Hi Bsu,
First of all, you should have individual emission inventories that devided by categories,such as agritulture.nc,industry.nc,power.nc
Then, you can change the line : setenv N_EMIS_GR 3 as there are 3 different emission inventories. And declare each emission inventories in run_cctm.csh.For gridded emission inventories,there should be individual EMISfile as emission file name,GR_EMIS as file path,GR_EMIS_LAB as the tags of emission file. As for point emissions,individual STK_GRPS,STK_EMIS,STK_EMIS_LAB,STK_EMIS_DIAG,STK_EM_SYM_DATE should be set.
Finally, you can modify isam_control.txt ,there must be individual TAG NAME ,REGION(S)
EMIS STREAM(S) for each emission inventories,and make sure that EMIS STREAM(S) are same with GR_EMIS_LAB.
C.W.Huang