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#!/bin/bash
#
# ./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
set -xv
#################################
#### User Defined Funtions ####
#################################
# check if args are ok
function check_args(){
NB_ARGS=$#
if [ $# -ne 1 ] ; then
echo
echo "USAGE: config_file "
echo "For example: ./nccf_atm_monthly.new.sh /home/$user/cfu_git/autosubmit/pp/atmos/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}/${SDATE}/${DIR}/outputs # hard coded
NFILE=`ls MMA*|wc -l`
for TMPFILE in `ls MMA*`
do
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
done
NLT=$((NFILE*NMONTH))
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
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
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
ncap2 -O -h -s "reftime(0)=reftime(1)" header.nc header.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
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
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
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 ${LEAD_LIST[@]} ];then
PATH_TO_SEARCH=${DATADIR}/${EXPID}/${SDATE}/$MEM
FILE_LIST=`find $PATH_TO_SEARCH -type f -iname "MMA*" 2> /dev/null`
else
YEAR0=${LEAD_LIST[0]}
MON0=${LEAD_LIST[1]}
YEARF=${LEAD_LIST[2]}
MONF=${LEAD_LIST[3]}
CHUNK_SIZE=${LEAD_LIST[4]}
YYYY0=`echo $SDATE | cut -b -4`
MM0=`echo $SDATE | cut -b 5-6`
LTIME0=1
LTIMEF=$(( ( ($YEARF - $YEAR0) * 12 + $MONF - $MON0+1 )/$CHUNK_SIZE ))
jt=$LTIME0
while [ $jt -le $((LTIMEF)) ]
do
YEAR1=$(( $YEAR0 +($MON0+($jt-1)*$CHUNK_SIZE-1)/ 12 ))
MON1=$(( ( $MON0 + ( $jt - 1 ) * ($CHUNK_SIZE) ) % 12))
YEAR2=$(( $YEAR1 + ( $MON1 + $CHUNK_SIZE-1 ) / 12 ))
MON2=$(( ( $MON1 + $CHUNK_SIZE-1 ) % 12 ))
if [ $MON1 -eq 0 ];then
MON1=12
YEAR1=`expr $YEAR1 - 1 `
fi
if [ $MON2 -eq 0 ];then
MON2=12
YEAR2=`expr $YEAR2 - 1 `
fi
jt=$(($jt+1))
FILE=` ls ${DATADIR}/${EXPID}/${SDATE}/$MEM/outputs/MMA_${EXPID}_${SDATE}_${MEM}_${YEAR1}$(printf "%02d" $MON1)01-${YEAR2}$(printf "%02d" $MON2)*.tar`
FILE_LIST="$FILE_LIST ${FILE}"
done
fi
echo ${FILE_LIST}
for f in ${FILE_LIST};do
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
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
done
}
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
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
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' `
case $GRID_TYPE in
GG)
[ $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
;;
SH)
[ $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(){
echo ${MEM_LST[@]}
for MEM in ${MEM_LST[@]}; do
FILES=`ls MMA*GG*.nc.$MEM`
nb_months_asked=$(( ( ($YEARF - $YEAR0) * 12 + $MONF - $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 + $MONF - $MON0+1 )))," check your configfile!"
