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@@ -0,0 +1,352 @@
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+#!/bin/bash
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+# PlaSim netcdf postprocessor script
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+# (c) 2019 Jost von Hardenberg - ISAC-CNR
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+
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+#set -ex
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+export LC_NUMERIC="en_US.UTF-8"
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+
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+function help {
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+ echo "Convert PLASIM service output file to netcdf format"
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+ echo "PlaSIM, ML ocean, ice model and LSG outputs are recognized"
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+ echo "Usage: srv2nc [-m] [-y] [-d code1,code2,...] [-f format] infile.srv outfile.nc"
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+ echo "Options:"
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+ echo " -m perform monthly means"
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+ echo " -y perform yearly means"
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+ echo " -p compute sea-level pressure"
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+ echo " -d codelist remove a comma-separated list of codes from the output"
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+ echo " -f format output format (default is zipped netcdf4 (HDF5))"
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+ echo " Alternatives: nc, nc1, nc4, nc4c, nc5"
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+ echo " -h print this help"
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+ exit
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+}
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+
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+fmonth=""
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+fyear=""
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+format="nc4 -z zip"
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+while getopts "d:ypmhf:" OPTION; do
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+ case $OPTION in
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+ d) delcodes=$OPTARG ;;
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+ m) fmonth="-monmean" ;;
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+ y) fyear="-yearmean" ;;
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+ p) psl=1 ;;
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+ f) format=$OPTARG ;;
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+ h) help ;;
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+ esac
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+done
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+shift $((OPTIND-1))
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+if [[ ! "nc nc1 nc2 nc4 nc4c nc5 nc4c -z zip nc4 -z zip" == *$format* ]]
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+then
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+echo "Invalid format: " $format
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+echo "Choose one of: nc, nc1, nc2, nc4, nc4c, nc5, nc4c -z zip, nc4 -z zip"
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+exit 1
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+fi
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+
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+if [ $# -lt 2 ]; then
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+ help
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+fi
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+
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+infile=$1
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+outfile=$2
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+
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+cdo="cdo -s"
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+cdonctab="cdo -t ./param$$.tab -f nc -s"
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+cdonc="cdo -f nc -s"
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+cdozip="cdo -f $format -s"
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+cdoziptab="cdo -t ./param$$.tab -f $format -s"
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+
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+cat > param$$.tab << EOT
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+110 mld Mixed Layer Depth [m]
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+129 sg Surf. Geopotential Orography [m2/s2]
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+130 ta Temperature [K]
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+131 ua Zonal Wind [m/s]
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+132 va Meridional Wind [m/s]
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+133 hus Specific Humidity [kg/kg]
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+134 ps Surface Pressure [hPa]
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+135 wap Vertical Pressure Velocity [Pa/s]
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+137 wa Vertical Wind [m/s]
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+138 zeta Vorticity [1/s]
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+139 ts Surface Temperature [K]
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+140 mrso Soil Wetness [m]
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+141 snd Snow Depth [m]
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+142 prl Large Scale Precipitation [m/s]
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+143 prc Convective Precipitation [m/s]
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+144 prsn Snow Fall [m/s]
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+145 bld Boundary Layer Dissipation [W/m**2]
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+146 hfss Surface Sensible Heat Flux [W/m**2]
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+147 hfls Surface Latent Heat Flux [W/m**2]
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+148 stf Streamfunction [m**2/s]
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+149 psi Velocity Potential [m**2/s]
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+151 psl Mean Sea Level Pressure [hPa]
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+152 pl Log Surface Pressure [1]
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+155 d Divergence [1/s]
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+156 zg Geopotential Height [m]
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+157 hur Relative Humidity [%]
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+158 tps Tendency of Surface Pressure [Pa/s]
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+159 u3 ustar **3 [m**3/s**3]
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+160 mrro Surface Runoff [m/s]
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+161 clw Liquid Water Content [kg/kg]
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+162 cl Cloud Cover [0-1]
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+163 tcc Total Cloud Cover [0-1]
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+164 clt Total Cloud Cover (Mean) [0-1]
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+165 uas Eastward Wind 10m [m/s]
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+166 vas Northward Wind 10m [m/s]
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+167 tas Temperature at 2m [K]
