Dear Ben,
Thank for the information. Here is the isam_control.txt file
!!! CMAQ-ISAM tag definition control file
!!! (lines begining with !!! - three exclamaition marks - are ignored by the text parser)
!!!
!!! Example file provided with CMAQ v5.3 release
!!! 05 June 2019: Sergey L. Napelenok
!!!
!!!
!!! The following line defines the tag classes to track for the simulation. Species in NITRATE and VOC classes depend on the
!!! the chemical mechanism used. The below definitions apply for the cb6r3_ae7_aq mechanism.
!!! Choose any/all from the list of nine: SULFATE, NITRATE, AMMONIUM, EC, OC, VOC, PM25_IONS, CO, OZONE
!!! SULFATE - ASO4J, ASO4I, SO2, SULF, SULRXN
!!! NITRATE - ANO3J, ANO3I, HNO3, NO, NO2, NO3, HONO, N2O5, PNA, PAN, PANX, NTR1, NTR2, INTR, CLNO2, CLNO3
!!! AMMONIUM - ANH4J, ANH4I, NH3
!!! EC - AECJ, AECI
!!! OC - APOCI, APOCJ, APNCOMI, APNCOMJ
!!! VOC - 22 species, check CCTM/src/isam/SA_DEFN.F for species names
!!! PM25_IONS - ANAI, ANAJ, AMGJ, AKJ, ACAJ, AFEJ, AALJ, ASIJ, ATIJ, AMNJ, AOTHRI, AOTHRJ
!!! CO - CO
!!! OZONE - all NITRATE species + all VOC species
!!! CHLORINE - ACLI, ACLJ, HCL
!!! The following are source definition text blocks in the format:
!!! TAG NAME |Three character text string
!!! REGION(S) |Keyword EVERYWHERE or variable names from the region file (multiple regions need to be comma delimited)
!!! FILENAME(S) |Emissions labels (multiple labels need to be comma delimited)
!!!TAG CLASSES | SULFATE, OZONE
TAG CLASSES | OZONE
TAG NAME | GR1
REGION(S) | CENSYD
EMIS STREAM(S) |GRIDDED_EMIS
TAG NAME | GR2
REGION(S) | ILLA
EMIS STREAM(S) |GMRELEV
ENDLIST eof
My runctm scripts has this reference to this isam_control.txt file
#> Integrated Source Apportionment Method (ISAM) Options
setenv CTM_ISAM Y
if ( $?CTM_ISAM ) then
if ( $CTM_ISAM == ‘Y’ || $CTM_ISAM == ‘T’ ) then
setenv SA_IOLIST ${WORKDIR}/isam_control.txt
setenv ISAM_BLEV_ELEV " 1 1"
setenv AISAM_BLEV_ELEV " 1 1"
#> Set Up ISAM Initial Condition Flags
if ($NEW_START == true || $NEW_START == TRUE ) then
setenv ISAM_NEW_START Y
setenv ISAM_PREVDAY
else
setenv ISAM_NEW_START N
setenv ISAM_PREVDAY "$OUTDIR/CCTM_SA_CGRID_${RUNID}_${YESTERDAY}.nc"
endif
#> Set Up ISAM Output Filenames
setenv SA_ACONC_1 "$OUTDIR/CCTM_SA_ACONC_${CTM_APPL}.nc -v"
setenv SA_CONC_1 "$OUTDIR/CCTM_SA_CONC_${CTM_APPL}.nc -v"
setenv SA_DD_1 "$OUTDIR/CCTM_SA_DRYDEP_${CTM_APPL}.nc -v"
setenv SA_WD_1 "$OUTDIR/CCTM_SA_WETDEP_${CTM_APPL}.nc -v"
setenv SA_CGRID_1 "$OUTDIR/CCTM_SA_CGRID_${CTM_APPL}.nc -v"
#> Set optional ISAM regions files
setenv CMAQ_REGIONS /home/duch/repository/5.3.1/ioapi-3.2/make_mask/output/reg_allmask_d01.ncf
endif
endif
As this CMAQ application is run on the domain in Sydney, Australia, I created the region mask file using m3tool (m3mask and m3merge). The header of this mask file (reg_allmask_d01.ncf) is followed
netcdf reg_allmask_d01 {
dimensions:
TSTEP = 1 ;
LAY = 1 ;
ROW = 373 ;
COL = 373 ;
DATE-TIME = 2 ;
VAR = 2 ;
variables:
float CENSYD(TSTEP, LAY, ROW, COL) ;
CENSYD:units = “None” ;
CENSYD:var_desc = "1==mask region, 0==outside-mask region " ;
CENSYD:long_name = "CENSYD " ;
float ILLA(TSTEP, LAY, ROW, COL) ;
ILLA:units = “None” ;
ILLA:var_desc = "1==mask region, 0==outside-mask region " ;
ILLA:long_name = "ILLA " ;
int TFLAG(TSTEP, VAR, DATE-TIME) ;
TFLAG:units = “<YYYYDDD,HHMMSS>None” ;
TFLAG:long_name = "TFLAG " ;
TFLAG:var_desc = "Timestep-valid flags: (1) YYYYDDD or (2) HHMMSS " ;
I carefully followed the previous tips and instruction in this forum on the creation of the mask file.
Thanks for your help
Best
Hiep Nguyen
Senior Atmospheric Scientist
Department of Planning, Industry and Environment, NSW, Sydney