Some questions about CMAQ CTM_LOG files

Dear all:
I’m doing a PM2.5 ISAM, and I have a few questions in the CTM_LOG today.
1.I find the CB06 contains BENZENE and XYL, why they are unused here?
|> Checking for unused Emissions Surrogates:
============================================
GR1 | Gridded Area Emissions File 1: 9 unused surrogates.
APIN
BENZENE
IVOC
NR
NVOL
PMFINE
UNK
UNR
XYL

 PT_NONEGU | Point Emissions File   1:  7 unused surrogates.
      BENZENE         
      NR              
      NVOL            
      UNK             
      UNR             
      XYL             
      PMFINE          

 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. 

2.There are 21 ISAM SPECIES not found in CHEMISTRY_SPC array, and they DO NOT participate in photochemistry. Are these species important in photochemistry? How can I change the CHEMISTRY_SPC array?
>>—>> WARNING in subroutine SA_IRR_INIT on PE 000
ISAM SPECIES: AECJ not found in CHEMISTRY_SPC array

 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: AECI not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ASO4J not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ASO4I not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ANO3J not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ANO3I not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ANH4J not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ANH4I not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: NH3 not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ANAJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ANAI not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: AMGJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: AKJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ACAJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: AFEJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: AALJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ASIJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: ATIJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: AMNJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: AOTHRJ not found in CHEMISTRY_SPC array
 
 
 >>--->> WARNING in subroutine SA_IRR_INIT on PE 000
 ISAM SPECIES: AOTHRI not found in CHEMISTRY_SPC array

Below isam species participate in photochemistry
SPC ISAM_SPC SPC PHOTOCHEM_SPC
3 APOCJ 132 APOCJ
4 APOCI 130 APOCI
5 APNCOMJ 133 APNCOMJ
6 APNCOMI 131 APNCOMI
9 SO2 14 SO2
10 SULF 15 SULF
11 SULRXN 16 SULRXN
14 HNO3 11 HNO3
15 NO 2 NO
16 NO2 1 NO2
17 NO3 5 NO3
18 HONO 12 HONO
19 N2O5 10 N2O5
20 PAN 20 PAN
21 XO2N 32 XO2N
22 NTR1 33 NTR1
23 NTR2 34 NTR2
24 INTR 59 INTR
25 PNA 13 PNA
26 PANX 26 PANX
27 CLNO2 92 CLNO2
28 CLNO3 93 CLNO3
29 XO2 31 XO2
30 XO2H 25 XO2H
31 MEO2 18 MEO2
32 ISO2 56 ISO2
33 C2O3 17 C2O3
34 CXO3 23 CXO3

Below isam species DO NOT participate in photochemistry
SPC ISAM_SPC
1 AECJ
2 AECI
7 ASO4J
8 ASO4I
12 ANO3J
13 ANO3I
35 ANH4J
36 ANH4I
37 NH3
38 ANAJ
39 ANAI
40 AMGJ
41 AKJ
42 ACAJ
43 AFEJ
44 AALJ
45 ASIJ
46 ATIJ
47 AMNJ
48 AOTHRJ
49 AOTHRI

  1. There aer many files not found, and it shows that :File not available. But CCTM match the files latter.
    Are there some bugs in the cctm runscrip?

    A_CONC_1 :/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_ACONC_v531_intel_tianshui_20190101.nc

    —>> WARNING in subroutine OPEN3
    File not available.
    Could not open A_CONC_1 file for update - try to open new

    Avg Conc File Header Description:
    Concentration file output
    Averaged over the synchronization time steps
    Timestamp represents beginning computed date/time
    Layer mapping (CGRID to AGRID):
    Layer 1 to 1
    => VNAME3D( 1 ): NO2
    => VNAME3D( 2 ): NO
    ………………
    => VNAME3D(235 ): TA
    => VNAME3D(236 ): PRES

    “A_CONC_1” opened as NEW(READ-WRITE )
    File name “/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_ACONC_v531_intel_tianshui_20190101.nc”
    File type GRDDED3
    Execution ID “CMAQ_CCTMv531_pbwang_20211228_221757_337125867”
    Grid name “CN5NC_156X117”
    Dimensions: 117 rows, 156 cols, 1 lays, 236 vbles
    NetCDF ID: 1048576 opened as VOLATILE READWRITE
    Starting date and time 2019001:000000 (0:00:00 Jan. 1, 2019)
    Timestep 010000 (1:00:00 hh:mm:ss)
    Maximum current record number 0
    |>— OPEN OR CREATE WET DEPOSITION FILE —<|

    CTM_WET_DEP_1 :/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_WETDEP1_v531_intel_tianshui_20190101.nc

    —>> WARNING in subroutine OPEN3
    File not available.

