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###############################################################################
# This file gathers a set of bash functions that rely on cdftools to #
# compute various ocean diagnostics : #
# #
# reduce_mmo #
# get_nemovar #
# get_diagsMMO #
# clean_diagsMMO #
# vertmeansal #
# heat_sal_mxl #
# cutsection #
# moc #
# psi #
# area_moc #
# max_moc #
# siasiesiv #
# ohc #
# interp3d #
# setminmax #
# concat #
# gather_memb #
# ohc_specified_layer #
# #
# Those functions would never have seen the day without Hui Du, #
# usually referred to as Super-Hui. #
# #
# He made a crucial work to develop what ended up below in the functions #
# that computes the sea ice extent, sea ice area, ocean heat content and #
# meridional overturning streamfunction. #
# Especially, he developped new options from the cdftools sources to be #
# able to compute the heat content in different basins. #
# #
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
# You want to make available a new diagnostic ? @
# @
# 1) Get an MMO tar files from any experiment on cfunas @
# 2) Write a bash function that works on a grid_T or grid_U or grid_V or @
# grid_W file or a combination from this MMO file @
# --> You can test your function by defining the CON_FILES and NEMOVERSION @
# variables and by sourcing the current file, the meshmasks will be @
# available after sourcing, remember to source again after any @
# modification of your function @
# --> Your function should work on input files of any resolution @
# ORCA1/ORCA025/ORCA2 @
# --> Your function should work on input files of any time length @
# --> The output file should contain a proper time axis that you can copy @
# from your input file @
# --> The output file should be at most a 3d field including the time @
# dimension @
# 3) Write a short description of your function, and add its name to the @
# list above @
# 4) Go the the ocean_pp.sh script to add a call to your function @
# @
# Any doubt ---> vguemas@ic3.cat @
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
# Link constant file for co #
###############################################################################
ln -sf ${CON_FILES}/mesh_mask_nemo.${NEMOVERSION}.nc mesh_hgr.nc
ln -sf ${CON_FILES}/mesh_mask_nemo.${NEMOVERSION}.nc mesh_zgr.nc
ln -sf ${CON_FILES}/mesh_mask_nemo.${NEMOVERSION}.nc mask.nc
ln -sf ${CON_FILES}/new_maskglo.${NEMOVERSION}.nc new_maskglo.nc
###############################################################################
# Reduced number of variables in diag files to save disk space #
# #
# $1 : input grid_T file name #
# $2 : input icemod file name #
# $3 : suffix of output files with nc extension #
# #
# Created in February 2012 Author : vguemas@ic3.cat #
###############################################################################
function reduce_mmo {
ncks -O -v sosstsst,sosaline,somixhgt,somxl010 $1 sstsssmld_${3}
typeset var lstvars=`cdo showvar $2`
if [[ ${lstvars/ileadfra} != ${lstvars} ]] ; then
ncks -O -v isnowthi,iicethic,ileadfra,iicetemp $2 ice_${3}
else
ncks -O -v isnowthi,iicethic,iiceconc,iicetemp $2 ice_${3}
fi
ncks -O -v votemper $1 t3d_${3}
}
###############################################################################
# Copy diags or MMO files from cfunas #
# #
# $1 : starting date #
# $2 : expid #
# $3 : member #
# $4 : starting leadtime #
# $5 : end leadtime #
# $6 : chunk length in month #
# $7 : nemo/ecearth #
# $8 : diags/MMO #
# $9 : storage frequency (daily/monthly) #
# #
# Created in May 2012 Author : vguemas@ic3.cat #
###############################################################################
function get_diagsMMO {
typeset var yyyy0=`echo $1|cut -c1-4`
typeset var mm0=`echo $1|cut -c5-6`
typeset var jt
typeset var year1
typeset var year2
typeset var mon1
typeset var mon2
for jt in $(seq $4 $6 $5) ; do
year1=$(($yyyy0+(10#$mm0+$jt-2)/12))
mon1=$(((10#$mm0+$jt-2)%12+1))
year2=$(($yyyy0+(10#$mm0+$jt+$6-3)/12))
mon2=$(((10#$mm0+$jt+$6-3)%12+1))
cp /cfunas/exp/$7/$2/$1/fc$3/outputs/$8_$2_$1_fc$3_${year1}$(printf "%02d" $mon1)01-${year2}$(printf "%02d" $mon2)*.tar .
