafractionalregionmapfileisnotprovidedforoneormoresourcecategories.

IfnofractionalareamapsareprovidedtoCAMx,thentheentireSAtreatmentdefaultsbackto

theoriginalareamapdefinition.CAMxincludesreportsintheoutputdiagnosticfiletoallow

theusertoreviewtheSAregionconfiguration.

March2016CAMxUser’sGuideVersion6.3

7.OzoneSourceApportionmentTechnology

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31 31 31 31 18 18 18 18 18 18 18 18 18 18 37 37 37 37 17 17 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 17 17 17 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 22 14 14 14 14 14 14 14 14

31 31 31 31 31 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 34 34 34 34 22 14 14 14 14 14 14 14 14

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 24 34 34 34 34 22 14 14 14 14 14 14 14 14

31 31 31 31 31 18 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 24 24 34 34 34 22 22 14 14 14 14 14 14 38 38

31 31 31 31 31 18 18 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 24 24 34 34 34 22 22 14 14 14 14 14 38 38 38

31 31 31 31 31 10 10 10 10 10 10 10 10 10 10 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 24 24 24 24 24 24 24 24 24 24 24 34 34 22 22 22 14 14 38 38 38 38 38 38

31 31 31 31 31 10 10 10 10 10 10 10 10 10 10 10 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 24 24 24 24 24 24 24 24 24 24 24 34 34 22 22 22 14 14 38 38 38 38 38 38

21 21 21 31 31 10 10 10 10 10 10 10 10 10 10 10 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 24 24 24 24 24 24 24 24 24 24 24 24 34 22 22 22 16 16 38 38 38 38 38 38

21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 10 10 8 8 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 24 24 24 24 24 24 24 24 24 24 24 24 24 16 16 16 16 16 16 16 38 38 38 38 38 38

21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 8 8 17 17 17 17 17 17 17 17 17 40 26 26 26 28 24 24 24 24 24 24 24 24 24 24 24 24 24 16 16 16 16 16 16 16 38 38 38 38 38 38

21 21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 9 9 17 17 17 17 17 17 17 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 24 24 24 3 3 3 29 29 16 16 16 38 38 38 38 38

21 21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 24 24 24 3 3 3 29 29 16 16 16 38 38 38 38 38

21 21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 23 24 24 3 3 24 24 29 16 16 16 38 38 38 38 38

21 21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 23 23 24 24 24 24 24 38 38 38 38 38 38 38 38 38

21 21 21 21 21 21 21 20 20 20 20 20 20 20 20 8 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 23 23 24 24 38 38 38 38 38 38 38 38 38 38 38 38

21 21 21 21 21 21 21 20 20 20 20 20 20 20 20 8 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 23 23 23 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 8 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 36 28 28 28 28 28 28 28 28 28 4 28 23 23 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 36 36 36 15 36 36 15 15 15 15 4 23 23 23 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 36 36 36 36 36 36 35 35 15 15 15 4 23 23 23 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 8 8 8 8 8 9 9 9 9 9 12 12 26 26 26 26 36 36 36 36 36 36 35 35 35 15 15 15 15 4 23 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 8 8 8 8 8 9 9 9 9 12 12 12 12 12 12 36 36 36 36 36 36 35 35 35 35 15 15 15 15 4 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 8 8 8 8 9 9 9 9 12 12 12 12 12 12 12 36 36 36 36 36 35 35 35 35 35 35 15 15 15 15 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 8 8 8 8 12 12 12 12 12 12 12 12 12 12 12 36 36 36 36 36 35 35 35 35 35 35 35 35 35 35 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 20 8 8 8 12 12 12 12 12 12 12 12 12 12 12 12 36 36 36 35 35 35 35 35 35 35 35 35 35 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 20 8 8 12 12 12 12 12 12 12 12 12 12 12 12 35 35 35 35 35 35 35 35 35 35 35 35 35 35 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 20 20 20 20 20 20 20 20 20 20 20 12 12 12 12 12 12 12 12 12 12 12 12 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 20 20 20 20 20 20 20 20 20 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 2 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 2 32 32 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 2 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 32 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 30 30 25 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 19 19 19 19 19 1 1 1 1 1 7 7 7 7 30 30 30 30 30 30 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 19 19 19 19 19 1 1 1 1 1 7 7 7 7 7 30 30 30 30 30 30 30 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 19 19 19 19 19 19 1 1 1 1 1 7 7 7 7 7 7 30 30 30 30 30 30 30 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 27 33 33 27 2 2 2 2 2 2 2 19 19 19 19 19 19 1 1 1 1 1 7 7 7 7 7 7 30 30 30 30 30 30 30 30 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 2 2 2 2 2 2 19 19 19 19 19 1 1 1 1 1 1 7 7 7 7 7 7 7 30 30 30 30 30 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 2 2 2 2 2 2 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 30 30 30 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 30 30 30 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 30 30 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 19 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 7 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 19 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 33 13 13 13 13 19 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 13 19 19 19 1 1 6 6 6 6 6 7 7 7 7 7 7 7 7 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 13 13 19 19 1 1 6 6 6 6 6 6 6 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 13 13 19 19 1 1 6 39 6 6 6 6 6 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 13 13 13 13 39 39 39 39 39 39 6 6 6 6 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 39 13 13 13 13 13 13 13 13 39 39 39 39 39 39 39 6 6 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 39 39 39 39 39 39 13 13 13 13 13 13 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 13 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38



Figure7‐8.ExampleoftheoriginalsourceareamapfileforthedomainandsourceareasshowninFigure7‐1.

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TheoriginalSAmapformatissimple:anarrayof3‐digitintegers(i3)spanningtheentiretyofa

particularCAMxgrid.Figure7‐8showsthesourceareamappingfileforthesinglegrid

correspondingtoFigure7‐1.SincetheCAMxdomaininFigure7‐1has63rowsand64columns

ofcells,thefileshowninFigure7‐8has63lineswith64numbersoneachline.Thefirst

numberinthetopleftcorneralwayscorrespondstothenorthwestcornerofthedomain.This

fileistypicallygeneratedusingGISsoftwarebyoverlayingthemodelinggridontogeopolitical

mapsandusingthedominantcoverageineachgridcellasitssourceregionassignment.

Tofacilitatemultipleintersectingregionswithineachgridcell,afractionalareamapforasingle

gridmayincludemultiple“panels”,wherethetotalnumberofpanelsisdeterminedbythe

maximumnumberofregionoverlapsfoundamongallgridcells.Forexample,ifaparticular

gridcellcontainsagrid‐widemaximumoffouroverlappingregions,thenthefractionalmap

containsfourpanels,eachlistingoneofthefourregionsanditsfractionalcoverageinthatcell.

ThefractionalSAmapfilehasthefollowingformat:

Loopovernumberofpanels

/SRCMAPnn-mm/Headerkeyword,wherennissource

category/groupID,mmispanelID

 Loopfromnygridrowsto1

(regn(i,j),frc(i,j),i=1,nx)Loopovernxgridcolumns,

500(i3,1x,f5.1)

Endloopoverrows

Endloopoverpanels

/END/Endoffilekeyword

Theintegervariablearrayregnistheregionindexthatexistsincell(i,j)andtherealvariable

arrayfrcisthefraction(percent)ofcell(i,j)coveredbythatregion.Fornon‐zerocell

fractions,bothregnandfrcmustbelisted,otherwiseregnisshownas0andfrcisblank

tomaximizevisualclarityofthefile.Thetotalcoverageamongallregionsineachgridcell

equals100.0%whensummedoverallpanels.AnexampleisshowninFigure7‐9forasmall

gridof10x10cells.

Theoriginalsourceareamap,andpossiblyeventhefractionalmap,maynotadequatelyresolve

theregiontowhichcertainpointsourcesshouldbeassigned.Toprovidefinercontrolofpoint

sourceassignmentstogeographicareas,theregionindexcanbespecifiedforanypointsource

usingthekcellvariableinthepointsourcefile(seefiledescriptioninSection3).Thisfeature

isreferredtoas“pointsourceoverride.”

7.3.3.1GeneratingFractionalAreaMapsFromSMOKEReports

AFortrantoolcalledREGNMAPhasbeendevelopedtosupportthedevelopmentoffractional

areamapsusinginformationderivedfromtheSparseMatrixOperatorKernelEmissions

(SMOKE)processingsystem.SMOKEcanbeconfiguredtooutputinformationto“reportfiles”

thatlistthespatialallocationofcounty‐levelemissionstoaparticularmodelinggridbycriteria

pollutant(NOx,VOC,SOx,andPM).Aseparatefractionalareamapcanbedevelopedforeach

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Figure7‐9.Examplefractionalareamapfileforasmall(10x10)grid.Thisfileisforsource

category/group#3andincludes2mappanels.Thegridcoverssourceregion#5and#6and

theseregionsoverlapinthemiddleofthedomain.Panel2showsjusttheremainingoverlap

informationforregion#6.



sourcesectororgroupofsectorsdependingonhowtheuserrunsSMOKEandconfiguresthe

listofsectorstobetrackedforSA(e.g.,considerspatialdifferencesbetweenurbanarea

sourcesandagriculturalnon‐roadsources).SMOKEspatialallocationreportsmustbeinvoked

inordertoutilizetheREGNMAPprogramtodevelopfractionalareamapsforCAMx.

Mobileemissionsarenotspatiallyallocatedinthesamewayasnon‐roadandstationary

sources,soSMOKEreportsarenotavailablefortheon‐roadsectorifSMOKE‐MOVESisused.

Therefore,theon‐roadsectormustcontinuetobetrackedinSAusingtheoriginalsourcearea

map.Additionally,SMOKEdoesnotallocateelevatedpointsourcestothemodelinggridlike

surfacecounty‐levelsources,andsoSMOKEspatialallocationreportsarenotavailableforpoint

sources.Allcategory‐specificpointsourcefilestobetrackedbySAareassignedtotheoriginal

regionmapdefinitionbydefault,exceptforthoseindividualpointsourcesflaggedforsource

regionoverride(seeSection3).

REGNMAPreadsSMOKEspatialallocationreportsforaspecificmodelinggridandsource

category(orgroupofcategories),extractsemissionsdatabygridcellandstate/countyFederal

InformationProcessingStandards(FIPS)code,andgeneratesafractionalareamapfileforthat

gridandsourcecategory/group.ThelistofSAregionstoprocessareexternallydefinedasa

countyorgroupofcounties,astateorgroupofstates,orallotherundefinedareas.REGNMAP

providesanoptiontoselectamongthecriteriapollutantsNOx,VOC,SOx,orPM2.5asthebasis

todefinethefractionalgridcellareasincasethespecificsourcecategory/grouptobe

processedisuniquelycharacterizedbyoneofthesespecies(e.g.,NOxformobilesources,SOx

forpowerplants).Alternatively,theusermayselect“All”criteriapollutants,inwhichcasethe

/SRCMAP03-01/

5 100.0 5 100.0 5 100.0 5 100.0 5 25.0 6 100.0 6 100.0 6 100.0 6 100.0 6 100.0

5 100.0 5 100.0 5 100.0 5 100.0 5 30.0 6 100.0 6 100.0 6 100.0 6 100.0 6 100.0

5 100.0 5 100.0 5 100.0 5 100.0 5 35.0 6 100.0 6 100.0 6 100.0 6 100.0 6 100.0

5 100.0 5 100.0 5 100.0 5 100.0 5 50.0 6 100.0 6 100.0 6 100.0 6 100.0 6 100.0

5 100.0 5 100.0 5 100.0 5 100.0 5 60.0 6 100.0 6 100.0 6 100.0 6 100.0 6 100.0

5 100.0 5 100.0 5 100.0 5 100.0 5 80.0 6 100.0 6 100.0 6 100.0 6 100.0 6 100.0

5 100.0 5 100.0 5 100.0 5 100.0 5 100.0 5 20.0 6 100.0 6 100.0 6 100.0 6 100.0

5 100.0 5 100.0 5 100.0 5 100.0 5 100.0 5 50.0 6 100.0 6 100.0 6 100.0 6 100.0

5 100.0 5 100.0 5 100.0 5 100.0 5 100.0 5 60.0 6 100.0 6 100.0 6 100.0 6 100.0

/SRCMAP03-02/

0 0 0 0 6 75.0 0 0 0 0 0

0 0 0 0 6 60.0 0 0 0 0 0

0 0 0 0 6 65.0 0 0 0 0 0

0 0 0 0 6 50.0 0 0 0 0 0

0 0 0 0 6 40.0 0 0 0 0 0

0 0 0 0 6 20.0 0 0 0 0 0

0 0 0 0 0 6 80.0 0 0 0 0

0 0 0 0 0 6 50.0 0 0 0 0

0 0 0 0 0 6 40.0 0 0 0 0

/END/

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fractionalallocationisbasedonthesumofallemissionsreportedpergridcellforthatsource

category/group.AdditionalinformationonhowtorunREGNMAPisprovidedwiththe

program.

7.3.4ReceptorDefinition

Tracerconcentrationscanbeoptionallyoutputtoatextfileforselectedreceptorlocationsat

themodel’soutputfrequency(usually1hour).Thereceptorsforeachmodelrunaredefinedin

the“receptordefinition”inputfile.Threetypesofreceptorsaresupported:

POINT apointspecifiedintheCAMxprojectioncoordinatesystem.

Concentrationsatthepointaredeterminedbybi‐linear

interpolationofthesurroundingfoursurfacegridcells.

SINGLECELLasinglesurfacegridcellidentifiedbygridcellindex.

CELLAVERAGEagroupofsurfacegridcellsidentifiedbyarangeofgridindices

thatareaveragedtogethertoprovidemulti‐cellaveragetracer

concentrations.

WALLOFCELLSagroupofgridcellsidentifiedbyarangeofgridandlayerindices

thatdefineawall(i.e.,afluxplane).

Forthereceptortypesthataredefinedbygridcellitisnecessarytospecifythegridcontaining

thereceptoronthereceptordefinitionrecord.Gridnumbersaredefinedusingtheinternal

CAMxgridordering.ThegridnumberingasdefinedbyCAMxisshowninatableinthe.diag

file.Eachreceptorcanbeidentifiedbya10charactername.Theformatsforspecifyingeach

receptortypearegiveninTable7‐2.Anexamplereceptorfileisshownbelow:



POINT City 1 1024.0 -272.0

SINGLE CELL Cell 1 1 45 18

CELL AVERAGE Region 10 2 8

31 19

32 19

33 19

34 19

31 18

32 18

33 18

34 18

WALL OF CELLS Boundary1 2 10 20

18 18

1 5

7.3.5OutputFileFormats

SAwritesseveraloutputfilesthatareintheCAMxFortranbinaryformat,asdescribedin

Section3.Theseincludethemasterandnestedgridtracerinstantaneousconcentrationfiles

(.sa.instand.sa.finst),thegrid‐specificsurfacetraceraverageconcentrationfile

(.sa.grdnn),andthegrid‐specificsurfacedepositedmassfile(.sa.depn.grdnn).In

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Table7‐2.Formatforthereceptordefinitionfile.

ReceptorType Line Columns Data

POIN

1 1‐15 Theword“POINT”

121‐30 Receptorname

131‐40 Xco‐ordinate

141‐50 Yco‐ordinate

SINGLECELL1 1‐15 Theword“SINGLECELL”

121‐30 Receptorname

131‐40 GridNumber

141‐50 Xcellnumber

151‐60 Ycellnumber

CELLAVERAGE1 1‐15 Thewords“CELLAVERAGE”

121‐30 Receptorname

131‐40 Gridnumber

141‐50 Thenumberofcellstoaverage(M)

2‐M 1‐10 Xcellnumber

2‐M11‐20 Ycellnumber

WALLOFCELLS1 1‐15 Thewords“WALLOFCELLS”

121‐30 Receptorname

131‐40 Gridnumber

141‐50 X‐cellbegin

151‐60 X‐cellend

241‐50 Y‐cellbegin

251‐60 Y‐cellend

341‐50 Z‐cellbegin

351‐60 Z‐cellend



addition,SAwritesouttracerconcentrationsforselectedreceptorlocationstoantextfile

(.sa.receptor).Thenamingconventionsfortracerspeciesandtheformatofthereceptor

concentrationfilearediscussedbelow.

7.3.5.1TracerSpeciesNames

Thenamesoftracerspeciesuniquelyidentifytheinformationcarriedbyeachspeciesand

togetheridentifytheSAconfiguration.Speciesnameshavelessthantencharacters,consistent

withtheCAMxconvention.Thenamingconventionsareasfollows:

EmissionSourcesSSSeeerrr

where:

SSSSpeciestype,e.g.,NOX,VOC,O3V,O3N,PSO4,etc.

eeeEmissionsgroup:

Singlegroup,always000

Multiplegroups,001,002,etc.

rrrRegiontracerreleasedfrom,001,002,003,etc.



Initial/Boundary SSSeeerrr

where:

SSSSpeciestype,e.g.,NOX,VOC,O3V,O3N,PSO4,etc.

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eeeInitialConcentrations:always000

BoundaryConcentrationsnotstratifiedbyboundary:always000

BoundaryConcentrationsstratifiedbyboundary:WST,EST,STH,NTH,

TOPindicatingboundaryoforigin

rrrICforInitialConcentrations,BCforBoundaryConcentrations

Examples:NOX000015,VOC002015,O3V000IC,O3NTOPBC

7.3.5.2ReceptorConcentrationFile

Tracerconcentrationsatuser‐specifiedreceptorlocationsareoutputtothe“receptor

concentration”file.Thefileisincommadelimitedtextformatsuitableforimportingintoa

spreadsheet.AnexampleoutputfileisshowninFigure7‐10.Twoheaderlinesatthetopof

thefileidentifythemodelversionandthedatetherunwasperformed.Next,twolinesidentify

thetimeperiodcoveredbythefileandtheaveraginginterval(generallyonehour,determined

bytheCAMxsimulationcontrolfile).Next,threelinesdefinetheSAconfiguration,followedby

thenumbersoftracerspeciesthatresultfromthisconfiguration.Thenamesofeachtracer

speciesarelistedbytracertype:theorderinwhichspeciesarelistedhereisthesameasthe

orderinwhichtracerconcentrationsaregivenlaterinthefile.

Thetracerspeciesnamesarefollowedbythenumberofreceptorsandreceptornamesas

specifiedinthe“receptordefinition”file.Thetracerconcentrationsarereportedinblockswith

adateandtimestampattheheadofeachblock.Withineachblock,receptorsarereportedin

numericalorder.Foreachreceptor,therearedataforthetracerspeciesidentifiedatthe

heading“TracerNames”.AllvaluesareinCAMxunitsofppmforgasesandg/m3forPM.

7.3.6Postprocessing

Thetracerconcentrationsinthegriddedsurfaceconcentrationfilescanbedisplayedusingany

post‐processingsoftwarenormallyusedfordisplayingCAMxaveragefileoutputformats.

Thereceptorconcentrationfilecontainsinformationforallreceptorsandallhourswithinthe

modelrunthatcreatedthefile.Itislefttotheusertodeveloppost‐processingtoolstoanalyze

theinformationcontainedinthisfile.

7.4StepsInDevelopingInputsAndRunningSA

BelowisasimplemethodologicallistofstepstofollowinsettingupandrunningSA.The

processissimilaramongtheOSAT/APCA,PSAT,andDDMProbingTools.

1) Definethesourcegroupsandregionsthatyouwishtotrack.Keepinmindthatmemory

resourcesincreasedramaticallyasthenumberoftracersgrows.ProbingTool

applicationswithlargenumbersoftracers,tracerclasses,nestedgridsorgridcellsmay

exceedavailablememory.

2) Buildasourceregionmap(Figure7‐8)thatdefinesthespatialallocationoftracer

emissions.Forsmalldomainsorsmallnumberofregions,thiscanbedonebyhand.We

suggestusingGISsoftwaretodevelopcomplexsourceregionmapsonlargegrids.

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CAMx,CAMx 6.30 Test Problem -- Mech6 CF CB05 SA.OMP,Source Apportionment, SA 160408,

Thu Mar 31 13:18:53 2016

File Duration , 02154, 0.00, 02154, 24.00,

Average Interval , 1.0000

Number of timing periods , 0

Number of source areas , 4

Number of emission groupings , 4

Number of tracer species , 180

Number of VOC species , 18

Number of O3N species , 18

Number of O3V species , 18

Number of OON species , 18

Number of OOV species , 18

Number of NIT species , 18

Number of RGN species , 18

Number of TPN species , 18

Number of NTR species , 18

Number of HN3 species , 18

Number of INERT TIME species , 0

Number of DECAY TIME species , 0

Tracer Names,

VOC000IC ,VOC000BC,VOC001001,VOC001002,VOC001003,VOC001004,VOC002001,…

O3N000IC ,O3N000BC,O3N001001,O3N001002,O3N001003,O3N001004,O3N002001,…

O3V000IC ,O3V000BC,O3V001001,O3V001002,O3V001003,O3V001004,O3V002001,…

(List continues for remaining tracer species names)

Number of receptors , 4

No, Name, Type, Grid#, Xloc, Yloc,

1, City 1 , 0, , 1024.0, -272.0,

2, Cell 1 , 1, 1, 45, 18,

3, Region 10, 8, 2, 31, 19,

32, 19,

33, 19,

34, 19,

31, 18,

32, 18,

33, 18,

34, 18,

4, Boundary1, 3, 2, 10, 20,

18, 18,

1, 5,

Time Varying Tracer Data,

Data for Period, 02154, 0.00, 02154, 1.00,

Receptor, 1,

1.3265E-02, 1.3544E-09, 1.0000E-16, 1.0974E-15, 1.0000E-16, 1.0000E-16,…

1.2237E-01, 3.3869E-08, 1.0000E-16, 1.6165E-14, 1.0000E-16, 1.0000E-16,…

8.7304E-02, 1.1926E-08, 1.0000E-16, 1.0000E-16, 1.0000E-16, 1.0000E-16,…

9.0300E-02, 1.5269E-08, 1.0188E-16, 2.6997E-15, 1.0213E-16, 1.0162E-16,…

1.0036E-16, 4.0640E-15, 1.0036E-16, 1.0036E-16, 1.0036E-16, 1.0029E-16,…

1.0000E-16, 3.7563E-15, 1.0000E-16, 1.0000E-16, 1.0000E-16, 1.0000E-16,…

Receptor, 2,

(File continues with data for remaining receptors and hours)



Figure7‐10.Examplereceptorconcentrationfile.Linesendingwith“…”aretruncatedtofit

thepage,andthefilewouldcontinuewithdataforadditionalreceptorsandhoursinthe

sameformat.

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3) Processtheemissionsinventoryintotheseparatesourcegroupfilesthatyouwantto

track(e.g.,mobile,area,point,biogenic,etc.).

a) Considerationofpotentialsourceapportionmentorsensitivityapplicationspriorto

anyemissionsprocessingcanbeverybeneficialsothatfilesbygroupareavailable

forlateruse.

b) Elevatedpointsourceswillautomaticallybeassignedtothesourceregioninwhich

theyreside.However,youmayoverridetheregiontowhicheachindividualpoint

sourceisassigned(seethedefinitionofkcellinSection3,ElevatedPointSource

File).Apointsourceregiondoesnotneedtobedefinedinthesourceregionmap,

e.g.,youcouldhaveamapwithtworegionsthatsplitthedomaininhalf,witha

thirdregionassignedarbitrarilytorepresentelevatedpointsourcesonly.

4) EdittheCAMxcontrolnamelistfile(Section2).

a) SettheProbing_Toolvariableto“SA”;thiswillactivatethe&SA_Control

namelistmodule.

b) Editoraddthe&SA_Controlnamelistmodule(describedearlier).Providethe

requiredinformation,including:

 outputpaths

 whethertostratifyboundaryconditions

 flagstoturnonspecificozoneorPMclasses

 numberofsourceregions

 numberofsourcegroups

 whethertousetheleftovergroupoption

 receptordefinitions

 listofinputemissionfilesbygroup.

c) NotethatAPCArequiresthatthebiogenicemissionfilesforeachgridarelistedfirst.

SeveralexamplesareshowninFigure7‐7.

5) ConfiguretheCAMxsourcecodetodefinethenumberoftracers,andbuildan

executable.ThiswillensurethatyouhavesufficientmemoryfortheProbingTool

application.

a) EditthefileIncludes/camx.prm

b) ChangetheparameterMXTRSP,followingtheinstructionsprovidedinthefile.

CAMxisdistributedwithMXTRSP=1tominimizememoryrequirementsfor

standardapplicationsofthemodel.IfyourunSAwithaninsufficientvalue,the

modelwillstopandtellyoutherequiredvalueofMXTRSPforyourapplication.

c) ExecutetheCAMxMakefiletobuildanexecutableprogram(Section2).

6) RunCAMxandreviewthediagnosticoutputfilestoensurethatthemodeliscorrectly

interpretingandrunningtheProbingToolconfigurationthatyouhavespecified.Ensure

thatCAMxisgeneratingtheproperoutputfilesthatyouareexpecting.Reviewthe

tableofemissionsbysourcegroupandregion.

March2016CAMxUser’sGuideVersion6.3

7.OzoneSourceApportionmentTechnology

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7) Reviewgriddedtracerfieldsusingcommonlyavailableplottingprograms.Utilitiessuch

asPAVEorVerdiwillreadProbingToolfilesdirectly.Useofanyothersoftwaremay

requirespecializedre‐formattingprocedures.

8) Youmaypost‐processandanalyzeSAreceptorfilesusingyourownspreadsheetor

databasesoftware.

9) ProbingToolgriddedtraceroutputfilesarewritteninthesameFortranbinaryformatas

theregularCAMxconcentrationoutputfiles.Youcanpost‐processgriddedoutputfields

usinganysoftwarethatreadsCAMxfiles,oryoucanadaptthoseprogramsorbuildyour

ownsoftwaretogeneratespecializedanalysisandgraphicalproducts.



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8.DECOUPLEDDIRECTMETHODFORSENSITIVITYANALYSIS

Photochemicalmodelershavetraditionallyusedsensitivityanalysisbothformodel

performanceevaluationandemissioncontrolstrategydesign.Thesimplestapproachto

sensitivityanalysis,oftenreferredtoasthe“brute‐force”approach,involveschangingamodel

inputparameter,rerunningthemodel,andthenevaluatingthechangeinmodeloutputfor

eachparametertobeinvestigated.Forexample,amodelperformanceevaluationmayuse

sensitivitysimulationstoevaluatetheimpactofchanginginitialorboundaryconditions(ICsand

BCs),biogenicemissions,anthropogenicemissions,etc.Controlstrategyevaluationmay

reduceVOCandNOxemissionstodeterminewhetherVOCand/orNOxreductionstrategiesare

themosteffectivepathtoreduceozone.

Theadvantagesofthe“bruteforce”methodforsensitivityanalysisare:

 Applicabletoanymodelinputparameter;

 Resultsareconceptuallyeasytoexplainandinterpret.

Thelimitationsofthe“bruteforce”methodare:

 Computationallyinefficient;

 Sensitivitydependsuponthemagnitudeoftheperturbationifthemodelresponseisnon‐

linear;

 Sensitivityderivedfromsmallperturbationsmaycontainsignificantlevelsofuncertainty

(numericalnoise).

Thelasttwopointsbearfurtherexplanation.Ifthemodelresponsetoaninputparameter

dependsuponnon‐linearcomponentswithinthemodel(e.g.,chemistry),thentherelative

magnitudeorevensignoftheoutputresponsemaychangeforperturbationsofdifferentsizes.

AnexampleistheozoneresponsetoNOxreductionsinaVOC‐limitedenvironment:smaller

reductionsinNOxemissionsincreaseozonelevelswhereaslargerNOxreductionsdecrease

ozone.

Thissituationcanbeillustratedmathematically.Wedefinea“sensitivitycoefficient”(s)which

representsthechangeinconcentration(c)withrespecttosomeinputparameter(

),evaluated

relativetothebasestate(

0),



Ingeneral,

canbeavector(denotedas

),whichcontainsmultipleparametersrelatedto

processesinthemodel(e.g.,rateconstants)orinputstothemodel(e.g.,emissions).The

concentrationresponsetoachangein

canberepresentedbyaTaylorseriesofsensitivity

coefficients:







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8.DecoupledDirectMethod

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wherenisthenumberof

vectorelements,xisthespatialdimensionvector,andtistime.In

theozonesensitivityexampleabove,thenon‐linearozoneresponsetolargeNOxemission

reductionsindicatesthathigh‐ordersensitivitycoefficients(curvaturesandinflections)are

significantrelativetothefirstordersensitivity(linearresponse).Asthemagnitudeoftheinput

perturbationtendstozero,theoutputresponsewillbecomedominatedbythefirst‐order

sensitivity.Therefore,verysmallchangesintheinputparametermayberequiredtousethe

“bruteforce”methodtoestimatethefirst‐order(local)sensitivity.Thepracticallimitationto

thisapproachisthatsincethechangeinoutputmustbedeterminedfromthedifference

betweentwosimulations,smalllevelsofnumericaluncertainty(noise)intwoverysimilar

outputswillcontaminatethesensitivitycalculation.

AnalternativemethodologyforevaluatingmodelsensitivitywasdevelopedbyDunker(1980,

1981)calledthedecoupleddirectmethod(DDM).TheDDMcanbeusedtocalculatethesame

typeofsensitivitycoefficientasthe“bruteforce”method.ThedifferenceisthatwithDDM,

sensitivitycoefficientsarecalculatedexplicitlybyspecializedalgorithmsimplementedinthe

hostmodel.Thus,theDDMoffersseveraladvantagesoverthebruteforcemethod:

 Improvedcomputationalefficiency,especiallyasmultiplesensitivitiescanbecalculated

simultaneously;

 Improvedaccuracysincesensitivitiesarenotcontaminatedbynumericalnoise.

8.1Implementation

TheoriginalCAMximplementationoftheDDMconsideredonlyfirst‐ordersensitivityforgas‐

phasespecies.Dunkeretal.(2002)performedarigorousanalysisofDDManddemonstrated

excellentagreementagainstbruteforcetests.High‐orderDDM(HDDM;Hakamietal.,2003;

Cohanetal.,2005)hassincebeenimplementedinCAMx.HDDMenablesCAMxtocalculate

second‐ordersensitivitiesalongwithfirst‐ordervaluesforgas‐phasespecies(Kooetal.,

2007a,2008).Thefirst‐orderDDMsensitivityhasbeenextendedtoPMspecies(Kooetal.,

2007b,2009).InthefollowingdiscussionweusethetermDDMgenericallytomeanfirstand/or

higherordersensitivity.

TheCAMxDDMcalculatesconcentrationsensitivitytoseveralsources(i.e.,emissions,ICsand

BCs)andtochemicalrateconstants.Thesensitivitytobeevaluatedmaybearasimple

relationshiptoamodelinputparameter,suchasscalingozoneBCsbyafactor(BCnew=

×BC0),

oradditivelyincreasingtheozoneBC’sbyaconstantamounteverywhere(BCnew=

+BC0).To

allowcompleteflexibility,thesensitivityperturbationsarespecifiedbyprovidingadditionalIC,

BC,and/oremissioninputfileswiththesameformatastheregularmodelinputfiles.

  



...

;,;,

termsorderhigherandthird

txctxc

























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Asaresult,theusercanperformmanydifferentsensitivitycalculationsinasinglerunaccording

tothecontentoftheDDMinputfiles.Forexample,ifthesameBCfileisspecifiedforboth

CAMxandDDM,theoutputsensitivityfieldsrepresentthesensitivityofthepredicted

concentrationstothoseparticularBCs.Simplyscalingtheoutputsensitivitycoefficientsfields

providestheincrementalconcentrationsresultingfromscalingtheBCs.IfaDDMBCfile

containsconstantconcentrationseverywhere,thesensitivitywillcorrespondtoauniform

absoluteincreaseintheBCsratherthanapercentageincreaseasdescribedabove.Another

possibilityincludesaDDMBCfilewithadifferentspatialpatternthantheCAMxinputfile.The

sensitivitycoefficientwouldthencorrespondtochangingboththegeographicdistributionand

magnitudeofBCs.Inshort,theDDMinputfilescanbearbitrary–differentfromtheCAMx

inputfileintheoverallmagnitudeofconcentrationsoremissions,differentinthegeographic

andtemporaldistribution,anddifferentintherelativeproportionsofthechemicalspecies.

However,theusermustunderstandwhatperturbationsarebeingconsideredinorderto

properlyinterprettheresultingoutputsensitivitycoefficientfields.

Inmathematicalterms,aregularmodelinputfile,forexampletheBCinputfile,represents

somesetoffunctionsofspaceandtimefi(x,t),whereeachchemicalspeciesicanbedefinedby

auniquefunction.AnadditionalinputfileprovidedtotheDDMrepresentsanothersetof

functionsofspace,time,andchemicalspeciesgi(x,t)thatcanbedifferentfromtheregular

inputfile.Thescalarparameter

iisthendefinedby



Here,

i×gi(x,t)istheperturbation,andtheuserdesiresinformationonhowthemodelwould

respondiftheinputfi(x,t)isreplacedbytheinputFi(x,t).Inthecaseofsensitivitytorate

constants,nouser‐definedinputfileisprovidedandtheperturbationisalwaysdefinedas

i×k

wherekisavectorofselectedrateconstants.TheDDMcalculatesthefirst‐ordersensitivity

si(1)(x,t)andsecond‐ordersensitivitysi(2)(x,t)withrespecttothescalarparameter

i.TheTaylor

seriestosecondorderthengivestheestimate:



wherecl(x;t;

i)istheestimatedmodelresultforspecieslwhenFi(x,t)isusedasinput,and

cl(x,t;

i=0)isthebasecasemodelresultwhenfi(x,t)isusedasinput.

Forexample,tocalculatethesensitivityofthepredictedozoneconcentrationtoscaling

boundaryozonebyafactor,CAMxwouldbeprovidedwithaDDMBCfilethathasthesame

ozonevaluesastheregularmodelBCfile.ThesensitivitycoefficientfieldsoutputbyCAMx

couldthenbeusedtoestimatetheresultingozoneconcentrationiftheozoneBCswere

increasedby20%,asfollows(forsimplicityhereafter,thedependenceonspace,time,and

chemicalspecieswillbeomitted):













.,,, txgtxftxF iiii







   

txstxstxctxc iiiiilil ,

,0;,;, )2(2)1( 

----

)2(2)1(

02.0 2.0

2.0 sscc  

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Tocalculatethesensitivityofthepredictedozoneconcentrationtoincreasingboundaryozone

by10ppb,CAMxwouldbeprovidedwithaDDMBCfilethathasaconstantozonevalueof10

ppb.Thesensitivitycoefficientfieldscouldbeusedtoestimatetheozoneconcentrationifthe

ozoneBCswereincreasedby10ppbasfollows:



whereeachsensitivityiscalculatedaccordingtothe10ppbadditioncarriedintheDDMBCfile

(thussensitivitiesarescaledbyunity).AnalternativeapproachwouldbetoprovideCAMxwith

aDDMBCfilethathasaconstantozonevalueof1ppb,andtoestimateozoneresponseifthe

ozoneBCswereincreasedby10ppbwouldrequirethateachsensitivityabovebescaledby10.

Theseareexamplesofrelativelysimplesensitivities.Amorecomplexexamplewouldbeto

calculateozonesensitivitytoscalingmorning(6‐9AM)NOxemissionsinaspecificgroupofgrid

cells.InthiscaseyouwouldprovideCAMxwithaDDMemissionsfilewhereallvaluesarezero

exceptfortheNOxemissionsintheselectedgridcellsbetween6AMand9AM,whichwould

havethesamevalueastheregularemissionsfile.Thesensitivitycoefficientcouldbeusedto

predicttheconcentrationafterascalarchange(

)inthemorningNOxemissionsusingthe

samegeneralequationasgivenabove:



Anytypeofsensitivityperturbationcanbedescribedviaaninputfile.However,theCAMxuser

interfacealsoprovideseasywaystodefinesomesensitivitiesthatarelikelytobeused

frequently.Inthefirstexampleabove,theDDMBCfilewasdescribedashavingthe“same

ozonevaluesastheregularmodelBCfile.”Toavoidtheeffortofpreparinganinputfilethatis

triviallydifferentfromtheregularmodelfile,theuserinterfaceallowsyoutoselectspecific

speciesfromaninputfiletotrack‐inthiscaseozone.Itispossibletoseparatelytrackthe

sensitivitytomorethanonespeciesfromthesamefile(e.g.ozoneandNO).Itisalsopossible

totrackthecombinedsensitivitytoagroupofspecies,suchasNOx,VOC,HRVOC,orALL.The

userinterfacealsoprovidesasimplewaytotracksensitivitiestoemissionsfromspecificgrid

cellsorgroupsofcells(sub‐regions).

8.1.1TrackingSensitivityCoefficientsWithinCAMx

DDMsensitivitycoefficientsarecalculatedinparalleltothecoreCAMxprocesses(emissions,

advection,diffusion,chemistry,deposition,etc.)thatstepthethree‐dimensionalconcentration

fieldsforwardintime.Forsomeprocesses(e.g.,chemistryandhorizontaladvection),the

sensitivityroutinesmakeuseofinformationsavedfromthecorrespondingcoremodelroutines

incaseswheretheresultsdependnon‐linearlyuponspeciesconcentrations.Inothercases,the

sensitivityalgorithmisidenticaltotheCAMxalgorithm(e.g.,horizontaldiffusion)andboth

concentrationsandsensitivitycoefficientscanbeprocessedbythesingleroiutine.Finally,

therearecaseswhereaspecializedmodulehasbeenwrittenforthesensitivitycoefficientsto

improvethecomputationalefficiency(e.g.,verticaladvection).

)2(2)1(

00.1 1

1sscc  

)2(2)1(

1sscc  

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PrioritiesintheDDMcodingimplementationwere:

 Ensuringaccuracybyusingconsistentnumericalmethodsfortheconcentrationsand

sensitivities;

 Ensuringaccuracybycalculatingtheconcentrationsandsensitivitieswithinthechemistry

solversoverthesamechemistrysub‐steps(fororiginalDDM);

 Optimizingtheefficiencyofthesensitivitycoefficientcalculationswithoutcompromising

accuracy;

 ProvidingaflexibleUserInterfacethatallowscalculationofsensitivitiestoallsourcesand

precursors;

 EnsuringthattheDDMalgorithmshaveminimalimpactoncomputerresource

requirements(memoryandCPUtime)whentheDDMisnotbeingused.

DDMandHDDMcanbeusedwitheitherofthetwohorizontaladvectionsolversavailablein

CAMx.Theoriginalfirst‐orderDDMimplementationwasdevelopedonlyfortheEBIchemistry

solver;itcannotbeusedwithLSODE.However,HDDMcanbeusedwithEBIorLSODE.

DDMandHDDMalgorithmsarenotcurrentlyimplementedfortheCAMxPlume‐in‐Grid(PiG)

submodelortheACM2verticaldiffusionschemes.

8.1.2Flexi‐DDM

AlthoughDDMiscomputationallymuchmoreefficientthantheBrute‐Forcemethod,itdoes

requiremuchmoreadditionalCPUtimeandmemoryspaceoverandaboveastandardCAMx

run,whichcanbesignificantespeciallywhenmanyfirstandsecond‐ordersensitivitiesare

requestedforanestedgridrunwithmultiplesourcecategoriesandmultiplesourceregions.

Theincreasedcomputationalcostmaynotalwaysbeworthwhileifonlypartofthemodeling

domainisofinterest.Onewaytoenhancecomputationalefficiencyinsuchcasesistouseone‐

waynesting,whereBCsforanestedgridareextractedfromtheparentgrid,andsosubsequent

runswithsensitivitiesareperformedwithoutoutergrids.However,differencesbetweenthe

twonestingschemes(i.e.1‐wayvs.2‐way)sometimescausediscrepanciesinthemodelresults.

Analternativeapproachistorunthefull2‐waynestedmodelwhile“turningoff”sensitivity

calculationsoutsidenestedgridsofinterest.

CAMxprovidesafeaturecalled“Flexi‐DDM”,whichallowstheusertoturnoffsensitivity

calculationsforselectedgrids(normallygridsfaroutsidetheareaofinterest)toimprove

computationalefficiencyofDDMruns(attheexpenseofaccuracy).ThisreducesCPUtimesbut

willnotreducememoryrequirements.Also,notethatturningoffsensitivitycalculationsfor

outergridsisonlyappropriateforcertaintypesofsensitivitycalculations:e.g.,sensitivityto

mastergridBCscannotbecalculatedwithFlexi‐DDM.

