Real.exe is successfully running with wrf_chem_input but producing a wrfinput without values for the chemical species.

[saadatshahidi12]

I am a relatively new user of WRF-Chem. I am using the version 3.9.1.1. When running real.exe with wrf_chem_input for a day the program runs, but the wrfinput file produced have zero values for the chemical species. The wrf_chem_input file I am using is actually the last wrfout from the previous days simulation. So, I am expecting that the wrfinput produced by real.exe should retain the chemical species values from the wrf_chem_input file. How can I fix this issue?

I asked a colleague to use my namelist.input, met_em files and wrf_chem_input files and run real.exe. When they did so, they got a wrfinput that has some nonzero values for the chemical species. It made me further confused about what might be the problem for my setup. I am attaching my namelist with this post.

 

[Jose Agustin]

Your compilation may be missing the required environment variables:
export WRF_KPP=1
export WRF_DA_CORE=0
export WRF_NMM_CORE=0
export WRF_CHEM=1
export WRF_EM_CORE=1
export WRFIO_NCD_LARGE_FILE_SUPPORT=1

Without these settings, real.exe will fail to generate the expected output.

 

[saadatshahidi12]

Your compilation may be missing the required environment variables:
export WRF_KPP=1
export WRF_DA_CORE=0
export WRF_NMM_CORE=0
export WRF_CHEM=1
export WRF_EM_CORE=1
export WRFIO_NCD_LARGE_FILE_SUPPORT=1

Without these settings, real.exe will fail to generate the expected output.

Thank you for your reply. I have doubled checked that my environment variables were correct. I have recompiled the model to check if it was a issue with the previous compilation. But I got the same result with the new compilation also.
To provide some more background, the model is running normally when restart = true. When I set restart = false to reinitialize the meteorology, then I am facing this issue. Real.exe produces an wrfinput with only zero values for the chemical species. When I use the wrfinput for running wrf.exe, the model is stuck in the first timestep.

 

[Jose Agustin]

We used the following script, it extracts and appends specific atmospheric variables from a WRF model output file to another NetCDF file, but only if the source file exists.

export fecha=`date -d "-1 days " +%Y'-'%m'-'%d'_00:00:00'`
file_path="/shared/pronostico/salidas/wrfout_d01_${fecha}"
# Check if the file exists
if [ -e "$file_path" ]; then
echo "The file exists: wrfout_d01_${fecha}"
/shared/mamba/bin/ncks -O -d Time,24,24 -v o3,no2,no,so2,co,hcho,PM2_5_DRY,PM10,T $file_path temp.nc
/shared/mamba/bin/ncks -A temp.nc wrfinput_d01
rm temp.nc
else
echo "The file does NOT exist: wrfout_d01_${fecha}"
fi