Hello, everyone!
I’m encountering some errors with the Combine module while trying to calculate PM2.5 concentrations for different areas labeled by ISAM (CMAQ-5.3.2), as shown in the picture. I have uploaded my run-combine scripts, running log and SpecDef.
Could anyone give me some advice? Thanks.

run_combine-XiXian-D02-ISAM.txt (7.4 KB)
combine-XiXian-D02-ISAM.txt (179.9 KB)
SpecDef_cb6r3_ae7_aq_XiXian.txt (8.0 KB)

Could you please double check your uploaded files? Despite the different names (run_combine-XiXian-D02-ISAM.csh vs. run_combine-XiXian-D02-ISAM.txt) of the links, the same underlying run script file seems to have been uploaded, while I cannot see the full log file.

Based on the image of the portions of the log file you posted, the species definition file opened by combine might not be the one you posted (SpecDef_cb6r3_ae7_aq_XiXian.txt) because in that file, NO2 is not referenced. The message “Starting Date > Ending Date” might also point to a mismatch of the time stamps between the different input files being opened, but we’ll have to see the full log file to really know what is happening.

I’m sorry, sir. I made a mistake and have updated the uploaded file for your review. Thank you very much for your response. The file named run_combine-XiXian-D02-ISAM is my running script, and combine-XiXian-D02-ISAM is the log file.

Thanks for posting the log file.

Lines 1 - 2095 of the log file show that combine successfully creates the COMBINE_ACONC_ISAM_v532_intel_2020{MM}{DD} files for July 1 - 3 and writes all of the PM2.5 variables defined in SpecDef_cb6r3_ae7_aq_XiXian.txt to these output files. No error is encountered while executing lines 1 - 136 of the run script, and based on your first post, these are the files you really want.

The error occurs when the run script then proceeds to creating the COMBINE_DEP output files. You specify the CCTM_SA_DRYDEP / CCTM_SA_WETDEP1 files as input, but the file defined as SPEC_DEP (SpecDef_Dep_cb6r3_ae7_aq.txt) lists standard species names from CCTM_DRYDEP / CCTM_WETDEP1, i.e. species names without the ISAM tags. If you indeed want a COMBINE_DEP output file using ISAM tags, you need to edit SpecDef_Dep_cb6r3_ae7_aq.txt with input species names that include the tag names, e.g. NO2_BJF, etc., just like you did when you created SpecDef_cb6r3_ae7_aq_XiXian.txt.

If you don’t want to create a COMBINE_DEP output file, just remove lines 136 - 185 from the run script or comment them out.

If you create a new SpecDef_Dep_cb6r3_ae7_aq.txt with the ISAM species names from CCTM_SA_DRYDEP / CCTM_SA_WETDEP1, make sure to first remove the existing /home/zhangyu/OutputData/XiXian/POST/COMBINE_DEP_ISAM_v532_intel_2020{MM}{DD} files from the run that crashed since there would be mismatch of species names in the header.

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Thank you very much for your detailed explanation. Your response has clarified my doubts, and I truly appreciate your help.

Hello Sir,
I have encountered an issue after using Combine to calculate the PM2.5 concentration in the tagged regions. While the IC and BC show concentrations, the PM2.5 concentrations in my tagged regions (XA, XY, LL, etc.) have no values. I am unsure why this is happening. If you need any reference files to help diagnose the issue, please let me know.
Thank you for your assistance.

Have you verified that at least some of the individual species included in your definition of PM25_XA have non-zero concentrations when you look at the raw CCTM_SA_ACONC (and/or CCTM_SA_CONC) output files from which combine calculates the aggregated concentrations?


The only way this can be zero is if either all of the individual aerosol species are zero, or the size cutoff fractions (PM25AT[3] and PM25AC[3]) are zero. Given that PM25_IC and PM25_BC which also use the size cutoff fractions are not zero, that points to the *_XAF PM concentrations from SA_ACONC / SA_CONC being zero.

Thank you for your attention. Following your advice, I checked the relevant variables, and as you mentioned, the *_XAF PM concentration is indeed zero. Based on other posts on the forum, I found the cause of the problem and am now working on resolving it. Thanks again for your help.