8.2RunningCAMxWithDDMandHDDM

TheDDMuserinterfacewasdesignedalongsimilarlinestotheSourceApportionment(SA)user

interface.Thismakesiteasiertolearnhowtousebothoptionsandpromotesconsistencyin

analysesperformedusingSAandDDM.DDMisinvokedsimilarlytotheotherProbingTools

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withintheCAMxcontrolfile.Inthe&CAMx_Controlnamelistmodule,thevariable

Probing_Toolmustbesettoeither“DDM”toutilizetheoriginalfirst‐order

implementation,or“HDDM”toutilizethehigh‐orderimplementation.Anadditionalnamelist

modulecalled&DDM_ControlmustthenbeprovidedinthecontrolfiletoconfiguretheDDM

portionofthemodel.Theadditionalnamelistmoduleisdescribedbelow.Theorderofthe

variablesfollowthetemplateavailablewiththesourcecode.AnexampleoftheDDMportion

oftheCAMxruncontrolfileisshowninFigure8‐1.



DescriptionofDDMControlintheCAMxRunControlFile



&DDM_Control   LabelfortheProbingToolnamelistmodulethatconfiguresthe

DDMoption;itmustbeginincolumn2



&Flagendinganamelist;itmustbeincolumn2



DDM_File_Root  Characterrootoutputpath/filename



DDM_Master_Sfc_OutputLogicalflagformastergridsurfaceoutput(TRUE=DDMfilewill

beoutputforallsensitivities,FALSE=DDMfilewillnotbe

output)



DDM_Nested_Sfc_OutputLogicalflagfornestedgridsurfaceoutput(TRUE=DDMfilewill

beoutputforallsensitivities,FALSE=DDMfilewillnotbe

output)



DDM_Stratify_BoundaryLogicalflagtostratifyboundarytypes(TRUE=separate

sensitivitytypeswillbeusedfortheN,S,E,W,andTop

boundaries,FALSE=asinglesensitivitytypewillbeusedforall5

boundaries)



DDM_Number_of_Source_RegionsIntegernumberofsourceregionstobetracked.This

mustbethesameasthenumberofsourceareasdefinedinthe

DDM_Source_Area_Mapfile.Thisvaluemustbegreater

thanzerowhensensitivitytoemissionsisrequested.



DDM_Number_of_Source_Groups Integernumberofemissiongroupstobetracked.This

determinesthenumberofemissionfilesthatmustbesupplied

(additionaldetailsbelow).Thisvaluemustbegreaterthanzero

whensensitivitytoemissionsisrequested.



Number_of_IC_Species_Groups Integernumberofspeciesorspeciesgroupsinthe

initialconditionstobetracked.Thisnumbermaybebetween

zeroandthenumberofspeciesbeingsimulatedplusfour

(allowingforthefourspeciesgroupsVOC,HRVOC,NOX,ALL).

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IC_Species_GroupsCharacterarray(byICgroup)namesofthespeciesorspecies

groupsintheinitialconditionstobetracked.Allowednames

areanyspeciesbeingsimulatedbythemechanisminuse(e.g.,

O3,PAR,NO,etc.)plusthespeciesgroupsNOX,VOC,HRVOC,

andALL.Itispermissibletospecifybothaspeciesandagroup

containingthatspecies,e.g.,bothNOandNOX.Eachname

mayhaveupto10characters.Notethatifyouselectaspecies

thatisnotpresentontheICfileprovided,theinitialsensitivities

forthatspecieswillbesettozero.Thisvariablemaybeleft

blankifthenumberofinitialconditionspeciesgroupsiszero.



Number_of_BC_Species_Groups Integernumberofspeciesorspeciesgroupsinthe

boundaryconditionstobetracked.Thisnumbermaybe

betweenzeroandthenumberofspeciesbeingsimulatedplus

four(allowingforthefourspeciesgroupsVOC,HRVOC,NOX,

ALL).



BC_species_GroupsCharacterarray(byBCgroup)namesofthespeciesorspecies

groupsintheboundaryconditionstobetracked.See

descriptionforIC_Species_Groupabove.



Number_of_EM_Species_Groups Integernumberofspeciesorspeciesgroupsinthe

emissionstobetracked.Thisnumbermaybebetweenzero

andthenumberofspeciesbeingsimulatedplusfour(allowing

forthefourspeciesgroupsVOC,HRVOC,NOX,ALL).



Emis_Species_GroupsCharacterarray(byemissionsgroup)namesofthespeciesor

speciesgroupsintheemissionstobetracked.Seedescription

forIC_Species_Groupabove.



Number_of_Rate_Const_Groups Integernumberofreactionratesensitivitygroupstobe

tracked.Thisnumbermaybezero.



Rate_Const_Groups Characterstringcontainingeachreactionratesensitivitygroup

nameandreactionnumbersthatbelongtothegroup.Group

nameandreactionnumbersareseparatedbycolon(:)andeach

reactionnumberisseparatedbycomma(,).

Number_of_HDDM_Sens_GroupsIntegernumberofsecond‐ordersensitivitygroupstobetracked

(additionaldetailsbelow).Thisnumbermaybezero.



HDDM_parametersCharacterarraynamesofthefirst‐ordersensitivityparameters

towhichsecond‐ordersensitivityiscomputed.Thenamingof

thefirst‐orderparametersisthesameasthelongnameof

sensitivitieswiththefirst4charactersomitted(seeDDM

sensitivitynamingconventions/formatsbelow).Foreach

HDDMsensitivitygroup,twofirst‐orderparametersare

required(thesamecanbeusedtwice).Allthefirst‐order

parametersmustbeincludedinthemodeling.

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DDM_Receptor_DefinitionsCharacterinputDDMreceptordefinitionpath/filename.(Thisis

anoptionalfile).



DDM_Source_Area_MapCharacterarray(byCAMxgrid)inputDDMsourcearea

definitionpath/filename(requiredformastergrid,optionalfor

nestedgrids).Sourceregionsaredefinedusingamapinthe

sameformatastheintegerSAsourceareamap(Section7);

fractionalsourceareamapsarenotsupportedbyDDM.Unlike

SA,DDMdoesnotrequirethatallpartsofthemodelingdomain

betracked,thereforeitispermissibletodefineanarea

numberedzerointhesourceareamap(emissionsfromthose

areaswillnotbetracked).Thenon‐zerosourceregionnumbers

mustbebetween1andthenumberofregions.



DDM_PT_OverrideLogicalflagtoallowpointsourceoverride(TRUE=lookforand

usethepointsourceoverrideflagsinsector‐specificpoint

sourcefiles,FALSE=ignorepointsourceoverrideflags)



DDM_Calc_Grid LogicalarraycontainingFlexi‐DDMflagforeachgrid(.TRUE.=

calculatesensitivitiesinthegrid;.FALSE.=donotcalculate

sensitivitiesinthegrid).

DDM_Initial_ConditionsThenameofthesensitivityinitialconditionfile.Leavethefile

nameblankforrestartdaysorifsensitivitytoinitialconditions

isnotbeingcalculated.



DDM_Boundary_ConditionsThenameofthesensitivitylateralboundaryconditionfile.

Leavethefilenameblankifsensitivitytoboundaryconditionsis

notbeingcalculated.



DDM_Master_RestartCharacterinputmastergridDDMrestartpath/filename

(ignoredifRestart=FALSE)



DDM_Nested_RestartCharacterinputnestedgridDDMrestartpath/filename

(ignoredifRestart=FALSEorNumber_of_Grids=1)



DDM_Points_GroupCharacterarray(bysourcegroup)inputDDMelevatedpoint

sourceemissionspath/filename(optional,ignoredif

Point_Emissions=FALSE)



DDM_Emiss_Group_GridCharacterarray(bysourcegroup,byCAMxgrid)inputDDM

griddedemissionspath/filename(optional,ignoredif

Gridded_Emissions=FALSE)

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

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

&DDM_Control

DDM_File_Root = './DDM_output/CAMx.020604’,

DDM_Master_Sfc_Output = .true.,

DDM_Nested_Sfc_Output = .true.,

DDM_Stratify_Boundary = .false.,

DDM_Number_of_Source_Regions = 4,

DDM_Number_of_Source_Groups = 2,

Number_of_IC_Species_Groups = 1,

IC_Species_Groups(1) = 'O3',

Number_of_BC_Species_Groups = 1,

BC_species_Groups(1) = 'O3',

Number_of_EM_Species_Groups = 2,

Emis_Species_Groups(1) = 'NOX',

Emis_Species_Groups(2) = 'VOC',

Number_of_Rate_Const_Groups = 1,

Rate_Const_Groups(1) = 'RXN1: 120,121,122',

Number_of_HDDM_Sens_Groups = 3,

HDDM_parameters(1,1) = 'EM0201NOX_',

HDDM_parameters(1,2) = 'EM0201NOX_',

HDDM_parameters(2,1) = 'EM0201VOC_',

HDDM_parameters(2,2) = 'EM0201VOC_',

HDDM_parameters(3,1) = 'EM0201NOX_',

HDDM_parameters(3,2) = 'EM0201VOC_',

DDM_Receptor_Definitions = './DDM_input/receptor.cities',

DDM_Source_Area_Map(1) = './DDM_input/source_map.DDM.4areas',

DDM_Source_Area_Map(2) = ' ',

DDM_PT_Override = .false.,

DDM_Calc_Grid(1) = .true.,

DDM_Calc_Grid(2) = .true.,

DDM_Initial_Conditions = './DDM_input/IC.020603',

DDM_Boundary_Conditions = './DDM_input/BC.020604',

DDM_Master_Restart = './DDM_output/CAMx.020603.ddm.inst',

DDM_Nested_Restart = './DDM_output/CAMx.020603.ddm.finst',

DDM_Points_Group(1) = ' ',

DDM_Points_Group(2) = './DDM_input/utils.020604',

DDM_Emiss_Group_Grid(1,1) = './OSAT_input/bio.grd1.020604',

DDM_Emiss_Group_Grid(1,2) = './OSAT_input/bio.grd2.020604',

DDM_Emiss_Group_Grid(2,1) = './OSAT_input/util.grd1.020604',

DDM_Emiss_Group_Grid(2,2) = './OSAT_input/util.grd2.020604',

Figure8‐1.ExampleofDDMinputsintheCAMxcontrolfile.CAMxisrunwithtwogrids,andDDMis

configuredtotrackemissionsfromfoursourceregionsandtwosourcegroups.Sensitivitytoozone

initialandboundaryconditionsaretracked,whilesensitivitiestoNOxandVOCemissionsaretracked.

Sensitivityforasinglerateconstantgroupwillbecalculatedinvolvingmechanismreactionnumbers

120,121,and122.Threegroupsofsecond‐ordersensitivitiestoanthropogenicNOxandVOC

emissions(fromemissionsgroup2,sourceregion1)willbecomputed(d2/dNOx2,d2/dVOC2and

d2/dNOxdVOC).Nosourceregionmapisprovidedforthenestedgrid(theregionassignmentsonthe

nestaredefinedbythemastergrid).Onlythegroup2pointsourcesaretracked(nobiogenicpoint

sourcesareavailable).

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8.3DDMOutputFiles

TheoutputfiletypesforaDDMsimulationaredescribedinTable8‐1.Thesefileshavethe

sameformatascorrespondingconcentrationoutputfiles,describedinSection3.



Table8‐1.DDMoutputfilesuffixnames.

FileNameSuffixDDMFileType

.ddm.inst Binarymastergridinstantaneoussensitivityfileatendofsimulation(usedforrestart),3‐

D,allsensitivities,inµmolm‐3forgasesandµgm‐3forPM.

.ddm.finst Binarynestedgridinstantaneoussensitivityfileatendofsimulation(usedforrestart),3‐

D,allsensitivities,inµmolm‐3forgasesandµgm‐3forPM.

.ddm.grdnn Binaryaveragesensitivityfileforgridnn,2‐D,surfacelayersensitivitiesonlyforaffected

speciesrequestedintheCAMxaveragefile,inppmforgasesandµgm‐3forPM.

.ddm.receptor Texthourlyaveragesensitivitiesatuserspecificreceptorlocations.Thisfileisincomma

delimitedtextformatsuitableforimportingintoaspreadsheet.



8.4DDMSensitivityCoefficientNames

EachDDMsensitivitycoefficienttrackstheinfluenceofaspeciesfromaspecificsource(the

influencingspecies)onapredictedconcentration(theaffectedspecies).Thesensitivity

coefficientnamesareconstructedtoshowthisrelationship,asfollows:

{AffectedSpecies}{PollutantSource}{InfluencingSpecies}

Thisisalotofinformationtoencodeinanamethatmustconformtothetencharacterlimit

imposedbythebinaryI/Ofileformats.Becauseofthis,twonamingsystemsareusedinCAMx:

 LongNames‐thesenamesareeasytoread,butsincetheyaremorethantencharacters

inlengththeycannotbeusedinsensitivitycoefficientbinaryoutputfiles.Ifanalternate

I/Oformatisimplementedinthefutureitmaybepossibletousethelongnameson

sensitivityoutputfiles.

 ShortNames‐theseconveythesameinformationasthelongnamesbutrequiremore

practicetolearn.Theyareusedinthesensitivitycoefficientbinaryoutputfiles.

AtthestartofeachCAMxrunaconcordanceofLongandShortsensitivitycoefficientnamesis

writtentothediagnosticoutputfile(.diagfile).AnexampleconcordanceisshowninFigure8‐

2,andadetailedexplanationofthenamingconventionfollows.



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8.DecoupledDirectMethod

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

Affected Influencing Source Long Short

Species Species Type Group Region Name Name

-------------------------------------------------------------------------------

NO ALL EM 1 2 NO__EM0102ALL_ 0160102ALL

NO2 ALL EM 1 2 NO2_EM0102ALL_ 0170102ALL

O3 ALL EM 1 2 O3__EM0102ALL_ 0180102ALL

PAN ALL EM 1 2 PAN_EM0102ALL_ 0190102ALL

PANX ALL EM 1 2 PANXEM0102ALL_ 0200102ALL

PNA ALL EM 1 2 PNA_EM0102ALL_ 0210102ALL

FACD ALL EM 1 2 FACDEM0102ALL_ 0220102ALL

FORM ALL EM 1 2 FORMEM0102ALL_ 0230102ALL

H2O2 ALL EM 1 2 H2O2EM0102ALL_ 0240102ALL

HNO3 ALL EM 1 2 HNO3EM0102ALL_ 0250102ALL

HONO ALL EM 1 2 HONOEM0102ALL_ 0260102ALL

IOLE ALL EM 1 2 IOLEEM0102ALL_ 0270102ALL

ISOP ALL EM 1 2 ISOPEM0102ALL_ 0280102ALL

ISPD ALL EM 1 2 ISPDEM0102ALL_ 0290102ALL

MEOH ALL EM 1 2 MEOHEM0102ALL_ 0300102ALL

MEPX ALL EM 1 2 MEPXEM0102ALL_ 0310102ALL

MGLY ALL EM 1 2 MGLYEM0102ALL_ 0320102ALL

AACD ALL EM 1 2 AACDEM0102ALL_ 0330102ALL

ALDX ALL EM 1 2 ALDXEM0102ALL_ 0340102ALL

CO ALL EM 1 2 CO__EM0102ALL_ 0350102ALL

ALD2 ALL EM 1 2 ALD2EM0102ALL_ 0360102ALL

NTR ALL EM 1 2 NTR_EM0102ALL_ 0370102ALL

Figure8‐2.Exampleconcordanceoflongandshortsensitivitycoefficientnamesfromthe

CAMxdiagnosticoutputfile.



8.4.1InitialConditionSensitivityNames



LongName NNNNIC____MMMM



where:

NNNN Affectedspeciesnamewithtrailingunderscoretopadblanks

IC Indicatesthesensitivitycoefficientisforinitialconditions

____ Fourunderscorestopadthenameto14characters

MMMM Influencingspeciesnamewithtrailingunderscoretopadblanks



Examples: O3__IC____O3__

HNO3IC____NOX_

ETH_IC____HRVO



ShortName nnnI___mmm



where:

nnn Affectedspeciesnumber

I Indicatesthesensitivitycoefficientisforinitialconditions

___ Threeunderscorestopadthenameto10characters

mmm Influencingspeciesnumberornameofaspeciesgroup(NOX,

VOC,HRVOCorALL).



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8.DecoupledDirectMethod

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

Examples: 018I___018 (whereO3isspeciesnumber18)

025I___NOX (whereHNO3isspeciesnumber25)

042I___HRV (whereETHisspeciesnumber42)



8.4.2BoundaryConditionSensitivityNames



LongName NNNNBCRRR_MMMM



where:

NNNN Affectedspeciesnamewithtrailingunderscoretopadblanks

BC Indicatesthesensitivitycoefficientisforboundaryconditions

RRR NTH,STH,EST,WSTorTOPifstratifiedbyboundary;ALLifnot

stratifiedbyboundary

_Underscoretopadthenameto14characters

MMMM Influencingspeciesnamewithtrailingunderscoretopadblanks



Examples: O3__BCTOP_O3__

HNO3BCEST_NOX_

ETH_BCALL_HRVO



ShortName nnnBRRRmmm



where:

nnn Affectedspeciesnumber

B Indicatesthesensitivitycoefficientisforinitialconditions

RRR NTH,STH,EST,WSTorTOPifstratifiedbyboundary;ALLifnot

stratifiedbyboundary

mmm Influencingspeciesnumberornameofaspeciesgroup(NOX,

VOC,HRVOCorALL)



Examples:018BTOP018 (whereO3isspeciesnumber18)

025BESTNOX (whereHNO3isspeciesnumber25)

042BALLHRV (whereETHisspeciesnumber42)



8.4.3EmissionsSensitivityNames



LongName NNNNEMGGRRMMMM



where:

NNNN Affectedspeciesnamewithtrailingunderscoretopadblanks

EM Indicatesthesensitivitycoefficientisforemissions

GG Emissionsgroupnumber

RR Emissionsregionnumber

MMMM Influencingspeciesnamewithtrailingunderscoretopadblanks

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8.DecoupledDirectMethod



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

Examples: O3__EM0101O3__

HNO3EM0201NOX_

ETH_EM0103HRVO



ShortName nnnGGRRmmm



where:

nnn Affectedspeciesnumber

GG Emissionsgroupnumber

RR Emissionsregionnumber

mmm Influencingspeciesnumberornameofaspeciesgroup(NOX,

VOC,HRVOCorALL)



Examples: 0180101018 (whereO3isspeciesnumber18)

0250201NOX (whereHNO3isspeciesnumber25)

0420103HRV (whereETHisspeciesnumber42)



8.4.4ReactionRateSensitivityNames



LongName NNNNRATE__MMMM



where:

NNNN Affectedspeciesnamewithtrailingunderscoretopadblanks

RATE Indicatesthesensitivitycoefficientisforrateconstants

__ Twounderscorestopadthenameto14characters

MMMM Reactionratesensitivitygroupnamewithtrailingunderscoreto

padblanks



Examples: NO__RATE__RXN1

O3__RATE__R28_



ShortName nnnRATEmmm



where:

nnn Affectedspeciesnumber

RATE Indicatesthesensitivitycoefficientisforrateconstants

mmm Reactionratesensitivitygroupnumber



Examples: 016RATE001 (whereNOisspeciesnumber16)

018RATE002 (whereO3isspeciesnumber18)





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8.4.5HDDMSensitivityNames



LongName NNNNHDDMLLLMMM



where:

NNNN Affectedspeciesnamewithtrailingunderscoretopadblanks

HDDM Indicatesthesensitivitycoefficientissecond‐order

LLL Theindexofthefirst1st‐ordersensitivityparameterintheinternal

listofthe1st‐orderparameters

MMM Theindexofthesecond1st‐ordersensitivityparameterinthe

internallistofthe1st‐orderparameters



Examples: NO__HDDM001001

O3__HDDM001002



ShortName nnnHlllmmm



where:

nnn Affectedspeciesnumber

H Indicatesthesensitivitycoefficientissecond‐order

lll Theindexofthefirst1st‐ordersensitivityparameterintheinternal

listofthe1st‐orderparameters

mmm Theindexofthesecond1st‐ordersensitivityparameterinthe

internallistofthe1st‐orderparameters



Examples: 016H001001 (whereNOisspeciesnumber16)

018H001002 (whereO3isspeciesnumber18)

8.5StepsInDevelopingInputsAndRunningDDM

BelowisasimplemethodologicallistofstepstofollowinsettingupandrunningDDM.The

processissimilaramongtheSAandDDMProbingTools.

1) Definethesourcegroupsandregionsthatyouwishtotrack.Keepinmindthatmemory

resourcesincreasedramaticallyasthenumberofsensitivitiesgrows.ProbingTool

applicationswithlargenumbersofsensitivities,nestedgridsorgridcellsmayexceed

availablememory.

2) Buildanintegersourceregionmap(seeSection7)thatdefinesthespatialallocationof

emissionsensitivities.Forsmalldomainsorsmallnumberofregions,thiscanbedoneby

hand.WesuggestusingGISsoftwaretodevelopcomplexsourceregionmapsonlarge

grids.

3) Processtheemissionsinventoryintotheseparatesourcegroupfilesthatyouwantto

track(e.g.,mobile,area,point,biogenic,etc.).

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a) Considerationofpotentialsourceapportionmentorsensitivityapplicationspriorto

anyemissionsprocessingcanbeverybeneficialsothatfilesbygroupareavailable

forlateruse.

b) Elevatedpointsourceswillautomaticallybeassignedtothesourceregioninwhich

theyreside.However,youmayoverridetheregiontowhicheachindividualpoint

sourceisassigned(seethedefinitionofkcellinSection3,ElevatedPointSource

File).Apointsourceregiondoesnotneedtobedefinedinthesourceregionmap,

e.g.,youcouldhaveamapwithtworegionsthatsplitthedomaininhalf,witha

thirdregionassignedarbitrarilytorepresentelevatedpointsourcesonly.

4) EdittheCAMxcontrolnamelistfile(Section2).

a) SettheProbing_Toolvariabletothetechnologyyouwishtouse(DDM,HDDM).

Thiswillactivatethe&DDM_Controlnamelistmodule.

b) Editoraddthe&DDM_Controlnamelistmodule(describedearlier).Providethe

requiredinformation,including:

 outputpaths

 whethertostratifyboundaryconditions

 numberofsourceregions

 numberofsourcegroups

 numbersandnamesofIC,BC,emissions,rateconstant,andHDDMgroups

 receptordefinitions

 IC/BCinputfiles

 listofinputemissionfilesbygroup.

5) ConfiguretheCAMxsourcecodetodefinethenumberoftracers,andbuildan

executable.ThiswillensurethatyouhavesufficientmemoryfortheProbingTool

application.

a) EditthefileIncludes/camx.prm

b) ChangetheparametersMXTRSPandMXFDDM,followingtheinstructionsprovided

inthefile.CAMxisdistributedwithMXTRSP = 1andMXFDDM = 1tominimize

memoryrequirementsforstandardapplicationsofthemodel.IfyourunDDMwith

aninsufficientvalue,themodelwillstopandtellyoutherequiredvalueofMXTRSP

andMXFDDMforyourapplication.

c) ExecutetheCAMxMakefiletobuildanexecutableprogram(Section2).

6) RunCAMxandreviewthediagnosticoutputfilestoensurethatthemodeliscorrectly

interpretingandrunningtheProbingToolconfigurationthatyouhavespecified.Ensure

thatCAMxisgeneratingtheproperoutputfilesthatyouareexpecting.Reviewthetable

ofconcordanceoflongandshortsensitivitycoefficientnames.

7) Reviewgriddedtracerfieldsusingcommonlyavailableplottingprograms.Utilitiessuchas

PAVEorVerdiwillreadProbingToolfilesdirectly.Useofanyothersoftwaremayrequire

specializedre‐formattingprocedures.

8) ProbingToolgriddedtraceroutputfilesarewritteninthesameFortranbinaryformatas

theregularCAMxconcentrationoutputfiles.Youcanpost‐processgriddedoutputfields

usinganysoftwarethatreadsCAMxfiles,oryoucanadaptthoseprogramsorbuildyour

ownsoftwaretogeneratespecializedanalysisandgraphicalproducts.

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9.ProcessAnalysis

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9.PROCESSANALYSIS

ProcessAnalysis(PA)allowsforin‐depthanalysisofphotochemicalmodelperformanceby

revealingthecontributionsfromindividualphysicalandchemicalprocessesoperatingwithin

themodel(JeffriesandTonnesen,1994).UsingPA,onecanmorefullyunderstandthecomplex

interactionsbetweenthedifferentprocesses,explainsimulationresultswithinthecontextof

themodelformulation,andimprovethedesignofcontrolstrategies.

Aconventionalmodelperformanceevaluationemploysstatisticalandgraphicalmethodsto

analyzepredictedconcentrationsagainstobservedconcentrations.Thisanswersthebasic

question:“Howwellisthemodelreplicatingmeasurements?”Whilesuchcomparisonsare

necessarytosummarizeperformance,theyarefarfromsufficienttodeterminewhetherthe

modelisadequatelyrepresentingtherealsituation.Thisisbecausecompensatingerrors

amongvariousmodelprocessescanresultinpredictionsthatserendipitouslyagreewithlimited

observationsbutforthewrongreasons.IncontrastPAprovidesinformationonhowthe

specificmodelpredictionswereobtained,whichcanbeinterpretedtoimprovemodel

performanceand/orinformcontrolstrategydecisions.

9.1ProcessAnalysisInCAMx

ThreecomponentsofPAareimplementedinCAMx:

1) IntegratedProcessesRate(IPR)analysis.TheIPRmethodprovidesdetailedprocessrate

informationforeachphysicalprocessinCAMx(i.e.,advection,diffusion,deposition,

emissions,andchemistry)forselectedgridcellsandselectedspecies(Wang,Langstaff,

andJeffries,1995).TheIPRoutputscanbeanalyzedtodeterminewhatprocesses

governedthemodel‐predictedconcentrationsatanytimeandplace.IPRinformationhas

oftenbeenplottedasatimeseriesofprocesscontributionsforspecificcellsorgroupsof

cells.IPRoutputshavealsobeenusedtocheckthemassbalanceinthehostmodel,i.e.,

todeterminewhethermodelconcentrationsarefullyexplainedbythediagnosedprocess

informationorwhetherunexpectedartifactsareoccurring.TheIPRdataarerelatively

easytointerpretandcanbeanalyzedusingsimpletoolssuchasspreadsheets.IPRworks

forallgasandPMmechanismsandwithPiG.IPRdoesnotworkwiththeACM2vertical

diffusionoption.

2) IntegratedReactionRate(IRR)analysis.TheIRRmethodprovidesdetailedreactionrate

informationforallreactionsinthechemicalmechanismforselectedgridcells(Jeffriesand

Tonnesen,1994).TheIRRdatacanbeanalyzedtodeterminehowthechemicalchanges

occurringinthemodelarerelatedtothechemicalmechanism.Forexample,byanalyzing

rateinformationovergroupsofreactionsitispossibletoquantifychemicallymeaningful

attributessuchasradicalinitiationrates,radicalpropagationefficiencies,chainlengths,

etc.Sincetheseanalysestendtobecomplex,IRRdatagenerallyrequirepost‐processing

tobeuseful.IRRisimplementedfortheCB05chemicalmechanism,andpartiallyfor

CB6r2;itisnotimplementedforotherCB6variantsorforSAPRC07(seeChapter5,Table

5‐1).

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3) ChemicalProcessAnalysis(CPA).CPAisrelatedtotheIRRmethodbutisdesignedtobe

moreuserfriendlyandaccessible.WithCPA,aselectionofusefulparametersis

calculatedfromIRRdatawithinCAMxandthenoutputtogriddedfilesforentiregrids

(TonnesenandDennis,2000).ThegriddedCPAfilesusethesameformatasthegridded

concentrationoutputsandcanbevisualizedandprocessedusingstandardpost‐

processingtools.CPAisimplementedfortheCB05chemicalmechanism,andpartiallyfor

CB6r2;itisnotimplementedforotherCB6variantsorforSAPRC07(seeChapter5,Table

5‐1).

9.1.1IntegratedProcessRateAnalysis

ThespecificprocessesthatarereportedbyIPRarelistedinTable9‐1.Thisinformationis

outputforeachchemicalspeciesselectedforinclusionintheaverageconcentrationoutputfile,

andforeachgridcellselectedforanalysis.Theprocessratesareintegratedacrosseachmodel

outputtimeinterval(normallyhourly).Takentogether,thisinformationprovidesacomplete

descriptionofhowthespeciesconcentrationchangedacrosstheoutputtimeintervalandthe

magnitudeofalloftheprocessesthatcausedthischange.Informationisoutputinthe

concentrationunitsusedinternallywithinCAMx(µmole/m3forgases,µg/m3forPMspecies).A

gasconversionfactor(ppm/µmole/m3)specifictothegridcell/timeperiodisalsooutputto

allowconversiontomixingratio(ppm)forcomparisonofgasspecieswithCAMxaverage

concentrationoutputs.ForPMspecies,theconversionfactorisalways1.Gridcellvolumeis

alsooutputtoallowaggregationacrossgridcells.

FormostoftheprocessrateslistedinTable9‐1theinterpretationisstraightforward,therateis

simplytheconcentrationchangecausedbythenamedprocessacrosstheoutputtimeinterval.

Thesignconventionissuchthatapositivefluxalwaystendstoincreasethecellconcentration.

Furtherexplanationisprovidedforseveralprocessesbelow:

Plume‐in‐Gridchange:ThegridcellconcentrationchangecausedbyPlume‐in‐Gridpuffs

thattransferredmasstothegridcellduringtheoutputtimeinterval.

Pointsourceemissions:DoesnotincludepointsourcesselectedforPiGtreatmentas

thesearereportedinPlume‐in‐GridChange.

Dilutioninthevertical:CAMxallowsforlayerinterfaceheightstochangeovertime

whichcanleadtoa“dilution”termforaffectedgridcells.

Boundarydiffusion:Insomecasesthistermwillbezerobydefinition,namely:the

bottomboundaryofsurfacelayergridcells;thetopboundaryoftoplayergridcells;any

lateralboundarythatcoincideswithanestboundary.

Drydeposition:Thistermiszerobydefinitionforallgridcellsabovethesurfacelayer.

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Table9‐1.ProcessinformationreportedbytheIPRoption.

IPRParameterProcessInformation Unitsa

1Initialconcentration µmole/m3(µg/m3)

2Gasphasechemistry µmole/m3(µg/m3)

3Griddedemissions µmole/m3(µg/m3)

4Pointsourceemissions µmole/m3(µg/m3)

5Plume‐in‐Gridchange µmole/m3(µg/m3)

6Westboundaryadvection µmole/m3(µg/m3)

7Eastboundaryadvection µmole/m3(µg/m3)

8Southboundaryadvection µmole/m3(µg/m3)

9Northboundaryadvection µmole/m3(µg/m3)

10Bottomboundaryadvection µmole/m3(µg/m3)

11Topboundaryadvection µmole/m3(µg/m3)

12Dilutioninthevertical µmole/m3(µg/m3)

13Westboundarydiffusion µmole/m3(µg/m3)

14Eastboundarydiffusion µmole/m3(µg/m3)

15Southboundarydiffusion µmole/m3(µg/m3)

16Northboundarydiffusion µmole/m3(µg/m3)

17Bottomboundarydiffusion µmole/m3(µg/m3)

18Topboundarydiffusion µmole/m3(µg/m3)

19Drydeposition µmole/m3(µg/m3)

20Wetdeposition µmole/m3(µg/m3)

21Inorganicaerosolchemistry µmole/m3(µg/m3)

22Organicaerosolchemistry µmole/m3(µg/m3)

23Aqueousaerosolchemistry µmole/m3(µg/m3)

24Finalconcentration µmole/m3(µg/m3)

25Unitsconversion ppm/(µmole/m3)(N/A)b

26Averagecellvolume m3

aUnitsintheparenthesesareforPMspecies.

bUnitconversionfactorforPMspeciesisalways1.

9.1.2IntegratedReactionRateAnalysis

IRRprovidestheintegratedrateofeachgas‐phasechemicalreactioninunitsofppmhr‐1for

eachgridcellselectedforprocessanalysis.Reactionratesareaccumulated(integrated)within

thechemistrysolveratthetimestepsbeingusedtosolvethechemicalequations,andoutput

attheCAMxoutputtimeinterval(usually1hour).

9.1.3ChemicalProcessAnalysis

TheCPAmethodcalculatesapre‐determinedsetofparametersaslistedinTable9‐2.TheCPA

parametersarecalculatedforallgridcellsineitherthesurfacelayeroralllayers.Theselection

betweensurfacelayeroralllayerCPAoutputsisdeterminedbythe“3‐Daveragefile”flag

specifiedintheCAMxControlFile(seeSection2).Thisisbasedonthepremisethat3‐DCPA

informationwillbeinterpretedinconjunctionwith3‐Dconcentrationfields.

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Table9‐2.ChemicalProcessAnalysis(CPA)variablescalculatedinCAMxfortheCB05and

CB6r2mechanisms.Concentrationsareppb;productionanddestructionareppb/hr;

photolysisratesarehr‐1,ratiosareunitless.

CB05CB6r2Description

OzoneandOxidantProductionandLoss

OxProdOxProdProductionofOx=Ozone+NOy‐NO

OxLossOxLossDestructionofOx

PO3_netPO3_netNetozoneproduced

PO3_VOCsnsPO3_VOCsnsNetozoneproducedunderVOCsensitiveconditions

PO3_NOxsnsPO3_NOxsnsNetozoneproducedunderNOxsensitiveconditions

PH2O2_PHN3PH2O2_PNH3RatioofH2O2produced/HNO3produced.Greaterthan0.35meansNOx

sensitiveozoneproduction

O3_destO3_destOzonedestructionbychemicalreactions

RadicalInitiation

OH_newNewOHproduced(initiated)

HO2_newNewHO2produced

HOx_newNewHOx(HOx=OH+HO2)produced

newOH_O1DProductionofOHfromozonephotolysis

newOH_HONOProductionofOHfromHONOphotolysis

nOH_O3_OLEProductionofOHfromozone‐alkenereactions

nwHO2_HCHOProductionofHO2fromformaldehydephotolysis

RO2_newNewRO2produced

RadicalPropagation

OHw_COOHw_COOHreactedwithcarbonmonoxide

OHw_CH4OHw_CH4OHreactedwithmethane

OHw_ECH4OHreactedwithlocallyemittedmethane

OHw_ETHAOHw_ETHAOHreactedwithalkanes

OHw_PAROHw_PAR

OHw_PRPAOHreactedwithpropane

OHw_BENZOHreactedwithbenzene

OHw_TOLOHw_TOLOHreactedwithtolueneandmono‐substitutedaromatics

OHw_XYLOHw_XYLOHreactedwithxylenesandpoly‐substitutedaromatics

OHw_ETHOHw_ETHOHreactedwithethene

OHw_ETHYOHreactedwithethylene

OHw_OLEOHw_OLEOHreactedwithterminalalkenes(R

–

HC=CH2,e.g.propene)

OHw_IOLEOHw_IOLEOHreactedwithinternalalkenes(R

–

HC=CH

–

R,e.g.2‐butene)

OHw_ISOPOHw_ISOPOHreactedwithisoprene

OHw_TERPOHw_TERPOHreactedwithterpenes

OHw_all_HCOHw_all_HCOHreactedwithallorganiccompounds(includingCO)

ISOPwOxIsoprenereactedwithO3,NO3andO(3P)

TERPwOxTerpenesreactedwithO3,NO3andO(3P)

OH_rctdOH_rctdTotalOHreacted

HO2_rctdTotalHO2reacted

HOx_rctdTotalHOxreacted

RO2_rctdTotalRO2reacted

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CB05CB6r2Description

OHfromHO2OHproducedfromreactionsofHO2

Y_OHperHO2YieldofOHperHO2reacted(=OHfromHO2/HO2_rctd)

RadicalTerminationandHOxChainLength

OH_termOHterminated

HO2_termHO2terminated

HOx_termHOxterminated

RO2_termRO2terminated

HOx_CLHOxchainlength(=HOx_rctd/{2xHOx_new})

FormaldehydeProduction

HCHOp_ethFormaldehydeproducedfromethene

HCHOp_ole

Formaldehydefromterminalalkenes(R

–

HC=CH2,e.g.propene)inthefirst

generationofproducts

HCHOp_iole

Formaldehydefrominternalalkenes(R

–

HC=CH

–

R,e.g.2‐butene)inthefirst

generationofproducts

HCHOp_terpFormaldehydefromterpenesinthefirstgenerationofproducts

HCHOp_isopFormaldehydefromisopreneinthefirstgenerationofproducts

HCHOp_ispd

Formaldehydefromisoprenedaughterproducts(isoprod,methacroleinand

methylvinylketone)

HCHOp_TotTotalformaldehydeproduced

NOyReactions

HNO3_OHNO2HNO3_OHNO2NitricacidproducedfromOHreactingwithNO2

HNO3_NO3HCHNO3_NO3HCNitricacidproducedfromNO3reactingwithorganics

HNO3_N2O5HNO3_N2O5NitricacidproducedfromN2O5reactingwithwater

PANprodNetNetPANproduced

PANlossNetNetPANdestroyed

NTR1_prodOrganicnitrateproduction

NTR2_prodOrganicnitrateproduction

INTR_prodOrganicnitrateproduction

NTR1toNTR2Organicnitrateconversion

INTRtoNTR2Organicnitrateconversion

RNO3_prodOrganicnitrates(RNO3)produced

NOxrecyclNOxrecyclNitrates(HNO3andRNO3)recycledtoNOx

NOw_HO2NOreactedwithHO2(formingNO2)

NOw_RO2sNOreactedwithRO2(formingNO2)

NOw_RCO3sNOreactedwithRCO3(formingNO2)

Photolysis

J_NO2J_NO2NO2photolysisrate

J_O3O1DJ_O3O1DO3photolysisratetoO(1D)atoms

J_CLDADJCloud/hazeadjustmentfactor

RadicalConcentrations

OHOHradicalconcentration

HO2HO2radicalconcentration

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9.2RunningProcessAnalysis

PAcanbeusedwithmostofthephysicaloptionsavailableforthe“core”CAMxmodel,e.g.,the

variousadvectionandchemistrymechanisms/solvers.However,PAcannotbeusedatthe

sametimeastheotherCAMx“ProbingTool”options(e.g.,SA,DDM,orRTRAC)becausethe

ProbingToolsshareinternaldatastructurestominimizethetotalmemoryresourcesrequired

byCAMx.IPRcannotbeusedwiththeACM2diffusionoption.

PAisinvokedsimilarlytotheotherProbingToolswithintheCAMxcontrolfile.Inthe

&CAMx_Controlnamelistmodule,thevariableProbing_Toolmustbesettoeither“PA”

(generatesallPAoutput),“IPR”,or“IRR”.Table9‐3summarizesthetypesofprocessanalysis

performedforeachkeywordandtheoutputfilesthatareproduced.



Table9‐3.ProcessanalysiskeywordsandassociatedCAMxoutputfiles.

ProcessAnalysisKeyWordOutput

Filename

File

Contains

IPRIRRPA

Yes No Yes *.ipr Integrated process rate (IPR)

information for all selected cells

No Yes Yes *.irr Integrated reaction rate (IRR)

information for all selected cells

No Yes Yes *.cpa.grdnn Chemical process analysis

(CPA) parameters for grid nn



Anadditionalnamelistmodulecalled&PA_Controlmustthenbeprovidedinthecontrolfile

toconfigurethePAportionofthemodel.Theadditionalnamelistmoduleisdescribedbelow.

Theorderofthevariablesfollowthetemplateavailablewiththesourcecode.Anexampleof

thePAportionoftheCAMxruncontrolfileisshowninFigure9‐1.

TherulesfordefiningPAsub‐domainsareasfollows:

1) TheymustbecontainedwithinasingleCAMxgrid;

2) Theymaynotincludecellsthatcontainanestedgrid;

3) Theymaycontainasfewas1gridcells;

4) TheymaycontainuptoallofthegridcellsinaCAMxgridprovidedthatthisdoesnot

violatethesecondrule;

5) Theymayintersectoroverlap–thesamegridcellmaybeinseveralprocessanalysis

domains.

