How to simulate OC with CMAQ

Dear all,
I made an inventory of a city in China.It contains 5 department and 9 air pollutants. I use SMOKE 4.7 to make emission files,andPOC is included in the PM2.5 species I input.I use CMAQ5.3.1 with cb6r3_ae6_aq to simulate PM2.5. But I find the concentration of OC is zero after running for a month.
I don’t konw which part I made some mistakes. Could you please give me some hints?

The amount of POC that can be extracted from my emission file. It shows in following:
Variable: sumPOC
Type: float
Total Size: 4 bytes
1 values
Number of Dimensions: 1
Dimensions and sizes: [1]
Coordinates:
(0) 3332361

Here is one of my specie list:

9928;“PM2_5”;“PAL”;0.000926;1;0.000926
9928;“PM2_5”;“PCA”;0.005505178;1;0.005505178
9928;“PM2_5”;“PCL”;0.001517406;1;0.001517406
9928;“PM2_5”;“PEC”;0.10178;1;0.10178
9928;“PM2_5”;“PFE”;0.010285188;1;0.010285188
9928;“PM2_5”;“PH2O”;0.000613;1;0.000613
9928;“PM2_5”;“PK”;0.000376;1;0.000376
9928;“PM2_5”;“PMG”;0.006732708;1;0.006732708
9928;“PM2_5”;“PMN”;0.0000826;1;0.0000826
9928;“PM2_5”;“PMOTHR”;0.30689824;1;0.30689824
9928;“PM2_5”;“PNA”;0.000494;1;0.000494
9928;“PM2_5”;“PNCOM”;0.062006847;1;0.062006847
9928;“PM2_5”;“PNH4”;0.056187;1;0.056187
9928;“PM2_5”;“PNO3”;0.078405;1;0.078405
9928;“PM2_5”;“POC”;0.33006;1;0.33006
9928;“PM2_5”;“PSI”;0.007219833;1;0.007219833
9928;“PM2_5”;“PSO4”;0.030586;1;0.030586
9928;“PM2_5”;“PTI”;0.000325;1;0.000325

I input 3 VOC sources, but the contributions to OC are all zero. And my EmissCtrl_t_cb6r3_ae6_aq.nml is dafault. The ISAM of CMAQ5.3.1 is based on the cb6r3_ae7_aq mechanis. So the ke of my problem should be the mechanis?

Dose cb6r3_ae6_aq has OC Generation mechanism?

It seems your posts in this thread touch on two issues:

  • Your earlier posts state that your simulated OC concentrations were zero despite your inclusion of primary OC emissions in your emissions file

  • Your latest posts mention zero OC contributions from VOC sources in ISAM

The lack of OC contributions from VOC sources in ISAM is expected because the current implementation of ISAM does not support source attribution of secondary OC. OC source attribution is supported for primary OC only.

While ISAM currently does not support source attribution for secondary OC, the cb6r3_ae6_aq mechanism includes the formation of secondary organic aerosols from anthropogenic and biogenic VOC precursor species so the simulated OC concentrations should not be zero if the relevant precursor species are present.

If your simulated OC concentrations are still zero, you want to examine the CTM_LOG files for potential errors or warnings in mapping the species from your emissions file(s) to the CMAQ model species for both primary OC and VOC precursors of secondary organic aerosols.

Thank you for you reply @hogrefe.christian
I ncdump the value of the SA_CONC, the OC’s concentration is about e-21, too small. As you told, the OC source attribution is supported for primary OC only. How to rise the primary OC? My PM2.5 species contain POC, should I input OC and BC source in the SMOKE in addition?

Before discussing ISAM results, can you please clarify whether or not the OC results in the CONC or ACONC files (not the SA_CONC or SA_ACONC files) seem reasonable? Your initial posts mention that they didn’t look reasonable, but it’s not clear if you fixed that problem before moving on to ISAM.

Given the example speciation profile you posted and given that you mentioned that you work with the default EmissCtrl file for cb6r3_ae6_aq (there seemed to be an extra “_t” in the file name you posted), you want to look at the magnitude and spatial pattern for species APOCJ and APNCOMJ. You can also compare these to AOTHRJ - based on your example speciation profile, AOTHRJ and APOCJ may have a similar magnitude.

