# Some questions about CMAQ CTM\_LOG files **URL:** \ **Category:** CMAQ-ISAM\ **Created:** [December 29, 2021, 7:51am UTC](https://forum.cmascenter.org/t/some-questions-about-cmaq-ctm-log-files/2934 "2021-12-29T07:51:29Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![pbwang](https://avatars.discourse-cdn.com/v4/letter/p/5daacb/32.png) [@pbwang](https://forum.cmascenter.org/u/pbwang)\ **Post date:** [December 29, 2021, 7:51am UTC](https://forum.cmascenter.org/t/some-questions-about-cmaq-ctm-log-files/2934/1 "2021-12-29T07:51:29Z")
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? 4.I want a CB06 input species list and CB06 output species list with their real name. Thank you for your help. ---
**Author:** ![hogrefe.christian](https://avatars.discourse-cdn.com/v4/letter/h/74df32/32.png) [@hogrefe.christian](https://forum.cmascenter.org/u/hogrefe.christian)\ **Post date:** [December 29, 2021, 2:27pm UTC](https://forum.cmascenter.org/t/some-questions-about-cmaq-ctm-log-files/2934/2 "2021-12-29T14:27:27Z")
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](https://github.com/USEPA/CMAQ/blob/5.3/DOCS/Release_Notes/aero7_overview.md#required-emission-updates)). 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](https://github.com/USEPA/CMAQ/blob/main/CCTM/src/MECHS/README.md), 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](https://github.com/USEPA/CMAQ/blob/main/CCTM/src/MECHS/mechanism_information/cb6r3_ae6_aq/cb6r3_ae6_aq_species_table.md). ---
**Author:** ![cjcoats](https://avatars.discourse-cdn.com/v4/letter/c/ac8455/32.png) [@cjcoats](https://forum.cmascenter.org/u/cjcoats)\ **Post date:** [December 29, 2021, 3:03pm UTC](https://forum.cmascenter.org/t/some-questions-about-cmaq-ctm-log-files/2934/3 "2021-12-29T15:03:29Z")
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 ---
**Author:** ![pbwang](https://avatars.discourse-cdn.com/v4/letter/p/5daacb/32.png) [@pbwang](https://forum.cmascenter.org/u/pbwang)\ **Post date:** [December 31, 2021, 8:45am UTC](https://forum.cmascenter.org/t/some-questions-about-cmaq-ctm-log-files/2934/4 "2021-12-31T08:45:27Z")
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. ---
**Author:** ![hogrefe.christian](https://avatars.discourse-cdn.com/v4/letter/h/74df32/32.png) [@hogrefe.christian](https://forum.cmascenter.org/u/hogrefe.christian)\ **Post date:** [December 31, 2021, 3:40pm UTC](https://forum.cmascenter.org/t/some-questions-about-cmaq-ctm-log-files/2934/5 "2021-12-31T15:40:54Z")
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.