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DescriptionofPAControlintheCAMxRunControlFile

&PA_Control LabelfortheProbingToolnamelistmodulethatconfiguresthe

PAoption;itmustbeginincolumn2

& Flagendinganamelist;itmustbeincolumn2

PA_File_Root Characterrootoutputpath/filename

Number_of_PA_Domains IntegernumberofPAanalysisdomainstobeevaluatedduring

thesimulation.

Within_CAMx_Grid Integerarray(byPAdomain)pointerintotheCAMxgridwithin

whichthePAdomainexists(1=mastergrid,etc.).UsetheCAMx

internalgridnumberreportedinthe*.diagfile.Notethatthis

maydifferfromthenestorderprovidedbytheuserinthe

CAMxcontrolfile.

PA_Beg_I_Index Integerarray(byPAdomain)gridcolumncontainingwestern

edgeofPAdomain.

PA_End_I_Index Integerarray(byPAdomain)gridcolumncontainingeastern

edgeofPAdomain.



PA_Beg_J_Index Integerarray(byPAdomain)gridrowcontainingsouthernedge

ofPAdomain.

PA_End_J_Index Integerarray(byPAdomain)gridrowcontainingnorthernedge

ofPAdomain.

PA_Beg_K_Index Integerarray(byPAdomain)gridlayercontainingbottomofPA

domain.



PA_End_K_Index Integerarray(byPAdomain)gridlayercontainingtopofPA

domain.

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Figure9‐1.ExamplesectionofaCAMxcontrolfilespecifyingoptionsforProcessAnalysis.



9.2.1SettingCAMxParameters

PAstoresinformationindatastructuresthataredimensionedusingFortranparameter

statements.TheseparametersmustbelargeenoughtoaccommodatethePAconfiguration

specifiedintheCAMxcontrolfile.IfoneoftheseparametersisexceededCAMxwillstopwith

anerrormessagestatingthataparametermustbechangedandthemodelrecompiled.Itis

alwaysagoodideatodoacompleterebuild(usetheUnixcommand“makeclean”)whena

parameterischanged.Theparametersthatmayneedtobechangedareintwoincludefiles,

“procan.inc”and“camx.prm”.

procan.inc

MXPADOM – ThemaximumnumberofProcessAnalysisdomains.

MXPACEL – ThemaximumnumberofProcessAnalysiscellsoveralldomains

camx.prm

MXTRSP – Thisparameterdefinesgriddeddatastructuresthatareusedbyseveral

probingtools.ForPAthedatastructuresstorechemicalprocessanalysis(CPA)

variables,soMXTRSPmustbesettoatleastthevalueofMXCPA(setinprocan.inc)

whichis99.

&PA_Control

PA_File_Root = 'CAMx.OTAG.950707.PA',

Number_of_PA_Domains = 2,

Within_CAMx_Grid(1) = 1,

PA_Beg_I_Index(1) = 8,

PA_End_I_Index(1) = 12,

PA_Beg_J_Index(1) = 9,

PA_End_J_Index(1) = 13,

PA_Beg_K_Index(1) = 1,

PA_End_K_Index(1) = 5,

Within_CAMx_Grid(2) = 2,

PA_Beg_I_Index(2) = 107,

PA_End_I_Index(2) = 110,

PA_Beg_J_Index(2) = 78,

PA_End_J_Index(2) = 82,

PA_Beg_K_Index(2) = 1,

PA_End_K_Index(2) = 7,

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9.ProcessAnalysis

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9.2.2OutputFileFormats

CAMxmayoutputuptofourfilescontainingPAinformationaccordingtothePAoption

selected(seeTable9‐3).AllofthesefilesareinFortranbinaryformattoconservediskspace.

Twofiles(the*.iprand*.irrfiles)containinformationforjustthegridcellsselectedfor

PA.TheformatsforthesefilesarenotdescribedheresincetwoFortranpost‐processor

programsareprovidedtoextractdatafromthesefilesinacomma‐delimitedtextformat.The

filescontainingCPAinformation(the*.cpa.grdnn)aregriddedfilescoveringthesamearea

astheregularmodelaveragefiles(*.avrg.grdnn).ThegriddedCPAfileshavethesame

formatasaregularmodelaveragefileasdescribedinSection3.

9.3Postprocessing

Twopost‐processorsareprovidedtoreadthebinary*.iprand*.irroutputfilesand

extractPAdataforfurtheranalysis.TheCPAoutputfilescanbevisualizeddirectly.

9.3.1IPROutputFiles

TheFortranprogram“ext_ipr”extractsIPRdatafromoneormoreCAMx*.iprbinaryfiles

andreformatsthedatatocommadelimitedtextformat(.csv)suitableforsubsequent

analysis(e.g.,usingspreadsheets).The“ext_ipr”programperformsthefollowingtasks:

 Readsandoutputsthedescriptiveheaderofthe*.iprfile;

 Optionallycombinesdatafromseveralconsecutive*.iprfilestoprovidemulti‐day

output;

 SelectsdataforanindividualcellwithinaPAsub‐domainoraggregatesdataovermultiple

cellswithinaPAsub‐domain;

 OutputstheselectedIPRdatain.csvformatineitherppbormolarunitsforgasspecies;

PMspeciesareineitherg/m3ormassunits.

Asamplescripttorunthe“ext_ipr”programisprovidedwithitssourcecode,andthescript

includesadescriptionofhowtousetheprogram.

The“ext_ipr”programcancombineIPRinformationacrossseveralcells.Thisisusefulfor

analyzingthecontributionsofmodelprocessestoageographicareathatspansmultiplecells

andlayers(e.g.,anurbanarea).Forsimplicity,themulti‐cellareamustbedefinedasa

rectangularbox.ThecapabilityofaggregatingIPRinformationacrossverticallayersis

particularlyimportantduringthedaybecauseverticalcolumnsofcellswithinthemixedlayer

becomestronglycoupledontimescalesshorterthanonehour.Thus,iftheprocess

contributionsforasurfacegridcellareanalyzedduringthedayverticaldiffusionwilloften

completelydominateallotherprocesses.Inthissituation,itismoreinformativetoanalyzea

columnofcellsextendingfromthesurfacetotheapproximateheightofthemixedlayer.When

the“ext_ipr”programaggregatesinformationacrossgridcellsitaccountsfordifferencesin

cellvolume.Iftheoutputforaggregatecellsisrequestedinppbunits,theoutputfromCAMx

inmicromole/volumeunitsisconvertedtoppbusingthevolume‐weightedaverageunits

conversionfactorforthecellsbeingaggregated.

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9.ProcessAnalysis

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OneusefulapproachtoanalyzingIPRdataistoplotthecontributionsofseveralprocessesasa

timeseries.Figure9‐2presentsanexampleasanillustrationofhowPAcanbeused.



Figure9‐2.ExampleIPRtimeseriesanalysisforPSO4;lateralboundaryandchemistryterms

arenotaggregated.



9.3.2IRROutputFiles

TheFortranprogram“ext_irr”extractsIRRdatafromoneormoreCAMx*.irrbinaryfiles

andreformatsthedataforsubsequentanalysis.The“ext_irr”programperformsthe

followingtasks:

 Readsandoutputsthedescriptiveheaderofthe*.irrfile;

 Optionallycombinesdatafromseveralconsecutive*.irrfilestoprovidemulti‐day

output;

 SelectsdataforanindividualcellormultiplecellswithinaPAsub‐domain;

 Optionally,outputstheselectedIRRdatatoa.csvformattextfile;

 Optionally,outputstheselectedIRRdatatoaUAMaverageformatbinaryfile.

Hourly PSO4 Change from Different Processes in Chicago Area.

Run = postproc_test

Grid cells used from grid number 1: (43, 47) to (52, 56) using layers 1 to 5

-1.5

-1

-0.5

0.5

Jun 13, 2002 Jun 14, 2002

Change in PSO4 (ug/m3)

Top Boundary Deposition Emissions

Gas-Phase Chemistry Heterogeneous Chemistry West Boundary

East Boundary South Boundary North Boundary

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9.ProcessAnalysis

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ThetextIRRdataaresuitableforsubsequentanalysis(e.g.,usingspreadsheets).ThebinaryIRR

outputfrom“ext_irr”canbedisplayedusinganypost‐processingsoftwarethatcandisplay

CAMxaverageconcentrationoutputs.

9.3.3CPAOutputFiles

CPAresultsareoutputfromCAMxasgriddedfilesinthesameformatastheaverage

concentrationfiles,andthereforecanbevisualizedusinganypost‐processingsoftwarethatcan

displayCAMxconcentrationoutputs.Thesefilesmayoptionallyincludejustthesurfacelayer

oralllayersaccordingtohowthe“3‐Doutput”flagissetintheCAMxcontrolfile.Surfacelayer

speciesconcentrationsreflectthebalancebetweenseveralmodelprocessesincludingsurface

emissions/deposition,verticalmixing,andchemicalreactionsinsurface(andpossiblyaloft)grid

cells.Incontrast,theCPAoutputdataaregridcellspecificandreflectchemicalchangeinsingle

gridcells.Thefactthatverticalmixingtendstoaveragespeciesconcentrationsovermultiple

layerswhereasCPAvariablesarelayerspecificmaycomplicateandbiastheinterpretationof

CPAresults.AsolutionistoplaceboththeconcentrationsandCPAvariablesonacomparable

basisbyaveragingthemoveralllayerswithintheplanetaryboundarylayer.

Apost‐processor(VERTAVG)wasdevelopedtoaverageCPAvariablesandconcentrationsover

multiplelayerscontainedwithinthedepthoftheplanetaryboundarylayer(PBL).ThePBL

depthvariesinspaceandtimeaccordingtothestrengthandverticalextentofturbulent

mixing.VerticalturbulentmixingisspecifiedforCAMxbytheinputdiffusivity(Kv)fields.The

VERTAVGprocessorreadsCAMxKv,height,temperature,andpressureinputfiles,andthen

calculatesthePBLdepthforeachgridcolumnateachhour.VERTAVGalsoreadsaCAMx3‐D

outputfileofCPAvariables(orspeciesconcentrations)andcalculatesair‐massweightedPBL

valuesforeachgridcolumnateachhour.TheoutputfromVERTAVGisa2‐Dfileinaveragefile

formatwherethesinglelayerrepresentsthePBLaveragevaluesratherthansurfacelayer

values.

VERTAVGappendstwoextravariablestothefilebeingprocessedtoaidwithinterpretationand

tomakeclearthatthedatahavebeenverticallyaveraged.Theaddedvariablesare:

 PBL_ZisthediagnosedheightofthePBLforeachgridcolumn.

 PBL_IisthelayerindexofthetoplayerwithinthediagnosedPBLforeachgridcolumn.

CAMxmustberunusingtheoptiontocreate3‐Dspeciesconcentration(andthereforeCPA)

outputfilesinordertouseVERTAVG.

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10.ReactiveTracers

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10.REACTIVETRACERS

TheCAMxreactivetraceralgorithmprovidesaflexibleapproachforsimulatingtheemission,

dispersion,chemistry,anddepositionofmultipletracegasandparticulatetracersonthe

computationalgrid(s)andwithintheIRONPiGtreatment.Originallydevelopedtomodelair

toxics,itwasextendedandgeneralizedtobeabletotrackavarietyofuser‐definedorganicand

inorganicspecies.

Reactivetracersarecarriedseparatelyfromthecoremodelphotochemical/PMchemistry

mechanisms,andthuscanbeusedtoaddressavarietyofissues,separatelyorincombination:

 Reactiveandinertgaseousandparticleairtoxiccompounds;

 ChemicaldecayofindividualVOCcompoundsintomultiplegenerationsofdaughter

products;

 Sourcetaggingofprimaryemittedinertandreactivecompoundsfromspecificsource

types/classes,orfromindividualstacks,facilitiesand/orcomplexes.

ThereactivetraceralgorithmisimplementedasaCAMx“ProbingTool”andthussharesmodel

datastructureswithotherProbingToolssuchastheSA,DDMandPA.Thisstreamlinesthe

CAMxcode,improvesefficiency,andmaximizesconsistencywiththecoremodelsinceitallows

reactivetracercalculationsforemissions,transport,anddepositiontousetheexistingCAMx

algorithms.However,thismeansthatreactivetracerscannotbeusedsimultaneouslywith

otherProbingTools.

Thereactivetracerimplementationemploystwoapproachestodefinetracerchemistry.The

originalapproach,referredtoasRTRAC,allowstracerstodecayandformmultiplegenerations

ofdaughterproductsthroughphotolysisanduser‐specifiedthermalreactionswithozoneand

radicals(OH,NO3)thatareextractedfromthecoremodel’sgas‐phasechemistry(CBorSAPRC).

Asecondapproach,referredtoastheRTRACChemicalMechanismCompiler(RTCMC),allows

theusertoexternallydefineafullchemistrymechanismwithnolimitsoncomplexity(within

availablecomputerresources).RTCMCcanalsoaccessanygas‐phaseconcentrationsfromthe

coregas‐phasemechanismaswell.Neitheroptionallowschemistryforparticulatetracers.

10.1DescriptionofRTRAC

ReactivetracersaredefinedforeachCAMxrunbyprovidinganRTRACchemistryparameters

filesimilartothatusedforthecoremodel.TheexampleinFigure10‐1illustratesanexample

RTRACairtoxicsapplication(ENVIRON,2002;Morrisetal.,2003).Thenumberandnamesof

thetracersarearbitrary;i.e.informationonthetracerspecies’chemicalidentities,structure,

reactionpathways,andkineticsarekeptseparatefromthecoremodel.Consistentwiththe

chemistryparametersfilesusedforthecoremodel’sphotochemistry,thephysical

characteristicsforeachreactivetracermustbespecifiedfordepositioncalculations,andtheir

reactionpathwaysandratesmustbedefined.

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Figure10‐1.ExampleRTRACchemistryinputfileformodelingspecifictoxicspecies.



ThestructureoftheRTRACtracerdefinitionprovidescompleteflexibilityintheselectionofthe

compoundsandtracerstobeincludedineachanalysis.Theuserisabletoeasilyalteror

expandthecompoundsasneeded.

Forgasspecies,therequireddepositionparametersaretheHenry’sLawconstantand

molecularweightMg,thelatterofwhichdefinesadiffusivityparameteraccordingto

OHg MM 2

/.Thedepositioncalculationforgasesthatreactinplanttissuealsoneedsa

reactivityparameterthatdescribeswhetheraspeciesreactswhendissolvedinsideleaftissues

(Wesely,1989).Thisparameterisintendedformodelingthedepositionofreactivespecies,

suchasozone,andshouldbesettozeroforairtoxics.Thedepositioncalculationforgasses

CAMx Version |VERSION6.3

Description |Example RTRAC Chemsitry for Toxics

No of gas tracers |6

No of aero tracers |8

No photolysis rxns |4

No thermal rxns |12

Gas Tracers

No. Name P/S SNAM lower bnd H-law T-fact Molwt Reactvty Rscale

1 PACET PRIM 1.00E-12 6.30e+03 -6492. 44.00 0.0 1.0

2 HCHO PRIM 1.00E-12 6.30e+03 -6492. 30.00 0.0 1.0

3 BENZ PRIM 1.00E-12 1.80e-01 0. 78.00 0.0 1.0

4 BUTA PRIM 1.00E-12 1.00e-02 0. 54.00 0.0 1.0

5 SACET SEC ALD2 1.00E-12 6.30e+03 -6492. 44.00 0.0 1.0

6 SFORM SEC FORM 1.00E-12 6.30e+03 -6492. 30.00 0.0 1.0

Aero Tracers

No. Name lower bnd Density Low cut Upper cut

7 DSLF 1.00E-09 1.5 0.10 2.50

8 ECF 1.00E-09 1.5 0.10 2.50

9 CRF 1.00E-09 1.5 0.10 2.50

10 CR6F 1.00E-09 1.5 0.10 2.50

11 DSLC 1.00E-09 1.5 2.50 10.00

12 ECC 1.00E-09 1.5 2.50 10.00

13 CRC 1.00E-09 1.5 2.50 10.00

14 CR6C 1.00E-09 1.5 2.50 10.00

Photolysis reactions

Toxic Rxn # Factor

PACET 108 1.0

SACET 108 1.0

HCHO 98 1.6

SFORM 98 1.6

Thermal reactions and rates

Toxic React A(ppm-1min-1) Ea(K) B Tref

PACET OH 8.2015E+03 -3.1099E+02 0.0 300.0

PACET NO3 2.0689E+03 1.8599E+03 0.0 300.0

HCHO OH 1.6699E+03 -6.4815E+02 2.0 300.0

HCHO NO3 4.1377E+03 2.5161E+03 0.0 300.0

BENZ OH 3.6944E+03 1.9978E+02 0.0 300.0

BUTA OH 2.1871E+04 -4.4787E+02 0.0 300.0

BUTA O3 4.8766E+01 2.5000E+03 0.0 300.0

BUTA NO3 2.1871E+04 1.4890E+03 0.0 300.0

SACET OH 8.2015E+03 -3.1099E+02 0.0 300.0

SACET NO3 2.0689E+03 1.8599E+03 0.0 300.0

SFORM OH 1.6699E+03 -6.4815E+02 2.0 300.0

SFORM NO3 4.1377E+03 2.5161E+03 0.0 300.0

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alsousesan“Rscale”factortoadjustthesurfaceresistance.Thisisusedtosetthesurface

resistancetozeroforstrongacids(e.g.,HNO3)andshouldbesetto1.0formodelingairtoxics.

Thedepositioncalculationforparticlesrequirestheparticledensityandsizeassociatedwith

eachspecies.Theparticlesizeiscalculatedasthegeometricmeanoftheloweranduppercut

points(seeFigure10‐1).Ifpossible,theparticlesizeanddensityshouldbebasedonthe

measuredsizeofparticlesassociatedwitheachRTRACspecies(e.g.,foracompoundassociated

withsootparticles,useadensityandsizerepresentingthesoot).

TheemissionratesfortheRTRACspeciesareprovidedbyanextrasetofemissionfiles(surface

and/orpointsource).Emissionsofgasesareinmolespertimeperiod(normallymoles/hour),

whereasparticlesareingramspertimeperiod.Theemissionsfileformatisthesameasfora

regularCAMxemissionsfile,asdescribedinSection3.

10.1.1RTRACGas‐PhaseChemistry

TheRTRACchemistrycalculationsuseaspecialchemistrymodule.Chemistrymaybemodeled

forprimaryandsecondarygasspecies,meaningthattracerscanbeformedfromthedecayof

primarytracersorfromthedecayofhostmodelspecies(e.g.,secondaryformaldehyde).The

chemicaldecayofgaseoustracerscanaccountforthermalreactionswithozone(O3),hydroxyl

radical(OH)andnitrateradical(NO3),aswellasphotolysis.Thealgorithmsarecodedsothatall

chemicaldecaypathwaysarezerobydefaultandonlybecomenon‐zeroifdecayratesare

explicitlyspecifiedintheinputfile(seeFigure10‐1).TheexampleRTRACchemistryinputfilein

Figure10‐1showshowthermalreactionsarespecifiedbynamingthetracerandoxidant,and

providingreactionrateparameters.NotethattheRTRACchemicalreactionratesdependon

theratesandparametersprovidedintheRTRACinputfile,andnottheratesinthehostmodel

chemicalmechanism;howeverthehostmodeldoesprovidetheoxidizingspecies

concentrations(i.e.,O3,OH,andNO3).

10.1.1.1ThermalReactions

Thermalreactionswithoxidantsaremodeledassecondorderreactions:



whereRisthedecayrateandtherateconstantkisdefinedusingthegeneralizedtemperature

dependentrateexpression:



TheArrheniusfactor(A)mustbeinunits(ppm‐1min‐1),theactivationenergy(Ea)mustbeKelvin

andBisdimensionless.Thisisthesameasexpression3inTable3‐3a.Oxidantconcentrations

forthedecaycalculationareobtainedfromtheCAMxphotochemicalsimulationforeachgrid

cellateachtimestep.RTRACcanbeusedwithanyofthephotochemicalmechanismsthatare

availableinthecurrentversionofCAMx(seeSection5).Choosingbetweenthecore









oxidanttracerkR



























T

Ak a

exp

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mechanismswillinfluencetheRTRACchemicaldecayratesbychangingtheoxidant

concentrationsinthehostmodel.

10.1.1.2Photolysis

Photolysisreactionsarespecifiedbynamingthetracerundergoingphotolysisandprovidinga

ratioofthetracerphotolysisratetooneofthephotolysisreactionsinthehostphotochemical

mechanism.Forexample,Figure10‐1showsthattherearebothprimaryandsecondary

acetaldehydereactivetracers(PACETandSACET)andthephotolysisrateforbothspeciesisset

equaltoCB6r2reaction108(photolysisofALD2),whichisbasedonacetaldehyde.Figure10‐1

alsoshowsthattherearetwotypesofformaldehyde(PFORMandSFORM).Modelingthe

photolysisofformaldehydewithRTRACiscomplicatedbythefactthattheCB6r2mechanism

includestwophotolysisreactionsforformaldehyde(reactions97and98).Thesolutionshown

inFigure10‐1istomodelformaldehydephotolysisas1.6timestherateofreaction98.The

CAMxhostmechanismsarediscussedinSection5andaredefinedbythetextchemistry

parametersfiles(Section3)andmechanismlistingsdistributedwithCAMxandavailablefrom

theCAMxwebpage(www.camx.com).

10.1.1.3SecondarySpecies

RTRACallowsforformationofsecondary/daughterproductsrelatedtothechemicaldecayof

oneoftheprimarytracers.Secondaryspeciescanalsobesubjecttochemicaldecay,justlike

primaryspecies,iftheuserdesires.Therefore,theRTRACchemistrymoduleallowsdecay

reactions(thermalandphotolysis)tobespecifiedforsecondaryspeciesusingthesamemethod

asforprimaryspecies.Inthismanner,concentrationsofsecondaryspeciesaredeterminedby

thebalancebetweenchemicalproductionanddestruction.RTRACrequiresthatanysecondary

daughtertracersmustbespecifiedaftertheirparenttracerinthechemistryparametersinput

file.

RTRACalsoallowstracersthattrackthesecondaryformationofanyspeciesthatisincludedin

thehostchemicalmechanism.Forexample,inFigure10‐1thespeciesSFORMisusedtotrack

secondaryformaldehyde,andsoSFORMisdefinedasasecondaryspeciesandidentifiedwith

thehostspeciesFORM.ThismeansthattheRTRACchemistrymodulewillidentifythechemical

productionofFORMineachgridcellateachtimestep,andaddthischemicalproductiontothe

SFORMtracer.SinceSFORMisintendedtotrackonlysecondaryformaldehyde,noprimary

emissionsshouldbeincludedforSFORM.

10.1.1.4ChemicalDecayRatesforNear‐SourceModeling

TheRTRACalgorithmcanoutputhourlychemicaldecayratesatuser‐specifiedlocationsto

supportexternalanalyses,forexample,asinputtoaGaussianplume/puffmodel.Theuser

providesthelocationsofeachreceptorusingtheCAMxProbingToolsreceptorfileinput

format.Figure10‐2displaysanexampleRTRACreceptorinputfileforthefivelocations.At

eachgridcell,hourlydecayratesforeachRTRACcompoundandeveryverticallayerareoutput

andcanthenbeinterfacedwithauser‐selectedplumemodel.

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Figure10‐2.ExampleRTRACreceptorinputfileidentifyingthegridcellswithlocationswhere

hourlydecayrateswillbeoutputforsubgrid‐scalepointsourcemodeling(seeformatforSA

receptorfileinTable7‐2).



Separatefamiliesofreactivetracercompoundscanbesimulatedbyprovidingseparate

emissioninputssimilarlytoSA(seeSection7).TrackingseparatefamiliesofRTRACtracers

allowsforsourceapportionmentandcanbeusedtoavoiddoublecountingwhenanexternal

plumemodelisusedtoobtainnear‐sourceimpacts.Forexample,separatefamiliesofairtoxic

tracerscanbespecifiedforeachpointsourcecomplextobemodeledbytheexternalplume

model,sothattotalconcentrationscouldincludethelocalpointsourceimpacts(plumemodel)

plustheregionalcontributionsfromallothersources(CAMxRTRAC).

10.2DescriptionofRTCMC

LikeRTRAC,thepurposeofRTCMCistoaddtracerspeciestoaCAMx“coremodel”simulation

andhavethetracersundergochemicalchangesthatdepend,inpart,upontheevolutionof

CAMxcoremodelspecies.TheRTCMCapproachdiffersfromtheoriginalRTRACapproachby

allowingarbitrarilycomplexchemicalreactionschemes,butitisexactlylikeRTRACinevery

otherrespect.ThecurrentimplementationofRTCMCisforgas‐phasereactions,i.e.,gas‐phase

tracersreactingwitheachotherand/orgas‐phasehostmodelspecies.Thecoremodel’s

photochemicalmechanismsremainintactandseparatefromthereactivetracerchemistry.

10.2.1RTCMCGas‐PhaseChemistry

TheRTCMCallowsuserstoinput,inatext‐basedformat,asetofchemicalreactions

(mechanism)forcertaintargetspeciestobetreatedbytheCAMxReactiveTracerProbingTool.

RTCMCisanextensionoftheoriginalRTRACalgorithmthatreads(andsolves)acompletely

independent,user‐definedchemicalmechanismforreactivetracersthatcanutilize

concentrationsofanyphotochemicalspeciesfromthecoremodelmechanism.Uponstartup,

RTCMCcompilesinformationonthechemicalmechanismandconfiguresthereactivetracer

chemistrysolver.Duringthemodelsimulation,theRTCMCchemistrysolverreceivesambient

pollutantinformationfromthecorephotochemicalmechanismandusesthistocalculatethe

evolutionofRTRACspecies.

TheformatoftheRTCMCinputfileisessentiallythesameasthe“IMC”inputfileformatofthe

SCICHEMLagrangianpuffmodel(EPRI,2000).AnexampleIMCformatfileisshowninFigure

10‐3.TherearefoursectionsinanIMCfilethatareidentifiedbyakeywordatthestartofeach

section,asfollows:

SINGLE CELL Test Cell 1 42 44

SINGLE CELL Test Cell 1 41 36

SINGLE CELL Test Cell 1 39 36

SINGLE CELL Test Cell 1 50 43

SINGLE CELL Test Cell 1 34 48

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Figure10‐3.Examplefree‐formatRTCMCIMCchemistryinputfile.

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#Control Configurationinformationidentifiedbykeywords

#Species Namesofchemicalspeciesandassociateddata

#Table Photolysisratedataforanyphotolyticreactions

#EquationsChemicalreactionsandthermalrateconstants

TheIMCfileusesspace‐delimitedfree‐formtextformat.Leadingwhitespaceatthestartof

anylinewillbeignored.CAMxreadstheIMCfileascaseinsensitive.

Thehashsymbol(#)beforeeachsectionkeywordmarksthestartofasectionandshouldbe

reservedforthispurpose.Thefoursectionsshouldappearintheordershownabove.Theonly

sectionthatmaybeunnecessaryinsomecases(i.e.,iftherearenophotolyticreactions)isthe

#Tablesectionandguidanceonhandlingthiscaseisprovidedbelow.

10.2.1.1TheControlSection

AccordingtotheSCICHEMdocumentation,the#ControlsectionoftheIMCfilemustalways

haveatleastthreelines,asfollows:

#CONTROL

&CONTROL

&END

#Control

rate_species_units = 'ppm'

rate_time_units = 'min'

solver = 'dlsode'

Jacobian = 'numeric'

#Name, Type, Ambient, ATol, Dep, Wet Scav, MW, Spec Map

O3 A 1.0 1.0E-12 0.0 0.0 0.0

OH A 1.0 1.0E-12 0.0 0.0 0.0

ATRAC F 1.0 1.0E-12 0.010 0.0 0.0

BTRAC F 1.0 1.0E-12 0.001 0.0 0.0

CTRAC F 1.0 1.0E-12 0.020 0.0 0.0

DTRAC F 1.0 1.0E-12 0.001 0.0 0.0

ETRAC F 1.0 1.0E-12 0.030 0.0 0.0

FTRAC F 1.0 1.0E-12 -0.001 0.0 0.0 NO2

#Table

0 0. 15. 30. 45. 60. 75.

80. 86. 87. 88.

1 4.1590E-04 4.0600E-04 3.7540E-04 3.27E-04 2.6040E-04 9.4990E-05

2.9930E-05 4.8590E-06 8.3030E-08 1.0000E-09

#Equations

1 [ATRAC] -> (2.0)[BTRAC] ; 0 0.000E-00

2 (1.5)[CTRAC] + [OH] -> (0.5)[DTRAC] ; 1 4.2000E+04

3 [ETRAC] + [O3] -> [FTRAC] ; 1 1.8000E-02

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Thefirstlineisthekeywordidentifyingthecontrolsection.Thesecondandthirdlinesare

additionalkeywordsdenotingthestartandendofthecontrolsection.Note,however,that

CAMxignoresthe&CONTROLand&ENDlines.

Oneormorecontroloptionsmaybespecifiedusingkeywords,insertedoneperline,aheadof

theclosing&ENDline,likethis:

#CONTROL

&CONTROL

Keyword = ‘option’

&END

ThekeywordsusedbyCAMxandSCICHEMarelistedinTable10‐1andarecaseinsensitive.Not

allkeywordsareusedbybothmodels,andCAMxwillignoreanynon‐recognizedkeyword.A

“=”symbolmustseparateeachkeywordandoption.Theoptionmustbeenclosedwithin

singlequotes.Inpractice,onlythefirstsixlettersofeachkeywordandthefirstthreelettersof

eachoptionareconsideredandyoumayabbreviateaccordingly(i.e.,keyword = ‘opt’).



Table10‐1.Keywords,optionsanddefaultvaluesfortheControlsectionoftheIMCfile.

Keyword

Usedby

SCICHEM

Usedby

CAMxOptionsAllowedbyCAMx

Ambient file ●

n/a

Species_units ●

n/a

Emission_units ●

n/a

Rate_species_units ● ● molecules/cm3(default)

ppm

Rate_time_units ● ●

seconds(default)

minutes

hours

Solver ●

DLSODE(default)

SLSODE

Rosenbrock

Rtol ● ● Realnumber(default=1.0E‐5)

Atol ● Realnumber(default=1.0E‐18)

Jacobian ● Numeric(default)

Algebraic

AllCAMxrecognizedkeywordshaveadefaultoptionthatwillbeusedifthekeywordisomitted,

meaningthattheCAMxRTCMCmayberunwithoutspecifyinganykeywordsprovidedthatthat

allotherinputdata(e.g.,rateconstants)areconsistentwiththedefaults.Theallowedkeyword

optionsinTable10‐1arediscussedbelow:

Rate_species_units

Theconcentrationunitsforthermalrateconstantexpressions.

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Rate_time_units

Thetimeunitsforphotolysisandthermalrateconstantexpressions.

Solver

Thenameofthenumericalintegratortobeusedasthechemistrysolver.SLSODEand

DLSODEare,respectively,thesingleanddoubleprecisionversionsoftheLivermore

SolverforOrdinaryDifferentialEquations(Hindmarsh1983).TheRosenbrocksolveris

thedoubleprecisionRODASsolver(HairerandWanner,1991).

Rtol

Therelativeerrortolerance(convergencecriterion)employedforallchemicalspeciesby

thechemistrysolver.

Atol

Theabsoluteerrortolerance(convergencecriterion)employedforallchemicalspecies

bythechemistrysolver.CAMxdoesnotusespecies‐specificAtolvaluesthatmay

appearinthespeciessection,asdiscussedbelow.

Jacobian

ThechemistrysolversemployaJacobianmatrixoffirst‐orderderivativesofeach

chemicalspecieswithrespecttoallspecies.TheJacobianmatrixisconstructed

automaticallybytheRTCMC.ThisoptioncontrolswhethertheJacobianisconstructed

algebraicallyornumerically.Bothoptionsmaybeusedwiththedoubleprecision

solversandnumericmaybemoreefficient.Thealgebraicoptionisstrongly

recommendedforthesingleprecisionSLSODEsolver(becausesingleprecisionmaybe

inadequateforconstructinganumericJacobianbyfinitedifference).

10.2.1.1.1ConcentrationUnits

CAMxdoesnotusetheSpecies_unitsorEmission_unitskeywordsandwillignore

themiftheyarepresent.CAMxwilloutputRTCMCspeciesaverageconcentrationsinppm

units.EmissionsofRTCMCspeciesmustbeprovidedinmoles/hour.

10.2.1.1.2SettingErrorTolerances

AllthreeRTCMCchemistrysolversusetheRtolandAtolparametersspecifiedinthecontrol

sectiontomanageerrorsinpredictedconcentrations.CAMxdoesnotusethespecies‐specific

Atolvaluesthatmayappearinthespeciessectionbecauseitisdifficulttoselectreliable

Atolvaluesforeachspecies.Theerror(err)inthepredictedconcentration(con)forspeciesi

shouldberoughlylessthan:

err(i) = rtol



con(i) + atol

ThecombinedRtolandAtoldetermineaccuracy.SettingAtoltozerowillresultinpure

relativeerrorcontrol.Relativeerrorcontrolhastheadvantageofbeingeasilyunderstood(the

errorsshouldbesmallerthanXpercent)butsuffersthedisadvantageofexcessive

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computationalresourcesthatmaybeexpendedtomanageerrorsinspeciesconcentrations

thatareessentiallyzero.NotethatRTCMCsetsaconcentrationfloorof1.0E‐16ppm.

ThedefaultsettingsforRtolandAtollistedinTable10‐1shouldbegenerallyapplicable

becausetheyareconservativeandeffectivelyresultinpurerelativeerrorcontrol.We

recommendagainstsettingRtolgreaterthan0.001.AppropriatesettingsforAtoldepend

uponthemagnitudeofconcentrationpredictionsandtheneedforaccuratepredictionsinhigh

vs.lowconcentrationareas(e.g.,plumecenterlinevs.outofplume).

DonotrequestinfeasibleaccuracyfromsingleprecisionSLSODEbysettingRtolandAtol

smallerthanabout1.0E‐7.

10.2.1.2TheSpeciesSection

ThespeciessectionoftheIMCfilelistschemicalspeciesandassociateddata.Allchemical

speciesreferredtointheequationsectionmustappearinthespeciessection.Extraspecies

mayappearinthespeciessection,butincludingnumerousextraspeciesmaycausearun‐time

errorbyexceedingthememoryavailableforstoringspeciesinformation(ifthishappens,delete

someoftheunusedspeciesfromthespeciessection).

Thefirstlineisthekeywordidentifyingthespeciessection.Thefollowinginformationmustbe

providedforeachlistedspecies:

Name

Speciesnamesmaybeupto8charactersandmuststartwithaletter.Theyarecase

insensitive.AccuratenamesareimportantbecauseotherCAMxinputdata(e.g.,

emissions,boundaryconditions)willbematchedtoRTRACspeciesbyname.

Type

Therearefourpermissiblespeciestypesidentifiedbyfirstletter:Ambient(A),Fast(F),

Slow(S),andEquilibrium(E).Settingthespeciestypeisdiscussedinmoredetailbelow.

Ambient

TheambientvalueisnotusedbyCAMx,butisusedbySCICHEM.Providearealnumber

(e.g.,0.0).

Atol

SpeciesspecificerrortolerancesarenotusedbyCAMx,butareusedbySCICHEM.

Providearealnumber(e.g.,0.0).

Dep

Thespeciesdepositionvelocityinm/s.Thisdepositionvelocitywillbeusedforallland

surfacetypes,whichisasimplificationcomparedtotheCAMxdrydepositionscheme.

Providearealnumber(e.g.,0.0).

Wet Scav

ThewetscavengingcoefficientisnotusedbyCAMx.ForSCICHEM,thisisawashout

ratio.CAMxdoesnotusethewashoutratiobecausethisapproachisincompatiblewith

theCAMxwetdepositionalgorithms.Providearealnumber(e.g.,0.0).

ThemolecularweightisnotneededbyCAMx.Providearealnumber(e.g.,1.0).

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Spec Map

Thecoremodelspeciesnamefromwhichtouseinternally‐calculateddrydeposition

velocityfortheRTCMCspecies.Thisistriggeredbyanegative“Dep”valueinthesame

record.Providea10‐characterstring.Intheexamplebelow,RTCMCtracerO3Awilluse

depositionvelocitiescalculatedbyCAMxforthecoremodelspeciesO3:

#Name, Type, Ambient, ATol, Dep, Wet Scav, MW, Spec Map

O3A F 1.0 1.000E-08 -3.00E-03 0.0 48.0 O3

10.2.1.2.1ChoosingtheSpeciesType

TheTypeforeachRTCMCspeciesshouldbesetaccordingto:(a)whetherthespecies

concentrationshouldbeobtainedfromthecoremodelormodeledusingtheRTCMC;and(b)

themostaccurateandefficientnumericalmethodforperformingchemistrywithinRTCMC.

Allspeciestobeobtainedfromthecoremodel(e.g.,O3,OH,NO,NO2,H2O,M,O2)mustbeset

totypeAmbient.ThisrulewillbeenforcedbyCAMxand,forexample,thespeciesO3must

besettotypeA,becauseitispartofallthecorechemicalmechanisms.

SpeciesthataresolvedbytheRTCMCmaybetypeF,SorE.Therecommendeddefaulttype

isF(fast)inwhichcasechemistrywillbeperformedusingtheselectedchemistrysolver(e.g.,

DLSODE).Speciesthatundergoslowchemicalchange(lifetimeofhoursorlonger)maybeset

totypeS(slow)withpotentialgaininefficiencybutsomelossinaccuracy.Speciesthat

undergoextremelyrapidchemicalchange(lifetimesmallerthanasecond)maybesettotypeE

(equilibrium)andsolvedusingasteady‐stateapproximationwithsomegaininefficiencybut

somelossinaccuracy.TheRosenbrocksolverdoesnotworkwellwithspeciestypesSorE.

EquilibriumspeciesmaybeusedeffectivelywiththesingleprecisionSLSODEsolvertoavoidthe

needfordoubleprecision.YoushouldusetypesSorEwithcautionandevaluateboth

computationalspeedandconcentrationaccuracybycomparingagainstresultswithusing

typeF.

10.2.1.3TheTableSection

ThetablesectionoftheIMCfileprovidesphotolysisratesforanyphotolyticreactionsinthe

RTCMCmechanism.Itmustcontainatleasttwolines:

#Table

0 zenith1, zenith2, zenith3, …

Thefirstlineisthekeywordidentifyingthetablesection.Thesecondlinemustbeginwith0

(zero)followedbyalistofspace‐delimitedzenithangles(indegrees)startingwithzerodegrees

andascendingtothelargestangle.Ifthelargestzenithanglespecifiedislessthan90degreesa

valueof90degreesisimplicitlyaddedtothelist.Bydefault,upto15zenithanglesareallowed

(thismaybechangedasdescribedunderadjustableparameters,below).Ifthefinalzenith

angleisnot90degrees,nomorethan14anglesshouldbelistedtoallowthe15thangletobe

implicitlysetto90degrees.

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Ifthereactionmechanismhasnophotolyticreactions,includejustthefirsttwolines(keyword

followedbyzenithangles)inthetablesection.Ifthereactionmechanismincludesphotolytic

reactions,listthemonereactionperspace‐delimitedlineafterthezenithangles:

reaction_ID, rate1, rate2, rate3, …

Thereaction_IDmustbetheintegeridentificationnumberofthephotolyticreaction

followedbythephotolysisrateateachzenithangle,fromzerotothelargestangle.Photolysis

reactionsarefirstorderandhaverateunitsofreciprocaltimetobeprovidedinthe

Rate_time_unitsspecifiedinthecontrolsectionoftheIMCfile.Aphotolysisrateofzero

isimplicitlyassumedat90degreesunlessyouspecifyotherwise.

Anegative“reaction_ID”inthetablesectioncausesthephotolysisratetobesettoacore

modelreactionnumber,whichissetinthepositionof“rate1”.Intheexamplebelow,

RTCMCreaction#1isphotolyticandrateswillbesetaccordingtotheCAMxcorephotolysis

reactionnumber9:

#Table

0 0. 10. 20. 30. 40. 50. 60. 70. 78. 86.

