| 1 | #!/usr/bin/bash |
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| 2 | # |
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| 3 | # Bash script to post-process files startphy_icosa.nc and start_icosa.nc |
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| 4 | # generated by start_archive2icosa and create files |
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| 5 | # start.nc and startphy.nc (usable as inputs for icosa_lmdz.exe) |
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| 6 | |
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| 7 | # load nco module |
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| 8 | module purge |
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| 9 | # change to your LMDZ install dir or set "export LMDZ=/path/lmdz" in your .bashrc |
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| 10 | LMDZ=${LMDZ:-../../..} |
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| 11 | source $LMDZ/XIOS/arch.env |
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| 12 | #module load nco/4.7.9-gcc-4.8.5-hdf5-1.8.18-openmpi-2.0.4 #Example of version of the module needed |
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| 13 | module load nco |
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| 14 | |
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| 15 | |
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| 16 | #conversion to netcdf 3 in order to rename and add variables, not properly done with netcdf4 files |
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| 17 | nccopy -k 'classic' startfi_prefinalize.nc startphy_icosa_nc3.nc |
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| 18 | |
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| 19 | # rename lat and lon variables as latitude and longitude and put result in |
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| 20 | # file startphy.nc |
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| 21 | ncrename -v lon,longitude -v lat,latitude -d cell,physical_points\ |
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| 22 | startphy_icosa_nc3.nc startphy_nc3.nc |
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| 23 | #Temporay soildepth array from Dynamico startphy_icosa_ref |
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| 24 | ncks -A -v soildepth startphy_icosa_ref.nc startphy_nc3.nc #You have to adapt to your own path |
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| 25 | # ncks -A -v subslope_dist startphy_icosa_ref.nc startphy_nc3.nc |
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| 26 | # ncks -A -v def_slope startphy_icosa_ref.nc startphy_nc3.nc |
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| 27 | |
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| 28 | nccopy -k 4 startphy_nc3.nc startfi.nc |
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| 29 | #cp startfi.nc startfi_before_finalize.nc |
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| 30 | |
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| 31 | #Temporary Time variable from start2archive; should be added with xios |
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| 32 | ncks -O -x -v time_counter startfi.nc startfi.nc_tmp |
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| 33 | #ncks -A -v Time start.nc startfi.nc_tmp |
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| 34 | # ncks -A -v flux_geo startphy_icosa_ref.nc startfi.nc_tmp |
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| 35 | # ncks -A -v wstar startphy_icosa_ref.nc startfi.nc_tmp |
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| 36 | # ncks -A -v hmons startphy_icosa_ref.nc startfi.nc_tmp |
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| 37 | # ncks -A -v summit startphy_icosa_ref.nc startfi.nc_tmp |
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| 38 | # ncks -A -v base startphy_icosa_ref.nc startfi.nc_tmp |
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| 39 | cp startfi.nc_tmp startfi.nc |
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| 40 | |
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| 41 | #./rearrange_startphy.e > rearrange_startphy.out 2>&1 |
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| 42 | |
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| 43 | # make a proper start.nc file based on start_icosa.nc |
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| 44 | cp start_icosa_prefinalize.nc start_icosa.nc |
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| 45 | |
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| 46 | # add u,u_lat,u_lon,bounds_lat_u and bound_lon_u from start_icosa_ref.nc |
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| 47 | ncks -A -v u,lon_u,lat_u,bounds_lon_u,bounds_lat_u \ |
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| 48 | start_icosa_ref.nc start_icosa.nc |
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| 49 | ncrename -d cell,cell_mesh \ |
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| 50 | start_icosa.nc |
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| 51 | ncrename -d nvertex,nvertex_mesh \ |
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| 52 | start_icosa.nc |
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| 53 | ncks -A -v xcell,ycell,zcell \ |
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| 54 | start_icosa_ref.nc start_icosa.nc |
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| 55 | |
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| 56 | #ncks -A -v q,nq start_icosa_ref.nc start_icosa.nc |
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| 57 | |
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| 58 | #ncks -A -v latitude,longitude startphy_icosa_ref.nc startfi.nc |
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| 59 | #ncks -A -v latitude,longitude startphy.nc startfi.nc |
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| 60 | # In the current version of Dynamico, the variable q for tracer is needed but unused. |
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| 61 | # To create this unused variable simply run this short python code |
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| 62 | |
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| 63 | # cleanup |
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| 64 | rm -rf startphy_icosa_nc3.nc startphy_nc3.nc startfi.nc_tmp |
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| 65 | |
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| 66 | # copy icosa start files in icosa_starts folder |
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| 67 | mkdir -p icosa_starts |
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| 68 | mv start_icosa.nc icosa_starts/start.nc |
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| 69 | mv startfi.nc icosa_starts/startfi.nc |
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