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+168 td2m Dew Point Temperature at 2m [K]
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+169 tsa Surface Temperature Accumulated [K]
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+170 tsod Deep Soil Temperature [K]
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+171 dsw Deep Soil Wetness [1]
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+172 lsm Land Sea Mask [0-1]
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+173 z0 Surface Roughness [m]
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+174 alb Surface Albedo [1]
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+175 as Surface Albedo [1]
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+176 rss Surface Solar Radiation [W/m2]
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+177 rls Surface Thermal Radiation [W/m2]
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+178 rst Top Solar Radiation [W/m2]
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+179 rlut Top Thermal Radiation [W/m2]
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+180 tauu U-Stress [Pa]
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+181 tauv V-Stress [Pa]
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+182 evap Evaporation [m/s]
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+183 tso Soil Temperature [K]
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+184 wsoi Soil Wetness [1]
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+199 vegc Vegetation Cover [0-1]
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+201 tasmax Maximum daily 2m temperature [K]
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+202 tasmin Minimum daily 2m temperature [K]
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+203 rsut Top Solar Radiation Upward [W/m2]
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+204 ssru Surface Solar Radiation Upward [W/m2]
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+205 stru Surface Therm Radiation Upward [W/m2]
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+207 tso2 Soil Temperature Level 2 [K]
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+208 tso3 Soil Temperature Level 3 [K]
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+209 tso4 Soil Temperature Level 4 [K]
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+210 sic Sea Ice Cover [0-1]
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+211 sit Sea Ice Thickness [m]
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+212 vegf Forest Cover [0-1]
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+218 snm Snow Melt [m/s]
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+221 sndc Snow Depth Change [m/s]
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+229 dwmax Field capacity [1]
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+230 prw Vert. Integrated Spec. Hum. [kg/m2]
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+232 glac Glacier Cover [0-1]
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+238 tsn Snow temperature [K]
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+259 spd Wind Speed [m/s]
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+260 pr Total Precipitation [m/s]
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+261 ntr Net Top Radiation [W/m2]
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+262 nbr Net Bottom Radiation [W/m2]
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+263 hfns Net Heat Flux [W/m2]
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+264 wfn Net Water Flux [m/s]
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+273 dpdx d(ps)/dx [Pa/m]
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+273 dpdy d(ps)/dy [Pa/m]
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+277 hlpr Half level pressure [Pa]
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+278 flpr Full level pressure [Pa]
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+701 heata Flux from the atmosphere [W/m2]
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+702 ofluxa Flux from the ocean [W/m2]
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+703 tsfluxa Flux to warm/cool ice/snow [W/m2]
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+704 smelta Flux for snow melt [W/m2]
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+705 imelta Flux used for ice melt [W/m2]
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+706 cfluxa Flux to the ocean [W/m2]
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+707 fluxca Cond. heatflux [W/m2]
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+708 qmelta Res flux to ice [W/m2]
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+709 xflxicea Flux correction [W/m2]
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+710 icec Ice cover [0-1]
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+711 iced Ice thickness [m]
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+712 scflxa Flux from snow -> ice conversion [W/m2]
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+713 cfluxra Flux for limiting ice to xmaxd [W/m2]
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+714 cfluxna Flux due to neg. ice [W/m2]
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+739 ts Surface temperature [K]
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+741 zsnow Snow depth [m h2o]
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+769 sst Sea surface temperature [K]
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+772 ls Land sea mask [0-1]
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+790 clicec2 Climatological ice cover [0-1]
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+791 cliced2 Climatological ice thickness [m]
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+792 icecc Ice cover computed prognostically [frac.]
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+794 cpmea Fresh water (p-e) for LSG [m/s]
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+795 croffa Runoff for LSG [m/s]
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+796 stoia Snow converted to ice [m h2o]
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+901 heata Heat flux from atm/ice [W/m2]
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+902 ifluxa Heat flux into ice [W/m2]
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+903 fssta Flux correction [W/m2]
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+904 dssta Vertical diffusion [m2/s]
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+905 qhda Horizontal diffusion [m2/s]
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+906 fldoa Flux from deep ocean (LSG) [W/m2]
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+910 icec Sea ice cover [0-1]
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+939 sst SST (ML ocean temperature) [K]
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+972 ls Land-sea mask [1]
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+990 clsst Climatological SST [K]
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+EOT
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+cat > paramlsg$$.tab << EOT
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+1 zeta surface elevation [m]
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+2 t potential temperature [K]
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+3 utot zonal velocity component [m/s]
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+4 vtot meridional velocity component [m/s]
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+5 s salinity [0/00]
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+7 w vertical velocity component [m/s]
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+13 sice ice thickness [m]
