1 | #!/bin/bash |
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2 | ### =========================================================================== |
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3 | ### |
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4 | ### Creates grids.nc, masks.nc and areas.nc for OASIS-MCT |
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5 | ### |
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6 | ### =========================================================================== |
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7 | ## |
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8 | ## Warning, to install, configure, run, use any of Olivier Marti's |
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9 | ## software or to read the associated documentation you'll need at least |
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10 | ## one (1) brain in a reasonably working order. Lack of this implement |
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11 | ## will void any warranties (either express or implied). |
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12 | ## O. Marti assumes no responsability for errors, omissions, |
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13 | ## data loss, or any other consequences caused directly or indirectly by |
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14 | ## the usage of his software by incorrectly or partially configured |
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15 | ## personal. |
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16 | ## |
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17 | ## SVN information |
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18 | # $Author$ |
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19 | # $Date$ |
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20 | # $Revision$ |
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21 | # $Id$ |
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22 | # $Log: $ |
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23 | |
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24 | ## |
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25 | ## Default configuration (may be overrided by command line parameters) |
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26 | ## =========================================================================== |
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27 | OCE=ORCA2.3 |
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28 | # OCE=eORCA1.2 |
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29 | ATM=ICO30 |
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30 | #ATM=ICO40 |
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31 | # ATM=ICO450 |
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32 | # ATM=LMD144142 |
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33 | # ATM=LMD9695 |
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34 | |
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35 | ## =========================================================================== |
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36 | ## |
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37 | ## You should not change anything below this line .... |
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38 | ## |
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39 | ## =========================================================================== |
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40 | |
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41 | # Defines computer |
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42 | # ================ |
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43 | if [[ $(hostname) = curie* ]] ; then arch=curie ; center=tgcc ; fi |
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44 | if [[ $(hostname) = irene* ]] ; then arch=irene ; center=tgcc ; fi |
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45 | PROGRAM=$(basename ${0}) |
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46 | |
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47 | case ${arch} in |
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48 | ( curie | irene ) |
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49 | set +vx |
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50 | module unload cdo nco ferret |
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51 | module unload netcdf hdf5 |
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52 | module load python # /2.7.12 |
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53 | module load netcdf/4.3.3.1_hdf5_parallel # Version for XIOS |
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54 | module load nco |
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55 | R_IN=$(ccc_home -u igcmg --cccwork)/IGCM |
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56 | TMPDIR=${SCRATCHDIR}/TMP |
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57 | SUBMIT_DIR=${BRIDGE_MSUB_PWD:-${SUBMIT_DIR}} |
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58 | ;; |
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59 | ( * ) |
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60 | exit -1 |
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61 | ;; |
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62 | esac |
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63 | ## |
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64 | ## Command line parameters |
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65 | ## =========================================================================== |
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66 | set -o verbose |
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67 | set -o xtrace |
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68 | |
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69 | while [[ ${1} = -* ]] ; do |
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70 | case ${1} in |
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71 | ( -- ) shift ; break ;; |
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72 | ( -o=* | --oce=* ) OCE=${1##*=} ; echo OCE:${OCE} ;; |
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73 | ( -o | --oce ) shift ; OCE=${1} ; echo OCE:${OCE} ;; |
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74 | ( -a=* | --atm=* ) ATM=${1##*=} ; echo ATM:${ATM} ;; |
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75 | ( -a | --atm ) shift ; ATM=${1} ; echo ATM:${ATM} ;; |
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76 | ( -v | --verbose ) set -o verbose ;; |