tar -xvf $8_$2_$1_fc$3_${year1}$(printf "%02d" $mon1)01-${year2}$(printf "%02d" $mon2)*.tar
rm -f $8_$2_$1_fc$3_${year1}$(printf "%02d" $mon1)01-${year2}$(printf "%02d" $mon2)*.tar
if [[ `ls *.gz` != '' ]] ; then gunzip *.gz ; fi
done
typeset var listroots
case $8 in
'diags' ) if [[ $6 -lt 12 || $5 -gt 12 ]] ; then listroots="t3d heat_sal_mxl ice moc psi sal_0-300m sal_300-5400m sstsssmld" ; fi ;;
'MMO' ) listroots="grid_T grid_U grid_V grid_W icemod" ;;
esac
case $9 in
'daily') freqexcl1='1m' ; freqexcl2='MM' ;;
'monthly' ) freqexcl1='1d' ; freqexcl2='DD' ;;
*) freqexcl1='1d' ; freqexcl2='DD' ;;
esac
typeset var root
typeset var lstfiles
for root in ${listroots[@]} ; do
lstfiles=`ls *${root}* | grep -v "${root}_$2_$1_fc*_$(($yyyy0+(10#$mm0+$4-2)/12))$(printf "%02d" $(((10#$mm0+$4-2)%12+1)))_${year2}$(printf "%02d" $mon2).nc" | grep -v "${freqexcl1}" | grep -v "${freqexcl2}" `
if [[ $root == 'grid_T' || $root == 't3d' ]] ; then
for file in $lstfiles ; do
ncatted -O -a valid_max,votemper,d,, $file $file
ncatted -O -a valid_min,votemper,d,, $file $file
done
fi
file1=`echo "${lstfiles}" | tail -1`
typeset var lstvars=`cdo showvar $file1`
if [[ ${lstvars/iicenflx} != ${lstvars} ]] ; then for file in $lstfiles ; do ncks -O -x -v iicenflx $file $file ; done ; fi
cdo mergetime $lstfiles ${root}_$2_$1_fc$3_$(($yyyy0+(10#$mm0+$4-2)/12))$(printf "%02d" $(((10#$mm0+$4-2)%12+1)))_${year2}$(printf "%02d" $mon2).nc
if [[ $root == 'moc' ]] ; then
ncrename -d gsize,y ${root}_$2_$1_fc$3_$(($yyyy0+(10#$mm0+$4-2)/12))$(printf "%02d" $(((10#$mm0+$4-2)%12+1)))_${year2}$(printf "%02d" $mon2).nc
ncks -A -v nav_lon,nav_lat `echo $lstfiles | awk '{print $1}' ` ${root}_$2_$1_fc$3_$(($yyyy0+(10#$mm0+$4-2)/12))$(printf "%02d" $(((10#$mm0+$4-2)%12+1)))_${year2}$(printf "%02d" $mon2).nc
fi
rm -f $lstfiles *${freqexcl1}* *${freqexcl2}*
done
}
###############################################################################
# Copy NEMOVAR files from cfunas #
# #
# $1 : expid #
# $2 : member #
# $3 : start year #
# $4 : end year #
# $5 : start month #
# $6 : end month #
# #
# Created in May 2012 Author : vguemas@ic3.cat #
###############################################################################
function get_nemovar {
if [ -z "$5" ] ; then
typeset var moni=9
else
typeset var moni=$5
fi
if [ -z "$5" ] ; then
typeset var monf=8
else
typeset var monf=$6
fi
typeset var path
typeset var yearf
case $1 in
'nemovar_s4') path=/cfunas/exp/ECMWF/NEMOVAR_S4/outputs/fc$2/s4 ;;
'nemovar_combine') path=/cfunas/exp/ECMWF/NEMOVAR_COMBINE/outputs/opa0/fa9p_1m ;;
esac
typeset var year
typeset var mon
for year in $(seq $3 $4) ; do
case $year in
$3) mona=${moni} ;;
*) mona=1 ;;
esac
case $year in
$4) monb=${monf} ;;
*) monb=12 ;;
esac
for mon in $(seq $mona $monb); do
cp ${path}_fc$2_${year}$(printf "%02d" $mon)*.gz .
