!#start   YYYYJJJ  
!#end     YYYYJJJ 
#layer         1

/
! This Species Definition File is for Use with the COMBINE tool built for 
! post-processing CAMx output. It is compatible with CAMxv7.0.
! Date: May 13 2019

! Output variables that begin with 'PM' represent those in which a size cut was 
! applied based on modeled aerosol mode parameters.  For example, PM25_NA is all 
! sodium that falls below 2.5 um diameter. These 'PM' variables are used for 
! comparisons at IMPROVE and CSN sites.

! Output variables that begin with 'PMAMS' represent the mass that would have
! been detected  by an Aerosol Mass Spectrometer.

! Output variables beginning with 'A' (aside from AIR_DENS) represent a 
! combination of aerosol species in which no size cut was applied.  For example, 
! ASO4IJ is the sum of i-mode and j-mode sulfate.  These 'A' variables are used 
! for comparisons at CASTNet sites.

! Output variables beginning with 'PMC' refer to the coarse fraction of total PM,
! computed by summing all modes and subtracting the PM2.5 fraction.  These 'PMC'
! variables are used for comparisons at SEARCH sites.

! This Species Definition File is just for use with the uncoupled, offline CMAQ,
! model. If you are processing WRF-CMAQ results, a different Species Definition
! file is required.

/ File [1]: CAMx average utput file converted to CMAQ conc/aconc file format
/ File [2]: METCRO3D file
/ File [3]: METCRO2D file
/
/new species    ,units     ,expression
                                         
!-------------------------------------------!
!------------- Meteorology -----------------!
!-------------------------------------------!
AIR_DENS        ,kg/m3     ,DENS[2]
!RH              ,%         ,100.00*RH[3]
SFC_TMP         ,C         ,(TEMP2[3]-273.15)
PBLH            ,m         ,PBL[3]
SOL_RAD         ,WATTS/m2  ,RGRND[3]
precip          ,cm        ,RN[3]+RC[3]
WSPD10          ,m/s       ,WSPD10[3]
WDIR10          ,deg       ,WDIR10[3]

!-------------------------------------------!
!--------------- Gases ---------------------!
!-------------------------------------------!
ALD2            ,ppbV      ,1000.0*ALD2[1]
BENZENE         ,ppbV      ,1000.0*BENZ[1]
CO              ,ppbV      ,1000.0*CO[1]
DMS             ,ppbV      ,1000.0*DMS[1]
ETH             ,ppbV      ,1000.0*ETH[1]
ETHA            ,ppbV      ,1000.0*ETHA[1]
FORM            ,ppbV      ,1000.0*FORM[1]
H2O2            ,ppbV      ,1000.0*H2O2[1]
HNO3            ,ppbV      ,1000.0*HNO3[1]
HNO3_UGM3       ,ug/m3     ,1000.0*(HNO3[1]*2.1756*DENS[2])
HONO            ,ppbV      ,1000.0*HONO[1]
ISOP            ,ppbV      ,1000.0*ISOP[1]
N2O5            ,ppbV      ,1000.0*N2O5[1]
NH3             ,ppbV      ,1000.0*NH3[1]
NH3_UGM3        ,ug/m3     ,1000.0*(NH3[1]*0.5880*DENS[2])
NHX             ,ug/m3     ,1000.0*(NH3[1]*0.5880*DENS[2])+PNH4[1]
NO              ,ppbV      ,1000.0*NO[1]
NO2             ,ppbV      ,1000.0*NO2[1]
NOX             ,ppbV      ,1000.0*(NO[1] + NO2[1])
ANO3_PPB	,ppbV      ,(PNO3[1])/(DENS[2]*(62.0/28.97))
NTR             ,ppbV      ,1000.0*(NTR1[1]+NTR2[1]+INTR[1])
PANS            ,ppbV      ,1000.0*(PAN[1]+PANX[1]+OPAN[1])
NOY             ,ppbV      ,1000.0* (NO[1]+NO2[1]+NO3[1]+2*N2O5[1]+HONO[1]+HNO3[1]+PNA[1] \
                                     +CRON[1])+PANS[0]+NTR[0]+ANO3_PPB[0]
O3              ,ppbV      ,1000.0*O3[1]
SO2             ,ppbV      ,1000.0*SO2[1]
SO2_UGM3        ,ug/m3     ,1000.0*(SO2[1]*2.2118*DENS[2])
SQT             ,ppbV      ,1000.0*SQT[1]
TERP            ,ppbV      ,1000.0*TERP[1]
TOL             ,ppbV      ,1000.0*TOL[1]
XYL             ,ppbV      ,1000.0*XYL[1]