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77 | ( -x | --xtrace ) set -o xtrace ;; |
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78 | ( -e ) set -e ;; |
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79 | ( -V | --noverbose ) set +o verbose ;; |
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80 | ( -X | --noxtrace ) set +o xtrace ;; |
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81 | ( -E ) set +e ;; |
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82 | ( -* ) echo ${Bold}"Unknown option : ${1}"${Norm} ; return 1 ;; |
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83 | esac |
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84 | shift |
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85 | done |
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86 | |
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87 | ## |
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88 | ## Short names (grid names in Oasis) |
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89 | ## =========================================================================== |
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90 | case ${OCE} in |
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91 | ( *ORC*) oce=orc ;; |
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92 | esac |
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93 | case ${ATM} in |
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94 | ( *ICO* ) atm=ico ;; |
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95 | ( *dynamico* ) atm=ico ;; |
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96 | ( *lmd* | *LMD* ) atm=lmd ;; |
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97 | esac |
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98 | |
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99 | CplModel=${OCE}x${ATM} |
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100 | |
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101 | ## |
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102 | ## Get input files |
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103 | ## =========================================================================== |
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104 | [[ -f ${OCE}_coordinates_mask.nc ]] || cp ${R_IN}/OCE/NEMO/${OCE}/${OCE}_coordinates_mask.nc . |
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105 | [[ -f ${ATM}_grid.nc ]] || cp ${R_IN}/ATM/${ATM}/${ATM}_grid.nc . |
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106 | |
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107 | # |
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108 | # Format for OASIS-MCT files : should be NetCDF3 classic or NetCDF3 64 bits |
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109 | # --------------------------------------------------------------------------- |
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110 | FL_FMT=64bit |
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111 | |
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112 | # |
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113 | # Cleaning |
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114 | # ---------------------------------------------------------------------------- |
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115 | rm -f grids_${CplModel}.nc masks_${CplModel}.nc areas_${CplModel}.nc |
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116 | rm -f *_tmp.nc |
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117 | |
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118 | # |
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119 | # Creates NetCDF3 version of input files |
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120 | # ---------------------------------------------------------------------------- |
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121 | ncks --overwrite --fl_fmt=${FL_FMT} --history ${OCE}_coordinates_mask.nc ${OCE}_coordinates_mask_${FL_FMT}.nc |
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122 | ncks --overwrite --fl_fmt=${FL_FMT} --history ${ATM}_grid_maskFrom_${OCE}.nc ${ATM}_grid_maskFrom_${OCE}_${FL_FMT}.nc |
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123 | # |
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124 | # Creates ocean fields |
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125 | # ---------------------------------------------------------------------------- |
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126 | |
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127 | for OCEGRID in T U V ; do |
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128 | ncks --fl_fmt=${FL_FMT} -C --history --append -v nav_lon_grid_${OCEGRID},nav_lat_grid_${OCEGRID},bounds_lon_grid_${OCEGRID},bounds_lat_grid_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT}.nc grids_${CplModel}.nc |
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129 | ncks --fl_fmt=${FL_FMT} -C --history --append -v area_grid_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT}.nc areas_${CplModel}.nc |
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130 | # Inverts mask values and switch to integer |
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131 | ncks --fl_fmt=${FL_FMT} --history -C -v mask_${OCEGRID} ${OCE}_coordinates_mask_${FL_FMT}.nc mask_${OCEGRID}_tmp.nc |
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132 | ncatted --history \ |
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133 | --attribute coordinates,mask_${OCEGRID},d,, \ |
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134 | --attribute online_operation,mask_${OCEGRID},d,, \ |
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135 | --attribute cell_measures,mask_${OCEGRID},d,, \ |
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136 | mask_${OCEGRID}_tmp.nc |
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137 | |
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138 | ncap2 --fl_fmt=${FL_FMT} --history --append -s "mask_${OCEGRID}=int(1-mask_${OCEGRID});" mask_${OCEGRID}_tmp.nc masks_${CplModel}.nc |
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139 | ncatted --history \ |
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140 | --attribute long_name,mask_${OCEGRID},o,c,"Land-sea mask" \ |
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141 | --attribute units,mask_${OCEGRID},o,c,"Land:1, Ocean:0" masks_${CplModel}.nc |
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142 | # Change order of dimensions |
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143 | mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc |
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144 | ncpdq --permute nvertex_grid_${OCEGRID},y_grid_${OCEGRID},x_grid_${OCEGRID} grids_${CplModel}_tmp.nc grids_${CplModel}.nc |
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145 | done |
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146 | |
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147 | ncks --history --append -v lon,lat ${ATM}_grid_maskFrom_${OCE}_${FL_FMT}.nc grids_${CplModel}.nc |
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148 | |
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149 | # |
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150 | # We need to have different names for dimensions and variables |
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151 | # ---------------------------------------------------------------------------- |
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152 | ncrename --history -v lon,alon grids_${CplModel}.nc |
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153 | ncrename --history -v lat,alat grids_${CplModel}.nc |
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154 | |
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155 | if [[ ${ATM} = dynamico* || ${ATM} = ICO* ]] ; then |
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156 | ncks --fl_fmt=${FL_FMT} --history --append -v bounds_lon,bounds_lat ${ATM}_grid_maskFrom_${OCE}_${FL_FMT}.nc grids_${CplModel}.nc |
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157 | fi |
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158 | |
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159 | ncks --fl_fmt=${FL_FMT} --history -C --append -v aire ${ATM}_grid_maskFrom_${OCE}_${FL_FMT}.nc areas_${CplModel}.nc |
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160 | ncatted --history --attribute coordinates,aire,d,, \ |
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161 | --attribute _FillValue,aire,d,, \ |
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162 | --attribute missing_value,aire,d,, \ |
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163 | --attribute online_operation,aire,d,, \ |
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164 | --attribute units,aire,o,c,"m2" \ |
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165 | --attribute standard_name,aire,o,c,"cell_area" \ |
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166 | areas_${CplModel}.nc |
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167 | |
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168 | ncks --fl_fmt=${FL_FMT} --history -C -v OceMask ${ATM}_grid_maskFrom_${OCE}_${FL_FMT}.nc OceMask_tmp.nc |
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169 | ncatted --history \ |
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170 | --attribute coordinates,OceMask,d,, \ |
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171 | --attribute online_operation,OceMask,d,, \ |
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172 | --attribute _FillValue,OceMask,d,, \ |
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173 | --attribute missing_value,OceMask,d,, \ |
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174 | OceMask_tmp.nc |
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175 | ncap2 --fl_fmt=${FL_FMT} --history --append -s "OceMask=int(1-OceMask)" OceMask_tmp.nc masks_${CplModel}.nc # For OASIS, ocean=0, land=1 |
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176 | ncatted --history \ |
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177 | --attribute long_name,OceMask,o,c,"Land-sea mask" \ |
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178 | --attribute units,OceMask,o,c,"Land:1, Ocean:0" masks_${CplModel}.nc |
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179 | |
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180 | ncatted --history --attribute history,global,d,, grids_${CplModel}.nc |
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181 | ncatted --history --attribute history,global,d,, masks_${CplModel}.nc |
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182 | ncatted --history --attribute history,global,d,, areas_${CplModel}.nc |
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183 | |
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184 | if [[ ${atm} = *dynamico* || ${atm} = ico* ]] ; then |
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185 | ncrename --history -d cell,ycell grids_${CplModel}.nc |
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186 | ncrename --history -d cell,ycell areas_${CplModel}.nc |
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187 | ncrename --history -d cell,ycell masks_${CplModel}.nc |
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188 | fi |
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189 | # if [[ ${atm} = *lmd* ]] ; then |
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190 | # ncrename -d lon,tlmdlon grids_${CplModel}.nc |
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191 | # ncrename -d lat,tlmdlat grids_${CplModel}.nc |
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192 | # ncrename -d lon,tlmdlon masks_${CplModel}.nc |
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193 | # ncrename -d lat,tlmdlat masks_${CplModel}.nc |
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194 | # ncrename -d lon,tlmdlon areas_${CplModel}.nc |
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195 | # ncrename -d lat,tlmdlat areas_${CplModel}.nc |
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196 | # fi |
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197 | |
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198 | # |
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199 | # DYNAMICO grids : |
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200 | # - Set correct order of dimensions |
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201 | # - Add a dimension |
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202 | # ---------------------------------------------------------------------------- |
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203 | if [[ ${atm} = dynamico* || ${atm} = ico* ]] ; then |
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204 | mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc |
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205 | ncpdq --permute nvertex,ycell,xcell grids_${CplModel}_tmp.nc grids_${CplModel}.nc |
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206 | |
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207 | mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc |
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208 | cat <<EOF >add_dim.nco |
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209 | // |
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210 | defdim("xcell",1) ; |
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211 | alat [ycell,xcell] = alat ; |
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212 | alon [ycell,xcell] = alon ; |
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213 | bounds_lat [nvertex,ycell,xcell] = bounds_lat ; |
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214 | bounds_lon [nvertex,ycell,xcell] = bounds_lon ; |
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215 | // |
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216 | EOF |
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217 | |
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218 | ncap2 --fl_fmt=${FL_FMT} --history --append -S add_dim.nco grids_${CplModel}_tmp.nc grids_${CplModel}.nc |
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219 | |
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220 | mv masks_${CplModel}.nc masks_${CplModel}_tmp.nc |
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221 | ncap2 --fl_fmt=${FL_FMT} --history --append -s 'defdim("xcell",1) ; OceMask[time_counter,ycell,xcell]=OceMask(:,:)' masks_${CplModel}_tmp.nc masks_${CplModel}.nc |
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222 | |
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223 | mv areas_${CplModel}.nc areas_${CplModel}_tmp.nc |
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224 | ncap2 --fl_fmt=${FL_FMT} --history --append -s 'defdim("xcell",1) ; aire[ycell,xcell]=aire(:) ; ' areas_${CplModel}_tmp.nc areas_${CplModel}.nc |
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225 | fi |
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226 | |
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227 | # |
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228 | # Some changes specific to LMDZ lon/lat grid |
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229 | # ---------------------------------------------------------------------------- |
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230 | if [[ ${atm} = lmd* ]] ; then |
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231 | # Spreads lon and lat to get 2D fields |
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232 | # ----------------------------------------------------------------------- |
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233 | mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc |
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234 | ncap2 --fl_fmt=${FL_FMT} --history --append -s "alon[lat,lon]=alon; alat[lat,lon]=alat" grids_${CplModel}_tmp.nc grids_${CplModel}.nc |
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235 | ncatted --history \ |
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236 | --attribute long_name,alon,o,c,"Longitude" \ |
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237 | --attribute long_name,alat,o,c,"Latitude" \ |
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238 | --attribute units,alon,o,c,"degrees_east" \ |
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239 | --attribute units,alat,o,c,"degrees_north" \ |
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240 | --attribute grid_type,alon,o,c,"P" \ |
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241 | --attribute grid_type,alat,o,c,"P" \ |
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242 | --attribute overlap,alon,o,i,0 \ |
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243 | --attribute overlap,alat,o,i,0 grids_${CplModel}.nc |
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244 | |
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245 | # Generates cell corners |
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246 | # ----------------------------------------------------------------------- |
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247 | cat <<EOF > add_bounds.nco |
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248 | defdim ("nvertex_lmd", 4) ; |
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249 | *delta_x = alon(0,1) - alon(0,0) ; |
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250 | *delta_y = alat(1,0) - alat(0,0) ; |
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251 | // |
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252 | bounds_lon[nvertex_lmd,lat,lon] = 0.0 ; |
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253 | bounds_lat[nvertex_lmd,lat,lon] = 0.0 ; |
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254 | // |
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255 | bounds_lon (0,:,:) = alon + delta_x*0.5 ; |
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256 | bounds_lat (0,:,:) = alat + delta_y*0.5 ; |
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257 | bounds_lon (1,:,:) = alon + delta_x*0.5 ; |
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258 | bounds_lat (1,:,:) = alat - delta_y*0.5 ; |
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259 | bounds_lon (2,:,:) = alon - delta_x*0.5 ; |
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260 | bounds_lat (2,:,:) = alat - delta_y*0.5 ; |
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261 | bounds_lon (3,:,:) = alon - delta_x*0.5 ; |
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262 | bounds_lat (3,:,:) = alat + delta_y*0.5 ; |
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263 | // |
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264 | where (bounds_lat > 90.0 ) bounds_lat = 90.0 ;; |
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265 | where (bounds_lat < -90.0 ) bounds_lat = -90.0 ;; |
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266 | // |
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267 | EOF |
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268 | mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc |
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269 | ncap2 --fl_fmt=${FL_FMT} --history -S add_bounds.nco -O grids_${CplModel}_tmp.nc grids_${CplModel}.nc |
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270 | fi |
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271 | |
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272 | # |
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273 | # Generates grid "aone" : same as t-ocean grid, with surfaces set to 1 |
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274 | # This grid is used when field are quantities instead of fluxes (i.e river flow) |
