CMAQ5.3.2 can't read emission file with zero pollutants in output files

Dear all,
I met a problem that all the pollutants is zero in using CMAQ5.3.2. I think this would be the problem that the emission file can’t be read in CMAQ5.3.2. But this emission file can be read in CMAQ5.3.2 and the pollutants increase apparently in the version 5.2.1. I checked the CTM_LOG file and found all the variables in emission file were not read in CMAQ5.3.2, but these variables are definitely in emission file and names are correct and consistant with names in CMAQ5.3.2, such as NO, NO2 and SO2. The run_cctm file, CTM_log file, and emission description file are attached. How can I solve this problem?
Thank you for your help.


     |> Checking for unused Emissions Surrogates:
     ============================================
     GRIDDED_EMIS | Gridded Area Emissions File   1: 46 unused surrogates.
          ALD2            
          ALDX            
          BENZENE         
          CH4             
          CO              
          DLUSE           
          ETH             
          ETHA            
          ETOH            
          FORM            
          HONO            
          IOLE            
          ISOP            
          MEOH            
          NH3             
          NO              
          NO2             
          NVOL            
          OLE             
          PAL             
          PAR             
          PCA             
          PCL             
          PEC             
          PFE             
          PH2O            
          PK              
          PMC             
          PMG             
          PMN             
          PMOTHR          
          PNA             
          PNCOM           
          PNH4            
          PNO3            
          POC             
          PSI             
          PSO4            
          PTI             
          SO2             
          SULF            
          TERP            
          TOL             
          UNK             
          UNR             
          XYL             
netcdf emis.mrg.regional.mycase.d02.cmaq_cb05ae6.25hrs.2022180 {
dimensions:
	TSTEP = UNLIMITED ; // (25 currently)
	DATE-TIME = 2 ;
	LAY = 37 ;
	VAR = 46 ;
	ROW = 200 ;
	COL = 176 ;
variables:
	int TFLAG(TSTEP, VAR, DATE-TIME) ;
		TFLAG:units = "<YYYYDDD,HHMMSS>" ;
		TFLAG:long_name = "TFLAG           " ;
		TFLAG:var_desc = "Timestep-valid flags:  (1) YYYYDDD or (2) HHMMSS                                " ;
	float ALD2(TSTEP, LAY, ROW, COL) ;
		ALD2:long_name = "ALD2            " ;
		ALD2:units = "moles/s         " ;
		ALD2:var_desc = "Hourly emission                                                                 " ;
	float ALDX(TSTEP, LAY, ROW, COL) ;
		ALDX:long_name = "ALDX            " ;
		ALDX:units = "moles/s         " ;
		ALDX:var_desc = "Hourly emission                                                                 " ;
	float BENZENE(TSTEP, LAY, ROW, COL) ;
		BENZENE:long_name = "BENZENE         " ;
		BENZENE:units = "moles/s         " ;
		BENZENE:var_desc = "Hourly emission                                                                 " ;
	float CH4(TSTEP, LAY, ROW, COL) ;
		CH4:long_name = "CH4             " ;
		CH4:units = "moles/s         " ;
		CH4:var_desc = "Hourly emission                                                                 " ;
	float CO(TSTEP, LAY, ROW, COL) ;
		CO:long_name = "CO              " ;
		CO:units = "moles/s         " ;
		CO:var_desc = "Hourly emission                                                                 " ;
	float DLUSE(TSTEP, LAY, ROW, COL) ;
		DLUSE:long_name = "DLUSE           " ;
		DLUSE:units = "g/s             " ;
		DLUSE:var_desc = "Hourly emission                                                                 " ;
	float ETH(TSTEP, LAY, ROW, COL) ;
		ETH:long_name = "ETH             " ;
		ETH:units = "moles/s         " ;
		ETH:var_desc = "Hourly emission                                                                 " ;
	float ETHA(TSTEP, LAY, ROW, COL) ;
		ETHA:long_name = "ETHA            " ;
		ETHA:units = "moles/s         " ;
		ETHA:var_desc = "Hourly emission                                                                 " ;
	float ETOH(TSTEP, LAY, ROW, COL) ;
		ETOH:long_name = "ETOH            " ;
		ETOH:units = "moles/s         " ;
		ETOH:var_desc = "Hourly emission                                                                 " ;
	float FORM(TSTEP, LAY, ROW, COL) ;
		FORM:long_name = "FORM            " ;
		FORM:units = "moles/s         " ;
		FORM:var_desc = "Hourly emission                                                                 " ;
	float HONO(TSTEP, LAY, ROW, COL) ;
		HONO:long_name = "HONO            " ;
		HONO:units = "moles/s         " ;
		HONO:var_desc = "Hourly emission                                                                 " ;
	float IOLE(TSTEP, LAY, ROW, COL) ;
		IOLE:long_name = "IOLE            " ;
		IOLE:units = "moles/s         " ;
		IOLE:var_desc = "Hourly emission                                                                 " ;
	float ISOP(TSTEP, LAY, ROW, COL) ;
		ISOP:long_name = "ISOP            " ;
		ISOP:units = "moles/s         " ;
		ISOP:var_desc = "Hourly emission                                                                 " ;
	float MEOH(TSTEP, LAY, ROW, COL) ;
		MEOH:long_name = "MEOH            " ;
		MEOH:units = "moles/s         " ;
		MEOH:var_desc = "Hourly emission                                                                 " ;
	float NH3(TSTEP, LAY, ROW, COL) ;
		NH3:long_name = "NH3             " ;
		NH3:units = "moles/s         " ;
		NH3:var_desc = "Hourly emission                                                                 " ;
	float NO(TSTEP, LAY, ROW, COL) ;
		NO:long_name = "NO              " ;
		NO:units = "moles/s         " ;
		NO:var_desc = "Hourly emission                                                                 " ;
	float NO2(TSTEP, LAY, ROW, COL) ;
		NO2:long_name = "NO2             " ;
		NO2:units = "moles/s         " ;
		NO2:var_desc = "Hourly emission                                                                 " ;
