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###############################################################################
# This file gathers a set of bash functions that rely on cdftools to #
# #
# reduce_mmo #
# get_diagsMMO #
# get_glorys #
# clean_diagsMMO #
# vertmeansal #
# heat_sal_mxl #
# area_moc #
# max_moc #
# siasiesiv #
# ohc #
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# interp3d #
# setminmax #
# concat #
# gather_memb #
# #
# 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
if [[ ! -f mask.nc ]] ; then
echo "No configuration files for cdftools"
exit
fi
###############################################################################
# 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 #
# May 2014 : Compatibility with PA changes to oce output - Virginie #
###############################################################################
function reduce_mmo {
ncks -O -v sosstsst,sosaline,somixhgt,somxl010,sossheig $1 oce_${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) #
# $10 : list of files extracted from the original tarballs
# #
# Created in May 2012 Author : vguemas@ic3.cat #
# Option 10: June 2013 isabel.andreu-burillo@ic3.cat
###############################################################################
function get_diagsMMO {
typeset var yyyy0=`echo $1|cut -c1-4`
typeset var mm0=`echo $1|cut -c5-6`
typeset var lstypes="grid_T grid_U grid_V grid_W icemod"
else
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 .
for filetype in $lstypes; do
tar --wildcards -xvf $8_$2_$1_fc$3_${year1}$(printf "%02d" $mon1)01-${year2}$(printf "%02d" $mon2)*.tar "*${freqkeep}*${filetype}*"
done
else
tar --wildcards -xvf $8_$2_$1_fc$3_${year1}$(printf "%02d" $mon1)01-${year2}$(printf "%02d" $mon2)*.tar
fi
rm -f $8_$2_$1_fc$3_${year1}$(printf "%02d" $mon1)01-${year2}$(printf "%02d" $mon2)*.tar
if [[ `ls *.gz` != '' ]] ; then gunzip -f *.gz ; fi
done
typeset var listroots
case $8 in
'diags' )
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listroots="t3d heat_sal_mxl ice moc psi sal_0-300m sal_300-5400m"
if [[ `ls sstsimld*` != '' ]] ; then
listroots=$listroots" sstsimld"
elif [[ `ls sstsssmld*` != '' ]] ; then
listroots=$listroots" sstsssmld"
else
listroots=$listroots" oce"
fi
'MMO' ) listroots=$lstypes ;;
esac
case $9 in
'daily') freqexcl1='1m' ; freqexcl2='MM' ;;
'monthly' ) freqexcl1='1d' ; freqexcl2='DD' ;;
*) freqexcl1='1d' ; freqexcl2='DD' ;;
esac
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function concat_startdate {
typeset var root
typeset var lstfiles
for root in ${listroots[@]} ; do
if [[ `ls *${root}*` != '' ]] && [[ `ls *${root}*` != ${root}_1m.nc ]] ; then
if [[ "$8" == "MMO" ]] ; then
lstfiles=`ls *${root}* | grep -v "${root}_$2_$1_fc" | grep -v "${freqexcl1}" | grep -v "${freqexcl2}" | grep -v "km" `
else
lstfiles=`ls ${root}* | grep -v "${root}_$2_$1_fc" | grep -v "${freqexcl1}" | grep -v "${freqexcl2}" | grep -v "km" `
fi
file1=`echo "${lstfiles}" | tail -1`
cdo_version=`cdo -V &> ff ; grep Climate ff | cut -d \ -f 5`
rm ff
#test on cdo version: if >1.5.6, remove valid_min/max attributes to avoid values out of that range to be replaced by NaN
if [[ "$cdo_version" = "`echo -e "$cdo_version\n1.5.6" | sort -V | head -n1`" ]] ; then
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
if [[ $root == 'heat_sal_mxl' ]] ; then
for file in $lstfiles ; do
ncatted -O -a valid_max,somxlheatc,d,, $file $file
