Hello Rain,
looking at your CMAQ run script run_isam.csh, you did not correctly set the GR_EMIS_LAB_* environment variables which are needed to associate the files defined by GR_EMIS_* with “labels” that are referenced in the EmissCtrl and isam_control files. Put differently, you need to set GR_EMIS_LAB_* to AG, AR, PP, TR< and IN, respectively, in order to successfully use these labels in EmissCtrl and isam_control.
So, you need to change this section
#> Gridded Emissions Files
setenv N_EMIS_GR 5
set EMISfile = AGarea.nc
setenv GR_EMIS_001 ${EMISpath}/${EMISfile}
# setenv GR_EMIS_LAB_001 GRIDDED_EMIS
setenv GR_EMIS_LAB_001 GR_RES_FIRES
setenv GR_EM_SYM_DATE_001 F # To change default behaviour please see Users Guide for EMIS_SYM_DATE
set EMISfile = ARarea.nc
setenv GR_EMIS_002 ${EMISpath}/${EMISfile}
setenv GR_EMIS_LAB_002 GR_RES_FIRES
setenv GR_EM_SYM_DATE_002 F # To change default behaviour please see Users Guide for EMIS_SYM_DATE
set EMISfile = INarea.nc
setenv GR_EMIS_003 ${EMISpath}/${EMISfile}
setenv GR_EMIS_LAB_003 GR_RES_FIRES
setenv GR_EM_SYM_DATE_003 F
set EMISfile = PParea.nc
setenv GR_EMIS_004 ${EMISpath}/${EMISfile}
setenv GR_EMIS_LAB_004 GR_RES_FIRES
setenv GR_EM_SYM_DATE_004 F
set EMISfile = TRarea.nc
setenv GR_EMIS_005 ${EMISpath}/${EMISfile}
setenv GR_EMIS_LAB_005 GR_RES_FIRES
setenv GR_EM_SYM_DATE_005 F
to
#> Gridded Emissions Files
setenv N_EMIS_GR 5
set EMISfile = AGarea.nc
setenv GR_EMIS_001 ${EMISpath}/${EMISfile}
# setenv GR_EMIS_LAB_001 GRIDDED_EMIS
setenv GR_EMIS_LAB_001 AG
setenv GR_EM_SYM_DATE_001 F # To change default behaviour please see Users Guide for EMIS_SYM_DATE
set EMISfile = ARarea.nc
setenv GR_EMIS_002 ${EMISpath}/${EMISfile}
setenv GR_EMIS_LAB_002 AR
setenv GR_EM_SYM_DATE_002 F # To change default behaviour please see Users Guide for EMIS_SYM_DATE
set EMISfile = INarea.nc
setenv GR_EMIS_003 ${EMISpath}/${EMISfile}
setenv GR_EMIS_LAB_003 IN
setenv GR_EM_SYM_DATE_003 F
set EMISfile = PParea.nc
setenv GR_EMIS_004 ${EMISpath}/${EMISfile}
setenv GR_EMIS_LAB_004 PP
setenv GR_EM_SYM_DATE_004 F
set EMISfile = TRarea.nc
setenv GR_EMIS_005 ${EMISpath}/${EMISfile}
setenv GR_EMIS_LAB_005 TR
setenv GR_EM_SYM_DATE_005 F
In general, you need to make sure that each label is set to a unique name, reusing the same label for multiple emission streams like in your example (GR_RES_FIRES) will likely cause unintended behavior not only in isam but also, more importantly, for the emission scaling instructions specified in EmissCtrl.