	float NVOL(TSTEP, LAY, ROW, COL) ;
		NVOL:long_name = "NVOL            " ;
		NVOL:units = "moles/s         " ;
		NVOL:var_desc = "Hourly emission                                                                 " ;
	float OLE(TSTEP, LAY, ROW, COL) ;
		OLE:long_name = "OLE             " ;
		OLE:units = "moles/s         " ;
		OLE:var_desc = "Hourly emission                                                                 " ;
	float PAL(TSTEP, LAY, ROW, COL) ;
		PAL:long_name = "PAL             " ;
		PAL:units = "g/s             " ;
		PAL:var_desc = "Hourly emission                                                                 " ;
	float PAR(TSTEP, LAY, ROW, COL) ;
		PAR:long_name = "PAR             " ;
		PAR:units = "moles/s         " ;
		PAR:var_desc = "Hourly emission                                                                 " ;
	float PCA(TSTEP, LAY, ROW, COL) ;
		PCA:long_name = "PCA             " ;
		PCA:units = "g/s             " ;
		PCA:var_desc = "Hourly emission                                                                 " ;
	float PCL(TSTEP, LAY, ROW, COL) ;
		PCL:long_name = "PCL             " ;
		PCL:units = "g/s             " ;
		PCL:var_desc = "Hourly emission                                                                 " ;
	float PEC(TSTEP, LAY, ROW, COL) ;
		PEC:long_name = "PEC             " ;
		PEC:units = "g/s             " ;
		PEC:var_desc = "Hourly emission                                                                 " ;
	float PFE(TSTEP, LAY, ROW, COL) ;
		PFE:long_name = "PFE             " ;
		PFE:units = "g/s             " ;
		PFE:var_desc = "Hourly emission                                                                 " ;
	float PH2O(TSTEP, LAY, ROW, COL) ;
		PH2O:long_name = "PH2O            " ;
		PH2O:units = "g/s             " ;
		PH2O:var_desc = "Hourly emission                                                                 " ;
	float PK(TSTEP, LAY, ROW, COL) ;
		PK:long_name = "PK              " ;
		PK:units = "g/s             " ;
		PK:var_desc = "Hourly emission                                                                 " ;
	float PMC(TSTEP, LAY, ROW, COL) ;
		PMC:long_name = "PMC             " ;
		PMC:units = "g/s             " ;
		PMC:var_desc = "Hourly emission                                                                 " ;
	float PMG(TSTEP, LAY, ROW, COL) ;
		PMG:long_name = "PMG             " ;
		PMG:units = "g/s             " ;
		PMG:var_desc = "Hourly emission                                                                 " ;
	float PMN(TSTEP, LAY, ROW, COL) ;
		PMN:long_name = "PMN             " ;
		PMN:units = "g/s             " ;
		PMN:var_desc = "Hourly emission                                                                 " ;
	float PMOTHR(TSTEP, LAY, ROW, COL) ;
		PMOTHR:long_name = "PMOTHR          " ;
		PMOTHR:units = "g/s             " ;
		PMOTHR:var_desc = "Hourly emission                                                                 " ;
	float PNA(TSTEP, LAY, ROW, COL) ;
		PNA:long_name = "PNA             " ;
		PNA:units = "g/s             " ;
		PNA:var_desc = "Hourly emission                                                                 " ;
	float PNCOM(TSTEP, LAY, ROW, COL) ;
		PNCOM:long_name = "PNCOM           " ;
		PNCOM:units = "g/s             " ;
		PNCOM:var_desc = "Hourly emission                                                                 " ;
	float PNH4(TSTEP, LAY, ROW, COL) ;
		PNH4:long_name = "PNH4            " ;
		PNH4:units = "g/s             " ;
		PNH4:var_desc = "Hourly emission                                                                 " ;
	float PNO3(TSTEP, LAY, ROW, COL) ;
		PNO3:long_name = "PNO3            " ;
		PNO3:units = "g/s             " ;
		PNO3:var_desc = "Hourly emission                                                                 " ;
	float POC(TSTEP, LAY, ROW, COL) ;
		POC:long_name = "POC             " ;
		POC:units = "g/s             " ;
		POC:var_desc = "Hourly emission                                                                 " ;
	float PSI(TSTEP, LAY, ROW, COL) ;
		PSI:long_name = "PSI             " ;
		PSI:units = "g/s             " ;
		PSI:var_desc = "Hourly emission                                                                 " ;
	float PSO4(TSTEP, LAY, ROW, COL) ;
		PSO4:long_name = "PSO4            " ;
		PSO4:units = "g/s             " ;
		PSO4:var_desc = "Hourly emission                                                                 " ;
	float PTI(TSTEP, LAY, ROW, COL) ;
		PTI:long_name = "PTI             " ;
		PTI:units = "g/s             " ;
		PTI:var_desc = "Hourly emission                                                                 " ;
	float SO2(TSTEP, LAY, ROW, COL) ;
		SO2:long_name = "SO2             " ;
		SO2:units = "moles/s         " ;
		SO2:var_desc = "Hourly emission                                                                 " ;
	float SULF(TSTEP, LAY, ROW, COL) ;
		SULF:long_name = "SULF            " ;
		SULF:units = "moles/s         " ;
		SULF:var_desc = "Hourly emission                                                                 " ;
	float TERP(TSTEP, LAY, ROW, COL) ;
		TERP:long_name = "TERP            " ;
		TERP:units = "moles/s         " ;
		TERP:var_desc = "Hourly emission                                                                 " ;
	float TOL(TSTEP, LAY, ROW, COL) ;
		TOL:long_name = "TOL             " ;
		TOL:units = "moles/s         " ;
		TOL:var_desc = "Hourly emission                                                                 " ;
	float UNK(TSTEP, LAY, ROW, COL) ;
		UNK:long_name = "UNK             " ;
		UNK:units = "moles/s         " ;
		UNK:var_desc = "Hourly emission                                                                 " ;
	float UNR(TSTEP, LAY, ROW, COL) ;
		UNR:long_name = "UNR             " ;
		UNR:units = "moles/s         " ;
		UNR:var_desc = "Hourly emission                                                                 " ;
	float XYL(TSTEP, LAY, ROW, COL) ;
		XYL:long_name = "XYL             " ;
		XYL:units = "moles/s         " ;
		XYL:var_desc = "Hourly emission                                                                 " ;

