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#
# ./nccf_atm_monthly.sh path_to_config_file >& EXPID-startdate.log &
#
#
# This script will extract variabls from EC-Earth monthly atmospheric output
# which is available in MMA files, save each variable in one file and also
# combine members together. It will modify the header informaton of the
# generated files according to CMIP5 standard and the variable names will be
# modified according PCMDI standard variable names.
#
# Written by Hui Du
#
# Institut Català de Ciències del Clima / Climate Forecasting Unit (IC3/CFU)
# Created: February 22, 2010
# Adapted: Pierre-Antoine Bretonnière - IC3 , January 2013
#module load NCO
#module load CDO
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msg='Your experiment crashed! Your workdir \($WORKDIR\) will be kept for one week from now and then deleted'
trap " echo $msg ; rm -rf $WORKDIR | at now + 7 days ; exit" SIGINT SIGHUP SIGTERM SIGSEGV SIGKILL EXIT
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#################################
#### User Defined Funtions ####
#################################
# check if args are ok
function check_args(){
NB_ARGS=$#
if [ $# -ne 1 ] ; then
echo
echo "USAGE: config_file "
echo "For example: ./nccf_atm_monthly.new.sh /home/Earth/$user/es_git/atmospheric_diagnostics/config_file "
echo
exit 1
fi
}
function get_leadtime(){
#gets lead_time and checks if all members have the same number of months
NMONTH=9999999
for DIR in $MEM_LST
do
cd ${DATADIR}/${EXPID}/original_files/${SDATE}/${DIR}/outputs
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NFILE=0
for file in $( find . -maxdepth 1 -name "MMA*" )
do
[[ $( echo $file | cut -f5 -d"_" | cut -f1 -d"-" ) -ge ${LEAD_LIST[0]}${LEAD_LIST[1]}01 ]] && [[ $( echo $file | cut -f5 -d"_" | cut -f1 -d"-" ) -le ${LEAD_LIST[2]}${LEAD_LIST[3]}01 ]] && NFILE=$(( NFILE + 1 ))
done
for TMPFILE in $( find . -maxdepth 1 -name "MMA*" | sed -e 's/\.\///g' )
do
# if [[ $( echo $TMPFILE | cut -f5 -d"_" | cut -f1 -d"-" ) -ge ${LEAD_LIST[0]}${LEAD_LIST[1]}01 ]]; then
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NMONTHS_LOC=$(tar tvf $TMPFILE | grep GG | wc -l)
[ $NMONTH -ne $NMONTHS_LOC ] && [ $NMONTH -ne 9999999 ] && echo "all members or start dates don't have the same number of months, be careful"
[ $NMONTH -ge $NMONTHS_LOC ] && NMONTH=$NMONTHS_LOC
# fi
cd ${WORKDIR}
done
}
function header(){
SD=$1
rtime 19500101 ${SD}
ncks -h -d ensemble,0,$((ENSEMBLE-1)),1 ${HEAD_DIR}/template.nc toto.nc # select sub member
cp toto.nc toto1.nc
TIME_BND1=0
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TIME_BND2=$(get_hours $SD)
LEADTIME=$(((TIME_BND1+TIME_BND2)/2))
ncap2 -O -h -s "leadtime(0)=${LEADTIME};time_bnd(,0)=${TIME_BND1};time_bnd(,1)=${TIME_BND2}" toto.nc toto.nc
for ((i=1;i<=$((NLT-1));i++)); do
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FORDATE=$(leadtime2date $SD $i)
INTERVAL=$(get_hours $FORDATE)
TIME_BND1=$TIME_BND2
TIME_BND2=$((TIME_BND1+INTERVAL))
LEADTIME=$(((TIME_BND1+TIME_BND2)/2))
echo $fordate $interval $time_bnd1 $time_bnd2
ncap2 -O -h -s "reftime(0)=${REFTIME_VALUE};leadtime(0)=${LEADTIME};time_bnd(,0)=${TIME_BND1};time_bnd(,1)=${TIME_BND2}" toto1.nc toto1.nc
ncrcat -O -h toto.nc toto1.nc toto.nc
done
mv toto.nc header.nc; rm toto1.nc
}
# function to get reftime time
function rtime(){
DATE1=$1
DATE2=$2
# FACTOR=day # h for hour, d for days
# echo "NFRP:",$NFRP
# FACTOR=day # h for hour, d for days
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YEAR1=$(echo $DATE1|cut -c1-4)
MONTH1=$(echo $DATE1|cut -c5-6)
DAY1=$(echo $DATE1|cut -c7-8)
YEAR2=$(echo $DATE2|cut -c1-4)
MONTH2=$(echo $DATE2|cut -c5-6)
DAY2=$(echo $DATE2|cut -c7-8)
SEC1=$(date --utc --date "${YEAR1}-${MONTH1}-${DAY1}" +%s)
SEC2=$(date --utc --date "${YEAR2}-${MONTH2}-${DAY2}" +%s)
# case $FACTOR in
# hour)
# FACTOR=3600 # 60*60
# ;;
# day)
# FACTOR=86400 # 60*60*24
# ;;
# esac
REFTIME_VALUE=$(((SEC2-SEC1)/FACTOR))
}
function leadtime2date(){
# function leadtime2date, based on starting date and lead time to calculate date(year & month) of the corresponding leadtime
INIDATE=$1
OFFSET=$2
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YY=$(echo $INIDATE|cut -c1-4)
MM=$(echo $INIDATE|cut -c5-6)
MM=$(echo $MM | sed 's/^0*//;s/^$/0/' )
YY1=$((YY+offset/12))
NMONTH=$((offset%12))
MM1=$((MM+NMONTH))
if [ $MM1 -gt 12 ]; then
YY1=$((YY1+1))
MM1=$((MM1-12))
fi
if [ $MM1 -lt 10 ]; then
MM1="0$MM1"
fi
}
# get the total number of HOURS for a specific MONTH
function get_hours(){
YYMM=$1
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YEAR=$(echo $YYMM|cut -c1-4)
MONTH=$(echo $YYMM|cut -c5-6)
