[3620] | 1 | #!/bin/bash |
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| 2 | #MSUB -r NemoAtm # nom de la requete |
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| 3 | #MSUB -o NemoAtm.out # nom du fichier de sortie |
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| 4 | #MSUB -e NemoAtm.out # nom du fichier de sortie |
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| 5 | #MSUB -eo |
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| 6 | #MSUB -n 16 # Reservation des processeurs pour le job |
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| 7 | #MSUB -T 1800 # Limite temps (en secondes) |
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| 8 | #MSUB -q standard |
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| 9 | #MSUB -Q test |
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| 10 | #MSUB -p devcmip6 |
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| 11 | |
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| 12 | ### =========================================================================== |
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| 13 | ### |
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| 14 | ### Creates interpolation weights between ORCA and DYNAMICO grids |
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| 15 | ### Interpolates ORCA mask to DYNAMICO grid |
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| 16 | ### |
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| 17 | ### =========================================================================== |
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| 18 | ## |
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| 19 | ## Warning, to install, configure, run, use any of Olivier Marti's |
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| 20 | ## software or to read the associated documentation you'll need at least |
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| 21 | ## one (1) brain in a reasonably working order. Lack of this implement |
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| 22 | ## will void any warranties (either express or implied). |
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| 23 | ## O. Marti assumes no responsability for errors, omissions, |
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| 24 | ## data loss, or any other consequences caused directly or indirectly by |
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| 25 | ## the usage of his software by incorrectly or partially configured |
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| 26 | ## personal. |
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| 27 | ## |
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| 28 | |
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| 29 | ## |
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| 30 | ## Configuration |
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| 31 | ## =========================================================================== |
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| 32 | |
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| 33 | # |
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| 34 | # Defines models |
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| 35 | # ============== |
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| 36 | OCE=ORCA2.3 |
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| 37 | OCE=eORCA1.2 |
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| 38 | #OCE=ORCA025 |
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| 39 | |
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| 40 | ATM=dynamico30 |
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| 41 | #ATM=dynamico40 |
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| 42 | #ATM=dynamico450 |
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| 43 | #ATM=LMD9695 |
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| 44 | #ATM=LMD144X142 |
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| 45 | |
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| 46 | |
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| 47 | |
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| 48 | # |
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| 49 | # Defines OCE grids to handle |
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| 50 | # =========================== |
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| 51 | |
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| 52 | OCEGRIDS="T" # " UV |
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| 53 | |
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| 54 | ### =========================================================================== |
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| 55 | ### |
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| 56 | ### You should not change anything below this line .... |
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| 57 | ### |
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| 58 | ### =========================================================================== |
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| 59 | SUBMIT_DIR=$(pwd) |
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| 60 | |
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| 61 | # Defines computer |
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| 62 | # ================ |
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| 63 | [[ $(hostname) = curie* ]] && arch=curie |
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| 64 | |
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| 65 | case ${arch} in |
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| 66 | ( curie | irene ) |
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| 67 | module load netcdf/4.3.3.1_hdf5_parallel |
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| 68 | module load nco/4.4.8 |
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| 69 | R_IN=$(ccc_home -u igcmg --cccwork)/IGCM |
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| 70 | TMPDIR=${SCRATCHDIR}/TMP/${OCE}x${ATM} |
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| 71 | ;; |
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| 72 | ( * ) |
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| 73 | exit -1 |
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| 74 | ;; |
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| 75 | esac |
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| 76 | |
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| 77 | |
