# ERROR in COMBINE for CMAQ5.3.2-ISAM **URL:** \ **Category:** CMAQ-ISAM\ **Created:** [June 9, 2024, 4:09am UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983 "2024-06-09T04:09:39Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Rain](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.cmascenter.org/rain/32/1939_2.png) [@Rain](https://forum.cmascenter.org/u/Rain)\ **Post date:** [June 9, 2024, 4:09am UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983/1 "2024-06-09T04:09:39Z")
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. ![微信图片_20240609115405](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/7/76496983c368da179b1cf81470a825816abeb468.png) [run\_combine-XiXian-D02-ISAM.txt](https://forum.cmascenter.org/uploads/short-url/2Vxm4zs1aHfv92A2eyTqlRzBiEu.txt) (7.4 KB) [combine-XiXian-D02-ISAM.txt](https://forum.cmascenter.org/uploads/short-url/hX2ljyOPyFS6SVcEKrJttVtpzhg.txt) (179.9 KB) [SpecDef\_cb6r3\_ae7\_aq\_XiXian.txt](https://forum.cmascenter.org/uploads/short-url/hZeyJpxcf7pnKOk8kKJ33Ezxt2y.txt) (8.0 KB) ---
**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:** [June 9, 2024, 9:23pm UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983/2 "2024-06-09T21:23:21Z")
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. ---
**Author:** ![Rain](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.cmascenter.org/rain/32/1939_2.png) [@Rain](https://forum.cmascenter.org/u/Rain)\ **Post date:** [June 11, 2024, 12:36am UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983/3 "2024-06-11T00:36:31Z")
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. ---
**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:** [June 11, 2024, 1:20am UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983/4 "2024-06-11T01:20:21Z")
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. ---
**Author:** ![Rain](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.cmascenter.org/rain/32/1939_2.png) [@Rain](https://forum.cmascenter.org/u/Rain)\ **Post date:** [June 12, 2024, 1:17am UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983/5 "2024-06-12T01:17:22Z")
Thank you very much for your detailed explanation. Your response has clarified my doubts, and I truly appreciate your help. ---
**Author:** ![Rain](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.cmascenter.org/rain/32/1939_2.png) [@Rain](https://forum.cmascenter.org/u/Rain)\ **Post date:** [June 16, 2024, 12:04pm UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983/6 "2024-06-16T12:04:18Z")
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. ![1](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/7/7227efbd7f15608b5637b71ed0903ce65d4cdf75.jpeg) ![2](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/c/cb87346ca2bebf15dd42077cefab2bcf6ec3277a.jpeg) ![3](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/f/f38551e71dac4946ecb8f56e05e7bb04d294bb59.png) ![4](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/5/537112d2293559804174c02b135c28a8da633c68.png) ---
**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:** [June 16, 2024, 9:49pm UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983/7 "2024-06-16T21:49:07Z")
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? As per your first post, PM25\_XA is defined as (ASO4I\_XAF[1]+ANO3I\_XAF[1]+ANH4I\_XAF[1]+ANAI\_XAF[1]+ACLI\_XAF[1]+AECI\_XAF[1]+AOTHRI\_XAF[1]+APOCI\_XAF[1]+APNCOMI\_XAF[1])\*PM25AT[3]+(ASO4J\_XAF[1]+ANO3J\_XAF[1]+ANH4J\_XAF[1]+ANAJ\_XAF[1]+ACLJ\_XAF[1]+AECJ\_XAF[1]+AOTHRJ\_XAF[1]+AFEJ\_XAF[1]+ASIJ\_XAF[1]+ATIJ\_XAF[1]+ACAJ\_XAF[1]+AMGJ\_XAF[1]+AMNJ\_XAF[1]+AALJ\_XAF[1]+AKJ\_XAF[1]+APOCJ\_XAF[1]+APNCOMJ\_XAF[1])\*PM25AC[3] 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. ---
**Author:** ![Rain](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.cmascenter.org/rain/32/1939_2.png) [@Rain](https://forum.cmascenter.org/u/Rain)\ **Post date:** [June 17, 2024, 9:37am UTC](https://forum.cmascenter.org/t/error-in-combine-for-cmaq5-3-2-isam/4983/8 "2024-06-17T09:37:43Z")
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. > [@CCTM output is all 0 after running CMAQ](https://forum.cmascenter.org/t/cctm-output-is-all-0-after-running-cmaq/3069/5): > > Hello, Yes, the variable in your region mask file should be in real format. You may straightforward use ncflint to convert them from integer to float or refer to Cristian’s suggestion, and see if your CMAQ/ISAM works. Try to use m3fake instead of t3mask in t3tool, please refer to [https://forum.cmascenter.org/t/error-creating-gridmask](https://forum.cmascenter.org/t/error-creating-gridmask) BTW, I created my mask files using ArcGIS and ncgen. Thanks. > [@How to make ISAM\_REGIONS file?](https://forum.cmascenter.org/t/how-to-make-isam-regions-file/2877/9): > > As far as computers are concerned, we don’t have “fractions” – only “bit patterns” that are interpreted according to variable-type. And fortunately the REAL and INTEGER bit-patterns are the same (all bit-zeros)…