CMAQ v5.3.2 ISAM Simulation - Regional Source Contributions All Zero in Output

Dear All,

I am encountering an issue with my ISAM simulation using CMAQ v5.3.2 for the period 20250720-20250730, and I would appreciate your assistance in troubleshooting this problem.

The ISAM regional source contributions in the output file CCTM_SA_ACONC_*.nc are showing zero values across the entire domain for all regional tags (SZE, DGE, etc.), while the total pollutant concentrations in CCTM_ACONC_*.nc appear normal and reasonable.(upload://rAs4JLDvH8120pvUDkF7JrwBgI2.png)

Configuration Details:

  • CMAQ Version: 5.3.2 with ISAM

  • Simulation Period: July 20-30, 2025

  • Grid: 3km resolution (153×121)

  • Chemical Mechanism: SAPRC07TC_AE6_AQ

  • Regional Tags: SZE, DGE,

  • Tag Classes: SULFATE, OZONE

Files Available for Analysis:

ISAM control file :

TAG CLASSES |SULFATE, OZONE

TAG NAME |SZE
REGION(S) |SZ
EMIS STREAM(S) |TR, RE, PO, IN, AG, BG

TAG NAME |DGE
REGION(S) |DG
EMIS STREAM(S) |TR, RE, PO, IN, AG, BG

Emission control configuration:

&RegionsRegistry
RGN_NML =
! | Region Label | File_Label | Variable on File
! ‘EVERYWHERE’ ,‘N/A’ ,‘N/A’,
! ‘WATER’ ,‘CMAQ_MASKS’ ,‘OPEN’,
! ‘ALL’ ,‘CMAQ_MASKS’ ,‘ALL’,
‘SZ’ ,‘ISAM_REGIONS’,‘SZ’,

‘DG’ ,‘ISAM_REGIONS’,‘DG’,

Run script :

   #> Gridded Emissions files
  setenv N_EMIS_GR 6
 # set EMISfile  = emis_mole_all_${YYYYMMDD}_12US1_nobeis_2016ff_16j.ncf
  set EMISfile  =  SAPRC07_transportation_${APPL}_${YYYYMMDD}.nc
  setenv GR_EMIS_001 ${EMISpath}/${EMISfile}
  setenv GR_EMIS_LAB_001 TR
  setenv GR_EM_SYM_DATE_001 F # To change default behaviour please see Users Guide for EMIS_SYM_DATE

  set EMISfile  =  SAPRC07_residential_${APPL}_${YYYYMMDD}.nc
  setenv GR_EMIS_002 ${EMISpath}/${EMISfile}
  setenv GR_EMIS_LAB_002 RE
  setenv GR_EM_SYM_DATE_002 F

  set EMISfile  =  SAPRC07_power_${APPL}_${YYYYMMDD}.nc
  setenv GR_EMIS_003 ${EMISpath}/${EMISfile}
  setenv GR_EMIS_LAB_003 PO
  setenv GR_EM_SYM_DATE_003 F

  set EMISfile  =  SAPRC07_industry_${APPL}_${YYYYMMDD}.nc
  setenv GR_EMIS_004 ${EMISpath}/${EMISfile}
  setenv GR_EMIS_LAB_004 IN
  setenv GR_EM_SYM_DATE_004 F

  set EMISfile  =  SAPRC07_agriculture_${APPL}_${YYYYMMDD}.nc
  setenv GR_EMIS_005 ${EMISpath}/${EMISfile}
  setenv GR_EMIS_LAB_005 AG
  setenv GR_EM_SYM_DATE_005 F

  #set EMISfile  = emis_mole_rwc_${YYYYMMDD}_12US1_cmaq_cb6_2016ff_16j.ncf
  set EMISfile  = MEGANv31.${APPL}.J4.SAPRC07.${YYYYMMDD}.BDSNP.ncf
  setenv GR_EMIS_006 ${EMISpath2}/${EMISfile}
  setenv GR_EMIS_LAB_006 BG
  setenv GR_EM_SYM_DATE_006 F # To change default behaviour please see Users Guide for EMIS_SYM_DATE