!Additional Toxic gases
!ACROLEIN        ,ug/m3     ,1000.0*(ACROLEIN[1]*1.9365*DENS[2]) 
!ACRO_PRIMARY    ,ug/m3     ,1000.0*(ACRO_PRIMARY*1.9365*DENS[2]) 
!ALD2_PRIMARY    ,ug/m3     ,1000.0*(ALD2_PRIMARY[1]*1.5188*DENS[2])     
!FORM_PRIMARY    ,ug/m3     ,1000.0*(FORM_PRIMARY[1]*1.0356*DENS[2])  
!BUTADIENE13     ,ug/m3     ,1000.0*(BUTADIENE13[1]*1.8674*DENS[2]) 
!HCL             ,ppbV      ,1000.0*HCL[1]                           
!TOLUENE         ,ppbV      ,1000.0*TOLU[1]                           

!Mercuric gas species
!HG_0            ,ng/m3     ,1000.0*(HG[1]*8.3330*DENS[2]*1000.0)       
!HG_II           ,ng/m3     ,1000.0*(HGIIGAS[1]*8.3330*DENS[2]*1000.0) 

!! Unused Gases. Presented Here for illustration. Users can uncomment
!! them if they choose.
!ALDX            ,ppbV      ,1000.0*ALDX[1]
!CLNO2           ,ppbV      ,1000.0*CLNO2[1] 
!IOLE            ,ppbV      ,1000.0*IOLE[1]
!OLE             ,ppbV      ,1000.0*OLE[1]
!PAR             ,ppbV      ,1000.0*PAR[1]
!PAN             ,ppbV      ,1000.0*PAN[1]
!PANX            ,ppbV      ,1000.0*PANX[1]
SULF            ,ppbV      ,1000.0*SULF[1]
!VOC             ,ppbC      ,1000.0* ( PAR[1]      + 2.0*ETH[1]  + MEOH[1]     + 2.0*ETOH[1]  \
!                                     +2.0*OLE[1]  + 7.0*TOL[1]  + 8.0*XYLMN[1]+ FORM[1]      \
!                                     +2.0*ALD2[1] + 2.0*ETHA[1] + 4.0*IOLE[1] + 2.0*ALDX[1]  \
!                                     +5.0*ISOP[1] + 10.0*TERP[1]+ 10.0*NAPH[1])


!-------------------------------------------!
!--------------- Particles -----------------!
!-------------------------------------------!
!! Crustal Elements !! Must output RTRAC for this to be output by CAMx
AFEJ            ,ug/m3     ,PFE[1]
AALJ            ,ug/m3     ,PAL[1]
ASIJ            ,ug/m3     ,PSI[1]
ATIJ            ,ug/m3     ,PTI[1]
ACAJ            ,ug/m3     ,PCA[1]
AMGJ            ,ug/m3     ,PMG[1]
AKJ             ,ug/m3     ,PK[1]
AMNJ            ,ug/m3     ,PMN[1]
FCRS            ,ug/m3     ,FCRS[1]
FCRS_SMAT       ,ug/m3     ,PAL[1]+PCA[1]+PFE[1]+PMG[1]+PK[1]+PMN[1]+PSI[1]+PTI[1]
FPRM            ,ug/m3     ,FPRM[1]
CCRS            ,ug/m3     ,CCRS[1]
CPRM            ,ug/m3     ,CPRM[1]
ASOILJ          ,ug/m3     ,2.20*PAL[1]+2.49*PSI[1]+1.63*PCA[1]+2.42*PFE[1]+1.94*PTI[1]
ASOILJ_SMAT     ,ug/m3     ,FCRS_SMAT[0]+FPRM[1]

!! Non-Crustal Inorganic Particle Species
!AHPLUSIJ        ,ug/m3     ,(AH3OPI[1]+AH3OPJ[1])*1.0/19.0
!ANAK            ,ug/m3     ,0.8373*ASEACAT[1]+0.0626*ASOIL[1]+0.0023*ACORS[1]
!AMGK            ,ug/m3     ,0.0997*ASEACAT[1]+0.0170*ASOIL[1]+0.0032*ACORS[1]
!AKK             ,ug/m3     ,0.0310*ASEACAT[1]+0.0242*ASOIL[1]+0.0176*ACORS[1]
!ACAK            ,ug/m3     ,0.0320*ASEACAT[1]+0.0838*ASOIL[1]+0.0562*ACORS[1]
ACLIJ           ,ug/m3     ,PCL[1]
AECIJ           ,ug/m3     ,PEC[1]
ANAIJ           ,ug/m3     ,NA[1]
ANO3IJ          ,ug/m3     ,PNO3[1]
!ANO3K           ,ug/m3     ,ANO3K[1]
TNO3            ,ug/m3     ,2175.6*(HNO3[1]*DENS[2])+PNO3[1]
ANH4IJ          ,ug/m3     ,PNH4[1]
!ANH4K           ,ug/m3     ,ANH4K[1]
ASO4IJ          ,ug/m3     ,PSO4[1]
!ASO4K           ,ug/m3     ,ASO4K[1]