done
done
gunzip *.gz
typeset var listroots="grid_T grid_U grid_V grid_W"
typeset var root
typeset var lstfiles
typeset var ntimes
typeset var jt
for root in ${listroots[@]} ; do
lstfiles=`ls *fc${2}*${root}* | grep -v "${root}_$1_195709_fc$2_${3}09_${4}$(printf "%02d" $monb).nc"`
ncrcat -O -x -v vorbiasp $lstfiles tmp_${root}.nc
cdo settaxis,${3}-$(printf "%02d" $moni)-15,12:00,1mon tmp_${root}.nc ${root}_$1_19570901_fc$2_${3}$(printf "%02d" $moni)_${4}$(printf "%02d" $monf).nc
rm -f $lstfiles tmp_${root}.nc
done
}
###############################################################################
# Clean diags or MMO files after postprocessing #
# #
# $1 : starting date #
# $2 : expid #
# $3 : member #
# $4 : starting leadtime #
# $5 : end leadtime #
# $6 : diags/MMO #
# #
# Created in May 2012 Author : vguemas@ic3.cat #
###############################################################################
function clean_diagsMMO {
typeset var yyyy0=`echo $1|cut -c1-4`
typeset var mm0=`echo $1|cut -c5-6`
typeset var year1=$(($yyyy0+(10#$mm0+$4-2)/12))
typeset var year2=$(($yyyy0+(10#$mm0+$5-2)/12))
typeset var mon1=$(((10#$mm0+$4-2)%12+1))
typeset var mon2=$(((10#$mm0+$5-2)%12+1))
typeset var listroots
case $6 in
'diags' ) listroots="t3d" ;;
'MMO' ) listroots="grid_T grid_U grid_V grid_W icemod" ;;
esac
typeset var root
typeset var lstfiles
for root in ${listroots[@]} ; do
rm -f ${root}_$2_$1_fc$3_${year1}$(printf "%02d" $mon1)_${year2}$(printf "%02d" $mon2).nc
done
}
###############################################################################
# Vertically averaged salt content #
# #
# $1 : input grid_T file name #
# $2 : upper depth of the layer (in meters) #
# $3 : lower depth of the layer (in meters) #
# $4 : output file name #
# #
# Created in February 2012 Author : vguemas@ic3.cat #
###############################################################################
function vertmeansal {
typeset var ntime=`cdo ntime $1`
typeset var list=""
typeset var jt
for jt in $(seq 1 $ntime); do
cdo seltimestep,$jt $1 intvertmeansal.nc
cdfvertmean intvertmeansal.nc vosaline T $2 $3
ncrename -O -v sovertmean,vertmeansal -d time_counter,time -v time_counter,time vertmean.nc
mv vertmean.nc outputvertmeansal_$jt.nc
list=$list" "outputvertmeansal_$jt.nc
rm -f intvertmeansal.nc
done
cdo cat $list $4
ncks -A -v time $1 $4
rm -f $list
setminmax $4 vertmeansal
}
###############################################################################
# Compute mixed layer heat and salt content #
# #
# $1 : input grid_T file name #
# $2 : output file name #
# #
# Created in February 2012 Author : vguemas@ic3.cat #
################################################################################
function heat_sal_mxl {
typeset var ntime=`cdo ntime $1`
typeset var list=""
typeset var jt
typeset var lstvars=`cdo showvar $1`
for jt in $(seq 1 $ntime); do
cdo seltimestep,$jt $1 intheat_sal_mxl.nc
if [[ ${lstvars/somxl010} == ${lstvars} ]] ; then
cdfmxl intheat_sal_mxl.nc mxl.nc
ncrename -d time_counter,time mxl.nc
ncks -A mxl.nc intheat_sal_mxl.nc
rm -f mxl.nc
fi
cdfmxlheatc intheat_sal_mxl.nc
if [[ $lstvars != ${lstvars/vosaline} ]] ; then
cdfmxlsaltc intheat_sal_mxl.nc
ncks -A mxlsaltc.nc mxlheatc.nc
rm -f mxlsaltc.nc
fi
mv mxlheatc.nc outputintheat_sal_mxl_$jt.nc
list=$list" "outputintheat_sal_mxl_$jt.nc
rm -f intheat_sal_mxl.nc
done
cdo cat $list $2
ncks -A -v time $1 $2
rm -f $list
setminmax $2 somxlheatc
if [[ $lstvars != ${lstvars/vosaline} ]] ; then setminmax $2 somxlsaltc ; fi
}
###############################################################################
# Pointwise Ocean Heat Content in a specified ocean thickness #
# (J/m-2)
# #
# $1 : input grid_T file name #
# $2 : upper depth of the layer (in meters) #
# $3 : lower depth of the layer (in meters) #
# $4 : output file name #
# #
# Created in June 2012 Author : isabel.andreu-burillo@ic3.cat #
###############################################################################