ncatted -O -a valid_min,somxlheatc,d,, $file $file
done
fi
fi
outfile=${root}_$2_$1_fc$3_$(($yyyy0+(10#$mm0+$4-2)/12))$(printf "%02d" $(((10#$mm0+$4-2)%12+1)))_${year2}$(printf "%02d" $mon2).nc
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 ${outfile}
timevar=`ncdump -h ${outfile} | grep UNLIMITED | awk '{print $1}'`
if [[ $timevar == 'time_counter' ]] ; then ncrename -v time_counter,time -d time_counter,time ${outfile} ; fi
if [[ $root == 'moc' ]] ; then
lstdims=`ncdump -h ${outfile} | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/gsize} != ${lstdims} ]] ; then
ncrename -d gsize,y ${outfile}
fi
lenx=`ncdump -h ${outfile} | grep 'x =' | head -1 | awk '{print $3}'`
if [[ $lenx > 1 ]] ; then
if [[ ${lstvars/nav_lon} != ${lstvars} ]] ; then
ncks -O -x -v nav_lon,nav_lat ${outfile} ${outfile}
fi
ncrename -d x,y ${outfile}
fi
ncks -A -v nav_lon,nav_lat `echo $lstfiles | awk '{print $1}' ` ${outfile}
fi
rm -f $lstfiles
if [[ $root == 'sstsimld' || $root == 'sstsssmld' ]] ; then mv ${outfile} oce_$2_$1_fc$3_$(($yyyy0+(10#$mm0+$4-2)/12))$(printf "%02d" $(((10#$mm0+$4-2)%12+1)))_${year2}$(printf "%02d" $mon2).nc ; fi
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done
}
concat_startdate $1 $2 $3 $4 $5 $6 $7 $8
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# These lines aim at concatenating the daily means as well and computing the monthly means from these daily means
if [[ $9 == 'monthly' ]] ; then
freqexcl1='1m' ; freqexcl2='MM'
for root in ${listroots[@]} ; do
outfile=${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 [[ -e $outfile ]] ; then
mv $outfile ${root}_1m.nc
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done
concat_startdate $1 $2 $3 $4 $5 $6 $7 $8
for root in ${listroots[@]} ; do
outfile=${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 [[ -e $outfile ]] ; then
cdo monmean $outfile ${root}_daily2monthly.nc
rm -f $outfile
if [[ -e ${root}_1m.nc ]] ; then
mv ${root}_1m.nc $outfile
ncks -A ${root}_daily2monthly.nc $outfile
rm -f ${root}_daily2monthly.nc
else
mv ${root}_daily2monthly.nc $outfile
fi
else
if [[ -e ${root}_1m.nc ]] ; then
mv ${root}_1m.nc $outfile
fi
fi
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done
fi
rm -f *${freqexcl1}* *${freqexcl2}*
}
###############################################################################
# Copy NEMOVAR files from cfunas #
# #
# $1 : expid #
# $2 : member #
# $3 : start year #
# $4 : end year #
# $5 : start month #
# $6 : end month #
# $7 : list of files extracted from the original tarballs
# #
# Created in May 2012 Author : vguemas@ic3.cat #
# Modified: June 2013 isabel.andreu-burillo@ic3.cat #
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###############################################################################
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
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
}
###############################################################################
# Copy GLORYS files from cfunas #
# #
# $1 : start year #
# $2 : end year #
# $3 : start month #
# $4 : end month #
# #
# Created in June 2013 Author : vguemas@ic3.cat #
###############################################################################
function get_glorys {
typeset var path=/cfunas/exp/MERCATOR/GLORYS2V1/outputs/ORCA1L46 #ORCA025L75_glorys
typeset var lstfiles=""
for year in $(seq $1 $2) ; do
cp ${path}/vosaline_${year}.nc .
cp ${path}/votemper_${year}.nc .
