#!/bin/bash ### =========================================================================== ### ### Creates grids.nc, masks.nc and areas.nc for OASIS-MCT ### ### =========================================================================== ## ## Warning, to install, configure, run, use any of Olivier Marti's ## software or to read the associated documentation you'll need at least ## one (1) brain in a reasonably working order. Lack of this implement ## will void any warranties (either express or implied). ## O. Marti assumes no responsability for errors, omissions, ## data loss, or any other consequences caused directly or indirectly by ## the usage of his software by incorrectly or partially configured ## personal. ## ### ### Documentation : https://forge.ipsl.jussieu.fr/igcmg/wiki/IPSLCM6/MOSAIX ### ## SVN information # $Author$ # $Date$ # $Revision$ # $Id$ # $HeadURL$ set +vx echo ${Titre}"Starting CreateOasisGrids.bash"${Norm} ## echo ${Titre}"Default configuration (may be overrided by command line parameters)"${Norm} ## =========================================================================== OCE=ORCA2.3 # OCE=eORCA1.2 ATM=ICO30 #ATM=ICO40 #ATM=ICO450 #ATM=LMD144142 #ATM=LMD9695 ## =========================================================================== ## ## You should not change anything below this line .... ## ## =========================================================================== echo ${Titre}"Defines computer"${Norm} # ================ if [[ $(hostname) = curie* ]] ; then arch=curie ; center=tgcc ; fi if [[ $(hostname) = irene* ]] ; then arch=irene ; center=tgcc ; fi if [[ $(hostname) = lsce3005* ]] ; then arch=spip ; center=spip ; fi PROGRAM=$(basename ${0}) case ${arch} in ( curie | irene ) set +vx module unload cdo nco ferret module unload netcdf hdf5 module load python # /2.7.12 module load netcdf/4.3.3.1_hdf5_parallel # Version for XIOS module load nco R_IN=$(ccc_home -u igcmg --cccwork)/IGCM TMPDIR=${SCRATCHDIR}/TMP SUBMIT_DIR=${BRIDGE_MSUB_PWD:-${SUBMIT_DIR}} ;; ( spip ) R_IN=${HOME}/Scratch/IGCM TMPDIR=${HOME}/Scratch/TMP SUBMIT_DIR=$(pwd) MPIRUN=/opt/local/bin/mpirun-openmpi-gcc49 -n 2 ;; ( * ) exit -1 ;; esac ## echo ${Titre}"Command line parameters"${Norm} ## =========================================================================== set -e set -o verbose set -o xtrace while [[ ${1} = -* ]] ; do case ${1} in ( -- ) shift ; break ;; ( -o=* | --oce=* ) OCE=${1##*=} ; echo OCE:${OCE} ;; ( -o | --oce ) shift ; OCE=${1} ; echo OCE:${OCE} ;; ( -a=* | --atm=* ) ATM=${1##*=} ; echo ATM:${ATM} ;; ( -a | --atm ) shift ; ATM=${1} ; echo ATM:${ATM} ;; ( -v | --verbose ) set -o verbose ;; ( -x | --xtrace ) set -o xtrace ;; ( -e ) set -e ;; ( -V | --noverbose ) set +o verbose ;; ( -X | --noxtrace ) set +o xtrace ;; ( -E ) set +e ;; ( -* ) echo ${Bold}"Unknown option : ${1}"${Norm} ; return 1 ;; esac shift done ## echo ${Titre}"Short names (grid names in Oasis)"${Norm} ## =========================================================================== case ${OCE} in ( *ORC*) oce=orc ;; esac case ${ATM} in ( *ICO* ) atm=ico ;; ( *dynamico* ) atm=ico ;; ( *lmd* | *LMD* ) atm=lmd ;; esac CplModel=${OCE}x${ATM} ## echo ${Titre}"Get input files"${Norm} ## =========================================================================== [[ -f ${OCE}_coordinates_mask.nc ]] || cp ${R_IN}/OCE/NEMO/${OCE}/${OCE}_coordinates_mask.nc . [[ -f ${ATM}_grid.nc ]] || cp ${R_IN}/ATM/GRID/${ATM}_grid.nc . # echo ${Titre}"Format for OASIS-MCT files : should be NetCDF3 classic