    Could not open CTM_WET_DEP_1 file for update - try to open new

    “CTM_WET_DEP_1” opened as NEW(READ-WRITE )
    File name “/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_WETDEP1_v531_intel_tianshui_20190101.nc”
    File type GRDDED3
    Execution ID “CMAQ_CCTMv531_pbwang_20211228_221757_337125867”
    Grid name “CN5NC_156X117”
    Dimensions: 117 rows, 156 cols, 1 lays, 141 vbles
    NetCDF ID: 1114112 opened as VOLATILE READWRITE
    Starting date and time 2019001:010000 (1:00:00 Jan. 1, 2019)
    Timestep 010000 (1:00:00 hh:mm:ss)
    Maximum current record number 0

    |>— CHECK INITIAL CONCENTRATIONS —<|

    Closing file ISAM_PREVDAY

    “SA_CONC_1” opened as NEW(READ-WRITE )
    File name “/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_SA_CONC_v531_intel_tianshui_20190101.nc”
    File type GRDDED3
    Execution ID “CMAQ_CCTMv531_pbwang_20211228_221757_337125867”
    Grid name “CN5NC_156X117”
    Dimensions: 117 rows, 156 cols, 40 lays, 686 vbles
    NetCDF ID: 589824 opened as VOLATILE READWRITE
    Starting date and time 2019001:000000 (0:00:00 Jan. 1, 2019)
    Timestep 010000 (1:00:00 hh:mm:ss)
    Maximum current record number 0
    SA_WD_1 :/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_SA_WETDEP_v531_intel_tianshui_20190101.nc

    —>> WARNING in subroutine OPEN3
    File not available.

    Could not open SA_WD_1 file for update - try to open new

    “SA_WD_1” opened as NEW(READ-WRITE )
    File name “/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_SA_WETDEP_v531_intel_tianshui_20190101.nc”
    File type GRDDED3
    Execution ID “CMAQ_CCTMv531_pbwang_20211228_221757_337125867”
    Grid name “CN5NC_156X117”
    Dimensions: 117 rows, 156 cols, 1 lays, 686 vbles
    NetCDF ID: 1179648 opened as VOLATILE READWRITE
    Starting date and time 2019001:010000 (1:00:00 Jan. 1, 2019)
    Timestep 010000 (1:00:00 hh:mm:ss)
    Maximum current record number 0
    After INITSCEN : Gas 1.508E-01 | Aer 1.605E+09 | Non 1.200E-03
    Value for CTM_IPR_1: ‘/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_PA_1_v531_intel_tianshui_20190101.nc -v’
    Value for CTM_IPR_1: ‘/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_PA_1_v531_intel_tianshui_20190101.nc -v’
    CTM_IPR_1 :/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_PA_1_v531_intel_tianshui_20190101.nc

    —>> WARNING in subroutine OPEN3
    File not available.

    Could not open CTM_IPR_1 file for update - try to open new

    “CTM_IPR_1” opened as NEW(READ-WRITE )
    File name “/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_PA_1_v531_intel_tianshui_20190101.nc”
    File type GRDDED3
    Execution ID “CMAQ_CCTMv531_pbwang_20211228_221757_337125867”
    Grid name “CN5NC_156X117_CR”
    Dimensions: 117 rows, 156 cols, 40 lays, 46 vbles
    NetCDF ID: 1245184 opened as VOLATILE READWRITE
    Starting date and time 2019001:010000 (1:00:00 Jan. 1, 2019)
    Timestep 010000 (1:00:00 hh:mm:ss)
    Maximum current record number 0
    Opened Integrated Reaction Rate Output File: CTM_IPR_1
    Value for CTM_IRR_1: ‘/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_IRR_1_v531_intel_tianshui_20190101.nc -v’
    Value for CTM_IRR_1: ‘/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_IRR_1_v531_intel_tianshui_20190101.nc -v’
    CTM_IRR_1 :/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_IRR_1_v531_intel_tianshui_20190101.nc

    —>> WARNING in subroutine OPEN3
    File not available.