If these magnitudes are lower than what you expect, you first want to double check that your emission file was read and mapped correctly by CMAQ. You do this carefully by reviewing this section in the CTM_LOG files

" ===========================================
|>— INITIALIZE EMISSIONS MODULE —<|
===========================================
"

all the way to

" ================================================================================
|> END EMISSIONS SCALING PREPARATION AND DIAGNOSTIC OUTPUT
"

If everything looks o.k. there, then the problem likely would be with the magnitude of the emissions. In that case, you’d want to tag your question with “SMOKE” and maybe start a new thread asking for help in reviewing the steps you took in preparing your CMAQ-ready emission files from your starting inventories.

Regarding this question, this really depends on what PM2.5 in your underlying inventory represents. Does it include OC and BC? It seems you may have separate OC and BC inventories, but opted to base your SMOKE processing on PM25 only and applied speciation profiles to estimate OC and EC from that PM25 number. If your PM25 total includes OC and BC and your speciation profiles are adequate, that’s probably o.k., but if you also do have OC and EC emissions and they were not included in the PM25 emissions, then you would need to account for them in your emissions processing.

Your suggestion are always helpful with my questions, thank you.@hogrefe.christian
I ncdump the value of AOTHRJ, and it looks right:
1.755064, 1.783399, 1.491545, 1.346599, 1.358861, 3.483655, 1.768755,
1.479154, 1.442184, 1.325247, 1.30257, 1.394619, 1.486664, 1.514659,
1.425774, 1.360975, 1.291046, 1.383237, 1.421548, 1.326904, 1.204934,
1.167239, 1.185602, 1.267868, 1.315572, 1.262768, 1.240267, 1.330585,
1.408326, 1.329302, 1.384865, 1.372679, 1.459593, 1.687707, 1.896025,
1.373465, 1.475192, 1.662637, 2.005848, 1.61383, 1.997012, 1.575644,

I checked my CTM_LOG files:

I find that the APOCI, APOCJ, APNCOMI, APNCOMJ are all zero in the area and point “SCALE”
So I wang to change the EmissCtrl_cb6r3_ae6_aq.nml:
! → Nonvolatile POA
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘APOC’ ,‘FINE’,0.5 ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘APNCOM’ ,‘FINE’,0.5 ,‘MASS’,‘a’,

Here is the CTM_LOG:
|>— INITIALIZE EMISSIONS MODULE —<|
===========================================
EMISDIAG_SUM | F
GR_EMIS_LAB_001 | GR1
GR_EMIS_APPLY_00 | T (default)
GR_EM_SYM_DATE_0 | F
GR_EMIS_DIAG_001 | TRUE (default)
STK_EMIS_LAB_001 | PT_NONEGU
STK_EMIS_APPLY_0 | T (default)
STK_EM_SYM_DATE_ | T
STK_EMIS_DIAG_00 | TRUE (default)

 |> Open Gridded Emissions:
 +===========================
 Number of Emissions Layers:          40
 out of total Number of Model Layers: 40

 |> Initialize Point Emissions:
 +===============================
 Using in-line 3d point source emissions option
 NOTE: Environment variable REP_LAYR_MIN is less than 1.  Turning off reporting...
 
 Value for PROMPTFLAG:  F returning FALSE

 |> Initialize Biogenic Emissions:
 +==================================

 |> Initialize Online Biogenic VOC Emissions Module (BEIS):
 +===========================================================

 |> Initialize Marine Gas Emissions:
 +====================================

 |> Initialize Lightning NO Emissions:
 +======================================

 |> Process Aerosol Emissions:
 +==============================
 Map SOA Precursors
 Note: Optional species ALK5RXN is not found in G2AE or N2AE values of
   the GC or NR namelist. Simulation will ignore this species.