ncks -A vosaline_${year}.nc votemper_${year}.nc
rm -f vosaline_${year}.nc
lstfiles=${lstfiles}" "votemper_${year}.nc
done
cdo cat ${lstfiles} tmp.nc
cdo settaxis,${1}-01-15,12:00,1mon tmp.nc tmp2.nc
cdo seldate,${1}-$(printf "%02d" $3)-00,${2}-$(printf "%02d" $4)-31 tmp2.nc grid_T_glorys2v1_19930101_fc0_${1}$(printf "%02d" $3)_${2}$(printf "%02d" $4).nc
rm -f ${lstfiles} tmp.nc tmp2.nc
ncks -O -x -v nav_lon,nav_lat,x_2,y_2 grid_T_glorys2v1_19930101_fc0_${1}$(printf "%02d" $3)_${2}$(printf "%02d" $4).nc grid_T_glorys2v1_19930101_fc0_${1}$(printf "%02d" $3)_${2}$(printf "%02d" $4).nc
ncks -A -v nav_lon,nav_lat mesh_hgr.nc grid_T_glorys2v1_19930101_fc0_${1}$(printf "%02d" $3)_${2}$(printf "%02d" $4).nc
}
###############################################################################
# Clean diags or MMO files after postprocessing #
# #
# $1 : starting date #
# $2 : expid #
# $3 : member #
# $4 : starting leadtime #
# $5 : end leadtime #
# $6 : diags/MMO #
# $7 : list of files extracted from the original tarballs
# #
# Created in May 2012 Author : vguemas@ic3.cat #
# Modified: June 2013 isabel.andreu-burillo@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 $6 in
'diags' ) listroots="t3d" ;;
'MMO' )
if [ -z "${7}" ] ; then
listroots="grid_T grid_U grid_V grid_W icemod"
else
listroots=${7}
fi
;;
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) #
# #
# Created in February 2012 Author : vguemas@ic3.cat #
###############################################################################
function vertmeansal {
cdo_version=`cdo -V &> ff ; grep Climate ff | cut -d \ -f 5`
rm ff
typeset var ntime=`cdo ntime $1`
typeset var list=""
typeset var jt
for jt in $(seq 1 $ntime); do
ncks -d time,$((jt-1)) $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
#test on cdo version: if >1.5.6, remove valid_min/max attributes to avoid values out of that range to be replaced by NaN
if [[ "$cdo_version" = "`echo -e "$cdo_version\n1.5.6" | sort -V | head -n1`" ]] ; then
ncatted -O -a valid_max,vertmeansal,d,, outputvertmeansal_$jt.nc outputvertmeansal_$jt.nc
ncatted -O -a valid_min,vertmeansal,d,, outputvertmeansal_$jt.nc outputvertmeansal_$jt.nc
fi
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 (=> 2D x-y ) #
# #
# 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 $ntime); do
ncks -d time,$((jt-1)) $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
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timevar=`ncdump -h outputintheat_sal_mxl_$jt.nc | grep UNLIMITED | awk '{print $1}'`
if [[ $timevar == 'time_counter' ]] ; then ncrename -v time_counter,time -d time_counter,time outputintheat_sal_mxl_$jt.nc ; fi
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 (=> 2D x-y ) #
# #
# Created in June 2012 Author : isabel.andreu-burillo@ic3.cat #
# May 2014 - Virginie Guemas - Way around the bc that does not work on moore #
###############################################################################
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` -> does not work on new moore
# strip out the .* from $3:
# addition with float returned:
lower_bnd=`echo $(printf "%f" $(( $stripped + 200)))`
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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 (=> 2D, depth-y) #
# #
# 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
ncks -O -x -v nav_lon,nav_lat outmoc_$jt.nc outmoc_$jt.nc