function ohc_specified_layer {
typeset var ntime=`cdo ntime $1`
typeset var list=""
typeset var jt
ncap2 -v -O -s "heatc_sl=tmask*e3t" mesh_zgr.nc e3t_file.nc
ncrename -d t,time -d z,deptht e3t_file.nc
for jt in $(seq 1 $ntime); do
cdo seltimestep,$jt $1 intohc_slayer.nc
ncks -O -v votemper intohc_slayer.nc intmeantem.nc
ncrename -v votemper,heatc_sl intmeantem.nc #to be commented
cdo mul intmeantem.nc e3t_file.nc heatc_sl_out.nc
#? ncks -A -m -v nav_lon,nav_lat $1 heatc_sl_out.nc
# extract the data between the two given depths --> heatc_sl_top.nc
ncks -d deptht,$2,$3 heatc_sl_out.nc heatc_sl_top.nc
#perform the integration of ohc down to that level (main contribution)
ncap2 -O -s 'heatc_sl=heatc_sl.total($deptht)' heatc_sl_top.nc heatc_sl_top.nc
# now extract a few levels below, to compute the residual ohc
lower_bnd=`echo "$3 + 200.0" | bc`
ncks -d deptht,$3,$lower_bnd heatc_sl_out.nc heatc_sl_bottom.nc
# obtain the weight for the extra level containing the 300 m
# deptht in the gridT files is positive
# weight = (300.0 - depth_top)/(depth_bottom - depth_top)
# and add the thickness down to 300 m in the next layer
ncpdq -a '-deptht' heatc_sl_top.nc heatc_sl_top_invert.nc
ncks -d deptht,0,0,1 heatc_sl_top_invert.nc level_above.nc
ncks -d deptht,0,0,1 heatc_sl_bottom.nc level_below.nc
## Here, add the residual contribution, before adding it to the main contribution
ncrename -v deptht,layerthcknss level_below.nc
ncrename -v deptht,layerthcknss level_above.nc
ncbo -A --op_typ=sub -v layerthcknss level_below.nc level_above.nc depth_diff_lay.nc
ncrename -v layerthcknss,heatc_sl depth_diff_lay.nc
ncap2 -s "heatc_sl=($3 - layerthcknss)" level_above.nc depth_diff_sublay.nc
ncbo --op_typ=/ -v heatc_sl depth_diff_sublay.nc depth_diff_lay.nc factor.nc
ncrename -v heatc_sl,factor factor.nc #to be commented
ncks -A -v factor factor.nc level_below.nc
rm -f depth_diff_sublay.nc depth_diff_lay.nc
ncap2 -O -s "heatc_sl=(factor * heatc_sl)" level_below.nc level_below.nc
ncwa -O -a deptht level_below.nc level_below.nc
ncbo --op_typ=+ -v heatc_sl heatc_sl_top.nc level_below.nc total_heatc_sl.nc
ncap2 -s "heatc_sl=1020.0*4000*heatc_sl" total_heatc_sl.nc heatc_sl_$jt.nc
list=$list" "heatc_sl_$jt.nc
rm -f depth_diff_lay.nc depth_diff_sublay.nc
rm -f heatc_sl_out.nc heatc_sl_top.nc heatc_sl_top_invert.nc heatc_sl_bottom.nc
rm -f level_above.nc level_below.nc
rm -f intohc_slayer.nc intmeantem.nc vertmean.nc total_heatc_sl.nc
rm -f factor.nc
done
cdo cat $list $4
ncks -A -v time $1 $4
rm -f $list
rm -f e3t_file.nc
setminmax $4 heatc_sl
}
###############################################################################
# Compute the MOC for oceanic basins #
# #
# $1 : input grid_V file name #
# $2 : output file name #
# #
# Created in March 2012 Author : vguemas@ic3.cat #
###############################################################################
function moc {
typeset var ntime=`cdo ntime $1`
typeset var list=""
typeset var jt
for jt in $(seq 1 $ntime); do
cdo seltimestep,$jt $1 intmoc.nc
cdfmoc intmoc.nc
ncwa -O -a x moc.nc outmoc_$jt.nc
list=$list" "outmoc_$jt.nc
rm -f intmoc.nc moc.nc
done
cdo cat $list $2
lstdims=`ncdump -h $2 | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/gsize} != ${lstdims} ]] ; then
ncrename -d gsize,y $2
fi
ncks -A -v nav_lon,nav_lat outmoc_1.nc $2
ncks -A -v time $1 $2
rm -f $list
}
###############################################################################
# #
# Compute the barotropic stream function #
# #
# $1 : input grid_U file name #
# $2 : input grid_V file name #
# $3 : output file name without nc extension #
# #
# Created in March 2012 Author : vguemas@ic3.cat #
################################################################################