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| 78 | set -vx ; set -e |
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| 79 | |
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| 80 | mkdir -p ${TMPDIR}/${OCE}x${ATM} || exit 1 |
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| 81 | cd ${TMPDIR}/${OCE}x${ATM} || exit 1 |
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| 82 | rm -f * |
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| 83 | |
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| 84 | # |
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| 85 | # Suffixes |
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| 86 | # --------------------------------------------------------------------------- |
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| 87 | ocegrids=${OCEGRIDS~} |
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| 88 | |
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| 89 | case ${OCE} in |
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| 90 | ( *ORC*) oce=orc ;; |
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| 91 | esac |
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| 92 | case ${ATM} in |
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| 93 | ( *dynamico* ) atm=ico ;; |
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| 94 | ( *lmd* | *LMD* ) atm=lmd ;; |
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| 95 | esac |
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| 96 | |
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| 97 | # |
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| 98 | # Format for OASIS files : should be NetCDF3 classic or NetCDF3 64 bits |
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| 99 | # --------------------------------------------------------------------------- |
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| 100 | FL_FMT=64bit |
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| 101 | |
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| 102 | ## |
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| 103 | ## NEMO T point towards ATM - 1st order |
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| 104 | ## =========================================================================== |
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| 105 | cp ${SUBMIT_DIR}/bin/interpol.exe . |
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| 106 | cp ${SUBMIT_DIR}/iodef_t${oce}_to_t${atm}_1storder.xml iodef.xml |
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| 107 | |
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| 108 | cp ${R_IN}/OCE/NEMO/${OCE}/${OCE}_coordinates_mask.nc . |
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| 109 | cp ${R_IN}/ATM/${ATM}/${ATM}_grid.nc . |
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| 110 | |
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| 111 | ln -s ${OCE}_coordinates_mask.nc oce_grid.nc |
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| 112 | ln -s ${ATM}_grid.nc atm_grid.nc |
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| 113 | |
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| 114 | sed --in-place -e 's/"mask_[TUV]"/"mask_T"/g' -e "s/[tuv]${oce}/t${oce}/" -e 's/_...order/_1storder/g' -e 's/order="."/order="1"/' iodef.xml |
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| 115 | time /usr/bin/time ccc_mprun ./interpol.exe --mask_src=yes --mask_dst=no |
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| 116 | |
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| 117 | ## |
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| 118 | ## Correct spurious values (extremes) |
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| 119 | ## =========================================================================== |
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| 120 | cat <<EOF > correction_masque.nco |
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| 121 | where (OceFrac < 0.00001 ) OceFrac=OceFrac.get_miss() ; |
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| 122 | where (OceFrac > 0.99999 ) OceFrac=1.0 ; |
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| 123 | OceFrac.delete_miss() ; |
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| 124 | // Fill masked values to land values |
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| 125 | where (OceFrac > 1.0 ) OceFrac=0.0 ; |
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| 126 | where (OceFrac < 0.0 ) OceFrac=0.0 ; |
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| 127 | EOF |
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| 128 | ncap2 -h --overwrite --script-file correction_masque.nco t${oce}_to_t${atm}_1storder.nc tmp_t${oce}_to_t${atm}_1storder.nc ; mv tmp_t${oce}_to_t${atm}_1storder.nc t${oce}_to_t${atm}_1storder.nc |
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| 129 | ncatted -h -a missing_value,OceFrac,d,,"" -a _FillValue,OceFrac,d,,"" t${oce}_to_t${atm}_1storder.nc |
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| 130 | |
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| 131 | ## |
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| 132 | ## Creates mask on ATM grid |
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| 133 | ## =========================================================================== |
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| 134 | cp t${oce}_to_t${atm}_1storder.nc t${oce}_to_t${atm}_1storder_mask.nc |
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| 135 | ncks -h --overwrite -v OceFrac t${oce}_to_t${atm}_1storder_mask.nc ${ATM}_grid_maskFrom_${OCE}.nc |
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| 136 | ncks -h --append -v aire atm_grid.nc ${ATM}_grid_maskFrom_${OCE}.nc |
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| 137 | [[ ${atm} = *ico* ]] && ncks -h --append -v bounds_lon,bounds_lat atm_grid.nc ${ATM}_grid_maskFrom_${OCE}.nc |
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| 138 | |
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| 139 | cat <<EOF > creation_masque.nco |
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| 140 | where (OceFrac > 0.0 ) OceFrac=1 ; |
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| 141 | where (OceFrac <= 0.0 ) OceFrac=0 ; |
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| 142 | EOF |
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| 143 | ncap2 -h --overwrite --script-file creation_masque.nco t${oce}_to_t${atm}_1storder_mask.nc tmp_t${oce}_to_t${atm}_1storder_mask.nc ; mv tmp_t${oce}_to_t${atm}_1storder_mask.nc t${oce}_to_t${atm}_1storder_mask.nc |
