### Author:  [@hiepnguyen](https://forum.cmascenter.org/u/hiepnguyen)
#### Post date: [May 13, 2021, 7:26am UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/1 "2021-05-13T07:26:39Z")
Hi all,
I am running WRF-CMAQ with ISAM. When I ran CMAQ-ISAM, i got this error
```
============================================
|>--- CHECK INITIAL CONCENTRATIONS ---<|
============================================
Variable name VNAME3D( 57 ) = "ASO4J_" duplicates VNAME3D( 1 ) = "ASO4J_" in file "SA_CONC_1"
Variable name VNAME3D( 58 ) = "ASO4I_" duplicates VNAME3D( 2 ) = "ASO4I_" in file "SA_CONC_1"
Variable name VNAME3D( 59 ) = "SO2_" duplicates VNAME3D( 3 ) = "SO2_" in file "SA_CONC_1"
Variable name VNAME3D( 60 ) = "SULF_" duplicates VNAME3D( 4 ) = "SULF_" in file "SA_CONC_1"
Variable name VNAME3D( 61 ) = "SULRXN_" duplicates VNAME3D( 5 ) = "SULRXN_" in file "SA_CONC_1"
Variable name VNAME3D( 62 ) = "ANO3J_" duplicates VNAME3D( 6 ) = "ANO3J_" in file "SA_CONC_1"
Variable name VNAME3D( 63 ) = "ANO3I_" duplicates VNAME3D( 7 ) = "ANO3I_" in file "SA_CONC_1"
Variable name VNAME3D( 64 ) = "HNO3_" duplicates VNAME3D( 8 ) = "HNO3_" in file "SA_CONC_1"
```
…
```
Error creating netCDF variable ASO4J_
netCDF error number -42 processing file "SA_CONC_1"
NetCDF: String match to name in use
*** ERROR ABORT in subroutine OP_SA on PE 000
Could not create SA_CONC_1 file
```
PM3EXIT: DTBUF 0:00:00 Jan. 14, 2019
Date and time 0:00:00 Jan. 14, 2019 (2019014:000000)
CMAQ reads isam\_cntrol.txt and the region file ok, but somehow the species name duplicate problem occurred.in the check initial concentration. Is this problem related to ICON ?
Any ideas ?
Thanks in advance
---
### Author:  [@Ben\_Murphy](https://forum.cmascenter.org/u/Ben_Murphy)
#### Post date: [May 14, 2021, 5:58pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/2 "2021-05-14T17:58:39Z")
Hi,
Can you send your isam\_control file? There should be an internal check to remove duplicates before the list of tagged model species is used to specify the output file, but it may have been bypassed somehow in the WRF-CMAQ system.
-Ben
---
### Author:  [@hiepnguyen](https://forum.cmascenter.org/u/hiepnguyen)
#### Post date: [May 14, 2021, 10:18pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/3 "2021-05-14T22:18:31Z")
Dear Ben,
Thank for the information. Here is the isam\_control.txt file
!!! CMAQ-ISAM tag definition control file
!!! (lines begining with !!! - three exclamaition marks - are ignored by the text parser)
!!!
!!! Example file provided with CMAQ v5.3 release
!!! 05 June 2019: Sergey L. Napelenok
!!!
!!!
!!! The following line defines the tag classes to track for the simulation. Species in NITRATE and VOC classes depend on the
!!! the chemical mechanism used. The below definitions apply for the cb6r3\_ae7\_aq mechanism.