NDAYS=$(cal $MONTH $YEAR |egrep "^[ 0-9][0-9]| [ 0-9][0-9]$" |wc -w)
HOURS=$((NDAYS*24))
echo $HOURS
}
function extract(){
#typeset var jt
#typeset var YEAR0
#typeset var YEARF
#typeset var MON0
#typeset var MONF
for MEM in ${MEM_LST[@]}; do
# untar and unzip MMA SH files and GG files
if [ -z $( echo ${LEAD_LIST[@]} ) ];then
PATH_TO_SEARCH=${DATADIR}/${EXPID}/original_files/${SDATE}/$MEM
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FILE_LIST=$(find $PATH_TO_SEARCH -type f -iname "MMA*" 2> /dev/null)
export YEAR0=${LEAD_LIST[0]}
export MON0=${LEAD_LIST[1]}
export YEARF=${LEAD_LIST[2]}
export MONF=${LEAD_LIST[3]}
export CHUNK_SIZE=${LEAD_LIST[4]}
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export YYYY0=$(echo $SDATE | cut -b -4)
export MM0=$(echo $SDATE | cut -b 5-6)
export LTIMEF=$(( ( ($YEARF - $YEAR0) * 12 + 10#$MONF - 10#$MON0+1 )/$CHUNK_SIZE ))
jt=$LTIME0
while [ $jt -le $((LTIMEF)) ]
do
FILE_LIST=""
YEAR1=$(( $YEAR0 +(10#$MON0+($jt-1)*$CHUNK_SIZE - 1 )/ 12 ))
MON1=$(( ( 10#$MON0 + ( $jt - 1 ) * ($CHUNK_SIZE) ) % 12))
MON1=$(echo $(printf "%02d" $(( 10#$MON1))) )
YEAR2=$(( $YEAR1 + ( 10#$MON1 + $CHUNK_SIZE-1 ) / 12 ))
MON2=$(( ( 10#$MON1 + $CHUNK_SIZE-1 ) % 12 ))
MON2=$(echo $(printf "%02d" $(( 10#$MON2))) )
[[ 10#$MON1 -eq 0 ]] && MON1=12
[[ 10#$MON2 -eq 0 ]] && MON2=12
[[ 10#$MON2 -eq 12 ]] && YEAR2=$(( $YEAR2 - 1 ))
FILE="$( find ${DATADIR}/${EXPID}/original_files/${SDATE}/*/outputs/ -maxdepth 1 -name "MMA_${EXPID}_${SDATE}_${MEM}_${YEAR1}"$(printf "%02d" $((10#$MON1)))"01-${YEAR2}"$(printf "%02d" $((10#$MON2)))"*.tar" )"
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if [[ -z ${FILE} ]]; then
echo "Expected file ${DATADIR}/${EXPID}/original_files/${SDATE}/${MEM}/outputs/MMA_${EXPID}_${SDATE}_${MEM}_${YEAR1}${MON1}01-${YEAR2}${MON2}*.tar not found, check your Namelist parameters"
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exit
fi
FILE_LIST="$FILE_LIST ${FILE}"
done
fi
echo ${FILE_LIST}
for f in ${FILE_LIST};do
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SH_FILES=$(tar tf ${f}|grep SH)
for FILE in ${SH_FILES};do
tar xvf ${f} ${FILE} ;gunzip -q ${FILE}; mv ${FILE%???} ${FILE%???}.$MEM
done
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GG_FILES=$(tar tf ${f}|grep GG)
for FILE in ${GG_FILES};do
tar xvf ${f} ${FILE} ;gunzip -q ${FILE}; mv ${FILE%???} ${FILE%???}.$MEM
done
done
echo "jt ltimef " $jt $((LTIMEF))
if [ $jt -le $((LTIMEF)) ]; then
echo le
else
echo gt
fi
echo "sortie de extract" $MEM -- ${MEM_LST[@]}
echo "sortie de extract"
}
function read_vars(){
#if no list of variables is provided in the namelist, looks for all variables in the files
OUTPUT_FILE=$1
GRID_TYPE=$2
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VAR_LST_DIM=$(ncdump -h $OUTPUT_FILE | grep float | sed -e s/float//g | sed -e s/\,\ /@/g | sed -e s/\;//g ) #get the names of the variables in output files
for VAR_DIM in $VAR_LST_DIM
do
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NB_DIMS=$(echo $VAR_DIM | sed -e s/[^@]/\ /g | wc -w) #count the number of dimensions of each variable
VAR=$(echo $VAR_DIM | sed -e 's/(.*)//g' )
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[ $NB_DIMS -eq 2 ] && VAR_LST_2D_GG=$(echo ${VAR_LST_2D_GG} $VAR) || VAR_LST_3D_GG=$(echo ${VAR_LST_3D_GG} $VAR) #create a separate list of variables for 2d and 3d
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[ $NB_DIMS -eq 2 ] && VAR_LST_2D_SH=$(echo ${VAR_LST_2D_SH} $VAR) || VAR_LST_3D_SH=$(echo ${VAR_LST_3D_SH} $VAR) #create a separate list of variables for 2d and 3d
;;
esac
done
}
# for surface variables (manipulate GG files)
function surface(){
export YEAR0=${LEAD_LIST[0]}
export MON0=${LEAD_LIST[1]}
export YEARF=${LEAD_LIST[2]}
export MONF=${LEAD_LIST[3]}
MONF=$(echo $(printf "%02d" $(( 10#$MONF))) )
#copy and format the mask
cp ${MASK_PATH} mask.nc
lstdims=`ncdump -h mask.nc | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/longitude} == ${lstdims} ]] && [[ ${lstdims/latitude} == ${lstdims} ]] ; then
ncrename -h -v lon,longitude -v lat,latitude mask.nc
ncrename -h -d lon,longitude -d lat,latitude mask.nc
fi
echo ${MEM_LST[@]}
for MEM in ${MEM_LST[@]}; do
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# FILES=$(ls MMA*GG*.nc.$MEM)
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FILES="$( find . -maxdepth 1 -name "MMA*GG*.nc.$MEM" | sed -e 's/\.\///g' | sort -u )"
nb_months_asked=$(( ( ($YEARF - $YEAR0) * 12 + 10#$MONF - 10#$MON0+1 ) ))
if [[ $NLT -ne $nb_months_asked ]];then
echo "Warning, the number of months in MMA ($nb_files) is different from the number of months you required according to the LEADLIST",$(( ( ($YEARF - $YEAR0) * 12 + 10#$MONF - $MON0+1 )))," check your configfile!"