function psi {
typeset var ntime=`cdo ntime $1`
typeset var list=""
typeset var jt
for jt in $(seq 1 $ntime); do
cdo seltimestep,$jt $1 intU.nc
cdo seltimestep,$jt $2 intV.nc
cdfpsi intU.nc intV.nc
mv psi.nc psi_U.nc
cdfpsi intU.nc intV.nc V
mv psi.nc psi_V.nc
ncea psi_U.nc psi_V.nc psi_${jt}.nc
list=$list" "psi_$jt.nc
rm -f intU.nc intV.nc psi_U.nc psi_V.nc
done
cdo cat $list ${3}
ncks -A -v time $1 ${3}
rm -f $list
}
###############################################################################
# #
# Compute an Atlantic MOC index by averaging the meridional overturning #
# in a latitude band between 1km and 2km #
# or any other index averaging the meridional overturning in #
# a given basin and a given domain #
# #
# $1 : input moc file name #
# $2 : latitude min #
# $3 : latitude max #
# $4 : output file name #
# $5 : depth min (default : 1km) #
# $6 : depth max (default : 2km) #
# $7 : basin (default : zomsfatl) #
# #
# Created in March 2012 Author : vguemas@ic3.cat #
###############################################################################
function area_moc {
if [ -z "$5" ] ; then
typeset var depmin=-1000.0
else
typeset var depmin=-$5
fi
if [ -z "$6" ] ; then
typeset var depmax=-2000.0
else
typeset var depmax=-$6
fi
if [ -z "$7" ] ; then
typeset var basin=zomsfatl
else
typeset var basin=$7
fi
ncrename -O -d y,lat -v nav_lat,lat $1 tmpmoc.nc
ncks -O -v $basin,time,depthw,lat tmpmoc.nc tmpmoc.nc
ncks -d lat,$2,$3 -d depthw,${depmax},${depmin} tmpmoc.nc area_moc.nc
cdo vertmean area_moc.nc area_ave_moc.nc
ncap -O -s "coslat[lat]=cos(lat[lat]*3.141592657/180.0)" area_ave_moc.nc area_ave_moc2.nc
ncwa -w coslat -a lat area_ave_moc2.nc area_ave_moc3.nc
ncks -O -v $basin,time area_ave_moc3.nc $4
rm -f tmpmoc.nc area_moc.nc area_ave_moc2.nc area_ave_moc3.nc
if [[ $4 != area_ave_moc.nc ]] ; then
rm -f area_ave_moc.nc
fi
}
###############################################################################
# #
# Compute an Atlantic MOC index by finding the maximum of the annual #
# mean meridional overturning in a latitude / depth region #
# #
# $1 : input moc file name #
# $2 : latitude min #
# $3 : latitude max #
# $4 : depth mean #
# $5 : depth max #
# $6 : output file name #
# #
# Created in March 2012 Author : vguemas@ic3.cat #
###############################################################################
function max_moc {
if [ ! -f $6 ] ; then
ncecat -h $1 tmpmoc1.nc
ncrename -d record,x tmpmoc1.nc
ncpdq -O -h -a time,x tmpmoc1.nc tmpmoc1.nc
ncpdq -O -h -a depthw,x tmpmoc1.nc tmpmoc1.nc
ncpdq -O -h -a y,x tmpmoc1.nc tmpmoc1.nc
cdo yearmean tmpmoc1.nc tmpmoc.nc
typeset var ntime=`cdo ntime tmpmoc.nc`
typeset var list=""
for jt in $(seq 1 $ntime) ; do
cdo seltimestep,$jt tmpmoc.nc tmpmoc2.nc
cdfmaxmoc tmpmoc2.nc atl $2 $3 $4 $5
mv maxmoc.nc maxmoc_$jt.nc
list=${list}" "maxmoc_$jt.nc
rm -f tmpmoc2.nc
done
cdo cat $list $6
ncks -A -v time tmpmoc.nc $6
rm -f $list tmpmoc.nc tmpmoc1.nc
fi
}
###############################################################################
# #
# Compute the sia extent, area and volume in both hemispheres #
# #
# $1 : input ice file name #
# $2 : output file name #
# #
# Created in April 2012 Author : vguemas@ic3.cat #
###############################################################################
function siasiesiv {
cp ${CON_FILES}/ice_template.nc toto_N.nc
cp ${CON_FILES}/ice_template.nc toto_S.nc
case ${NEMOVERSION} in
#'Ec3.0_O1L46'|'Ec3.0_O25L46') ncrename -v ice_pres,ileadfra $1 ;;
'Ec3.0_O1L46'|'Ec3.0_O25L46') ncrename -v iiceconc,ileadfra $1 ;;
esac
typeset var ntime=`cdo ntime $1`
typeset var list1=""
typeset var list2=""
typeset var jt
for jt in $(seq 1 $ntime) ; do
cdo seltimestep,$jt $1 tmpice.nc
cdficediags tmpice.nc>ice.txt
for d in N S;do
ncdump toto_${d}.nc > ice_template.cdl