!!! Choose any/all from the list of nine: SULFATE, NITRATE, AMMONIUM, EC, OC, VOC, PM25\_IONS, CO, OZONE
!!! SULFATE - ASO4J, ASO4I, SO2, SULF, SULRXN
!!! NITRATE - ANO3J, ANO3I, HNO3, NO, NO2, NO3, HONO, N2O5, PNA, PAN, PANX, NTR1, NTR2, INTR, CLNO2, CLNO3
!!! AMMONIUM - ANH4J, ANH4I, NH3
!!! EC - AECJ, AECI
!!! OC - APOCI, APOCJ, APNCOMI, APNCOMJ
!!! VOC - 22 species, check CCTM/src/isam/SA\_DEFN.F for species names
!!! PM25\_IONS - ANAI, ANAJ, AMGJ, AKJ, ACAJ, AFEJ, AALJ, ASIJ, ATIJ, AMNJ, AOTHRI, AOTHRJ
!!! CO - CO
!!! OZONE - all NITRATE species + all VOC species
!!! CHLORINE - ACLI, ACLJ, HCL
!!! The following are source definition text blocks in the format:
!!! TAG NAME |Three character text string
!!! REGION(S) |Keyword EVERYWHERE or variable names from the region file (multiple regions need to be comma delimited)
!!! FILENAME(S) |Emissions labels (multiple labels need to be comma delimited)
!!!TAG CLASSES | SULFATE, OZONE
TAG CLASSES | OZONE
TAG NAME | GR1
REGION(S) | CENSYD
EMIS STREAM(S) |GRIDDED\_EMIS
TAG NAME | GR2
REGION(S) | ILLA
EMIS STREAM(S) |GMRELEV
ENDLIST eof
My runctm scripts has this reference to this isam\_control.txt file
#\> Integrated Source Apportionment Method (ISAM) Options
setenv CTM\_ISAM Y
if ( $?CTM\_ISAM ) then
if ( $CTM\_ISAM == ‘Y’ || $CTM\_ISAM == ‘T’ ) then
```
setenv SA_IOLIST ${WORKDIR}/isam_control.txt
setenv ISAM_BLEV_ELEV " 1 1"
setenv AISAM_BLEV_ELEV " 1 1"
#> Set Up ISAM Initial Condition Flags
if ($NEW_START == true || $NEW_START == TRUE ) then
setenv ISAM_NEW_START Y
setenv ISAM_PREVDAY
else
setenv ISAM_NEW_START N
setenv ISAM_PREVDAY "$OUTDIR/CCTM_SA_CGRID_${RUNID}_${YESTERDAY}.nc"
endif
#> Set Up ISAM Output Filenames
setenv SA_ACONC_1 "$OUTDIR/CCTM_SA_ACONC_${CTM_APPL}.nc -v"
setenv SA_CONC_1 "$OUTDIR/CCTM_SA_CONC_${CTM_APPL}.nc -v"
setenv SA_DD_1 "$OUTDIR/CCTM_SA_DRYDEP_${CTM_APPL}.nc -v"
setenv SA_WD_1 "$OUTDIR/CCTM_SA_WETDEP_${CTM_APPL}.nc -v"
setenv SA_CGRID_1 "$OUTDIR/CCTM_SA_CGRID_${CTM_APPL}.nc -v"
#> Set optional ISAM regions files
setenv CMAQ_REGIONS /home/duch/repository/5.3.1/ioapi-3.2/make_mask/output/reg_allmask_d01.ncf
endif
```
endif
As this CMAQ application is run on the domain in Sydney, Australia, I created the region mask file using m3tool (m3mask and m3merge). The header of this mask file (reg\_allmask\_d01.ncf) is followed
netcdf reg\_allmask\_d01 {
dimensions:
TSTEP = 1 ;
LAY = 1 ;
ROW = 373 ;
COL = 373 ;
DATE-TIME = 2 ;
VAR = 2 ;
variables:
float CENSYD(TSTEP, LAY, ROW, COL) ;
CENSYD:units = “None” ;
CENSYD:var\_desc = "1==mask region, 0==outside-mask region " ;
CENSYD:long\_name = "CENSYD " ;
float ILLA(TSTEP, LAY, ROW, COL) ;
ILLA:units = “None” ;
ILLA:var\_desc = "1==mask region, 0==outside-mask region " ;
ILLA:long\_name = "ILLA " ;
int TFLAG(TSTEP, VAR, DATE-TIME) ;
TFLAG:units = “\None” ;
TFLAG:long\_name = "TFLAG " ;
TFLAG:var\_desc = "Timestep-valid flags: (1) YYYYDDD or (2) HHMMSS " ;
I carefully followed the previous tips and instruction in this forum on the creation of the mask file.