#### process each variable ####
for VAR in ${VAR_LST_2D[@]}; do # untar once and extract all the variables
new_name $VAR
case $VAR in
"PRECIP") # for precip, have to add CP and LSP to get total precip
varnew=prlr
for f in ${FILES}; do
cdo chname,LSP,$varnew -divc,${FACTOR} -add -selname,LSP $f -selname,CP $f ${varnew}.${SUFFIX}
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# prlr_files=$(ls ${varnew}*)
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prlr_files="$(find . -maxdepth 1 -name "${varnew}*${MEM}*" | sed -e 's/\.\///g' | sort -u )"
cdo -O mergetime ${prlr_files} tmp_${varnew}_$SDATE.$MEM.nc # combine all the time steps in one file
;;
"SSRU")
varnew=rsus
for f in ${FILES}; do
cdo chname,SSR,$varnew -divc,${FACTOR} -sub -selname,SSR $f -selname,SSRD $f ${varnew}.${SUFFIX}
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# rsus_files=$(ls ${varnew}*)
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rsus_files="$(find . -maxdepth 1 -name "${varnew}*${MEM}*" | sed -e 's/\.\///g' | sort -u )"
cdo -O mergetime ${rsus_files} tmp_${varnew}_$SDATE.$MEM.nc # combine all the time steps in one file
;;
"STRU")
varnew=rlus
for f in ${FILES}; do
cdo chvar,STRD,rlus -divc,${FACTOR} -sub -selname,STRD $f -selname,STR $f ${varnew}.${SUFFIX}
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# rsus_files=$(ls ${varnew}*)
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rsus_files="$( find . -maxdepth 1 -name "${varnew}*${MEM}*" | sed -e 's/\.\///g' | sort -u )"
cdo -O mergetime ${rsus_files} tmp_${varnew}_$SDATE.$MEM.nc # combine all the time steps in one file
"SWVL") # for soil moisture, have to average SWVL1 SWVL3 SWVL2 SWVL4
varnew=mrso
for f in ${FILES}; do
fact1=$(echo "scale=8;7/255."|bc)
fact2=$(echo "scale=8;21/255."|bc)
fact3=$(echo "scale=8;72/255."|bc)
fact4=$(echo "scale=8;155/255."|bc)
cdo vertmean -chname,SWVL1,mrso \
-add -add -divc,$fact1 \
-selname,SWVL1 $f\
-divc,$fact2 \
-selname,SWVL2 $f \
-add -divc,$fact3 \
-selname,SWVL3 $f \
-divc,$fact4 \
-selname,SWVL4 $f \
${varnew}_aux.${SUFFIX}
ncwa -h -O -a depth ${varnew}_aux.${SUFFIX} -o ${varnew}.${SUFFIX}
rm -f ${varnew}_aux.${SUFFIX}
mrso_files="$(find . -maxdepth 1 -name "${varnew}*${MEM}*" | sed -e 's/\.\///g' | sort -u )"
cdo -O mergetime ${mrso_files} tmp_${varnew}_$SDATE.$MEM.nc # combine all the time steps in one file
;;
*)
new_name $VAR
for f in ${FILES};do
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echo $f --
cdo selname,${VAR} ${f} ${VAR}.$MEM.${f%.*}
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TMP_FILES="$( find . -maxdepth 1 -name "${VAR}*.nc" | sed -e 's/\.\///g' | sort -u )"
TMP_OUT=tmp_${varnew}_$SDATE.$MEM.nc
# combine all the time steps in one file
cdo -O mergetime ${TMP_FILES} ${TMP_OUT}
[[ ${VAR} != ${varnew} ]] && ncrename -h -v ${VAR},${varnew} ${TMP_OUT}
"prsn|rss"|"rls"|"rsscs"|"rsds"|"rlds"|"hflsd"|"hfssd"|"rlt"|"rst"|"rltcs"|"rstcs")
cdo divc,${FACTOR} ${TMP_OUT} toto.nc; rm -rf ${TMP_OUT}; mv toto.nc ${TMP_OUT}
[[ ${varnew} != "prsn" ]] && ncatted -O -h -a units,${varnew},m,c,"W m-2" ${TMP_OUT}
#mask the continent for tos
if [[ $varnew == tos ]]
then
cdo div ${TMP_OUT} -ltc,0.5 mask.nc ${TMP_OUT}_aux
#replace the fill value
ncatted -O -a _FillValue,$varnew,d,, ${TMP_OUT}_aux
ncatted -O -a missing_value,$varnew,d,, ${TMP_OUT}_aux
cdo setrtoc,-9e34,-2000,1.e+12 ${TMP_OUT}_aux ${TMP_OUT}
rm -rf ${TMP_OUT}_aux
fi
rm -rf ${TMP_FILES}
;;
esac
done # loop for VAR
done # loop for members
echo "after loop on members in surface"
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# finish selecting the variables
# combine members and change the attributes
for VAR in ${VAR_LST_2D[@]}; do
new_name $VAR
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pathout=${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h
pathout=${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h
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mkdir -m ug+w -m o-w -p $pathout
LSMBSH="${LISTMEMB[0]}-${LISTMEMB[${#LISTMEMB[@]}-1]}"
# PREVIOUS_FILE="$(ls -tr ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/${varnew}_${SDATE}_*.nc | tail -1)" (if left like this, we have the "no such file" pb. but if we chose the "find" option, we can sort the files and get hte last one edited => have to make a find to be sure there are some previous_files and then, if so, get the actual previous_file with the ls command.