-001 9

10.2.1.4TheEquationsSection

TheequationssectionoftheIMCfileliststhechemicalreactionsandrateconstantsforthe

RTCMCreactionmechanismandmustcontainatleasttwolines:

#Equations

reaction_ID [Reactants] > (Stoichiometry) [Products] ; Rate_Constant

Thefirstlineisthekeywordidentifyingtheequationssectionandmustbefollowedbyatleast

onereactionline.Reactionlineslistreactionsandrateconstantsandaredelimitedbywhite

spaceandseparators.Thereaction_IDandtheReactantsmustbeseparatedbywhite

space.TheReactantsandProductsmustbeseparatedbyarightarrowsymbol(theright

arrowmaybeprecededbycharacters,e.g.,=>or−>).TheProductsandthe

Rate_Constantmustbeseparatedbyasemi‐colon.

Thereaction_IDmustbeanintegervaluethatuniquelyidentifieseachreaction.Reactions

identifiersneednotbeinorderorcontinuous.

ThenameofReactantsandProductsmustbeenclosedwithinsquarebrackets,begin

withaletter,andnotexceed8charactersinlength.Allspeciesnamesusedintheequations

sectionmustalsoappearinthespeciessection.Zerotothreereactantsareallowed.Zeroto20

productsareallowed(themaximumisauseradjustableparameter).Reactantandproduct

namesmaybeprecededbyastoichiometriccoefficientenclosedwithinroundbrackets.Ifthe

stoichiometriccoefficientisomitteditisassumedtobeunity.

RateconstantsarespecifiedusingSCICHEMconventionsandmustbeintheunitsspecifiedby

thekeywordsRate_species_unitsandRate_time_unitsinthecontrolsection(the

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defaultsaremoleculescm‐3andseconds,respectively).SCICHEMsupportsnumerousrate

constantexpressiontypesandCAMxshouldinterpretallofthemcorrectly,althoughnotall

havebeenthoroughlytested.Table10‐2definesasub‐setoftheSCICHEMrateconstant

expressiontypesthatarerecommendedforusewithCAMx.Theformatforspecifyingrate

expressionsistheintegerexpressiontypefollowedbyalistofthenumericalvaluesrequiredby

thatexpressiontype.Itisimportantthatrateexpressionsaredefinedinunitsthatare

consistentwiththereactionorder,andTable10‐3defineshowthereactionorderandrate

constantunitdimensionsmaybedetermined.



Table10‐2a.RecommendedSCICHEMrateconstantexpressiontypesforuseinCAMx.

ExpressionTypeDescriptionExpression

0 Photolysis k=0

1 Constant 0





2 General temperature

dependence



TBc eTAk /



3 Troe-type temperature and

pressure dependence

kMk

k

















/][1

][



TAk 

0

TCk 



6.0



F









0/][log1















 kMkG 

8 Equilibrium with a previously

defined reaction (kref)



ref eAkk /



13 Lindemann - Hinshelwood

as used for OH + HNO3

0/}[1

][

kMk

kk 

 



eAk /

0



eCk /

2



eEk /

3

Simple pressure

dependence used for OH +





Pkk 6.01

0





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Table10‐2b.ParametersrequiredbySCICHEMrateconstantexpressiontypes.

Expression

TypeParameters

12 3 4 56

0



1

o

2AB



3AB

D

8

A B 

13AB

D E

7

o



Table10‐3.Determiningthereactionorderandconsequentunitdimensionsforrate

constants.

NumberofReactantsReactionOrder

ConcentrationUnit

DimensionTimeUnitDimension

0ZeroNone Time‐1

1FirstNone Time‐1

2SecondConcentration‐1Time‐1

3ThirdConcentration‐2Time‐1



TheCAMxoutput“diag”filelistsdiagnosticinformationonthemechanismandrateconstant

expressionsreadbyfromtheIMCfile.Youshouldreviewthisdiagnosticoutputtoensurethat

CAMxcorrectlyreadandconfiguredtheRTCMCchemistrymechanism.

10.3ReactiveTracersInIRONPiG

RTRAC/RTCMCcalculationsforemissionsandchemistryhavebeenintegratedintotheIRONPiG

algorithms.TherearetwowaysinwhichRTRACtracersmayenteraPiGplume:asprimary

emissionsfromspecificallyflaggedsourceswithintheRTRACpointsourcefile,orbyformation

ofsecondaryspeciesfromdecayofprimaryplumeemissions.Thereisnoentrainmentof

tracersfromthegridtotheplumeasthisislikelytoresultinnegativetracerconcentrations,

especiallyiftheentrainedtracerisasecondaryproductofahostmodelspecies(e.g.,secondary

formaldehyde).TracersareassumedtohavenegligibleimpactonPiGpuffchemistryoroxidant

levels.Ifthetracerconcentrationintheplumeishighenoughtoenhanceorsuppressthe

plumeoxidantlevels,thenthephotochemicalimpactsofthetracercanbeaccountedforby

separatelyaddingthetraceremissionsintothehostmodellumpedemissions;e.g.,fortracing

highconcentrationsofpropeneandbuteneinaplume,onewouldtrackthepropene/butene

concentrationsusingRTRACtracersbutalsoaddCB‐OLEorSAPRC‐OLE1emissionstotheplume

toaccountfortheoxidantimpacts.RTRACcheckstoensurethatitisreadingitsowninput

pointsourcefile.RTRACandhostmodelpointsourcefilesmusthavethesamenumberof

sourcesinthesameorder;however,thelistofspeciesoneachfilemaybedifferent,andthe

sourcesflaggedtoreceivethePiGtreatmentmayvary.Apre‐processorprogramwascodedto

helpprepareconsistentRTRACandhostmodelpointsourcefiles.

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TracersreleasedfromPiGsourcesdecayaccordingtotheoxidantandphotolyticenvironment

oftheplumeusinguser‐suppliedchemicalrateparameters(asdescribedearlier).Oxidant

concentrationsforthedecaycalculationareobtainedfromtheCAMxPiGincremental

photochemicalsimulationforeachpuffateachtimestep.RTRACtracersineachpuffreactor

areupdatedbasedonthetotaloxidantconcentrationsforthereactor,i.e.,puffincrementplus

puffambient/background.RTRACenforcesarulethatnosecondarytracerformationfromthe

decayofhostmodelspeciesareallowedifIRONPiGisactive(e.g.,nosecondaryformaldehyde

tracerformationisallowedwithIRONPiG).Secondarytracerproductionfromprimarytracer

decayisallowed.

TracersaretransferredfromthePiGtothegridusingthesameapproachasforanyotherhost

modelspecies(seeSection6).Tracerconcentrationsatanypointarethesuperpositionofthe

gridconcentrationplusanycollocatedPiGpuffs.

RTRACoptionallyemployssurface‐layerIRONpuffsamplingoftracersonauser‐defined

samplinggrid(seeSection6).Samplinggridsareentirelypassive,andintendedtoprovidea

displayofthereactivetracerplumeconcentrationsatscalesmuchsmallerthantypicallyused

forthefinestcomputationalgrids(i.e.,<1km).

10.4RunningCAMxWithReactiveTracers

10.4.1CAMxControlFile

RTRACisinvokedsimilarlytotheotherProbingToolswithintheCAMxcontrolfile.Inthe

&CAMx_Controlnamelistmodule,thevariableProbing_Toolmustbesetto“RTRAC”or

“RTCMC”.Anadditionalnamelistmodulecalled&RT_Controlmustthenbeprovidedinthe

controlfiletoconfiguretheRTRACportionofthemodel.Theadditionalnamelistmoduleis

describedbelow.Theorderofthevariablesfollowsthetemplateavailablewiththesource

code.Figure10‐5providesanexampleoftheRTRACcontrolmodule.



DescriptionofRTRACControlintheCAMxRunControlFile



&RT_Control LabelfortheProbingToolnamelistmodulethatconfiguresthe

RTRACoption;itmustbeginincolumn2



& Flagendinganamelist;itmustbeincolumn2



RT_File_Root Characterrootoutputpath/filename



RT_Initial_Conditions CharacterinputmastergridRTRACinitialconditions

path/filename(optional,ignoredif Restart=TRUE)



RT_Boundary_Conditions CharacterinputmastergridRTRACboundaryconditions

path/filename(optional)

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RT_Master_Restart CharacterinputmastergridRTRACrestartpath/filename

(ignoredif Restart=FALSE)



RT_Nested_Restart CharacterinputnestedgridRTRACrestartpath/filename

(ignoredif Restart=FALSE or Number_of_Grids=1)



RT_Chemistry_Parameters CharacterinputRTRACchemistryparameterspath/filename,or

RTCMCIMCchemistrydefinitionpath/filename



RT_Receptor_Definitions CharacterinputRTRACreceptordefinitionpath/filename

(optional)



RT_Point_Sources CharacterinputRTRACelevatedpointsourceemissions

path/filename(optional,ignoredif

Point_Emissions=FALSE)



RT_Emiss_Grid Characterarray(byCAMxgrid)inputRTRACgriddedemissions

path/filename(optional,ignoredif

Gridded_Emissions=FALSE)



RT_PiG_Sample LogicalsamplinggridflagforRTRACIRONPiGoutput;sampling

gridsaredefinedinthemain &CAMx_Controlnamelist

(TRUE=samplinggridoutputwillbegenerated,FALSE=sampling

gridoutputwillnotbegenerated)



Figure10‐4.ExampleinputofRTRACoptionsandfilenameswithintheCAMxcontrolfile.

&RT_Control

RT_File_Root = 'CAMx6.test.020614',

RT_Initial_Conditions = ' ',

RT_Boundary_Conditions = ' ',

RT_Master_Restart = 'CAMx6.test.020613.rt.inst',

RT_Nested_Restart = 'CAMx6.test.020613.rt.finst',

RT_Chemistry_Parameters = 'CAMx6.chemparam.rtrac_test',

RT_Receptor_Definitions = 'receptor.rtrac.test',

RT_Point_Sources = 'pt.rtrac.test',

RT_Emiss_Grid(1) = 'emiss.rtrac.36km',

RT_Emiss_Grid(2) = 'emiss.rtrac.12km',

RT_Emiss_Grid(3) = 'emiss.rtrac.04km',

RT_PiG_Sample = .true.,

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AswiththeoutputforthehostmodelandotherProbingTools,a“root”filenameisspecified

andsuffixesareaddeddependinguponthetypeofoutputproduced.Aseparaterootnamefor

RTRAC(andotherProbingTools)allowstheusertodirecttheoutputtoacompletelydifferent

path.RTRACwritesseveraloutputfilesthatareinFortranbinaryformat,asdescribedin

Section3.Theseincludethemasterandnestedgridtracerinstantaneousconcentrationfiles

(.rt.instand.rt.finst),thegrid‐specificsurfacetraceraverageconcentrationfile

(.rt.grdnn).Thesefilesarewritteninthesameformatasfortheregularmodelspecies

describedinSection3.

The“RT_Chemistry_Parameter”namelistvariablespecifiesthepath/filenameofeither

theRTRACchemistryparametersfileortheRTCMCIMCchemistrydefinitionfile.Thechoiceof

whichtypeoffileformatisreadissetaccordingthemain“Probing_Tool”variable(i.e.,

RTRACorRTCMC).

RTRAC/IRONPiGsamplinggridsareinvokedintheRTRACnamelistbysettingalogicalflag.If

settoTRUE,theusermustprovidethenumberofsamplinggridsandthegridparametersof

eachinthemain&CAMx_Controlnamelist.Samplinggridsaresetidenticallytotheway

nestedgridsarespecifiedforthehostmodel,withoneexception:therearenoverticallevelsto

define(samplinggridsarecurrentlyonly2‐Dsurfacefields).Thesamerulesthatapplyforthe

specificationofnestedgridsholdsforthespecificationofallsamplinggrids(seeSections2,4,

and6).The“meshfactor”setstheresolutionorcellsizeofthesamplinggridrelativetothe

mastergrid.TheCAMxdiagnosticoutputfileprovidesinformationonthelocationandsizeof

eachsamplinggridtohelpensurepropersetup.

10.4.2UserAdjustableParameters

OncetheRTRAC/RTCMCchemistryparameters/definitionfileisestablished,theusershouldbe

surethatasufficientallocationofmemoryisprovidedforthisProbingTool.Thisisdoneby

examiningthemainProbingToolparameterandcommonblockfilein

Includes/camx.prm.TheparameterMXTRSPshouldbesettothetotalnumberofspecies

definedinthechemistryparametersfile.Ifsamplinggridsaretobeused,theusershould

ensurethatsufficientmemoryisavailabletodefinethesizeofsamplinggridarrays.Thisisalso

setinIncludes/camx.prm.

UseradjustableparametersforRTCMCaresetintheCAMxincludefile

Includes/rtcmcchm.inc.Ifanerrorisencounteredatmodelstartupbecauseoneof

theseRTCMCparameterhasbeenexceeded,consultthelistofparametersinTable10‐4and

thenchangetheparameterappropriatelyinthertcmcchm.incincludefile.Rebuildthe

CAMxexecutable(werecommendperforminga“make clean”beforemakinganewCAMx

executable)afterchanginganyRTCMCparameter.



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Table10‐4.RTCMCparametersdefaultsettingsintheIncludes/rtcmcchm.incinclude

file.

NameDescriptionDefault

MXRX maximumnumberofRTCMCreactions 20

MXPHOT maximumnumberofphotolysisreactions 10

MXZEN maximumnumberofphotolysisreactionzenithangles 15

MXRCTMaximumnumberofreactantsineachreaction 3

MXPRD maximumnumberofproductsineachreaction 20

MXEQM maximumnumberofequilibriumspecies 5

MXSLOmaximumnumberofslowspecies 25

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11.REFERENCES

Anthes,R.A.andT.T.Warner.1978.DevelopmentofHydrodynamicModelsSuitableforAir

PollutionandOtherMesometeorologicalStudies.Mon.Wea.Rev.,106,1045‐1078.

Arey,J.,S.M.Aschmann,E.S.C.Kwok,R.Atkinson.2001.Alkylnitrate,hydroxyalkylnitrate,and

hydroxycarbonylformationfromtheNOx‐airphotooxidationsofC5‐C8n‐alkanes.J.

Phys.Chem.,A105,1020‐1027.

Ariya,P.A.,A.KhalizovandA.Gidas.2002.Reactionsofgaseousmercurywithatomicand

molecularhalogens:kinetics,productstudies,andatmosphericimplications.J.Phys.

Chem.,106,7310‐7320.

AstithaM.,C.Spyrou,G.Kallos,H.DenierVanderGon,A.VisschedijkandJ.Lelieveld.2009.

Chemicalcompositionchangeofaerosolsalonglong‐rangetransportpaths.30th

NATO/SPSITMonAirPollutionModellinganditsApplications,May2009,SanFrancisco,

CA.

Atkinson,R.,W.P.Carter,A.M.Winer.1983.Effectsoftemperatureandpressureonalkyl

nitrateyieldsinthenitrogenoxide(NOx)photooxidationsofn‐pentaneandn‐heptane.

J.Phys.Chem.,87(11),2012‐2018.

Atkinson,R.A.,D.L.Baulch,R.A.Cox,J.N.Crowley,R.F.Hampson,R.G.Hynes,M.E.Jenkin,J.A.

Kerr,M.J.Rossi,J.Troe.2010.“Evaluatedkineticandphotochemicaldatafor

atmosphericchemistry‐IUPACsubcommitteeongaskineticdataevaluationfor

atmosphericchemistry.”January3,2010webversionavailableathttp://www.iupac‐

kinetic.ch.cam.ac.uk/index.html.

Barlage,M.,F.Chen,M.Tewari,K.Ikeda,D.Gochis,J.Dudhia,R.Rasmussen,B.Livneh,M.Ek,

K.Mitchell.2010.Noahlandsurfacemodelmodificationstoimprovesnowpack

predictionintheColoradoRockyMountains.J.Geophys.Res.,115,D22101,

doi:10.1029/2009JD013470.

Bertram,T.H.,Thornton,J.A.2009.TowardageneralparameterizationofN2O5reactivityon

aqueousparticles:thecompetingeffectsofparticleliquidwater,nitrateandchloride.

Atmos.Chem.Phys.,9,8351‐8363.

Bott,A.1989.APositiveDefiniteAdvectionSchemeObtainedbyNonlinearRenormalizationof

theAdvectiveFluxes.Mon.Wea.Rev.,117,1006‐1015.

Brown,S.S.,Ryerson,T.B.,Wollny,A.G.,Brock,C.A.,Peltier,R.,Sullivan,A.P.,Weber,R.J.,Dube,

W.P.,Trainer,M.,Meagher,J.F.,Fehsenfeld,F.C.,Ravishankara,A.R.2006.Variabilityin

nocturnalnitrogenoxideprocessinganditsroleinregionalairquality.Science,311,67‐

70.

Carlton,A.G.,B.J.Turpin,K.E.Altieri,S.Seitzinger,A.Reff,H.‐J.Lim,B.Ervens.2007.

AtmosphericoxalicacidandSOAproductionfromglyoxal:Resultsofaqueous

photooxidationexperiments.Atmos.Environ.,41,7588‐7602.

Carpenter,L.J.2003.Iodineinthemarineboundarylayer.ChemicalReviews,103,4953‐4962.

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 220www.camx.com



Carter,W.P.L.1996.CondensedAtmosphericPhotooxidationMechanismsforIsoprene.

Atmos.Environ.,30,4275‐4290.

Carter,W.P.L.2010.DevelopmentoftheSAPRC‐07chemicalmechanism.Atmos.Environ.,44,

5324‐5335.

Carter,W.P.andG.Heo.2013.DevelopmentofrevisedSAPRCaromaticsmechanisms.Atmos.

Environ.,77,404‐414.

Chang,J.S.,R.A.Brost,I.S.A.Isaksen,S.Madronich,P.Middleton,W.R.Stockwell,andC.J,

Walcek.1987.AThree‐dimensionalEulerianAcidDepositionModel:PhysicalConcepts

andFormulation.J.Geophys.Res.,92,14,681‐14,700.

Clever,H.,S.A.JohnsonandE.M.Derrick.1985.Thesolubilityofmercuryandsomesparingly

solublemercurysaltsinwaterandaqueoussolutions.J.Phys.Chem.Ref.Data,14,631‐

680.

Cohan,D.S.,A.Hakami,Y.Hu,andA.G.Russell.2005.NonlinearResponseofOzoneto

Emissions:SourceApportionmentandSensitivityAnalysis.Environ.Sci.Technol.,39,

6739‐6748.

Colella,P.,andP.R.Woodward.1984.ThePiecewiseParabolicMethod(PPM)forGas‐

dynamicalSimulations.J.Comp.Phys.,54,174‐201.

DelGenio,A.D.,M.S.Yao,W.Kovari,K.K.W.Lo.1996.Aprognosticcloudwater

parameterizationforglobalclimatemodels.J.Climate,9,270‐304.

Donahue,N.M.,A.L.Robinson,C.O.Stanier,S.N.Pandis.2006.Coupledpartitioning,dilution,

andchemicalagingofsemivolatileorganics.Environ.Sci.Technol.,40,2635‐2643.

Donahue,N.M.,S.A.Epstein,S.N.Pandis,A.L.Robinson.2011.Atwo‐dimensionalvolatility

basisset:1.organic‐aerosolmixingthermodynamics.Atmos.Chem.Phys.,11,3303‐

3318.

Donahue,N.M.,J.H.Kroll,S.N.Pandis,A.L.Robinson.2012.Atwo‐dimensionalvolatilitybasis

set–Part2:Diagnosticsoforganic‐aerosolevolution.Atmos.Chem.Phys.,12,615‐634.

Dunker,A.M.1980.Theresponseofanatmosphericreaction‐transportmodeltochangesin

inputfunctions.Atmos.Environ.,14,671‐679.

Dunker,A.M.1981.Efficientcalculationsofsensitivitycoefficientsforcomplexatmospheric

models.Atmos.Environ.15,1155‐1161.

DunkerA.M.,G.Yarwood,J.P.Ortmann,G.M.Wilson.2002.Thedecoupleddirectmethodfor

sensitivityanalysisinathree‐dimensionalairqualitymodel–implementation,accuracy

andefficiency.Environ.Sci.Technol.,36,2965‐2976.

Edgerton,E.S.,B.E.HartsellandJ.J.Jansen.2001.Atmosphericmercurymeasurementsata

ruralandurbansitenearAtlanta,GA,USA.6thInternationalConferenceonMercuryasa

GlobalPollutant,15‐19October2001,Minamata,Japan.

Ek,M.B.,K.E.Mitchell,Y.Lin,E.Rogers,P.Grunmann,V.Koren,G.Gayno,J.D.Tarpley.2003.

ImplementationofNoahlandsurfacemodeladvancesintheNationalCentersfor

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 221www.camx.com



EnvironmentalPredictionoperationalmesoscaleEtamodel.J.Geophys.Res.,108(D22),

8851,doi:10.1029/2002JD003296.

Elterman,L.1968.“UV,Visible,andIRAttenuationforAltitudesto50km,1968.”USAirForce

CambridgeResearchLaboratoryReport,AFCRL68‐0153.

Emery,C.,J.Jung,J.Johnson,G.Yarwood,S.Madronich,G.Grell.2010.Improvingthe

CharacterizationofCloudsandtheirImpactonPhotolysisRateswithintheCAMx

PhotochemicalGridModel.PreparedfortheTexasCommissiononEnvironmental

Quality,Austin,TX.PreparedbyENVIRONInternationalCorporation,Novato,CAand

theNationalCenterforAtmosphericResearch,Boulder,CO(August27,2010).

Emery,C.,E.Tai,G.Yarwood,R.Morris.2011.Investigationintoapproachestoreduce

excessiveverticaltransportovercomplexterraininaregionalphotochemicalgrid

model.Atmos.Environ.,45,7341‐7351,doi:10.1016/j.atmosenv.2011.07.052.

Emery,C.,J.Jung,B.Koo,G.Yarwood.2015.ImprovementstoCAMxSnowCoverTreatments

andCarbonBondChemicalMechanismforWinterOzone.PreparedfortheUtah

DepartmentofEnvironmentalQuality,DivisionofAirQuality,SaltLakeCity,UT.

PreparedbyRambollEnviron,Novato,CA(August2015).

ENVIRON.2002.Development,Application,andEvaluationofanAdvancedPhotochemicalAir

ToxicsModelingSystem.PreparedfortheCoordinatingResearchCouncil,Alpharetta,

GA,andtheU.S.DepartmentofEnergy,OfficeofHeavyVehicleTechnologies

(September27,2002).Availablefromwww.crcao.com.

EPA.1990.User’sGuidefortheUrbanAirshedModel‐VolumeI;User’sManualforUAM(CB‐

IV).U.S.EnvironmentalProtectionAgency,ResearchTrianglePark,NC,EPA‐450/4‐90‐

007a.

EPA.1998.User’sGuidefortheAERMODMeteorologicalPreprocessor(RevisedDraft).

PreparedbytheU.S.EnvironmentalProtectionAgency,ResearchTrianglePark,NC

(November,1998).

EPRI.2000.SCICHEMVersion1.2:TechnicalDocumentation.FinalReportpreparedby

ARAP/TitanCorporation,Princeton,NJ,forEPRI,PaloAlto,CA.December2000

(1000713).

Fahey,K.M.andS.N.Pandis.2001.Optimizingmodelperformance:variablesizeresolutionin

cloudchemistrymodeling.Atmos.Environ.35,4471‐4478.

FLAG.2000.“FederalLandManagers’AirQualityRelatedValuesWorkgroup(FLAG),PhaseI

Report.”PreparedbytheUSForestService,AirQualityProgram;NationalParkService,

AirResourcesDivision;andUSFishandWildlifeService,AirQualityBranch(December

2000).

Gallagher,W.M.,K.M.Beswick,J.Duyzer,H.Westrate,T.W.Choularton,J.P.Hummelsho.1997.

MeasurementsofaerosolfluxestoSpeulderforestusingamicrometeorological

technique.Atmos.Environ.,31,359–373.

Ganzeveld,L.,D.Helmig,C.W.Fairall,J.Hare,andA.Pozzer.2009.Atmosphere‐oceanozone

exchange:Aglobalmodelingstudyofbiogeochemical,atmospheric,andwaterside

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 222www.camx.com



turbulencedependencies.GlobalBiogeochem.Cycles,23,GB4021,

doi:10.1029/2008GB003301.

Gardfeldt,K.andM.Johnson.2003.IsbimolecularreductionofHg(II)complexespossiblein

aqueoussystemsofenvironmentalimportance?J.Phys.Chem.,107,4478‐4482.

Gear,C.W.1971.NumericalInitialValueProblemsinOrdinaryDifferentialEquations.Prentice‐

Hall,EnglewoodCliffs,NJ.

Gery,M.W.,G.Z.Whitten,J.P.Killus,andM.C.Dodge.1989.APhotochemicalKinetics

MechanismforUrbanandRegionalScaleComputerModeling.J.Geophys.Res.,94,

925‐956.

Goliff,W.S.,W.R.Stockwell,C.V.Lawson.2013.Theregionalatmosphericchemistry

mechanism,version2.Atmos.Environ.,68,174‐185.

Hairer,E.,andG.Wanner.1991.SolvingordinarydifferentialequationsIIStiffanddifferential‐

algebraicproblems.Springer‐Verlag,Berlin.

Hakami,A.,M.T.Odman,andA.G.Russell.2003.High‐order,directsensitivityanalysisof

multidimensionalairqualitymodels.Environ.Sci.Technol.,37,2442‐2452.

Hall,B.1995.Thegas‐phaseoxidationofelementalmercurybyozone.WaterAirSoilPollut.,

80,301‐315.

Helmig,D.,E.K.Lang,L.Bariteau,P.Boylan,C.W.Fairall,L.Ganzeveld,J.E.Hare,J.Hueber,M.

Pallandt.2012.Atmospherie‐oceanozonefluxesduringtheTexAQS2006,STRATUS

2006,GOMECC2007,GasEx2008andAMMA2008Cruises.J.Geophys.Res.,117,

D04305,doi:10.1029/2011JD015955.

Herman,J.R.andE.A.Celarier.1997.Earthsurfacereflectivityclimatologyat340‐380nmfrom

TOMSdata.J.Geophys.Res.,102,No.23.

HertelO.,R.Berkowics,J.ChristensenandO.Hov.1993.Testoftwonumericalschemesfor

useinatmospherictransport‐chemistrymodels.Atmos.Env.,27,2591‐2611.

HildebrandtRuiz,L.H,andG.Yarwood.2013.InteractionsbetweenorganicaerosolandNOy:

Influenceonoxidantproduction.PreparedfortheTexasAQRP(Project12‐012),bythe

UniversityofTexasatAustin,andENVIRONInternationalCorporation,Novato,CA

(http://aqrp.ceer.utexas.edu/projectinfoFY12_13/12‐012/12‐

012%20Final%20Report.pdf).

HildebrandtRuiz,L.,Koo,B.,Yarwood,G.2015.SourcesofOrganicParticulateMatterin

Houston:EvidencefromDISCOVER‐AQdata‐ModelingandExperiments.FinalReport

preparedfortheTexasAQRP(Project14‐024),bytheUniversityofTexasatAustin,and

RambollEnviron,Novato,CA(http://aqrp.ceer.utexas.edu/projectinfoFY14_15/14‐

024/14‐024%20Final%20Report.pdf).

Hindmarsh,A.C.1983.ODEPACK,aSystematizedCollectionofODESolvers.InNumerical

MethodsforScientificComputation,55,R.S.Stepleman,Ed.,North‐Holland,NewYork.

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 223www.camx.com



Holmes,C.D.,D.J.Jacob,andX.Yang.2006.Globallifetimeofelementalmercuryagainst

oxidationbyatomicbromineinthefreetroposphere.Geophys.Res.Lett.,33,L20808,

doi:10.1029/2006GL027176.

Holtslag,A.A.M.andB.A.Boville.1993.Localversusnonlocalboundary‐layerdiffusionina

globalclimatemodel.J.Climate,6,1825–1842.

Huebert,B.J.,andC.H.Robert.1985.TheDryDepositionofNitricAcidtoGrass.J.Geophys.

Res.,90(D1),2085‐2090(doi:10.1029/JD090iD01p02085).

Hutzell,W.T.,Luecken,D.J.,Appel,K.W.,Carter,W.P.L.2012.Interpretingpredictionsfromthe

SAPRC07mechanismbasedonregionalandcontinentalsimulations.Atmos.Environ.,

46,417‐429.

IUPAC.1992.EvaluatedKineticandPhotochemicalDataforAtmosphericChemistry.

SupplementIV.IUPACSubcommitteeonGasKineticDataEvaluationforAtmospheric

Chemistry(R.Atkinson,D.L.Baulch,R.A.Cox,R.F.Hampson,Jr.,J.A.Kerr,andJ.Troe).

JournalofPhysicalandChemicalReferenceData,21,No.6,1125‐1568.

IUPAC.2014a.“SummaryofReactionsandPreferredRateData,Volume3‐InorganicHalogen

Species.”Availableathttp://iupac.pole‐

ether.fr/datasheets/summary/vol3_summary.xml.

IUPAC.2014b.“SummaryofReactionsandPreferredRateData,Volume‐OrganicHalogen

Species.”Availableathttp://iupac.pole‐

ether.fr/datasheets/summary/vol4_summary.xml.

IUPAC.2015.“TaskGrouponAtmosphericChemicalKineticDataEvaluation–DataSheet

NOx33.”Availableathttp://iupac.pole‐

ether.fr/htdocs/datasheets/pdf/NOx33_N2O5_H2O.pdf.

Jacob,D.J.2000.Heterogeneouschemistryandtroposphericozone.Atmos.Environ.,34,

2131‐2159.

Jaegle,L.,D.J.Jacob,W.H.BruneandP.O.Wennberg.2001.ChemistryofHOxradicalsinthe

uppertroposphere.Atmos.Environ.,35,469‐489.

Jathar,S.H.,Gordon,T.D.,Hennigan,C.J.,Pye,H.O.T.,Pouliot,G.,Adams,P.J.,Donahue,N.M.,

Robinson,A.L.2014.Unspeciatedorganicemissionsfromcombustionsourcesandtheir

influenceonthesecondaryorganicaerosolbudgetintheUnitedStates.Proc.Natl.

Acad.Sci.,111,10473‐10478.

Jeffries,H.E.,andG.S.Tonnesen.1994.Comparisonoftwophotochemicalreaction

mechanismsusingamassbalanceandprocessanalysis.Atmos.Environ.,28,2991‐3003.

Kalberer,M.,D.Paulson,M.Sax,M.Steinbacher,J.Dommen,A.S.H.Prevot,R.Fisseha,E.

Weingartner,V.Franhevich,R.Zenob,andU.Balternsperger.2004.Identificationof

polymersasmajorcomponentsofatmosphericorganicaerosols.Science,303,1659‐

1662.

Karamchandani,P.,A.Koo,C.Seigneur.1998.Reducedgas‐phasekineticmechanismfor

atmosphericplumechemistry.Environ.Sci.Technol.,32,1709‐1720.

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 224www.camx.com



Koo,B.,A.S.Ansari,andS.N.Pandis.2003.IntegratedApproachestoModelingtheOrganic

andInorganicAtmosphericAerosolComponents.Atmos.Environ.,37,4757‐4768.

Koo,B.,G.Yarwood,D.S.Cohan.2007a.IncorporationofHigh‐orderDecoupledDirectMethod

(HDDM)SensitivityAnalysisCapabilityintoCAMx.PreparedfortheTexasCommission

onEnvironmentalQuality,Austin,TX.PreparedbyENVIRONInternationalCorporation,

Novato,CAandRiceUniversity,Houston,TX.

Koo,B.,A.M.Dunker,G.Yarwood.2007b.ImplementingtheDecoupledDirectMethodfor

SensitivityAnalysisinaParticulateMatterAirQualityModel.Environ.Sci.Technol.,41,

2847‐2854.

Koo,B.,G.Yarwood,D.S.Cohan.2008.Higher‐orderDecoupledDirectMethod(HDDM)for

OzoneModelingSensitivityAnalysesandCodeRefinements.PreparedfortheTexas

CommissiononEnvironmentalQuality,Austin,TX.PreparedbyENVIRONInternational

Corporation,Novato,CAandRiceUniversity,Houston,TX.

Koo,B.,G.M.Wilson,R.E.Morris,A.M.Dunker,G.Yarwood.2009.ComparisonofSource

ApportionmentandSensitivityAnalysisinaParticulateMatterAirQualityModel.

Environ.Sci.Technol.,43,6669‐6675.

Koo,B.,G.YarwoodandJ.Roberts.2012.AnAssessmentofNitrylChlorideFormation

ChemistryanditsImportanceinOzoneNon‐AttainmentAreasinTexas.Finalreportfor

TexasAirQualityResearchProgramproject10‐015.PreparedbyENVIRONInternational

Corporation,Novato,CAandNOAA/ESRL,Boulder,CO.Availableat

http://aqrp.ceer.utexas.edu/projectinfo%5C10‐015%5C10‐015%20Final%20Report.pdf.

Koo,B.,E.Knipping,G.Yarwood.2014.1.5‐Dimensionalvolatilitybasissetapproachfor

modelingorganicaerosolinCAMxandCMAQ.Atmos.Environ.,95,158‐164.

Kumar,N.,F.W.Lurmann,A.S.Wexler,S.Pandis,andJ.H.Seinfeld.1996.Developmentand

ApplicationofaThreeDimensionalAerosolModel.PresentedattheA&WMASpecialty

ConferenceonComputinginEnvironmentalResourceManagement,ResearchTriangle

Park,NC,December2‐4,1996.

Kumar,N.andA.G.Russell.1996.DevelopmentofaComputationallyefficient,ReactiveSub‐

Grid‐ScalePlumeModelandtheImpactintheNortheasternUnitedStatesUsing

IncreasingLevelsofChemicalDetail.J.Geophys.Res.,101,16,737‐16,744.

Landis,M.S.andG.Keeler.2002.AtmosphericmercurydepositiontoLakeMichiganduringthe

LakeMichiganMassBalanceStudy.Environ.Sci.Technol.,36,4518‐4524.

Lane,T.E.,N.M.Donahue,S.N.Pandis.2008.Simulatingsecondaryorganicaerosolformation

usingthevolatilitybasis‐setapproachinachemicaltransportmodel.Atmos.Environ.,

42,7439‐7451.

Lee,L.,P.J.Wooldridge,J.B.Gilman,C.Warneke,J.deGouw,R.C.Cohen.2014.Low

temperaturesenhanceorganicnitrateformation:evidencefromobservationsinthe

2012UintahBasinWinterOzoneStudy.Atmos.Chem.Phys.Disc.,14(11),17401‐17438.

Lin,C.J.andS.O.Pehkonen.1997.Aqueous‐freeradicalchemistryofmercuryinthepresence

ofironoxidesandambientaerosol.Atmos.Environ.,31,4125‐4137.

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 225www.camx.com



Lin,C.J.andS.O.Pehkonen.1998.Oxidationofelementalmercurybyaqueouschlorine

(HOCl/OCl‐):Implicationsfortroposphericmercurychemistry.J.Geophys.Res.,103,

28093‐28102.

Lindberg,S.,O.R.Bullock,R.Ebinghaus,D.Engstrom,X.Feng,W.Fitzgerald,N.Pirrone,E.

Prestbo,andC.Seigneur.2007.Asynthesisofprogressanduncertaintiesinattributing

thesourcesofmercuryindeposition.Ambio,36,19‐33.

Lindqvist,O.andH.Rodhe.1985.Atmosphericmercury‐areview.Tellus,37B,136‐159.

Liu,M.andJ.Carroll.1996.Ahighresolutionairpollutionmodelsuitablefordispersionstudies

incomplexterrain.Mon.Wea.Rev.,124,10,2396‐2409.

Livneh,B.,Y.Xia,K.E.Mitchell,M.B.Ek.2010.NoahLSMsnowmodeldiagnosticsand

enhancements.J.Hydromet.,11,doi:10.1175/2009JHM1174.1.

Locatelli,J.D.andP.V.Hobbs.1974.Fallspeedsandmassesofsolidprecipitationparticles.J.

Geophys.Res.,79(15),2185‐2197.

Louis,J.F.1979.AParametricModelofVerticalEddyFluxesintheAtmosphere.Bound.Lay.

Meteor.17,187‐202.

May,A.A.,A.A.Presto,C.J.Hennigan,N.T.Nguyen,T.D.Gordon,A.L.Robinson.2013a.Gas‐

particlepartitioningofprimaryorganicaerosolemissions:(1)Gasolinevehicleexhaust.

Atmos.Environ.,77,128‐139.

May,A.A.,A.A.Presto,C.J.Hennigan,N.T.Nguyen,T.D.Gordon,A.L.Robinson.2013b.Gas‐

ParticlePartitioningofPrimaryOrganicAerosolEmissions:(2)DieselVehicles.Environ.

Sci.Technol.,47,8288‐8296.

May,A.A.,E.J.T.Levin,C.J.Hennigan,I.Riipinen,T.Lee,J.L.CollettJr.,J.L.Jimenez,S.M.

Kreidenweis,A.L.Robinson.2013c.Gas‐particlepartitioningofprimaryorganicaerosol

emissions:3.Biomassburning.J.Geophys.Res.,118,11327‐11338.

Moore,R.andTokarczyk,R.1993.VolatileBiogenicHalocarbonsintheNorthwestAtlantic.

GlobalBiogeochem.Cy.,7,195–210,

Moore,R.andZafiriou,O.1994.Photochemicalproductionofmethyliodideinseawater.J.

Geophys.Res.,99,16415–16420,doi:10.1029/94JD00786.

Morris,R.E.,S.Lau,andG.Yarwood.2003.DevelopmentandApplicationofanAdvancedAir

ToxicsHybridPhotochemicalGridModelingSystem.Presentedat96thAnnual

ConferenceandExhibitionoftheA&WMA,SanDiego,California(June2003).

Munthe,J.1992.Theaqueousoxidationofelementalmercurybyozone.Atmos.Environ.,Part

A,26,1461‐1468.

Murphy,B.N.,S.N.Pandis.2009.SimulatingtheFormationofSemivolatilePrimaryand

SecondaryOrganicAerosolinaRegionalChemicalTransportModel.Environ.Sci.

Technol.,43,4722‐4728.

NASA.1997.ChemicalKineticsandPhotochemicalDataforUseinStratosphericModeling,JPL

Publication97‐4.JetPropulsionLaboratory,CaliforniaInstituteofTechnology,

Pasadena,California.January15.

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 226www.camx.com



NCAR.2011.TheTroposphericVisibleandUltraviolet(TUV)RadiationModelwebpage.

NationalCenterforAtmosphericResearch,AtmosphericChemistryDivision,Boulder,

Colorado,http://cprm.acd.ucar.edu/Models/TUV/index.shtml.

Nenes,A,C.Pilinis,andS.N.Pandis.1998.ISORROPIA:ANewThermodynamicModelfor

MultiphaseMulticomponentInorganicAerosols.AquaticGeochemistry,4,123‐152.

Nenes,A.,C.Pilinis,andS.N.Pandis.1999.ContinuedDevelopmentandTestingofaNew

ThermodynamicAerosolModuleforUrbanandRegionalAirQualityModels.Atmos.

Environ.33,1553‐1560.

Odman,M.T.andIngram,C.L.1993.MultiscaleAirQualitySimulationPlatform(MAQSIP):

SourceCodeDocumentationandValidation.Technicalreport,83pp.,ENV‐96TR002,

MCNC–NorthCarolinaSupercomputingCenter,ResearchTrianglePark,NorthCarolina,

1996.

Ordóñez,C.,J.‐F.Lamarque,S.Tilmes,D.E.Kinnison,E.L.Atlas,D.R.Blake,G.SousaSantos,G.

Brasseur,andA.Saiz‐Lopez.2012.Bromineandiodinechemistryinaglobalchemistry‐

climatemodel:descriptionandevaluationofveryshort‐livedoceanicsources.Atmos.

Chem.Phys.,12,1423‐1447,doi:10.5194/acp‐12‐1423‐2012.

Pal,B.,andP.A.Ariya.2003.Atmosphericreactionsofgaseousmercurywithozoneand

hydroxylradical:kineticsandproductstudies.J.Phys.,107,189–192.