Thanks for your help
Best
Hiep Nguyen
Senior Atmospheric Scientist
Department of Planning, Industry and Environment, NSW, Sydney
---
### Author:  [@hiepnguyen](https://forum.cmascenter.org/u/hiepnguyen)
#### Post date: [May 15, 2021, 12:42pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/4 "2021-05-15T12:42:05Z")
It may have something to do with ICON tag. In the error messages, the duplicate species names, such as ASO4J\_, do not have tag at the end. Why don’t the tags attached to the species names in the check initial concentration check ?
I looked into the source code in isam directory. I found the sa\_array\_init.F has this section on checking ICON tag
```
DO JSPCTAG = 1, NSPCTAG
!KRT: extract sa_conc_1 from previous day
IF ( .NOT. XTRACT3( INNAME, VNAME3D( JSPCTAG ),
& 1, NLAYS3D, STARTROW, ENDROW, STARTCOL, ENDCOL,
& JDATE, JTIME, TEMP ) ) THEN
Print*, PNAME, JDATE, JTIME,
& 'Read failure: file ' // INNAME //
& ' variable ' // VNAME3D( JSPCTAG )
stop ' end of file...'
END IF
!KRT: identify isam indices from input species names
IBGN = INDEX( VNAME3D( JSPCTAG ),'_', .FALSE. )
S = INDEX1( VNAME3D( JSPCTAG )( 1:IBGN-1 ),NSPC_SA,SPCNAME1 )
K = INDEX1( VNAME3D( JSPCTAG )( IBGN+1:LEN_TRIM(VNAME3D(JSPCTAG))),
& NTAG_SA, TAGNAME )
IF ( S .GT. 0 ) THEN
IF ( K .GT. 0 ) THEN
DO C = 1, NCOLS
DO R = 1, NROWS
DO L = 1, NLAYS3D
ISAM( C,R,L,S,K ) = TEMP( C,R,L )
END DO
END DO
END DO
ELSE ! bcon, othr, or icon tags
CK_SUFFX: SELECT CASE ( VNAME3D(JSPCTAG)(IBGN+1:LEN_TRIM(VNAME3D(JSPCTAG))) )
CASE ( 'BCON' )
K = NTAG_SA - 2
CASE ( 'OTHR' )
K = NTAG_SA - 1
CASE ( 'ICON' )
K = NTAG_SA
END SELECT CK_SUFFX
DO L = 1, NLAYS3D
DO R = 1, NROWS
DO C = 1, NCOLS
ISAM( C,R,L,S,K ) = TEMP( C,R,L )
END DO
END DO
END DO
ENDIF ! emission tags
ENDIF ! species exist in tags
END DO ! jspctag
```
How can I set this tag (ICON) on or do something to avoid the duplicate errors in creating the SA\_CONC\_1 file ?.
Thanks in advance
Hiep
---
### Author:  [@Ben\_Murphy](https://forum.cmascenter.org/u/Ben_Murphy)
#### Post date: [May 17, 2021, 4:08pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/5 "2021-05-17T16:08:44Z")
This is indeed odd. You’ve only declared one Tag Class (ozone), so I wouldn’t expect ISAM to be requiring ASO4 at all in the first place. Try adding sulfate to the Tag Classes to see if that straightens things out.
-Ben
---
### Author:  [@sergey](https://forum.cmascenter.org/u/sergey)
#### Post date: [May 17, 2021, 5:13pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/6 "2021-05-17T17:13:07Z")
I agree with Ben - it should not have anything to do with the sulfate related species. Is this the first day and first hour of the simulation or are you reading some kind of initial conditions for the apportionment?