#savedir
PREVIOUS_FILE="$( find ${pathout} -maxdepth 1 -name "${varnew}_${SDATE}_*.nc" )"
echo okkkk
if [ ! -z $( ls $PREVIOUS_FILE ) ] ; then
PREVIOUS_FILE="$(ls -tr ${pathout}/${varnew}_${SDATE}_*.nc | tail -1)"
cd ${pathout}
FILE_NAME_PREVIOUS="$( find . -maxdepth 1 -name "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"
cd -
IDX_1ST=$(echo ${varnew}_${SDATE}_fc | wc -m )
FIRST_MEMBER_PREVIOUS=$(echo $FILE_NAME_PREVIOUS | cut -b$IDX_1ST )
IDX_LST=$( expr $IDX_1ST + 2 )
LAST_MEMBER_PREVIOUS=$(echo $FILE_NAME_PREVIOUS | cut -b$IDX_LST )
#security check:
if [ $LAST_MEMBER_PREVIOUS -le $(expr ${LISTMEMB[0]} - 1 ) ] ; then
cp $PREVIOUS_FILE tmp_$FILE_NAME_PREVIOUS
if [ $LAST_MEMBER_PREVIOUS -eq $(expr ${LISTMEMB[0]} - 1 ) ] ; then
LSMBSH=${FIRST_MEMBER_PREVIOUS}-${LISTMEMB[${#LISTMEMB[@]}-1]}
else
echo "Actual list of members does not follow directly the ones already post-processed! Check you did not forget any members at the beginning of your list"
MISSING_FIRST=$(expr ${LAST_MEMBER_PREVIOUS} + 1 )
MISSING_LAST=$(expr ${LISTMEMB[0]} - 1 )
LSMBSH=${FIRST_MEMBER_PREVIOUS}_${LISTMEMB[${#LISTMEMB[@]}-1]}-${MISSING_FIRST}_${MISSING_LAST}
fi
else
echo "Some members are going to be treated twice! If you are not adding new lead_times, revise the consistency between your member list and the previously processed files"
fi
echo ok2
fi
echo ok3
pwd
ls
YRSO=${YEAR0}$(printf "%02d" $(( 10#$MON0)))_${YEARF}$(printf "%02d" $(( 10#$MONF)))
gather_memb tmp_${varnew}_$SDATE ${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc $varnew $VAR
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output=${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc
##### Change the header informations #####
#
# Get the CFU standard attributes to be written in the variable
#
variables="$(cat ${HEAD_DIR}/table_of_variable | cut -f$idx -d'|' | sed -e 's/ /@/g')" #to be changed into more interactive with xml table
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 $variables | cut -f9 -d' ' | sed -e 's/@/ /g')" # variable level unit
#
# Adding the variable level
#
# ncap2 -h -O -s level_${varnew}="$cfulevel_number" ${output} ${output}
#
# Removing unnecessary attributes
#
#if [[ $idx -ne 40 ]]; then
for att in units valid_range actual_range code table GRID_TYPE ; do
ncatted -O -h -a ${att},${varnew},d,c, ${output}
done
#
# Adding and modifying the {varnew}iable attributes
#
ncatted -O -h -a _FillValue,${varnew},a,f,1.e+12 ${output}
ncatted -O -h -a standard_name,${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" ${output} # {varnew}iable cell methods
ncatted -O -h -a unit_long,${varnew},o,c,"$cfuunit_long" ${output} # {varnew}iable long unit name
ncatted -O -h -a units,${varnew},o,c,"$cfuunit" ${output} # {varnew}iable units
#fi
# ncatted -O -h -a data_type,level_${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}" ${output} # variable coordinates
ncatted -O -h -a coordinates,${varnew},o,c,"longitude latitude reftime leadtime time_bnd experiment_id source realization institution " ${output} # variable coordinates
#
# If the NetCDF file had a horizontal axis name different from longitude
#
ncrename -h -d lon,longitude -v lon,longitude ${output}
[[ ! -z $( ncdump -h ${output} | grep record ) ]] && ncrename -h -d record,ensemble ${output}
# [[ ! -z $( ncdump -h ${output} | grep ensemble ) ]] && ncrename -h -d record,ensemble ${output}
#
# If the NetCDF file had a vertical axis name different from latitude
#
ncrename -h -d lat,latitude -v lat,latitude ${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
#[[ $idx -ne 40 ]] &&
# ncatted -O -h -a axis,level_${varnew},o,c,"Z" ${output} # variable level axis
# modify level information
# reshape the dimension and make time unlimited
# [[ ! -z $( ncdump -h ${output} | grep record ) ]] && ncpdq -O -h -a time,ensemble ${output} ${output}
[[ ! -z $( ncdump -h ${output} | grep ensemble ) ]] && ncpdq -O -h -a time,ensemble ${output} ${output}
cp ${output} hhh.nc
ncks -h -A header.nc ${output}
#if [[ $idx -ne 40 ]]; then
nt=$(cdo ntime ${output})
# ncatted -O -h -a standard_name,level_${varnew},c,c,"height" ${output} # standard name
# ncatted -O -h -a long_name,level_${varnew},c,c,"reference height" ${output} # long name
# ncatted -O -h -a data_type,level_${varnew},c,c,"float" ${output} # data type
# ncatted -O -h -a units,level_${varnew},c,c,"m" ${output} # units
# ncatted -O -h -a axis,level_${varnew},c,c,"Z" ${output} # axis
# ncatted -O -h -a positive,level_${varnew},c,c,"up" ${output}
# ncap2 -O -h -s "level_${varnew}=float(${cfulevel_number})" $output $output
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#fi