Pal,B.andP.A.Ariya.2004.Gas‐phaseHO‐initiatedreactionsofelementalmercury:Kinetics,

productstudiesandatmosphericimplications.Environ.Sci.Technol.,38,5555‐5566.

Pandis,S.N.,A.S.Wexler,andJ.H.Seinfeld.1993.Secondaryorganicaerosolformationand

transport,II,Predictingtheambientsecondaryorganicaerosolsizedistribution.Atmos.

Environ.,27A,2403‐2416.

Parrella,J.P.,D.J.Jacob,Q.Liang,Y.Zhang,L.J.Mickley,B.Miller,M.J.Evansetal.2012.

Troposphericbrominechemistry:implicationsforpresentandpre‐industrialozoneand

mercury.Atmos.Chem.Phys.,12,no.15:6723‐6740.

Paulot,F.,J.D.Crounse,H.G.Kjaergaard,J.H.Kroll,J.H.Seinfeld,P.O.Wennberg.2009a.

Isoprenephotooxidation:newinsightsintotheproductionofacidsandorganicnitrates.

Atmos.Chem.Phys.,9,1479‐1501.

Paulot,F,J.D.Crounse,H.G.Kjaergaard,A.Kurten,J.M.St.Clair,J.H.Seinfeld,P.O.Wennberg.

2009b.UnexpectedEpoxideFormationintheGas‐PhasePhotooxidationofIsoprene.

Science,325,730‐733.

Peeters,J.,Nguyen,T.L.,Vereecken,L.2009.HOxradicalregenerationintheoxidationof

isoprene.Phys.Chem.andChem.Phys.,11,5935‐5939

Pehkonen,S.O.andC.J.Lin.1998.Aqueousphotochemistryofdivalentmercurywithorganic

acids.J.AirWasteManage.Assoc.,48,144‐150.

Perring,A.E.,S.E.Pusede,R.C.Cohen.2013.Anobservationalperspectiveontheatmospheric

impactsofalkylandmultifunctionalnitratesonozoneandsecondaryorganicaerosol.

ChemicalReviews,113(8),5848‐5870.

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 227www.camx.com



Pleim,J.2007.Acombinedlocalandnonlocalclosuremodelfortheatmosphericboundary

layer.PartI:Modeldescriptionandtesting.J.Appl.Met.andClim.,46,1383‐1395.

Radhakrishnan,K.andA.C.Hindmarsh.1993.DescriptionandUseofLSODE,theLivermore

SolverforOrdinaryDifferentialEquations.NASAreferencePublication1327.Lawrence

LivermoreNationalLaboratory,Livermore,CA.

Ranjan,M.,A.A.Presto,A.A.May,A.L.Robinson.2012.TemperatureDependenceofGas–

ParticlePartitioningofPrimaryOrganicAerosolEmissionsfromaSmallDieselEngine.

AerosolSci.Technol.,46,13‐21.

Raofie,F.andP.A.Ariya.2003.ReactionsofBrOwithmercury:kineticstudies.J.Phys.IV,107,

1119–1121.

Robinson,A.L.,N.M.Donahue,M.K.Shrivastava,E.A.Weitkamp,A.M.Sage,A.P.Grieshop,T.E.

Lane,J.R.Pierce,S.N.Pandis.2007.Rethinkingorganicaerosols:semivolatileemissions

andphotochemicalaging.Science,315,1259‐1262.

Russell,L.M.,S.N.Pandis,andJ.H.Seinfeld.1994.Aerosolproductionandgrowthinthe

marineboundarylayer.J.Geophys.Res.,99,20989‐21003.

Rutter,A.P.,andJ.J.Schauer.2007a.Theeffectoftemperatureonthegas‐particlepartitioning

ofreactivemercuryinatmosphericaerosols.Atmos.Environ.,41,8647‐8657.

Rutter,A.P.;Schauer,J.J.2007b.Theimpactofaerosolcompositionontheparticletogas

partitioningofreactivemercury.Environ.Sci.Technol.,41,3934‐3939.

Ryaboshapko,A.,R.Bullock,R.Ebinghaus,I.Ilyin,K.Lohman,J.Munthe,G.Petersen,C.

SeigneurandI.Wängberg.2002.Comparisonofmercurychemistrymodels.Atmos.

Environ.,36,3881‐3898.

Sander,S.P.,R.R.Friedl,D.M.Golden,M.J.Kurylo,R.E.Huie,V.L.Orkin,G.K.Moortgat,P.H.

Wine,A.R.Ravishankara,C.E.Kolb,M.J.Molina,B.J.Finlayson‐Pitts.2006.Evaluation

number15:Chemicalkineticsandphotochemicaldataforuseinatmosphericstudies.

NASAPanelforDataEvaluation,JPLPublication06‐2,JetPropulsionLaboratory,

CaliforniaInsituteofTechnology,Pasadena,California.

Sanemasa,I.1975.Thesolubilityofelementalmercuryvaporinwater.Bull.Chem.Soc.Jpn.,

48,1795‐1798.

Sauter,D.P.andP.K.Wang.1989.Anexperimentalstudyofthescavengingofaerosolparticles

bynaturalsnowcrystals.J.Atmos.Sci.,46,1650‐1655.

Schroeder,W.H.andJ.Munthe.1998.Atmosphericmercury–Anoverview.Atmos.Environ.,

32,809‐822.

Scott,B.C.1978.Parameterizationofsulfateremovalbyprecipitation.J.Appl.Meteor.,17,

1375‐1389.

Sehmel,G.A.1980.ParticleandGasDeposition,aReview.Atmos.Environ.,14,983‐1011.

Seigneur,C.,H.Abeck,G.Chia,M.Reinhard,N.S.Bloom,E.PrestboandP.Saxena.1998.

Mercuryadsorptiontoelementalcarbon(soot)particlesandatmosphericparticulate

matter.Atmos.Environ.,32,2649‐2657.

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 228www.camx.com



Seigneur,C.,P.Karamchandani,K.Lohman,K.VijayaraghavanandR.‐L.Shia.2001a.Multiscale

modelingoftheatmosphericfateandtransportofmercury.J.Geophys.Res.,106,

27795‐27809.

Seigneur,C.,P.Karamchandani,K.LohmanandJ.Jansen.2001b.Modelingofmercuryin

powerplantplumes.6thInternationalConferenceonMercuryasaGlobalPollutant,15‐

19October2001,Minamata,Japan.

Seigneur,C.,P.Karamchandani,K.Vijayaraghavan,K.LohmanandG.Yelluru.2003.Scoping

StudyforMercuryDepositionintheUpperMidwest.AERReportCP149‐03‐01a,

preparedfortheMidwestRegionalPlanningOrganization,DesPlaines,IL.

Seigneur,C.,K.Vijayaraghavan,K.LohmanandP.Karamchandani.2004.Modelingthe

atmosphericfateandtransportofmercuryoverNorthAmerica.FuelProcessing

Technol.,85,441‐450.

Seigneur,C.andK.Lohman.2008.Effectofbrominechemistryontheatmosphericmercury

cycle.J.Geophys.Res.,113,D23309,doi:10.1029/2008JD010262.

Seinfeld,J.H.,andS.N.Pandis.1998.AtmosphericChemistryandPhysics,FromAirPollutionto

ClimateChange.JohnWileyandSons,Inc.,NY.

Sillen,G.L.andA.E.Martell,(Eds.).1964.Stabilityconstantsofmetalioncomplexes,Spec.

Publ.Chem.Soc.,17,754.

Sillman,S.1995.TheUseofNOy,H2O2,andHNO3asIndicatorsforOzone‐NOX‐Hydrocarbon

SensitivityinUrbanLocations.J.Geophys.Res.,100,14,175‐14,188.

Slinn,S.A.andW.G.N.Slinn.1980.Predictionsforparticledepositiononnaturalwaters.

Atmos.Environ.,24,1013‐1016.

Slinn,W.G.N.1982.Predictionsforparticledepositiontovegetativesurfaces.Atmos.Environ.,

16,1785‐1794.

Smagorinsky,J.1963.GeneralCirculationExperimentswiththePrimitiveEquations:I.The

BasicExperiment.Mon.Wea.Rev.,91,99‐164.

Smoydzin,L.,andR.vonGlasow.2009.ModellingchemistryovertheDeadSea:bromineand

ozonechemistry.AtmosphericChemistryandPhysics,9(14),5057‐5072.

Sommar,J.,K.Gårdfeldt,D.StrömbergandX.Feng.2001.Akineticstudyofthegas‐phase

reactionbetweenthehydroxylradicalandatomicmercury.Atmos.Environ.,35,3049‐

3054.

Strader,R.,F.Lurmann,andS.N.Pandis.1999.Evaluationofsecondaryorganicaerosol

formationinwinter.Atmos.Environ.,33,4849‐4863.

Takemura,T.,T.Nakajima,O.Dubovik,B.N.Holben,S.Kinne.2002.Single‐scatteringalbedo

andradiativeforcingofvariousaerosolspecieswithaglobalthree‐dimensionalmodel.

J.Climate,15(4),333‐352.

Tanaka,P.L.,D.T.Allen,E.C.McDonald‐Buller,S.Chang,Y.Kimura,C.B.Mullins,G.Yarwood,

andJ.D.Neece.2003.Developmentofachlorinemechanismforuseinthecarbon

bondIVchemistrymodel.J.Geophys.Res.:Atmos.,108(D4),1984–2012.

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 229www.camx.com



Tokos,J.J.S.,B.Hall,J.A.Calhoun,andE.M.Prestbo.1998.Homogeneousgas‐phasereactionof

Hg0withH2O2,O3,CH3I,and(CH3)2S:ImplicationsforatmosphericHgcycling.Atmos.

Environ.,32,823‐827.

Tonnesen,G.S.andR.L.Dennis.2000.Analysisofradicalpropagationefficiencytoassess

ozonesensitivitytohydrocarbonsandNOx.Part1:Localindicatorsofoddoxygen

productionsensitivity.J.Geophys.Res.,105,9213‐9225.

Turner,D.B.,T.Chico,andA.Catalano.1986.TUPOS:AMultipleSourceGaussianDispersion

AlgorithmUsingOn‐SiteTurbulenceData.U.SEnvironmentalProtectionAgency,

ResearchTrianglePark,NorthCarolina(EPA‐600/8‐86/010).

Turner,D.B.andR.H.Schulze.2007.PracticalGuidetoAtmosphericDispersionModeling.Air

andWasteManagementAssociation.

vanLoon,L.,E.Mader,andS.L.Scott.2000.Reductionoftheaqueousmercuricionbysulfite:

UVspectrumofHgSO3anditsintramolecularredoxreactions.J.Phys.Chem.,104,

1621‐1626.

vanLoon,L.L.,E.A.Mader,andS.L.Scott.2001.Sulfitestabilizationandreductionofthe

aqueousmercuricion:kineticdeterminationofsequentialformationconstants.J.Phys.

Chem.,105,3190‐3195.

Vijayaraghavan,K.,P.Karamchandani,C.Seigneur,R.Balmori,andS.‐Y.Chen.2008.Plume‐in‐

gridmodelingofatmosphericmercury.J.Geophys.Res.,113,D24305,

doi:10.1029/2008JD010580.

Vogt,R.,R.Sander,R.vonGlasow,andP.J.Crutzen.1999.Iodinechemistryanditsrolein

halogenactivationandozonelossinthemarineboundarylayer:Amodelstudy.J.

Atmos.Chem.,32(3),375‐395.

Voulgarakis,A.,N.H.Savage,O.Wild,G.D.Carver,K.C.Clemitshaw,J.A.Pyle.2009.Upgrading

photolysisinthep‐TOMCATCTM:modelevaluationandassessmentoftheroleof

clouds.Geo.Mod.Devel.,2,59‐72.

Wang,Z.,J.E.Langstaff,andH.E.Jeffries.1995.TheApplicationoftheIntegratedProcessRate

AnalysisMethodforInvestigationofUrbanAirshedModel(UAM)Sensitivityto

SpeciationinVOCEmissionsData.Air&WasteManagementAssociationannual

meeting,SanAntonio,TX.

Wang,Z.,andX.Zeng.2010.Evaluationofsnowalbedoinlandmodelsforweatherand

climatestudies.J.Appl.MetClim.,49,doi:10.1175/2009JAMC2134.1.

Wesely,M.L.1989.ParameterizationofSurfaceResistancestoGaseousDryDepositionin

Regional‐ScaleNumericalModels.Atmos.Environ.,23,1293‐1304.

Wesely,M.L.,andB.B.Hicks.2000.Areviewofthecurrentstatusofknowledgeondry

deposition.Atmos.Environ.,34,2261.

Whitten,G.,H.P.Deuel,C.S.Burton,andJ.L.Haney.1996.“OverviewoftheImplementationof

anUpdatedIsopreneChemistryMechanisminCB4/UAM‐V.”(RevisedMemorandumto

OTAGParticipants,July22).

March2016CAMxUser’sGuideVersion6.3

11.References



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 230www.camx.com



Whitten,G.Z.,andG.Yarwood.2008.TheOzoneProductivityofn‐PropylBromide:Part2—An

ExceptiontotheMaximumIncrementalReactivityScale.J.AirWasteManag.Assoc.,

58(7),891‐901.

Whitten,G.Z.,G.Heo,Y.Kimura,E.McDonald‐Buller,D.T.Allen,W.P.I.Carter,G.Yarwood.

2010.ANewCondensedTolueneMechanismforCarbonBond:CB05‐TU.Atmos.

Environ.,44(40),doi:10.1016/j.atmosenv.2009.12.029.

Woody,M.C.,Baker,K.R.,Hayes,P.L.,Jimenez,J.L.,Koo,B.,Pye,H.O.T.2016.Understanding

sourcesoforganicaerosolduringCalNex‐2010usingtheCMAQ‐VBS.Atmos.Chem.

Phys.,16,4081‐4100(doi:10.5194/acp‐16‐4081‐2016).

Yamartino,R.2000.RefinementofHorizontalDiffusioninPhotochemicalGridModels.

PresentedattheAmericanMeteorologicalSociety11thJointConferenceonthe

ApplicationsofAirPollutionMeteorologywiththeAirandWasteManagement

Association,LongBeach,CA,January9‐13.

Yang,X.,R.A.Cox,N.J.Warwick,J.A.Pyle,G.D.Carver,F.M.O'Connor,andN.H.Savage.2005.

Troposphericbrominechemistryanditsimpactsonozone:Amodelstudy.J.Geophys.

Res.:Atmos.,110(D23),DOI:10.1029/2005JD006244.

Yarwood,G.,R.E.Morris,M.A.Yocke,H.HogoandT.Chico.1996a.Developmentofa

MethodologyforSourceApportionmentofOzoneConcentrationEstimatesfroma

PhotochemicalGridModel.Presentedatthe89thAWMAAnnualMeeting,Nashville

TN,June23‐28.

Yarwood,G.,T.E.Stoeckenius,G.Wilson,R.E.Morris,andM.A.Yocke.1996b.Developmentof

aMethodologytoAssessGeographicandTemporalOzoneControlStrategiesforthe

SouthCoastAirBasin.PreparedforSouthCoastAirQualityManagementDistrict,

DiamondBar,CA.

Yarwood,G.,R.E.Morris,G.M.Wilson.2004.ParticulateMatterSourceApportionment

Technology(PSAT)intheCAMxPhotochemicalGridModel.Proceedingsofthe27th

NATO/CCMSInternationalTechnicalMeetingonAirPollutionModelingand

Application.SpringerVerlag(Availablefrom

http://camx.com/publ/pdfs/yarwood_itm_paper.pdf).

Yarwood.G.,G.Z.Whitten,andS.Rao.2005a.UpdatestotheCarbonBond4Photochemical

Mechanism.PreparedfortheLakeMichiganAirDirectorsConsortium,DesPlains,

Illinois.

Yarwood.G.,S.Rao,M.Yocke,andG.Z.Whitten.2005b.UpdatestotheCarbonBondchemical

mechanism:CB05.FinalReportpreparedforUSEPA.Availableat

http://www.camx.com/publ/pdfs/CB05_Final_Report_120805.pdf.

Yarwood,G.,J.Jung,G.Z.Whitten,G.Heo,J.MellbergandE.Estes.2010.Updatestothe

CarbonBondMechanismforVersion6(CB6).Presentedatthe9thAnnualCMAS

Conference,ChapelHill,October.

Yarwood,G.,H.Gookyoung,W.P.L.Carter,G.Z.Whitten.2012a.EnvironmentalChamber

ExperimentstoEvaluateNOxSinksandRecyclinginAtmosphericChemicalMechanisms.

March2016CAMxUser’sGuideVersion6.3

11.References

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FinalReportpreparedfortheTexasAirQualityResearchProgram,UniversityofTexas,

Austin,Texas(AQRPProject10‐042,February2012).

Yarwood,G.,J.Jung,U.Nopmongcol,C.Emery.2012b.ImprovingCAMxPerformancein

SimulatingOzoneTransportfromtheGulfofMexico.FinalReportpreparedforthe

TexasCommissiononEnvironmentalQuality,Austin,Texas(September2012).Prepared

byENVIRONInternationalCorporation,Novato,CA.

Yarwood,G.,T.Sakulyanontvittaya,U.Nopmongcol,B.Koo.2014.OzoneDepletionby

BromineandIodineovertheGulfofMexico.FinalReportpreparedfortheTexas

CommisisiononEnvironmentalQuality,Austin,Texas(November2014).Preparedby

ENVIRONInternationalCorporation,Novato,CA.

Yarwood,G.andB.Koo.2015.ImprovedOSAT,APCAandPSATAlgorithmsforCAMx.Final

reportpreparedfortheTexasCommissiononEnvironmentalQuality,Austin,Texas

(August,2015).PreparedbyRambollEnviron,Novato,CA.

Yeh,G.K.andP.J.Ziemann.2014.AlkylNitrateFormationfromtheReactionsofC8–C14n‐

AlkaneswithOHRadicalsinthePresenceofNOx:MeasuredYieldswithEssential

CorrectionsforGas–WallPartitioning.J.Phys.Chem.,118(38),8797‐8806.

Zhang,L.,S.Gong,J.Padro,L.Barrie.2001.Asize‐segregatedparticledrydepositionscheme

foranatmosphericaerosolmodule.Atmos.Environ.,35,549‐560.

Zhang,L.,J.R.Brook,andR.Vet.2003.Arevisedparameterizationforgaseousdrydeposition

inair‐qualitymodels.Atmos.Chem.Phys.,3,2067–2082.

Zhang,X.,S.Kondragunta,C.Schmidt,andF.Kogan.2008.Nearrealtimemonitoringof

biomassburningparticulateemissions(PM2.5)acrosscontiguousUnitedStatesusing

multiplesatelliteinstruments.AtmosphericEnvironment,42,6959‐6972.

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AppendixA

CAMxMechanism2:CB6r2Gas‐PhaseChemistry

TableA‐1.ReactionsandrateconstantexpressionsfortheCB6r2mechanism.k298istherate

constantat298Kand1atmosphereusingunitsinmolecules/cm3and1/s.Forphotolysis

reactionsk298showsthephotolysisrateatasolarzenithangleof60°andheightof600m

MSL/AGL.SeeTable5‐2forspeciesnames.SeeSection3.1ontemperatureandpressure

dependencies.

NumberReactantsandProductsRateConstantExpressionk298

1NO2=NO+OPhotolysis6.30E‐3

2O+O2+M=O3+Mk=5.68E‐34(T/300)^‐2.65.78E‐34

3O3+NO=NO2k=1.40E‐12exp(‐1310/T)1.73E‐14

4O+NO+M=NO2+Mk=1.00E‐31(T/300)^‐1.61.01E‐31

5O+NO2=NOk=5.50E‐12exp(188/T)1.03E‐11

6O+NO2=NO3Falloff:F=0.6;n=1

k(0)=1.30E‐31(T/300)^‐1.5

k(inf)=2.30E‐11(T/300)^0.24

2.11E‐12

7O+O3=k=8.00E‐12exp(‐2060/T)7.96E‐15

8O3=OPhotolysis3.33E‐4

9O3=O1DPhotolysis8.78E‐6

10O1D+M=O+Mk=2.23E‐11exp(115/T)3.28E‐11

11O1D+H2O=2OHk=2.14E‐102.14E‐10

12O3+OH=HO2k=1.70E‐12exp(‐940/T)7.25E‐14

13O3+HO2=OHk=2.03E‐16(T/300)^4.57exp(693/T)2.01E‐15

14OH+O=HO2k=2.40E‐11exp(110/T)3.47E‐11

15HO2+O=OHk=2.70E‐11exp(224/T)5.73E‐11

16OH+OH=Ok=6.20E‐14(T/298)^2.6exp(945/T)1.48E‐12

17OH+OH=H2O2Falloff:F=0.5;n=1.13

k(0)=6.90E‐31(T/300)^‐0.8

k(inf)=2.60E‐11

5.25E‐12

18OH+HO2=k=4.80E‐11exp(250/T)1.11E‐10

19HO2+HO2=H2O2k=k1+k2[M]

k1=2.20E‐13exp(600/T)

k2=1.90E‐33exp(980/T)

2.90E‐12

20HO2+HO2+H2O=H2O2k=k1+k2[M]

k1=3.08E‐34exp(2800/T)

k2=2.66E‐54exp(3180/T)

6.53E‐30

21H2O2=2OHPhotolysis3.78E‐6

22H2O2+OH=HO2k=2.90E‐12exp(‐160/T)1.70E‐12

23H2O2+O=OH+HO2k=1.40E‐12exp(‐2000/T)1.70E‐15

24NO+NO+O2=2NO2k=3.30E‐39exp(530/T)1.95E‐38

25HO2+NO=OH+NO2k=3.45E‐12exp(270/T)8.54E‐12

26NO2+O3=NO3k=1.40E‐13exp(‐2470/T)3.52E‐17

27NO3=NO2+OPhotolysis1.56E‐1

28NO3=NOPhotolysis1.98E‐2

29NO3+NO=2NO2k=1.80E‐11exp(110/T)2.60E‐11

30NO3+NO2=NO+NO2k=4.50E‐14exp(‐1260/T)6.56E‐16

31NO3+O=NO2k=1.70E‐111.70E‐11

32NO3+OH=HO2+NO2k=2.00E‐112.00E‐11

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NumberReactantsandProductsRateConstantExpressionk298

33NO3+HO2=OH+NO2k=4.00E‐124.00E‐12

34NO3+O3=NO2k=1.00E‐171.00E‐17

35NO3+NO3=2NO2k=8.50E‐13exp(‐2450/T)2.28E‐16

36NO3+NO2=N2O5Falloff:F=0.35;n=1.33

k(0)=3.60E‐30(T/300)^‐4.1

k(inf)=1.90E‐12(T/300)^0.2

1.24E‐12

37N2O5=NO3+NO2Falloff:F=0.35;n=1.33

k(0)=1.30E‐3(T/300)^‐3.5exp(‐11000/T)

k(inf)=9.70E+14(T/300)^0.1exp(‐

11080/T)

4.46E‐2

38N2O5=NO2+NO3Photolysis2.52E‐5

39N2O5+H2O=2HNO3k=1.00E‐221.00E‐22

40NO+OH=HONOFalloff:F=0.81;n=0.87

k(0)=7.40E‐31(T/300)^‐2.4

k(inf)=3.30E‐11(T/300)^‐0.3

9.77E‐12

41NO+NO2+H2O=2HONOk=5.00E‐405.00E‐40

42HONO+HONO=NO+NO2k=1.00E‐201.00E‐20

43HONO=NO+OHPhotolysis1.04E‐3

44HONO+OH=NO2k=2.50E‐12exp(260/T)5.98E‐12

45NO2+OH=HNO3Falloff:F=0.6;n=1

k(0)=1.80E‐30(T/300)^‐3

k(inf)=2.80E‐11

1.06E‐11

46HNO3+OH=NO3k=k1+k3[M]/(1+k3[M]/k2)

k1=2.40E‐14exp(460/T)

k2=2.70E‐17exp(2199/T)

k3=6.50E‐34exp(1335/T)

1.54E‐13

47HNO3=OH+NO2Photolysis2.54E‐7

48HO2+NO2=PNAFalloff:F=0.6;n=1

k(0)=1.80E‐31(T/300)^‐3.2

k(inf)=4.70E‐12

1.38E‐12

49PNA=HO2+NO2Falloff:F=0.6;n=1

k(0)=4.10E‐5exp(‐10650/T)

k(inf)=4.80E+15exp(‐11170/T)

8.31E‐2

50PNA=0.59HO2+0.59NO2+0.41OH+

0.41NO3

Photolysis2.36E‐6

51PNA+OH=NO2k=3.20E‐13exp(690/T)3.24E‐12

52SO2+OH=SULF+HO2Falloff:F=0.53;n=1.1

k(0)=4.50E‐31(T/300)^‐3.9

k(inf)=1.30E‐12(T/300)^‐0.7

8.12E‐13

53C2O3+NO=NO2+MEO2+RO2k=7.50E‐12exp(290/T)1.98E‐11

54C2O3+NO2=PANFalloff:F=0.3;n=1.41

k(0)=2.70E‐28(T/300)^‐7.1

k(inf)=1.20E‐11(T/300)^‐0.9

9.40E‐12

55PAN=NO2+C2O3Falloff:F=0.3;n=1.41

k(0)=4.90E‐3exp(‐12100/T)

k(inf)=5.40E+16exp(‐13830/T)

2.98E‐4

56PAN=0.6NO2+0.6C2O3+0.4NO3+0.4

MEO2+0.4RO2

Photolysis3.47E‐7

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AppendixA:Mechanism2–CB6r2

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NumberReactantsandProductsRateConstantExpressionk298

57C2O3+HO2=0.41PACD+0.15AACD+

0.15O3+0.44MEO2+0.44RO2+0.44OH

k=5.20E‐13exp(980/T)1.39E‐11

58C2O3+RO2=C2O3k=8.90E‐13exp(800/T)1.30E‐11

59C2O3+C2O3=2MEO2+2RO2k=2.90E‐12exp(500/T)1.55E‐11

60C2O3+CXO3=MEO2+ALD2+XO2H+2

RO2

k=2.90E‐12exp(500/T)1.55E‐11

61CXO3+NO=NO2+ALD2+XO2H+RO2k=6.70E‐12exp(340/T)2.10E‐11

62CXO3+NO2=PANXk=k(ref)K

k(ref)=k(54)

K=1.00E+0

9.40E‐12

63PANX=NO2+CXO3k=k(ref)K

k(ref)=k(55)

K=1.00E+0

2.98E‐4

64PANX=0.6NO2+0.6CXO3+0.4NO3+0.4

ALD2+0.4XO2H+0.4RO2

Photolysis3.47E‐7

65CXO3+HO2=0.41PACD+0.15AACD+

0.15O3+0.44ALD2+0.44XO2H+0.44

RO2+0.44OH

k=5.20E‐13exp(980/T)1.39E‐11

66CXO3+RO2=0.8ALD2+0.8XO2H+0.8

RO2

k=8.90E‐13exp(800/T)1.30E‐11

67CXO3+CXO3=2ALD2+2XO2H+2RO2k=3.20E‐12exp(500/T)1.71E‐11

68RO2+NO=NOk=2.40E‐12exp(360/T)8.03E‐12

69RO2+HO2=HO2k=4.80E‐13exp(800/T)7.03E‐12

70RO2+RO2=k=6.50E‐14exp(500/T)3.48E‐13

71MEO2+NO=FORM+HO2+NO2k=2.30E‐12exp(360/T)7.70E‐12

72MEO2+HO2=0.9MEPX+0.1FORMk=3.80E‐13exp(780/T)5.21E‐12

73MEO2+C2O3=FORM+0.9HO2+0.9

MEO2+0.1AACD+0.9RO2

k=2.00E‐12exp(500/T)1.07E‐11

74MEO2+RO2=0.685FORM+0.315MEOH

+0.37HO2+RO2

k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

75XO2H+NO=NO2+HO2k=2.70E‐12exp(360/T)9.04E‐12

76XO2H+HO2=ROOHk=6.80E‐13exp(800/T)9.96E‐12

77XO2H+C2O3=0.8HO2+0.8MEO2+0.2

AACD+0.8RO2

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

78XO2H+RO2=0.6HO2+RO2k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

79XO2+NO=NO2k=k(ref)K

k(ref)=k(75)

K=1.00E+0

9.04E‐12

80XO2+HO2=ROOHk=k(ref)K

k(ref)=k(76)

K=1.00E+0

9.96E‐12

81XO2+C2O3=0.8MEO2+0.2AACD+0.8

RO2

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixA:Mechanism2–CB6r2



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 235www.camx.com



NumberReactantsandProductsRateConstantExpressionk298

82XO2+RO2=RO2k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

83XO2N+NO=0.5NTR1+0.5NTR2k=k(ref)K

k(ref)=k(75)

K=1.00E+0

9.04E‐12

84XO2N+HO2=ROOHk=k(ref)K

k(ref)=k(76)

K=1.00E+0

9.96E‐12

85XO2N+C2O3=0.8HO2+0.8MEO2+0.2

AACD+0.8RO2

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

86XO2N+RO2=RO2k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

87MEPX+OH=0.6MEO2+0.6RO2+0.4

FORM+0.4OH

k=5.30E‐12exp(190/T)1.00E‐11

88MEPX=MEO2+RO2+OHPhotolysis2.68E‐6

89ROOH+OH=0.54XO2H+0.06XO2N+0.6

RO2+0.4OH

k=5.30E‐12exp(190/T)1.00E‐11

90ROOH=HO2+OHPhotolysis2.68E‐6

91NTR1+OH=NTR2k=2.00E‐122.00E‐12

92NTR1=NO2Photolysis1.06E‐6

93FACD+OH=HO2k=4.50E‐134.50E‐13

94AACD+OH=MEO2+RO2k=4.00E‐14exp(850/T)6.93E‐13

95PACD+OH=C2O3k=5.30E‐12exp(190/T)1.00E‐11

96FORM+OH=HO2+COk=5.40E‐12exp(135/T)8.49E‐12

97FORM=2HO2+COPhotolysis1.78E‐5

98FORM=CO+H2Photolysis2.38E‐5

99FORM+O=OH+HO2+COk=3.40E‐11exp(‐1600/T)1.58E‐13

100FORM+NO3=HNO3+HO2+COk=5.50E‐165.50E‐16

101FORM+HO2=HCO3k=9.70E‐15exp(625/T)7.90E‐14

102HCO3=FORM+HO2k=2.40E+12exp(‐7000/T)1.51E+2

103HCO3+NO=FACD+NO2+HO2k=5.60E‐125.60E‐12

104HCO3+HO2=0.5MEPX+0.5FACD+0.2

OH+0.2HO2

k=5.60E‐15exp(2300/T)1.26E‐11

105ALD2+O=C2O3+OHk=1.80E‐11exp(‐1100/T)4.49E‐13

106ALD2+OH=C2O3k=4.70E‐12exp(345/T)1.50E‐11

107ALD2+NO3=C2O3+HNO3k=1.40E‐12exp(‐1860/T)2.73E‐15

108ALD2=MEO2+RO2+CO+HO2Photolysis1.76E‐6

109ALDX+O=CXO3+OHk=1.30E‐11exp(‐870/T)7.02E‐13

110ALDX+OH=CXO3k=4.90E‐12exp(405/T)1.91E‐11

111ALDX+NO3=CXO3+HNO3k=6.30E‐156.30E‐15

112ALDX=ALD2+XO2H+RO2+CO+HO2Photolysis6.96E‐6

113GLYD+OH=0.2GLY+0.2HO2+0.8C2O3k=8.00E‐128.00E‐12

114GLYD=0.74FORM+0.89CO+1.4HO2+

0.15MEOH+0.19OH+0.11GLY+0.11

XO2H+0.11RO2

Photolysis1.56E‐6

115GLYD+NO3=HNO3+C2O3k=1.40E‐12exp(‐1860/T)2.73E‐15

March2016CAMxUser’sGuideVersion6.3

AppendixA:Mechanism2–CB6r2



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 236www.camx.com



NumberReactantsandProductsRateConstantExpressionk298

116GLY+OH=1.8CO+0.2XO2+0.2RO2+

HO2

k=3.10E‐12exp(340/T)9.70E‐12

117GLY=2HO2+2COPhotolysis5.50E‐5

118GLY+NO3=HNO3+1.5CO+0.5XO2+0.5

RO2+HO2

k=1.40E‐12exp(‐1860/T)2.73E‐15

119MGLY=C2O3+HO2+COPhotolysis1.46E‐4

120MGLY+NO3=HNO3+C2O3+XO2+RO2k=1.40E‐12exp(‐1860/T)2.73E‐15

121MGLY+OH=C2O3+COk=1.90E‐12exp(575/T)1.31E‐11

122H2+OH=HO2k=7.70E‐12exp(‐2100/T)6.70E‐15

123CO+OH=HO2k=k1+k2[M]

k1=1.44E‐13

k2=3.43E‐33

2.28E‐13

124CH4+OH=MEO2+RO2k=1.85E‐12exp(‐1690/T)6.37E‐15

125ETHA+OH=0.991ALD2+0.991XO2H+

0.009XO2N+RO2

k=6.90E‐12exp(‐1000/T)2.41E‐13

126MEOH+OH=FORM+HO2k=2.85E‐12exp(‐345/T)8.95E‐13

127ETOH+OH=0.95ALD2+0.9HO2+0.1

XO2H+0.1RO2+0.078FORM+0.011

GLYD

k=3.00E‐12exp(20/T)3.21E‐12

128KET=0.5ALD2+0.5C2O3+0.5XO2H+0.5

CXO3+0.5MEO2+RO2‐2.5PAR

Photolysis2.27E‐7

129ACET=0.38CO+1.38MEO2+1.38RO2+

0.62C2O3

Photolysis2.08E‐7

130ACET+OH=FORM+C2O3+XO2+RO2k=1.41E‐12exp(‐620.6/T)1.76E‐13

131PRPA+OH=0.71ACET+0.26ALDX+0.26

PAR+0.97XO2H+0.03XO2N+RO2

k=7.60E‐12exp(‐585/T)1.07E‐12

132PAR+OH=0.11ALDX+0.76ROR+0.13

XO2N+0.11XO2H+0.76XO2+RO2‐0.11

PAR

k=8.10E‐138.10E‐13

133ROR=0.2KET+0.42ACET+0.74ALD2+

0.37ALDX+0.04XO2N+0.94XO2H+0.98

RO2+0.02ROR‐2.7PAR

k=5.70E+12exp(‐5780/T)2.15E+4

134ROR+O2=KET+HO2k=1.50E‐14exp(‐200/T)7.67E‐15

135ROR+NO2=NTR1k=8.60E‐12exp(400/T)3.29E‐11

136ETHY+OH=0.7GLY+0.7OH+0.3FACD+

0.3CO+0.3HO2

Falloff:F=0.37;n=1.3

k(0)=5.00E‐30(T/300)^‐1.5

k(inf)=1.00E‐12

7.52E‐13

137ETH+O=FORM+HO2+CO+0.7XO2H+

0.7RO2+0.3OH

k=1.04E‐11exp(‐792/T)7.29E‐13

138ETH+OH=XO2H+RO2+1.56FORM+

0.22GLYD

Falloff:F=0.48;n=1.15

k(0)=8.60E‐29(T/300)^‐3.1

k(inf)=9.00E‐12(T/300)^‐0.85

7.84E‐12

139ETH+O3=FORM+0.51CO+0.16HO2+

0.16OH+0.37FACD

k=9.10E‐15exp(‐2580/T)1.58E‐18

140ETH+NO3=0.5NO2+0.5NTR1+0.5

XO2H+0.5XO2+RO2+1.125FORM

k=3.30E‐12exp(‐2880/T)2.10E‐16

141OLE+O=0.2ALD2+0.3ALDX+0.1HO2+

0.2XO2H+0.2CO+0.2FORM+0.01XO2N

+0.21RO2+0.2PAR+0.1OH

k=1.00E‐11exp(‐280/T)3.91E‐12

March2016CAMxUser’sGuideVersion6.3

AppendixA:Mechanism2–CB6r2



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 237www.camx.com



NumberReactantsandProductsRateConstantExpressionk298

142OLE+OH=0.781FORM+0.488ALD2+

0.488ALDX+0.976XO2H+0.195XO2+

0.024XO2N+1.195RO2‐0.73PAR

Falloff:F=0.5;n=1.13

k(0)=8.00E‐27(T/300)^‐3.5

k(inf)=3.00E‐11(T/300)^‐1

2.86E‐11

143OLE+O3=0.295ALD2+0.555FORM+

0.27ALDX+0.15XO2H+0.15RO2+0.334

OH+0.08HO2+0.378CO+0.075GLY+

0.075MGLY+0.09FACD+0.13AACD+

0.04H2O2‐0.79PAR

k=5.50E‐15exp(‐1880/T)1.00E‐17

144OLE+NO3=0.5NO2+0.5NTR1+0.48

XO2+0.48XO2H+0.04XO2N+RO2+0.5

FORM+0.25ALD2+0.375ALDX‐1PAR

k=4.60E‐13exp(‐1155/T)9.54E‐15

145IOLE+O=1.24ALD2+0.66ALDX+0.1

XO2H+0.1RO2+0.1CO+0.1PAR

k=2.30E‐112.30E‐11

146IOLE+OH=1.3ALD2+0.7ALDX+XO2H+

RO2

k=1.05E‐11exp(519/T)5.99E‐11

147IOLE+O3=0.732ALD2+0.442ALDX+

0.128FORM+0.245CO+0.5OH+0.3

XO2H+0.3RO2+0.24GLY+0.06MGLY+

0.29PAR+0.08AACD+0.08H2O2

k=4.70E‐15exp(‐1013/T)1.57E‐16

148IOLE+NO3=0.5NO2+0.5NTR1+0.48

XO2+0.48XO2H+0.04XO2N+RO2+0.5

ALD2+0.625ALDX+PAR

k=3.70E‐133.70E‐13

149ISOP+OH=ISO2+RO2k=2.70E‐11exp(390/T)9.99E‐11

150ISOP+O=0.75ISPD+0.5FORM+0.25

XO2+0.25RO2+0.25HO2+0.25CXO3+

0.25PAR

k=3.00E‐113.00E‐11

151ISO2+NO=0.1INTR+0.9NO2+0.673

FORM+0.9ISPD+0.818HO2+0.082

XO2H+0.082RO2

k=2.39E‐12exp(365/T)8.13E‐12

152ISO2+HO2=0.88ISPX+0.12OH+0.12

HO2+0.12FORM+0.12ISPD

k=7.43E‐13exp(700/T)7.78E‐12

153ISO2+C2O3=0.598FORM+1ISPD+

0.728HO2+0.072XO2H+0.8MEO2+0.2

AACD+0.872RO2

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

154ISO2+RO2=0.598FORM+1ISPD+0.728

HO2+0.072XO2H+0.072RO2

k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

155ISO2=HO2+HPLDk=3.30E+9exp(‐8300/T)2.64E‐3

156ISOP+O3=0.6FORM+0.65ISPD+0.15

ALDX+0.2CXO3+0.35PAR+0.266OH+

0.2XO2+0.2RO2+0.066HO2+0.066CO

k=1.03E‐14exp(‐1995/T)1.27E‐17

157ISOP+NO3=0.35NO2+0.65NTR2+0.64

XO2H+0.33XO2+0.03XO2N+RO2+0.35

FORM+0.35ISPD

k=3.03E‐12exp(‐448/T)6.74E‐13

158ISPD+OH=0.022XO2N+0.521XO2+

0.115MGLY+0.115MEO2+0.269GLYD+

0.269C2O3+0.457OPO3+0.117PAR+

0.137ACET+0.137CO+0.137HO2+0.658

RO2

k=5.58E‐12exp(511/T)3.10E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixA:Mechanism2–CB6r2



