# CMAQ ACONC outputs using 2014 NEI emissions

**URL:** <https://forum.cmascenter.org/t/cmaq-aconc-outputs-using-2014-nei-emissions/951>\
**Category:** Chemistry and Aerosols\
**Created:** [September 18, 2019, 6:08pm UTC](https://forum.cmascenter.org/t/cmaq-aconc-outputs-using-2014-nei-emissions/951 "2019-09-18T18:08:46Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![zyj.jess](https://avatars.discourse-cdn.com/v4/letter/z/8dc957/32.png) [@zyj.jess](https://forum.cmascenter.org/u/zyj.jess)\
**Post date:** [September 18, 2019, 6:08pm UTC](https://forum.cmascenter.org/t/cmaq-aconc-outputs-using-2014-nei-emissions/951/1 "2019-09-18T18:08:46Z")

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Dear all;

I am developing a new ammonia emission inventory for animal production operations in NC. I have used it for 4 CMAQ simulations, January, April, July, and October. Each run simulated 3-day with the domain of 12US1.

Somehow, I need to test my simulation method and setup. Therefore, I went back to test on the NEI original emission inputs. But I have observed something not making a lot of sense in the CMAQ outputs. Mainly the nitrogen species are not looking correct to me. So I want to show you the ACONC outputs of some nitrogen compounds and perhaps you can give me some ideas.

For this 1-d simulation on 20140703, the emission gridded input file is “emis\_mole\_all\_20140703\_12US1\_cmaq\_cb6\_2014fb\_cdc\_cb6cmaq\_14j.ncf”. This is the original NEI emission file for 2014. I did not modify or make any changes on it. I know it is a single day simulation. The outputs could be impacted by ICON and BCON a lot. This reason could not be excluded. But I am still skeptical about the chemistry setup in the running script. Below is the setup in the script.

##################################################################################  
#\> CCTM Configuration Options

# =====================================================================

#\> Set Start and End Days for looping  
setenv NEW\_START TRUE #\> Set to FALSE for model restart  
set START\_DATE = “2014-07-03” #\> beginning date (June 20, 2014)  
set END\_DATE = “2014-07-03” #\> ending date (July 30, 2014)

#\> Set Timestepping Parameters  
set STTIME = 000000 #\> beginning GMT time (HHMMSS)  
set NSTEPS = 240000 #\> time duration (HHMMSS) for this run  
set TSTEP = 010000 #\> output time step interval (HHMMSS)

#\> Horizontal domain decomposition  
if ( $PROC == serial ) then  
setenv NPCOL\_NPROW “1 1”; set NPROCS = 1 # single processor setting  
else  
@ NPCOL = 8; @ NPROW = 6  
@ NPROCS = $NPCOL \* $NPROW  
setenv NPCOL\_NPROW “$NPCOL $NPROW”;  
endif

#\> Define Execution ID: e.g. [CMAQ-Version-Info]_[User]_[Date]_[Time]  
setenv EXECUTION\_ID "CMAQ\_CCTM${VRSN}_`id -u -n`\_`date -u +%Y%m%d_%H%M%S_%N`" #\> Inform IO/API of the Execution ID  
echo “”  
echo “—CMAQ EXECUTION ID: $EXECUTION\_ID —”

#\> Logfile Options  
#\> Master Log File Name; uncomment to write standard output to a log, otherwise write to screen  
#setenv LOGFILE $CMAQ\_HOME/$RUNID.log  
if (! -e $LOGDIR ) then  
mkdir -p $LOGDIR  
endif  
setenv PRINT\_PROC\_TIME Y #\> Print timing for all science subprocesses to Logfile  
#\> [default: TRUE or Y]  
setenv STDOUT T #\> Override I/O-API trying to write information to both the processor  
#\> logs and STDOUT [options: T | F]

setenv GRID\_NAME 12US1 #\> check GRIDDESC file for GRID\_NAME options  
setenv GRIDDESC $INPDIR/GRIDDESC #\> grid description file

#\> Retrieve the number of columns, rows, and layers in this simulation  
set NZ = 35  
set NX = `grep -A 1 ${GRID_NAME} ${GRIDDESC} | tail -1 | sed 's/ */ /g' | cut -d' ' -f6`  
set NY = `grep -A 1 ${GRID_NAME} ${GRIDDESC} | tail -1 | sed 's/ */ /g' | cut -d' ' -f7`  
set NCELLS = `echo "${NX} * ${NY} * ${NZ}" | bc -l`

**#\> Output Species and Layer Options**  
\*\* #\> CONC file species; comment or set to “ALL” to write all species to CONC\*\*  
\*\* #setenv CONC\_SPCS “O3 NO ANO3I ANO3J NO2 FORM ISOP ANH4J ASO4I ASO4J” \*\*  
\*\* #setenv CONC\_BLEV\_ELEV " 1 4" #\> CONC file layer range; comment to write all layers to CONC\*\*