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timevar=`ncdump -h outmoc_$jt.nc | grep UNLIMITED | awk '{print $1}'`
if [[ $timevar == 'time_counter' ]] ; then ncrename -v time_counter,time -d time_counter,time outmoc_$jt.nc ; fi
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 $1 $2
ncks -A -v time $1 $2
rm -f $list
}
###############################################################################
# #
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# Compute the intensity of convection in the four main convection sites #
# #
# $1 : input oce file name containing somxl010 #
# $2 : input grid #
# $3 : output file name (=> index) #
# #
# Created in October 2013 Author : vguemas@ic3.cat #
###############################################################################
function convection {
case $2 in
'Ec2.3_O1L42'|'Ec3.0_O1L46'|'N3.2_O1L42'|'N3.3_O1L46'|'nemovar_O1L42')
A1=225;A2=245;A3=215;A4=255;
B1=245;B2=290;B3=215;B4=245;
C1=260;C2=310;C3=245;C4=291;
D1=225;D2=280;D3=1;D4=50;;
'Ec3.0_O25L46'|'Ec3.0_O25L75'|'glorys2v1_O25L75')
stop"Option convection not available yet for this configuration"
;;
esac
cdo fldmax -selindexbox,${A1},${A2},${A3},${A4} $1 Labrador.nc
ncrename -v somxl010,Labrador Labrador.nc
ncks -v Labrador Labrador.nc convection.nc
rm -f Labrador.nc
cdo fldmax -selindexbox,${B1},${B2},${B3},${B4} $1 Irminger.nc
ncrename -v somxl010,Irminger Irminger.nc
ncks -A -v Irminger Irminger.nc convection.nc
rm -f Irminger.nc
cdo fldmax -selindexbox,${C1},${C2},${C3},${C4} $1 GIN.nc
ncrename -v somxl010,GIN GIN.nc
ncks -A -v GIN GIN.nc convection.nc
rm -f GIN.nc
cdo fldmax -selindexbox,${D1},${D2},${D3},${D4} $1 Wedell.nc
ncrename -v somxl010,Wedell Wedell.nc
ncks -A -v Wedell Wedell.nc convection.nc
rm -f Wedell.nc
mv convection.nc $3
}
###############################################################################
# #
# Compute the barotropic stream function #
# #
# $1 : input grid_U file name #
# $2 : input grid_V file name #
# $3 : output file name without nc extension (=> 2D x-y) #
# #
# 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
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timevar=`ncdump -h psi_$jt.nc | grep UNLIMITED | awk '{print $1}'`
if [[ $timevar == 'time_counter' ]] ; then ncrename -v time_counter,time -d time_counter,time psi_$jt.nc ; fi
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
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}
###############################################################################
# #
# Compute the intensity of the subtropical and subpolar gyres #
# #
# $1 : input psi file name #
# $2 : input grid #
# $3 : output file name ( => index ) #
# #
# Created in October 2013 Author : vguemas@ic3.cat #
###############################################################################
function gyres {
case $2 in
'Ec2.3_O1L42'|'Ec3.0_O1L46'|'N3.2_O1L42'|'N3.3_O1L46'|'nemovar_O1L42')
A1=230;A2=275;A3=215;A4=245;
B1=70;B2=145;B3=195;B4=235;
C1=45;C2=175;C3=165;C4=220;
D1=195;D2=275;D3=175;D4=225;
E1=70;E2=205;E3=120;E4=145;
F1=235;F2=300;F3=120;F4=145;
G1=320;G2=30;G3=110;G4=180;
H1=1;H2=361;H3=1;H4=65;;
'Ec3.0_O25L46'|'Ec3.0_O25L75'|'glorys2v1_O25L75')
stop"Option gyres not available yet for this configuration"
;;
esac
cdo fldmin -selindexbox,${A1},${A2},${A3},${A4} $1 subpolar_NAtl.nc
ncrename -v sobarstf,subpolNAtl subpolar_NAtl.nc
