| 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 | source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.env #You have to adapt to your own path |
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| 10 | #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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| 11 | module load nco |
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| 12 | |
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| 13 | #conversion to netcdf 3 in order to rename and add variables, not properly done with netcdf4 files |
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| 14 | nccopy -k 'classic' startfi_prefinalize.nc startphy_icosa_nc3.nc |
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| 15 | |
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| 16 | # rename lat and lon variables as latitude and longitude and put result in |
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| 17 | # file startphy.nc |
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| 18 | ncrename -v lon,longitude -v lat,latitude -d cell,physical_points\ |
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| 19 | startphy_icosa_nc3.nc startphy_nc3.nc |
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| 20 | # Temporarily added because program is not yet able to read topography |
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| 21 | # SSO parameters are now taken from a dedicated startarchive.nc |
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| 22 | # see start2archive_SSO.f90 |
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| 23 | #ncks -A -v albedodat,ZMEA,ZSTD,ZSIG,ZGAM,ZTHE \ |
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| 24 | # startphy_icosa_ref.nc startphy_nc3.nc |
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| 25 | #Temporay soildepth array from Dynamico restartfi |
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| 26 | ncks -A -v soildepth \ |
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| 27 | ../../mars_dynamico_update_basic/startfi_0.nc startphy_nc3.nc #You have to adapt to your own path |
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| 28 | |
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| 29 | nccopy -k 4 startphy_nc3.nc startfi.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 -A -v Time \ |
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| 33 | # start_archive_nc4.nc startfi.nc |
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| 34 | ncks -O -x -v time_counter startfi.nc startfi.nc_tmp |
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| 35 | ncks -A -v Time start.nc startfi.nc_tmp |
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| 36 | cp startfi.nc_tmp startfi.nc |
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| 37 | |
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| 38 | rearrange_startphy > rearrange_startphy.out 2>&1 |
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| 39 | |
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| 40 | # make a proper start.nc file based on start_icosa.nc |
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| 41 | cp start_icosa_prefinalize.nc start_icosa.nc |
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| 42 | |
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| 43 | # add u,u_lat,u_lon,bounds_lat_u and bound_lon_u from start_icosa_ref.nc |
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| 44 | ncks -A -v u,lon_u,lat_u,bounds_lon_u,bounds_lat_u \ |
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| 45 | start_icosa_ref.nc start_icosa.nc |
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| 46 | ncrename -d cell,cell_mesh \ |
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| 47 | start_icosa.nc |
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| 48 | ncrename -d nvertex,nvertex_mesh \ |
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| 49 | start_icosa.nc |
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| 50 | ncks -A -v xcell,ycell,zcell \ |
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| 51 | start_icosa_ref.nc start_icosa.nc |
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| 52 | |
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| 53 | # In the current version of Dynamico, the variable q for tracer is needed but unused. |
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| 54 | # To create this unused variable simply run this short python code |
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| 55 | |
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| 56 | #import numpy as np |
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| 57 | #import netCDF4 as nc |
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| 58 | |
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| 59 | #fn = 'start_icosa.nc' |
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| 60 | #ds = nc.Dataset(fn, 'a', format='NETCDF4') |
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| 61 | #nq = ds.createDimension('nq', 7) |
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| 62 | |
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| 63 | #q = ds.createVariable('q', 'f8', ('nq','lev', 'cell_mesh',)) |
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| 64 | #nqq = ds.createVariable('nq', 'f8', ('nq',)) |
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| 65 | #q[:,:,:]=0. |
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| 66 | #q.online_operation = "once" |
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| 67 | #q.coordinates = "lat lon" |
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| 68 | #ds.close() |
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| 69 | |
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| 70 | # cleanup |
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| 71 | rm -rf startphy_icosa_nc3.nc startphy_nc3.nc |
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