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 238www.camx.com



NumberReactantsandProductsRateConstantExpressionk298

159ISPD+O3=0.04ALD2+0.231FORM+

0.531MGLY+0.17GLY+0.17ACET+0.543

CO+0.461OH+0.15FACD+0.398HO2+

0.143C2O3

k=3.88E‐15exp(‐1770/T)1.02E‐17

160ISPD+NO3=0.717HNO3+0.142NTR2+

0.142NO2+0.142XO2+0.142XO2H+

0.113GLYD+0.113MGLY+0.717PAR+

0.717CXO3+0.284RO2

k=4.10E‐12exp(‐1860/T)7.98E‐15

161ISPD=0.76HO2+0.34XO2H+0.16XO2+

0.34MEO2+0.208C2O3+0.26FORM+

0.24OLE+0.24PAR+0.17ACET+0.128

GLYD+0.84RO2

Photolysis1.60E‐5

162ISPX+OH=0.904EPOX+0.933OH+0.067

ISO2+0.067RO2+0.029IOLE+0.029

ALDX

k=2.23E‐11exp(372/T)7.77E‐11

163HPLD=OH+ISPDPhotolysis4.41E‐4

164HPLD+NO3=HNO3+ISPDk=6.00E‐12exp(‐1860/T)1.17E‐14

165EPOX+OH=EPX2+RO2k=5.78E‐11exp(‐400/T)1.51E‐11

166EPX2+HO2=0.275GLYD+0.275GLY+

0.275MGLY+1.125OH+0.825HO2+

0.375FORM+0.074FACD+0.251CO+

2.175PAR

k=7.43E‐13exp(700/T)7.78E‐12

167EPX2+NO=0.275GLYD+0.275GLY+

0.275MGLY+0.125OH+0.825HO2+

0.375FORM+NO2+0.251CO+2.175PAR

k=2.39E‐12exp(365/T)8.13E‐12

168EPX2+C2O3=0.22GLYD+0.22GLY+0.22

MGLY+0.1OH+0.66HO2+0.3FORM+

0.2CO+1.74PAR+0.8MEO2+0.2AACD+

0.8RO2

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

169EPX2+RO2=0.275GLYD+0.275GLY+

0.275MGLY+0.125OH+0.825HO2+

0.375FORM+0.251CO+2.175PAR+RO2

k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

170INTR+OH=0.63XO2+0.37XO2H+RO2+

0.444NO2+0.185NO3+0.104INTR+

0.592FORM+0.331GLYD+0.185FACD+

2.7PAR+0.098OLE+0.078ALDX+0.266

NTR2

k=3.10E‐113.10E‐11

171TERP+O=0.15ALDX+5.12PARk=3.60E‐113.60E‐11

172TERP+OH=0.75XO2H+0.5XO2+0.25

XO2N+1.5RO2+0.28FORM+1.66PAR+

0.47ALDX

k=1.50E‐11exp(449/T)6.77E‐11

173TERP+O3=0.57OH+0.07XO2H+0.69

XO2+0.18XO2N+0.94RO2+0.24FORM

+0.001CO+7PAR+0.21ALDX+0.39

CXO3

k=1.20E‐15exp(‐821/T)7.63E‐17

174TERP+NO3=0.47NO2+0.28XO2H+0.75

XO2+0.25XO2N+1.28RO2+0.47ALDX+

0.53NTR2

k=3.70E‐12exp(175/T)6.66E‐12

175BENZ+OH=0.53CRES+0.352BZO2+

0.352RO2+0.118OPEN+0.118OH+0.53

HO2

k=2.30E‐12exp(‐190/T)1.22E‐12

March2016CAMxUser’sGuideVersion6.3

AppendixA:Mechanism2–CB6r2



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 239www.camx.com



NumberReactantsandProductsRateConstantExpressionk298

176BZO2+NO=0.918NO2+0.082NTR2+

0.918GLY+0.918OPEN+0.918HO2

k=2.70E‐12exp(360/T)9.04E‐12

177BZO2+C2O3=GLY+OPEN+HO2+MEO2

+RO2

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

178BZO2+HO2=k=1.90E‐13exp(1300/T)1.49E‐11

179BZO2+RO2=GLY+OPEN+HO2+RO2k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

180TOL+OH=0.18CRES+0.65TO2+0.72

RO2+0.1OPEN+0.1OH+0.07XO2H+

0.18HO2

k=1.80E‐12exp(340/T)5.63E‐12

181TO2+NO=0.86NO2+0.14NTR2+0.417

GLY+0.443MGLY+0.66OPEN+0.2XOPN

+0.86HO2

k=2.70E‐12exp(360/T)9.04E‐12

182TO2+C2O3=0.48GLY+0.52MGLY+0.77

OPEN+0.23XOPN+HO2+MEO2+RO2

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

183TO2+HO2=k=1.90E‐13exp(1300/T)1.49E‐11

184TO2+RO2=0.48GLY+0.52MGLY+0.77

OPEN+0.23XOPN+HO2+RO2

k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

185XYL+OH=0.155CRES+0.544XLO2+

0.602RO2+0.244XOPN+0.244OH+

0.058XO2H+0.155HO2

k=1.85E‐111.85E‐11

186XLO2+NO=0.86NO2+0.14NTR2+0.221

GLY+0.675MGLY+0.3OPEN+0.56XOPN

+0.86HO2

k=2.70E‐12exp(360/T)9.04E‐12

187XLO2+HO2=k=1.90E‐13exp(1300/T)1.49E‐11

188XLO2+C2O3=0.26GLY+0.77MGLY+

0.35OPEN+0.65XOPN+HO2+MEO2+

RO2

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

189XLO2+RO2=0.26GLY+0.77MGLY+0.35

OPEN+0.65XOPN+HO2+RO2

k=k(ref)K

k(ref)=k(70)

K=1.00E+0

3.48E‐13

190CRES+OH=0.025GLY+0.025OPEN+

HO2+0.2CRO+0.732CAT1+0.02XO2N+

0.02RO2

k=1.70E‐12exp(950/T)4.12E‐11

191CRES+NO3=0.3CRO+HNO3+0.48XO2+

0.12XO2H+0.24GLY+0.24MGLY+0.48

OPO3+0.1XO2N+0.7RO2

k=1.40E‐111.40E‐11

192CRO+NO2=CRONk=2.10E‐122.10E‐12

193CRO+HO2=CRESk=5.50E‐125.50E‐12

194CRON+OH=NTR2+0.5CROk=1.53E‐121.53E‐12

195CRON+NO3=NTR2+0.5CRO+HNO3k=3.80E‐123.80E‐12

196CRON=HONO+HO2+FORM+OPENPhotolysis9.45E‐5

197XOPN=0.4GLY+XO2H+0.7HO2+0.7CO

+0.3C2O3

Photolysis5.04E‐4

March2016CAMxUser’sGuideVersion6.3

AppendixA:Mechanism2–CB6r2

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

NumberReactantsandProductsRateConstantExpressionk298

198XOPN+OH=MGLY+0.4GLY+2XO2H+2

RO2

k=9.00E‐119.00E‐11

199XOPN+O3=1.2MGLY+0.5OH+0.6C2O3

+0.1ALD2+0.5CO+0.3XO2H+0.3RO2

k=1.08E‐16exp(‐500/T)2.02E‐17

200XOPN+NO3=0.5NO2+0.5NTR2+0.45

XO2H+0.45XO2+0.1XO2N+RO2+0.25

OPEN+0.25MGLY

k=3.00E‐123.00E‐12

201OPEN=OPO3+HO2+COPhotolysis5.04E‐4

202OPEN+OH=0.6OPO3+0.4XO2H+0.4

RO2+0.4GLY

k=4.40E‐114.40E‐11

203OPEN+O3=1.4GLY+0.24MGLY+0.5OH

+0.12C2O3+0.08FORM+0.02ALD2+

1.98CO+0.56HO2

k=5.40E‐17exp(‐500/T)1.01E‐17

204OPEN+NO3=OPO3+HNO3k=3.80E‐123.80E‐12

205CAT1+OH=0.14FORM+0.2HO2+0.5

CRO

k=5.00E‐115.00E‐11

206CAT1+NO3=CRO+HNO3k=1.70E‐101.70E‐10

207OPO3+NO=NO2+0.5GLY+0.5CO+0.8

HO2+0.2CXO3

k=1.00E‐111.00E‐11

208OPO3+NO2=OPANk=k(ref)K

k(ref)=k(54)

K=1.00E+0

9.40E‐12

209OPAN=OPO3+NO2k=k(ref)K

k(ref)=k(55)

K=1.00E+0

2.98E‐4

210OPO3+HO2=0.41PACD+0.15AACD+

0.15O3+0.44ALDX+0.44XO2H+0.44

RO2+0.44OH

k=k(ref)K

k(ref)=k(57)

K=1.00E+0

1.39E‐11

211OPO3+C2O3=MEO2+XO2+ALDX+2

RO2

k=k(ref)K

k(ref)=k(59)

K=1.00E+0

1.55E‐11

212OPO3+RO2=0.8XO2H+0.8ALDX+1.8

RO2+0.2AACD

k=k(ref)K

k(ref)=k(58)

K=1.00E+0

1.30E‐11

213OPAN+OH=0.5NO2+0.5GLY+CO+0.5

NTR2

k=3.60E‐113.60E‐11

214PANX+OH=ALD2+NO2k=3.00E‐123.00E‐12

215NTR2=HNO3k=2.30E‐52.30E‐5

216ECH4+OH=MEO2+RO2k=1.85E‐12exp(‐1690/T)6.37E‐15



March2016CAMxUser’sGuideVersion6.3

AppendixB:Mechanism3–CB6r2withHalogenChemistry

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

AppendixB

CAMxMechanism3:CB6r2withHalogenChemistry

TableB‐1.ListingoftheCB6r2halogenmechanism(seeTableA‐1foracompletelistingof

CB6r2).k298istherateconstantat298Kand1atmosphereusingunitsinmolecules/cm3and

1/s.Forphotolysisreactionsk298showsthephotolysisrateatasolarzenithangleof60°and

heightof600mMSL/AGL.SeeTableB‐2forspeciesnames.SeeSection3.1ontemperature

andpressuredependencies.

NumberReactantsandProductsRateConstantExpression k298

1CL2=2CL Photolysis 1.56E‐3

2HOCL=CL+OH Photolysis 1.34E‐4

3CL+O3=CLO k=2.30E‐11exp(‐200/T) 1.18E‐11

4CLO+CLO=0.3CL2+1.4CL k=1.63E‐14 1.63E‐14

5CLO+NO=CL+NO2 k=6.40E‐12exp(290/T) 1.69E‐11

6CLO+HO2=HOCL k=2.70E‐12exp(220/T) 5.65E‐12

7CLO+NO2=CLN3 Falloff:F=0.6;n=1

k(0)=1.80E‐31(T/300)^‐3.4

k(inf)=1.50E‐11(T/300)^‐1.9

2.34E‐12

8CLN3=CLO+NO2 Falloff:F=0.6;n=1

k(0)=4.48E‐5(T/300)^‐1exp(‐12530/T)

k(inf)=3.71E+15(T/300)^3.5exp(‐

12530/T)

3.11E‐4

9CLN3=CLO+NO2 Photolysis 4.97E‐6

10CLN3=CL+NO3 Photolysis 4.67E‐4

11CLN3+H2O=HOCL+HNO3 k=2.50E‐22 2.50E‐22

12OH+HCL=CL k=6.58E‐13(T/300)^1.2exp(58/T)7.93E‐13

13OH+FMCL=CL+CO k=3.67E‐11exp(‐1419/T) 3.14E‐13

14FMCL=CL+CO+HO2 Photolysis 6.10E‐8

15CLO+MEO2=CL+FORM+HO2 k=4.10E‐13exp(‐800/T) 2.80E‐14

16CL+CH4=HCL+MEO2 k=6.60E‐12exp(‐1240/T) 1.03E‐13

17CL+PAR=HCL k=5.00E‐11 5.00E‐11

18CL+ETHA=HCL+0.991ALD2+0.991

XO2H+0.009XO2N+RO2

k=8.30E‐11exp(‐100/T) 5.93E‐11

19CL+PRPA=HCL+ACET+0.97XO2H+

0.03XO2N+RO2

k=1.40E‐10 1.40E‐10

20CL+ISOP=FMCL+ISPD+0.96XO2H+

0.04XO2N+RO2

k=4.30E‐10 4.30E‐10

21HCL+N2O5=CLN2+HNO3 k=6.00E‐13 6.00E‐13

22CLN2=CL+NO2 Photolysis 2.86E‐4

23BR2=2BR Photolysis 2.79E‐2

24HOBR=BR+OH Photolysis 1.51E‐3

25BR2+OH=HOBR+BR k=5.40E‐11exp(180/T) 9.88E‐11

26HBR+OH=BR k=5.50E‐12exp(‐200/T) 2.81E‐12

27BR+O3=BRO k=1.60E‐11exp(780/T) 2.19E‐10

28BR+HO2=HBR k=4.80E‐12exp(310/T) 1.36E‐11

29BR+NO2=BRN2 Falloff:F=0.6;n=1

k(0)=4.20E‐31(T/300)^‐2.4

k(inf)=2.70E‐11

4.89E‐12

30BR+NO3=BRO+NO2 k=1.60E‐11 1.60E‐11

31BRO=BR+O Photolysis 2.05E‐2

32BRO+HO2=HOBR k=4.50E‐12exp(460/T) 2.11E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixB:Mechanism3–CB6r2withHalogenChemistry



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

NumberReactantsandProductsRateConstantExpression k298

33BRO+OH=BR+HO2 k=1.70E‐11exp(250/T) 3.93E‐11

34BRO+BRO=2BR k=2.40E‐12exp(40/T) 2.74E‐12

35BRO+BRO=BR2 k=2.80E‐14exp(860/T) 5.02E‐13

36BRO+NO=BR+NO2 k=8.80E‐12exp(260/T) 2.11E‐11

37BRO+NO2=BRN3 Falloff:F=0.6;n=1

k(0)=5.20E‐31(T/300)^‐3.2

k(inf)=6.90E‐12

2.81E‐12

38BRN2=BR+NO2 Photolysis 3.21E‐3

39BRN3=BR+NO3 Photolysis 9.76E‐4

40BRN3+H2O=HOBR+HNO3 k=2.50E‐22 2.50E‐22

41FMBR+OH=BR+CO k=5.00E‐12 5.00E‐12

42FMBR=BR+CO+HO2 Photolysis 4.15E‐6

43BRO+MEO2=0.75HOBR+0.25BR+

FORM

k=4.10E‐13exp(‐800/T) 2.80E‐14

44BR+FORM=HBR+CO+HO2 k=7.70E‐11exp(‐580/T) 1.10E‐11

45BR+ALD2=HBR+C2O3 k=1.80E‐11exp(‐460/T) 3.84E‐12

46BR+OLE=FMBR+ALD2+XO2H‐ 1PAR

+RO2

k=3.60E‐12 3.60E‐12

47BR+ISOP=FMBR+ISPD+0.96XO2H+

0.04XO2N+RO2

k=5.00E‐12 5.00E‐12

48I2=2I Photolysis 1.30E‐1

49HOI=I+OH Photolysis 6.36E‐2

50I2+OH=I+HOI k=2.10E‐10 2.10E‐10

51I2+NO3=I+INO3 k=1.50E‐12 1.50E‐12

52HI+OH=I k=1.60E‐11exp(440/T) 7.00E‐11

53I+O3=IO k=2.10E‐11exp(‐830/T) 1.30E‐12

54I+HO2=HI k=1.50E‐11exp(‐1090/T) 3.87E‐13

55I+NO2=INO2 Falloff:F=0.63;n=1

k(0)=3.00E‐31(T/300)^‐1

k(inf)=6.60E‐11

5.24E‐12

56IO=I+O Photolysis 1.18E‐1

57IO+IO=0.4I+0.4OIO+0.6I2O2 k=5.40E‐11exp(180/T) 9.88E‐11

58IO+HO2=HOI k=1.40E‐11exp(540/T) 8.57E‐11

59IO+NO=I+NO2 k=7.15E‐12exp(300/T) 1.96E‐11

60IO+NO2=INO3 Falloff:F=0.4;n=1

k(0)=7.70E‐31(T/300)^‐5

k(inf)=1.60E‐11

3.55E‐12

61HOI+OH=IO k=5.00E‐12 5.00E‐12

62OIO=I Photolysis 1.28E‐1

63OIO+OH=HIO3 Falloff:F=0.3;n=1

k(0)=1.50E‐27(T/300)^‐3.93

k(inf)=5.50E‐10exp(46/T)

4.72E‐10

64OIO+IO=IXOY k=1.00E‐10 1.00E‐10

65OIO+OIO=IXOY k=1.50E‐10 1.50E‐10

66OIO+NO=IO+NO2 k=1.10E‐12exp(542/T) 6.78E‐12

67I2O2=I+OIO k=1.00E+1 1.00E+1

68I2O2+O3=IXOY k=1.00E‐12 1.00E‐12

69INO2=I+NO2 Photolysis 3.21E‐3

70INO2+INO2=I2+2NO2 k=4.70E‐13exp(‐1670/T) 1.73E‐15

71INO3=I+NO3 Photolysis 1.25E‐2

72INO3+H2O=HOI+HNO3 k=2.50E‐22 2.50E‐22

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NumberReactantsandProductsRateConstantExpression k298

73CLO+BRO=CL+BR k=4.70E‐12exp(320/T) 1.38E‐11

74CLO+IO=CL+I k=4.70E‐12exp(280/T) 1.20E‐11

75BRO+IO=BR+I k=1.50E‐11exp(510/T) 8.31E‐11

76CH3I=I+MEO2 Photolysis 3.19E‐6

77MI2=2I+FORM Photolysis 4.69E‐3

78MIB=I+BR+FORM Photolysis 2.53E‐4

79MIC=I+CL+FORM Photolysis 7.48E‐5

80MB3=3BR+HO2+CO Photolysis 4.64E‐7

81MB3+OH=3BR+CO k=1.35E‐12exp(‐600/T) 1.80E‐13

82MB2+OH=2BR+HO2+CO k=2.00E‐12exp(‐840/T) 1.19E‐13

83MBC+OH=BR+MEO2 k=2.35E‐12exp(‐1300/T) 3.00E‐14

84MBC2+OH=BR+MEO2 k=9.00E‐13exp(‐600/T) 1.20E‐13

85MB2C+OH=BR+MEO2 k=9.00E‐13exp(‐600/T) 1.20E‐13

86IALK=I+ALDX+XO2H+RO2Photolysis 5.88E‐7

87SSCL+HNO3=HCL+SSN3 k=1.00E‐12 1.00E‐12

88SSBR+HOBR=BR2 k=1.00E‐12 1.00E‐12



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AppendixB:Mechanism3–CB6r2withHalogenChemistry

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TableB‐2.ChemicalspeciesincludedinCB6r2h.

SpeciesDescription

Constituents

Mol.Wt.C H O N ClBrI

CL2Molecularchlorine270.9

CLChlorineatom135.5

CLOChlorinemonoxide1 151.4

HCLHydrogenchloride1 136.5

HOCLHypochlorousacid1 1 152.4

CLN2Nitrylchloride:ClNO22 181.4

CLN3Chlorinenitrate:ClONO23 197.4

FMCLFormylchloride:HC(O)Cl1 1 1 164.5

BR2Molecularbromine2 159.8

BRBromineatom179.9

BROBrominemonoxide1 195.9

HBRHydrogenbromide1 180.9

HOBRHypobromousacid1 1 196.9

BRN2Nitrylbroride:BrNO22 1125.9

BRN3Brominenitrate:BrONO23 1141.9

FMBRFormylbromide:HC(O)Br1 1 1 1108.9

I2Moleculariodine2253.8

IIodineatom1126.9

IOIodinemonoxide1 1142.9

OIOIodinedioxide2 1158.9

I2O2Diiodinedioxide2 2285.8

IXOYCondensableiodineoxides(>I2O2) 3 2301.8

HIHydrogeniodide1 1127.9

HOIHypoiodousacid1 1 1143.9

HIO3Iodicacid:HONO21 3 1175.9

INO2Nitryliodide:INO22 1172.9

INO3Iodinenitrate:IONO23  1188.9

CH3IIodomethane1 3   1141.9

MI2Diiodomethane:CH2I21 2 2267.8

MIBBromoiodomethane:CH2BrI1 2 11220.8

MICChloroiodomethane:CH2ClI1 2 11176.4

MBCChlorobromomethane:CH2ClBr 1 2 11129.4

MB2Dibromomethane:CH2Br21 2 2173.8

MBC2Dichlorobromomethane:CHCl2Br 1 3 21165.8

MB2CChlorodibromomethane:CHClBr21 3 12210.3

MB3BromoformCHBr31 1 3252.7

IALKAlkyliodides3 7   1170.0

SSCLPseudogas‐phasespeciesforseasaltchloride 0 1  35.5

SSBRPseudogas‐phasespeciesforseasaltbromide 0 179.9

SSN3Pseudogas‐phasespeciesforseasaltnitrate 0 3 1    62.0

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AppendixC:Mechanism6–CB05

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AppendixC

CAMxMechanism6:CB05Gas‐PhaseChemistry

TableC‐1.ReactionsandrateconstantexpressionsfortheCB05mechanism.k298istherate

constantat298Kand1atmosphereusingunitsinmolecules/cm3and1/s.SeeTable5‐2for

speciesnames.SeeSection3.1ontemperatureandpressuredependencies.

NumberReactantsandProductsRateConstantExpressionk298

1NO2=NO+OPhotolysis5.89E‐3

2O+O2+M=O3+Mk=6.00E‐34(T/300)^‐2.46.10E‐34

3O3+NO=NO2k=3.00E‐12exp(‐1500/T)1.95E‐14

4O+NO2=NOk=5.60E‐12exp(180/T)1.02E‐11

5O+NO2=NO3Falloff:F=0.6;n=1

k(0)=2.50E‐31(T/300)^‐1.8exp(‐2/T)

k(inf)=2.20E‐11(T/300)^‐0.7exp(‐3/T)

3.26E‐12

6O+NO=NO2Falloff:F=0.6;n=1

k(0)=9.00E‐32(T/300)^‐1.5

k(inf)=3.00E‐11

1.66E‐12

7NO2+O3=NO3k=1.20E‐13exp(‐2450/T)3.23E‐17

8O3=OPhotolysis3.34E‐4

9O3=O1DPhotolysis8.95E‐6

10O1D+M=O+Mk=2.10E‐11exp(102/T)2.96E‐11

11O1D+H2O=2OHk=2.20E‐102.20E‐10

12O3+OH=HO2k=1.70E‐12exp(‐940/T)7.25E‐14

13O3+HO2=OHk=1.00E‐14exp(‐490/T)1.93E‐15

14NO3=NO2+OPhotolysis1.51E‐1

15NO3=NOPhotolysis1.64E‐2

16NO3+NO=2NO2k=1.50E‐11exp(170/T)2.65E‐11

17NO3+NO2=NO+NO2k=4.50E‐14exp(‐1260/T)6.56E‐16

18NO3+NO2=N2O5Falloff:F=0.6;n=1

k(0)=2.00E‐30(T/300)^‐4.4

k(inf)=1.40E‐12(T/300)^‐0.7

1.18E‐12

19N2O5+H2O=2HNO3k=2.50E‐222.50E‐22

20N2O5+H2O+H2O=2HNO3k=1.80E‐391.80E‐39

21N2O5=NO3+NO2Falloff:F=0.45;n=1

k(0)=1.00E‐3(T/300)^‐3.5exp(‐11000/T)

k(inf)=9.70E+14(T/300)^0.1exp(‐

11080/T)

5.28E‐2

22NO+NO+O2=2NO2k=3.30E‐39exp(530/T)1.95E‐38

23NO+NO2+H2O=2HONOk=5.00E‐405.00E‐40

24NO+OH=HONOFalloff:F=0.6;n=1

k(0)=7.00E‐31(T/300)^‐2.6

k(inf)=3.60E‐11(T/300)^‐0.1

7.41E‐12

25HONO=NO+OHPhotolysis1.05E‐3

26OH+HONO=NO2k=1.80E‐11exp(‐390/T)4.86E‐12

27HONO+HONO=NO+NO2k=1.00E‐201.00E‐20

28NO2+OH=HNO3Falloff:F=0.6;n=1

k(0)=2.00E‐30(T/300)^‐3

k(inf)=2.50E‐11

1.05E‐11

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AppendixC:Mechanism6–CB05

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NumberReactantsandProductsRateConstantExpressionk298

29OH+HNO3=NO3k=k1+k3[M]/(1+k3[M]/k2)

k1=2.40E‐14exp(460/T)

k2=2.70E‐17exp(2199/T)

k3=6.50E‐34exp(1335/T)

1.54E‐13

30HO2+NO=OH+NO2k=3.50E‐12exp(250/T)8.10E‐12

31HO2+NO2=PNAFalloff:F=0.6;n=1

k(0)=3.00E‐31(T/300)^‐3.2

k(inf)=4.70E‐12

1.77E‐12

32PNA=HO2+NO2Falloff:F=0.6;n=1

k(0)=4.10E‐5exp(‐10650/T)

k(inf)=4.80E+15exp(‐11170/T)

8.31E‐2

33OH+PNA=NO2k=1.30E‐12exp(380/T)4.65E‐12

34HO2+HO2=H2O2k=k1+k2[M]

k1=2.30E‐13exp(600/T)

k2=1.70E‐33exp(1000/T)

2.92E‐12

35HO2+HO2+H2O=H2O2k=k1+k2[M]

k1=3.22E‐34exp(2800/T)

k2=2.38E‐54exp(3200/T)

6.58E‐30

36H2O2=2OHPhotolysis3.78E‐6

37OH+H2O2=HO2k=2.90E‐12exp(‐160/T)1.70E‐12

38O1D+H2=OH+HO2k=1.10E‐101.10E‐10

39OH+H2=HO2k=5.50E‐12exp(‐2000/T)6.69E‐15

40OH+O=HO2k=2.20E‐11exp(120/T)3.29E‐11

41OH+OH=Ok=4.20E‐12exp(‐240/T)1.88E‐12

42OH+OH=H2O2Falloff:F=0.6;n=1

k(0)=6.90E‐31(T/300)^‐1

k(inf)=2.60E‐11

6.29E‐12

43OH+HO2=k=4.80E‐11exp(250/T)1.11E‐10

44HO2+O=OHk=3.00E‐11exp(200/T)5.87E‐11

45H2O2+O=OH+HO2k=1.40E‐12exp(‐2000/T)1.70E‐15

46NO3+O=NO2k=1.00E‐111.00E‐11

47NO3+OH=HO2+NO2k=2.20E‐112.20E‐11

48NO3+HO2=HNO3k=3.50E‐123.50E‐12

49NO3+O3=NO2k=1.00E‐171.00E‐17

50NO3+NO3=2NO2k=8.50E‐13exp(‐2450/T)2.28E‐16

51PNA=0.61HO2+0.61NO2+0.39OH+

0.39NO3

Photolysis2.53E‐6

52HNO3=OH+NO2Photolysis2.55E‐7

53N2O5=NO2+NO3Photolysis2.52E‐5

54XO2+NO=NO2k=2.60E‐12exp(365/T)8.85E‐12

55XO2N+NO=NTRk=2.60E‐12exp(365/T)8.85E‐12

56XO2+HO2=ROOHk=7.50E‐13exp(700/T)7.86E‐12

57XO2N+HO2=ROOHk=7.50E‐13exp(700/T)7.86E‐12

58XO2+XO2=k=6.80E‐146.80E‐14

59XO2N+XO2N=k=6.80E‐146.80E‐14

60XO2+XO2N=k=6.80E‐146.80E‐14

61NTR+OH=HNO3+HO2+0.33FORM+

0.33ALD2+0.33ALDX‐0.66PAR

k=5.90E‐13exp(‐360/T)1.76E‐13

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AppendixC:Mechanism6–CB05

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NumberReactantsandProductsRateConstantExpressionk298

62NTR=NO2+HO2+0.33FORM+0.33ALD2

+0.33ALDX‐0.66PAR

Photolysis1.06E‐6

63SO2+OH=SULF+HO2Falloff:F=0.6;n=1

k(0)=3.00E‐31(T/300)^‐3.3

k(inf)=1.50E‐12

8.89E‐13

64ROOH+OH=XO2+0.5ALD2+0.5ALDXk=3.01E‐12exp(190/T)5.69E‐12

65ROOH=OH+HO2+0.5ALD2+0.5ALDXPhotolysis2.72E‐6

66OH+CO=HO2k=k1+k2[M]

k1=1.44E‐13

k2=3.43E‐33

2.28E‐13

67OH+CH4=MEO2k=2.45E‐12exp(‐1775/T)6.34E‐15

68MEO2+NO=FORM+HO2+NO2k=2.80E‐12exp(300/T)7.66E‐12

69MEO2+HO2=MEPXk=4.10E‐13exp(750/T)5.08E‐12

70MEO2+MEO2=1.37FORM+0.74HO2+

0.63MEOH

k=9.50E‐14exp(390/T)3.52E‐13

71MEPX+OH=0.7MEO2+0.3XO2+0.3

HO2

k=3.80E‐12exp(200/T)7.43E‐12

72MEPX=FORM+HO2+OHPhotolysis2.72E‐6

73MEOH+OH=FORM+HO2k=7.30E‐12exp(‐620/T)9.12E‐13

74FORM+OH=HO2+COk=9.00E‐129.00E‐12

75FORM=2HO2+COPhotolysis1.40E‐5

76FORM=COPhotolysis2.43E‐5

77FORM+O=OH+HO2+COk=3.40E‐11exp(‐1600/T)1.58E‐13

78FORM+NO3=HNO3+HO2+COk=5.80E‐165.80E‐16

79FORM+HO2=HCO3k=9.70E‐15exp(625/T)7.90E‐14

80HCO3=FORM+HO2k=2.40E+12exp(‐7000/T)1.51E+2

81HCO3+NO=FACD+NO2+HO2k=5.60E‐125.60E‐12

82HCO3+HO2=MEPXk=5.60E‐15exp(2300/T)1.26E‐11

83FACD+OH=HO2k=4.00E‐134.00E‐13

84ALD2+O=C2O3+OHk=1.80E‐11exp(‐1100/T)4.49E‐13

85ALD2+OH=C2O3k=5.60E‐12exp(270/T)1.39E‐11

86ALD2+NO3=C2O3+HNO3k=1.40E‐12exp(‐1900/T)2.38E‐15

87ALD2=MEO2+CO+HO2Photolysis1.76E‐6

88C2O3+NO=MEO2+NO2k=8.10E‐12exp(270/T)2.00E‐11

89C2O3+NO2=PANFalloff:F=0.3;n=1

k(0)=2.70E‐28(T/300)^‐7.1

k(inf)=1.20E‐11(T/300)^‐0.9

1.05E‐11

90PAN=C2O3+NO2Falloff:F=0.3;n=1

k(0)=4.90E‐3exp(‐12100/T)

k(inf)=5.40E+16exp(‐13830/T)

3.31E‐4

91PAN=C2O3+NO2Photolysis3.47E‐7

92C2O3+HO2=0.8PACD+0.2AACD+0.2

O3

k=4.30E‐13exp(1040/T)1.41E‐11

93C2O3+MEO2=0.9MEO2+0.9HO2+

FORM+0.1AACD

k=2.00E‐12exp(500/T)1.07E‐11

94C2O3+XO2=0.9MEO2+0.1AACDk=4.40E‐13exp(1070/T)1.60E‐11

95C2O3+C2O3=2MEO2k=2.90E‐12exp(500/T)1.55E‐11

96PACD+OH=C2O3k=4.00E‐13exp(200/T)7.83E‐13

97PACD=MEO2+OHPhotolysis0.00E+0

March2016CAMxUser’sGuideVersion6.3

AppendixC:Mechanism6–CB05

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

NumberReactantsandProductsRateConstantExpressionk298

98AACD+OH=MEO2k=4.00E‐13exp(200/T)7.83E‐13

99ALDX+O=CXO3+OHk=1.30E‐11exp(‐870/T)7.02E‐13

100ALDX+OH=CXO3k=5.10E‐12exp(405/T)1.99E‐11

101ALDX+NO3=CXO3+HNO3k=6.50E‐156.50E‐15

102ALDX=MEO2+CO+HO2Photolysis6.96E‐6

103CXO3+NO=ALD2+NO2+HO2+XO2k=6.70E‐12exp(340/T)2.10E‐11

104CXO3+NO2=PANXFalloff:F=0.3;n=1

k(0)=2.70E‐28(T/300)^‐7.1

k(inf)=1.20E‐11(T/300)^‐0.9

1.05E‐11

105PANX=CXO3+NO2Falloff:F=0.3;n=1

k(0)=4.90E‐3exp(‐12100/T)

k(inf)=5.40E+16exp(‐13830/T)

3.31E‐4

106PANX=CXO3+NO2Photolysis3.47E‐7

107PANX+OH=ALD2+NO2k=3.00E‐133.00E‐13

108CXO3+HO2=0.8PACD+0.2AACD+0.2

O3

k=4.30E‐13exp(1040/T)1.41E‐11

109CXO3+MEO2=0.9ALD2+0.9XO2+HO2

+0.1AACD+0.1FORM

k=2.00E‐12exp(500/T)1.07E‐11

110CXO3+XO2=0.9ALD2+0.1AACDk=4.40E‐13exp(1070/T)1.60E‐11

111CXO3+CXO3=2ALD2+2XO2+2HO2k=2.90E‐12exp(500/T)1.55E‐11

112CXO3+C2O3=MEO2+XO2+HO2+ALD2k=2.90E‐12exp(500/T)1.55E‐11

113OH+ETHA=0.991ALD2+0.991XO2+

0.009XO2N+HO2

k=8.70E‐12exp(‐1070/T)2.40E‐13

114OH+ETOH=HO2+0.9ALD2+0.05ALDX+

0.1FORM+0.1XO2

k=6.90E‐12exp(‐230/T)3.19E‐12

115PAR+OH=0.87XO2+0.13XO2N+0.11

HO2+0.06ALD2‐0.11PAR+0.76ROR+

0.05ALDX

k=8.10E‐138.10E‐13

116ROR=0.96XO2+0.6ALD2+0.94HO2‐2.1

PAR+0.04XO2N+0.02ROR+0.5ALDX

k=1.00E+15exp(‐8000/T)2.19E+3

117ROR=HO2k=1.60E+31.60E+3

118ROR+NO2=NTRk=1.50E‐111.50E‐11

119O+OLE=0.2ALD2+0.3ALDX+0.3HO2+

0.2XO2+0.2CO+0.2FORM+0.01XO2N

+0.2PAR+0.1OH

k=1.00E‐11exp(‐280/T)3.91E‐12

120OH+OLE=0.8FORM+0.33ALD2+0.62

ALDX+0.8XO2+0.95HO2‐0.7PAR

k=3.20E‐113.20E‐11

121O3+OLE=0.18ALD2+0.74FORM+0.32

ALDX+0.22XO2+0.1OH+0.33CO+0.44

HO2‐1PAR

k=6.50E‐15exp(‐1900/T)1.11E‐17

122NO3+OLE=NO2+FORM+0.91XO2+

0.09XO2N+0.56ALDX+0.35ALD2‐1PAR

k=7.00E‐13exp(‐2160/T)4.98E‐16

123O+ETH=FORM+1.7HO2+CO+0.7XO2

+0.3OH

k=1.04E‐11exp(‐792/T)7.29E‐13

124OH+ETH=XO2+1.56FORM+0.22ALDX

+HO2

Falloff:F=0.6;n=1

k(0)=1.00E‐28(T/300)^‐0.8

k(inf)=8.80E‐12

8.15E‐12

125O3+ETH=FORM+0.63CO+0.13HO2+

0.13OH+0.37FACD

k=1.20E‐14exp(‐2630/T)1.76E‐18

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NumberReactantsandProductsRateConstantExpressionk298

126NO3+ETH=NO2+XO2+2FORMk=3.30E‐12exp(‐2880/T)2.10E‐16

127IOLE+O=1.24ALD2+0.66ALDX+0.1

HO2+0.1XO2+0.1CO+0.1PAR

k=2.30E‐112.30E‐11

128IOLE+OH=1.3ALD2+0.7ALDX+HO2+

XO2

k=1.00E‐11exp(550/T)6.33E‐11

129IOLE+O3=0.65ALD2+0.35ALDX+0.25

FORM+0.25CO+0.5O+0.5OH+0.5HO2

k=8.40E‐15exp(‐1100/T)2.09E‐16

130IOLE+NO3=1.18ALD2+0.64ALDX+HO2

+NO2

k=9.60E‐13exp(‐270/T)3.88E‐13

131TOL+OH=0.44HO2+0.08XO2+0.36

CRES+0.56TO2

k=1.80E‐12exp(355/T)5.92E‐12

132TO2+NO=0.9NO2+0.9HO2+0.9OPEN

+0.1NTR

k=8.10E‐128.10E‐12

133TO2=CRES+HO2k=4.20E+04.20E+0

134OH+CRES=0.4CRO+0.6XO2+0.6HO2+

0.3OPEN

k=4.10E‐114.10E‐11

135CRES+NO3=CRO+HNO3k=2.20E‐112.20E‐11

136CRO+NO2=NTRk=1.40E‐111.40E‐11

137CRO+HO2=CRESk=5.50E‐125.50E‐12

138OPEN=C2O3+HO2+COPhotolysis1.26E‐4

139OPEN+OH=XO2+2CO+2HO2+C2O3+

FORM

k=3.00E‐113.00E‐11

140OPEN+O3=0.03ALDX+0.62C2O3+0.7

FORM+0.03XO2+0.69CO+0.08OH+

0.76HO2+0.2MGLY

k=5.40E‐17exp(‐500/T)1.01E‐17

141OH+XYL=0.7HO2+0.5XO2+0.2CRES+

0.8MGLY+1.1PAR+0.3TO2

k=1.70E‐11exp(116/T)2.51E‐11

142OH+MGLY=XO2+C2O3k=1.70E‐111.70E‐11

143MGLY=C2O3+HO2+COPhotolysis1.54E‐4

144O+ISOP=0.75ISPD+0.5FORM+0.25

XO2+0.25HO2+0.25CXO3+0.25PAR

k=3.60E‐113.60E‐11

145OH+ISOP=0.912ISPD+0.629FORM+

0.991XO2+0.912HO2+0.088XO2N

k=2.54E‐11exp(407.6/T)9.97E‐11

146O3+ISOP=0.65ISPD+0.6FORM+0.2

XO2+0.066HO2+0.266OH+0.2CXO3+

0.15ALDX+0.35PAR+0.066CO

k=7.86E‐15exp(‐1912/T)1.29E‐17

147NO3+ISOP=0.2ISPD+0.8NTR+XO2+

0.8HO2+0.2NO2+0.8ALDX+2.4PAR

k=3.03E‐12exp(‐448/T)6.74E‐13

148NO2+ISOP=0.2ISPD+0.8NTR+XO2+

0.8HO2+0.2NO+0.8ALDX+2.4PAR

k=1.50E‐191.50E‐19

149OH+ISPD=1.565PAR+0.167FORM+

0.713XO2+0.503HO2+0.334CO+0.168

MGLY+0.252ALD2+0.21C2O3+0.25

CXO3+0.12ALDX

k=3.36E‐113.36E‐11

150O3+ISPD=0.114C2O3+0.15FORM+

0.85MGLY+0.154HO2+0.268OH+0.064

XO2+0.02ALD2+0.36PAR+0.225CO

k=7.10E‐187.10E‐18

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NumberReactantsandProductsRateConstantExpressionk298

151NO3+ISPD=0.357ALDX+0.282FORM+

1.282PAR+0.925HO2+0.643CO+0.85

NTR+0.075CXO3+0.075XO2+0.15

HNO3

k=1.00E‐151.00E‐15

152ISPD=0.333CO+0.067ALD2+0.9FORM

+0.832PAR+1.033HO2+0.7XO2+0.967

C2O3

Photolysis1.11E‐6

153TERP+O=0.15ALDX+5.12PARk=3.60E‐113.60E‐11

154TERP+OH=0.75HO2+1.25XO2+0.25

XO2N+0.28FORM+1.66PAR+0.47ALDX

k=1.50E‐11exp(449/T)6.77E‐11

155TERP+O3=0.57OH+0.07HO2+0.76

XO2+0.18XO2N+0.24FORM+0.001CO

+7PAR+0.21ALDX+0.39CXO3

k=1.20E‐15exp(‐821/T)7.63E‐17

156TERP+NO3=0.47NO2+0.28HO2+1.03

XO2+0.25XO2N+0.47ALDX+0.53NTR

k=3.70E‐12exp(175/T)6.66E‐12

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AppendixD:Mechanism5–SAPRC07TC

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AppendixD

CAMxMechanism5:SAPRC07TCGas‐PhaseChemistry

TableD‐1.ReactionsandrateconstantsfortheSAPRC07TCmechanism.k300istherate

constantat300Kand1atmosphereusingunitsinmolecules/cm‐3and1/s.SeeTableD‐2for

speciesnames.SeeSection3.1ontemperatureandpressuredependencies.