Sergey
---
### Author:  [@hiepnguyen](https://forum.cmascenter.org/u/hiepnguyen)
#### Post date: [May 18, 2021, 1:56am UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/7 "2021-05-18T01:56:40Z")
Hi Ben and Sergey,
The above error messages were from the run with TAG CLASSES | SULPHATE, OZONE.
With TAG CLASSES | OZONE, errors as followed
```
CTM_WET_DEP_1 :/mnt/scratch3/CMAQ_installation/data/CTM-hd/casestudy1/2019-01-14/d01/CCTM_WETDEP1_v531_intel_d01_20190114.nc
============================================
|>--- CHECK INITIAL CONCENTRATIONS ---<|
============================================
Variable name VNAME3D( 52 ) = "ANO3J_" duplicates VNAME3D( 1 ) = "ANO3J_" in file "SA_CONC_1"
Variable name VNAME3D( 53 ) = "ANO3I_" duplicates VNAME3D( 2 ) = "ANO3I_" in file "SA_CONC_1"
Variable name VNAME3D( 54 ) = "HNO3_" duplicates VNAME3D( 3 ) = "HNO3_" in file "SA_CONC_1"
Variable name VNAME3D( 55 ) = "NO_" duplicates VNAME3D( 4 ) = "NO_" in file "SA_CONC_1"
Variable name VNAME3D( 56 ) = "NO2_" duplicates VNAME3D( 5 ) = "NO2_" in file "SA_CONC_1"
Variable name VNAME3D( 57 ) = "NO3_" duplicates VNAME3D( 6 ) = "NO3_" in file "SA_CONC_1"
Variable name VNAME3D( 58 ) = "HONO_" duplicates VNAME3D( 7 ) = "HONO_" in file "SA_CONC_1"
Variable name VNAME3D( 59 ) = "N2O5_" duplicates VNAME3D( 8 ) = "N2O5_" in file "SA_CONC_1"
Variable name VNAME3D( 60 ) = "PAN_" duplicates VNAME3D( 9 ) = "PAN_" in file "SA_CONC_1"
Variable name VNAME3D( 61 ) = "XO2N_" duplicates VNAME3D( 10 ) = "XO2N_" in file "SA_CONC_1"
Variable name VNAME3D( 62 ) = "NTR1_" duplicates VNAME3D( 11 ) = "NTR1_" in file "SA_CONC_1"
Variable name VNAME3D( 63 ) = "NTR2_" duplicates VNAME3D( 12 ) = "NTR2_" in file "SA_CONC_1"
Variable name VNAME3D( 64 ) = "INTR_" duplicates VNAME3D( 13 ) = "INTR_" in file "SA_CONC_1"
Variable name VNAME3D( 65 ) = "PNA_" duplicates VNAME3D( 14 ) = "PNA_" in file "SA_CONC_1"
```
Sergey, this is the first day and first hour of the simulation.
Thanks
Hiep
---
### Author:  [@sergey](https://forum.cmascenter.org/u/sergey)
#### Post date: [May 24, 2021, 4:17pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/8 "2021-05-24T16:17:25Z")
Can you post the exact control file you used for the run that resulted in the errors? The “duplicates” text normally results from having non-unique tag names specified in the control file.
Sergey
---
### Author:  [@hiepnguyen](https://forum.cmascenter.org/u/hiepnguyen)
#### Post date: [May 27, 2021, 12:25pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/9 "2021-05-27T12:25:31Z")
Thank you, Sergey. I post here the isam\_control.txt file for your information
!!! CMAQ-ISAM tag definition control file
!!! (lines begining with !!! - three exclamaition marks - are ignored by the text parser)
!!!
!!! Example file provided with CMAQ v5.3 release
!!! 05 June 2019: Sergey L. Napelenok
!!!
!!!
!!! The following line defines the tag classes to track for the simulation. Species in NITRATE and VOC classes depend on the
!!! the chemical mechanism used. The below definitions apply for the cb6r3\_ae7\_aq mechanism.