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+18 fluxhea heat flux [W/m2]
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+27 psi horizontal barotropic stream function [m3/s]
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+37 ub zonal component of barotropic velocity [m/s]
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+38 vb meridional component of barotropic velocity [m/s]
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+40 wet land-sea mask for scalar points [0-1]
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+41 wetvec land-sea mask for vector points [0-1]
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+52 taux zonal component of wind stress [Pa]
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+53 tauy meridional component of wind stress [Pa]
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+62 tc potential temperature [C]
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+65 fluwat net fresh water flux (P-E) [m/s]
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+66 convadd potential energy dissipation due to convection [mW/m2]
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+67 flukwat fresh water flux due to Newtonian coupling [m/s]
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+68 flukhea heat flux due to Newtonian coupling [W/m2]
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+69 convad convective adjustment events [1]
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+80 fldsst sst differences lsg-plasim [K]
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+81 fldice ice-differences lsg-plasim [1]
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+82 fldpme pme-differences lsg-plasim [m/s]
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+83 fldtaux taux-differences lsg-plasim [Pa]
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+84 fldtauy tauy-differences lsg-plasim [Pa]
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+92 tbound boundary value of t [K]
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+97 dQ/dt coupling coefficient [W/m2K]
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+98 depp depth in scalar-points [m]
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+99 depv depth in vector-points [m]
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+EOT
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+
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+ysize=$($cdo -s griddes $infile | grep ysize | head -1 | cut -d= -f2|sed 's/ //g')
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+case $ysize in
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+ 32) spgrid=t21; gpgrid=n16;;
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+ 48) spgrid=t31; gpgrid=n24;;
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+ 64) spgrid=t42; gpgrid=n32;;
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+ 96) spgrid=t63; gpgrid=n48;;
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+ 128) spgrid=t85; gpgrid=n64;;
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+ 160) spgrid=t106; gpgrid=n80;;
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+ 76) gpgridt=lsggridt$$.txt; gpgridu=lsggridu$$.txt; flsg=1;;
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+esac
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+
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+if [ -z "$flsg" ]; then
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+ fsp=$($cdo griddes $infile | grep "gridID 2") # Spectral or not?
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+ $cdo zaxisdes $infile > inzgrid$$.txt
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+ f3d=$(grep "zaxisID 2" inzgrid$$.txt) # Vertical sigma axis or not
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+else
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+
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+# vertical axes for LSG
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+cat > zaxislsgu$$.txt << EOT
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+zaxistype = depth_below_sea
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+size = 22
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+levels = 25 75 125 175 225 275 350 450 550 650 750 850 950 1100 1300 1500 1800 2250 2750 3500 4500 5500
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+EOT
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+cat > zaxislsgc$$.txt << EOT
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+zaxistype = depth_below_sea
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+size = 21
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+levels = 75 125 175 225 275 350 450 550 650 750 850 950 1100 1300 1500 1800 2250 2750 3500 4500 5500
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+EOT
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+cat > zaxislsgw$$.txt << EOT
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+zaxistype = depth_below_sea
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+size = 22
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+levels = 50 100 150 200 250 312.5 400 500 600 700 800 900 1025 1200 1400 1650 2025 2500 3125 4000 5000 6000
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+EOT
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+
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+ # Create scalar grid
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+ cat > $gpgridt <<EOT
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+#
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+# gridID 1
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+#
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+gridtype = curvilinear
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+gridsize = 5472
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+xsize = 72
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+ysize = 76
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+xname = lon
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+xdimname = west_east
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+xlongname = "longitude"
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+xunits = "degrees_east"
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+yname = lat
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+ydimname = south_north
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+ylongname = "latitude"
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+yunits = "degrees_north"
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+xvals =
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+ $(awk "BEGIN {off=-2.5; for(y=93.75; y>=-93.75; y=y-2.5) {for(x=0.; x<=357.5; x=x+5.0) {printf x-off \" \" }; printf \"\n\"; off=2.5+off}}")
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+yvals =
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+ $(awk "BEGIN {for(y=93.75; y>=-93.75; y=y-2.5) {for(i=1; i<=72; ++i) {printf y \" \" } printf \"\n\"}}")
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+scanningMode = 64
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+EOT
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+
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+ # Create vector grid
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+ cat > $gpgridu <<EOT
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+#
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+# gridID 1
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+#
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+gridtype = curvilinear
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+gridsize = 5472