 |> Check Emissions Mapping:
 +============================


 =============================================================================
 |> SCALING EMISSIONS CONSISTENT WITH EMISSIONS CONTROL FILE SUPPLIED BY USER
 =============================================================================

 |> Regions Available for Scaling:
 =================================
    Number  Region Label        File Label          Variable
    ------  ------------        ----------          --------
      1     EVERYWHERE          N/A                 N/A
      2     R01                 ISAM_REGIONS        M01
      3     R02                 ISAM_REGIONS        M02
      4     R03                 ISAM_REGIONS        M03
      5     R04                 ISAM_REGIONS        M04
      6     R05                 ISAM_REGIONS        M05
      7     R06                 ISAM_REGIONS        M06
      8     R07                 ISAM_REGIONS        M07
      9     R08                 ISAM_REGIONS        M08
     10     R09                 ISAM_REGIONS        M09
     11     R10                 ISAM_REGIONS        M10
     12     R11                 ISAM_REGIONS        M11

 |> Map Available Emissions Surrogates to Defaults:
 ==================================================

 |> Checking Emissions Surrogate Units:
 ======================================

 |> Emission Stream Family Definitions:
 ======================================
    Stream Family Label               Stream Family Members
    -------------------               ---------------------

 |> CMAQ Species Family Definitions:
 ======================================
    Species Family Label              Species Family Members
    --------------------              ---------------------

 |> Mapping Particle Size Distributions to Each Emission Stream:
 ===============================================================

 ATTENTION: The Emissions Stream Label (WBDUST) applied for Rule   1
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 ATTENTION: The Emissions Stream Label (WBDUST) applied for Rule   2
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 ATTENTION: The Emissions Stream Label (SEASPRAY) applied for Rule   3
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 ATTENTION: The Emissions Stream Label (SEASPRAY) applied for Rule   4
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 *** ATTENTION **********************************************:
 The emission surrogate or member of family CL2
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family HCL
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family SESQ
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family SOAALK
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family ACROLEIN
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family ALD2_PRIMARY
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family FORM_PRIMARY
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family ACROLEIN
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family BUTADIENE13
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family TOLU
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 ATTENTION: The Emissions Stream Label (PT_FIRES) applied for Rule  87
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 ATTENTION: The Emissions Stream Label (PT_RXFIRES) applied for Rule  88
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 ATTENTION: The Emissions Stream Label (PT_AGFIRES) applied for Rule  89
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 ATTENTION: The Emissions Stream Label (PT_OTHFIRES) applied for Rule  90
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 ATTENTION: The Emissions Stream Label (PT_FIRES_MXCA) applied for Rule  91
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 ATTENTION: The Emissions Stream Label (GR_RES_FIRES) applied for Rule  92
 in the Emissions Control Namelist does not match any of the emissions streams 
 labels or families provided to CMAQ. Please check the 
 runscript against your emissions control inputs
 confirm that this stream should be ignored.


 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_SO4
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_NO3
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_CL
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_NH4
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_NA
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_CA
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_MG
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_K
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_FE
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_AL
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_SI
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_TI
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_MN
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_H2O
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_OTHR
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_LVPO1
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMFINE_LVOO1
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMCOARSE_SO4
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMCOARSE_NO3
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMCOARSE_CL
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMCOARSE_H2O
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMCOARSE_SOIL
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************

 *** ATTENTION **********************************************:
 The emission surrogate or member of family PMCOARSE_SEACAT
 was not found in the requested emission streams but the 
 CTM_EMISCHK environment variable set to False so simulation 
 will proceed.
 *************************************************************
|> Checking for unused Emissions Surrogates:
 ============================================
 GR1 | Gridded Area Emissions File   1: 28 unused surrogates.
      ALDX“;0.122358

 PT_NONEGU | Point Emissions File   1: 26 unused surrogates.
      ALDX“;0.122358

 NOTE: Some Emissions Surrogates are unused by your current
 emission control configuration. You may want to include these 
 emissions if they are relevant to your application.

 |> Checking status of used Emissions Surrogates:
 ================================================


 |> EMISSIONS SCALING DIAGNOSTIC:
 ==================================
   Note: these are populated using rules from the
         Emission Control File Supplied by the User.