# 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
echo "before modify ncvalue" $output ; ncdump -h $output
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
##
ncrename -O -h -v time,kaka $output # delete time variable
ncks -O -h -x -v kaka $output $output # delete time variable
save_final_output $varnew $output
done # loop for variables
}
function new_name(){ #to be rethought: make a match between var_name and xml table
case $1 in # rename variable names in model output to the standard names which should be used in post-processed files
"T2M")
varnew=tas
idx=1
;;
"D2M")
varnew=d2m
idx=25
;;
"U10M")
varnew=uas
idx=15
;;
"V10M")
varnew=vas
idx=16
;;
"PRECIP")
varnew=prlr
idx=7
;;
"CP")
varnew=prc
idx=26
;;
"SF")
varnew=prsn
idx=27
;;
"E")
varnew=evspsbl
idx=28
;;
"SSTK")
# "SST")
#weird... VAR=SSTK
varnew=tos
idx=10
;;
"MSL")
varnew=psl
idx=2
;;
"SSR")
varnew=rss
idx=5
;;
"SSRU")
varnew=rsus
idx=30
;;
"SSRC")
varnew=rsscs
idx=29
;;
"TSR")
varnew=rst
idx=21
;;
"TSRC")
varnew=rstcs
idx=22
;;
"TTR")
varnew=rlt
idx=23
;;
"TTRC")
varnew=rltcs
idx=24
;;
"STR")
varnew=rls
idx=6
;;
"STRD")
varnew=rlds
idx=31
;;
"STRU")
varnew=rlus
idx=32
;;
"SLHF")
varnew=hflsd
idx=9
;;
"SSHF")
varnew=hfssd
idx=8
;;
"SSRD")
varnew=rsds
idx=20
;;
"T")
varnew=ta
idx=11
;;
"U")
varnew=ua
idx=12
;;
"V")
varnew=va
idx=13
;;
"W")
varnew=wap
idx=34
;;
"CLWC")
varnew=clw
idx=36
;;
"CIWC")
varnew=cli
idx=37
;;
"Z")
varnew=g
idx=14
;;
"Q")
varnew=hus
idx=19
;;
"tasmax")
varnew=tasmax
idx=17
;;
"tasmin")
varnew=tasmin
idx=18
;;
"TCC")
varnew=clt
idx=33
;;
"CC")
varnew=cl
idx=35
;;
#pab!!!! new variables to be added when variable list read directly in outputs, some are missing
"var78")
varnew=tclw
idx=38
;;
"AL")
varnew=al
idx=39
;;
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varnew=$( echo $1 | tr [A-Z] [a-z] )
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function gather_memb() {
# Gather the members in a single netcdf file
# $1 : prefix netcdf file name for all the members
# $2 : output file name
# Created in May 2012 Author : vguemas@ic3.cat
# Adapted for atmospherical outputs January 2013 pierre-antoine.bretonniere@ic3.cat
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# OLD_FILE=$(ls ${1}_* || echo "")
# NEW_FILES=$(ls "${1}".*)
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OLD_FILE="$( find . -maxdepth 1 -name "${1}_*" | sed -e 's/\.\///g' | sort -u )"
NEW_FILES="$( find . -maxdepth 1 -name "${1}.*" | sed -e 's/\.\///g'| sort -u )"
VAR_LOC=$3
VAR_OLD=$4
rm -f tmp_cat.nc tmp_0_${OLD_FILE} tmp_${OLD_FILE}
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if [[ $( echo $NEW_FILES | wc -w ) -gt 1 ]]; then
ncecat ${NEW_FILES} tmp_cat.nc || exit
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ncrename -h -d record,ensemble tmp_cat.nc
ncecat -O -h tmp_cat.nc tmp_cat2.nc
ncpdq -O -h -a ensemble,record tmp_cat2.nc tmp_cat2.nc
ncwa -O -h -a record tmp_cat2.nc tmp_cat2.nc
mv tmp_cat2.nc tmp_cat.nc #new
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else
mv ${NEW_FILES} tmp_cat.nc
fi
for var_check in $VAR_LST_3D_GG
do
if [ $VAR_OLD == $var_check ];then
ncks -O -h -a -v lon,lat,$VAR_LOC tmp_cat.nc tmp_cat.nc
# ncks -O -h -a -v lon,lat,$VAR_LOC tmp_cat2.nc tmp_cat3.nc
# mv tmp_cat3.nc tmp_cat.nc
# else
# mv tmp_cat2.nc tmp_cat.nc
fi
done
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if [ ! -z $OLD_FILE ] ; then
ncks -C -O -v longitude,latitude,$VAR_LOC $OLD_FILE tmp_0_${OLD_FILE}
ncecat -O -h tmp_0_${OLD_FILE} tmp_${OLD_FILE}
ncpdq -O -h -a ensemble,record tmp_${OLD_FILE} tmp_${OLD_FILE}
ncwa -O -h -a record tmp_${OLD_FILE} tmp_${OLD_FILE}
ncrcat tmp_cat.nc tmp_${OLD_FILE} $2
else
mv tmp_cat.nc $2
fi
}
function save_final_output(){
# save final post-processed output (file in *.nc format)
varnew=$1
output=$2
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TARDIR=${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h
[ ! -d $TARDIR ] && mkdir -p $TARDIR
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echo ${TARDIR} -- ${output}
chmod 770 ${output}
mv ${output} ${TARDIR}/${output}
#to make a smooth transition between the 2 versions of nccf_atm_monthly, as R functions look for atmospherical monthly means called $var_yyyymmdd.nc (without the members), a link between the 2 naming conventions is created so that R functions still work while they have not been updated.