sia=`grep ${d}Area ice.txt |awk '{print $4}'`
sie=`grep ${d}Extend ice.txt|awk '{print $4}'`
siv=`grep ${d}Volume ice.txt|awk '{print $4}'`
sed -e "s/sia =.*/sia = $sia ;/" ice_template.cdl > ice_template2.cdl
sed -e "s/sie =.*/sie = $sie ;/" ice_template2.cdl > ice_template3.cdl
sed -e "s/siv =.*/siv = $siv ;/" ice_template3.cdl > ice_template.cdl
ncgen -o ice_${d}_${jt}.nc ice_template.cdl
rm -f ice_template.cdl ice_template2.cdl ice_template3.cdl
done
list1=$list1" "ice_N_${jt}.nc
list2=$list2" "ice_S_${jt}.nc
rm -f ice.txt tmpice.nc icediags.nc
done
cdo cat $list1 ice_N_${2}
cdo cat $list2 ice_S_${2}
ncks -A -v time $1 ice_N_${2}
ncks -A -v time $1 ice_S_${2}
rm -f $list1 $list2 toto_N.nc toto_S.nc
setminmax ice_N_${2} sia sie siv
setminmax ice_S_${2} sia sie siv
}
###############################################################################
# #
# Compute the total ocean heat extent #
# #
# $1 : input temperature file name #
# $2 : output file name #
# $3 : basin (NAtl, NPac, TAtl, TPac, TInd, Anta, Arct, Glob) Default : Glob #
# $4 = 0 if $3 = Glob #
# $4 : mixed layer (1=only, 0=included, -1=without) Default : 0 #
# $5 : upper level of the layer (optional) Default : top #
# $6 : lower level of the layer (optional) Default : bottom #
# #
# Created in May 2012 Author : vguemas@ic3.cat #
###############################################################################
function ohc {
cp ${CON_FILES}/depth.${NEMOVERSION}.txt depth.txt
#
# Input arguments
#
if [ -z "$3" ] ; then
typeset var basin='Glob'
else
typeset var basin=$3
fi
if [ -z "$4" ] ; then
typeset var mxl=0
else
typeset var mxl=$4
fi
if [ -z "$5" ] ; then
typeset var up=1
else
typeset var up=$5
fi
if [ -z "$6" ] ; then
typeset var down=`cat depth.txt | wc -l`
else
typeset var down=$6
fi
if [[ ${up} -eq 1 ]] ; then
typeset var depmin=0
else
typeset var depmin=`cat depth.txt |head -${up} |tail -1 | awk '{print $2}' | awk '{printf "%.0f",$1}'`
fi
typeset var depmax=`cat depth.txt |head -${down} |tail -1 | awk '{print $2}' | awk '{printf "%.0f",$1}'`
cp ${CON_FILES}/heatc_template.nc template_heatc.nc
ncdump template_heatc.nc > template_heatc.cdl
#exec=/home/huidu/download/CDFTOOLS_2.1/cdfheatc-cfu
exec=/home/vguemas/CDFTOOLS_2.1/cdfheatc-cfu
#
# Define some parameters
#
typeset var para
typeset var output
typeset var nlev=`cat depth.txt | wc -l`
if [[ ! -z "$depmin" && ! -z "$depmax" ]] ; then
if [[ $depmin != 0 || ${down} != ${nlev} && ${down} != 0 ]] ; then
output=${depmin}-${depmax}'_'
fi
fi
case $basin in
'NAtl') para="atl $mxl 0 0 10 65"; output='NAtl_10N65N_'${output} ;;
'TAtl') para="atl $mxl 0 0 -30 30" ; output='TAtl_30S30N_'${output} ;;
'NPac') para="pac $mxl 0 0 10 70" ; output='NPac_10N70N_'${output} ;;
'TPac') para="pac $mxl 0 0 -30 30" ; output='TPac_30S30N_'${output} ;;
'Arct') para="atl $mxl 0 0 65 90" ; output='Arc_65N90N_'${output} ;;
'Anta') para="all $mxl 0 0 -90 -60" ; output='Ant_90S60S_'${output} ;;
'TInd') para="ind $mxl 0 0 -30 30" ; output='TInd_30S30N_'${output} ;;
'Glob') para="all $mxl 0 0 0 0" ;;
esac
case $mxl in
1) output='mxl_'${output} ;;
-1) output='nonmxl_'${output} ;;
esac
#
# Compute ohc
#
typeset var lstvars=`cdo showvar $1`
typeset var ntime=`cdo ntime $1`
typeset var list=""
typeset var jt
for jt in $(seq 1 $ntime) ; do
cdo seltimestep,$jt $1 tmpohc.nc
if [[ ${lstvars/somxl010} != ${lstvars} ]] ; then
ncks -v somxl010 tmpohc.nc mxl.nc
else
cdfmxl tmpohc.nc mxl.nc
fi
$exec tmpohc.nc $para $up $down > tmp.log
cat tmp.log
thc=`cat tmp.log | grep "Total Heat content :" | awk '{print $5}'`;
uhc=`cat tmp.log | grep "Total Heat content/volume" | awk '{print $5}'`;
sed -e "s/thc =.*/thc = $thc ;/" template_heatc.cdl > template_heatc2.cdl
sed -e "s/uhc =.*/uhc = $uhc ;/" template_heatc2.cdl > template_heatc.cdl
ncgen -o heatc_${jt}.nc template_heatc.cdl
rm -f template_heatc2.cdl tmpohc.nc mxl.nc tmp.log