 >--------------------------------------------------------------------------------
 Stream Type: "Gridded Area Emissions File   1" | Sector Label: GR1 (01)

    Table of Aerosol Size Distributions Available for Use Sector-Wide.
    Note that Mode 1 is reserved for gas-phase species and surrogates.
      Number  Surrogate Mode  Reference Mode (see AERO_DATA.F)
      ------  --------------  --------------------------------
      2       FINE                        FINE_REF
      3       COARSE                    COARSE_REF

    CMAQ Species     Phase/Mode  Surrogate         Region             Op ScaleFac Basis FinalFac
    ------------     ----------  ---------         ------             -- -------- ----- --------
      NO2              GAS        NO2              EVERYWHERE         a   1.000    UNIT   1.000
      NO               GAS        NO               EVERYWHERE         a   1.000    UNIT   1.000
      HONO             GAS        HONO             EVERYWHERE         a   1.000    UNIT   1.000
      SO2              GAS        SO2              EVERYWHERE         a   1.000    UNIT   1.000
      SULF             GAS        SULF             EVERYWHERE         a   0.000    UNIT   0.000
      AACD             GAS        AACD             EVERYWHERE         a   1.000    UNIT   1.000
      ALD2             GAS        ALD2             EVERYWHERE         a   1.000    UNIT   1.000
      FORM             GAS        FORM             EVERYWHERE         a   1.000    UNIT   1.000
      MEOH             GAS        MEOH             EVERYWHERE         a   1.000    UNIT   1.000
      FACD             GAS        FACD             EVERYWHERE         a   1.000    UNIT   1.000
      CO               GAS        CO               EVERYWHERE         a   1.000    UNIT   1.000
      ALDX             GAS        ALDX             EVERYWHERE         a   1.000    UNIT   1.000
      ETHA             GAS        ETHA             EVERYWHERE         a   1.000    UNIT   1.000
      ETOH             GAS        ETOH             EVERYWHERE         a   1.000    UNIT   1.000
      KET              GAS        KET              EVERYWHERE         a   1.000    UNIT   1.000
      PAR              GAS        PAR              EVERYWHERE         a   1.000    UNIT   1.000
      ACET             GAS        ACET             EVERYWHERE         a   1.000    UNIT   1.000
      PRPA             GAS        PRPA             EVERYWHERE         a   1.000    UNIT   1.000
      ETHY             GAS        ETHY             EVERYWHERE         a   1.000    UNIT   1.000
      ETH              GAS        ETH              EVERYWHERE         a   1.000    UNIT   1.000
      OLE              GAS        OLE              EVERYWHERE         a   1.000    UNIT   1.000
      IOLE             GAS        IOLE             EVERYWHERE         a   1.000    UNIT   1.000
      ISOP             GAS        ISOP             EVERYWHERE         a   1.000    UNIT   1.000
      TERP             GAS        TERP             EVERYWHERE         a   1.000    UNIT   1.000
      BENZENE          GAS        BENZ             EVERYWHERE         a   1.000    UNIT   1.000
      TOL              GAS        TOL              EVERYWHERE         a   1.000    UNIT   1.000
      XYLMN            GAS        XYLMN            EVERYWHERE         a   1.000    UNIT   1.000
      NAPH             GAS        NAPH             EVERYWHERE         a   1.000    UNIT   1.000
      ECH4             GAS        CH4              EVERYWHERE         a   1.000    UNIT   1.000
      VLVPO1           GAS        POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      VSVPO1           GAS        POC              EVERYWHERE         a   0.045    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.045    MASS   0.000
      VSVPO2           GAS        POC              EVERYWHERE         a   0.140    MASS   0.001
                                  PNCOM            EVERYWHERE         a   0.140    MASS   0.001
      VSVPO3           GAS        POC              EVERYWHERE         a   0.180    MASS   0.001
                                  PNCOM            EVERYWHERE         a   0.180    MASS   0.001
      VIVPO1           GAS        POC              EVERYWHERE         a   0.500    MASS   0.002
                                  PNCOM            EVERYWHERE         a   0.500    MASS   0.002
      PCVOC            GAS        POC              EVERYWHERE         a   6.579    MASS   0.039
                                  PNCOM            EVERYWHERE         a   6.579    MASS   0.039
