nccf_atm_monthly.sh

# for maximum and minimum temperature (manipulate daily data files)
function maxmin(){
for VAR in ${VAR_LST_MXMN[@]}; do
 new_name $VAR
 echo "llll"  $SDATE
 output=${VAR}_${SDATE}.nc
 cp $DATADIR/${EXPID}/daily/$VAR/${VAR}_${SDATE}_*.nc.gz .
 gunzip ${VAR}_${SDATE}_*.nc.gz 
 SDATE1=$(echo ${SDATE}|cut -c1-6)
 cdo timmean ${VAR}_${SDATE}_${SDATE1}.nc ${output} ; rm -f ${VAR}_${SDATE}_${SDATE1}.nc
 files="$(find . -maxdepth 1 -name "${VAR}_${SDATE}_*.nc" | sed -e 's/\.\///g' )"  
 for f in $files;do
  cdo timmean $f toto.nc;rm -f $f
  ncrcat -O -h ${output} toto.nc ${output};rm -f toto.nc
 done # loop for files


 ncrename -h -d lev,ensemble ${output}
 ncrename -O -h -v lev,kaka ${output} #delete lev var
 ncks -O -h -x -v kaka ${output} ${output} #delete lev var
 ncks -h -A header.nc ${output}
#
# Get the CFU standard attributes to be written in the variable
#
variables="$(cat ${HEAD_DIR}/table_of_variable | cut -f$idx -d'|' | sed -e 's/ /@/g')"
cfustandard_name="$(echo $variables | cut -f2 -d' ' | sed -e 's/@/ /g')"  # variable standard name
cfulong_name="$(echo $variables     | cut -f3 -d' ' | sed -e 's/@/ /g')"  # variable long name
cfucell_methods="$(echo $variables  | cut -f4 -d' ' | sed -e 's/@/ /g')"  # variable cell methods
cfuunit="$(echo $variables          | cut -f5 -d' ' | sed -e 's/@/ /g')"  # variable unit
cfuunit_long="$(echo $variables     | cut -f6 -d' ' | sed -e 's/@/ /g')"  # variable unit long name
cfulevel_number="$(echo $variables  | cut -f7 -d' ' | sed -e 's/@/ /g')"  # variable level
cfulevel_type="$(echo $variables    | cut -f8 -d' ' | sed -e 's/@/ /g')"  # variable level type
cfulevel_units="$(echo $variables   | cut -f9 -d' ' | sed -e 's/@/ /g')"  # variable level unit
#
# Adding the variable level
#
ncap2 -s level_${varnew}="$cfulevel_number" ${output} -h -O ${output}
#
# Removing unnecessary attributes
#
for att in GRID_TYPE ; do 
 ncatted -O -h -a ${att},${varnew},d,c, ${output}      
done
#
# Adding and modifying the {varnew}iable attributes
#
ncatted -O -h -a standard_name,${varnew},o,c,"$cfustandard_name" ${output} # {varnew}iable standard name
ncatted -O -h -a long_name,${varnew},o,c,"$cfulong_name" ${output}         # {varnew}iable long name
ncatted -O -h -a cell_methods,${varnew},o,c,"$cfucell_methods" ${output}   # {varnew}iable cell methods
ncatted -O -h -a data_type,level_${varnew},o,c,"$cfulevel_type" ${output}  # {varnew}iable level type
ncatted -O -h -a units,level_${varnew},o,c,"$cfulevel_units" ${output}     # {varnew}iable level units
ncatted -O -h -a coordinates,${varnew},o,c,"longitude latitude reftime leadtime time_bnd experiment_id source realization institution level_${varnew}" ${output}
#
# Adding variable axis
#
ncatted -O -h -a axis,longitude,o,c,"X" ${output}       # variable longitude axis
ncatted -O -h -a axis,latitude,o,c,"Y" ${output}        # variable latitude axis
ncatted -O -h -a axis,level_${varnew},o,c,"Z" ${output} # variable level axis
# delete history
ncatted -h -a history,global,d,, $output
# change institution name
ncatted -h -a institution,global,m,c,"IC3" $output 

# create a script to change the EXPID, insitutution, ensember, source and realiazation 
	i=0 # index
	for mem in ${LISTMEMB[@]}; do
cat>modify_ncvalue<<EOF
ncap2 -O -h -s 'experiment_id($i,0:3)="$EXPID";realization($i)=$MEM;institution($i,0:$(( ${#INSTITUTION} -1  )))="$INSTITUTION";source($i,0:$(( ${#SOURCE} -1  )))="$SOURCE"' \$1 \$1
EOF

		cat modify_ncvalue
		bash modify_ncvalue $output; rm modify_ncvalue
		i=$((i+1))
	done
##

    save_final_output $varnew $output
done # loop for variables 
}
####  End of the User Defined Functions  #### 