cdo mulc,-1 subpolar_NAtl.nc gyres.nc
rm -f subpolar_NAtl.nc
cdo fldmin -selindexbox,${B1},${B2},${B3},${B4} $1 subpolar_NPac.nc
ncrename -v sobarstf,subpolNPac subpolar_NPac.nc
cdo mulc,-1 subpolar_NPac.nc tmp.nc
ncks -A tmp.nc gyres.nc
rm -f subpolar_NPac.nc tmp.nc
cdo fldmax -selindexbox,${C1},${C2},${C3},${C4} $1 subtrop_NPac.nc
ncrename -v sobarstf,subtropNPac subtrop_NPac.nc
ncks -A subtrop_NPac.nc gyres.nc
rm -f subtrop_NPac.nc
cdo fldmax -selindexbox,${E1},${E2},${E3},${E4} $1 subtrop_SPac.nc
ncrename -v sobarstf,subtropSPac subtrop_SPac.nc
ncks -A subtrop_SPac.nc gyres.nc
rm -f subtrop_SPac.nc
cdo fldmax -selindexbox,${D1},${D2},${D3},${D4} $1 subtrop_NAtl.nc
ncrename -v sobarstf,subtropNAtl subtrop_NAtl.nc
ncks -A subtrop_NAtl.nc gyres.nc
rm -f subtrop_NAtl.nc
cdo fldmax -selindexbox,${F1},${F2},${F3},${F4} $1 subtrop_SAtl.nc
ncrename -v sobarstf,subtropSAtl subtrop_SAtl.nc
ncks -A subtrop_SAtl.nc gyres.nc
rm -f subtrop_SAtl.nc
cdo fldmax -selindexbox,${G1},${G2},${G3},${G4} $1 subtrop_Ind.nc
ncrename -v sobarstf,subtropInd subtrop_Ind.nc
ncks -A subtrop_Ind.nc gyres.nc
rm -f subtrop_Ind.nc
cdo fldmax -selindexbox,${H1},${H2},${H3},${H4} $1 ACC.nc
ncrename -v sobarstf,ACC ACC.nc
ncks -A ACC.nc gyres.nc
rm -f ACC.nc
mv gyres.nc $3
}
###############################################################################
# #
# 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 ( => index ) #
# $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
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lstdims=`ncdump -h $1 | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/x} != ${lstdims} ]] ; then
ncwa -O -a x $1 tmpmoc.nc
ncrename -O -d y,lat -v nav_lat,lat tmpmoc.nc 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 ( => index ) #
# #
# Created in March 2012 Author : vguemas@ic3.cat #
###############################################################################
function max_moc {
if [ ! -f $6 ] ; then
ncecat -h $1 tmpmoc1.nc
lstdims=`ncdump -h tmpmoc1.nc | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/x} != ${lstdims} ]] ; then
ncwa -O -a x tmpmoc1.nc tmpmoc1.nc
fi
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
timevar=`ncdump -h maxmoc_$jt.nc | grep UNLIMITED | awk '{print $1}'`
if [[ $timevar == 'time_counter' ]] ; then ncrename -v time_counter,time -d time_counter,time maxmoc_$jt.nc ; fi
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 ( => index ) #
# #
# 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'|'Ec3.0_O25L75') for var in `cdo showvar $1 | head -1`
do
[[ $var = "ice_pres" || $var = "iiceconc" ]] && ncrename -v $var,ileadfra $1
done;;
#'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}Exnsidc 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 ( => 2D x-y ) #
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# $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
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lstdims=`ncdump -h tmpohc.nc | awk /dimensions:/,/variables:/ | grep -v dimensions: | grep -v variables: | awk '{print $1}'`
if [[ ${lstdims/x_2} != ${lstdims} ]] ; then
if [[ ${lstdims/x} != ${lstdims} ]] ; then
ncwa -O -a x tmpohc.nc tmpohc.nc
fi
ncrename -d x_2,x tmpohc.nc
fi
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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 #
# #
# 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')