// global attributes:
		:IOAPI_VERSION = "$Id: @(#) ioapi library version 3.1 $                                           " ;
		:EXEC_ID = "????????????????                                                                " ;
		:FTYPE = 1 ;
		:CDATE = 2023353 ;
		:CTIME = 13424 ;
		:WDATE = 2023353 ;
		:WTIME = 13424 ;
		:SDATE = 2022180 ;
		:STIME = 0 ;
		:TSTEP = 10000 ;
		:NTHIK = 1 ;
		:NCOLS = 176 ;
		:NROWS = 200 ;
		:NLAYS = 37 ;
		:NVARS = 46 ;
		:GDTYP = 2 ;
		:P_ALP = 30. ;
		:P_BET = 60. ;
		:P_GAM = 118.281 ;
		:XCENT = 118.281 ;
		:YCENT = 45. ;
		:XORIG = -277498.84375 ;
		:YORIG = -2399273.5 ;
		:XCELL = 3000. ;
		:YCELL = 3000. ;
		:VGTYP = 7 ;
		:VGTOP = 5000.f ;
		:VGLVLS = 1.f, 0.998f, 0.99f, 0.985f, 0.98f, 0.97f, 0.96f, 0.95f, 0.94f, 0.93f, 0.92f, 0.91f, 0.9f, 0.88f, 0.86f, 0.83f, 0.8f, 0.77f, 0.74f, 0.71f, 0.68f, 0.64f, 0.6f, 0.56f, 0.52f, 0.48f, 0.44f, 0.4f, 0.36f, 0.32f, 0.28f, 0.24f, 0.2f, 0.16f, 0.12f, 0.08f, 0.05f, 0.f ;
		:GDNAM = "LAM_27N109E     " ;
		:UPNAM = "MRGGRID         " ;
		:VAR-LIST = "ALD2            ALDX            BENZENE         CH4             CO              DLUSE           ETH             ETHA            ETOH            FORM            HONO            IOLE            ISOP            MEOH            NH3             NO              NO2             NVOL            OLE             PAL             PAR             PCA             PCL             PEC             PFE             PH2O            PK              PMC             PMG             PMN             PMOTHR          PNA             PNCOM           PNH4            PNO3            POC             PSI             PSO4            PTI             SO2             SULF            TERP            TOL             UNK             UNR             XYL             " ;
		:FILEDESC = "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                " ;
		:HISTORY = "" ;
}

emission_ncdump.txt (16.4 KB)
CTM_LOG_000.v532_gcc_2022FJ_20220629.txt (242.8 KB)
run_cctm_hj.csh (35.4 KB)

This section of your log file:

 |> Checking for unused Emissions Surrogates:
     ============================================
 GRIDDED_EMIS | Gridded Area Emissions File   1: 46 unused surrogates.

indicates that all of the species in your gridded emissions file are not being used.
You have commented out EMISSCTRL_NML. This is likely your problem–though I’m surprised the model did not crash without finding this file.

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