      ASO4J            FINE       SULF             EVERYWHERE         a   1.000    MASS  88.200
                                  PSO4             EVERYWHERE         a   1.000    UNIT   0.900
      ASO4I            FINE       SULF             EVERYWHERE         a   1.000    MASS   9.800
                                  PSO4             EVERYWHERE         a   1.000    UNIT   0.100
      ANH4J            FINE       PNH4             EVERYWHERE         a   1.000    UNIT   0.900
      ANH4I            FINE       PNH4             EVERYWHERE         a   1.000    UNIT   0.100
      ANO3J            FINE       PNO3             EVERYWHERE         a   1.000    UNIT   0.900
      ANO3I            FINE       PNO3             EVERYWHERE         a   1.000    UNIT   0.100
      AECJ             FINE       PEC              EVERYWHERE         a   1.000    UNIT   0.900
      AECI             FINE       PEC              EVERYWHERE         a   1.000    UNIT   0.100
      AOTHRJ           FINE       PMOTHR           EVERYWHERE         a   1.000    UNIT   0.900
      AOTHRI           FINE       PMOTHR           EVERYWHERE         a   1.000    UNIT   0.100
      AFEJ             FINE       PFE              EVERYWHERE         a   1.000    UNIT   1.000
      AALJ             FINE       PAL              EVERYWHERE         a   1.000    UNIT   1.000
      ASIJ             FINE       PSI              EVERYWHERE         a   1.000    UNIT   1.000
      ATIJ             FINE       PTI              EVERYWHERE         a   1.000    UNIT   1.000
      ACAJ             FINE       PCA              EVERYWHERE         a   1.000    UNIT   1.000
      AMGJ             FINE       PMG              EVERYWHERE         a   1.000    UNIT   1.000
      AKJ              FINE       PK               EVERYWHERE         a   1.000    UNIT   1.000
      AMNJ             FINE       PMN              EVERYWHERE         a   1.000    UNIT   1.000
      ACORS            COARSE     PMC              EVERYWHERE         a   0.997    UNIT   0.997
      AH2OJ            FINE       PH2O             EVERYWHERE         a   1.000    UNIT   0.900
      AH2OI            FINE       PH2O             EVERYWHERE         a   1.000    UNIT   0.100
      ANAJ             FINE       PNA              EVERYWHERE         a   1.000    UNIT   0.900
      ANAI             FINE       PNA              EVERYWHERE         a   1.000    UNIT   0.100
      ACLJ             FINE       PCL              EVERYWHERE         a   1.000    UNIT   0.900
      ACLI             FINE       PCL              EVERYWHERE         a   1.000    UNIT   0.100
      ACLK             COARSE     PMC              EVERYWHERE         a   0.001    UNIT   0.001
      ASO4K            COARSE     PMC              EVERYWHERE         a   0.001    UNIT   0.001
      ANO3K            COARSE     PMC              EVERYWHERE         a   0.000    UNIT   0.000
      AH2OK            COARSE     PMC              EVERYWHERE         a   0.000    UNIT   0.000
      APOCI            FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
      APOCJ            FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
      APNCOMI          FINE       PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      APNCOMJ          FINE       PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      ALVPO1I          FINE       POC              EVERYWHERE         a   0.090    MASS   0.009
                                  PNCOM            EVERYWHERE         a   0.090    MASS   0.009
      ASVPO1I          FINE       POC              EVERYWHERE         a   0.045    MASS   0.005
                                  PNCOM            EVERYWHERE         a   0.045    MASS   0.005
      ASVPO2I          FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      ALVPO1J          FINE       POC              EVERYWHERE         a   0.090    MASS   0.081
                                  PNCOM            EVERYWHERE         a   0.090    MASS   0.081
      ASVPO1J          FINE       POC              EVERYWHERE         a   0.045    MASS   0.041
                                  PNCOM            EVERYWHERE         a   0.045    MASS   0.041
      ASVPO2J          FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      ASVPO3J          FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      AIVPO1J          FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      NH3              GAS        NH3              EVERYWHERE         a   1.000    UNIT   1.000

