#!/bin/bash
#
# Generate external parameters for HDCP2 simulations
# using GLOBCOVER2009, FAO DSMW, ASTER, Lake Database
# 06.2014 Daniel Klocke
# Adapted for Blizzard by Anurag Dipankar
# Adapted for mistral by Pavan Siligam

#=====================================
# slrum batch job parameters
# these are specified in cylc suite.rc
#-------------------------------------
#SBATCH --account=bm0682
#SBATCH --job-name=extpar_icon_mistral.run
#SBATCH --partition=compute2
#SBATCH --nodes=1
#SBATCH --threads-per-core=2
#SBATCH --output=LOG.extpar_icon_mistral.run.%j.o
#SBATCH --error=LOG.extpar_icon_mistral.run.%j.o
#SBATCH --exclusive
# #
#========================================
# GENERAL REMARKS (Guido)
# Depending on the selection of globcover and orography things can get weird.
# so please not the following:
# -ASTER topography only goes to 35N, if you want to go south you won't get far
# -GLOBCOVER HDCP2 only works for northern Europe
# 
# REMOVE EVERYTHING FROM EXP FOLDER BEFORE LAUNCHING WHEN CHANGING GRID!!!!
#-----------------------------------------------------------------------------
# openmp environment variables
# ----------------------------
export OMP_NUM_THREADS=24
export OMP_SCHEDULE=static,16
export OMP_DYNAMIC="false"
export OMP_STACKSIZE=128M
ulimit -s unlimited

set -e

SWROOT=/sw/rhel6-x64
GRIBROOT=${SWROOT}/grib_api/grib_api-1.13.0-intel14
export GRIB_DEFINITION_PATH=${GRIBROOT}/share/grib_api/definitions/:${GRIBROOT}/share/grib_api/definitions/grib2/localConcepts/edzw
export GRIB_SAMPLE_PATH=${GRIBROOT}/share/grib_api/samples

data_dir=/work/bm0834/k203095/pool/EXTPAR_INPUT

#For input grid
filename=hdcp2_R2B07-grid
#
#Where Binaries are
progdir=/work/mh0731/m300382/extpar_lem/bin
#
workdir=/work/mh0731/m300382/extpar_lem/exp
#
#Grid dir
#icon_grid_dir=/work/mh0731/m300382/icon-GridGenerator-dev/grids
icon_grid_dir=/scratch/m/m300382/temp

#
# set target grid definition 
icon_grid_file=${filename}.nc


if [[ ! -d ${workdir} ]] ; then
  mkdir -p ${workdir} 
fi
cd ${workdir}
pwd

binary_extpar_consistency_check=extpar_consistency_check.exe
binary_aot=extpar_aot_to_buffer.exe
binary_tclim=extpar_cru_to_buffer.exe
binary_lu=extpar_landuse_to_buffer.exe
binary_topo=extpar_topo_to_buffer.exe
binary_ndvi=extpar_ndvi_to_buffer.exe
binary_soil=extpar_soil_to_buffer.exe
binary_flake=extpar_flake_to_buffer.exe
binary_alb=extpar_alb_to_buffer.exe



cat > INPUT_grid_org << EOF_go
&GRID_DEF 
 igrid_type = 1,
 domain_def_namelist='INPUT_ICON_GRID'
/ 
EOF_go


cat > INPUT_ICON_GRID << EOF5
&icon_grid_info
  icon_grid_dir='${icon_grid_dir}',
  icon_grid_nc_file ='${filename}.nc'
/
EOF5

#---

grib_output_filename="extpar_${filename}.g2"
netcdf_output_filename="extpar_${filename}.nc"
grib_sample='GRIB2'

echo $netcdf_output_filename
echo $grib_output_filename
#----

raw_data_alb='month_alb.nc'
raw_data_alnid='month_alnid.nc'
raw_data_aluvd='month_aluvd.nc'
buffer_alb='month_alb_BUFFER.nc'
output_alb='month_alb_extpar_ICON.nc'

raw_data_aot='aerosol_optical_thickness.nc'
buffer_aot='extpar_aot_BUFFER.nc'
output_aot='aot_extpar_ICON.nc'

raw_data_tclim_coarse='absolute_hadcrut3.nc'
raw_data_tclim_fine='CRU_T2M_SURF_clim.nc'
buffer_tclim='crutemp_climF_extpar_BUFFER.nc'
output_tclim='crutemp_climF_extpar_ICON.nc'

raw_data_glc2000='glc2000_byte.nc'
buffer_glc2000='extpar_landuse_BUFFER.nc'
output_glc2000='extpar_landuse_ICON.nc'
raw_data_glcc='glcc_usgs_class_byte.nc'
buffer_glcc='glcc_landuse_BUFFER.nc'
output_glcc='glcc_landuse_ICON.nc'