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| 144 | ncrename -h -v OceFrac,OceMask t${oce}_to_t${atm}_1storder_mask.nc |
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| 145 | |
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| 146 | ncks -h --append -v OceMask t${oce}_to_t${atm}_1storder_mask.nc ${ATM}_grid_maskFrom_${OCE}.nc |
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| 147 | |
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| 148 | ## |
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| 149 | ## NEMO T point towards ATM - 2nd order |
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| 150 | ## =========================================================================== |
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| 151 | sed --in-place -e 's/"mask_[TUV]"/"mask_T"/g' -e "s/[tuv]${oce}/t${oce}/" -e 's/_...order/_2ndorder/g' -e 's/order="."/order="2"/' iodef.xml |
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| 152 | #time /usr/bin/time ccc_mprun ./interpol.exe --mask_src=yes --mask_dst=yes |
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| 153 | |
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| 154 | ## |
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| 155 | ## ATM towards NEMO T point - 1st order |
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| 156 | ## =========================================================================== |
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| 157 | cp ${SUBMIT_DIR}/iodef_t${atm}_to_t${oce}_1storder.xml iodef.xml |
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| 158 | sed --in-place -e 's/"mask_[TUV]"/"mask_T"/g' -e "s/[tuv]${oce}/t${oce}/" -e 's/_...order/_1storder/g' -e 's/order="."/order="1"/' iodef.xml |
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| 159 | time /usr/bin/time ccc_mprun ./interpol.exe --mask_src=yes --mask_dst=yes |
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| 160 | |
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| 161 | ## |
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| 162 | ## ATM towards NEMO U Point - 1st order |
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| 163 | ## =========================================================================== |
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| 164 | sed --in-place -e 's/"mask_[TUV]"/"mask_U"/g' -e "s/[tuv]${oce}/u${oce}/" -e 's/_...order/_1storder/g' -e 's/order="."/order="1"/' iodef.xml |
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| 165 | #time /usr/bin/time ccc_mprun ./interpol.exe --mask_src=yes --mask_dst=yes |
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| 166 | |
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| 167 | ## |
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| 168 | ## ATM towards NEMO V Point - 1st order |
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| 169 | ## =========================================================================== |
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| 170 | sed --in-place -e 's/"mask_[TUV]"/"mask_V"/g' -e "s/[tuv]${oce}/v${oce}/" -e 's/_...order/_1storder/g' -e 's/order="."/order="1"/' iodef.xml |
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| 171 | #time /usr/bin/time ccc_mprun ./interpol.exe --mask_src=yes --mask_dst=yes |
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| 172 | |
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| 173 | ## |
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| 174 | ## ATM verstowards NEMO T point - 2nd order |
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| 175 | ## =========================================================================== |
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| 176 | sed --in-place -e 's/"mask_[TUV]"/"mask_T"/g' -e "s/[tuv]${oce}/t${oce}/" -e 's/_...order/_2ndorder/g' -e 's/order="."/order="2"/' iodef.xml |
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| 177 | #/usr/bin/time ccc_mprun ./interpol.exe --mask_src=yes --mask_dst=yes |
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| 178 | |
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| 179 | |
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| 180 | ## |
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| 181 | ## Change all NetCDF files to NetCDF 3 format (needed for OASIS) |
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| 182 | ## =========================================================================== |
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| 183 | for InFile in *.nc ; do |
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| 184 | if [[ $(ncdump -k ${InFile}) = *netCDF-4* ]] ; then |
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| 185 | mv ${InFile} tmp_${InFile} |
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| 186 | ncks --fl_fmt=${FL_FMT} -h tmp_${InFile} ${InFile} |
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| 187 | fi |
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| 188 | done |
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| 189 | |
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| 190 | |
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| 191 | ## |
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| 192 | ## Add time axis and coordinates information |
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| 193 | ## (needed if files need to be read by XIOS) |
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| 194 | ## =========================================================================== |
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| 195 | if [[ ${atm} = ico ]] ; then |
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| 196 | cat <<EOF > add_time.nco |
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| 197 | defdim("time_counter",1) ; |
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| 198 | OceFrac [time_counter,cell] = OceFrac (:) ; |
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| 199 | OceMask [time_counter,cell] = OceMask (:) ; |
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| 200 | EOF |
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| 201 | ncap2 -O -h -S add_time.nco ${ATM}_grid_maskFrom_${OCE}.nc tmp_${ATM}_grid_maskFrom_${OCE}.nc ; mv tmp_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc |
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| 202 | ncks -O --mk_rec time_counter ${ATM}_grid_maskFrom_${OCE}.nc tmp_${ATM}_grid_maskFrom_${OCE}.nc ; mv tmp_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc |
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| 203 | ncatted -h \ |
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| 204 | -a coordinates,OceFrac,c,c,"time_counter cell" \ |
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| 205 | -a coordinates,OceMask,c,c,"time_counter cell" \ |
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| 206 | -a coordinates,aire,c,c,"time_counter cell" ${ATM}_grid_maskFrom_${OCE}.nc |
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| 207 | fi |
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| 208 | if [[ ${atm} = lmd ]] ; then |
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| 209 | cat <<EOF > add_time.nco |
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| 210 | defdim("time_counter",1) ; |
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| 211 | OceFrac [time_counter,lat,lon] = OceFrac (:,:) ; |
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| 212 | OceMask [time_counter,lat,lon] = OceMask (:,:) ; |
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| 213 | EOF |
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| 214 | ncap2 -O -h -S add_time.nco ${ATM}_grid_maskFrom_${OCE}.nc tmp_${ATM}_grid_maskFrom_${OCE}.nc ; mv tmp_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc |
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| 215 | ncks -O --mk_rec time_counter ${ATM}_grid_maskFrom_${OCE}.nc tmp_${ATM}_grid_maskFrom_${OCE}.nc ; mv tmp_${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}.nc |
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| 216 | ncatted -h \ |
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| 217 | -a coordinates,OceFrac,c,c,"time_counter lat lon" \ |
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| 218 | -a coordinates,OceMask,c,c,"time_counter lat lon" \ |
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| 219 | -a coordinates,aire,c,c,"time_counter lat lon" ${ATM}_grid_maskFrom_${OCE}.nc |
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| 220 | fi |
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| 221 | |
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| 222 | ## |
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| 223 | ## Add some information in file headers |
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| 224 | ## =========================================================================== |
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| 225 | |
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| 226 | UUID=$(uuid) |
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| 227 | NCO="$(ncks --version |& tail -1|sed 's/ncks //')" |
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| 228 | for InFile in *${oce}_to_*${atm}_*.nc *${atm}_to_*${oce}_*.nc ${ATM}_grid_maskFrom_${OCE}.nc ; do |
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| 229 | ncatted -h \ |
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| 230 | --attribute uuid,global,d,, \ |
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| 231 | --attribute LongName,global,d,, \ |
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| 232 | --attribute nco_openmp_thread_number,global,d,, \ |
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| 233 | --attribute Conventions,global,o,c,"CF-1.6" \ |
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| 234 | --attribute source,global,o,c,"IPSL Earth system model" \ |
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| 235 | --attribute group,global,o,c,"ICMC IPSL Climate Modelling Center" \ |
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| 236 | --attribute Institution,global,o,c,"IPSL" \ |
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| 237 | --attribute Ocean,global,o,c,"${OCE}" \ |
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| 238 | --attribute Atmosphere,global,o,c,"${ATM}" \ |
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| 239 | --attribute production,global,o,c,"$(finger ${LOGNAME} | head -1 | awk '{print $4, $5}') " \ |
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| 240 | --attribute originalFiles,global,o,c,"${OCE}_coordinates_mask.nc ${ATM}_grid_mask.nc" \ |
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| 241 | --attribute associatedFiles,global,o,c,"grids_${OCE}x${ATM}.nc areas_${OCE}x${ATM}.nc masks_${OCE}x${ATM}.nc" \ |
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| 242 | --attribute directory,global,o,c,"$(pwd)" \ |
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| 243 | --attribute description,global,o,c,"Fields needed by OASIS-MCT" \ |
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| 244 | --attribute title,global,o,c,"${type}_${OCE}x${ATM}.nc" \ |
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| 245 | --attribute timeStamp,global,o,c,"$(date)" \ |
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| 246 | --attribute uuid,global,o,c,"${UUID}" \ |
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| 247 | --attribute HOSTNAME,global,o,c,"$(hostname)" \ |
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| 248 | --attribute LOGNAME,global,o,c,"$(whoami)" \ |
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| 249 | --attribute NCO,global,o,c,"NCO ${NCO}" \ |
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| 250 | --attribute OS,global,o,c,"$(uname -o)" \ |
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| 251 | --attribute release,global,o,c,"$(uname -r)" \ |
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| 252 | --attribute hardware,global,o,c,"$(uname -i)" \ |
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| 253 | --attribute directory,global,o,c,"$(pwd)" \ |
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| 254 | --attribute description,global,o,c,"Generated with XIOS" \ |
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| 255 | --attribute Comment,global,o,c,"Preliminary attempt - Do not trust !" \ |
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| 256 | ${InFile} |
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| 257 | done |
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| 258 | |
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| 259 | |
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| 260 | ## |
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| 261 | ## Update and complete weights file to fit OASIS requested format |
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| 262 | ## =========================================================================== |
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| 263 | cat <<EOF > add_dim.nco |