    Could not open CTM_IRR_1 file for update - try to open new

    “CTM_IRR_1” opened as NEW(READ-WRITE )
    File name “/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_IRR_1_v531_intel_tianshui_20190101.nc”
    File type GRDDED3
    Execution ID “CMAQ_CCTMv531_pbwang_20211228_221757_337125867”
    Grid name “CN5NC_156X117_CR”
    Dimensions: 117 rows, 156 cols, 40 lays, 43 vbles
    NetCDF ID: 1310720 opened as VOLATILE READWRITE
    Starting date and time 2019001:010000 (1:00:00 Jan. 1, 2019)
    Timestep 010000 (1:00:00 hh:mm:ss)
    Maximum current record number 0
    Opened Integrated Reaction Rate Output File: CTM_IRR_1
    |>— INITIALIZE SURFACE EXCHANGE MODULE —<|

    DEPV_INIT: completed INIT_GAS_DV block

    CTM_DRY_DEP_1 :/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_DRYDEP_v531_intel_tianshui_20190101.nc

    —>> WARNING in subroutine OPEN3
    File not available.

    Could not open CTM_DRY_DEP_1 file for update - try to open new

    “CTM_DRY_DEP_1” opened as NEW(READ-WRITE )
    File name “/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_DRYDEP_v531_intel_tianshui_20190101.nc”
    File type GRDDED3
    Execution ID “CMAQ_CCTMv531_pbwang_20211228_221757_337125867”
    Grid name “CN5NC_156X117”
    Dimensions: 117 rows, 156 cols, 1 lays, 172 vbles
    NetCDF ID: 1441792 opened as VOLATILE READWRITE
    Starting date and time 2019001:010000 (1:00:00 Jan. 1, 2019)
    Timestep 010000 (1:00:00 hh:mm:ss)
    Maximum current record number 0
    SA_DD_1 :/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_SA_DRYDEP_v531_intel_tianshui_20190101.nc

    —>> WARNING in subroutine OPEN3
    File not available.

    Could not open SA_DD_1 file for update - try to open new

    “SA_DD_1” opened as NEW(READ-WRITE )
    File name “/home/pbwang/CMAQ5.3/data/cctm/111/CN5NC_156X117/CCTM_SA_DRYDEP_v531_intel_tianshui_20190101.nc”
    File type GRDDED3
    Execution ID “CMAQ_CCTMv531_pbwang_20211228_221757_337125867”
    Grid name “CN5NC_156X117”
    Dimensions: 117 rows, 156 cols, 1 lays, 686 vbles
    NetCDF ID: 1507328 opened as VOLATILE READWRITE
    Starting date and time 2019001:010000 (1:00:00 Jan. 1, 2019)
    Timestep 010000 (1:00:00 hh:mm:ss)
    Maximum current record number 0

4.I want a CB06 input species list and CB06 output species list with their real name.
Thank you for your help.

Thanks for reading your log file carefully and asking specific questions about the warnings and messages you’re seeing. Here are my thoughts, others may want to weigh in, too, if I miss something or don’t characterize something correctly:

  1. Some of these warnings about unused surrogates definitely need to be addressed as they point to a mismatch between what was assumed during speciation in the emissions processing and what is specified in EmissCtrl for how the emissions are mapped to CMAQ species. You don’t need to worry about NR, NVOL, UNK, and UNR, but you should address the warnings about BENZENE, XYL, APIN, PMFINE, and possibly IVOC.

Looking at EmissCtr for cb6r3_ae6_aq, you see that it expects the emitted species to be called BENZ, not BENZENE. If your emissions file only contains BENZENE but not BENZ, you should change the existing assignment 'EVERYWHERE', 'ALL' ,'BENZ' ,'BENZENE' ,'GAS' ,1. ,'UNIT','a', to 'EVERYWHERE', 'ALL' ,'BENZENE' ,'BENZENE' ,'GAS' ,1. ,'UNIT','a',. If your emissions file contains both BENZ and BENZENE (maybe it was merged from different sectors and they used different speciation profiles with different names for benzene) and they both represent benzene emissions you’d like CMAQ to consider, you’d leave the existing assignment but also add a second assignment of 'EVERYWHERE', 'ALL' ,'BENZENE' ,'BENZENE' ,'GAS' ,1. ,'UNIT','a',. This would result in adding both BENZ and BENZENE emissions to the CMAQ species BENZENE.