 >--------------------------------------------------------------------------------
 Stream Type: "Point Emissions File   1" | Sector Label: PT_NONEGU (02)

    Table of Aerosol Size Distributions Available for Use Sector-Wide.
    Note that Mode 1 is reserved for gas-phase species and surrogates.
      Number  Surrogate Mode  Reference Mode (see AERO_DATA.F)
      ------  --------------  --------------------------------
      2       FINE                        FINE_REF
      3       COARSE                    COARSE_REF

    CMAQ Species     Phase/Mode  Surrogate         Region             Op ScaleFac Basis FinalFac
    ------------     ----------  ---------         ------             -- -------- ----- --------
      NO2              GAS        NO2              EVERYWHERE         a   1.000    UNIT   1.000
      NO               GAS        NO               EVERYWHERE         a   1.000    UNIT   1.000
      HONO             GAS        HONO             EVERYWHERE         a   1.000    UNIT   1.000
      SO2              GAS        SO2              EVERYWHERE         a   1.000    UNIT   1.000
      SULF             GAS        SULF             EVERYWHERE         a   0.000    UNIT   0.000
      ALD2             GAS        ALD2             EVERYWHERE         a   1.000    UNIT   1.000
      FORM             GAS        FORM             EVERYWHERE         a   1.000    UNIT   1.000
      MEOH             GAS        MEOH             EVERYWHERE         a   1.000    UNIT   1.000
      CO               GAS        CO               EVERYWHERE         a   1.000    UNIT   1.000
      ALDX             GAS        ALDX             EVERYWHERE         a   1.000    UNIT   1.000
      ETHA             GAS        ETHA             EVERYWHERE         a   1.000    UNIT   1.000
      ETOH             GAS        ETOH             EVERYWHERE         a   1.000    UNIT   1.000
      KET              GAS        KET              EVERYWHERE         a   1.000    UNIT   1.000
      PAR              GAS        PAR              EVERYWHERE         a   1.000    UNIT   1.000
      ACET             GAS        ACET             EVERYWHERE         a   1.000    UNIT   1.000
      PRPA             GAS        PRPA             EVERYWHERE         a   1.000    UNIT   1.000
      ETHY             GAS        ETHY             EVERYWHERE         a   1.000    UNIT   1.000
      ETH              GAS        ETH              EVERYWHERE         a   1.000    UNIT   1.000
      OLE              GAS        OLE              EVERYWHERE         a   1.000    UNIT   1.000
      IOLE             GAS        IOLE             EVERYWHERE         a   1.000    UNIT   1.000
      ISOP             GAS        ISOP             EVERYWHERE         a   1.000    UNIT   1.000
      TERP             GAS        TERP             EVERYWHERE         a   1.000    UNIT   1.000
      BENZENE          GAS        BENZ             EVERYWHERE         a   1.000    UNIT   1.000
      TOL              GAS        TOL              EVERYWHERE         a   1.000    UNIT   1.000
      ECH4             GAS        CH4              EVERYWHERE         a   1.000    UNIT   1.000
      VLVPO1           GAS        POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      VSVPO1           GAS        POC              EVERYWHERE         a   0.045    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.045    MASS   0.000
      VSVPO2           GAS        POC              EVERYWHERE         a   0.140    MASS   0.001
                                  PNCOM            EVERYWHERE         a   0.140    MASS   0.001
      VSVPO3           GAS        POC              EVERYWHERE         a   0.180    MASS   0.001
                                  PNCOM            EVERYWHERE         a   0.180    MASS   0.001
      VIVPO1           GAS        POC              EVERYWHERE         a   0.500    MASS   0.002
                                  PNCOM            EVERYWHERE         a   0.500    MASS   0.002
      PCVOC            GAS        POC              EVERYWHERE         a   6.579    MASS   0.039
                                  PNCOM            EVERYWHERE         a   6.579    MASS   0.039
      ASO4J            FINE       SULF             EVERYWHERE         a   1.000    MASS  88.200
                                  PSO4             EVERYWHERE         a   1.000    UNIT   0.900
