1. Run RegIPSL (WRF+ORCHIDEE) with default initial conditions for ORCHIDEE.
   1. This run should at least be of one year.
   2. The routing module should not be activated.
2. Generate from the output of this first simulation the atmospheric conditions to drive ORCHIDEE off-line (see script below).
3. Run ORCHIDEE for a number of years off-line with all the options desired. This can be done on Climserv.
4. Restart the RegIPSL simulation now with appropriate initial conditions for ORCHIDEE. These initial conditions should be taken from the step 3.

#!/bin/bash
# Job name 
# @ job_name = ExtractForcing
# Standard output file name
# @ output = ExtractForcing.000001
# Error output file name
# @ error = ExtractForcing.000001
# Job type
# @ job_type = serial
# Specific option for OpenMP parallelization: Number of OpenMP threads per MPI task
# Memory : as_limit=3.5gb max per process per core. With 4 threads per process use max as_limit=14gb
# @ as_limit = 15gb
# Maximum CPU time per task hh:mm:ss
# @ wall_clock_limit = 20:00:00
# End of the header options
# @ queue
#
######################################################################################################
#
# Functions
#
######################################################################################################
function concat2dfields {
    infile=$1
    outfile=$2
    #
    echo "==> Working on ${infile}"
    #
    # LWdown:long_name = "Mean surface incident longwave" ;
    echo "==> LWdown:long_name = Mean surface incident longwave"
    ncks -h -v rlds ${infile} LWdown.nc
    ncrename -h -O -v rlds,LWdown LWdown.nc
    ncatted -h -a cell_methods,LWdown,o,c,"Time: mean(center)" LWdown.nc
    # SWdown:long_name = "Mean surface incident shortwave" ;
    echo "==> SWdown:long_name = Mean surface incident shortwave"
    ncks -h -v rsds  ${infile} SWdown.nc
    ncrename -h -O -v rsds,SWdown SWdown.nc
    ncatted -h -a cell_methods,SWdown,o,c,"Time: mean(center)" SWdown.nc
    # PSurf:long_name = "Surface pressure at time stamp" ;
    echo "==> PSurf:long_name = Surface pressure at time stamp"
    ncks -h -v ps ${infile} PSurf.nc
    ncrename -h -O -v ps,PSurf  PSurf.nc
    ncatted -h -a cell_methods,PSurf,o,c,"Time: instantaneous" PSurf.nc
    # Rainf:long_name = "Mean rainfall rate" ;
    # Snowf:long_name = "Mean snowfall rate" ;
    echo "==> Snowf:long_name = Mean snowfall rate"
    echo "==> Rainf:long_name = Mean rainfall rate"
    ncap2 -h -v -s 'Snowf=pr*SR;Rainf=pr-(pr*SR)' ${infile} Precipitation.nc
    ncks -h -v Snowf Precipitation.nc Snowf.nc
    # Ensure we do not have negative values
    ncatted -h -a long_name,Snowf,o,c,"Mean snowfall rate" Snowf.nc
    ncatted -h -a cell_methods,Snowf,o,c,"Time: mean(center)" Snowf.nc
    ncks -h -v Rainf Precipitation.nc Rainf.nc
    # Ensure we do not have negative values
    ncatted -h -a long_name,Rainf,o,c,"Mean rainfall rate" Rainf.nc
    ncatted -h -a cell_methods,Rainf,o,c,"Time: mean(center)" Rainf.nc
    /bin/rm -rf Precipitation.nc Snowfa.nc Rainfa.nc
