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Older
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 #
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# #
# 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
orca_res=`echo $NEMOVERSION | cut -c 7-9`
if ((${orca_res} \= "O25")); then
cdo invertlatdata tmp3out.nc $3
else
cp tmp3out.nc $3
fi
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rm -f tmp_* tmpout.nc tmp2out.nc tmp3out.nc rmp_${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}
}
Eleftheria Exarchou
committed
###############################################################################
# Choose vertical level in ocean, or vertically average between
# 2 or more ocean levels #
# #
# $1 : input file name #
# $2: input variable name (votemper or vosaline) #
# $3 : upper depth of the layer (in level number) #
# $4 : lower depth of the layer (in level number. If same as the #
# upper layer, then the script just selects this layer. If its #
# different, a vertical integral (weighted) between upper and lower #
# level is computed #
# $5 : output file name (=> 2D field ) #
# #
# Created in February 2012 Author : vguemas@ic3.cat #
# Modified (more generic,
# i.e. for any input var) in December 2014 #
# Author : eleftheria.exarchou@ic3.cat #
###############################################################################
Eleftheria Exarchou
committed
function vertmeanvar {
typeset var ntime=`cdo ntime $1`
typeset var list=""
typeset var jt
for jt in $(seq 1 $ntime); do
ncks -d time,$((jt-1)) $1 a1
l1=$(($3+1))
l2=$(($4+1))
lev1=`echo $(cdo info -seltimestep,1 -selvar,gdept mesh_zgr.nc | sed -n ${l1}p | awk '{ print $10 }')`
lev2=`echo $(cdo info -seltimestep,1 -selvar,gdept mesh_zgr.nc | sed -n ${l2}p | awk '{ print $10 }')`
if [ "`uname -n`" == "moore" ] ; then
cdfvertmean_elfi=/home/eexarchou/moore_cdftools/CDFTOOLS_2.1/cdfvertmean
fi
if [ "`uname -n`" == "amdahl" ] ; then
cdfvertmean_elfi=/home/eexarchou//amdahl_cdftools/CDFTOOLS_2.1/cdfvertmean
fi
${cdfvertmean_elfi} a1 $2 T $lev1 $lev2
Eleftheria Exarchou
committed
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rm -f a1
ncrename -O -v sovertmean,vertmean -d time_counter,time -v time_counter,time vertmean.nc
mv vertmean.nc outputvertmean_$jt.nc
list=$list" "outputvertmean_$jt.nc
rm -f intvertmean.nc a?
# #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
ncatted -O -a valid_max,vertmean,d,, outputvertmean_$jt.nc outputvertmean_$jt.nc
ncatted -O -a valid_min,vertmean,d,, outputvertmean_$jt.nc outputvertmean_$jt.nc
ncatted -O -a standard_name,time,a,c,time outputvertmean_$jt.nc outputvertmean_$jt.nc
ncatted -O -a units,time,o,c,'seconds since 1993-05-01 00:00:00' outputvertmean_$jt.nc outputvertmean_$jt.nc
ncatted -O -a long_name,time,a,c,'Time axis' outputvertmean_$jt.nc outputvertmean_$jt.nc
done
cdo cat $list $5
ncks -A -v time $1 $5
rm -f $list
setminmax $5 vertmean
ncrename -v vertmean,$2 $5
#typeset var level=`echo $(cdo info -selvar,$2 -setctomiss,0 $5 | sed -n 2p | awk '{ print $7 }')`
#typeset var lev=`echo $(cdo info -seltimestep,1 -selvar,$2 -setctomiss,0 $1 | grep $level | awk '{ print $1 }')`
lev=$3
echo $lev
cp $5 tmp_${lev}.nc
## Here we interpolate horizontally onto a regular grid
ln -sf /cfu/autosubmit/con_files/weigths/${NEMOVERSION}/rmp_${NEMOVERSION}_to_*_lev${lev}.nc rmp_${NEMOVERSION}_to_regular_lev${lev}.nc
ln -sf /cfu/pub/scripts/interpolation/scrip_use scrip_use
cat > scrip_use_in <<EOF
&remap_inputs
remap_wgt = 'rmp_${NEMOVERSION}_to_regular_lev${lev}.nc'
infile = 'tmp_${lev}.nc'
invertlat = FALSE
var = '$2'
fromregular = FALSE
outfile = 'tmp_${lev}_int.nc'
/
EOF
./scrip_use
cdo setgrid,t106grid tmp_${lev}_int.nc tmpout1.nc
cdo invertlatdata tmpout1.nc $5
ncatted -O -a long_name,${2},o,c,'vertical average of temp/sal between '${lev1}'m and '${lev2}'m' $5
rm -f tmp_* tmpout* rmp_${NEMOVERSION}_to_regular_lev* scrip_use scrip_use_in
}