#> 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 ISAM_REGIONS $INPDIR/data/MEIC/mask1.nc

    endif
 endif

CTM log files (CTM_LOG_*.txt)

================================================================================          
|                                                                              |          
|               The Community Multiscale Air Quality (CMAQ) Model              |          
|                                   Version 5.3.2                              |          
|                                                                              |          
|                          Built and Maintained by the                         |          
|                        Office of Research and Development                    |          
|                   United States Environmental Protection Agency              |          
|                                                                              |          
|                            https://www.epa.gov/cmaq                          |          
|                                                                              |          
|       Source Code:   https://www.github.com/USEPA/cmaq/tree/master           |          
|       Documentation: https://www.github.com/USEPA/cmaq/tree/master/DOCS      |          
|                                                                              |          
|         The CMAQ Model is tested and released with cooperation from          |          
|         the Community Modeling and Analysis System (CMAS) Center via         |          
|         contract support. CMAS is managed by the Institute for the           |          
|         Environment, University of North Carolina at Chapel Hill.            |          
|         CMAS URL: (https://www.cmascenter.org)                               |          
|                                                                              |          
================================================================================          

                                                                                          
     This program uses the EPA-AREAL/MCNC-EnvPgms/BAMS/ UNC IE                            
     Models-3 I/O Applications Programming Interface, [I/O API]                           
     which is built on top of the netCDF I/O library (Copyright                           
     993, 1996 University Corporation for Atmospheric Research                            
     Unidata Program) and the PVM parallel-programming library                            
     (from Oak Ridge National Laboratory).                                                
     Copyright (C) 1992-2002 MCNC,                                                        
     (C) 1992-2018 Carlie J. Coats, Jr.,                                                  
     (C) 2003-2012 Baron Advanced Meteorological Systems, LLC, and                        
     (C) 2014-2023 UNC Institute for the Environment.                                     
     Released under the GNU LGPL  License, version 2.1.  See URL                          
                                                                                          
         https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html                          
                                                                                          
     for conditions of use.                                                               
                                                                                          
     ioapi-3.2: $Id: init3.F90 247 2023-03-22 15:59:19Z coats $                           
     $Tag: 2023075 $                                                                      
     Version with PARMS3.EXT/PARAMETER::MXVARS3= 2048                                     
     netCDF version 4.9.2 of Aug 11 2025 11:44:45 $                                       
                                                                                          
                                                                                          
     EXECUTION_ID: CMAQ_CCTMv532_ISAM_wlx_20251121_033249_291869758                       
     Value for IOAPI_CHECK_HEADERS:  N returning FALSE
      
     "MET_CRO_3D" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/mcipout/domain3/METCRO3D_20250731.nc"
     File type GRDDED3 
     Execution ID "mcip"
     Grid name "3km_153X121_CROS"
     Dimensions: 121 rows, 153 cols, 34 lays, 16 vbles
     NetCDF ID:     65536  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25

     MET data determined based on WRF ARW version 4.3

     Closing file MET_CRO_3D


     ========================================
     |>---   RETRIEVE HORIZONTAL GRID   ---<|
     ========================================

     File "GRIDDESC" opened for input on unit:  98
     /disk1/modelout/mcipout/domain3/GRIDDESC



     ======================================
     |>---   RETRIEVE VERTICAL GRID   ---<|
     ======================================
      
     "MET_CRO_3D" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/mcipout/domain3/METCRO3D_20250731.nc"
     File type GRDDED3 
     Execution ID "mcip"
     Grid name "3km_153X121_CROS"
     Dimensions: 121 rows, 153 cols, 34 lays, 16 vbles
     NetCDF ID:     65536  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25

     =========================================
     |>---   RETRIEVE SPECIES NAMELIST   ---<|
     =========================================