raw_data_globcover_0='GLOBCOVER_0_16bit.nc'
raw_data_globcover_1='GLOBCOVER_1_16bit.nc'
raw_data_globcover_2='GLOBCOVER_2_16bit.nc'
raw_data_globcover_3='GLOBCOVER_3_16bit.nc'
raw_data_globcover_4='GLOBCOVER_4_16bit.nc'
raw_data_globcover_5='GLOBCOVER_5_16bit.nc'
raw_data_globcover='GLOBCOVER_USERSPECIF_HDCP2.nc'
buffer_lu='extpar_landuse_BUFFER.nc'
output_lu='extpar_landuse_ICON.nc'

raw_data_globe_A10='GLOBE_A10.nc'
raw_data_globe_B10='GLOBE_B10.nc'
raw_data_globe_C10='GLOBE_C10.nc'
raw_data_globe_D10='GLOBE_D10.nc'
raw_data_globe_E10='GLOBE_E10.nc'
raw_data_globe_F10='GLOBE_F10.nc'
raw_data_globe_G10='GLOBE_G10.nc'
raw_data_globe_H10='GLOBE_H10.nc'
raw_data_globe_I10='GLOBE_I10.nc'
raw_data_globe_J10='GLOBE_J10.nc'
raw_data_globe_K10='GLOBE_K10.nc'
raw_data_globe_L10='GLOBE_L10.nc'
raw_data_globe_M10='GLOBE_M10.nc'
raw_data_globe_N10='GLOBE_N10.nc'
raw_data_globe_O10='GLOBE_O10.nc'
raw_data_globe_P10='GLOBE_P10.nc'

buffer_topo='topography_BUFFER.nc'
output_topo='topography_ICON.nc'

raw_data_ndvi='NDVI_1998_2003.nc'
buffer_ndvi='NDVI_BUFFER.nc'
output_ndvi='ndvi_extpar_ICON.nc'

raw_data_soil_FAO='FAO_DSMW_DP.nc'
raw_data_soil_HWSD='HWSD0_30_texture_2.nc'
raw_data_deep_soil='HWSD30_100_texture_2.nc'
buffer_soil='SOIL_BUFFER.nc'
output_soil='SOIL_ICON.nc'

raw_lookup_table_HWSD='LU_TAB_HWSD_UF.data'
raw_HWSD_data='HWSD_DATA_COSMO.data'
raw_HWSD_data_deep='HWSD_DATA_COSMO_S.data'
raw_HWSD_data_extpar='HWSD_DATA_COSMO_EXTPAR.asc'

raw_data_flake='lakedepth.nc'
buffer_flake='flake_BUFFER.nc'
output_flake='ext_par_flake_ICON.nc'



# create input namelists 
cat > INPUT_AOT << EOF_aot
&aerosol_raw_data
  raw_data_aot_path='',
  raw_data_aot_filename='${raw_data_aot}'
/  
&aerosol_io_extpar
  aot_buffer_file='${buffer_aot}',
  aot_output_file='${output_aot}'
/
EOF_aot
#---
cat > INPUT_TCLIM << EOF_tclim
&t_clim_raw_data
  raw_data_t_clim_path='',
  raw_data_t_clim_filename='${raw_data_tclim_coarse}'
  raw_data_t_id = 2
/  

&t_clim_io_extpar
  t_clim_buffer_file='crutemp_climC_extpar_BUFFER.nc',
  t_clim_output_file='crutemp_climC_extpar_ICON.nc'
/  
EOF_tclim
#---
# &lu_raw_data
#    raw_data_lu_path='',
#    raw_data_lu_filename='${raw_data_globcover}',
#    i_landuse_data=1,
#    ilookup_table_lu=1,
#    ntiles_globcover=1
# /