###################################
####  Main Part of the Script  ####
###################################

# NCO and CDO must be available in $PATH

date

config_file=$1
check_args $@ 
#read config_file and initialize variables
#check config file syntaxis problems
sed -i -e 's/= /=/g' ${config_file}
. ${config_file}
export WORKDIR

FACTOR=$((NFRP*3600))
ENSEMBLE=${#MEM_LST[@]}
if [[ $ENSEMBLE -eq 0 ]]; then
  MEM_LST=( $( ls ${DATADIR}/${EXPID}/${SDATE} ) ) 
  ENSEMBLE=${#MEM_LST[@]}
  echo "Warning: you passed an empty member list. By default, it will treat all the available members: " ${MEM_LST[@]}
fi
LISTMEMB=( $(echo ${MEM_LST[@]} | sed -e 's/fc//g') ) #member list without "fc"
echo ${MEM_LST[0]}
echo $LISTMEMB
echo  ${LISTMEMB[0]}
echo ${LISTMEMB[${#LISTMEMB[@]}-1]}
echo ${#LISTMEMB[@]}

rm -rf ${WORKDIR}
mkdir -p ${WORKDIR}
if [[ ! -d ${WORKDIR} ]]; then
 exit 1
fi

cd ${WORKDIR}

base_path=${DATADIR}/${EXPID}/${SDATE}
mkdir -p ${SAVEDIR}/${EXPID}; # chmod -R 775 $SAVEDIR/${EXPID} 

#exit stop
get_leadtime
header $SDATE
extract
echo "after extract"

if [ -z ${VAR_LST_2D[@]}  ]; then
# GG=$(ls *GG* | head -1)
 GG="$(find . -maxdepth 1 -name "*GG*" | head -1 | sed -e 's/\.\///g' )"
 read_vars $GG GG
# SH=$(ls *SH* | head -1)
 SH="$(find . -maxdepth 1 -name "*SH*" | head -1 | sed -e 's/\.\///g' )"
 read_vars $SH SH
rm -f /scratch/Earth/${USER}/pp/VAR_LST_2D.txt 
VAR_LST_2D=$(echo ${VAR_LST_2D_GG} ${VAR_LST_2D_SH} 'PRECIP')
echo $VAR_LST_2D >> /scratch/Earth/${USER}/pp/VAR_LST_2D.txt
VAR_LST_3D=$(echo ${VAR_LST_3D_GG} ${VAR_LST_3D_SH})
rm -f /scratch/Earth/${USER}/pp/VAR_LST_3D.txt 
else
 VAR_LST_3D_SH_DEFAULT='T U V W Z'
 VAR_LST_3D_GG_DEFAULT='Q CC CIWC CLWC'
 VAR_LST_2D_GG_DEFAULT='T2M D2M SSTK MSL PRECIP SSR STR TTR TSR TSRC TTRC SLHF SSHF U10M V10M SSRD CP SF E SSRU SSRC STRU STRD TCC'
#if list of variables read from config_file, separation between GG and SH variables
 for var in ${VAR_LST_3D[@]}
 do
  for var_sh in ${VAR_LST_3D_SH_DEFAULT[@]} 
  do
   [ $var == $var_sh ] && VAR_LST_3D_SH=$(echo $VAR_LST_3D_SH $var)
  done
  for var_gg in ${VAR_LST_3D_GG_DEFAULT[@]}
  do
   [ $var == $var_gg ] && VAR_LST_3D_GG=$(echo $VAR_LST_3D_GG $var)
  done
 done  
 for var in ${VAR_LST_2D[@]}
 do
  for var_gg in ${VAR_LST_2D_GG_DEFAULT[@]}
  do
   [ $var == $var_gg ] && VAR_LST_2D_GG=$(echo $VAR_LST_2D_GG $var)
  done
 done 
fi

echo $YEARF - $YEAR0 - $MONF - 10#$MONF - $MON0 

echo "before surface"
surface  

echo "after surface"
combine_3d
regrid2x2
upper


if [[ ${#VAR_LST_MXMN[@]} > 0 ]]; then
 maxmin
#else 
# echo "" #empty line to avoid trap issue
fi

cd ~/; rm -rf $WORKDIR # clean up

date
trap - EXIT
####  End of the Main Part of Script  ####