     ===========================================
     |>---   INITIALIZE PROCESS ANALYSIS   ---<|
     ===========================================
     PA_DATAGEN: Process Analysis is not activated


     ==================================
     |>---   CONFIGURE SCENARIO   ---<|
     ==================================
 SA_IO_LIST Sucessfully Opened
 Start counting the list...
 Reading ISAM control file
 TAGCLASSES = SULFATE, OZONE
   for            2  tags
Tagged species found,   76, equals expected,   76, for the SAPRC07TC_AE6_AQ mechanism.
ISAM_INIT: SPC_LIST:    1 ASO4J           
ISAM_INIT: SPC_LIST:    2 ASO4I           
ISAM_INIT: SPC_LIST:    3 SO2             
ISAM_INIT: SPC_LIST:    4 SULF            
ISAM_INIT: SPC_LIST:    5 SULRXN          
ISAM_INIT: SPC_LIST:    6 ANO3J           
ISAM_INIT: SPC_LIST:    7 ANO3I           
ISAM_INIT: SPC_LIST:    8 HNO3            
ISAM_INIT: SPC_LIST:    9 NO              
ISAM_INIT: SPC_LIST:   10 NO2             
ISAM_INIT: SPC_LIST:   11 NO3             
ISAM_INIT: SPC_LIST:   12 HONO            
ISAM_INIT: SPC_LIST:   13 N2O5            
ISAM_INIT: SPC_LIST:   14 PAN             
ISAM_INIT: SPC_LIST:   15 HNO4            
ISAM_INIT: SPC_LIST:   16 RNO3            
ISAM_INIT: SPC_LIST:   17 PAN2            
ISAM_INIT: SPC_LIST:   18 CLNO            
ISAM_INIT: SPC_LIST:   19 CLONO           
ISAM_INIT: SPC_LIST:   20 CLONO2          
ISAM_INIT: SPC_LIST:   21 xNO2            
ISAM_INIT: SPC_LIST:   22 MEO2            
ISAM_INIT: SPC_LIST:   23 xMEO2           
ISAM_INIT: SPC_LIST:   24 RO2C            
ISAM_INIT: SPC_LIST:   25 RO2XC           
ISAM_INIT: SPC_LIST:   26 MECO3           
ISAM_INIT: SPC_LIST:   27 xMECO3          
ISAM_INIT: SPC_LIST:   28 RCO3            
ISAM_INIT: SPC_LIST:   29 xRCO3           
ISAM_INIT: SPC_LIST:   30 BZCO3           
ISAM_INIT: SPC_LIST:   31 PBZN            
ISAM_INIT: SPC_LIST:   32 MACO3           
ISAM_INIT: SPC_LIST:   33 CO              
ISAM_INIT: SPC_LIST:   34 HCHO            
ISAM_INIT: SPC_LIST:   35 CCHO            
ISAM_INIT: SPC_LIST:   36 RCHO            
ISAM_INIT: SPC_LIST:   37 xHCHO           
ISAM_INIT: SPC_LIST:   38 xCCHO           
ISAM_INIT: SPC_LIST:   39 xRCHO           
ISAM_INIT: SPC_LIST:   40 ALK1            
ISAM_INIT: SPC_LIST:   41 ALK2            
ISAM_INIT: SPC_LIST:   42 ALK3            
ISAM_INIT: SPC_LIST:   43 ALK4            
ISAM_INIT: SPC_LIST:   44 ALK5            
ISAM_INIT: SPC_LIST:   45 ETHENE          
ISAM_INIT: SPC_LIST:   46 ACETYLENE       
ISAM_INIT: SPC_LIST:   47 PROPENE         
ISAM_INIT: SPC_LIST:   48 ISOPRENE        
ISAM_INIT: SPC_LIST:   49 TERP            
ISAM_INIT: SPC_LIST:   50 SESQ            
ISAM_INIT: SPC_LIST:   51 APIN            
ISAM_INIT: SPC_LIST:   52 OLE1            
ISAM_INIT: SPC_LIST:   53 OLE2            
ISAM_INIT: SPC_LIST:   54 ETOH            
ISAM_INIT: SPC_LIST:   55 MEOH            
ISAM_INIT: SPC_LIST:   56 GLY             
ISAM_INIT: SPC_LIST:   57 MGLY            
ISAM_INIT: SPC_LIST:   58 BENZENE         
ISAM_INIT: SPC_LIST:   59 TMBENZ124       
ISAM_INIT: SPC_LIST:   60 TOLUENE         
ISAM_INIT: SPC_LIST:   61 MXYL            
ISAM_INIT: SPC_LIST:   62 OXYL            
ISAM_INIT: SPC_LIST:   63 PXYL            
ISAM_INIT: SPC_LIST:   64 NAPHTHAL        