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ln -sf ${TARDIR}/${output} ${TARDIR}/${varnew}_${SDATE}.nc
}
# Select variables and levels
function combine_3d(){
for MEM in ${MEM_LST[@]}; do
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# FILES=$(ls MMA*SH*.nc.$MEM)
FILES="$(find . -maxdepth 1 -name "MMA*SH*.nc.$MEM" | sed -e 's/\.\///g' )"
echo $FILES
for f in ${FILES}; do
for var in ${VAR_LST_3D_SH[@]}; do
new_name $var
TMP_OUT=tmp_${varnew}_$f
cdo selname,${var} -sellevel,${LEVEL_LST} ${f} ${TMP_OUT}
done
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# FILES=$(ls MMA*GG*.nc.$MEM)
FILES=$(find . -maxdepth 1 -name "MMA*GG*.nc.$MEM" | sed -e 's/\.\///g' )
for f in ${FILES}; do
for var in ${VAR_LST_3D_GG[@]}; do
new_name $var
TMP_OUT=tmp_${varnew}_$f
case $var in #pab
Q)
cdo selname,${var} -sellevel,${LEVEL_LST} ${f} ${TMP_OUT} #
;;
*)
cdo selname,${var} ${f} ${TMP_OUT} #pab
;;
esac
done
done
# combine all time step in one file
for var in ${VAR_LST_3D[@]}; do
new_name $var
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# FILES=$(ls tmp_${varnew}_*)
FILES="$(find . -maxdepth 1 -name "tmp_${varnew}_*" | sed -e 's/\.\///g' )"
output=${varnew}_$SDATE.$MEM.nc
cdo -O mergetime ${FILES} ${output} # combine all the time steps in one file
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ncrename -h -v ${var},${varnew} ${output}
rm -rf ${FILES}
done #loop for variables
done # loop for members
}
######end of combine3d ##########
# interpolate from SH to regular grid
function regrid2x2(){
for var in ${VAR_LST_3D_SH[@]}; do
new_name $var
FILES=$( find . -maxdepth 1 -name "${varnew}_$SDATE.*.nc" | sed -e 's/\.\///g' )
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cdo -r sp2gpl -selname,${varnew} ${f} rg_${f}; rm -f ${f}
done
done
for var in ${VAR_LST_3D_GG[@]}; do
new_name $var
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# FILES="$(ls ${varnew}_$SDATE.*.nc)"
FILES=$(find . -maxdepth 1 -name "${varnew}_$SDATE.*.nc" | sed -e 's/\.\///g' )
cdo selname,${varnew} ${f} rg_${f}; rm -f ${f}
done
done
}
function upper(){
for var in ${VAR_LST_3D[@]}; do
new_name $var
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echo ${LISTMEMB[0]} -- ${#LISTMEMB[@]} -- ${LISTMEMB[${#LISTMEMB[@]}-1]}
LSMBSH="${LISTMEMB[0]}-${LISTMEMB[${#LISTMEMB[@]}-1]}"
# PREVIOUS_FILE="$(ls ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/${varnew}_${SDATE}_*.nc | tail -1)"
# PREVIOUS_FILE="$( find . -maxdepth 1 -name "${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"
#savedir
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# PREVIOUS_FILE="$( find ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly -maxdepth -name "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"
PREVIOUS_FILE="$( find ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h -maxdepth -name "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"
if [ ! -z $PREVIOUS_FILE ] ; then
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# cd ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/;
cd ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_f${NFRP}h/;
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FILE_NAME_PREVIOUS="$( find . -maxdepth 1 -name "${varnew}_${SDATE}_*.nc" | tail -1 | sed -e 's/\.\///g' )"; cd -
IDX_1ST=$(echo ${varnew}_${SDATE}_ | wc -m )
FIRST_MEMBER_PREVIOUS=$(echo $FILE_NAME_PREVIOUS | cut -b$IDX_1ST )
IDX_LST=$( expr $IDX_1ST + 2 )
LAST_MEMBER_PREVIOUS=$(echo $FILE_NAME_PREVIOUS | cut -b$IDX_LST )
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if [ $LAST_MEMBER_PREVIOUS -le $(expr ${LISTMEMB[0]} - 1 ) ] ; then
cp $PREVIOUS_FILE rg_$FILE_NAME_PREVIOUS
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if [ $LAST_MEMBER_PREVIOUS -eq $(expr ${LISTMEMB[0]} - 1 ) ] ; then
LSMBSH=${FIRST_MEMBER_PREVIOUS}-${LISTMEMB[${#LISTMEMB[@]}-1]}
else
echo "Actual list of members does not follow directly the ones already post-processed! Check you did not forget any members at the beginning of your list"
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MISSING_FIRST=$(expr ${LAST_MEMBER_PREVIOUS} + 1 )
MISSING_LAST=$(expr ${LISTMEMB[0]} - 1 )
LSMBSH=${FIRST_MEMBER_PREVIOUS}_${LISTMEMB[${#LISTMEMB[@]}-1]}-${MISSING_FIRST}_${MISSING_LAST}
fi
else
echo "Some members are going to be treated twice! Revise the consistency between your member list and the previously processed files"
fi
fi
YRSO=${YEAR0}$(printf "%02d" $(( 10#$MON0)))_${YEARF}$(printf "%02d" $((10#$MONF))).nc
[[ 10#${MONF} -le 9 ]] && [[ $( echo $MONF | wc -c) -eq 2 ]] && YRSO=${YEAR0}${MON0}_${YEARF}$(printf "%02d" ${MONF}).nc