      ASO4I            FINE       SULF             EVERYWHERE         a   1.000    MASS   9.800
                                  PSO4             EVERYWHERE         a   1.000    UNIT   0.100
      ANH4J            FINE       PNH4             EVERYWHERE         a   1.000    UNIT   0.900
      ANH4I            FINE       PNH4             EVERYWHERE         a   1.000    UNIT   0.100
      ANO3J            FINE       PNO3             EVERYWHERE         a   1.000    UNIT   0.900
      ANO3I            FINE       PNO3             EVERYWHERE         a   1.000    UNIT   0.100
      AECJ             FINE       PEC              EVERYWHERE         a   1.000    UNIT   0.900
      AECI             FINE       PEC              EVERYWHERE         a   1.000    UNIT   0.100
      AOTHRJ           FINE       PMOTHR           EVERYWHERE         a   1.000    UNIT   0.900
      AOTHRI           FINE       PMOTHR           EVERYWHERE         a   1.000    UNIT   0.100
      AFEJ             FINE       PFE              EVERYWHERE         a   1.000    UNIT   1.000
      AALJ             FINE       PAL              EVERYWHERE         a   1.000    UNIT   1.000
      ASIJ             FINE       PSI              EVERYWHERE         a   1.000    UNIT   1.000
      ATIJ             FINE       PTI              EVERYWHERE         a   1.000    UNIT   1.000
      ACAJ             FINE       PCA              EVERYWHERE         a   1.000    UNIT   1.000
      AMGJ             FINE       PMG              EVERYWHERE         a   1.000    UNIT   1.000
      AKJ              FINE       PK               EVERYWHERE         a   1.000    UNIT   1.000
      AMNJ             FINE       PMN              EVERYWHERE         a   1.000    UNIT   1.000
      ACORS            COARSE     PMC              EVERYWHERE         a   0.997    UNIT   0.997
      AH2OJ            FINE       PH2O             EVERYWHERE         a   1.000    UNIT   0.900
      AH2OI            FINE       PH2O             EVERYWHERE         a   1.000    UNIT   0.100
      ANAJ             FINE       PNA              EVERYWHERE         a   1.000    UNIT   0.900
      ANAI             FINE       PNA              EVERYWHERE         a   1.000    UNIT   0.100
      ACLJ             FINE       PCL              EVERYWHERE         a   1.000    UNIT   0.900
      ACLI             FINE       PCL              EVERYWHERE         a   1.000    UNIT   0.100
      ACLK             COARSE     PMC              EVERYWHERE         a   0.001    UNIT   0.001
      ASO4K            COARSE     PMC              EVERYWHERE         a   0.001    UNIT   0.001
      ANO3K            COARSE     PMC              EVERYWHERE         a   0.000    UNIT   0.000
      AH2OK            COARSE     PMC              EVERYWHERE         a   0.000    UNIT   0.000
      APOCI            FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
      APOCJ            FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
      APNCOMI          FINE       PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      APNCOMJ          FINE       PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      ALVPO1I          FINE       POC              EVERYWHERE         a   0.090    MASS   0.009
                                  PNCOM            EVERYWHERE         a   0.090    MASS   0.009
      ASVPO1I          FINE       POC              EVERYWHERE         a   0.045    MASS   0.005
                                  PNCOM            EVERYWHERE         a   0.045    MASS   0.005
      ASVPO2I          FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      ALVPO1J          FINE       POC              EVERYWHERE         a   0.090    MASS   0.081
                                  PNCOM            EVERYWHERE         a   0.090    MASS   0.081
      ASVPO1J          FINE       POC              EVERYWHERE         a   0.045    MASS   0.041
                                  PNCOM            EVERYWHERE         a   0.045    MASS   0.041
      ASVPO2J          FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      ASVPO3J          FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      AIVPO1J          FINE       POC              EVERYWHERE         a   0.000    MASS   0.000
                                  PNCOM            EVERYWHERE         a   0.000    MASS   0.000
      NH3              GAS        NH3              EVERYWHERE         a   1.000    UNIT   1.000