ISAM_INIT: SPC_LIST:   65 ARO1            
ISAM_INIT: SPC_LIST:   66 ARO2MN          
ISAM_INIT: SPC_LIST:   67 BUTADIENE13     
ISAM_INIT: SPC_LIST:   68 ACROLEIN        
ISAM_INIT: SPC_LIST:   69 ACETONE         
ISAM_INIT: SPC_LIST:   70 MEK             
ISAM_INIT: SPC_LIST:   71 MVK             
ISAM_INIT: SPC_LIST:   72 MACR            
ISAM_INIT: SPC_LIST:   73 HO2             
ISAM_INIT: SPC_LIST:   74 O3              
ISAM_INIT: SPC_LIST:   75 O1D             
ISAM_INIT: SPC_LIST:   76 O3P             
ISAM_INIT: SPC_LIST:    1 ASO4J           
ISAM_INIT: SPC_LIST:    2 ASO4I           
ISAM_INIT: SPC_LIST:    3 SO2             
ISAM_INIT: SPC_LIST:    4 SULF            
ISAM_INIT: SPC_LIST:    5 SULRXN          
ISAM_INIT: SPC_LIST:    6 ANO3J           
ISAM_INIT: SPC_LIST:    7 ANO3I           
ISAM_INIT: SPC_LIST:    8 HNO3            
ISAM_INIT: SPC_LIST:    9 NO              
ISAM_INIT: SPC_LIST:   10 NO2             
ISAM_INIT: SPC_LIST:   11 NO3             
ISAM_INIT: SPC_LIST:   12 HONO            
ISAM_INIT: SPC_LIST:   13 N2O5            
ISAM_INIT: SPC_LIST:   14 PAN             
ISAM_INIT: SPC_LIST:   15 HNO4            
ISAM_INIT: SPC_LIST:   16 RNO3            
ISAM_INIT: SPC_LIST:   17 PAN2            
ISAM_INIT: SPC_LIST:   18 CLNO            
ISAM_INIT: SPC_LIST:   19 CLONO           
ISAM_INIT: SPC_LIST:   20 CLONO2          
ISAM_INIT: SPC_LIST:   21 xNO2            
ISAM_INIT: SPC_LIST:   22 MEO2            
ISAM_INIT: SPC_LIST:   23 xMEO2           
ISAM_INIT: SPC_LIST:   24 RO2C            
ISAM_INIT: SPC_LIST:   25 RO2XC           
ISAM_INIT: SPC_LIST:   26 MECO3           
ISAM_INIT: SPC_LIST:   27 xMECO3          
ISAM_INIT: SPC_LIST:   28 RCO3            
ISAM_INIT: SPC_LIST:   29 xRCO3           
ISAM_INIT: SPC_LIST:   30 BZCO3           
ISAM_INIT: SPC_LIST:   31 PBZN            
ISAM_INIT: SPC_LIST:   32 MACO3           
ISAM_INIT: SPC_LIST:   33 CO              
ISAM_INIT: SPC_LIST:   34 HCHO            
ISAM_INIT: SPC_LIST:   35 CCHO            
ISAM_INIT: SPC_LIST:   36 RCHO            
ISAM_INIT: SPC_LIST:   37 xHCHO           
ISAM_INIT: SPC_LIST:   38 xCCHO           
ISAM_INIT: SPC_LIST:   39 xRCHO           
ISAM_INIT: SPC_LIST:   40 ALK1            
ISAM_INIT: SPC_LIST:   41 ALK2            
ISAM_INIT: SPC_LIST:   42 ALK3            
ISAM_INIT: SPC_LIST:   43 ALK4            
ISAM_INIT: SPC_LIST:   44 ALK5            
ISAM_INIT: SPC_LIST:   45 ETHENE          
ISAM_INIT: SPC_LIST:   46 ACETYLENE       
ISAM_INIT: SPC_LIST:   47 PROPENE         
ISAM_INIT: SPC_LIST:   48 ISOPRENE        
ISAM_INIT: SPC_LIST:   49 TERP            
ISAM_INIT: SPC_LIST:   50 SESQ            
ISAM_INIT: SPC_LIST:   51 APIN            
ISAM_INIT: SPC_LIST:   52 OLE1            
ISAM_INIT: SPC_LIST:   53 OLE2            
ISAM_INIT: SPC_LIST:   54 ETOH            
ISAM_INIT: SPC_LIST:   55 MEOH            
ISAM_INIT: SPC_LIST:   56 GLY             
ISAM_INIT: SPC_LIST:   57 MGLY            
ISAM_INIT: SPC_LIST:   58 BENZENE         
ISAM_INIT: SPC_LIST:   59 TMBENZ124       
ISAM_INIT: SPC_LIST:   60 TOLUENE         
ISAM_INIT: SPC_LIST:   61 MXYL            
ISAM_INIT: SPC_LIST:   62 OXYL            
ISAM_INIT: SPC_LIST:   63 PXYL            
ISAM_INIT: SPC_LIST:   64 NAPHTHAL        
ISAM_INIT: SPC_LIST:   65 ARO1            