\*\* #\> ACONC file species; comment or set to “ALL” to write all species to ACONC\*\*  
\*\* #setenv AVG\_CONC\_SPCS “O3 NO CO NO2 ASO4I ASO4J NH3” \*\*  
\*\* setenv AVG\_CONC\_SPCS “ALL” \*\*  
\*\* setenv ACONC\_BLEV\_ELEV " 1 1" #\> ACONC file layer range; comment to write all layers to ACONC\*\*  
\*\* setenv AVG\_FILE\_ENDTIME N #\> override default beginning ACONC timestamp [default: N]\*\*

#\> Synchronization Time Step and Tolerance Options  
setenv CTM\_MAXSYNC 300 #\> max sync time step (sec) [default: 720]  
setenv CTM\_MINSYNC 60 #\> min sync time step (sec) [default: 60]  
setenv SIGMA\_SYNC\_TOP 0.7 #\> top sigma level thru which sync step determined [default: 0.7]  
#setenv ADV\_HDIV\_LIM 0.95 #\> maximum horiz. div. limit for adv step adjust [default: 0.9]  
setenv CTM\_ADV\_CFL 0.95 #\> max CFL [default: 0.75]  
#setenv RB\_ATOL 1.0E-09 #\> global ROS3 solver absolute tolerance [default: 1.0E-07]

**#\> Science Options**  
**setenv CTM\_SS\_AERO Y #\> use inline Sea Spray Aerosol emissions [default: Y]**  
**setenv CTM\_WB\_DUST Y #\> use inline windblown dust emissions [default: Y]**  
**setenv CTM\_ERODE\_AGLAND N #\> use agricultural activity for windblown dust \*\*  
\*\* #\> [default: N]; ignore if CTM\_WB\_DUST = N**  
**setenv CTM\_WBDUST\_BELD BELD3 #\> landuse database for identifying dust source regions \*\*  
\*\* #\> [default: UNKNOWN]; ignore if CTM\_WB\_DUST = N \*\*  
 setenv CTM\_LTNG\_NO N #\> turn on lightning NOx [default: N]  
 setenv CTM\_WVEL Y #\> save derived vertical velocity component to conc \*\*  
\*\* #\> file [default: N]  
 setenv KZMIN Y #\> use Min Kz option in edyintb [default: Y], \*\*  
\*\* #\> otherwise revert to Kz0UT  
 setenv CTM\_ILDEPV Y #\> calculate in-line deposition velocities [default: Y]  
 setenv CTM\_MOSAIC N #\> landuse specific deposition velocities [default: N]  
 setenv CTM\_FST N #\> mosaic method to get land-use specific stomatal flux \*\*  
\*\* #\> [default: N]  
 setenv PX\_VERSION Y #\> WRF PX LSM  
 setenv CLM\_VERSION N #\> WRF CLM LSM  
 setenv NOAH\_VERSION N #\> WRF NOAH LSM  
 setenv CTM\_ABFLUX N #\> ammonia bi-directional flux for in-line deposition \*\*  
\*\* #\> velocities [default: N]; ignore if CTM\_ILDEPV = N  
 setenv CTM\_BIDI\_FERT\_NH3 T #\> subtract fertilizer NH3 from emissions because it will be handled  
\*\* #\> by the BiDi calculation [default: Y]**  
**setenv CTM\_HGBIDI N #\> mercury bi-directional flux for in-line deposition \*\*  
\*\* #\> velocities [default: N]; ignore if CTM\_ILDEPV = N**  
**setenv CTM\_SFC\_HONO Y #\> surface HONO interaction [default: Y]; ignore if CTM\_ILDEPV = N**  
**setenv CTM\_GRAV\_SETL Y #\> vdiff aerosol gravitational sedimentation [default: Y]**  
**setenv CTM\_BIOGEMIS Y #\> calculate in-line biogenic emissions [default: N]**  
**setenv CTM\_ZERO\_PCSOA N #\> zero out emissions of VOC precursor for pcSOA formation.**  
\*\* #\> The CMAQ dev team recommends leaving pcSOA mass in the\*\*  
\*\* #\> model for production runs. [default: N]\*\*

#\> Vertical Extraction Options  
setenv VERTEXT N  
setenv VERTEXT\_COORD\_PATH ${WORKDIR}/lonlat.csv