or NetCDF3 64 bits"${Norm} # --------------------------------------------------------------------------- FL_FMT3=64bit # echo ${Titre}"Cleaning"${Norm} # ---------------------------------------------------------------------------- rm -f grids_${CplModel}.nc masks_${CplModel}.nc areas_${CplModel}.nc rm -f *_tmp.nc # echo ${Titre}"Creates NetCDF3 version of input files"${Norm} # ---------------------------------------------------------------------------- ncks --overwrite --fl_fmt=${FL_FMT} --history ${OCE}_coordinates_mask.nc ${OCE}_coordinates_mask_${FL_FMT3}.nc ncks --overwrite --fl_fmt=${FL_FMT} --history ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc # echo ${Titre}"Creates ocean fields"${Norm} # ---------------------------------------------------------------------------- for OCEGRID in T U V ; do ncks --fl_fmt=${FL_FMT3} -C --history --append --variable nav_lon_grid_${OCEGRID},nav_lat_grid_${OCEGRID},bounds_lon_grid_${OCEGRID},bounds_lat_grid_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT3}.nc grids_${CplModel}.nc ncks --fl_fmt=${FL_FMT3} -C --history --append --variable area_grid_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT3}.nc areas_${CplModel}.nc # Inverts mask values and switch to integer ncks --fl_fmt=${FL_FMT33} --history -C --variable mask_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT3}.nc mask_${OCEGRID}_tmp.nc ncatted --history \ --attribute coordinates,mask_${OCEGRID},d,, \ --attribute online_operation,mask_${OCEGRID},d,, \ --attribute cell_measures,mask_${OCEGRID},d,, \ mask_${OCEGRID}_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --append --script "mask_${OCEGRID}=int(1-mask_${OCEGRID});" mask_${OCEGRID}_tmp.nc masks_${CplModel}.nc rm mask_${OCEGRID}_tmp.nc ncatted --history \ --attribute long_name,mask_${OCEGRID},o,c,"Land-sea mask" \ --attribute units,mask_${OCEGRID},o,c,"Land:1, Ocean:0" masks_${CplModel}.nc # Change order of dimensions mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc ncpdq --permute nvertex_grid_${OCEGRID},y_grid_${OCEGRID},x_grid_${OCEGRID} grids_${CplModel}_tmp.nc grids_${CplModel}.nc rm grids_${CplModel}_tmp.nc done ncks --history --append --variable lon,lat ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc grids_${CplModel}.nc # echo ${Titre}"We need to have different names for dimensions and variables"${Norm} # ---------------------------------------------------------------------------- ncrename --history --variable lon,alon grids_${CplModel}.nc ncrename --history --variable lat,alat grids_${CplModel}.nc if [[ ${ATM} = dynamico* || ${ATM} = ICO* ]] ; then ncks --fl_fmt=${FL_FMT3} --history --append --variable bounds_lon,bounds_lat ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc grids_${CplModel}.nc fi ncks --fl_fmt=${FL_FMT3} --history -C --append --variable aire ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc areas_${CplModel}.nc ncatted --history --attribute coordinates,aire,d,, \ --attribute _FillValue,aire,d,, \ --attribute missing_value,aire,d,, \ --attribute online_operation,aire,d,, \ --attribute units,aire,o,c,"m2" \ --attribute standard_name,aire,o,c,"cell_area" \ areas_${CplModel}.nc ncks --fl_fmt=${FL_FMT3} --history -C --variable OceMask ${ATM}_grid_maskFrom_${OCE}_${FL_FMT3}.nc OceMask_tmp.nc ncatted --history \ --attribute coordinates,OceMask,d,, \ --attribute online_operation,OceMask,d,, \ --attribute _FillValue,OceMask,d,, \ --attribute missing_value,OceMask,d,, \ OceMask_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --append --script "OceMask=int(1-OceMask)" OceMask_tmp.nc masks_${CplModel}.nc # For OASIS, ocean=0, land=1 rm OceMask_tmp.nc ncatted --history \ --attribute long_name,OceMask,o,c,"Land-sea mask" \ --attribute units,OceMask,o,c,"Land:1, Ocean:0" masks_${CplModel}.nc ncatted --history --attribute history,global,d,, grids_${CplModel}.nc ncatted --history --attribute history,global,d,, masks_${CplModel}.nc ncatted --history --attribute history,global,d,, areas_${CplModel}.nc if [[ ${atm} = *dynamico* || ${atm} = ico* ]] ; then ncrename --history --dimension cell,ycell grids_${CplModel}.nc ncrename --history --dimension cell,ycell areas_${CplModel}.nc ncrename --history --dimension cell,ycell masks_${CplModel}.nc fi # if [[ ${atm} = *lmd* ]] ; then # ncrename --dimension lon,tlmdlon grids_${CplModel}.nc # ncrename --dimension lat,tlmdlat grids_${CplModel}.nc # ncrename --dimension lon,tlmdlon masks_${CplModel}.nc # ncrename --dimension lat,tlmdlat masks_${CplModel}.nc # ncrename --dimension lon,tlmdlon areas_${CplModel}.nc # ncrename --dimension lat,tlmdlat areas_${CplModel}.nc # fi # echo ${Titre}"DYNAMICO grids : 1) Set correct order of dimensions, 2) Add a dimension"${Norm} # ---------------------------------------------------------------------------- if [[ ${atm} = dynamico* || ${atm} = ico* ]] ; then mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc ncpdq --permute nvertex,ycell,xcell grids_${CplModel}_tmp.nc grids_${CplModel}.nc mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc cat <add_dim.nco // defdim("xcell",1) ; alat [ycell,xcell] = alat ; alon [ycell,xcell] = alon ; bounds_lat [nvertex,ycell,xcell] = bounds_lat ; bounds_lon [nvertex,ycell,xcell] = bounds_lon ; // EOF ncap2 --fl_fmt=${FL_FMT3} --history --append --script-file add_dim.nco grids_${CplModel}_tmp.nc grids_${CplModel}.nc mv masks_${CplModel}.nc masks_${CplModel}_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --append --script 'defdim("xcell",1) ; OceMask[time_counter,ycell,xcell]=OceMask(:,:)' masks_${CplModel}_tmp.nc masks_${CplModel}.nc mv areas_${CplModel}.nc areas_${CplModel}_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --append --script 'defdim("xcell",1) ; aire[ycell,xcell]=aire(:) ; ' areas_${CplModel}_tmp.nc areas_${CplModel}.nc rm -f grids_${CplModel}_tmp.nc areas_${CplModel}_tmp.nc masks_${CplModel}_tmp.nc fi # echo ${Titre}"Some changes specific to LMDZ lon/lat grid"${Norm} # ---------------------------------------------------------------------------- if [[ ${atm} = lmd* ]] ; then echo ${Titre}"Spreads lon and lat to get 2D fields"${Norm} # ----------------------------------------------------------------------- mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --append --script "alon[lat,lon]=alon; alat[lat,lon]=alat" grids_${CplModel}_tmp.nc grids_${CplModel}.nc rm -f grids_${CplModel}_tmp.nc ncatted --history \ --attribute long_name,alon,o,c,"Longitude" \ --attribute long_name,alat,o,c,"Latitude" \ --attribute units,alon,o,c,"degrees_east" \ --attribute units,alat,o,c,"degrees_north" \ --attribute grid_type,alon,o,c,"P" \ --attribute grid_type,alat,o,c,"P" \ --attribute overlap,alon,o,i,0 \ --attribute overlap,alat,o,i,0 grids_${CplModel}.nc echo ${Titre}"Generates cell corners"${Norm} # ----------------------------------------------------------------------- cat < add_bounds.nco defdim ("nvertex_lmd", 4) ; *delta_x = alon(0,1) - alon(0,0) ; *delta_y = alat(1,0) - alat(0,0) ; // bounds_lon[nvertex_lmd,lat,lon] = 0.0 ; bounds_lat[nvertex_lmd,lat,lon] = 0.0 ; // bounds_lon (0,:,:) = alon + delta_x*0.5 ; bounds_lat (0,:,:) = alat + delta_y*0.5 ; bounds_lon (1,:,:) = alon + delta_x*0.5 ; bounds_lat (1,:,:) = alat - delta_y*0.5 ; bounds_lon (2,:,:) = alon - delta_x*0.5 ; bounds_lat (2,:,:) = alat - delta_y*0.5 ; bounds_lon (3,:,:) = alon - delta_x*0.5 ; bounds_lat (3,:,:) = alat + delta_y*0.5 ; // where (bounds_lat > 90.0 ) bounds_lat = 90.0 ;; where (bounds_lat < -90.0 ) bounds_lat = -90.0 ;; // EOF mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --script-file add_bounds.nco -O grids_${CplModel}_tmp.nc grids_${CplModel}.nc rm grids_${CplModel}_tmp.nc fi # echo ${Titre}"Generates grid o${atm}, 'o' meaning 'one'"${Norm} # same as t${atm} grid, with surfaces set to 1 # and mask to 0 (ocean everywhere, to compute integral over the whole grid)) # This grid is used when field are quantities instead of fluxes (i.e river flow) # ---------------------------------------------------------------------------- mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --script "o${atm}_lon=alon; o${atm}_lat=alat; bounds_o${atm}_lon=bounds_lon; bounds_o${atm}_lat=bounds_lat; " grids_${CplModel}_tmp.nc grids_${CplModel}.nc mv areas_${CplModel}.nc areas_${CplModel}_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --script "o${atm}_aire=aire*0.0d+1.0d; " areas_${CplModel}_tmp.nc areas_${CplModel}.nc mv masks_${CplModel}.nc masks_${CplModel}_tmp.nc ncap2 --fl_fmt=${FL_FMT3} --history --script "o${atm}_mask=int(OceMask)*0+0; " masks_${CplModel}_tmp.nc masks_${CplModel}.nc rm grids_${CplModel}_tmp.nc areas_${CplModel}_tmp.nc masks_${CplModel}_tmp.nc # echo ${Titre}"Final renaming"${Norm} # ---------------------------------------------------------------------------- for OCEGRID in T U V do ocegrid=${OCEGRID~} # To lowercase ncrename --history --variable nav_lon_grid_${OCEGRID},${ocegrid}${oce}.lon grids_${CplModel}.nc ncrename --history --variable nav_lat_grid_${OCEGRID},${ocegrid}${oce}.lat grids_${CplModel}.nc ncrename --history --variable bounds_lon_grid_${OCEGRID},${ocegrid}${oce}.clo grids_${CplModel}.nc ncrename --history --variable bounds_lat_grid_${OCEGRID},${ocegrid}${oce}.cla grids_${CplModel}.nc ncrename --history --variable mask_${OCEGRID},${ocegrid}${oce}.msk masks_${CplModel}.nc ncrename --history --variable area_grid_${OCEGRID},${ocegrid}${oce}.srf areas_${CplModel}.nc ncatted --history \ --attribute bounds,${ocegrid}${oce}.lon,m,c,"${ocegrid}${oce}.clo" \ --attribute bounds,${ocegrid}${oce}.lat,m,c,"${ocegrid}${oce}.cla" \ --attribute units,${ocegrid}${oce}.clo,o,c,"degrees_east" \ --attribute units,${ocegrid}${oce}.clo,o,c,"degrees_north" grids_${CplModel}.nc done ncrename --history --variable alon,t${atm}.lon grids_${CplModel}.nc ncrename --history --variable alat,t${atm}.lat grids_${CplModel}.nc ncrename --history --variable o${atm}_lon,o${atm}.lon grids_${CplModel}.nc ncrename --history --variable o${atm}_lat,o${atm}.lat grids_${CplModel}.nc ncrename --history --variable OceMask,t${atm}.msk masks_${CplModel}.nc ncrename --history --variable o${atm}_mask,o${atm}.msk masks_${CplModel}.nc ncrename --history --variable aire,t${atm}.srf areas_${CplModel}.nc ncrename --history --variable o${atm}_aire,o${atm}.srf areas_${CplModel}.nc ncrename --history --variable bounds_lon,t${atm}.clo grids_${CplModel}.nc ncrename --history --variable bounds_lat,t${atm}.cla grids_${CplModel}.nc ncrename --history --variable bounds_o${atm}_lon,o${atm}.clo grids_${CplModel}.nc ncrename --history --variable bounds_o${atm}_lat,o${atm}.cla