!!! Choose any/all from the list of nine: SULFATE, NITRATE, AMMONIUM, EC, OC, VOC, PM25\_IONS, CO, OZONE
!!! SULFATE - ASO4J, ASO4I, SO2, SULF, SULRXN
!!! NITRATE - ANO3J, ANO3I, HNO3, NO, NO2, NO3, HONO, N2O5, PNA, PAN, PANX, NTR1, NTR2, INTR, CLNO2, CLNO3
!!! AMMONIUM - ANH4J, ANH4I, NH3
!!! EC - AECJ, AECI
!!! OC - APOCI, APOCJ, APNCOMI, APNCOMJ
!!! VOC - 22 species, check CCTM/src/isam/SA\_DEFN.F for species names
!!! PM25\_IONS - ANAI, ANAJ, AMGJ, AKJ, ACAJ, AFEJ, AALJ, ASIJ, ATIJ, AMNJ, AOTHRI, AOTHRJ
!!! CO - CO
!!! OZONE - all NITRATE species + all VOC species
!!! CHLORINE - ACLI, ACLJ, HCL
!!! The following are source definition text blocks in the format:
!!! TAG NAME |Three character text string
!!! REGION(S) |Keyword EVERYWHERE or variable names from the region file (multiple regions need to be comma delimited)
!!! FILENAME(S) |Emissions labels (multiple labels need to be comma delimited)
!!!TAG CLASSES | SULFATE, OZONE
TAG CLASSES | OZONE
TAG NAME | GR1
!!!REGION(S) | CENSYD
!!!REGION(S) | reg\_sydcen
REGION(S) | EVERYWHERE
!!!REGION(S) | WATER, CENSYD
EMIS STREAM(S) |GRIDDED\_EMIS
TAG NAME | GR2
!!!REGION(S) | ILLA
!!!REGION(S) | reg\_ill
REGION(S) | EVERYWHERE
!!!REGION(S) | WATER, ILLA
!!!EMIS STREAM(S) |GRIDDED\_EMIS, GMRELEV
EMIS STREAM(S) |GMRELEV
ENDLIST eof
The run file contains this reference to the above file
#\> Integrated Source Apportionment Method (ISAM) Options
setenv CTM\_ISAM Y
if ( $?CTM\_ISAM ) then
if ( $CTM\_ISAM == ‘Y’ || $CTM\_ISAM == ‘T’ ) then
```
setenv SA_IOLIST ${WORKDIR}/isam_control.txt
setenv ISAM_BLEV_ELEV " 1 1"
setenv AISAM_BLEV_ELEV " 1 1"
#> Set Up ISAM Initial Condition Flags
if ($NEW_START == true || $NEW_START == TRUE ) then
setenv ISAM_NEW_START Y
setenv ISAM_PREVDAY
else
setenv ISAM_NEW_START N
setenv ISAM_PREVDAY "$OUTDIR/CCTM_SA_CGRID_${RUNID}_${YESTERDAY}.nc"
endif
#> Set Up ISAM Output Filenames
setenv SA_ACONC_1 "$OUTDIR/CCTM_SA_ACONC_${CTM_APPL}.nc -v"
setenv SA_CONC_1 "$OUTDIR/CCTM_SA_CONC_${CTM_APPL}.nc -v"
setenv SA_DD_1 "$OUTDIR/CCTM_SA_DRYDEP_${CTM_APPL}.nc -v"
setenv SA_WD_1 "$OUTDIR/CCTM_SA_WETDEP_${CTM_APPL}.nc -v"
setenv SA_CGRID_1 "$OUTDIR/CCTM_SA_CGRID_${CTM_APPL}.nc -v"
#> Set optional ISAM regions files
```
# setenv ISAM\_REGIONS /work/MOD3EVAL/nsu/isam\_v53/CCTM/scripts/input/RGN\_ISAM.nc
```
setenv CMAQ_REGIONS /home/duch/repository/5.3.1/ioapi-3.2/make_mask/output/reg_allmask_d01.ncf
endif
```
endif
---
### Author:  [@sergey](https://forum.cmascenter.org/u/sergey)
#### Post date: [June 1, 2021, 2:12pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/10 "2021-06-01T14:12:22Z")
I don’t see any problems with what you are trying to do. Perhaps, try to simplify to just one and see if it works?