cat > INPUT_LU << EOF_lu
&lu_raw_data
  raw_data_lu_path='',
  raw_data_lu_filename='${raw_data_globcover_0}' '${raw_data_globcover_1}' '${raw_data_globcover_2}' '${raw_data_globcover_3}' '${raw_data_globcover_4}' '${raw_data_globcover_5}',
  i_landuse_data=1,
  ilookup_table_lu=1,
  ntiles_globcover=6
/
&lu_io_extpar
   lu_buffer_file='${buffer_lu}',
   lu_output_file='${output_lu}'
/
&glcc_raw_data
   raw_data_glcc_path='',
   raw_data_glcc_filename='${raw_data_glcc}'
/
&glcc_io_extpar
   glcc_buffer_file='${buffer_glcc}',
   glcc_output_file='${output_glcc}'
/
EOF_lu
#---
#cat > INPUT_ORO << EOF_oro
#&orography_io_extpar
#orography_buffer_file='${buffer_topo}',
#orography_output_file='${output_topo}'
#/
#&orography_raw_data
#itopo_type = 2
#lsso_param = .TRUE., 
#raw_data_orography_path='',
#ntiles_column = 2,
#ntiles_row = 4,
#topo_files = 'topo.ASTER_orig_T006.nc' 'topo.ASTER_orig_T007.nc' 'topo.ASTER_orig_T018.nc' 'topo.ASTER_orig_T019.nc' 'topo.ASTER_orig_T030.nc' 'topo.ASTER_orig_T031.nc ' 'topo.ASTER_orig_T042.nc' 'topo.ASTER_orig_T043.nc' 
#/
#EOF_oro
cat > INPUT_ORO << EOF_oro
   &orography_io_extpar
     orography_buffer_file='${buffer_topo}',
     orography_output_file='${output_topo}'
  /
   &orography_raw_data
    itopo_type = 1
    lsso_param = .TRUE., 
    raw_data_orography_path='',
    ntiles_column = 4,
    ntiles_row = 4,
    topo_files = ${raw_data_globe_A10} ${raw_data_globe_B10}  ${raw_data_globe_C10}  ${raw_data_globe_D10}  ${raw_data_globe_E10}  ${raw_data_globe_F10}  ${raw_data_globe_G10}  ${raw_data_globe_H10}  ${raw_data_globe_I10}  ${raw_data_globe_J10}  ${raw_data_globe_K10}  ${raw_data_globe_L10}  ${raw_data_globe_M10}  ${raw_data_globe_N10}  ${raw_data_globe_O10}  ${raw_data_globe_P10}  
   /
EOF_oro
#----
cat > INPUT_OROSMOOTH << EOF_orosmooth
&orography_smoothing
  lfilter_oro=.FALSE.
/
EOF_orosmooth
#---
cat > INPUT_RADTOPO << EOF_rad
&radtopo
  lradtopo=.FALSE.,
  nhori=24,
/
EOF_rad
#---
#---
cat > INPUT_NDVI << EOF_ndvi
&ndvi_raw_data
  raw_data_ndvi_path='',
  raw_data_ndvi_filename='${raw_data_ndvi}'
/  
&ndvi_io_extpar
 ndvi_buffer_file='${buffer_ndvi}',
 ndvi_output_file='${output_ndvi}'
/
EOF_ndvi
#---
cat > INPUT_SOIL << EOF_soil
&soil_raw_data
 isoil_data = 2,
 ldeep_soil = .false.,
 raw_data_soil_path='',
 raw_data_soil_filename='${raw_data_soil_HWSD}'
 raw_data_deep_soil_filename='${raw_data_deep_soil}'
/
&soil_io_extpar
  soil_buffer_file='${buffer_soil}',
  soil_output_file='${output_soil}'
/ 
&HWSD_index_files
 path_HWSD_index_files='',
 lookup_table_HWSD='${raw_lookup_table_HWSD}', 
 HWSD_data='${raw_HWSD_data}',
 HWSD_data_deep='${raw_HWSD_data_deep}',
 HWSD_data_extpar='${raw_HWSD_data_extpar}'
/
EOF_soil
#---
cat > INPUT_FLAKE << EOF_flake
&flake_raw_data
   raw_data_flake_path='',
   raw_data_flake_filename='${raw_data_flake}'
/
&flake_io_extpar
   flake_buffer_file='${buffer_flake}'
   flake_output_file='${output_flake}'
/
EOF_flake

#---

cat > INPUT_ALB << EOF_alb
&alb_raw_data
  raw_data_alb_path='',
  raw_data_alb_filename='${raw_data_alb}'
/
&alnid_raw_data
  raw_data_alb_path='',
  raw_data_alnid_filename='${raw_data_alnid}'
/
&aluvd_raw_data
  raw_data_alb_path='',
  raw_data_aluvd_filename='${raw_data_aluvd}'
/
&alb_io_extpar
  alb_buffer_file='${buffer_alb}',
  alb_output_file='${output_alb}'
/
&alb_source_file     
  alb_source='al'
  alnid_source='alnid'
  aluvd_source='aluvd'
/
EOF_alb


# consistency check
cat > INPUT_CHECK << EOF_check
&extpar_consistency_check_io
  grib_output_filename='${grib_output_filename}',
  netcdf_output_filename='${netcdf_output_filename}',
  orography_buffer_file='${buffer_topo}',
  soil_buffer_file='${buffer_soil}',
  lu_buffer_file='${buffer_lu}',
  glcc_buffer_file='${buffer_glcc}',
  flake_buffer_file='${buffer_flake}',
  ndvi_buffer_file='${buffer_ndvi}',
  t_clim_buffer_file='${buffer_tclim}',
  aot_buffer_file='${buffer_aot}',
  alb_buffer_file='${buffer_alb}',
  i_lsm_data=1,
  land_sea_mask_file="",
  number_special_points=0
/  
EOF_check