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+xsize = 72
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+ysize = 76
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+xname = lon
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+xdimname = west_east
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+xlongname = "longitude"
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+xunits = "degrees_east"
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+yname = lat
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+ydimname = south_north
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+ylongname = "latitude"
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+yunits = "degrees_north"
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+xvals =
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+ $(awk "BEGIN {off=-5.; for(y=93.75; y>=-93.75; y=y-2.5) {for(x=0.; x<=357.5; x=x+5.0) {printf x-off \" \" }; printf \"\n\"; off=2.5+off}}")
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+yvals =
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+ $(awk "BEGIN {for(y=93.75; y>=-93.75; y=y-2.5) {for(i=1; i<=72; ++i) {printf y \" \" } printf \"\n\"}}")
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+scanningMode = 64
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+EOT
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+
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+fi
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+
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+# If 3D Field, adjust vertical grid
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+if [ ! -z "$f3d" ]; then
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+nlev=$( grep size inzgrid$$.txt|tail -1|cut -d= -f2|sed 's/ //g' )
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+#sigmas=$($cdo outputf,%19.16f -selindexbox,1,$nlev,1,1 -selcode,333 $infile | awk ' BEGIN{p=0.} {s=($1+p)/2.; p=$1} {printf("%19.16f\n", s)}')
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+sigmas=$($cdo outputf,%19.16f -selindexbox,1,$nlev,1,1 -selcode,333 $infile)
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+grep -m 1 -B 1000 -A 1 "zaxisID 2" inzgrid$$.txt >zgrid$$.txt
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+cat >> zgrid$$.txt << EOT
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+zaxistype = hybrid
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+size = $nlev
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+levels = $( seq 1 $nlev )
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+vctsize = $(( nlev*2 + 2 ))
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+vct = $( printf "%.s0 " $(seq 1 $((nlev + 1)) ) )
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+ 0 $sigmas
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+EOT
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+fixzgrid="-setzaxis,zgrid$$.txt"
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+delcode333="-delcode,333"
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+else
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+fixzgrid=""
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+delcode333=""
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+fi
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+
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+if [ -z "$flsg" ]; then
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+# If not LSG
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+# If spectral fix grids
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+if [ ! -z "$fsp" ]; then
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+ $cdo splitgrid ${infile} grid_$$_
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+ if [ ! -z "$psl" ]; then
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+ $cdonctab $fixzgrid -setgrid,$spgrid grid_$$_02.srv spectral$$.nc
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+ $cdonctab $fixzgrid $delcode333 -setgrid,$gpgrid grid_$$_01.srv gaussian$$.nc
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+ $cdonctab merge spectral$$.nc gaussian$$.nc tempfile0$$.nc
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+ $cdonctab sealevelpressure -sp2gp tempfile0$$.nc press$$.nc
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+ $cdozip $fmonth $fyear -merge tempfile0$$.nc press$$.nc tempfile$$.nc
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+ else
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+ $cdonctab $fmonth $fyear $fixzgrid -setgrid,$spgrid grid_$$_02.srv spectral$$.nc
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+ $cdonctab $fmonth $fyear $fixzgrid $delcode333 -setgrid,$gpgrid grid_$$_01.srv gaussian$$.nc
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+ $cdozip merge spectral$$.nc gaussian$$.nc tempfile$$.nc
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+ fi
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+else
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+ $cdoziptab setgrid,$gpgrid $fmonth $fyear $infile tempfile$$.nc
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+fi
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+else
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+# If LSG
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+ #$cdonc copy $fmonth $fyear $infile tempinfile$$.nc
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+ $cdonc splitzaxis $infile zaxis$$_
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+ $cdonc setzaxis,zaxislsgu$$.txt -delcode,7 zaxis$$_01.nc fixzaxis$$_01u.nc # code 7 is w
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+ $cdonc setzaxis,zaxislsgw$$.txt -selcode,7 zaxis$$_01.nc fixzaxis$$_01w.nc
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+ $cdonc setzaxis,zaxislsgc$$.txt zaxis$$_03.nc fixzaxis$$_03.nc
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+ $cdonc merge fixzaxis$$_01u.nc fixzaxis$$_01w.nc zaxis$$_02.nc fixzaxis$$_03.nc tempin$$.nc
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+ $cdonc setpartab,paramlsg$$.tab $fmonth $fyear tempin$$.nc tempinpar$$.nc
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+ uvars="taux,tauy,depv,ub,vb,utot,vtot,wetvec"
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+ $cdonc setgrid,$gpgridu $fmonth $fyear -selname,$uvars tempinpar$$.nc ufields$$.nc
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+ $cdonc setgrid,$gpgridt $fmonth $fyear -delname,$uvars tempinpar$$.nc tfields$$.nc
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+ $cdozip merge tfields$$.nc ufields$$.nc tempfile$$.nc
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|
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+fi
|
|
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+
|
|
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+if [ -z "$delcodes" ]
|
|
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+then
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+ mv tempfile$$.nc $outfile
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|
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+else
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+ $cdozip delcode,$delcodes tempfile$$.nc $outfile
|
|
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+fi
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+rm -f spectral$$.nc gaussian$$.nc grid_$$_01.srv grid_$$_02.srv inzgrid$$.txt zgrid$$.txt tempfile$$.nc param$$.tab lsggridt$$.txt lsggridu$$.txt ufields$$.nc tfields$$.nc zaxislsgu$$.txt zaxislsgw$$.txt zaxislsgc$$.txt zaxis$$_* fixzaxis$$_* tempin$$.nc tempinpar$$.nc paramlsg$$.tab press$$.nc tempfile0$$.nc
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