The other thing to check is to make sure you are moving out all existing output files and writing out to a clean directory.
Sergey
---
### Author:  [@hiepnguyen](https://forum.cmascenter.org/u/hiepnguyen)
#### Post date: [June 9, 2021, 2:12pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/11 "2021-06-09T14:12:06Z")
Dear Sergey,
# I tried your suggestion using TAG CLASSES | CO which has only one species (CO). Still the error as followed
```
|>--- CHECK INITIAL CONCENTRATIONS ---<|
============================================
Variable name VNAME3D( 2 ) = "CO_" duplicates VNAME3D( 1 ) = "CO_" in file "SA_CONC_1"
Error creating netCDF variable CO_
netCDF error number -42 processing file "SA_CONC_1"
NetCDF: String match to name in use
*** ERROR ABORT in subroutine OP_SA on PE 000
Could not create SA_CONC_1 file
```
The SA\_CONC\_1 file should have species name as “CO\_ICON” rather than “CO\_”. The error message tells me that the problem is in subroutine OP\_SA.
I looked into the source code, the file op\_sa.F contains this relevant code
IF ( ITAG .EQ. BCONTAG ) THEN
CSUFFX = 'BCON ’
CALL WR\_VARNAME( SPECIE\_NAME, LENGTH, NTAG\_SA, NSPC\_SA,
& CSUFFX, VNAME( JSPC,ITAG ) )
ELSEIF ( ITAG .EQ. OTHRTAG ) THEN
CSUFFX = 'OTHR ’
CALL WR\_VARNAME( SPECIE\_NAME, LENGTH, NTAG\_SA, NSPC\_SA,
& CSUFFX, VNAME( JSPC,ITAG ) )
ELSEIF ( ITAG .EQ. ICONTAG ) THEN
CSUFFX = 'ICON ’
CALL WR\_VARNAME( SPECIE\_NAME, LENGTH, NTAG\_SA, NSPC\_SA,
& CSUFFX, VNAME( JSPC,ITAG ) )
It tells us that when there is an icontag then the suffix would be 'ICON ’ (16 characters). And then add this suffix to the species name by calling the subroutine WR\_VARNAME.
The subroutine WR\_VARNAME is as follows
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
c
c this subroutine must be implemented to overcome Character_1 X 16
c to Character_16 conversion.
c new varname will be created by this way.
c
c by bo wang
c
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
```
subroutine wr_varname(input, length, ntag_tssa, nspc_tssa,
& src_name, varname)
```
c …argument
integer length
character_1 :: input(length)
integer ntag\_tssa, nspc\_tssa
character_16 src\_name
character\*16 varname
c …local variable
integer i
CHARACTER_7 CHAR1
Ckrt CHARACTER(len=16-length) :: CHAR1
character(len=length) output
character_16 temp
c …external function
integer len\_trim
c…
```
do i = 1, length
output(i:i) = input(i)
end do
temp = src_name
```
!0711 do i = 1, 7
do i = 1, min( 7, 16-length-1 )
char1(i:i) = temp(i:i)
end do
```
VARNAME = output // '_' // char1
```
end
So somewhere the ‘ICON’ suffix tag failed to be added to the species name (CO) to become ‘CO\_ICON’ to be created in the SA\_CONC\_1 file.
I don’t know how this happened.
---
### Author:  [@sergey](https://forum.cmascenter.org/u/sergey)
#### Post date: [June 14, 2021, 2:38pm UTC](https://forum.cmascenter.org/t/cmaq-isam-initial-condition-error/2333/12 "2021-06-14T14:38:45Z")
Please, try running only 1 parameter. Something like this:
TAG CLASSES | CO
TAG NAME | GR1
REGION(S) | EVERYWHERE
EMIS STREAM(S) |GRIDDED\_EMIS
Are you writing output to a an empty directory?
Sergey