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275 | # ---------------------------------------------------------------------------- |
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276 | mv grids_${CplModel}.nc grids_${CplModel}_tmp.nc |
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277 | ncap2 --fl_fmt=${FL_FMT} --history -s "aone_lon=alon; aone_lat=alat; bounds_aone_lon=bounds_lon; bounds_aone_lat=bounds_lat; " grids_${CplModel}_tmp.nc grids_${CplModel}.nc |
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278 | |
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279 | mv areas_${CplModel}.nc areas_${CplModel}_tmp.nc |
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280 | ncap2 --fl_fmt=${FL_FMT} --history -s "aone_aire=aire*0+1; " areas_${CplModel}_tmp.nc areas_${CplModel}.nc |
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281 | |
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282 | mv masks_${CplModel}.nc masks_${CplModel}_tmp.nc |
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283 | ncap2 --fl_fmt=${FL_FMT} --history -s "aone_mask=int(OceMask); " masks_${CplModel}_tmp.nc masks_${CplModel}.nc |
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284 | |
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285 | # |
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286 | # Final renaming |
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287 | # ---------------------------------------------------------------------------- |
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288 | for OCEGRID in T U V |
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289 | do |
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290 | ocegrid=${OCEGRID~} # To lowercase |
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291 | ncrename --history -v nav_lon_grid_${OCEGRID},${ocegrid}${oce}.lon grids_${CplModel}.nc |
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292 | ncrename --history -v nav_lat_grid_${OCEGRID},${ocegrid}${oce}.lat grids_${CplModel}.nc |
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293 | ncrename --history -v bounds_lon_grid_${OCEGRID},${ocegrid}${oce}.clo grids_${CplModel}.nc |
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294 | ncrename --history -v bounds_lat_grid_${OCEGRID},${ocegrid}${oce}.cla grids_${CplModel}.nc |
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295 | ncrename --history -v mask_${OCEGRID},${ocegrid}${oce}.msk masks_${CplModel}.nc |
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296 | ncrename --history -v area_grid_${OCEGRID},${ocegrid}${oce}.srf areas_${CplModel}.nc |
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297 | |
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298 | ncatted --history \ |
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299 | --attribute bounds,${ocegrid}${oce}.lon,m,c,"${ocegrid}${oce}.clo" \ |
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300 | --attribute bounds,${ocegrid}${oce}.lat,m,c,"${ocegrid}${oce}.cla" \ |
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301 | --attribute units,${ocegrid}${oce}.clo,o,c,"degrees_east" \ |
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302 | --attribute units,${ocegrid}${oce}.clo,o,c,"degrees_north" grids_${CplModel}.nc |
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303 | done |
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304 | |
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305 | ncrename --history -v alon,t${atm}.lon grids_${CplModel}.nc |
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306 | ncrename --history -v alat,t${atm}.lat grids_${CplModel}.nc |
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307 | ncrename --history -v aone_lon,o${atm}.lon grids_${CplModel}.nc |
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308 | ncrename --history -v aone_lat,o${atm}.lat grids_${CplModel}.nc |
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309 | ncrename --history -v OceMask,t${atm}.msk masks_${CplModel}.nc |
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310 | ncrename --history -v aone_mask,o${atm}.msk masks_${CplModel}.nc |
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311 | ncrename --history -v aire,t${atm}.srf areas_${CplModel}.nc |
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312 | ncrename --history -v aone_aire,o${atm}.srf areas_${CplModel}.nc |
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313 | |
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314 | ncrename --history -v bounds_lon,t${atm}.clo grids_${CplModel}.nc |
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315 | ncrename --history -v bounds_lat,t${atm}.cla grids_${CplModel}.nc |
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316 | ncrename --history -v bounds_aone_lon,o${atm}.clo grids_${CplModel}.nc |
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317 | ncrename --history -v bounds_aone_lat,o${atm}.cla grids_${CplModel}.nc |
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318 | |
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319 | for atmgrid in t o ; do |
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320 | ncatted --history \ |
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321 | --attribute bounds,${atmgrid}${atm}.lon,c,c,"${atmgrid}${atm}.clo" \ |
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322 | --attribute bounds,${atmgrid}${atm}.lat,c,c,"${atmgrid}${atm}.cla" \ |
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323 | --attribute units,${atmgrid}${atm}.clo,o,c,"degrees_east" \ |
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324 | --attribute units,${atmgrid}${atm}.cla,o,c,"degrees_north" grids_${CplModel}.nc |
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325 | done |
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326 | |
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327 | ## |
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328 | ## Change all NetCDF files to NetCDF 3 format |
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329 | ## =========================================================================== |
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330 | for InFile in areas_${CplModel}.nc grids_${CplModel}.nc masks_${CplModel}.nc ; do |
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331 | if [[ $(ncdump -k ${InFile}) = *netCDF-4* ]] ; then |
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332 | mv ${InFile} tmp_${InFile} |
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333 | ncks --fl_fmt=${FL_FMT} --history tmp_${InFile} ${InFile} |
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334 | fi |
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335 | done |
