#!/usr/bin/env bash ### =========================================================================== ### ### Creates initial state for coupler, ocean side ### Take data from NEMO grid_T and icemod files ### ### =========================================================================== ## ## 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 # $Author$ # $Date$ # $Revision$ # $Id$ # $HeadURL$ ## Usage exemples : # # CreateRestartOce4Oasis.bash --ocefile /ccc/store/cont003/dsm/p25sepul/IGCM_OUT/IPSLCM5A2/PROD/piControl/CM5A2.1.pi.00/OCE/Output/MO/CM5A2.1.pi.00_40100101_40191231_1M_grid_T.nc --icefile /ccc/store/cont003/dsm/p25sepul/IGCM_OUT/IPSLCM5A2/PROD/piControl/CM5A2.1.pi.00/ICE/Output/MO/CM5A2.1.pi.00_40100101_40191231_1M_icemod.nc --icefrc ice_pres --icetem tsice --icealb ialb # # CreateRestartOce4Oasis.bash --ocefile /ccc/store/cont003/gencmip6/p86mart/IGCM_OUT/IPSLCM6/DEVT/pdControl/CM6010.2.rivgeo-LR-pdCtrl/OCE/Output/MO/CM6010.2.rivgeo-LR-pdCtrl_22400101_22491231_1M_grid_T.nc --icefrc siconc # CreateRestartOce4Oasis.bash --ocefile /ccc/store/cont003/gen7451/personr/IGCM_OUT/ORCA025_LIM3_PISCES/DEVT/ORCA025ia/eOR025L3P-IA-REF07-MUSCL/OCE/Output/MO/eOR025L3P-IA-REF07-MUSCL_20090101_20091231_1M_grid_T.nc # # CreateRestartOce4Oasis.bash --ocefile /ccc/work/cont003/gencmip6/p48ethe/ICMC-TOOLS/DATA/eOR025L3P-IA-REF07-MUSCL_20090101_20091231_1M_grid_T.nc --icefile /ccc/work/cont003/gencmip6/p48ethe/ICMC-TOOLS/DATA/eOR025L3P-IA-REF07-MUSCL_20090101_20091231_1M_icemod.nc --icefrc siconc/oce --icetem sistem # # ## =========================================================================== ## ## You should not change anything below this line .... ## ## =========================================================================== ## ## Command line parameters ## =========================================================================== # Default values Comment="Preliminary attempt - Do not trust !" # # --ocefile : file in which sea surface temperature is read # --icefile : file in which sea ice fraction, albedo and surface temperature are read. # if not specified, these variables are readed in the ocean file # ## Variable in ocean file : OceSst=tos #> Variable containing sea surface temperature (°C) : --ocesst tos ## Variables in ice file IceFrc=ice_pres #> Variable containing sea ice fraction [0-1] : --icefrc ice_pres IceAlb=none #> Variable containing sea ice albedo [0-1]. If 'none', set to 0.65 : --icealb ialb IceTem=none #> Variable containing sea ice surface temperature (°C). If 'none', set to -20°C : --icetem tsice # Complementary syntaxes for variables names # --icefrc siconc/oce means that siconc variable should be taken in the ocean file ... # --icealb ialb/oce # --icetem tsice/oce ## Filling # If the ocean in the coupled model has a different geometry that the one in the files. # In general, the forced ocean does run with no closed sea, when the coupled model does. # This step is he mandatory Fill=yes # If yes, fill the continents. --fill / --nofill # nperio parameter for ORCA. Normally guess from name or dimensions. For ORCA2, set to nperio=4, but should be set to nperio=6 for some paleo configs # --nperio 4 DefaultIceAlb=0.65 DefaultIceTem=-20.0 #OceFile=/ccc/store/cont003/dsm/p25sepul/IGCM_OUT/IPSLCM5A2/PROD/piControl/CM5A2.1.pi.00/OCE/Output/MO/CM5A2.1.pi.00_40100101_40191231_1M_grid_T.nc #OceFile=/ccc/store/cont003/gencmip6/p86mart/IGCM_OUT/IPSLCM6/DEVT/pdControl/CM6010.2.rivgeo-LR-pdCtrl/OCE/Output/MO/CM6010.2.rivgeo-LR-pdCtrl_22400101_22491231_1M_grid_T.nc # # # Defines computer # ================ if [[ $(hostname) = irene* ]] ; then arch=irene ; center=tgcc ; fi case ${arch} in ( irene ) set +vx module unload cdo nco ferret module unload netcdf hdf5 module load python # /2.7.12 #module load netcdf/4.3.3.1_hdf5_parallel # Version for XIOS module load nco module load