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| 264 | defdim("num_wgts",1) ; |
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| 265 | weight[n_weight, num_wgts] = weight ; |
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| 266 | EOF |
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| 267 | |
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| 268 | for file in rmp_*${oce}_to_*${atm}_*.nc rmp_*${atm}_to_*${oce}_*.nc ; do |
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| 269 | mv ${file} xios_${file} |
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| 270 | ncap2 --fl_fmt=${FL_FMT} -h --script-file add_dim.nco xios_${file} ${file} |
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| 271 | |
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| 272 | ncrename -h --dimension n_weight,num_links ${file} |
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| 273 | ncrename -h --variable src_idx,src_address ${file} |
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| 274 | ncrename -h --variable dst_idx,dst_address ${file} |
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| 275 | ncrename -h --variable weight,remap_matrix ${file} |
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| 276 | case ${file} in |
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| 277 | ( *1storder.nc ) ncatted -h --attribute map_method,global,o,c,"Conservative Remapping - 1st order" ${file} ;; |
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| 278 | ( *2ndorder.nc ) ncatted -h --attribute map_method,global,o,c,"Conservative Remapping - 2nd order" ${file} ;; |
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| 279 | esac |
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| 280 | ncatted -h --attribute conventions,global,o,c,"SCRIP" ${file} |
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| 281 | ncatted -h --attribute normalization,global,o,c,"none" ${file} |
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| 282 | |
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| 283 | case ${file} in |
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| 284 | ( rmp_*${oce}_to_t${atm}_* ) |
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| 285 | ncatted -h \ |
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| 286 | --attribute title,global,o,c,"Weights ${OCE} to ${ATM}" \ |
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| 287 | --attribute source_grid,global,o,c,"curvilinear" \ |
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| 288 | --attribute dest_grid,global,o,c,"unstructured" \ |
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| 289 | ${file} |
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| 290 | ;; |
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| 291 | ( rmp_*${atm}_to_*${oce}_* ) |
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| 292 | ncatted -h \ |
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| 293 | --attribute title,global,o,c,"Weights ${ATM} to ${OCE}" \ |
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| 294 | --attribute source_grid,global,o,c,"unstructured" \ |
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| 295 | --attribute dest_grid,global,o,c,"curvilinear" \ |
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| 296 | ${file} |
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| 297 | ;; |
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| 298 | esac |
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| 299 | done |
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| 300 | |
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| 301 | ## |
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| 302 | ## Save results |
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| 303 | ## =========================================================================== |
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| 304 | cp ${ATM}_grid_maskFrom_${OCE}.nc ${SUBMIT_DIR} |
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| 305 | for order in 1st # 2nd |
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| 306 | do |
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| 307 | cp t${oce}_to_t${atm}_${order}order.nc ${SUBMIT_DIR}/t${OCE}_to_t${ATM}_${order}order.nc |
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| 308 | cp rmp_t${oce}_to_t${atm}_${order}order.nc ${SUBMIT_DIR}/rmp_t${OCE}_to_t${ATM}_${order}order.nc |
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| 309 | for grid in ${ocegrids} ; do |
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| 310 | cp rmp_t${atm}_to_${grid}${oce}_${order}order.nc ${SUBMIT_DIR}/rmp_t${ATM}_to_${grid}${OCE}_${order}order.nc |
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| 311 | cp t${atm}_to_${grid}${oce}_${order}order.nc ${SUBMIT_DIR}/t${ATM}_to_${grid}${OCE}_${order}order.nc |
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| 312 | done |
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| 313 | done |
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| 314 | |
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| 315 | ## |
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| 316 | ## Creates and save auxiliary files for OASIS |
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| 317 | ## =========================================================================== |
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| 318 | bash ${SUBMIT_DIR}/GenerateOasisGrids.bash --oce ${OCE} --atm ${ATM} |
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| 319 | |
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| 320 | cp areas_${OCE}_${ATM}.nc ${SUBMIT_DIR} |
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| 321 | cp grids_${OCE}_${ATM}.nc ${SUBMIT_DIR} |
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| 322 | cp masks_${OCE}_${ATM}.nc ${SUBMIT_DIR} |
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| 323 | |
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| 324 | |
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| 325 | ### =========================================================================== |
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| 326 | ### |
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| 327 | ### That's all folk's !!! |
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| 328 | ### |
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| 329 | ### =========================================================================== |
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| 330 | |
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