NumberReactantsandProductsRateConstantExpression k300

1NO2=NO+O3PPhotolysis 6.37E‐3

2O3P+O2+M=O3k=5.68E‐34(T/300)^‐2.6 5.68E‐34

3O3P+O3= k=8.00E‐12exp(‐2060/T) 8.34E‐15

4O3P+NO=NO2Falloff:F=0.6;n=1

k(0)=9.00E‐32(T/300)^‐1.5

k(inf)=3.00E‐11

1.64E‐12

5O3P+NO2=NOk=5.50E‐12exp(188/T) 1.03E‐11

6O3P+NO2=NO3Falloff:F=0.6;n=1

k(0)=2.50E‐31(T/300)^‐1.8

k(inf)=2.20E‐11(T/300)^‐0.7

3.24E‐12

7O3+NO=NO2k=3.00E‐12exp(‐1500/T) 2.02E‐14

8O3+NO2=NO3k=1.40E‐13exp(‐2470/T) 3.72E‐17

9NO+NO3=2.NO2k=1.80E‐11exp(110/T) 2.60E‐11

10NO+NO+O2=2.NO2k=3.30E‐39exp(530/T) 1.93E‐38

11NO2+NO3=N2O5Falloff:F=0.35;n=1.33

k(0)=3.60E‐30(T/300)^‐4.1

k(inf)=1.90E‐12(T/300)^0.2

1.24E‐12

12N2O5=NO2+NO3Falloff:F=0.35;n=1.33

k(0)=1.30E‐3(T/300)^‐3.5exp(‐11000/T)

k(inf)=9.70E+14(T/300)^0.1exp(‐11080/T)

5.69E‐2

13N2O5+H2O=2.HNO3k=1.00E‐22 1.00E‐22

14N2O5+H2O+H2O=2.HNO3k=0.00E+0 0.00E+0

15NO2+NO3=NO+NO2k=4.50E‐14exp(‐1260/T) 6.75E‐16

16NO3=NOPhotolysis 1.98E‐2

17NO3=NO2+O3PPhotolysis 1.56E‐1

18O3=O1DPhotolysis 9.47E‐6

19O3=O3PPhotolysis 3.40E‐4

20O1D+H2O=2.OHk=1.63E‐10exp(60/T) 1.99E‐10

21O1D+M=O3Pk=2.38E‐11exp(96/T) 3.28E‐11

22OH+NO=HONOFalloff:F=0.6;n=1

k(0)=7.00E‐31(T/300)^‐2.6

k(inf)=3.60E‐11(T/300)^‐0.1

7.31E‐12

23HONO=OH+NOPhotolysis 9.88E‐4

24OH+HONO=NO2k=2.50E‐12exp(260/T) 5.95E‐12

25OH+NO2=HNO3Falloff:F=0.6;n=1

k(0)=1.80E‐30(T/300)^‐3

k(inf)=2.80E‐11

1.05E‐11

26OH+NO3=HO2+NO2k=2.00E‐11 2.00E‐11

27OH+HNO3=NO3k=k1+k3[M]/(1+k3[M]/k2)

k1=2.40E‐14exp(460/T)

k2=2.70E‐17exp(2199/T)

k3=6.50E‐34exp(1335/T)

1.51E‐13

28HNO3=OH+NO2Photolysis 2.55E‐7

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AppendixD:Mechanism5–SAPRC07TC

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NumberReactantsandProductsRateConstantExpression k300

29OH+CO=HO2+CO2k=k1+k2[M]

k1=1.44E‐13

k2=3.43E‐33

2.28E‐13

30OH+O3=HO2k=1.70E‐12exp(‐940/T) 7.41E‐14

31HO2+NO=OH+NO2k=3.60E‐12exp(270/T) 8.85E‐12

32HO2+NO2=PNAFalloff:F=0.6;n=1

k(0)=2.00E‐31(T/300)^‐3.4

k(inf)=2.90E‐12(T/300)^‐1.1

1.12E‐12

33PNA=HO2+NO2Falloff:F=0.6;n=1

k(0)=3.72E‐5(T/300)^‐2.4exp(‐10650/T)

k(inf)=5.42E+15(T/300)^‐2.3exp(‐11170/T)

1.07E‐1

34PNA=0.61HO2+0.61NO2+0.39OH+0.39

NO3

Photolysis 3.17E‐6

35PNA+OH=NO2 k=1.30E‐12exp(380/T) 4.61E‐12

36HO2+O3=OHk=2.03E‐16(

/300)^4.57exp(693/T)2.05E‐15

37HO2+HO2=H2O2k=k1+k2[M]

k1=2.20E‐13exp(600/T)

k2=1.90E‐33exp(980/T)

2.84E‐12

38HO2+HO2+H2O=H2O2k=k1+k2[M]

k1=3.08E‐34exp(2800/T)

k2=2.66E‐54exp(3180/T)

6.09E‐30

39NO3+HO2=0.8OH+0.8NO2+0.2HNO3 k=4.00E‐12 4.00E‐12

40NO3+NO3=2.NO2k=8.50E‐13exp(‐2450/T) 2.41E‐16

41H2O2=2.OHPhotolysis 3.78E‐6

42H2O2+OH=HO2k=1.80E‐12 1.80E‐12

43OH+HO2= k=4.80E‐11exp(250/T) 1.10E‐10

44OH+SO2=HO2+SULFFalloff:F=0.6;n=1

k(0)=3.30E‐31(T/300)^‐4.3

k(inf)=1.60E‐12

9.49E‐13

45OH+H2=HO2k=7.70E‐12exp(‐2100/T) 7.02E‐15

46MEO2+NO=NO2+HCHO+HO2 k=2.30E‐12exp(360/T) 7.64E‐12

47MEO2+HO2=COOHk=3.46E‐13(T/300)^0.36exp(780/T)4.66E‐12

48MEO2+HO2=HCHOk=3.34E‐14(T/300)^‐3.53exp(780/T)4.50E‐13

49MEO2+NO3=HCHO+HO2+NO2 k=1.30E‐12 1.30E‐12

50MEO2+MEO2=MEOH+HCHOk=6.39E‐14(T/300)^‐1.8exp(365/T)2.16E‐13

51MEO2+MEO2=2.HCHO+2.HO2 k=7.40E‐13exp(‐520/T) 1.31E‐13

52RO2C+NO=NO2k=2.60E‐12exp(380/T) 9.23E‐12

53RO2C+HO2= k=3.80E‐13exp(900/T) 7.63E‐12

54RO2C+NO3=NO2k=2.30E‐12 2.30E‐12

55RO2C+MEO2=0.5HO2+0.75HCHO+0.25

MEOH

k=2.00E‐13 2.00E‐13

56RO2C+RO2C= k=3.50E‐14 3.50E‐14

57RO2X+NO=XNk=k(52) 9.23E‐12

58RO2X+HO2= k=k(53) 7.63E‐12

59RO2X+NO3=NO2k=k(54) 2.30E‐12

60RO2X+MEO2=0.5HO2+0.75HCHO+0.25

MEOH

k=k(55) 2.00E‐13

61RO2X+RO2C= k=k(56) 3.50E‐14

62RO2X+RO2X= k=k(56) 3.50E‐14

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 253www.camx.com



NumberReactantsandProductsRateConstantExpression k300

63MCO3+NO2=PANFalloff:F=0.3;n=1.41

k(0)=2.70E‐28(T/300)^‐7.1

k(inf)=1.21E‐11(T/300)^‐0.9

9.38E‐12

64PAN=MCO3+NO2Falloff:F=0.3;n=1.41

k(0)=4.90E‐3exp(‐12100/T)

k(inf)=4.00E+16exp(‐13600/T)

6.27E‐4

65PAN=0.6MCO3+0.6NO2+0.4MEO2+0.4

CO2+0.4NO3

Photolysis 3.50E‐7

66MCO3+NO=MEO2+CO2+NO2 k=7.50E‐12exp(290/T) 1.97E‐11

67MCO3+HO2=0.7CO3H+0.3AACD+0.3O3 k=5.20E‐13exp(980/T) 1.36E‐11

68MCO3+NO3=MEO2+CO2+NO2 k=k(54) 2.30E‐12

69MCO3+MEO2=0.1AACD+HCHO+0.9HO2

+0.9MEO2+0.9CO2

k=2.00E‐12exp(500/T) 1.06E‐11

70MCO3+RO2C=MEO2+CO2k=4.40E‐13exp(1070/T) 1.56E‐11

71MCO3+RO2X=MEO2+CO2k=k(70) 1.56E‐11

72MCO3+MCO3=2.MEO2+2.CO2 k=2.90E‐12exp(500/T) 1.54E‐11

73RCO3+NO2=PAN2k=1.21E‐11(T/300)^‐1.07 1.21E‐11

74PAN2=RCO3+NO2k=8.30E+16exp(‐13940/T) 5.48E‐4

75PAN2=0.6RCO3+0.6NO2+0.4RO2C+0.4

XHO2+0.4YRPX+0.4XCCH+0.4CO2+0.4

NO3

Photolysis 3.50E‐7

76RCO3+NO=NO2+RO2C+XHO2+YRPX+

XCCH+CO2

k=6.70E‐12exp(340/T) 2.08E‐11

77RCO3+HO2=0.75RO3H+0.25PACD+0.25

O3

k=k(67) 1.36E‐11

78RCO3+NO3=NO2+RO2C+XHO2+YRPX+

XCCH+CO2

k=k(54) 2.30E‐12

79RCO3+MEO2=HCHO+HO2+RO2C+XHO2

+XCCH+YRPX+CO2

k=k(69) 1.06E‐11

80RCO3+RO2C=RO2C+XHO2+XCCH+YRPX+

CO2

k=k(70) 1.56E‐11

81RCO3+RO2X=RO2C+XHO2+XCCH+YRPX+

CO2

k=k(70) 1.56E‐11

82RCO3+MCO3=2.CO2+MEO2+RO2C+

XHO2+YRPX+XCCH

k=k(72) 1.54E‐11

83RCO3+RCO3=2.RO2C+2.XHO2+2.XCCH+

2.YRPX+2.CO2

k=k(72) 1.54E‐11

84BZC3+NO2=PBZNk=1.37E‐11 1.37E‐11

85PBZN=BZC3+NO2k=7.90E+16exp(‐14000/T) 4.27E‐4

86PBZN=0.6BZC3+0.6NO2+0.4CO2+0.4

BZO+0.4RO2C+0.4NO3

Photolysis 3.50E‐7

87BZC3+NO=NO2+CO2+BZO+RO2C k=k(76) 2.08E‐11

88BZC3+HO2=0.75RO3H+0.25PACD+0.25

O3+4.XC

k=k(67) 1.36E‐11

89BZC3+NO3=NO2+CO2+BZO+RO2C k =k(54) 2.30E‐12

90BZC3+MEO2=HCHO+HO2+RO2C+BZO+

CO2

k=k(69) 1.06E‐11

91BZC3+RO2C=RO2C+BZO+CO2 k=k(70) 1.56E‐11

92BZC3+RO2X=RO2C+BZO+CO2 k=k(70) 1.56E‐11

93BZC3+MCO3=2.CO2+MEO2+BZO+RO2C k=k(72) 1.54E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 254www.camx.com



NumberReactantsandProductsRateConstantExpression k300

94BZC3+RCO3=2.CO2+2.RO2C+XHO2+

YRPX+XCCH+BZO

k=k(72) 1.54E‐11

95BZC3+BZC3=2.BZO+2.RO2C+2.CO2 k=k(72) 1.54E‐11

96MAC3+NO2=MPANk=k(73) 1.21E‐11

97MPAN=MAC3+NO2k=1.60E+16exp(‐13486/T) 4.80E‐4

98MPAN=0.6MAC3+0.6NO2+0.4CO2+0.4

HCHO+0.4MCO3+0.4NO3

Photolysis 3.50E‐7

99MAC3+NO=NO2+CO2+HCHO+MCO3 k=k(76) 2.08E‐11

100MAC3+HO2=0.75RO3H+0.25PACD+0.25

O3+XC

k=k(67) 1.36E‐11

101MAC3+NO3=NO2+CO2+HCHO+MCO3 k=k(54) 2.30E‐12

102MAC3+MEO2=2.HCHO+HO2+CO2+

MCO3

k=k(69) 1.06E‐11

103MAC3+RO2C=CO2+HCHO+MCO3 k=k(70) 1.56E‐11

104MAC3+RO2X=CO2+HCHO+MCO3 k=k(70) 1.56E‐11

105MAC3+MCO3=2.CO2+MEO2+HCHO+

MCO3

k=k(72) 1.54E‐11

106MAC3+RCO3=HCHO+MCO3+RO2C+

XHO2+YRPX+XCCH+2.CO2

k=k(72) 1.54E‐11

107MAC3+BZC3=HCHO+MCO3+BZO+RO2C

+2.CO2

k=k(72) 1.54E‐11

108MAC3+MAC3=2.HCHO+2.MCO3+2.CO2 k=k(72) 1.54E‐11

109TBUO+NO2=RNO3‐2.XCk=2.40E‐11 2.40E‐11

110TBUO=ACET+MEO2k=7.50E+14exp(‐8152/T) 1.19E+3

111BZO+NO2=NPHEk=2.30E‐11exp(150/T) 3.79E‐11

112BZO+HO2=CRES‐1.XCk=k(53) 7.63E‐12

113BZO=CRES+RO2C+XHO2‐1.XC k=1.00E‐31.00E‐3

114XHO2+NO=NO+HO2k=k(52) 9.23E‐12

115XHO2+HO2=HO2k=k(53) 7.63E‐12

116XHO2+NO3=NO3+HO2k=k(54) 2.30E‐12

117XHO2+MEO2=MEO2+0.5HO2 k=k(55) 2.00E‐13

118XHO2+RO2C=RO2C+0.5HO2k=k(56) 3.50E‐14

119XHO2+RO2X=RO2X+0.5HO2k=k(56) 3.50E‐14

120XHO2+MCO3=MCO3+HO2k=k(70) 1.56E‐11

121XHO2+RCO3=RCO3+HO2k=k(70) 1.56E‐11

122XHO2+BZC3=BZC3+HO2k=k(70) 1.56E‐11

123XHO2+MAC3=MAC3+HO2k=k(70) 1.56E‐11

124XOH+NO=NO+OHk=k(52) 9.23E‐12

125XOH+HO2=HO2k=k(53) 7.63E‐12

126XOH+NO3=NO3+OHk=k(54) 2.30E‐12

127XOH+MEO2=MEO2+0.5OHk=k(55) 2.00E‐13

128XOH+RO2C=RO2C+0.5OHk=k(56) 3.50E‐14

129XOH+RO2X=RO2X+0.5OHk=k(56) 3.50E‐14

130XOH+MCO3=MCO3+OHk=k(70) 1.56E‐11

131XOH+RCO3=RCO3+OHk=k(70) 1.56E‐11

132XOH+BZC3=BZC3+OHk=k(70) 1.56E‐11

133XOH+MAC3=MAC3+OHk=k(70) 1.56E‐11

134XNO2+NO=NO+NO2k=k(52) 9.23E‐12

135XNO2+HO2=HO2+XNk=k(53) 7.63E‐12

136XNO2+NO3=NO3+NO2k=k(54) 2.30E‐12

137XNO2+MEO2=MEO2+0.5NO2+0.5XN k=k(55) 2.00E‐13

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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NumberReactantsandProductsRateConstantExpression k300

138XNO2+RO2C=RO2C+0.5NO2+0.5XN k=k(56) 3.50E‐14

139XNO2+RO2X=RO2X+0.5NO2+0.5XN k=k(56) 3.50E‐14

140XNO2+MCO3=MCO3+NO2k=k(70) 1.56E‐11

141XNO2+RCO3=RCO3+NO2k=k(70) 1.56E‐11

142XNO2+BZC3=BZC3+NO2k=k(70) 1.56E‐11

143XNO2+MAC3=MAC3+NO2k=k(70) 1.56E‐11

144XMEO+NO=NO+MEO2k=k(52) 9.23E‐12

145XMEO+HO2=HO2+XCk=k(53) 7.63E‐12

146XMEO+NO3=NO3+MEO2k=k(54) 2.30E‐12

147XMEO+MEO2=1.5MEO2+0.5XC k=k(55) 2.00E‐13

148XMEO+RO2C=RO2C+0.5MEO2+0.5XC k=k(56) 3.50E‐14

149XMEO+RO2X=RO2X+0.5MEO2+0.5XC k=k(56) 3.50E‐14

150XMEO+MCO3=MCO3+MEO2k=k(70) 1.56E‐11

151XMEO+RCO3=RCO3+MEO2k=k(70) 1.56E‐11

152XMEO+BZC3=BZC3+MEO2k=k(70) 1.56E‐11

153XMEO+MAC3=MAC3+MEO2k=k(70) 1.56E‐11

154XMC3+NO=NO+MCO3k=k(52) 9.23E‐12

155XMC3+HO2=HO2+2.XCk=k(53) 7.63E‐12

156XMC3+NO3=NO3+MCO3k=k(54) 2.30E‐12

157XMC3+MEO2=MEO2+0.5MCO3+XC k=k(55) 2.00E‐13

158XMC3+RO2C=RO2C+0.5MCO3+XC k=k(56) 3.50E‐14

159XMC3+RO2X=RO2X+0.5MCO3+XC k=k(56) 3.50E‐14

160XMC3+MCO3=2.MCO3k=k(70) 1.56E‐11

161XMC3+RCO3=RCO3+MCO3k=k(70) 1.56E‐11

162XMC3+BZC3=BZC3+MCO3k=k(70) 1.56E‐11

163XMC3+MAC3=MAC3+MCO3k=k(70) 1.56E‐11

164XRC3+NO=NO+RCO3k=k(52) 9.23E‐12

165XRC3+HO2=HO2+3.XCk=k(53) 7.63E‐12

166XRC3+NO3=NO3+RCO3k=k(54) 2.30E‐12

167XRC3+MEO2=MEO2+0.5RCO3+1.5XC k=k(55) 2.00E‐13

168XRC3+RO2C=RO2C+0.5RCO3 +1.5XC k=k(56) 3.50E‐14

169XRC3+RO2X=RO2X+0.5RCO3+1.5XC k=k(56) 3.50E‐14

170XRC3+MCO3=MCO3+RCO3k=k(70) 1.56E‐11

171XRC3+RCO3=2.RCO3k=k(70) 1.56E‐11

172XRC3+BZC3=BZC3+RCO3k=k(70) 1.56E‐11

173XRC3+MAC3=MAC3+RCO3k=k(70) 1.56E‐11

174XMA3+NO=NO+MAC3k=k(52) 9.23E‐12

175XMA3+HO2=HO2+4.XCk=k(53) 7.63E‐12

176XMA3+NO3=NO3+MAC3k=k(54) 2.30E‐12

177XMA3+MEO2=MEO2+0.5MAC3+2.XC k=k(55) 2.00E‐13

178XMA3+RO2C=RO2C+0.5MAC3+2.XC k=k(56) 3.50E‐14

179XMA3+RO2X=RO2X+0.5MAC3+2.XC k=k(56) 3.50E‐14

180XMA3+MCO3=MCO3+MAC3k=k(70) 1.56E‐11

181XMA3+RCO3=RCO3+MAC3k=k(70) 1.56E‐11

182XMA3+BZC3=BZC3+MAC3k=k(70) 1.56E‐11

183XMA3+MAC3=2.MAC3k=k(70) 1.56E‐11

184XTBU+NO=NO+TBUOk=k(52) 9.23E‐12

185XTBU+HO2=HO2+4.XCk=k(53) 7.63E‐12

186XTBU+NO3=NO3+TBUOk=k(54) 2.30E‐12

187XTBU+MEO2=MEO2+0.5TBUO+2.XC k=k(55) 2.00E‐13

188XTBU+RO2C=RO2C+0.5TBUO+2.XC k=k(56) 3.50E‐14

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 256www.camx.com

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NumberReactantsandProductsRateConstantExpression k300

189XTBU+RO2X=RO2X+0.5TBUO+2.XC k=k(56) 3.50E‐14

190XTBU+MCO3=MCO3+TBUOk=k(70) 1.56E‐11

191XTBU+RCO3=RCO3+TBUOk=k(70) 1.56E‐11

192XTBU+BZC3=BZC3+TBUOk=k(70) 1.56E‐11

193XTBU+MAC3=MAC3+TBUOk=k(70) 1.56E‐11

194XCO+NO=NO+COk=k(52) 9.23E‐12

195XCO+HO2=HO2+XCk=k(53) 7.63E‐12

196XCO+NO3=NO3+COk=k(54) 2.30E‐12

197XCO+MEO2=MEO2+0.5CO+0.5XC k=k(55) 2.00E‐13

198XCO+RO2C=RO2C+0.5CO+0.5XC k=k(56) 3.50E‐14

199XCO+RO2X=RO2X+0.5CO+0.5XC k=k(56) 3.50E‐14

200XCO+MCO3=MCO3+COk=k(70) 1.56E‐11

201XCO+RCO3=RCO3+COk=k(70) 1.56E‐11

202XCO+BZC3=BZC3+COk=k(70) 1.56E‐11

203XCO+MAC3=MAC3+COk=k(70) 1.56E‐11

204HCHO=2.HO2+COPhotolysis 1.78E‐5

205HCHO=COPhotolysis 2.38E‐5

206HCHO+OH=HO2+COk=5.40E‐12exp(135/T) 8.47E‐12

207HCHO+NO3=HNO3+HO2+CO k=2.00E‐12exp(‐2431/T) 6.05E‐16

208CCHO+OH=MCO3k=4.40E‐12exp(365/T) 1.49E‐11

209CCHO=CO+HO2+MEO2Photolysis 1.77E‐6

210CCHO+NO3=HNO3+MCO3k=1.40E‐12exp(‐1860/T) 2.84E‐15

211RCHO+OH=0.965RCO3+0.035RO2C+

0.035XHO2+0.035XCO+0.035XCCH+

0.035YRPX

k=5.10E‐12exp(405/T) 1.97E‐11

212RCHO=RO2C+XHO2+YRPX+XCCH+CO+

HO2

Photolysis 6.95E‐6

213RCHO+NO3=HNO3+RCO3k=1.40E‐12exp(‐1601/T) 6.74E‐15

214ACET+OH=RO2C+XMC3+XHCH+YRPX k=4.56E‐14(T/300)^3.65exp(429/T)1.91E‐13

215ACET=0.62MCO3+1.38MEO2+0.38CO Photolysis 1.04E‐7

216MEK+OH=0.967RO2C+0.039RO2X+0.039

ZRN3+0.376XHO2+0.51XMC3+0.074

XRC3+0.088XHCH+0.504XCCH+0.376

XRCH+YRPX+0.3XC

k=1.30E‐12(T/300)^2exp(‐25/T)1.20E‐12

217MEK=MCO3+RO2C+XHO2+XCCH+YRPX Photolysis 8.13E‐7

218MEOH+OH=HCHO+HO2k=2.85E‐12exp(‐345/T) 9.02E‐13

219FACD+OH=HO2+CO2k=4.50E‐13 4.50E‐13

220AACD+OH=0.509MEO2+0.491RO2C+

0.509CO2+0.491XHO2+0.491XMGL+

0.491YRPX‐0.491XC

k=4.20E‐14exp(855/T) 7.26E‐13

221PACD+OH=RO2C+XHO2+0.143CO2+

0.142XCCH+0.4XRCH+0.457XBAC+YRPX‐

0.455XC

k=1.20E‐12 1.20E‐12

222COOH+OH=0.3HCHO+0.3OH+0.7MEO2 k=3.80E‐12exp(200/T) 7.40E‐12

223COOH=HCHO+HO2+OHPhotolysis 2.72E‐6

224ROOH+OH=0.744OH+0.251RO2C+0.004

RO2X+0.004ZRN3+0.744RCHO+0.239

XHO2+0.012XOH+0.012XHCH+0.012

XCCH+0.205XRCH+0.034XPD2+0.256

YRPX‐0.115XC

k =2.50E‐11 2.50E‐11

225ROOH=RCHO+HO2+OHPhotolysis 2.72E‐6

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 257www.camx.com

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NumberReactantsandProductsRateConstantExpression k300

226R6PX+OH=0.84OH+0.222RO2C+0.029

RO2X+0.029ZRN3+0.84PRD2+0.09XHO2

+0.041XOH+0.02XCCH+0.075XRCH+

0.084XPD2+0.16YRPX+0.02XC

k=5.60E‐11 5.60E‐11

227R6PX=OH+0.142HO2+0.782RO2C+0.077

RO2X+0.077ZRN3+0.085RCHO+0.142

PRD2+0.782XHO2+0.026XCCH+0.058

XRCH+0.698XPD2+0.858Y6PX+0.017XC

Photolysis 2.72E‐6

228RAPX+OH=0.139OH+0.148HO2+0.589

RO2C+0.124RO2X+0.124ZRN3+0.074

PRD2+0.147MGLY+0.139IPRD+0.565

XHO2+0.024XOH+0.448XRCH+0.026XGLY

+0.03XMEK+0.252XMGL+0.073XAF1+

0.073XAF2+0.713Y6PX+2.674XC

k=1.41E‐10 1.41E‐10

229RAPX=OH+HO2+0.5GLY+0.5MGLY+0.5

AFG1+0.5AFG2+0.5XC

Photolysis 2.72E‐6

230GLY=2.CO+2.HO2Photolysis 7.88E‐5

231GLY=HCHO+COPhotolysis 2.23E‐5

232GLY+OH=0.63HO2+1.26CO+0.37RCO3‐

0.37XC

k=1.10E‐11 1.10E‐11

233GLY+NO3=HNO3+0.63HO2+1.26CO+

0.37RCO3‐0.37XC

k=2.80E‐12exp(‐2376/T) 1.02E‐15

234MGLY=HO2+CO+MCO3Photolysis 1.39E‐4

235MGLY+OH=CO+MCO3k=1.50E‐11 1.50E‐11

236MGLY+NO3=HNO3+CO+MCO3 k=1.40E‐12exp(‐1895/T) 2.53E‐15

237BACL=2.MCO3Photolysis 2.45E‐4

238CRES+OH=0.2BZO+0.8RO2C+0.8XHO2+

0.8Y6PX+0.25XMGL+5.05XC

k=1.70E‐12exp(950/T) 4.03E‐11

239CRES+NO3=HNO3+BZO+XCk=1.40E‐11 1.40E‐11

240NPHE+OH=BZO+XNk=3.50E‐12 3.50E‐12

241NPHE=HONO+6.XCPhotolysis 9.55E‐6

242NPHE=6.XC+XNPhotolysis 9.55E‐5

243BALD+OH=BZC3k=1.20E‐11 1.20E‐11

244BALD=7.XCPhotolysis 2.48E‐5

245BALD+NO3=HNO3+BZC3k=1.34E‐12exp(‐1860/T) 2.72E‐15

246AFG1+OH=0.217MAC3+0.723RO2C+0.06

RO2X+0.06ZRN3+0.521XHO2+0.201

XMC3+0.334XCO+0.407XRCH+0.129

XMEK+0.107XGLY+0.267XMGL+0.783

Y6PX+0.284XC

k=7.40E‐11 7.40E‐11

247AFG1+O3=0.826OH+0.522HO2+0.652

RO2C+0.522CO+0.174CO2+0.432GLY+

0.568MGLY+0.652XRC3+0.652XHCH+

0.652Y6PX‐0.872XC

k=9.66E‐18 9.66E‐18

248AFG1=1.023HO2+0.173MEO2+0.305

MCO3+0.5MAC3+0.695CO+0.195GLY+

0.305MGLY+0.217XC

Photolysis 3.07E‐3

249AFG2+OH=0.217MAC3+0.723RO2C+0.06

RO2X+0.06ZRN3+0.521XHO2+0.201

XMC3+0.334XCO+0.407XRCH+0.129

XMEK+0.107XGLY+0.267XMGL+0.783

Y6PX+0.284XC

k=7.40E‐11 7.40E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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NumberReactantsandProductsRateConstantExpression k300

250AFG2+O3=0.826OH+0.522HO2+0.652

RO2C+0.522CO+0.174CO2+0.432GLY+

0.568MGLY+0.652XRC3+0.652XHCH+

0.652Y6PX‐0.872XC

k=9.66E‐18 9.66E‐18

251AFG2=PRD2‐1.XCPhotolysis 3.07E‐3

252AFG3+OH=0.206MAC3+0.733RO2C+

0.117RO2X+0.117ZRN3+0.561XHO2+

0.117XMC3+0.114XCO+0.274XGLY+0.153

XMGL+0.019XBAC+0.195XAF1+0.195

XAF2+0.231XIPR+0.794Y6PX+0.938XC

k=9.35E‐11 9.35E‐11

253AFG3+O3=0.471OH+0.554HO2+0.013

MCO3+0.258RO2C+0.007RO2X+0.007

ZRN3+0.58CO+0.19CO2+0.366GLY+

0.184MGLY+0.35AFG1+0.35AFG2+0.139

AFG3+0.003MACR+0.004MVK+0.003

IPRD+0.095XHO2+0.163XRC3+0.163

XHCH+0.095XMGL+0.264Y6PX‐0.575XC

k=1.43E‐17 1.43E‐17

254MACR+OH=0.5MAC3+0.5RO2C+0.5

XHO2+0.416XCO+0.084XHCH+0.416

XMEK+0.084XMGL+0.5YRPX‐0.416XC

k=8.00E‐12exp(380/T) 2.84E‐11

255MACR+O3=0.208OH+0.108HO2+0.1

RO2C+0.45CO+0.117CO2+0.1HCHO+0.9

MGLY+0.333FACD+0.1XRC3+0.1XHCH+

0.1YRPX‐0.1XC

k=1.40E‐15exp(‐2100/T) 1.28E‐18

256MACR+NO3=0.5MAC3+0.5RO2C+0.5

HNO3+0.5XHO2+0.5XCO+0.5YRPX+1.5

XC+0.5XN

k=1.50E‐12exp(‐1815/T) 3.54E‐15

257MACR+O3P=RCHO+XCk=6.34E‐12 6.34E‐12

258MACR=0.33OH+0.67HO2+0.34MCO3+

0.33MAC3+0.33RO2C+0.67CO+0.34

HCHO+0.33XMC3+0.33XHCH+0.33YRPX

Photolysis 1.39E‐6

259MVK+OH=0.975RO2C+0.025RO2X+0.025

ZRN3+0.3XHO2+0.675XMC3+0.3XHCH+

0.675XGLD+0.3XMGL+YRPX‐0.05XC

k=2.60E‐12exp(610/T) 1.99E‐11

260MVK+O3=0.164OH+0.064HO2+0.05

RO2C+0.05XHO2+0.475CO+0.124CO2+

0.05HCHO+0.95MGLY+0.351FACD+0.05

XRC3+0.05XHCH+0.05YRPX‐0.05XC

k=8.50E‐16exp(‐1520/T) 5.36E‐18

261MVK+O3P=0.45RCHO+0.55MEK+0.45XC k=4.32E‐12 4.32E‐12

262MVK=0.4MEO2+0.6CO+0.6PRD2+0.4

MAC3‐2.2XC

Photolysis 5.25E‐7

263IPRD+OH=0.289MAC3+0.67RO2C+0.67

XHO2+0.041RO2X+0.041ZRN3+0.336XCO

+0.055XHCH+0.129XGLD+0.013XRCH+

0.15XMEK+0.332XPD2+0.15XGLY+0.174

XMGL‐0.504XC+0.711Y6PX

k=6.19E‐11 6.19E‐11

264IPRD+O3=0.285OH+0.4HO2+0.048 RO2C

+0.048XRC3+0.498CO+0.14CO2+0.124

HCHO+0.21MEK+0.023GLY+0.742MGLY+

0.1FACD+0.372PACD+0.047XGLD+0.001

XHCH+0.048Y6PX‐0.329XC

k=4.18E‐18 4.18E‐18

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 259www.camx.com

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NumberReactantsandProductsRateConstantExpression k300

265IPRD+NO3=0.15MAC3+0.15HNO3+0.799

RO2C+0.799XHO2+0.051RO2X+0.051

ZRN3+0.572XCO+0.227XHCH+0.218XRCH

+0.008XMGL+0.572XRN3+0.85Y6PX+

0.278XN‐0.815XC

k=1.00E‐13 1.00E‐13

266IPRD=1.233HO2+0.467MCO3+0.3RCO3+

1.233CO+0.3HCHO+0.467GLYD+0.233

MEK‐0.233XC

Photolysis 1.39E‐6

267PRD2+OH=0.472HO2+0.379XHO2+0.029

XMC3+0.049XRC3+0.473RO2C+0.071

RO2X+0.071ZRN3+0.002HCHO+0.211

XHCH+0.001CCHO+0.083XCCH+0.143

RCHO+0.402XRCH+0.115XMEK+0.329

PRD2+0.007XPD2+0.528Y6PX+0.877XC

k =1.55E‐11 1.55E‐11

268PRD2=0.913XHO2+0.4MCO3+0.6RCO3+

1.59RO2C+0.087RO2X+0.087ZRN3+0.303

XHCH+0.163XCCH+0.78XRCH+Y6PX‐

0.091XC

Photolysis 2.26E‐8

269RNO3+OH=0.189HO2+0.305XHO2+0.019

NO2+0.313XNO2+0.976RO2C+0.175

RO2X+0.175ZRN3+0.011XHCH+0.429

XCCH+0.001RCHO+0.036XRCH+0.004

XACE+0.01MEK+0.17XMEK+0.008PRD2+

0.031XPD2+0.189RNO3+0.305XRN3+

0.157YRPX+0.636Y6PX+0.174XN+0.04XC

k=7.20E‐12 7.20E‐12

270RNO3=0.344HO2+0.554XHO2+NO2+

0.721RO2C+0.102RO2X+0.102ZRN3+

0.074HCHO+0.061XHCH+0.214CCHO+

0.23XCCH+0.074RCHO+0.063XRCH+

0.008XACE+0.124MEK+0.083XMEK+0.19

PRD2+0.261XPD2+0.066YRPX+0.591Y6PX

+0.396XC

Photolysis 1.20E‐6

271GLYD+OH=MCO3k=k(208) 1.49E‐11

272GLYD=CO+2.HO2+HCHOPhotolysis 2.75E‐6

273GLYD+NO3=HNO3+MCO3k=k(210) 2.84E‐15

274ACRO+OH=0.25XHO2+0.75MAC3+0.25

RO2C+0.167XCO+0.083XHCH+0.167XCCH

+0.083XGLY+0.25YRPX‐0.75XC

k=1.99E‐11 1.99E‐11

275ACRO+O3=0.83HO2+0.33OH+1.005CO+

0.31CO2+0.5HCHO+0.185FACD+0.5GLY

k=1.40E‐15exp(‐2528/T) 3.07E‐19

276ACRO+NO3=0.031XHO2+0.967MAC3+

0.031RO2C+0.002RO2X+0.002ZRN3+

0.967HNO3+0.031XCO+0.031XRN3+

0.033YRPX+0.002XN‐1.097XC

k=1.18E‐15 1.18E‐15

277ACRO+O3P=RCHOk=2.37E‐12 2.37E‐12

278ACRO=1.066HO2+0.178OH+0.234MEO2

+0.33MAC3+1.188CO+0.102CO2+0.34

HCHO+0.05AACD‐0.284XC

Photolysis 1.28E‐6

279CO3H+OH=0.98MCO3+0.02RO2C+0.02

CO2+0.02XOH+0.02XHCH+0.02YRPX

k=5.28E‐12 5.28E‐12

280CO3H=MEO2+CO2+OHPhotolysis 3.60E‐7

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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

NumberReactantsandProductsRateConstantExpression k300

281RO3H+OH=0.806RCO3+0.194RO2C+

0.194YRPX+0.11CO2+0.11XOH+0.11

XCCH+0.084XHO2+0.084XRCH

k=6.42E‐12 6.42E‐12

282RO3H=XHO2+XCCH+YRPX+CO2+OH Photolysis 3.60E‐7

283XHCH+NO=NO+HCHOk=k(52) 9.23E‐12

284XHCH+HO2=HO2+XCk=k(53) 7.63E‐12

285XHCH+NO3=NO3+HCHOk=k(54) 2.30E‐12

286XHCH+MEO2=MEO2+0.5HCHO+0.5XC k=k(55) 2.00E‐13

287XHCH+RO2C=RO2C+0.5HCHO+0.5XC k=k(56) 3.50E‐14

288XHCH+RO2X=RO2X+0.5HCHO+0.5XC k=k(56) 3.50E‐14

289XHCH+MCO3=MCO3+HCHOk=k(70) 1.56E‐11

290XHCH+RCO3=RCO3+HCHOk=k(70) 1.56E‐11

291XHCH+BZC3=BZC3+HCHOk=k(70) 1.56E‐11

292XHCH+MAC3=MAC3+HCHOk=k(70) 1.56E‐11

293XCCH+NO=NO+CCHOk=k(52) 9.23E‐12

294XCCH+HO2=HO2+2.XCk=k(53) 7.63E‐12

295XCCH+NO3=NO3+CCHOk=k(54) 2.30E‐12

296XCCH+MEO2=MEO2+0.5CCHO+XC k=k(55) 2.00E‐13

297XCCH+RO2C=RO2C+0.5CCHO+XC k=k(56) 3.50E‐14

298XCCH+RO2X=RO2X+0.5CCHO+XC k=k(56) 3.50E‐14

299XCCH+MCO3=MCO3+CCHOk=k(70) 1.56E‐11

300XCCH+RCO3=RCO3+CCHOk=k(70) 1.56E‐11

301XCCH+BZC3=BZC3+CCHOk=k(70) 1.56E‐11

302XCCH+MAC3=MAC3+CCHOk=k(70) 1.56E‐11

303XRCH+NO=NO+RCHOk=k(52) 9.23E‐12

304XRCH+HO2=HO2+3.XCk=k(53) 7.63E‐12

305XRCH+NO3=NO3+RCHOk=k(54) 2.30E‐12

306XRCH+MEO2=MEO2+0.5RCHO+1.5XC k=k(55) 2.00E‐13

307XRCH+RO2C=RO2C+0.5RCHO+1.5XC k=k(56) 3.50E‐14

308XRCH+RO2X=RO2X+0.5RCHO+1.5XC k=k(56) 3.50E‐14

309XRCH+MCO3=MCO3+RCHOk=k(70) 1.56E‐11

310XRCH+RCO3=RCO3+RCHOk=k(70) 1.56E‐11

311XRCH+BZC3=BZC3+RCHOk=k(70) 1.56E‐11

312XRCH+MAC3=MAC3+RCHOk=k(70) 1.56E‐11

313XACE+NO=NO+ACETk=k(52) 9.23E‐12

314XACE+HO2=HO2+3.XCk=k(53) 7.63E‐12

315XACE+NO3=NO3+ACETk=k(54) 2.30E‐12

316XACE+MEO2=MEO2+0.5ACET+1.5XC k=k(55) 2.00E‐13

317XACE+RO2C=RO2C+0.5ACET+1.5XC k=k(56) 3.50E‐14

318XACE+RO2X=RO2X+0.5ACET+1.5XC k=k(56) 3.50E‐14

319XACE+MCO3=MCO3+ACETk=k(70) 1.56E‐11

320XACE+RCO3=RCO3+ACE

k=k(70) 1.56E‐11

321XACE+BZC3=BZC3+ACE

k=k(70) 1.56E‐11

322XACE+MAC3=MAC3+ACETk=k(70) 1.56E‐11

323XMEK+NO=NO+MEKk=k(52) 9.23E‐12

324XMEK+HO2=HO2+4.XCk=k(53) 7.63E‐12

325XMEK+NO3=NO3+MEKk=k(54) 2.30E‐12

326XMEK+MEO2=MEO2+0.5MEK+2.XC k=k(55) 2.00E‐13

327XMEK+RO2C=RO2C+0.5MEK+2.XC k=k(56) 3.50E‐14

328XMEK+RO2X=RO2X+0.5MEK+2.XC k=k(56) 3.50E‐14

329XMEK+MCO3=MCO3+MEKk=k(70) 1.56E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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