# link raw data files to local workdir
ln -s -f ${data_dir}/${raw_data_alb}
ln -s -f ${data_dir}/${raw_data_alnid}
ln -s -f ${data_dir}/${raw_data_aluvd}

ln -s -f ${data_dir}/${raw_data_aot}

ln -s -f ${data_dir}/${raw_data_tclim_coarse}
ln -s -f ${data_dir}/${raw_data_tclim_fine}

ln -s -f ${data_dir}/${raw_data_glc2000}
ln -s -f ${data_dir}/${raw_data_glcc}

ln -s -f ${data_dir}/${raw_data_globcover_0}
ln -s -f ${data_dir}/${raw_data_globcover_1}
ln -s -f ${data_dir}/${raw_data_globcover_2}
ln -s -f ${data_dir}/${raw_data_globcover_3}
ln -s -f ${data_dir}/${raw_data_globcover_4}
ln -s -f ${data_dir}/${raw_data_globcover_5}
ln -s -f ${data_dir}/${raw_data_globcover}

ln -s -f ${data_dir}/${raw_data_globe_A10} 
ln -s -f ${data_dir}/${raw_data_globe_B10}
ln -s -f ${data_dir}/${raw_data_globe_C10} 
ln -s -f ${data_dir}/${raw_data_globe_D10} 
ln -s -f ${data_dir}/${raw_data_globe_E10}
ln -s -f ${data_dir}/${raw_data_globe_F10} 
ln -s -f ${data_dir}/${raw_data_globe_G10} 
ln -s -f ${data_dir}/${raw_data_globe_H10} 
ln -s -f ${data_dir}/${raw_data_globe_I10} 
ln -s -f ${data_dir}/${raw_data_globe_J10} 
ln -s -f ${data_dir}/${raw_data_globe_K10} 
ln -s -f ${data_dir}/${raw_data_globe_L10} 
ln -s -f ${data_dir}/${raw_data_globe_M10} 
ln -s -f ${data_dir}/${raw_data_globe_N10} 
ln -s -f ${data_dir}/${raw_data_globe_O10} 
ln -s -f ${data_dir}/${raw_data_globe_P10} 

ln -s -f ${data_dir}/topo.ASTER_orig_T006.nc 
ln -s -f ${data_dir}/topo.ASTER_orig_T007.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T008.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T018.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T019.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T020.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T030.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T031.nc 
ln -s -f ${data_dir}/topo.ASTER_orig_T032.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T042.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T043.nc
ln -s -f ${data_dir}/topo.ASTER_orig_T044.nc
#ln -s -f ${data_dir}/topo.ASTER_orig_T054.nc
#ln -s -f ${data_dir}/topo.ASTER_orig_T055.nc


ln -s -f ${data_dir}/${raw_data_ndvi}

ln -s -f ${data_dir}/${raw_data_soil_FAO}

ln -s -f ${data_dir}/${raw_data_soil_HWSD}
ln -s -f ${data_dir}/${raw_data_deep_soil}

ln -s -f ${data_dir}/${raw_lookup_table_HWSD}
ln -s -f ${data_dir}/${raw_HWSD_data}
ln -s -f ${data_dir}/${raw_HWSD_data_deep}

ln -s -f ${data_dir}/${raw_data_flake}
ln -s -f ${icon_grid_dir}/${icon_grid_file}


# run the programs
# the next seven programs can run independent of each other 
 time ${progdir}/${binary_tclim}
#---
cat > INPUT_TCLIM << EOF_tclim
&t_clim_raw_data
  raw_data_t_clim_path='',
  raw_data_t_clim_filename='${raw_data_tclim_fine}',
  raw_data_t_id = 1
/  

&t_clim_io_extpar
  t_clim_buffer_file='${buffer_tclim}',
  t_clim_output_file='${output_tclim}'
/  
EOF_tclim
 time ${progdir}/${binary_lu}
 time ${progdir}/${binary_tclim}
 time ${progdir}/${binary_alb}
 time ${progdir}/${binary_aot}
 time ${progdir}/${binary_topo}
 time ${progdir}/${binary_ndvi}
 time ${progdir}/${binary_soil}
 time ${progdir}/${binary_flake}

printenv | grep GRIB_

cat > INPUT_TCLIM_FINAL << EOF_tclim
&t_clim_raw_data
  raw_data_t_clim_path='',
  raw_data_t_clim_filename='${raw_data_tclim_fine}',
  raw_data_t_id = 1
/  

&t_clim_io_extpar
  t_clim_buffer_file='crutemp_climF_extpar_BUFFER.nc',
  t_clim_output_file='crutemp_climC_extpar_BUFFER.nc'
/  
EOF_tclim

time ${progdir}/${binary_extpar_consistency_check}

echo 'External parameters for refinement grid of ICON model generated in'
echo  $workdir