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336 | |
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337 | ## |
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338 | ## Add some useful information in NetCDF headers |
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339 | ## =========================================================================== |
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340 | UUID=$(uuid) |
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341 | NCO=$(ncks --version |& tail -1|sed 's/ncks //') |
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342 | for type in areas masks grids ; do |
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343 | ncatted --history \ |
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344 | --attribute nco_openmp_thread_number,global,d,, \ |
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345 | --attribute uuid,global,d,, \ |
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346 | --attribute LongName,global,d,, \ |
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347 | --attribute NCO,global,o,c,"NCO netCDF Operator ${NCO} http://nco.sourceforge.net" \ |
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348 | --attribute Conventions,global,o,c,"CF-1.6" \ |
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349 | --attribute source,global,o,c,"IPSL Earth system model" \ |
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350 | --attribute group,global,o,c,"ICMC IPSL Climate Modelling Center" \ |
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351 | --attribute production,global,o,c,"$(finger ${LOGNAME} | head -1 | awk '{print $4, $5}') " \ |
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352 | --attribute Institution,global,o,c,"IPSL https://www.ipsl.fr" \ |
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353 | --attribute Ocean,global,o,c,"${OCE} https://www.nemo-ocean.eu" \ |
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354 | --attribute Atmosphere,global,o,c,"${ATM} http://lmdz.lmd.jussieu.fr" \ |
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355 | --attribute HOSTNAME,global,o,c,"$(hostname)" \ |
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356 | --attribute LOGNAME,global,o,c,"$(whoami)" \ |
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357 | --attribute Program,global,o,c,"Generated by ${0}" \ |
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358 | --attribute name,global,o,c,"${type}_${CplModel}.nc" \ |
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359 | --attribute directory,global,o,c,"$(pwd)" \ |
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360 | --attribute description,global,o,c,"Fields needed by OASIS-MCT" \ |
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361 | --attribute title,global,o,c,"${type}_${CplModel}.nc" \ |
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362 | --attribute timeStamp,global,o,c,"$(date)" \ |
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363 | --attribute associatedFiles,global,o,c,"grids_${CplModel}.nc areas_${CplModel}.nc masks_${CplModel}.nc" \ |
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364 | --attribute originalFiles,global,o,c,"${OCE}_coordinates_mask.nc ${ATM}_grid_mask.nc"\ |
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365 | --attribute uuid,global,o,c,"${UUID}" \ |
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366 | --attribute OS,global,o,c,"$(uname -o)" \ |
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367 | --attribute release,global,o,c,"$(uname -r)" \ |
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368 | --attribute hardware,global,o,c,"$(uname -i)" \ |
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369 | --attribute Comment,global,o,c,"Preliminary attempt - Do not trust !" \ |
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370 | --attribute SVN_Author,global,o,c,"$Author$" \ |
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371 | --attribute SVN_Date,global,o,c,"$Date$" \ |
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372 | --attribute SVN_Revision,global,o,c,"$Revision$" \ |
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373 | --attribute SVN_Id,global,o,c,"$Id$" \ |
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374 | --attribute SVN_Lo,global,o,c,"$Log: $" \ |
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375 | ${type}_${CplModel}.nc |
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376 | done |
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377 | |
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378 | ## |
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379 | ## Cleaning |
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380 | ## =========================================================================== |
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381 | #rm *_tmp.nc ${OCE}_coordinates_mask_${FL_FMT}.nc ${ATM}_grid_maskFrom_${OCE}_${FL_FMT}.nc *.nco |
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382 | |
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383 | exit |
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384 | # |
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385 | # Name of the dimensions ? |
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386 | # ---------------------------------------------------------------------------- |
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387 | for OCEGRID in T U V ; do |
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388 | ocegrid=${OCEGRID~} # Downcase name of grids |
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389 | ncrename --history -d x_grid_${OCEGRID},x${ocegrid}${oce} grids_${CplModel}.nc |
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390 | ncrename --history -d y_grid_${OCEGRID},y${ocegrid}${oce} grids_${CplModel}.nc |
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391 | ncrename --history -d nvertex_grid_${OCEGRID},crn${ocegrid}${oce} grids_${CplModel}.nc |
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392 | done |
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393 | |
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394 | ## =========================================================================== |
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395 | ## |
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396 | ## That's all folk's !!! |
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397 | ## |
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398 | ## =========================================================================== |
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