ISAM_INIT: SPC_LIST:   66 ARO2MN          
ISAM_INIT: SPC_LIST:   67 BUTADIENE13     
ISAM_INIT: SPC_LIST:   68 ACROLEIN        
ISAM_INIT: SPC_LIST:   69 ACETONE         
ISAM_INIT: SPC_LIST:   70 MEK             
ISAM_INIT: SPC_LIST:   71 MVK             
ISAM_INIT: SPC_LIST:   72 MACR            
ISAM_INIT: SPC_LIST:   73 HO2             
ISAM_INIT: SPC_LIST:   74 O3              
ISAM_INIT: SPC_LIST:   75 O1D             
ISAM_INIT: SPC_LIST:   76 O3P             
 # FINAL List of ISAM species =           76
   1 ASO4J           
   2 ASO4I           
   3 SO2             
   4 SULF            
   5 SULRXN          
   6 ANO3J           
   7 ANO3I           
   8 HNO3            
   9 NO              
  10 NO2             
  11 NO3             
  12 HONO            
  13 N2O5            
  14 PAN             
  15 HNO4            
  16 RNO3            
  17 PAN2            
  18 CLNO            
  19 CLONO           
  20 CLONO2          
  21 xNO2            
  22 MEO2            
  23 xMEO2           
  24 RO2C            
  25 RO2XC           
  26 MECO3           
  27 xMECO3          
  28 RCO3            
  29 xRCO3           
  30 BZCO3           
  31 PBZN            
  32 MACO3           
  33 CO              
  34 HCHO            
  35 CCHO            
  36 RCHO            
  37 xHCHO           
  38 xCCHO           
  39 xRCHO           
  40 ALK1            
  41 ALK2            
  42 ALK3            
  43 ALK4            
  44 ALK5            
  45 ETHENE          
  46 ACETYLENE       
  47 PROPENE         
  48 ISOPRENE        
  49 TERP            
  50 SESQ            
  51 APIN            
  52 OLE1            
  53 OLE2            
  54 ETOH            
  55 MEOH            
  56 GLY             
  57 MGLY            
  58 BENZENE         
  59 TMBENZ124       
  60 TOLUENE         
  61 MXYL            
  62 OXYL            
  63 PXYL            
  64 NAPHTHAL        
  65 ARO1            
  66 ARO2MN          
  67 BUTADIENE13     
  68 ACROLEIN        
  69 ACETONE         
  70 MEK             
  71 MVK             
  72 MACR            
  73 HO2             
  74 O3              
  75 O1D             
  76 O3P             
ISAM WARNING: Tagged Species, SULRXN not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, xNO2 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, MEO2 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, xMEO2 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, RO2C not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, RO2XC not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, MECO3 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, xMECO3 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, RCO3 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, xRCO3 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, MACO3 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, xHCHO not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, xCCHO not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, xRCHO not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, HO2 not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, O1D not transported. Modify species namelist(s) to include process.
ISAM WARNING: Tagged Species, O3P not transported. Modify species namelist(s) to include process.
     