APIN in your emissions file might be coming from offline biogenic sources, but in aero6 SOA formation from alpha-pinenes was not explicitly considered (this was introduced in aero7 as documented in the release notes). Assuming your (biogenic) speciation profile generated both APIN and TERP and TERP did not include APIN, in aero6 you would then want to map both of them to the CMAQ species TERP by adding 'EVERYWHERE', 'ALL' ,'APIN' ,'TERP' ,'GAS' ,1. ,'UNIT','a', to your EmissCtrl file (you can see that the aero7 EmissCtrl file maps APIN to the new CMAQ species APIN)

XYL is not a cb6r3 species, the relevant CMAQ species are XYLMN (xylene minus naphtalene) and NAPH (naphtalene). Depending on whether you know if your XYL emissions include naphtalene and - if so - which fraction of these emissions are naphtalene, and depending on whether your emissions file also includes XYLMN and NAPH, you want to either modify the lines 'EVERYWHERE', 'ALL' ,'XYLMN' ,'XYLMN' ,'GAS' ,1. ,'UNIT','a', and 'EVERYWHERE', 'ALL' ,'NAPH' ,'NAPH' ,'GAS' ,1. ,'UNIT','a' to use XYL in the “emission surrogate” column and split it up between these two species, making sure that the total weights add up to one, or add new lines with these instructions while leaving the existing lines for XYLMN and NAPH.

PMFINE is not a CMAQ species but apparently was used in one or more of the speciation profiles used in your emissions processing. You either want to revisit that speciation profile to speciate PM25 emissions from those sources into the CMAQ primary PM emission surrogates PSO4, PNO3, PNH4, PMOTHR, POC, PNCOM, and crustal elements, or - if you know that PMFINE is equivalent to one of those surrogates (e.g. PMOTHR) - add a rule that maps PMFINE to AOTHR ('EVERYWHERE', 'ALL' ,'PMFINE' ,'AOTHR' ,'FINE' ,1. ,'UNIT','a'). It depends on what you know about these PMFINE emissions.

I don’t really know what IVOC represents in your emission files and whether or not it might be appropriate to map it to one or more of the VBS VOC surrogates used in cb6r3_ae6_aq. It may or may not require any action.

  1. This is not a problem. CMAQ simply tries to first open output files in case they exist already to add to them before creating them if they do not yet exist. These warnings simply reflect that process.

  2. Not a problem either, these warnings simply tell you that some of the ISAM species do not participate in photochemistry (and therefore are not part of the CHEMISTRY_SPC array) which is correct. There is nothing you can (or should) change here.

  3. As linked in the user’s guide, markdown tables of mechanism species can be found in the mechanism_information folder of CCTM/src/MECHS. The table for cb6r3_ae6_aq can be found here.

1 Like

Re (2) from Christian Hogrefe:

The original model-architecture called for attempting first to open output files for READ-WRITE and if successful use these files to provide initial conditions. If the files did not exist, the model would open and read the corresponding initial conditions files, and create new output files to match.

At some point, it was decided always to use initial-conditions files; the output-file code should have been changed to open the output files as UNKNOWN (if file exists, open it and check its file-description against the model; else create it according to the file-description).

As it stands, there is the “dangling”

if file exists, open it for READ-WRITE (generating log messages either for success or failure); else create it as NEW (also generating log-messages).

which is further obscured by the fact that these two steps happen in two distinct subroutines… and not doing the consistency-checks automatically.

FWIW

Carlie J. Coats, Jr.
Original Models-3 systems architect

Thank you for your detailed information@hogrefe.christian
I look up the EmissCtrl_cb6r3_ae6_aq.nml, the PMFINE is a kind of species that concerning with Wind-Blown Dust and Sea Spray Scaling.

Regarding PMFINE, you are correct that the CMAQ code for the inline dust and sea spray emission streams generates emission surrogates PMFINE_#### which are then mapped to CMAQ model species according to the rules in that section of the EmissCtrl file.

However, the PMFINE (not PMFINE_###) emission surrogates reported in your log file occurred in the GR1 and PT_NONEGU emission streams, i.e. the emission files you prepared offline. Since there are no rules in EmissCtrl to map this PMFINE surrogate to any CMAQ species, the mass associated with its emissions would not be accounted for in the CMAQ simulations. As noted in my previous post, if these PMFINE emissions in your emission input file represent mass that you want to include in your CMAQ simulations, you either need to trace your way back through your emission processing and speciate them into emission surrogates actually present in the EmissCtrl file, or you need to decide “manually” which CMAQ model species you would like to map these emissions to and add a corresponding line to the EmissCtrl file.