exit
fi
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#### 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 ${FILES}; do
SUFFIX=$MEM.${f%????}
cdo selname,CP $f CP.$SUFFIX # select CP
ncrename -h -v CP,prlr CP.$SUFFIX
cdo selname,LSP $f LSP.$SUFFIX # select LSP
ncrename -h -v LSP,prlr LSP.$SUFFIX
cdo add CP.$SUFFIX LSP.$SUFFIX ${varnew}.${SUFFIX} # add CP and LSP to get total precipitation
cdo divc,${FACTOR} ${varnew}.${SUFFIX} toto.nc;rm ${varnew}.${SUFFIX}; mv toto.nc ${varnew}.${SUFFIX}
done
prlr_files=`ls ${varnew}*`
cdo copy ${prlr_files} tmp_${varnew}_$SDATE.$MEM.nc # combine all the time steps in one file
rm -r prlr*.nc CP* LSP*
;;
"SSRU")
varnew=rsus
for f in ${FILES}; do
SUFFIX=$MEM.${f%????}
cdo selname,SSRD $f SSRD.$SUFFIX
ncrename -h -v SSRD,rsus SSRD.$SUFFIX
cdo selname,SSR $f SSR.$SUFFIX
ncrename -h -v SSR,rsus SSR.$SUFFIX
cdo sub SSR.$SUFFIX SSRD.$SUFFIX ${varnew}.${SUFFIX}
cdo divc,${FACTOR} ${varnew}.${SUFFIX} toto.nc;rm ${varnew}.${SUFFIX}; mv toto.nc ${varnew}.${SUFFIX}
done
rsus_files=`ls ${varnew}*`
cdo copy ${rsus_files} tmp_${varnew}_$SDATE.$MEM.nc # combine all the time steps in one file
rm -r rsus*.nc SSR* SSRD*
;;
"STRU")
varnew=rlus
for f in ${FILES}; do
SUFFIX=$MEM.${f%????}
cdo selname,STRD $f STRD.$SUFFIX
ncrename -h -v STRD,rlus STRD.$SUFFIX
cdo selname,STR $f STR.$SUFFIX
ncrename -h -v STR,rlus STR.$SUFFIX
cdo sub STR.$SUFFIX STRD.$SUFFIX ${varnew}.${SUFFIX}
cdo divc,${FACTOR} ${varnew}.${SUFFIX} toto.nc;rm ${varnew}.${SUFFIX}; mv toto.nc ${varnew}.${SUFFIX}
done
rsus_files=`ls ${varnew}*`
cdo copy ${rsus_files} tmp_${varnew}_$SDATE.$MEM.nc # combine all the time steps in one file
rm -r rlus*.nc STR* STRD*
;;
*)
new_name $VAR
for f in ${FILES};do
cdo selname,${VAR} ${f} ${VAR}.$MEM.${f%????}
done
TMP_FILES=`ls ${VAR}*.nc`
TMP_OUT=tmp_${varnew}_$SDATE.$MEM.nc
cdo copy ${TMP_FILES} ${TMP_OUT} # combine all the time steps in one file
ncrename -v ${VAR},${varnew} ${TMP_OUT}
case ${varnew} in
"rss"|"rls"|"rsscs"|"rsds"|"rlds"|"hflsd"|"hfssd"|"rlt"|"rst"|"rltcs"|"rstcs")
cdo divc,${FACTOR} ${TMP_OUT} toto.nc; rm ${TMP_OUT};mv toto.nc ${TMP_OUT}
ncatted -O -a units,${varnew},m,c,"W m-2" ${TMP_OUT}
;;
esac
rm ${TMP_FILES}
# cdo divc,${FACTOR} ${TMP_OUT} toto.nc; rm ${TMP_OUT};mv toto.nc ${TMP_OUT}
;;
esac
done # loop for VAR
done # loop for members
# finish selecting the variables
# combine members and change the attributes
for VAR in ${VAR_LST_2D[@]}; do
new_name $VAR
LSMBSH=${LISTMEMB[0]}-${LISTMEMB[${#LISTMEMB[@]}-1]}
PREVIOUS_FILE=`ls -tr ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/${varnew}_${SDATE}_*.nc | tail -1`
if [ ! -z $PREVIOUS_FILE ] ; then
cd ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/; FILE_NAME_PREVIOUS=`ls ${varnew}_${SDATE}_*.nc | tail -1 `; cd -
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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 `
#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