     >>--->> WARNING in subroutine GET_SPC_INDEX on PE 000
     Above Problems Encountered
     
     INIT_MEDC_1     :/disk1/modelout/data/output_CCTM_region_v532_ISAM_gcc_3km_153X121/CCTM_MEDIA_CONC_v532_ISAM_gcc_3km_153X121_20250730.nc
     
     >>--->> WARNING in subroutine OPEN3
     File not available.
     
      
     "GRID_CRO_2D" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/mcipout/domain3/GRIDCRO2D_20250731.nc"
     File type GRDDED3 
     Execution ID "mcip"
     Grid name "3km_153X121_CROS"
     Dimensions: 121 rows, 153 cols, 1 lays, 7 vbles
     NetCDF ID:    131072  opened as READONLY            
     Time-independent data.
      
     "GRID_DOT_2D" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/mcipout/domain3/GRIDDOT2D_20250731.nc"
     File type GRDDED3 
     Execution ID "mcip"
     Grid name "3km_153X121_DOT"
     Dimensions: 122 rows, 154 cols, 1 lays, 9 vbles
     NetCDF ID:    196608  opened as READONLY            
     Time-independent data.
      
     "LUFRAC_CRO" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/mcipout/domain3/LUFRAC_CRO_20250731.nc"
     File type GRDDED3 
     Execution ID "mcip"
     Grid name "3km_153X121_CROS"
     Dimensions: 121 rows, 153 cols, 21 lays, 1 vbles
     NetCDF ID:    262144  opened as READONLY            
     Time-independent data.
      
     "MET_CRO_2D" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/mcipout/domain3/METCRO2D_20250731.nc"
     File type GRDDED3 
     Execution ID "mcip"
     Grid name "3km_153X121_CROS"
     Dimensions: 121 rows, 153 cols, 1 lays, 35 vbles
     NetCDF ID:    327680  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25
      
     "MET_DOT_3D" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/mcipout/domain3/METDOT3D_20250731.nc"
     File type GRDDED3 
     Execution ID "mcip"
     Grid name "3km_153X121_DOT"
     Dimensions: 122 rows, 154 cols, 34 lays, 6 vbles
     NetCDF ID:    393216  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25
      
     "GR_EMIS_001" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/data/MEIC/MEIC3km_1/SAPRC07_transportation_3km_153X121_20250731.nc"
     File type GRDDED3 
     Execution ID "GRIDDESC"
     Grid name "3km_153X121"
     Dimensions: 121 rows, 153 cols, 1 lays, 59 vbles
     NetCDF ID:    458752  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25
GR_EM_SYM_DATE_0  |          F
      