grids_${CplModel}.nc for atmgrid in t o ; do ncatted --history \ --attribute bounds,${atmgrid}${atm}.lon,c,c,"${atmgrid}${atm}.clo" \ --attribute bounds,${atmgrid}${atm}.lat,c,c,"${atmgrid}${atm}.cla" \ --attribute units,${atmgrid}${atm}.clo,o,c,"degrees_east" \ --attribute units,${atmgrid}${atm}.cla,o,c,"degrees_north" grids_${CplModel}.nc done ## echo ${Titre}"Change all NetCDF files to NetCDF 3 format"${Norm} ## =========================================================================== for InFile in areas_${CplModel}.nc grids_${CplModel}.nc masks_${CplModel}.nc ; do if [[ $(ncdump -k ${InFile}) = *netCDF-4* ]] ; then mv ${InFile} tmp_${InFile} ncks --fl_fmt=${FL_FMT3} --history tmp_${InFile} ${InFile} rm tmp_${InFile} fi done ## echo ${Titre}"Add some useful information in NetCDF headers"${Norm} ## =========================================================================== UUID=$(uuid) NCO=$(ncks --version |& tail -1|sed 's/ncks //') for type in areas masks grids ; do ncatted --history \ --attribute nco_openmp_thread_number,global,d,, \ --attribute uuid,global,d,, \ --attribute LongName,global,d,, \ --attribute NCO,global,o,c,"NCO netCDF Operator ${NCO} http://nco.sourceforge.net" \ --attribute Conventions,global,o,c,"CF-1.6" \ --attribute source,global,o,c,"IPSL Earth system model" \ --attribute group,global,o,c,"ICMC IPSL Climate Modelling Center" \ --attribute production,global,o,c,"$(finger ${LOGNAME} | head -1 | awk '{print $4, $5}') " \ --attribute Institution,global,o,c,"IPSL https://www.ipsl.fr" \ --attribute Ocean,global,o,c,"${OCE} https://www.nemo-ocean.eu" \ --attribute Atmosphere,global,o,c,"${ATM} http://lmdz.lmd.jussieu.fr" \ --attribute HOSTNAME,global,o,c,"$(hostname)" \ --attribute LOGNAME,global,o,c,"$(whoami)" \ --attribute Program,global,o,c,"Generated by ${0}" \ --attribute name,global,o,c,"${type}_${CplModel}.nc" \ --attribute directory,global,o,c,"$(pwd)" \ --attribute description,global,o,c,"Fields needed by OASIS-MCT" \ --attribute title,global,o,c,"${type}_${CplModel}.nc" \ --attribute timeStamp,global,o,c,"$(date)" \ --attribute associatedFiles,global,o,c,"grids_${CplModel}.nc areas_${CplModel}.nc masks_${CplModel}.nc" \ --attribute originalFiles,global,o,c,"${OCE}_coordinates_mask.nc ${ATM}_grid_mask.nc"\ --attribute uuid,global,o,c,"${UUID}" \ --attribute OS,global,o,c,"$(uname -o)" \ --attribute release,global,o,c,"$(uname -r)" \ --attribute hardware,global,o,c,"$(uname -i)" \ --attribute SVN_Author,global,o,c,"$Author$" \ --attribute SVN_Date,global,o,c,"$Date$" \ --attribute SVN_Revision,global,o,c,"$Revision$" \ --attribute SVN_Id,global,o,c,"$Id$" \ --attribute SVN_HeardURL,global,o,c,"$HeadURL $" \ ${type}_${CplModel}.nc done exit # echo ${Titre}"Name of the dimensions ?"${Norm} # ---------------------------------------------------------------------------- for OCEGRID in T U V ; do ocegrid=${OCEGRID~} # Downcase name of grids ncrename --history --dimension x_grid_${OCEGRID},x${ocegrid}${oce} grids_${CplModel}.nc ncrename --history --dimension y_grid_${OCEGRID},y${ocegrid}${oce} grids_${CplModel}.nc ncrename --history --dimension nvertex_grid_${OCEGRID},crn${ocegrid}${oce} grids_${CplModel}.nc done ## =========================================================================== echo ${Titre}"exit from CreateOasisGrids "${Norm} ## =========================================================================== ## echo ${Titre}" That's all folk's !!! "${Norm} ## ## ===========================================================================