fi
gather_memb tmp_${varnew}_$SDATE ${varnew}_${SDATE}_${LSMBSH}.nc $varnew $VAR
output=${varnew}_${SDATE}_${LSMBSH}.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 $variables | cut -f9 -d' ' | sed -e 's/@/ /g'` # variable level unit
#
# Adding the variable level
#
ncap2 -s level_${varnew}="$cfulevel_number" ${output} -h -O ${output}
#
# Removing unnecessary attributes
#
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" ${output} # {varnew}iable units
ncatted -O -h -a data_type,level_${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
#
# If the NetCDF file had a horizontal axis name different from longitude
#
ncrename -h -d lon,longitude -v lon,longitude ${output}
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" ${output} # variable latitude axis
ncatted -O -h -a axis,level_${varnew},o,c,"Z" ${output} # variable level axis
# modify level information
# reshape the dimension and make time unlimited
ncpdq -O -h -a time,ensemble ${output} ${output}
ncks -h -A header.nc ${output}
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
# 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,0:14)="$INSTITUTION";source($i,0:59)="$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
;;
*)
varnew=` echo $1 | tr [A-Z] [a-z] `
idx=000
;;
esac
}
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
OLD_FILE=`ls ${1}_*`
NEW_FILES=`ls ${1}.*`
VAR_LOC=$3
VAR_OLD=$4
rm -f tmp_cat.nc tmp_0_${OLD_FILE} tmp_${OLD_FILE}
ncecat ${NEW_FILES} tmp_cat.nc || exit
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ncrename -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
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
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=$2
TARDIR=${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly
[ ! -d $TARDIR ] && mkdir -p $TARDIR
find ${SAVEDIR}/${EXPID}/monthly_mean/. -type d | xargs chmod 775 2>/dev/null
find ${SAVEDIR}/${EXPID}/monthly_mean/. -type f | xargs chmod 664 2>/dev/null
if [ -e ${TARDIR}/${output} ] ; then
mv ${output} new_${output}
ncpdq -O -h -a ensemble,time new_${output} new_${output} # shape the dimensions
mv ${TARDIR}/${output} old_${output}
ncpdq -O -h -a ensemble,time old_${output} old_${output} # shape the dimensions
ncrcat -O -h old_${output} new_${output} ${output}
ncpdq -O -h -a time,ensemble ${output} ${output} # again reshape the dimensions as per requirement of final output
rm old_${output} new_${output}
fi
chmod 770 ${output}
mv ${output} ${TARDIR}
#for tos, change value on land from 0 to NaN
if [ $varnew == "tos" ]; then
# ln -sf /cfunas/exp/ecearth/land_sea_mask_320x160.nc .
ln -sf ${MASK_PATH} .
cdo div `basename ${MASK_PATH}` `basename ${MASK_PATH}` mask1.nc
# cdo div land_sea_mask_320x160.nc land_sea_mask_320x160.nc mask1.nc
cdo div $output mask1.nc $output.tmp
mv $output.tmp $output
rm mask1.nc `basename ${MASK_PATH}`
fi
#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.