     "GR_EMIS_002" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/data/MEIC/MEIC3km_1/SAPRC07_residential_3km_153X121_20250731.nc"
     File type GRDDED3 
     Execution ID "GRIDDESC"
     Grid name "3km_153X121"
     Dimensions: 121 rows, 153 cols, 1 lays, 59 vbles
     NetCDF ID:    524288  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25
GR_EM_SYM_DATE_0  |          F
      
     "GR_EMIS_003" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/data/MEIC/MEIC3km_1/SAPRC07_power_3km_153X121_20250731.nc"
     File type GRDDED3 
     Execution ID "GRIDDESC"
     Grid name "3km_153X121"
     Dimensions: 121 rows, 153 cols, 1 lays, 59 vbles
     NetCDF ID:    589824  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25
GR_EM_SYM_DATE_0  |          F
      
     "GR_EMIS_004" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/data/MEIC/MEIC3km_1/SAPRC07_industry_3km_153X121_20250731.nc"
     File type GRDDED3 
     Execution ID "GRIDDESC"
     Grid name "3km_153X121"
     Dimensions: 121 rows, 153 cols, 1 lays, 59 vbles
     NetCDF ID:    655360  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25
GR_EM_SYM_DATE_0  |          F
      
     "GR_EMIS_005" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/data/MEIC/MEIC3km_1/SAPRC07_agriculture_3km_153X121_20250731.nc"
     File type GRDDED3 
     Execution ID "GRIDDESC"
     Grid name "3km_153X121"
     Dimensions: 121 rows, 153 cols, 1 lays, 59 vbles
     NetCDF ID:    720896  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25
GR_EM_SYM_DATE_0  |          F
      
     "GR_EMIS_006" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/data/BVOCs/MEGANv31.3km_153X121.J4.SAPRC07.20250731.BDSNP.ncf"
     File type GRDDED3 
     Execution ID "????????????????"
     Grid name "3km_153X121_CROS"
     Dimensions: 121 rows, 153 cols, 1 lays, 44 vbles
     NetCDF ID:    786432  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number        25
GR_EM_SYM_DATE_0  |          F
      
     "INIT_CONC_1" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/data/output_CCTM_region_v532_ISAM_gcc_3km_153X121/CCTM_CGRID_v532_ISAM_gcc_3km_153X121_20250730.nc"
     File type GRDDED3 
     Execution ID "CMAQ_CCTMv532_ISAM_wlx_20251121_033249_291869758"
     Grid name "3km_153X121"
     Dimensions: 121 rows, 153 cols, 34 lays, 277 vbles
     NetCDF ID:    851968  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number         1
      
     "ISAM_PREVDAY" opened as OLD:READ-ONLY   
     File name "/disk1/modelout/data/output_CCTM_region_v532_ISAM_gcc_3km_153X121/CCTM_SA_CGRID_v532_ISAM_gcc_3km_153X121_20250730.nc"
     File type GRDDED3 
     Execution ID "CMAQ_CCTMv532_ISAM_wlx_20251121_033249_291869758"
     Grid name "3km_153X121"
     Dimensions: 121 rows, 153 cols, 34 lays, 380 vbles
     NetCDF ID:    917504  opened as READONLY            
     Starting date and time  2025211:160000 (16:00:00  July 30, 2025)
     Timestep                          010000 (1:00:00 hh:mm:ss)
     Maximum current record number         1


ISAM regional definition files
![ScreenShot_2025-11-23_131741_445|633x500](upload://xN7IeV1XezEqW1AI7i62A96lZmR.png)
![ScreenShot_2025-11-23_131756_924|690x473](upload://ohciDKFiZCMviU9OfGIsZw6erjj.png)

Hi Lucy,

I am not exactly sure why you are getting all zeros, but the first thing I would check would be the contents of the “mask1.nc” file. Make sure that the values for the variables “SZ” and “DG” exist and are between 0.0 and 1.0 in the geographical area where you expect them. Also, make sure there is some notice in the log files where the model is opening and reading this file without issue.

Sergey