#\> I/O Controls

setenv IOAPI\_LOG\_WRITE F #\> turn on excess WRITE3 logging [options: T | F]  
setenv FL\_ERR\_STOP N #\> stop on inconsistent input files  
setenv PROMPTFLAG F #\> turn on I/O-API PROMPT\*FILE interactive mode [options: T | F]  
setenv IOAPI\_OFFSET\_64 YES #\> support large timestep records (\>2GB/timestep record) [options: YES | NO]  
setenv IOAPI\_CHECK\_HEADERS N #\> check file headers [options: Y | N]  
setenv IOAPI\_CFMETA YES  
setenv CTM\_EMISCHK N #\> Abort CMAQ if missing surrogates from emissions Input files  
setenv EMISDIAG F #\> Print Emission Rates at the output time step after they have been  
#\> scaled and modified by the user Rules [options: F | T or 2D | 3D | 2DSUM]  
#\> Individual streams can be modified using the variables:  
#\> GR\_EMIS\_DIAG\_## | STK\_EMIS\_DIAG\_## | BIOG\_EMIS\_DIAG  
#\> MG\_EMIS\_DIAG | LTNG\_EMIS\_DIAG | DUST\_EMIS\_DIAG  
#\> SEASPRAY\_EMIS\_DIAG  
#\> Note that these diagnostics are different than other emissions diagnostic  
#\> output because they occur after scaling.  
setenv EMIS\_DATE\_OVRD N #\> Master switch for allowing CMAQ to use the date from each Emission file  
#\> rather than checking the emissions date against the internal model date.  
#\> [options: T | F or Y | N]. If false (F/N), then the date from CMAQ’s internal  
#\> time will be used and an error check will be performed (recommended). Users  
#\> may switch the behavior for individual emission files below using the variables:  
#\> GR\_EM\_DTOVRD\_## | STK\_EM\_DTOVRD\_##

#\> Aerosol Diagnostic Controls  
setenv CTM\_PMDIAG Y #\> Instantaneous Aerosol Diagnostic File [default: Y]  
setenv CTM\_APMDIAG Y #\> Hourly-Average Aerosol Diagnostic File [default: Y]  
#setenv APMDIAG\_BLEV\_ELEV “1 3” #\> layer range for average pmdiag  
setenv APMDIAG\_BLEV\_ELEV “” #\> layer range for average pmdiag = NLAYS

#\> Diagnostic Output Flags  
setenv CTM\_CKSUM Y #\> checksum report [default: Y]  
setenv CLD\_DIAG Y #\> cloud diagnostic file [default: N]  
setenv CTM\_AERDIAG Y #\> aerosol diagnostic file [default: N]

setenv CTM\_PHOTDIAG Y #\> photolysis diagnostic file [default: N]  
setenv NLAYS\_PHOTDIAG “3” #\> Number of layers for PHOTDIAG2 and PHOTDIAG3 from  
#\> Layer 1 to NLAYS\_PHOTDIAG [default: all layers]  
#setenv NWAVE\_PHOTDIAG “294 303 310 316 333 381 607” #\> Wavelengths written for variables  
#\> in PHOTDIAG2 and PHOTDIAG3  
#\> [default: all wavelengths]

setenv CTM\_SSEMDIAG Y #\> sea-spray emissions diagnostic file [default: N]  
setenv CTM\_DUSTEM\_DIAG Y #\> windblown dust emissions diagnostic file [default: N];  
#\> Ignore if CTM\_WB\_DUST = N  
setenv CTM\_DEPV\_FILE Y #\> deposition velocities diagnostic file [default: N]  
setenv VDIFF\_DIAG\_FILE Y #\> vdiff & possibly aero grav. sedimentation diagnostic file [default: N]  
setenv LTNGDIAG Y #\> lightning diagnostic file [default: N]  
setenv B3GTS\_DIAG Y #\> BEIS mass emissions diagnostic file [default: N]  
setenv PT3DDIAG N #\> 3D point source emissions diagnostic file [default: N];  
setenv PT3DFRAC N #\> layer fractions diagnostic file(s) [default: N];  
setenv REP\_LAYER\_MIN -1 #\> Minimum layer for reporting plume rise info [default: -1]

set DISP = delete #\> [delete | keep] existing output files

##################################################################################

Based on the script, I have two concerns.

1. Note that the parameter “CTM\_LTING\_NO” is set to be N.
2. I set the ACONC\_BLEV\_ELEV to be “1 1”. What does it mean? Doe it mean surface level of the average of all layers?

The NO3 and HNO3 avg. concentration are shown below. They seem not right.

 ![ACONC_NO3](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/1X/c9ed33f6a3a94da4c8e0eccb39b98752adc4da51.gif)  
 ![ACONC_HNO3](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/1X/71d401e628796cb6cedaa31acafb1b1e2990e245.gif)

Could you give me some advice on the outputs? If you need any supporting files, please let me know and I can upload them.

Thanks very much!

Yijia

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<div class="post-metadata">

**Author:** ![zyj.jess](https://avatars.discourse-cdn.com/v4/letter/z/8dc957/32.png) [@zyj.jess](https://forum.cmascenter.org/u/zyj.jess)\
**Post date:** [September 20, 2019, 4:10pm UTC](https://forum.cmascenter.org/t/cmaq-aconc-outputs-using-2014-nei-emissions/951/2 "2019-09-20T16:10:00Z")

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Does anyone know any publications on CMAQ application on 2014 emission inventory? For example, the study of reactive nitrogen or PM2.5 using CMAQ.