ln -sf ${TARDIR}/${output} ${TARDIR}/${varnew}_${SDATE}.nc
}
# Select variables and levels
function combine_3d(){
for MEM in ${MEM_LST[@]}; do
FILES=`ls MMA*SH*.nc.$MEM`
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
rm ${f}
done
FILES=`ls MMA*GG*.nc.$MEM`
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 $var
FILES=`ls tmp_${varnew}_*`
output=${varnew}_$SDATE.$MEM.nc
cdo copy ${FILES} ${output} # combine all the time steps in one file
ncrename -v ${var},${varnew} ${output}
rm -r ${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=`ls ${varnew}_$SDATE.*.nc`
for f in ${FILES}; do
cdo -r sp2gp -selname,${varnew} ${f} rg_${f}; rm ${f}
done
done
for var in ${VAR_LST_3D_GG[@]}; do
new_name $var
FILES=`ls ${varnew}_$SDATE.*.nc`
for f in ${FILES}; do
cdo selname,${varnew} ${f} rg_${f}; rm ${f}
done
done
}
function upper(){
for var in ${VAR_LST_3D[@]}; do
new_name $var
LSMBSH=${LISTMEMB[0]}-${LISTMEMB[${#LISTMEMB[@]}-1]}
PREVIOUS_FILE=`ls ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/${varnew}_${SDATE}_*.nc | tail -1`
if [ ! -z $PREVIOUS_FILE ] ; then
cd ${SAVEDIR}/${EXPID}/monthly_mean/${varnew}_${NFRP}hourly/; FILE_NAME_PREVIOUS=`ls ${varnew}_${SDATE}_*.nc | tail -1 `; cd -
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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 `
#security check:
if [ $LAST_MEMBER_PREVIOUS -le `expr ${LISTMEMB[0]} - 1 ` ] ; then
cp $PREVIOUS_FILE rg_$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! Revise the consistency between your member list and the previously processed files"
fi
fi
gather_memb rg_${varnew}_$SDATE ${varnew}_${SDATE}_${LSMBSH}.nc $varnew $VAR
output=${varnew}_${SDATE}_${LSMBSH}.nc
rm ${FILES}
for CHECK_VAR in $VAR_LST_3D_SH
do
if [ $CHECK_VAR == $var ];then
ncrename -d lon,longitude -d lat,latitude -d lev,level ${output}
ncrename -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 -d lon,longitude -d lat,latitude -d mlev,level ${output}
# ncrename -v lon,longitude -v lat,latitude -v mlev,level ${output}
ncrename -d lon,longitude -d lat,latitude ${output}
ncrename -d mlev,level ${output}
ncrename -v lon,longitude -v lat,latitude ${output}
ncrename -v mlev,level ${output}
fi
done
#
# 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
#
# modify variable attributes
#
for att in units valid_range actual_range code table GRID_TYPE truncation; do
ncatted -O -h -a ${att},${varnew},d,, ${output}
done
ncatted -O -h -a _FillValue,${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" ${output} # variable units
ncatted -O -h -a data_type,level,o,c,"$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
#
ncrename -d record,ensemble ${output}
#
# 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}
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 ${LISTMEMB[@]}; do
cat>modify_ncvalue<<EOF
ncap2 -O -h -s 'experiment_id($i,0:3)="$EXPID";realization($i)=$mem;institution($i,0:14)="$INSTITUTION";source($i,0:59)="$SOURCE"' \$1 \$1
EOF
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 $VAR
output=${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 ${VAR}_${SDATE}_${SDATE1}.nc
files=`ls ${VAR}_${SDATE}_*.nc`
for f in $files;do
cdo timmean $f toto.nc;rm $f
ncrcat -O -h ${output} toto.nc ${output};rm 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,0:14)="$INSTITUTION";source($i,0:59)="$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}
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. ${config_file}
#check 1st_month and last_month formats
[ $MON0 -lt 10 ] && MON0=`echo $MON0 | cut -b 2 `
[ $MONF -lt 10 ] && MONF=`echo $MONF | cut -b 2 `
FACTOR=$((NFRP*3600))
ENSEMBLE=${#MEM_LST[@]}
#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}
LISTMEMB=(`echo ${MEM_LST[@]} | sed -e 's/fc//g'`) #member list without "fc"
get_leadtime
header $SDATE
extract
if [ -z ${VAR_LST_2D[@]} ]; then
GG=`ls *GG* | head -1`
read_vars $GG GG
SH=`ls *SH* | head -1`
read_vars $SH SH
rm /scratch/${USER}/pp/VAR_LST_2D.txt
VAR_LST_2D=`echo ${VAR_LST_2D_GG} ${VAR_LST_2D_SH}`
echo $VAR_LST_2D >> /scratch/${USER}/pp/VAR_LST_2D.txt
rm /scratch/${USER}/pp/VAR_LST_3D.txt
VAR_LST_3D=`echo ${VAR_LST_3D_GG} ${VAR_LST_3D_SH}`
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
surface