!! Organic Particle Species
APOCIJ          ,ugC/m3    ,POA[1]*0.588

!APOMI           ,ug/m3     ,APOCI[1]  + APNCOMI[1]
!APOMJ           ,ug/m3     ,APOCJ[1]  + APNCOMJ[1]
APOMIJ          ,ug/m3     ,POA[1]

ASOCJ           ,ugC/m3    ,0.5*(SOA1[1]+SOA2[1])+0.476*(SOPA[1]+SOPB[1])+0.625*(SOA3[1]+SOA4[1])
ASOMJ           ,ug/m3     ,SOA1[1]+SOA2[1]+SOPA[1]+SOA3[1]+SOA4[1]+SOPB[1] 

!AOCI            ,ugC/m3    ,APOCI[1]
!AOCJ            ,ugC/m3    ,APOCJ[1]  + ASOCJ[0]
AOCIJ           ,ugC/m3    ,APOCIJ[0] + ASOCJ[0]

!AOMI            ,ug/m3     ,APOMI[0] 
!AOMJ            ,ug/m3     ,APOMJ[0]  + ASOMJ[0]
AOMIJ           ,ug/m3     ,APOMIJ[0] + ASOMJ[0]

!!! Anthropogenic-VOC Derived Organic Aerosol
AORGAJ          ,ug/m3     ,SOA1[1]+SOA2[1]+SOPA[1]

!!! Biogenic-VOC Derived Organic Aerosol
AORGBJ          ,ug/m3     ,SOA3[1]+SOA4[1]+SOPB[1]

!!! Cloud-Processed  SOA
!AORGCJ          ,ug/m3     ,AORGCJ[1]

!!! OM/OC ratios
!AOMOCRAT_TOT    ,none      ,AOMIJ[0]/AOCIJ[0]

!! Total PM Aggregates
!ATOTI           ,ug/m3     ,ASO4I[1]+ANO3I[1]+ANH4I[1]+ANAI[1]+ACLI[1] \
!                           +AECI[1]+AOMI[0]+AOTHRI[1] 
!ATOTJ           ,ug/m3     ,ASO4J[1]+ANO3J[1]+ANH4J[1]+ANAJ[1]+ACLJ[1] \
!                           +AECJ[1]+AOMJ[0]+AOTHRJ[1]+AFEJ[1]+ASIJ[1]  \
!                           +ATIJ[1]+ACAJ[1]+AMGJ[1]+AMNJ[1]+AALJ[1]+AKJ[1]
!ATOTK           ,ug/m3     ,ASOIL[1]+ACORS[1]+ASEACAT[1]+ACLK[1]+ASO4K[1] \
!                           +ANO3K[1]+ANH4K[1]
ATOTIJ          ,ug/m3     ,PSO4[1]+PNO3[1]+PNH4[1]+PEC[1]+NA[1]+PCL[1]+ASOILJ[0]+SOA1[1]+SOA2[1]+SOA3[1]+SOA4[1]+SOPA[1]+SOPB[1]+POA[1]
ATOTIJ_SMAT     ,ug/m3     ,PSO4[1]+PNO3[1]+PNH4[1]+PEC[1]+NA[1]+PCL[1]+ASOILJ_SMAT[0]+SOA1[1]+SOA2[1]+SOA3[1]+SOA4[1]+SOPA[1]+SOPB[1]+POA[1]
ATOTIJK         ,ug/m3     ,ATOTIJ[0]+CCRS[1]+CPRM[1]

!! Unspeciated PM including non-carbon organic mass
!AUNSPEC1IJ      ,ug/m3     ,ATOTIJ[0] - (ASOILJ[0] + ANO3IJ[0] + ASO4IJ[0] + ANH4IJ[0] \
!                                      +AOCIJ[0]  + AECIJ[0]  + ANAIJ[0]  + ACLIJ[0])
!! Non-Carbon Organic Mass
ANCOMIJ         ,ug/m3     ,AOMIJ[0]-AOCIJ[0]