    # contfrac
    ncks -h -v LANDMASK geo_em.d01.nc contfrac.nc
    ncrename  -h -O -v LANDMASK,contfrac -d south_north,y_grid_M -d west_east,x_grid_M contfrac.nc
    #
    # Merge these variables into the forcing :
    #
    echo "==> Concatenate Surface fields"
    ncwa -a Time contfrac.nc ${outfile}
    ncks -h -A -v LWdown LWdown.nc ${outfile}
    ncks -h -A -v SWdown SWdown.nc ${outfile}
    ncks -h -A -v PSurf PSurf.nc ${outfile}
    ncks -h -A -v Rainf Rainf.nc ${outfile}
    ncks -h -A -v Snowf Snowf.nc ${outfile}
    #
    echo "==> Clean-up 2D"
    /bin/rm -rf contfrac.nc LWdown.nc SWdown.nc PSurf.nc Rainf.nc Snowf.nc
}
function add3dfields {
    #
    infile=$1
    outfile=$2
    # Levels:long_name = "relative height at the first vertical level over surface on the Mass grid" ;
    echo "==> Compute first level height"
    ncap2 -h -v -s 'ZZ0=(PHB(0,:,:)+PH(:,0,:,:))/9.81;ZZ1=(PHB(1,:,:)+PH(:,1,:,:))/9.81' ${infile} ZZ.nc
    ncap2 -h -v -s 'Levels=0.5*(ZZ1-ZZ0)' ZZ.nc Levels.nc
    ncatted -h -a long_name,Levels,o,c,"Height of lowest atmospheric level" Levels.nc
    ncatted -h -a units,Levels,o,c,"m" Levels.nc
    /bin/rm -rf ZZ.nc
    # Compute conversion coefficient for temperature
    echo "==> Conversion for temperature (with P in Pa)"
    ncap2 -h -v -s 'cf=((PB(0,:,:)+P(:,0,:,:))*0.01/1000.0)^0.2854' ${infile} cf.nc
    #
    #
    # Tair:long_name = "air temperature" ;
    echo "==> Tair:long_name = air temperature"
    ncks -h -A -v ta ${infile} cf.nc
    ncap2 -h -v -s 'Tair=ta(:,0,:,:)*cf' cf.nc Tair.nc
    /bin/rm -rf cf.nc
    ncatted -h -a long_name,Tair,o,c,"Near Surface Air Temperature" Tair.nc
    ncatted -h -a cell_methods,Tair,o,c,"Time: instantaneous" Tair.nc
    #
    echo "==> Slicing the 3D fields"
    ncap2 -h -v -s 'Qair=hus(:,0,:,:);WindX=Um(:,0,:,:);WindY=Vm(:,0,:,:)' ${infile} tmp.nc
    ncks -h -A -v SINALPHA,COSALPHA ${infile} tmp.nc
    echo "==> Qair:long_name = Near surface specific humidity"
    ncks -h -v Qair tmp.nc Qair.nc
    ncatted -h -a long_name,Qair,o,c,"Near Surface Specific Air Humidity" Qair.nc
    ncatted -h -a cell_methods,Qair,o,c,"Time: instantaneous" Qair.nc
    echo "==> Wind_E:long_name = Near surface eastward wind speed"
    ncap2 -h -v -s 'Wind_E=WindX*COSALPHA - WindY*SINALPHA' tmp.nc Wind_E.nc
    ncatted -h -a long_name,Wind_E,o,c,"Near Surface Eastward wind" Wind_E.nc
    ncatted -h -a cell_methods,Wind_E,o,c,"Time: instantaneous" Wind_E.nc
    echo "==> Wind_N:long_name = Near surface northward wind speed"
    ncap2 -h -v -s 'Wind_N=WindX*SINALPHA + WindY*COSALPHA' tmp.nc Wind_N.nc
    ncatted -h -a long_name,Wind_N,o,c,"Near Surface Northward wind" Wind_N.nc
    ncatted -h -a cell_methods,Wind_N,o,c,"Time: instantaneous" Wind_N.nc
    #
    # Merge 3D var into the forcing file
    #
    echo "==> Add atmospheric fields"
    ncks -A -v Levels Levels.nc ${outfile}
    ncks -A -v Tair Tair.nc ${outfile}
    ncks -A -v Qair Qair.nc ${outfile}
    ncks -A -v Wind_E Wind_E.nc ${outfile}