gather_memb rg_${varnew}_$SDATE ${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc $varnew $VAR
output=${varnew}_${SDATE}_fc${LSMBSH}_${YRSO}.nc
# gather_memb rg_${varnew}_$SDATE ${varnew}_${SDATE}_${LSMBSH}.nc $varnew $VAR
# output=${varnew}_${SDATE}_${LSMBSH}.nc
rm -f ${FILES}
for CHECK_VAR in $VAR_LST_3D_SH
do
if [ $CHECK_VAR == $var ];then
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ncrename -h -d lon,longitude -d lat,latitude -d lev,level ${output}
ncrename -h -v lon,longitude -v lat,latitude -v lev,level ${output}
fi
done
for CHECK_VAR in $VAR_LST_3D_GG
do
if [ $CHECK_VAR == $var ];then
ncrename -h -d lon,longitude -d lat,latitude ${output}
[[ ! -z $( ncdump -h ${output} | grep "mlev =" ) ]] && ncrename -h -d mlev,level -v mlev,level ${output}
[[ ! -z $( ncdump -h ${output} | grep "lev =" ) ]] && ncrename -h -d lev,level -v lev,level ${output}
if [[ ! -z $( ncdump -h ${output} | grep "depth =" ) ]]; then
ncrename -h -d depth,level ${output}
ncrename -h -v depth,level ${output}
fi
ncrename -h -v lon,longitude -v lat,latitude ${output}
fi
done
#
# Get the CFU standard attributes to be written in the variable
#
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variables="$(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
#
# modify variable attributes
#
for att in units valid_range actual_range code table GRID_TYPE truncation; do
ncatted -O -h -a ${att},${varnew},d,, ${output}
done
#moved when the mask is applied (by Chloe)
ncatted -O -h -a _FillValue,${varnew},a,f,1.e+12 ${output}
ncatted -O -h -a standard_name,${varnew},o,c,"$cfustandard_name" ${output} # variable standard name
ncatted -O -h -a long_name,${varnew},o,c,"$cfulong_name" ${output} # variable long name
ncatted -O -h -a cell_methods,${varnew},o,c,"$cfucell_methods" ${output} # variable cell methods
ncatted -O -h -a unit_long,${varnew},o,c,"$cfuunit_long" ${output} # variable long unit name
ncatted -O -h -a units,${varnew},o,c,"$cfuunit" ${output} # variable units
lstdims=`ncdump -h ${output} | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/lev_2} != ${lstdims} ]] ; then
ncrename -d lev_2,level -v lev_2,level $output
fi
if [[ ${lstdims/depth_2} != ${lstdims} ]] ; then
ncrename -d depth_2,level -v depth_2,level $output
fi
if [[ ${lstdims/depth_3} != ${lstdims} ]] ; then
ncrename -d depth_3,level -v depth_3,level $output
fi
if [[ ${lstdims/depth_4} != ${lstdims} ]] ; then
ncrename -d depth_4,level -v depth_4,level $output
fi
lstdims=`ncdump -h ${output} | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/depth} != ${lstdims} ]] ; then
ncrename -d depth,level -v depth,level $output
fi
lstdims=`ncdump -h ${output} | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/level} == ${lstdims} ]] ; then
ncrename -d lev,level -v lev,level $output
fi
ncatted -O -h -a data_type,level,o,c,"$cfulevel_type" ${output} # variable level type
ncatted -O -h -a units,level,o,c,"$cfulevel_units" ${output} # variable level units
ncatted -O -h -a coordinates,${varnew},o,c,"longitude latitude leadtime reftime time_bnd experiment_id source realization institution level" ${output}
#
# If the NetCDF file had a horizontal axis name different from longitude
#
[[ ! -z $( ncdump -h $output | grep record ) ]] && ncrename -h -d record,ensemble ${output}
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#
# modify logitude attributes
#
lon_min=0
lon_max=359.25
lat_min=-89.4270841760375
lat_max=89.4270841760375 # These valuse shoud be obtaind from the file instead of hardcoded
ncatted -O -h -a axis,longitude,o,c,"X" ${output} # variable longitude axis
ncatted -O -h -a topology,longitude,c,c,"circular" ${output} # variable longitude axis
ncatted -O -h -a modulo,longitude,c,f,"360" ${output} # variable longitude axis
ncatted -O -h -a valid_min,longitude,c,f,"$lon_min" ${output} # variable longitude valid_min
ncatted -O -h -a valid_max,longitude,c,f,"$lon_max" ${output} # variable longitude valid_max
# modify latitude attributes
ncatted -O -h -a axis,latitude,o,c,"Y" ${output} # variable latitude axis
ncatted -O -h -a valid_min,latitude,c,f,"$lat_min" ${output} # variable latitude valid_min
ncatted -O -h -a valid_max,latitude,c,f,"$lat_max" ${output} # variable latitude valin_max
# modify level attributes
ncatted -O -h -a standard_name,level,o,c,"air_pressure" ${output} # standard name
ncatted -O -h -a long_name,level,o,c,"air pressure" ${output} # long name
ncatted -O -h -a data_type,level,o,c,"float" ${output} # data type
ncatted -O -h -a units,level,o,c,"hPa" ${output} # units