!! Unspeciated PM excluding non-carbon organic mass
!AUNSPEC2IJ      ,ug/m3     ,AUNSPEC1IJ[0] - ANCOMIJ[0]

!! AMS Projection of Output Concentrations
!PMAMS_CL        ,ug/m3     ,ACLI[1]*AMSAT[3]+ACLJ[1]*AMSAC[3]+ACLK[1]*AMSCO[3]
!PMAMS_NH4       ,ug/m3     ,ANH4I[1]*AMSAT[3]+ANH4J[1]*AMSAC[3]+ANH4K[1]*AMSCO[3]
!PMAMS_NO3       ,ug/m3     ,ANO3I[1]*AMSAT[3]+ANO3J[1]*AMSAC[3]+ANO3K[1]*AMSCO[3]
!PMAMS_OM        ,ugC/m3    ,AOMI[0]*AMSAT[3]+AOMJ[0]*AMSAC[3]
!PMAMS_SO4       ,ug/m3     ,ASO4I[1]*AMSAT[3]+ASO4J[1]*AMSAC[3]+ASO4K[1]*AMSCO[3]

!! PM1 Cutoff Output
!PM1_TOT         ,ug/m3     ,ATOTI[0]*PM1AT[3]+ATOTJ[0]*PM1AC[3]+ATOTK[0]*PM1CO[3]

!! Unused PM1 Species. Included Here for demonstration
!PM1_EC         ,ug/m3     ,AECI[1]*PM1AT[3]+AECJ[1]*PM1AC[3]
!PM1_OC         ,ugC/m3    ,AOCI[0]*PM1AT[3]+AOCJ[0]*PM1AC[3]
!PM1_OM         ,ug/m3     ,AOMI[0]*PM1AT[3]+AOMJ[0]*PM1AC[3]
!PM1_SO4        ,ug/m3     ,ASO4I[1]*PM1AT[3]+ASO4J[1]*PM1AC[3]+ASO4K[1]*PM1CO[3]
!PM1_CL         ,ug/m3     ,ACLI[1]*PM1AT[3]+ACLJ[1]*PM1AC[3]+ACLK[1]*PM1CO[3]
!PM1_NA         ,ug/m3     ,ANAI[1]*PM1AT[3]+ANAJ[1]*PM1AC[3]+ANAK[0]*PM1CO[3]
!PM1_MG         ,ug/m3     ,                  AMGJ[1]*PM1AC[3]+AMGK[0]*PM1CO[3]
!PM1_K          ,ug/m3     ,                  AKJ[1] *PM1AC[3]+AKK[0] *PM1CO[3]
!PM1_CA         ,ug/m3     ,                  ACAJ[1]*PM1AC[3]+ACAK[0]*PM1CO[3]
!PM1_NH4        ,ug/m3     ,ANH4I[1]*PM1AT[3]+ANH4J[1]*PM1AC[3]+ANH4K[1]*PM1CO[3]
!PM1_NO3        ,ug/m3     ,ANO3I[1]*PM1AT[3]+ANO3J[1]*PM1AC[3]+ANO3K[1]*PM1CO[3] 
!PM1_SOIL       ,ug/m3     ,ASOILJ[0]*PM1AC[3]+(ASOIL[1]+ACORS[1])*PM1CO[3]
!PM1_UNSPEC1    ,ug/m3     ,PM1_TOT[0]-(PM1_CL[0]+PM1_EC[0]+PM1_NA[0]+PM1_NH4[0]+PM1_NO3[0]+PM1_OC[0]+PM1_SOIL[0]+PM1_SO4[0]) 