python3 R_IN=$(ccc_home -u igcmg --cccwork)/IGCM TMPDIR=${SCRATCHDIR}/TMP SUBMIT_DIR=${BRIDGE_MSUB_PWD:-${SUBMIT_DIR}} ;; ( * ) exit -1 ;; esac set -o verbose set -o xtrace set -e Nperio="" while [[ ${1} = -* ]] ; do case ${1} in ( -- ) shift ; break ;; ( -c | --comment ) shift ; Comment=${1} ;; ( --ocefile ) shift ; OceFile=${1} ;; ( --icefile ) shift ; IceFile=${1} ;; ( --ocesst ) shift ; OceSst=${1} ;; ( --icefrc ) shift ; IceFrc=${1} ;; ( --icetem ) shift ; IceTem=${1} ;; ( --icealb ) shift ; IceAlb=${1} ;; ( --fill ) Fill="yes" ;; ( --nofill ) Fill="no" ;; ( --nperio ) shift ; Nperio="--nperio ${1}" ;; ( -v | --verbose ) set -o verbose ;; ( -x | --xtrace ) set -o xtrace ;; ( -xv | -vx ) set -o xtrace verbose ;; ( -e ) set -e ;; ( -V | --noverbose ) set +o verbose ;; ( -X | --noxtrace ) set +o xtrace ;; ( -XV | -VX ) set +o xtrace verbose ;; ( -E ) set +e ;; ( -* ) echo ${Bold}"Unknown option : ${1}"${Norm} ; exit 1 ;; esac shift done # # Format for OASIS files : should be NetCDF3 classic or NetCDF3 64 bits # --------------------------------------------------------------------------- FL_FMT=64bit ## ## Defines associated sea ice file ## =========================================================================== if [[ -z ${IceFile} ]] ; then IceFile=${OceFile} ; fi IceFrcFile=${IceFile} IceTemFile=${IceFile} IceAlbFile=${IceFile} ## Select file for each variable OceSstFile=${OceFile} if [[ ${OceSst} = */ice ]] ; then OceSstFile=${IceFile} OceSst=${OceSst%%/*} fi if [[ ${IceAlb} = */oce ]] ; then IceAlbFile=${OceFile} IceAlb=${IceFrc%%/*} fi if [[ ${IceFrc} = */oce ]] ; then IceFrcFile=${OceFile} IceFrc=${IceFrc%%/*} fi if [[ ${IceTem} = */oce ]] ; then IceTemFile=${OceFile} IceTem=${IceTem%%/*} fi echo "Oce sst - Variable ${OceSst} - File ${OceSstFile}" echo "Ice fraction - Variable ${IceFrc} - File ${IceFrcFile}" echo "Ice albedo - Variable ${IceAlb} - File ${IceAlbFile}" echo "Ice temperature - Variable ${IceTem} - File ${IcetemFile}" ## ## Extract variables ## =========================================================================== ncks --overwrite --fl_fmt=${FL_FMT} --history -d time_counter,0,0 --variable ${IceFrc} ${IceFrcFile} sstoce_fields.nc ncks --overwrite --fl_fmt=${FL_FMT} --history -d time_counter,0,0 --variable ${OceSst} ${OceSstFile} oce_sst.nc ncks --append --fl_fmt=${FL_FMT} --history oce_sst.nc sstoce_fields.nc if [[ "X${IceAlb}" != "Xnone" ]] ; then ncks --overwrite --fl_fmt=${FL_FMT} --history -d time_counter,0,0 --variable ${IceAlb} ${IceAlbFile} ice_alb.nc ncks --append --fl_fmt=${FL_FMT} --history ice_alb.nc sstoce_fields.nc fi if [[ "X${IceTem}" != "Xnone" ]] ; then ncks --overwrite --fl_fmt=${FL_FMT} --history -d time_counter,0,0 --variable ${IceTem} ${IceTemFile} ice_tem.nc ncks --append --fl_fmt=${FL_FMT} --history ice_tem.nc sstoce_fields.nc fi ncwa --overwrite --fl_fmt=${FL_FMT} --history --average time_counter sstoce_fields.nc sstoce_fields_notime.nc # Remove time dimension ncatted --history --attribute history,global,d,c,"" sstoce_fields_notime.nc # Clean attributes ## ## Find ocean name ## =========================================================================== dim_y=$(ncdump -h sstoce_fields_notime.nc | grep "y *=" | grep -v "nvertex" | awk '{print $3}' ) dim_x=$(ncdump -h sstoce_fields_notime.nc | grep "x *=" | grep -v "nvertex" | awk '{print $3}' ) echo ${dim_x} ${dim_y} [[ ${dim_x} = 182 && ${dim_y} = 149 ]] && OCE=ORCA2.3 [[ ${dim_x} = 362 && ${dim_y} = 332 ]] && OCE=eORCA1.2 [[ ${dim_x} = 1442 && ${dim_y} = 1207 ]] && OCE=eORCA025.1 ## ## Creates sstoce file ## =========================================================================== cat < create_sstoce.nco *OceSst[y,x] = double ( ${OceSst}(:,:) + 273.15d ) ; OIceFrc[y,x] = double ( ${IceFrc}(:,:) ) ; // EOF if [[ "X${IceAlb}" != "Xnone" ]] ; then cat <> create_sstoce.nco *IceAlb[y,x] = double ( ${IceAlb}(:,:) ) ; // EOF else cat <> create_sstoce.nco *IceAlb[y,x] = double ( ${DefaultIceAlb}d ) ; // EOF fi if [[ "X${IceTem}" != "Xnone" ]] ; then cat <> create_sstoce.nco *IceTem[y,x] = double ( ${IceTem}(:,:) + 273.15d ) ; // EOF else cat <> create_sstoce.nco *IceTem[y,x] = double ( ${DefaultIceTem}d + 273.15d ) ; // EOF fi cat <> create_sstoce.nco O_SSTSST[y,x] = OceSst (:,:) * (1.0d-OIceFrc(:,:)) ; O_AlbIce[y,x] = IceAlb (:,:) * OIceFrc(:,:) ; O_TepIce[y,x] = IceTem (:,:) * OIceFrc(:,:) ; O_OCurx1[y,x] = 0.0d ; O_OCury1[y,x] = 0.0d ; O_OCurz1[y,x] = 0.0d ; EOF ncap2 --overwrite --fl_fmt=${FL_FMT} --history --script-file create_sstoce.nco sstoce_fields_notime.nc tmp_sstoc.nc ncks --fl_fmt=${FL_FMT} --overwrite --history --variable OIceFrc,O_SSTSST,O_AlbIce,O_TepIce,O_OCurx1,O_OCury1,O_OCurz1 tmp_sstoc.nc sstoc.nc ncatted --history --attribute long_name,O_SSTSST,o,c,"SST weighted by fraction of open ocean" sstoc.nc ncatted --history --attribute long_name,O_AlbIce,o,c,"Albedo weighted by fraction of sea ice" sstoc.nc ncatted --history --attribute long_name,O_TepIce,o,c,"Ice temperature weighted by fraction of sea ice" sstoc.nc ncatted --history --attribute comment,O_SSTSST,o,c,"Variable ${OceSst} taken in ${OceSstFile}" sstoc.nc ncatted --history --attribute comment,OIceFrc,o,c,"Variable ${IceFrc} taken in ${IceFrcFile}" sstoc.nc if [[ ${IceAlb} = none ]] ; then ncatted --history --attribute comment,O_AlbIce,o,c,"Set to ${DefaultIceAlb}" sstoc.nc else ncatted --history --attribute comment,O_AlbIce,o,c,"Variable ${IceAlb} taken in ${IceAlbFile}" sstoc.nc fi if [[ ${IceTem} = none ]] ; then ncatted --history --attribute comment,O_TepIce,o,c,"Set to ${DefaultIceTem}" sstoc.nc else ncatted --history --attribute comment,O_TepIce,o,c,"Variable ${IceTem} taken in ${IceTemFile}" sstoc.nc fi ## ## Filling the fields ## =========================================================================== if [[ ${Fill} = yes ]] ; then mv sstoc.nc sstoc_nofilled.nc python3 FillOceRestart.py --input sstoc_nofilled.nc --output sstoc.nc ${Nperio} fi ## ## Add some information in file header ## =========================================================================== UUID=$(uuid) NCO="$(ncks --version |& tail -1|sed 's/ncks //')" ncatted --history \ --attribute nco_openmp_thread_number,global,d,, \ --attribute source,global,o,c,"IPSL Earth system model" \ --attribute group,global,o,c,"ICMC IPSL Climate Modelling Center" \ --attribute Institution,global,o,c,"IPSL https://www.ipsl.fr" \ --attribute Model,global,o,c,"${OCE} https://www.nemo-ocean.eu" \ --attribute production,global,o,c,"$(finger ${LOGNAME} | head -1 | awk '{print $4, $5}')" \ --attribute originalFiles,global,o,c,"${OceFile} ${IceFile}" \ --attribute directory,global,o,c,"$(pwd)" \ --attribute description,global,o,c,"Fields needed by OASIS-MCT" \ --attribute timeStamp,global,o,c,"$(date)" \ --attribute uuid,global,o,c,"${UUID}" \ --attribute Program,global,o,c,"Generated by ${0}" \ --attribute HOSTNAME,global,o,c,"$(hostname)" \ --attribute LOGNAME,global,o,c,"$(whoami)" \ --attribute NCO,global,o,c,"NCO netCDF Operator ${NCO} http://nco.sourceforge.net" \ --attribute OS,global,o,c,"$(uname -o)" \ --attribute release,global,o,c,"$(uname -r)" \ --attribute hardware,global,o,c,"$(uname -i)" \ --attribute directory,global,o,c,"$(pwd)" \ --attribute Comment,global,o,c,"${Comment}" \ --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,"$Id$" \ sstoc.nc ## ## Cleaning ## =========================================================================== #rm -f sstoce_fields.nc sstoce_fields_notime.nc tmp_sstoce.nc oce_fields.nc mv sstoc.nc sstoc_${OCE}.nc ## =========================================================================== ## ## That's all folk's !!! ## ## ===========================================================================