ncatted -O -h -a axis,level,o,c,"Z" ${output} # axis
ncatted -O -h -a positive,level,c,c,"up" ${output}
###
# modify the level values, should be hPa instead of Pa
ncap2 -O -h -s "level()=level()/100" ${output} ${output}
lstdims=`ncdump -h ${output} | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/ensemble} == ${lstdims} ]] ; then
ncecat -h ${output} tmp_${output}
rm -f $output
mv tmp_${output} ${output}
ncrename -h -O -d record,ensemble $output $output
fi
ncpdq -O -h -a time,ensemble ${output} ${output} # reshape the dimension and make time unlimited
# ncks -h -A $HEAD_DIR/${SDATE}.nc ${output}
ncks -h -A header.nc ${output}
ncrename -O -h -v time,kaka $output # delete time variable
ncks -O -h -x -v kaka $output $output # delete time variable
ncatted -h -a history,global,d,, $output #delete history
ncatted -h -a institution,global,m,c,"IC3" $output ## change institution name in global attributes
# create a script to change the EXPID, insitutution, ensember, source and realiazation
i=0 # index
for mem in ${LISTMEMB[@]}; do
ncap2 -O -h -s 'experiment_id($i,0:3)="$EXPID";realization($i)=$mem;institution($i,0:$(( ${#INSTITUTION} -1 )))="$INSTITUTION";source($i,0:$(( ${#SOURCE} -1 )))="$SOURCE"' \$1 \$1
cat modify_ncvalue
bash modify_ncvalue $output; rm modify_ncvalue
i=$((i+1))
done
##
# rm -f ${files}*
save_final_output $varnew $output
done # loop over variables
}
# 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
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SDATE1=$(echo ${SDATE}|cut -c1-6)
cdo timmean ${VAR}_${SDATE}_${SDATE1}.nc ${output} ; rm -f ${VAR}_${SDATE}_${SDATE1}.nc
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files="$(find . -maxdepth 1 -name "${VAR}_${SDATE}_*.nc" | sed -e 's/\.\///g' )"
cdo timmean $f toto.nc;rm -f $f
ncrcat -O -h ${output} toto.nc ${output};rm -f toto.nc
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 ${output}
#
# Get the CFU standard attributes to be written in the variable
#
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variables="$(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 $variables | cut -f9 -d' ' | sed -e 's/@/ /g')" # variable level unit
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#
# Adding the variable level
#
ncap2 -s level_${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
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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' ${config_file}
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export WORKDIR
FACTOR=$((NFRP*3600))
ENSEMBLE=${#MEM_LST[@]}
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if [[ $ENSEMBLE -eq 0 ]]; then
MEM_LST=( $( ls ${DATADIR}/${EXPID}/original_files/${SDATE} ) )
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ENSEMBLE=${#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[@]}
mkdir -p ${WORKDIR}
if [[ ! -d ${WORKDIR} ]]; then
exit 1
fi
cd ${WORKDIR}
if [[ ! -d ${DATADIR}/${EXPID} ]]; then
[[ -d /esarchive/exp/ecearth/${EXPID} ]] && DATADIR=/esarchive/exp/ecearth
fi
base_path=${DATADIR}/${EXPID}/original_files/${SDATE}
mkdir -p ${SAVEDIR}/${EXPID}; # chmod -R 775 $SAVEDIR/${EXPID}
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#exit stop
get_leadtime
header $SDATE
extract
echo "after extract"
if [ -z ${VAR_LST_2D[@]} ]; then
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# GG=$(ls *GG* | head -1)
GG="$(find . -maxdepth 1 -name "*GG*" | head -1 | sed -e 's/\.\///g' )"
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# SH=$(ls *SH* | head -1)
SH="$(find . -maxdepth 1 -name "*SH*" | head -1 | sed -e 's/\.\///g' )"
rm -f /scratch/Earth/${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
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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
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[ $var == $var_sh ] && VAR_LST_3D_SH=$(echo $VAR_LST_3D_SH $var)
done
for var_gg in ${VAR_LST_3D_GG_DEFAULT[@]}
do
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[ $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
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[ $var == $var_gg ] && VAR_LST_2D_GG=$(echo $VAR_LST_2D_GG $var)
echo $YEARF - $YEAR0 - $MONF - 10#$MONF - $MON0
echo "before surface"
echo "after surface"
combine_3d
regrid2x2
upper
if [[ ${#VAR_LST_MXMN[@]} > 0 ]]; then
maxmin
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#else
# echo "" #empty line to avoid trap issue
cd ~/; rm -rf $WORKDIR # clean up
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trap - EXIT
#### End of the Main Part of Script ####