NumberReactantsandProductsRateConstantExpression k300

330XMEK+RCO3=RCO3+MEKk=k(70) 1.56E‐11

331XMEK+BZC3=BZC3+MEKk=k(70) 1.56E‐11

332XMEK+MAC3=MAC3+MEKk=k(70) 1.56E‐11

333XPD2+NO=NO+PRD2k=k(52) 9.23E‐12

334XPD2+HO2=HO2+6.XCk=k(53) 7.63E‐12

335XPD2+NO3=NO3+PRD2k=k(54) 2.30E‐12

336XPD2+MEO2=MEO2+0.5PRD2+3.XC k=k(55) 2.00E‐13

337XPD2+RO2C=RO2C+0.5PRD2+3.XC k=k(56) 3.50E‐14

338XPD2+RO2X=RO2X+0.5PRD2+3.XC k=k(56) 3.50E‐14

339XPD2+MCO3=MCO3+PRD2k=k(70) 1.56E‐11

340XPD2+RCO3=RCO3+PRD2k=k(70) 1.56E‐11

341XPD2+BZC3=BZC3+PRD2k=k(70) 1.56E‐11

342XPD2+MAC3=MAC3+PRD2k=k(70) 1.56E‐11

343XGLY+NO=NO+GLYk=k(52) 9.23E‐12

344XGLY+HO2=HO2+2.XCk=k(53) 7.63E‐12

345XGLY+NO3=NO3+GLYk=k(54) 2.30E‐12

346XGLY+MEO2=MEO2+0.5GLY+XC k=k(55) 2.00E‐13

347XGLY+RO2C=RO2C+0.5GLY+XC k=k(56) 3.50E‐14

348XGLY+RO2X=RO2X+0.5GLY+XC k=k(56) 3.50E‐14

349XGLY+MCO3=MCO3+GLYk=k(70) 1.56E‐11

350XGLY+RCO3=RCO3+GLYk=k(70) 1.56E‐11

351XGLY+BZC3=BZC3+GLYk=k(70) 1.56E‐11

352XGLY+MAC3=MAC3+GLYk=k(70) 1.56E‐11

353XMGL+NO=NO+MGLYk=k(52) 9.23E‐12

354XMGL+HO2=HO2+3.XCk=k(53) 7.63E‐12

355XMGL+NO3=NO3+MGLYk=k(54) 2.30E‐12

356XMGL+MEO2=MEO2+0.5MGLY+1.5XC k=k(55) 2.00E‐13

357XMGL+RO2C=RO2C+0.5MGLY+1.5XC k=k(56) 3.50E‐14

358XMGL+RO2X=RO2X+0.5MGLY+1.5XC k=k(56) 3.50E‐14

359XMGL+MCO3=MCO3+MGLYk=k(70) 1.56E‐11

360XMGL+RCO3=RCO3+MGLYk=k(70) 1.56E‐11

361XMGL+BZC3=BZC3+MGLYk=k(70) 1.56E‐11

362XMGL+MAC3=MAC3+MGLYk=k(70) 1.56E‐11

363XBAC+NO=NO+BACLk=k(52) 9.23E‐12

364XBAC+HO2=HO2+4.XCk=k(53) 7.63E‐12

365XBAC+NO3=NO3+BACLk=k(54) 2.30E‐12

366XBAC+MEO2=MEO2+0.5BACL+2.XC k=k(55) 2.00E‐13

367XBAC+RO2C=RO2C+0.5BACL+2.XC k=k(56) 3.50E‐14

368XBAC+RO2X=RO2X+0.5BACL+2.XC k=k(56) 3.50E‐14

369XBAC+MCO3=MCO3+BACLk=k(70) 1.56E‐11

370XBAC+RCO3=RCO3+BACLk=k(70) 1.56E‐11

371XBAC+BZC3=BZC3+BACLk=k(70) 1.56E‐11

372XBAC+MAC3=MAC3+BACLk=k(70) 1.56E‐11

373XBAL+NO=NO+BALDk=k(52) 9.23E‐12

374XBAL+HO2=HO2+7.XCk=k(53) 7.63E‐12

375XBAL+NO3=NO3+BALDk=k(54) 2.30E‐12

376XBAL+MEO2=MEO2+0.5BALD+3.5XC k=k(55) 2.00E‐13

377XBAL+RO2C=RO2C+0.5BALD+3.5XC k=k(56) 3.50E‐14

378XBAL+RO2X=RO2X+0.5BALD+3.5XC k=k(56) 3.50E‐14

379XBAL+MCO3=MCO3+BALDk=k(70) 1.56E‐11

380XBAL+RCO3=RCO3+BALDk=k(70) 1.56E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 262www.camx.com



NumberReactantsandProductsRateConstantExpression k300

381XBAL+BZC3=BZC3+BALDk=k(70) 1.56E‐11

382XBAL+MAC3=MAC3+BALDk=k(70) 1.56E‐11

383XAF1+NO=NO+AFG1k=k(52) 9.23E‐12

384XAF1+HO2=HO2+5.XCk=k(53) 7.63E‐12

385XAF1+NO3=NO3+AFG1k=k(54) 2.30E‐12

386XAF1+MEO2=MEO2+0.5AFG1+2.5XC k=k(55) 2.00E‐13

387XAF1+RO2C=RO2C+0.5AFG1+2.5XC k=k(56) 3.50E‐14

388XAF1+RO2X=RO2X+0.5AFG1+2.5XC k=k(56) 3.50E‐14

389XAF1+MCO3=MCO3+AFG1k=k(70) 1.56E‐11

390XAF1+RCO3=RCO3+AFG1k=k(70) 1.56E‐11

391XAF1+BZC3=BZC3+AFG1k=k(70) 1.56E‐11

392XAF1+MAC3=MAC3+AFG1k=k(70) 1.56E‐11

393XAF2+NO=NO+AFG2k=k(52) 9.23E‐12

394XAF2+HO2=HO2+5.XCk=k(53) 7.63E‐12

395XAF2+NO3=NO3+AFG2k=k(54) 2.30E‐12

396XAF2+MEO2=MEO2+0.5AFG2+2.5XC k=k(55) 2.00E‐13

397XAF2+RO2C=RO2C+0.5AFG2+2.5XC k=k(56) 3.50E‐14

398XAF2+RO2X=RO2X+0.5AFG2+2.5XC k=k(56) 3.50E‐14

399XAF2+MCO3=MCO3+AFG2k=k(70) 1.56E‐11

400XAF2+RCO3=RCO3+AFG2k=k(70) 1.56E‐11

401XAF2+BZC3=BZC3+AFG2k=k(70) 1.56E‐11

402XAF2+MAC3=MAC3+AFG2k=k(70) 1.56E‐11

403XAF3+NO=NO+AFG3k=k(52) 9.23E‐12

404XAF3+HO2=HO2+7.XCk=k(53) 7.63E‐12

405XAF3+NO3=NO3+AFG3k=k(54) 2.30E‐12

406XAF3+MEO2=MEO2+0.5AFG3+3.5XC k=k(55) 2.00E‐13

407XAF3+RO2C=RO2C+0.5AFG3+3.5XC k=k(56) 3.50E‐14

408XAF3+RO2X=RO2X+0.5AFG3+3.5XC k=k(56) 3.50E‐14

409XAF3+MCO3=MCO3+AFG3k=k(70) 1.56E‐11

410XAF3+RCO3=RCO3+AFG3k=k(70) 1.56E‐11

411XAF3+BZC3=BZC3+AFG3k=k(70) 1.56E‐11

412XAF3+MAC3=MAC3+AFG3k=k(70) 1.56E‐11

413XMAC+NO=NO+MACRk=k(52) 9.23E‐12

414XMAC+HO2=HO2+4.XCk=k(53) 7.63E‐12

415XMAC+NO3=NO3+MACRk=k(54) 2.30E‐12

416XMAC+MEO2=MEO2+0.5MACR+2.XC k=k(55) 2.00E‐13

417XMAC+RO2C=RO2C+0.5MACR+2.XC k=k(56) 3.50E‐14

418XMAC+RO2X=RO2X+0.5MACR+2.XC k=k(56) 3.50E‐14

419XMAC+MCO3=MCO3+MACRk=k(70) 1.56E‐11

420XMAC+RCO3=RCO3+MACRk=k(70) 1.56E‐11

421XMAC+BZC3=BZC3+MACRk=k(70) 1.56E‐11

422XMAC+MAC3=MAC3+MACRk=k(70) 1.56E‐11

423XMVK+NO=NO+MVKk=k(52) 9.23E‐12

424XMVK+HO2=HO2+4.XCk=k(53) 7.63E‐12

425XMVK+NO3=NO3+MVKk=k(54) 2.30E‐12

426XMVK+MEO2=MEO2+0.5MVK+2.XC k=k(55) 2.00E‐13

427XMVK+RO2C=RO2C+0.5MVK+2.XC k=k(56) 3.50E‐14

428XMVK+RO2X=RO2X+0.5MVK+2.XC k=k(56) 3.50E‐14

429XMVK+MCO3=MCO3+MVKk=k(70) 1.56E‐11

430XMVK+RCO3=RCO3+MVKk=k(70) 1.56E‐11

431XMVK+BZC3=BZC3+MVKk=k(70) 1.56E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 263www.camx.com

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NumberReactantsandProductsRateConstantExpression k300

432XMVK+MAC3=MAC3+MVKk=k(70) 1.56E‐11

433XIPR+NO=NO+IPRDk=k(52) 9.23E‐12

434XIPR+HO2=HO2+5.XCk=k(53) 7.63E‐12

435XIPR+NO3=NO3+IPRDk=k(54) 2.30E‐12

436XIPR+MEO2=MEO2+0.5IPRD+2.5XC k=k(55) 2.00E‐13

437XIPR+RO2C=RO2C+0.5IPRD+2.5XC k=k(56) 3.50E‐14

438XIPR+RO2X=RO2X+0.5IPRD+2.5XC k=k(56) 3.50E‐14

439XIPR+MCO3=MCO3+IPRDk=k(70) 1.56E‐11

440XIPR+RCO3=RCO3+IPRDk=k(70) 1.56E‐11

441XIPR+BZC3=BZC3+IPRDk=k(70) 1.56E‐11

442XIPR+MAC3=MAC3+IPRDk=k(70) 1.56E‐11

443XRN3+NO=NO+RNO3k=k(52) 9.23E‐12

444XRN3+HO2=HO2+6.XC+XNk=k(53) 7.63E‐12

445XRN3+NO3=NO3+RNO3k=k(54) 2.30E‐12

446XRN3+MEO2=MEO2+0.5RNO3+0.5XN+

3.XC

k=k(55) 2.00E‐13

447XRN3+RO2C=RO2C+0.5RNO3 +0.5XN+3.

XC

k=k(56) 3.50E‐14

448XRN3+RO2X=RO2X+0.5RNO3+0.5XN+3.

XC

k=k(56) 3.50E‐14

449XRN3+MCO3=MCO3+RNO3k=k(70) 1.56E‐11

450XRN3+RCO3=RCO3+RNO3k=k(70) 1.56E‐11

451XRN3+BZC3=BZC3+RNO3k=k(70) 1.56E‐11

452XRN3+MAC3=MAC3+RNO3k=k(70) 1.56E‐11

453YRPX+NO=NOk=k(52) 9.23E‐12

454YRPX+HO2=HO2+ROOH‐3.XC k=k(53) 7.63E‐12

455YRPX+NO3=NO3k=k(54) 2.30E‐12

456YRPX+MEO2=MEO2+0.5MEK‐ 2.XC k=k(55) 2.00E‐13

457YRPX+RO2C=RO2C+0.5MEK‐ 2.XC k=k(56) 3.50E‐14

458YRPX+RO2X=RO2X+0.5MEK‐ 2.XC k=k(56) 3.50E‐14

459YRPX+MCO3=MCO3k=k(70) 1.56E‐11

460YRPX+RCO3=RCO3k=k(70) 1.56E‐11

461YRPX+BZC3=BZC3k=k(70) 1.56E‐11

462YRPX+MAC3=MAC3k=k(70) 1.56E‐11

463Y6PX+NO=NOk=k(52) 9.23E‐12

464Y6PX+HO2=HO2+R6PX‐6.XC k=k(53) 7.63E‐12

465Y6PX+NO3=NO3k=k(54) 2.30E‐12

466Y6PX+MEO2=MEO2+0.5PRD2‐ 3.XC k=k(55) 2.00E‐13

467Y6PX+RO2C=RO2C+0.5PRD2‐ 3.XC k=k(56) 3.50E‐14

468Y6PX+RO2X=RO2X+0.5PRD2‐ 3.XC k=k(56) 3.50E‐14

469Y6PX+MCO3=MCO3k=k(70) 1.56E‐11

470Y6PX+RCO3=RCO3k=k(70) 1.56E‐11

471Y6PX+BZC3=BZC3k=k(70) 1.56E‐11

472Y6PX+MAC3=MAC3k=k(70) 1.56E‐11

473YAPX+NO=NOk=k(52) 9.23E‐12

474YAPX+HO2=HO2+RAPX‐8.XC k=k(53) 7.63E‐12

475YAPX+NO3=NO3k=k(54) 2.30E‐12

476YAPX+MEO2=MEO2+0.5PRD2‐ 3.XC k=k(55) 2.00E‐13

477YAPX+RO2C=RO2C+0.5PRD2‐ 3.XC k=k(56) 3.50E‐14

478YAPX+RO2X=RO2X+0.5PRD2‐ 3.XC k=k(56) 3.50E‐14

479YAPX+MCO3=MCO3k=k(70) 1.56E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 264www.camx.com



NumberReactantsandProductsRateConstantExpression k300

480YAPX+RCO3=RCO3k=k(70) 1.56E‐11

481YAPX+BZC3=BZC3k=k(70) 1.56E‐11

482YAPX+MAC3=MAC3k=k(70) 1.56E‐11

483ZRN3+NO=NO+RNO3‐1.XNk=k(52) 9.23E‐12

484ZRN3+HO2=HO2+6.XCk=k(53) 7.63E‐12

485ZRN3+NO3=NO3+PRD2+HO2 k=k(54) 2.30E‐12

486ZRN3+MEO2=MEO2+0.5PRD2+0.5HO2+

3.XC

k=k(55) 2.00E‐13

487ZRN3+RO2C=RO2C+0.5PRD2+0.5HO2+

3.XC

k=k(56) 3.50E‐14

488ZRN3+RO2X=RO2X+0.5PRD2+0.5HO2+

3.XC

k=k(56) 3.50E‐14

489ZRN3+MCO3=MCO3+PRD2+HO2 k=k(70) 1.56E‐11

490ZRN3+RCO3=RCO3+PRD2+HO2 k=k(70) 1.56E‐11

491ZRN3+BZC3=BZC3+PRD2+HO2 k=k(70) 1.56E‐11

492ZRN3+MAC3=MAC3+PRD2+HO2 k=k(70) 1.56E‐11

493XGLD+NO=NO+GLYDk=k(52) 9.23E‐12

494XGLD+HO2=HO2+2.XCk=k(53) 7.63E‐12

495XGLD+NO3=NO3+GLYDk=k(54) 2.30E‐12

496XGLD+MEO2=MEO2+0.5GLYD+XC k=k(55) 2.00E‐13

497XGLD+RO2C=RO2C+0.5GLYD+XC k=k(56) 3.50E‐14

498XGLD+RO2X=RO2X+0.5GLYD+XC k=k(56) 3.50E‐14

499XGLD+MCO3=MCO3+GLYDk=k(70) 1.56E‐11

500XGLD+RCO3=RCO3+GLYDk=k(70) 1.56E‐11

501XGLD+BZC3=BZC3+GLYDk=k(70) 1.56E‐11

502XGLD+MAC3=MAC3+GLYDk=k(70) 1.56E‐11

503XACR+NO=NO+ACROk=k(52) 9.23E‐12

504XACR+HO2=HO2+3.XCk=k(53) 7.63E‐12

505XACR+NO3=NO3+ACROk=k(54) 2.30E‐12

506XACR+MEO2=MEO2+0.5ACRO+1.5XC k=k(55) 2.00E‐13

507XACR+RO2C=RO2C+0.5ACRO+1.5XC k=k(56) 3.50E‐14

508XACR+RO2X=RO2X+0.5ACRO+1.5XC k=k(56) 3.50E‐14

509XACR+MCO3=MCO3+ACROk=k(70) 1.56E‐11

510XACR+RCO3=RCO3+ACROk=k(70) 1.56E‐11

511XACR+BZC3=BZC3+ACROk=k(70) 1.56E‐11

512XACR+MAC3=MAC3+ACROk=k(70) 1.56E‐11

513CH4+OH=MEO2k=1.85E‐12exp(‐1690/T) 6.62E‐15

514ETHE+OH=XHO2+RO2C+1.61XHCH+

0.195XGLD+YRPX

Falloff:F=0.6;n=1

k(0)=1.00E‐28(T/300)^‐4.5

k(inf)=8.80E‐12(T/300)^‐0.85

8.15E‐12

515ETHE+O3=0.16HO2+0.16OH+0.51CO+

0.12CO2+HCHO+0.37FACD

k=9.14E‐15exp(‐2580/T) 1.68E‐18

516ETHE+NO3=XHO2+RO2C+XRCH+YRPX+

XN‐1.XC

k=3.30E‐12(T/300)^2exp(‐2880/T)2.24E‐16

517ETHE+O3P=0.8HO2+0.29XHO2+0.51

MEO2+0.29RO2C+0.51CO+0.278XCO+

0.278XHCH+0.1CCHO+0.012XGLY+0.29

YRPX+0.2XC

k=1.07E‐11exp(‐800/T) 7.43E‐13

518PRPE+OH=0.984XHO2+0.984RO2C+

0.016RO2X+0.016ZRN3+0.984XHCH+

0.984XCCH+YRPX‐0.048XC

k=4.85E‐12exp(504/T) 2.60E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 265www.camx.com



NumberReactantsandProductsRateConstantExpression k300

519PRPE+O3=0.165HO2+0.35OH+0.355

MEO2+0.525CO+0.215CO2+0.5HCHO+

0.5CCHO+0.185FACD+0.075AACD+0.07

XC

k=5.51E‐15exp(‐1878/T) 1.05E‐17

520PRPE+NO3=0.949XHO2+0.949RO2C+

0.051RO2X+0.051ZRN3+YRPX+XN+2.694

XC

k=4.59E‐13exp(‐1156/T) 9.73E‐15

521PRPE+O3P=0.45RCHO+0.55MEK‐ 0.55XC k=1.02E‐11exp(‐280/T) 4.01E‐12

522BD13+OH=0.951XHO2+1.189RO2C+

0.049RO2X+0.049ZRN3+0.708XHCH+0.48

XACR+0.471XIPR+YRPX‐0.797XC

k=1.48E‐11exp(448/T) 6.59E‐11

523BD13+O3=0.08HO2+0.08OH+0.255CO+

0.185CO2+0.5HCHO+0.185FACD+0.5

ACRO+0.375MVK+0.125PRD2‐0.875XC

k=1.34E‐14exp(‐2283/T) 6.64E‐18

524BD13+NO3=0.815XHO2+0.12XNO2+

1.055RO2C+0.065RO2X+0.065ZRN3+

0.115XHCH+0.46XMVK+0.12XIPR+0.355

XRN3+YRPX+0.525XN‐1.075XC

k=1.00E‐13 1.00E‐13

525BD13+O3P=0.25HO2+0.117XHO2+0.118

XMA3+0.235RO2C+0.015RO2X+0.015

ZRN3+0.115XCO+0.115XACR+0.001XAF1

+0.001XAF2+0.75PRD2+0.25YRPX‐1.532

XC

k=2.26E‐11exp(‐40/T) 1.98E‐11

526ISOP+OH=0.907XHO2+0.986RO2C+0.093

RO2X+0.093ZRN3+0.624XHCH+0.23

XMAC+0.32XMVK+0.357XIPR+Y6PX‐

0.167XC

k=2.54E‐11exp(410/T) 9.96E‐11

527ISOP+O3=0.066HO2+0.266OH+0.192

XMA3+0.192RO2C+0.008RO2X+0.008

ZRN3+0.275CO+0.122CO2+0.4HCHO+

0.192XHCH+0.204FACD+0.39MACR+0.16

MVK+0.15IPRD+0.1PRD2+0.2Y6PX‐

0.559XC

k=7.86E‐15exp(‐1912/T) 1.34E‐17

528ISOP+NO3=0.749XHO2+0.187XNO2+

0.936RO2C+0.064RO2X+0.064ZRN3+

0.936XIPR+Y6PX+0.813XN‐0.064XC

k=3.03E‐12exp(‐448/T) 6.81E‐13

529ISOP+O3P=0.25MEO2+0.24XMA3+0.24

RO2C+0.01RO2X+0.01ZRN3+0.24XHCH+

0.75PRD2+0.25Y6PX‐1.01XC

k=3.50E‐11 3.50E‐11

530APIN+OH=0.799XHO2+0.004XRC3+1.042

RO2C+0.197RO2X+0.197ZRN3+0.002XCO

+0.022XHCH+0.776XRCH+0.034XACE+

0.02XMGL+0.023XBAC+Y6PX+6.2XC

k=1.21E‐11exp(436/T) 5.18E‐11

531APIN+O3=0.009HO2+0.102XHO2+0.728

OH+0.001XMC3+0.297XRC3+1.511RO2C

+0.337RO2X+0.337ZRN3+0.029CO+

0.051XCO+0.017CO2+0.344XHCH+0.24

XRCH+0.345XACE+0.008MEK+0.002XGLY

+0.081XBAC+0.255PRD2+0.737Y6PX+

2.999XC

k=5.00E‐16exp(‐530/T) 8.55E‐17

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 266www.camx.com



NumberReactantsandProductsRateConstantExpression k300

532APIN+NO3=0.056XHO2+0.643XNO2+

0.007XRC3+1.05RO2C+0.293RO2X+0.293

ZRN3+0.005XCO+0.007XHCH+0.684XRCH

+0.069XACE+0.002XMGL+0.056XRN3+

Y6PX+0.301XN+5.608XC

k=1.19E‐12exp(490/T) 6.09E‐12

533APIN+O3P=PRD2+4.XCk=3.20E‐11 3.20E‐11

534ACYE+OH=0.3HO2+0.7OH+0.3CO+0.3

FACD+0.7GLY

Falloff:F=0.6;n=1

k(0)=5.50E‐30(T/300)^‐2

k(inf)=8.30E‐13

7.56E‐13

535ACYE+O3=1.5HO2+0.5OH+1.5CO+0.5

CO2

k=1.00E‐14exp(‐4100/T) 1.16E‐20

536BENZ+OH=0.57HO2+0.29XHO2+0.116

OH+0.29RO2C+0.024RO2X+0.024ZRN3+

0.29XGLY+0.57CRES+0.029XAF1+0.261

XAF2+0.116AFG3+0.314YAPX‐0.976XC

k=2.33E‐12exp(‐193/T) 1.22E‐12

537TOLU+OH=0.181HO2+0.454XHO2+0.312

OH+0.454RO2C+0.054RO2X+0.054ZRN3

+0.238XGLY+0.151XMGL+0.181CRES+

0.065XBAL+0.195XAF1+0.195XAF2+0.312

AFG3+0.073Y6PX+0.435YAPX‐0.109XC

k=1.81E‐12exp(338/T) 5.58E‐12

538MXYL+OH=0.159HO2+0.52XHO2+0.239

OH+0.52RO2C+0.082RO2X+0.082ZRN3+

0.1XGLY+0.38XMGL+0.159CRES+0.041

XBAL+0.336XAF1+0.144XAF2+0.239AFG3

+0.047Y6PX+0.555YAPX+0.695XC

k=2.31E‐11 2.31E‐11

539OXYL+OH=0.161HO2+0.554XHO2+0.198

OH+0.554RO2C+0.087RO2X+0.087ZRN3

+0.084XGLY+0.238XMGL+0.185XBAC+

0.161CRES+0.047XBAL+0.253XAF1+0.253

XAF2+0.198AFG3+0.055Y6PX+0.586YAPX

+0.484XC

k=1.36E‐11 1.36E‐11

540PXYL+OH=0.159HO2+0.487XHO2+0.278

OH+0.487RO2C+0.076RO2X+0.076ZRN3

+0.286XGLY+0.112XMGL+0.159CRES+

0.088XBAL+0.045XAF1+0.067XAF2+0.278

AFG3+0.286XAF3+0.102Y6PX+0.461YAPX

+0.399XC

k=1.43E‐11 1.43E‐11

541B124+OH=0.022HO2+0.627XHO2+0.23

OH+0.627RO2C+0.121RO2X+0.121ZRN3

+0.074XGLY+0.405XMGL+0.112XBAC+

0.022CRES+0.036XBAL+0.088XAF1+0.352

XAF2+0.23AFG3+0.151XAF3+0.043Y6PX

+0.705YAPX+1.19XC

k=3.25E‐11 3.25E‐11

542ETOH+OH=0.95HO2+0.05XHO2+0.05

RO2C+0.081XHCH+0.95CCHO+0.01XGLD

+0.05YRPX‐0.001XC

k=5.49E‐13(T/300)^2exp(530/T)3.21E‐12

543ALK1+OH=XHO2+RO2C+XCCH+YRPX k=1.34E‐12(T/300)^2exp(‐499/T)2.54E‐13

544ALK2+OH=0.965XHO2+0.965RO2C+

0.035RO2X+0.035ZRN3+0.261XRCH+

0.704XACE+YRPX‐0.105XC

k=1.49E‐12(T/300)^2exp(‐87/T)1.11E‐12

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 267www.camx.com



NumberReactantsandProductsRateConstantExpression k300

545ALK3+OH=0.695XHO2+0.236XTBU+

1.253RO2C+0.07RO2X+0.07ZRN3+0.026

XHCH+0.445XCCH+0.122XRCH+0.024

XACE+0.332XMEK+0.983YRPX+0.017

Y6PX‐0.046XC

k=1.51E‐12exp(126/T) 2.30E‐12

546ALK4+OH=0.83XHO2+0.01XMEO+0.011

XMC3+1.763RO2C+0.149RO2X+0.149

ZRN3+0.002XCO+0.029XHCH+0.438XCCH

+0.236XRCH+0.426XACE+0.106XMEK+

0.146XPD2+Y6PX‐0.119XC

k=3.75E‐12exp(44/T) 4.34E‐12

547ALK5+OH=0.647XHO2+1.605RO2C+

0.353RO2X+0.353ZRN3+0.04XHCH+0.106

XCCH+0.209XRCH+0.071XACE+0.086

XMEK+0.407XPD2+Y6PX+2.004XC

k=2.70E‐12exp(374/T) 9.39E‐12

548OLE1+OH=0.871XHO2+0.001XMEO+

1.202RO2C+0.128RO2X+0.128ZRN3+

0.582XHCH+0.01XCCH+0.007XGLD+0.666

XRCH+0.007XACE+0.036XACR+0.001

XMAC+0.012XMVK+0.009XIPR+0.168

XPD2+0.169YRPX+0.831Y6PX+0.383XC

k=6.72E‐12exp(501/T) 3.57E‐11

549OLE1+O3=0.095HO2+0.057XHO2+0.128

OH+0.09RO2C+0.005RO2X+0.005ZRN3+

0.303CO+0.088CO2+0.5HCHO+0.011

XCCH+0.5RCHO+0.044XRCH+0.003XACE

+0.009MEK+0.185FACD+0.159PACD+

0.268PRD2+0.011YRPX+0.052Y6PX+0.11

XC

k=3.19E‐15exp(‐1701/T) 1.10E‐17

550OLE1+NO3=0.772XHO2+1.463RO2C+

0.228RO2X+0.228ZRN3+0.013XCCH+

0.003XRCH+0.034XACE+0.774XRN3+

0.169YRPX+0.831Y6PX+0.226XN‐1.149

XC

k=5.37E‐13exp(‐1047/T) 1.64E‐14

551OLE1+O3P=0.45RCHO+0.39MEK+0.16

PRD2+1.13XC

k=1.61E‐11exp(‐326/T) 5.43E‐12

552OLE2+OH=0.912XHO2+0.953RO2C+

0.088RO2X+0.088ZRN3+0.179XHCH+

0.835XCCH+0.51XRCH+0.144XACE+0.08

XMEK+0.002XMVK+0.012XIPR+0.023

XPD2+0.319YRPX+0.681Y6PX+0.135XC

k=1.26E‐11exp(488/T) 6.41E‐11

553OLE2+O3=0.094HO2+0.041XHO2+0.443

OH+0.307MEO2+0.156XMC3+0.008XRC3

+0.212RO2C+0.003RO2X+0.003ZRN3+

0.299CO+0.161CO2+0.131HCHO+0.114

XHCH+0.453CCHO+0.071XCCH+0.333

RCHO+0.019XRCH+0.051ACET+0.033

MEK+0.001XMEK+0.024FACD+0.065

AACD+0.235PACD+0.037PRD2+0.073

YRPX+0.136Y6PX+0.16XC

k=8.59E‐15exp(‐1255/T) 1.31E‐16

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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NumberReactantsandProductsRateConstantExpression k300

554OLE2+NO3=0.4XHO2+0.426XNO2+0.035

XMEO+1.193RO2C+0.14RO2X+0.14ZRN3

+0.072XHCH+0.579XCCH+0.163XRCH+

0.116XACE+0.002XMEK+0.32XRN3+

0.319YRPX+0.681Y6PX+0.254XN+0.13XC

k=2.31E‐13exp(382/T) 8.25E‐13

555OLE2+O3P=0.079RCHO+0.751MEK+0.17

PRD2+0.739XC

k=1.43E‐11exp(111/T) 2.07E‐11

556ARO1+OH=0.123HO2+0.566XHO2+0.202

OH+0.566RO2C+0.11RO2X+0.11ZRN3+

0.158XGLY+0.1XMGL+0.123CRES+0.072

XAF1+0.185XAF2+0.202AFG3+0.309XPD2

+0.369Y6PX+0.31XC

k=7.84E‐12 7.84E‐12

557ARO2+OH=0.077HO2+0.617XHO2+0.178

OH+0.617RO2C+0.128RO2X+0.128ZRN3

+0.088XGLY+0.312XMGL+0.134XBAC+

0.077CRES+0.026XBAL+0.221XAF1+0.247

XAF2+0.178AFG3+0.068XAF3+0.057XPD2

+0.101Y6PX+1.459XC

k=3.09E‐11 3.09E‐11

558TERP+OH=0.734XHO2+0.064XRC3+1.211

RO2C+0.201RO2X+0.201ZRN3+0.001XCO

+0.411XHCH+0.385XRCH+0.037XACE+

0.007XMEK+0.003XMGL+0.009XBAC+

0.003XMVK+0.002XIPR+0.409XPD2+Y6PX

+4.375XC

k=2.27E‐11exp(435/T) 9.68E‐11

559TERP+O3=0.078HO2+0.046XHO2+0.499

OH+0.202XMC3+0.059XRC3+0.49RO2C+

0.121RO2X+0.121ZRN3+0.249CO+0.063

CO2+0.127HCHO+0.033XHCH+0.208

XRCH+0.057XACE+0.002MEK+0.172FACD

+0.068PACD+0.003XMGL+0.039XBAC+

0.002XMAC+0.001XIPR+0.502PRD2+

0.428Y6PX+3.852XC

k=8.28E‐16exp(‐785/T) 6.05E‐17

560TERP+NO3=0.227XHO2+0.287XNO2+

0.026XRC3+1.786RO2C+0.46RO2X+0.46

ZRN3+0.012XCO+0.023XHCH+0.002XGLD

+0.403XRCH+0.239XACE+0.005XMAC+

0.001XMVK+0.004XIPR+0.228XRN3+

Y6PX+0.485XN+3.785XC

k=1.33E‐12exp(490/T) 6.81E‐12

561TERP+O3P=0.237RCHO+0.763PRD2+

4.711XC

k=4.02E‐11 4.02E‐11

562SESQ+OH=0.734XHO2+0.064XRC3+

1.211RO2C+0.201RO2X+0.201ZRN3+

0.001XCO+0.411XHCH+0.385XRCH+

0.037XACE+0.007XMEK+0.003XMGL+

0.009XBAC+0.003XMVK+0.002XIPR+

0.409XPD2+Y6PX+9.375XC

k=k(558) 9.68E‐11

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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NumberReactantsandProductsRateConstantExpression k300

563SESQ+O3=0.078HO2+0.046XHO2+0.499

OH+0.202XMC3+0.059XRC3+0.49RO2C+

0.121RO2X+0.121ZRN3+0.249CO+0.063

CO2+0.127HCHO+0.033XHCH+0.208

XRCH+0.057XACE+0.002MEK+0.172FACD

+0.068PACD+0.003XMGL+0.039XBAC+

0.002XMAC+0.001XIPR+0.502PRD2+

0.428Y6PX+8.852XC

k=k(559) 6.05E‐17

564SESQ+NO3=0.227XHO2+0.287XNO2+

0.026XRC3+1.786RO2C+0.46RO2X+0.46

ZRN3+0.012XCO+0.023XHCH+0.002XCCH

+0.403XRCH+0.239XACE+0.005XMAC+

0.001XMVK+0.004XIPR+0.228XRN3+

Y6PX+0.485XN+8.785XC

k=k(560) 6.81E‐12

565SESQ+O3P=0.237RCHO+0.763PRD2+

9.711XC

k=k(561) 4.02E‐11



March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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TableD‐2.ExplicitspeciesintheSAPRC07TCmechanism.

SpeciesNameDescription

BD131,3‐butadiene

AACDAceticacid

ACE

Acetone

ACROAcrolein

ACYEAcetylene

AFG1Lumpedphotoreactivemonounsaturateddicarbonyl

aromaticfragmentationproductsthatphotolyzetoform

radicals

AFG2Lumped photoreactivemonounsaturateddicarbonyl

aromaticfragmentationproductsthatphotolyzetoform

non‐radicalproducts

AFG3Lumpeddiunsaturatreddicarbonylaromaticfragmentation

product.

ALK1Alkanesandothernon‐aromaticcompoundsthatreactonly

withOH,andhavekOHbetween2and5E2ppm‐1min‐1.

(Primarilyethane)

ALK2Alkanesandothernon‐aromaticcompoundsthatreactonly

withOH,andhavekOHbetween5E2and2.5E3ppm‐1min‐1.

(Primarilypropaneandacetylene)

ALK3Alkanesandothernon‐aromaticcompoundsthatreactonly

withOH,andhavekOHbetween2.5E3and5E3ppm‐1min‐1.

ALK4Alkanesandothernon‐aromaticcompoundsthatreactonly

withOH,andhavekOHbetween5E3and1E4ppm‐1min‐1.

ALK5Alkanesandothernon‐aromaticcompoundsthatreactonly

withOH,andhavekOHgreaterthan1E4ppm‐1min‐1.

APIN‐pinene

ARO1AromaticswithkOH <2E4ppm‐1min‐1.

ARO2AromaticswithkOH >2E4ppm‐1min‐1.

B1241,2,4‐trimethylbenzene

BACLBiacetyl

BALDAromaticaldehydes(e.g.,benzaldehyde)

BENZBenzene

BZC3PeroxyacylradicalformedfromAromaticAldehydes

BZOPhenoxyRadicals

CCHOAcetaldehyde

CO3HPeroxyaceticacid

CH4Methane

COCarbonMonoxide

CO2CarbonDioxide

COOHMethylHydroperoxide

CRESPhenolsandCresols

ETHEEthene

ETOHEthanol

FACDFormicAcid

GLYGlyoxal

H2Hydrogen

H2OWater

HCHOFormaldehyde

HNO3NitricAcid

PNAPeroxynitricAcid

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC

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SpeciesNameDescription

HO2HydroperoxideRadicals

H2O2HydrogenPeroxide

GLYDGlycolaldehyde

HONONitrousAcid

IPRDLumpedisopreneproductspecies

ISOPIsoprene

MAtmosphericpressure

MAC3Peroxyacylradicalsformedfrommethacroleinandother

acroleins.

MACRMethacrolein

MPANPANanalogueformedfromMethacrolein

MCO3AcetylPeroxyRadicals

MEKKetonesandothernon‐aldehydeoxygenatedproducts

whichreactwithOHradicalsfasterthan5E‐13butslower

than5E‐12cm3molec‐2sec‐1.(Basedonmechanismfor

methylethylketone).

MEO2MethylPeroxyRadicals

MEOHMethanol

MGLYMethylGlyoxal

MVKMethylVinylKetone

MXYLm‐xylene

N2O5NitrogenPentoxide

NONitricOxide

NO2NitrogenDioxide

NO3NitrateRadical

NPHENitrophenols

O1DExcitedOxygenAtoms

O2Oxygen

O3Ozone

O3PGroundStateOxygenAtoms

OHHydroxylRadicals

OLE1Alkenes(otherthanethene)withkOH <7E4ppm‐1min‐1.

OLE2AlkeneswithkOH >7E4ppm‐1min‐1.

OXYLo‐xylene

PACDPropanoicacid

PANPeroxyAcetylNitrate

PAN2PPNandotherhigheralkylPANanalogues

PBZNPANanaloguesformedfromAromaticAldehydes

PRD2Ketonesandothernon‐aldehydeoxygenatedproducts

whichreactwithOHradicalsfasterthan5E‐12cm3molec‐2

sec‐1

PRPEPropene

PXYLp‐xylene

R6PXLumpedorganichydroperoxideswith5ormorecarbons

(otherthanthoseformedfollowingOHadditiontoaromatic

rings,whichisreprsentedseparately).Mechanismbasedon

thatestimatedfor3‐hexylhydroperoxide.

RAPXOrganichydroperoxidesformedfollowingOHadditionto

aromaticrings,whichisreprsentedseparatelybecauseof

theirprobableroleinSOAformation.Mechanismbasedon

twoisomersexpectedtobeformedinthem‐xylenesystem.

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 272www.camx.com



SpeciesNameDescription

RCHOLumpedC3+Aldehydes(mechanismbasedon

propionaldehyde)

RCO3PeroxyPropionylandhigherperoxyacylRadicals

RO3HHigherorganicperoxyacids(mechanismbasedon

peroxypropionicacid).

RNO3LumpedOrganicNitrates

RO2CPeroxyRadicalOperatorrepresentingNOtoNO2andNO3

toNO2conversions,andtheeffectsofperoxyradical

reactionsonacylperoxyandotherperoxyradicals.

RO2XPeroxyRadicalOperatorrepresentingNOconsumption

(usedinconjunctionwithorganicnitrateformation),and

theeffectsofperoxyradicalreactionsonNO3,acylperoxy

radicals,andotherperoxyradicals.

ROOHLumpedorganichydroperoxideswith2‐4carbons.

Mechanismbasedonthatestimatedforn‐propyl

hydroperoxide.

SES

Sesquiterpenes

SO2SulfurDioxide

SULFSulfates(SO3orH2SO4)

TBUOt‐ButoxyRadicals

TERPTerpenes

TOLUToluene

XACEAsforxHO2

XACRAsforxHO2

XAF1AsforxHO2

XAF2AsforxHO2

XAF3AsforxHO2

XBACAsforxHO2

XBALAsforxHO2

XCLostCarbonorcarboninunreactiveproducts

XCCHAsforxHO2

XCOAsforxHO2

XGLYAsforxHO2

XHCHAsforxHO2

XHO2FormationofHO2fromalkoxyradicalsformedinperoxy

radicalreactionswithNOandNO3(100%yields)andRO2

(50%yields)

XGLDAsforxHO2

XIPRAsforxHO2

XMA3AsforxHO2

XMACAsforxHO2

XMC3AsforxHO2

XMEKAsforxHO2

XMEOAsforxHO2

XMGLAsforxHO2

XMVKAsforxHO2

XNLostNitrogenornitrogeninunreactiveproducts

XNO2AsforxHO2

XOHAsforxHO2

XPD2AsforxHO2

XRCHAsforxHO2

March2016CAMxUser’sGuideVersion6.3

AppendixD:Mechanism5–SAPRC07TC



COMPREHENSIVEAIRQUALITYMODELWITHEXTENSIONS 273www.camx.com



SpeciesNameDescription

XRC3AsforxHO2

XRN3AsforxHO2

XTBUAsforxHO2

Y6PXAsforROOH,butforR6PX

YAPXAsforROOH,butforRAPX

YRPXFormationofROOHfollowingRO2+HO2reactions

ZRN3FormationofRNO3intheRO2+NO,reaction.



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