list=$list" "heatc_${jt}.nc
done
cdo cat $list ${output}$2
ncks -h -A -v time $1 ${output}$2
rm -f $list template_heatc.nc template_heatc.cdl depth.txt
setminmax ${output}$2 thc uhc
}
###############################################################################
# #
# Cut a meridional or zonal section #
# #
# #
# $1 : input file #
# $2 : input var #
# $3 : Z/M (zonal / meridional section) #
# $4 : lat/lon #
# $5 : output file #
# #
# Created in September 2012 Author : vguemas@ic3.cat #
# #
###############################################################################
function cutsection {
typeset var ntime=`cdo ntime $1`
typeset var nx=`ncdump -h $1|grep 'x = '|head -1|cut -f3 -d" "`
typeset var ny=`ncdump -h $1|grep 'y = '|head -1|cut -f3 -d" "`
typeset var nz=`ncdump -h $1|grep 'depth'|head -1|cut -f3 -d" "`
cat>section.R<<EOF1
library(ncdf)
# Get latitudes, longitudes, depth, mask
fncm=open.ncdf('mesh_hgr.nc')
lon=get.var.ncdf(fncm,'nav_lon')
lat=get.var.ncdf(fncm,'nav_lat')
close.ncdf(fncm)
fncm=open.ncdf('mesh_zgr.nc')
depth=get.var.ncdf(fncm,'nav_lev')
close.ncdf(fncm)
fncm=open.ncdf('mask.nc')
mask=get.var.ncdf(fncm,switch('$2','vozocrtx'='umask','vomecrty'='vmask','tmask'))
close.ncdf(fncm)
# Latitude / longitude of the zonal / meridional section
exactpos=$4
if ('$3'=='M') {
while (exactpos<min(lon)) {exactpos=exactpos+360}
while (exactpos>max(lon)) {exactpos=exactpos-360}
}
# Collect the indexes defining the section
listi=array(dim=switch('$3','Z'=$nx-2,'M'=$ny-1))
listj=array(dim=switch('$3','Z'=$nx-2,'M'=$ny-1))
for (jpt in 1:length(listi)) {
vect=switch('$3','Z'=lat[jpt,],'M'=lon[,jpt+1])
if (min(abs(vect-exactpos))<(2*360./$nx)) {
pos=sort(abs(vect-exactpos),index.return=T)\$ix[1]
listi[jpt]=switch('$3','Z'=jpt+1,'M'=pos)
listj[jpt]=switch('$3','Z'=pos,'M'=jpt)
}
}
listi=listi[is.na(listi)==F]
listj=listj[is.na(listj)==F]
print(listi)
print(listj)
# Select variable at those indexes
fnc1=open.ncdf('$1')
varout=array(dim=c(length(listi),$nz,$ntime))
for (jt in 1:$ntime) {
varin=get.var.ncdf(fnc1,'$2',start=c(1,1,1,jt),count=c($nx,$ny,$nz,1))
varin[which(mask<0.5)]=1e20
for (jpt in 1:length(listi)) {
varout[jpt,,jt]=varin[listi[jpt],listj[jpt],]
}
}
close.ncdf(fnc1)
# Write the output
wtime=dim.def.ncdf("time","",seq(1,$ntime),unlim=TRUE)
dimout=array(dim=length(listi))
for (jpt in 1:length(listi)) {
dimout[jpt]=switch('$3','Z'=lon[listi[jpt],listj[jpt]],'M'=lat[listi[jpt],listj[jpt]])
}
wsec=switch('$3','Z'=dim.def.ncdf("lon","",dimout),'M'=dim.def.ncdf("lat","",dimout))
wdep=dim.def.ncdf("deptht","",depth)
wvar=var.def.ncdf("$2","",list(wsec,wdep,wtime),1e20)
fnc2=create.ncdf('$5',wvar)
put.var.ncdf(fnc2,wvar,varout)
close.ncdf(fnc2)
EOF1
R CMD BATCH section.R
ncks -h -A -v time $1 $5
}
###############################################################################
# #
# 3-dimensional conservative interpolation to the regular atmospheric grid #
# #
# $1 : input file #
# $2 : input var #
# $3 : output file #
# #
# Created in November 2012 Author : vguemas@ic3.cat #
# #
###############################################################################
function interp3d {
typeset var nz=`ncdump -h $1|grep 'deptht'|head -1|cut -f3 -d" "`
ln -sf /cfu/pub/scripts/interpolation/scrip_use scrip_use
for lev in $(seq 1 $nz) ; do
ncks -d deptht,$((lev-1)) -v $2 $1 tmp_${lev}.nc
ncwa -O -h -a deptht tmp_${lev}.nc tmp_${lev}.nc
ln -sf /cfu/autosubmit/con_files/weigths/${NEMOVERSION}/rmp_${NEMOVERSION}_to_*_lev${lev}.nc rmp_${NEMOVERSION}_to_regular_lev${lev}.nc
cat > scrip_use_in <<EOF
&remap_inputs
remap_wgt = 'rmp_${NEMOVERSION}_to_regular_lev${lev}.nc'
infile = 'tmp_${lev}.nc'
invertlat = FALSE
var = '$2'
fromregular = FALSE
outfile = 'tmp_$(printf "%02d" $lev).nc'
/
EOF
./scrip_use
ncecat -O -h tmp_$(printf "%02d" $lev).nc tmp_$(printf "%02d" $lev).nc