    ncks -A -v Wind_N Wind_N.nc ${outfile}
    #
    echo "==> Clean-up 3D"
    /bin/rm -rf Levels.nc Tair.nc Qair.nc Wind_E.nc Wind_N.nc tmp.nc 
}
function rshfilesize {
    TEST=$(rsh ergon "test -e $1 && echo \"0\" || echo \"1\"")
    if [  -eq 0 ] ;  then
	filesz=$(rsh ergon stat --printf="%s" $1)
    else
        filesz=0
    fi
    echo 
}
function cleanupfile {
    infile=$1
    # Delete unneeded variables
    ncrename -h -O -d time_counter,Time 
    ncrename -h -O -v time_centered,Time 
    ncrename -h -O -d y_grid_M,south_north -d x_grid_M,west_east 
    ncks -h -x -v time_counter,time_counter_bounds,time_instant  tmp.nc
    /bin/mv tmp.nc 
    # Correct coordinates
    vars="LWdown SWdown PSurf Levels Tair Qair Wind_E Wind_N Rainf Snowf"
    for v in  ; do
	ncatted -h -a coordinates,,o,c,"Time nav_lat_grid_M nav_lon_grid_M" 
    done
    ncatted -h -O -a history,global,o,c,'Built by ExtractForcing.sh' 
    /bin/rm -rf tmp.nc
}
#
######################################################################################################
#
# Main script
#
######################################################################################################
#
cd 
#
EXP="MEDCORDEX-A"
FPATH="IGCM_OUT/RegIPSL/PROD/${EXP}/WRFORCH/ATM/Output/HF/"
module load nco/4.4.6
module load cdo/1.5.9
module load python/2.7.10
#
# Clean-up
#
/bin/rm -rf *.nc *.tmp
mfget ${FPATH}/${FILE}
mfget ../rron960/rron600/MORCE2/FICHIERS/WRF-GEOGRID/GEOGRID-MORCE-STREAM2/geo_em.d01.nc
ls -l
#
cp ~/NetCDFTools/rebasetime.py .
#
# Using only NCO tools we extract from a WRF simulation (using XIOS output) the forcing data needed
# for ORCHIDEE. The 3hourly file will be the basis for the extraction.
#
EXISTS=($(rsh ergon ls "WRF_Forcing/${EXP}"))
#
for YEAR in 
0115eq 1979 1999
0032; do
    #
    RESFILE=flux_${YEAR}.nc
    fsz=$(rshfilesize "WRF_Forcing/${EXP}/${RESFILE}")
    #
    # Only do the work if the file is too small
    #
    if [ ${fsz} -lt 8000000000 ] ; then
	#
	# Get list of files to treat
	#
	LIST=($(rsh ergon ls "/*_*_*.nc"))
	#
	if [ ${#LIST[@]} -eq 4 ] ; then
	    for ff in ${LIST[*]} ; do
		#
		mfget 
		FILE=$(basename )
		EXT=$(echo  | cut -d '_' -f 2-3)
		#
		# Uncompress
		ncks --fl_fmt=classic ${FILE} workfile.nc
		forcingfile="forcing_${EXT}.nc"
		#
		concat2dfields workfile.nc ${forcingfile}
		add3dfields workfile.nc ${forcingfile}
		#
		/bin/rm workfile.nc
		#
	    done
	    #
	    # Transfer the forcing file to the mass store.
	    #
	    ncrcat -h forcing_${YEAR}*.nc ${RESFILE}
	    cleanupfile ${RESFILE}
	    python rebasetime.py -d 1979-01-01 ${RESFILE}
	    mfput ${RESFILE} WRF_Forcing/${EXP}
	    /bin/rm forcing_1979*.nc ${RESFILE}
	    #
	    # Should the geo_em file not already be there, transfer it.
	    #
	    fsz=$(rshfilesize "WRF_Forcing/${EXP}/geo_em.d01.nc")
	    if [ ${fsz} -lt 10 ] ; then
		mfput geo_em.d01.nc WRF_Forcing/${EXP}
	    fi
	else
	    echo " does not have enough semesters for building forcing"
	fi

    fi
    
done