ecearth3/sources/util/ece2evt/ece2evt-nemo.sh

#!/bin/bash

set -eu

# experiemnt name
expname=$1

# read configuration file
. $2

tmpdir=$tmpdir_root/nemo
mkdir -p $tmpdir

start_yyyymmdd=${start_yyyy}0101
end_yyymmdd=${end_yyyy}1231

d=$resdir

nprocs=$nprocs_nemo

# land-sea mask for nemo
lsm_file=/nobackup/rossby17/sm_wyser/ece2esmvaltool/lsm_orca1.nc

# area for each ocean gridcell (undef over land)
area_file=/nobackup/rossby17/sm_wyser/ece2esmvaltool/area_orca1.nc

# variable names to be processed
var_2d_list="tos sic"
var_1d_list="tos sos zos heatc saltc sienh siesh sivolnh sivolsh"

var_list=
for var in $var_2d_list $var_1d_list
do
    awk -v var=$var -f split_ptab.awk $nemo_par > $tmpdir/nemo-par-$var
    eval $(sed -n "/name[[:blank:]]*=/ p" $tmpdir/nemo-par-$var | tr -d [:blank:])
    var_list=$var_list" "$name
done
# remove duplicates
var_list=$(echo $var_list | tr '[:blank:]' '\n' | sort | uniq | tr '\n' ' ')

# create list with filenames to be included
# NB: the approach with "find" may not be the best possible choice in case of
# very long simulations
rm -f  $tmpdir/fname_list
for fname in $(find $d/nemo -regextype posix-extended -regex '.*_1m_.*(grid_T|icemod).nc$' | sort )
do
    f=$(basename $fname)
    fstart=$(echo $f | cut -d _ -f 3)
    fend=$(echo $f | cut -d _ -f 4)
    [ $fend -ge $start_yyyymmdd ] && [ $fstart -le $end_yyymmdd ] && echo $fname >> $tmpdir/fname_list
done

# loop over all filenames; execute in parallel
icount=0
while read fname
do
    (( icount+=1 ))
    echo "...now processing $(basename $fname)"

    iiii=$(printf %04d $icount)
    # cdo on bi has problems with pipes and compressed netcdf files
    # therefore save temporary files with -f nc (maybe only on bi?)
    cdo  -s -f nc splitvar -ifthen $lsm_file \
        -selvar,$(echo $var_list | tr -s '[:blank:]' ',') \
        $fname $tmpdir/x_${iiii}_ &
    if (( icount%nprocs == 0 )); then wait; fi
done < $tmpdir/fname_list
wait

# concatenate files
icount=0
for var in $var_list
do
    (( icount+=1 ))
    echo "...concatenating $var"

    ( rm -f $tmpdir/y_${var}.nc
      cdo -s cat $tmpdir/x_*_$var.nc $tmpdir/y_${var}.nc

      # change time variable
      ncrename -O  \
               -d time_counter,time -v time_counter,time \
               $tmpdir/y_${var}.nc $tmpdir/z_${var}.nc ) &

    if (( icount%nprocs == 0 )); then wait; fi
done
wait

# save files
icount=0
for out_name in $var_2d_list
do
    (( icount+=1 ))
    echo "...now processing $out_name"

    ( # get variable name from $nemo_par
      var=$(grep ' name ' $tmpdir/nemo-par-$out_name | cut -d = -f 2 | tr -d '[:blank:]')

      # convert units (this may become superfluos once UDUNITS2 support
      # has been activated when compiling cdo
      case $out_name in
      ( tos ) unit_conv='-addc,273.15' ;;
      ( sic ) unit_conv='-mulc,100' ;;
      ( * ) unit_conv= ;;
      esac

      outfile=$outdir/CMIP5_Omon_historical_${expname}_r1i1p1_T2Ms_${out_name}_${start_yyyy}-${end_yyyy}.nc
      rm -f $outfile

      cdo -s -f nc4c -z zip setpartabn,$tmpdir/nemo-par-$out_name \
          -setreftime,$refdate,00:00:00,days \
          -invertlat \
          $unit_conv -remapdis,n128 \
          $tmpdir/z_${var}.nc $outfile ) &

    if (( icount%nprocs == 0 )); then wait; fi
done
wait
 
icount=0
for out_name in $var_1d_list
do
    (( icount+=1 ))
    echo "...now processing $out_name"

    ( # get variable name from $nemo_par
      var=$(grep ' name ' $tmpdir/nemo-par-$out_name | cut -d = -f 2 | tr -d '[:blank:]')

      # convert units (this may become superfluos once UDUNITS2 support
      # has been activated when compiling cdo
      case $out_name in
      ( tos ) unit_conv='-addc,273.15' ;;
      ( sie* ) unit_conv='-divc,1e12' ;;
      ( sivol* ) unit_conv='-divc,1e12' ;;
      ( * ) unit_conv= ;;
      esac

      # threshold for sea-ice extent
      case $out_name in
      ( sie* ) ext_thresh='-gtc,.15' ;;
      ( * ) ext_thresh= ;;
      esac

      outfile=$outdir/CMIP5_Omon_historical_${expname}_r1i1p1_T1Ms_${out_name}_${start_yyyy}-${end_yyyy}.nc
      rm -f $outfile

      case $out_name in
      ( sienh | sivolnh )
          cdo -s -f nc4c -z zip setpartabn,$tmpdir/nemo-par-$out_name \
            -setreftime,$refdate,00:00:00,days $unit_conv \
            -fldsum -maskindexbox,1,362,147,292 \
            -mul $ext_thresh $tmpdir/z_${var}.nc $area_file \
            $outfile ;;
      ( siesh | sivolsh )
          cdo -s -f nc4c -z zip setpartabn,$tmpdir/nemo-par-$out_name \
            -setreftime,$refdate,00:00:00,days $unit_conv \
            -fldsum -maskindexbox,1,362,1,146 \
            -mul $ext_thresh $tmpdir/z_${var}.nc $area_file \
            $outfile ;;
      ( * )
          cdo -s  -f nc4c -z zip setpartabn,$tmpdir/nemo-par-$out_name \
            -setreftime,$refdate,00:00:00,days $unit_conv \
            -div -fldsum -mul $area_file $tmpdir/z_${var}.nc \
            -fldsum $area_file $outfile ;;
      esac ) &

    if (( icount%nprocs == 0 )); then wait; fi
done
wait

# clean up
rm -r $tmpdir

echo "!!! ece2evt-nemo done !!!"
exit 0