ncrename -h -O -d record,deptht tmp_$(printf "%02d" $lev).nc tmp_$(printf "%02d" $lev).nc
done
ncrcat -n $nz,2,1 -v $2 tmp_01.nc tmpout.nc
ncpdq -O -h -a time,deptht tmpout.nc tmp2out.nc
ncks -A -v deptht $1 tmp2out.nc
cdo setgrid,t106grid tmp2out.nc tmp3out.nc
cdo invertlatdata tmp3out.nc $3
rm -f tmp_* tmpout.nc tmp2out.nc tmp3out.nc rmp_${NEMOVERSION}_to_regular_lev* scrip_use scrip_use_in
}
###############################################################################
# #
# Set minimum and maximum attributes #
# #
# $1 : input file #
# $2 : input vars provided as a list #
# #
# Created in May 2012 Author : vguemas@ic3.cat #
###############################################################################
function setminmax {
cdo fldmax -timmax $1 intmax.nc
cdo fldmin -timmin $1 intmin.nc
typeset var listvars=""
typeset args=("$@")
typeset var ind
for ((ind=1;ind<$#;ind++)) ; do
listvars=$listvars" "${args[$ind]}
done
typeset name
for name in ${listvars[@]} ; do
typeset var var_max=`ncdump -v $name intmax.nc | tail -2 | head -1 | awk '{print $1}'`
ncatted -h -a valid_max,$name,m,f,$var_max $1
typeset var var_min=`ncdump -v $name intmin.nc | tail -2 | head -1 | awk '{print $1}'`
ncatted -h -a valid_min,$name,m,f,$var_min $1
done
rm -f intmax.nc intmin.nc
}
###############################################################################
# #
# Concatenate with a weight of the results obtained #
# on partial years #
# #
# $1 : input file 1 #
# $2 : input file 2 #
# $3 : ending month file 1 #
# $4 : output file #
# #
# Created in May 2012 Author : vguemas@ic3.cat #
###############################################################################
function concat {
typeset var wgt=$((10#${3}%12))
typeset var ntimes=`cdo ntime $1`
ncks -O -d time,$(($ntimes-1)) $1 part1.nc
ncks -O -d time,0 $2 part2.nc
cdo mulc,$wgt part1.nc part1_bis.nc
cdo mulc,$((12-$wgt)) part2.nc part2_bis.nc
cdo add part1_bis.nc part2_bis.nc tmp2_bis.nc
cdo divc,12 tmp2_bis.nc tmp2.nc
lstdims=`ncdump -h tmp2.nc | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/lev} != ${lstdims} ]] ; then
ncrename -d lev,ensemble tmp2.nc
else
ncecat -O -h tmp2.nc tmp2.nc
ncrename -h -O -d record,ensemble tmp2.nc tmp2.nc
ncpdq -O -h -a time,ensemble tmp2.nc tmp2.nc
fi
rm -f part1.nc part2.nc part1_bis.nc part2_bis.nc tmp2_bis.nc
ncks -O -d time,0,$((ntimes-2+10#${3}/12)) $1 tmp1.nc
ncks -O -d time,1, $2 tmp3.nc
ncrcat -O tmp1.nc tmp2.nc tmp3.nc $4
rm -f tmp1.nc tmp2.nc tmp3.nc
}
###############################################################################
# #
# Gather the members in a single netcdf file #
# #
# $1 : prefix netcdf file name for all the members #
# $2 : suffix netcdf file name for all the members #
# $3 : output file name #
# #
# Created in May 2012 Author : vguemas@ic3.cat #
###############################################################################
function gather_memb {
typeset var lstfiles1=`ls ${1}*${2}`
typeset var file
typeset var ind=1
typeset var lstfiles2=""
for file in ${lstfiles1[@]} ; do
typeset var lstvars=`cdo showvar $file`
typeset var lstexclude="nav_lon nav_lat"
for varex in $lstexclude ; do
if [[ ${lstvars/${varex}/} != ${lstvars} ]] ; then
ncks -O -x -v ${varex} $file $file
fi
done
if [[ ! -z "`ncdump -h ${file} | grep ensemble | head -1 | awk '{print $3}' | grep [0-9]`" ]] ; then
typeset var nrec=`ncdump -h ${file} | grep ensemble | head -1 | awk '{print $3}' | grep [0-9]`
typeset var jrec
for jrec in $(seq 1 $nrec) ; do
ncks -d ensemble,$((jrec-1)) $file tmp_record_${ind}.nc
ncwa -O -a ensemble tmp_record_${ind}.nc tmp_record_${ind}.nc
lstfiles2=${lstfiles2}" "tmp_record_${ind}.nc
ind=$((ind+1))
done
else
lstfiles2=${lstfiles2}" "$file
fi
done
ncecat -h ${lstfiles2} ${3}
rm -f tmp_record_*.nc
ncrename -h -O -d record,ensemble ${3} ${3}
ncpdq -O -h -a time,ensemble ${3} ${3}
}