!! PM2.5 species computed using modeled size distribution
!PM25_HP         ,ug/m3     ,(AH3OPI[1]*PM25AT[3]+AH3OPJ[1]*PM25AC[3]+AH3OPK[1]*PM25CO[3])*1.0/19.0
PM25_CL         ,ug/m3     ,ACLIJ[0]
PM25_EC         ,ug/m3     ,AECIJ[0]
PM25_NA         ,ug/m3     ,ANAIJ[0]
PM25_MG         ,ug/m3     ,AMGJ[0]
PM25_K          ,ug/m3     ,AKJ[0]
PM25_CA         ,ug/m3     ,ACAJ[0]
PM25_NH4        ,ug/m3     ,ANH4IJ[0]
PM25_NO3        ,ug/m3     ,ANO3IJ[0]
PM25_OC         ,ugC/m3    ,AOCIJ[0]
PM25_OM         ,ug/m3     ,AOMIJ[0]
PM25_SOIL       ,ug/m3     ,ASOILJ[0]
PM25_SO4        ,ug/m3     ,ASO4IJ[0]
PM25_TOT        ,ug/m3     ,PSO4[1]+PNO3[1]+PNH4[1]+PEC[1]+NA[1]+PCL[1]+ASOILJ[0]+SOA1[1]+SOA2[1]+SOA3[1]+SOA4[1]+SOPA[1]+SOPB[1]+POA[1]
PM25_TOT_SMAT   ,ug/m3     ,PSO4[1]+PNO3[1]+PNH4[1]+PEC[1]+NA[1]+PCL[1]+ASOILJ_SMAT[0]+SOA1[1]+SOA2[1]+SOA3[1]+SOA4[1]+SOPA[1]+SOPB[1]+POA[1]
!PM25_UNSPEC1    ,ug/m3     ,PM25_TOT[0]-(PM25_CL[0]+PM25_EC[0]+PM25_NA[0]+PM25_NH4[0] \
!                             +PM25_NO3[0]+PM25_OC[0]+PM25_SOIL[0]+PM25_SO4[0])

!! PM10.0 and Coarse-Sized Species
!PM10            ,ug/m3     ,ATOTI[0]*PM10AT[3]+ATOTJ[0]*PM10AC[3]+ATOTK[0]*PM10CO[3]

!PMC_CL          ,ug/m3     ,ACLI[1]+ACLJ[1]+ACLK[1]-PM25_CL[0]
!PMC_NA          ,ug/m3     ,ANAIJ[0]+ANAK[0]-PM25_NA[0]
!PMC_NH4         ,ug/m3     ,ANH4I[1]+ANH4J[1]+ANH4K[1]-PM25_NH4[0]
!PMC_NO3         ,ug/m3     ,ANO3I[1]+ANO3J[1]+ANO3K[1]-PM25_NO3[0]
!PMC_SO4         ,ug/m3     ,ASO4I[1]+ASO4J[1]+ASO4K[1]-PM25_SO4[0]
PMC_TOT         ,ug/m3     ,CCRS[1]+CPRM[1]

!! FRM PM Equivalent Calculation
!! This section calculates the FRM applicable PM species, PMIJ_FRM and
!! PM25_FRM. The intermediate variablse K...ANH4IJ_loss are needed to 
!! calculate the final quantities.
!K               ,ppb^2	   ,exp(118.87-24084/TEMP2[4]-6.025*log(TEMP2[4]))
!P1              ,          ,exp(8763/TEMP2[4]+19.12*log(TEMP2[4])-135.94)
!P2              ,          ,exp(9969/TEMP2[4]+16.22*log(TEMP2[4])-122.65)
!P3              ,          ,exp(13875/TEMP2[4]+24.46*log(TEMP2[4])-182.61)
!a               ,          ,1-RH[0]/100
!K_prime         ,ppb^2     ,(P1[0]-P2[0]*a[0]+(P3[0]*a[0]*a[0]))*(a[0]^1.75)*K[0]
!sqrt_Ki         ,ppb       ,sqrt(RH[0]<=61 ? K[0] : K_prime[0])
!max_NO3_loss    ,ug/m3     ,745.7/TEMP2[4]*sqrt_Ki[0]
!PM25_NO3_loss   ,ug/m3     ,max_NO3_loss[0]<=PM25_NO3[0] ? max_NO3_loss[0] : PM25_NO3[0]
!ANO3IJ_loss     ,ug/m3     ,max_NO3_loss[0]<=ANO3IJ[0] ? max_NO3_loss[0] : ANO3IJ[0]
!PM25_NH4_loss   ,ug/m3     ,PM25_NO3_loss[0]*(18/62)
!ANH4IJ_loss     ,ug/m3     ,ANO3IJ_loss[0]*(18/62)
!PMIJ_FRM        ,ug/m3     ,ATOTIJ[0]-(ANO3IJ_loss[0]+ANH4IJ_loss[0]) \
!                            +0.24*(ASO4IJ[0]+ANH4IJ[0]-ANH4IJ_loss[0])+0.5
!PM25_FRM        ,ug/m3     ,PM25_TOT[0]-(PM25_NO3_loss[0]+PM25_NH4_loss[0]) \
!                            +0.24*(PM25_SO4[0]+PM25_NH4[0]-PM25_NH4_loss[0])+0.5