 ================================================================================
 |> END EMISSIONS SCALING PREPARATION AND DIAGNOSTIC OUTPUT

I changed the EmissCtrl_cb6r3_ae6_aq.nml, and the result is much batter.
! → Nonvolatile POA
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘APOC’ ,‘FINE’,0.5 ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘APNCOM’ ,‘FINE’,0.5 ,‘MASS’,‘a’,
The APOCI result:
0.0003859454, 0.0003458597, 8.374572e-05, 4.012762e-05, 2.425514e-05,
9.798936e-06, 2.233077e-05, 2.787977e-05, 7.107879e-05, 0.0001624645,
4.399491e-05, 0.000560355, 0.001437822, 0.0003073164, 0.0001333524,
3.981777e-05, 6.980577e-05, 0.0004842946, 0.00329925, 0.00728748,
0.005447648, 0.005448489, 0.01265273, 0.01499518, 0.01089952, 0.01007447,
0.01069152, 0.01828291, 0.03009181, 0.03380717, 0.03124777, 0.03679941,
0.04196794, 0.06416969, 0.1085059, 0.1319689, 0.1107287, 0.07522821,
0.04031098, 0.03245287, 0.03063439, 0.0281356, 0.02543317, 0.02502372,
0.02326598, 0.02320218, 0.02862192, 0.03389805, 0.03995613, 0.04590014,
0.05111884, 0.05639008, 0.05816591, 0.05716435, 0.05564224, 0.0618072,
0.06963018, 0.07750133, 0.08066913, 0.08117459, 0.08170985, 0.08174985,
0.0862453, 0.0930794, 0.08366204, 0.08752195, 0.0805624, 0.05493547,
0.03257544, 0.02000036, 0.01243351, 0.007555791, 0.005960271,
0.005756504, 0.007126107, 0.006909362,

So how to give the Scale of Nonvolatile POA? Do they have a empirical value?

O.k., this makes sense now. Others on this forum certainly are more knowledgeable than me about this topic, but here is the basic idea:

First, you need to decide if you want to map your primary OC emissions into a nonvolatile or semivolatile framework. For the former, 100% of POC is mapped to APOC and 100% of PNCOM is mapped to APNCOM. For the latter, POC and PNCOM are each distributed across the gas phase species VLVPO1, VSVPO1, VSVPO2, VSVPO3, VIVPO1 and the aerosol species ALVPO1, ASVPO1, ASVPO2, ASVPO3, AIVPO1, though some of the default weights are zero. The weights for POC and PNCOM add up to 1 each. If you use the semivolatile framework, you cannot currently perform source apportionment of (primary) OC, but you would gain a more realistic representation of how primary OC emissions affect ambient OC and OM concentrations.

Regardless of your choice, you want to make sure that the scaling factors applied to your POC and PNCOM emissions each add up to 1 to avoid losing or gaining mass. In the case of selecting the nonvolatile framework, this portion of EmissCtrl would look as follows:

! → Nonvolatile POA
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘APOC’ ,‘FINE’,1. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘APNCOM’ ,‘FINE’,1. ,‘MASS’,‘a’,
! → Semivolatile POA
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘VLVPO1’ ,‘GAS’ ,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘VLVPO1’ ,‘GAS’ ,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘VSVPO1’ ,‘GAS’ ,0.,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘VSVPO1’ ,‘GAS’ ,0.,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘VSVPO2’ ,‘GAS’ ,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘VSVPO2’ ,‘GAS’ ,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘VSVPO3’ ,‘GAS’ ,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘VSVPO3’ ,‘GAS’ ,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘VIVPO1’ ,‘GAS’ ,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘VIVPO1’ ,‘GAS’ ,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘ALVPO1’ ,‘FINE’,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘ALVPO1’ ,‘FINE’,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘ASVPO1’ ,‘FINE’,0.,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘ASVPO1’ ,‘FINE’,0.,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘ASVPO2’ ,‘FINE’,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘ASVPO2’ ,‘FINE’,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘ASVPO3’ ,‘FINE’,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘ASVPO3’ ,‘FINE’,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘POC’ ,‘AIVPO1’ ,‘FINE’,0. ,‘MASS’,‘a’,
‘EVERYWHERE’, ‘ALL’ ,‘PNCOM’ ,‘AIVPO1’ ,‘FINE’,0. ,‘MASS’,‘a’,

When you look at the SpecDef file used for post-processing CMAQ output, you’ll see that the definitions of APOCI, APOCJ, AOMI, and AOMJ include both the non-volatile and semi-volatile primary organic carbon species, with the understanding that the user selected either framework in EmissCtrl and set the emission scaling factors for the non-selected framework to zero. Thus, when you mentioned in your initial post that OC was zero, you may only have looked at APOCI, APOCJ, ANCOMI, and ANCOMJ but not all of the other primary organic aerosol species used in your default emissions assignment (ALVPO1, ASVPO1, ASVPO2, ASVPO3, AIVPO1).

Really apreciate you @hogrefe.christian
I’ll have a try.