#! /bin/bash

##########################################################
laphysiq="mars_lmd" ## default value
config="" ## default value
while getopts "p:c:" options; do
  case $options in
   p ) laphysiq="${OPTARG}";;     ## choose physics
   c ) config="${OPTARG}";;     ## choose config
  esac
done
##########################################################
echo '*** copying physics: '$laphysiq
##########################################################

echo '*** linking sources from ...'
WRFSRC=$PWD/SRC/
if [[ "${config}" == "les" ]]
then
  WRFSRC=$PWD/SRC/LES/
fi
echo $WRFSRC
echo '*** to ...'
HERE=$PWD
echo $HERE


#mkdir WPS
#cd WPS
#ln -sf $WRFSRC/WPS/wps_mars .
#ln -sf $WRFSRC/WPS/switch_WPS_Mars .
#cd ..

mkdir zeWRFV2
#ln -sf $WRFSRC/prepare_ini .
cd zeWRFV2 

echo '*** start defining folders and links'
ln -sf $WRFSRC/WRFV2/clean . 
ln -sf $WRFSRC/WRFV2/compile .
#ln -sf $WRFSRC/WRFV2/makemeso .
ln -sf $WRFSRC/WRFV2/configure .
ln -sf $WRFSRC/WRFV2/Makefile .
#ln -sf $WRFSRC/WRFV2/mars.sed* .
ln -sf $WRFSRC/WRFV2/*.h .
ln -sf $WRFSRC/WRFV2/configure.defaults.* .
ln -sf $WRFSRC/WRFV2/call_meso_inifis?.inc .
ln -sf $WRFSRC/WRFV2/call_meso_physiq?.inc .

#\rm meso_dimphys.h
#cp $WRFSRC/WRFV2/meso_dimphys.h .
#cp $WRFSRC/WRFV2/call_*.inc .
#cp $WRFSRC/WRFV2/custom*.inc .
mkdir Registry
ln -sf $WRFSRC/WRFV2/Registry/* Registry/
  ### this is to allow one to change Registry somewhere without it being changed everywhere !
  rm Registry/Registry.EM
  cp $WRFSRC/WRFV2/Registry/Registry.EM Registry/
mkdir arch
ln -sf $WRFSRC/WRFV2/arch/* arch/
mkdir dyn_em
ln -sf $WRFSRC/WRFV2/dyn_em/* dyn_em/
mkdir dyn_exp
ln -sf $WRFSRC/WRFV2/dyn_exp/* dyn_exp/
mkdir dyn_nmm
ln -sf $WRFSRC/WRFV2/dyn_nmm/* dyn_nmm/
mkdir frame
ln -sf $WRFSRC/WRFV2/frame/* frame/
mkdir inc
ln -sf $WRFSRC/WRFV2/inc/* inc/
mkdir main
ln -sf $WRFSRC/WRFV2/main/* main/
mkdir phys
ln -sf $WRFSRC/WRFV2/phys/* phys/
echo $laphysiq
ln -sf $WRFSRC/WRFV2/phys/dynphy_wrf_$laphysiq/* phys/
mkdir run
ln -sf $WRFSRC/WRFV2/run/* run/
mkdir share
ln -sf $WRFSRC/WRFV2/share/* share/
mkdir tools
ln -sf $WRFSRC/WRFV2/tools/* tools/
\rm tools/DOMAIN_TIME_TEST
\rm tools/CodeBase
mkdir tools/DOMAIN_TIME_TEST
ln -sf $WRFSRC/WRFV2/tools/DOMAIN_TIME_TEST/* tools/DOMAIN_TIME_TEST/
mkdir tools/CodeBase
ln -sf $WRFSRC/WRFV2/tools/CodeBase/* tools/CodeBase/
mkdir external
ln -sf $WRFSRC/WRFV2/external/Makefile external/
mkdir external/io_int
ln -sf $WRFSRC/WRFV2/external/io_int/* external/io_int/
mkdir external/esmf_time_f90
ln -sf $WRFSRC/WRFV2/external/esmf_time_f90/* external/esmf_time_f90/
mkdir external/io_netcdf
ln -sf $WRFSRC/WRFV2/external/io_netcdf/* external/io_netcdf/
mkdir external/io_grib1
ln -sf $WRFSRC/WRFV2/external/io_grib1/* external/io_grib1/
\rm external/io_grib1/MEL_grib1
\rm external/io_grib1/WGRIB
\rm external/io_grib1/build
\rm external/io_grib1/grib1_util
mkdir external/io_grib1/MEL_grib1
ln -sf $WRFSRC/WRFV2/external/io_grib1/MEL_grib1/* external/io_grib1/MEL_grib1/
mkdir external/io_grib1/WGRIB
ln -sf $WRFSRC/WRFV2/external/io_grib1/WGRIB/* external/io_grib1/WGRIB/
mkdir external/io_grib1/grib1_util
ln -sf $WRFSRC/WRFV2/external/io_grib1/grib1_util/* external/io_grib1/grib1_util/
mkdir external/io_grib1/build
mkdir external/io_grib_share
ln -sf $WRFSRC/WRFV2/external/io_grib_share/* external/io_grib_share/
\rm external/io_grib_share/build
mkdir external/io_grib_share/build
ln -sf $WRFSRC/WRFV2/external/io_grib_share/build/* external/io_grib_share/build/
mkdir external/ioapi_share
ln -sf $WRFSRC/WRFV2/external/ioapi_share/* external/ioapi_share/
mkdir external/io_phdf5
ln -sf $WRFSRC/WRFV2/external/io_phdf5/* external/io_phdf5/
mkdir external/RSL_LITE
ln -sf $WRFSRC/WRFV2/external/RSL_LITE/* external/RSL_LITE/
mkdir external/io_grib2
ln -sf $WRFSRC/WRFV2/external/io_grib2/* external/io_grib2/
\rm external/io_grib2/bacio-1.3
\rm external/io_grib2/g2lib
mkdir external/io_grib2/bacio-1.3
ln -sf $WRFSRC/WRFV2/external/io_grib2/bacio-1.3/* external/io_grib2/bacio-1.3/
mkdir external/io_grib2/g2lib
ln -sf $WRFSRC/WRFV2/external/io_grib2/g2lib/* external/io_grib2/g2lib/
mkdir external/io_pnetcdf
ln -sf $WRFSRC/WRFV2/external/io_pnetcdf/* external/io_pnetcdf/
mkdir external/RSL
ln -sf $WRFSRC/WRFV2/external/RSL/* external/RSL/
\rm external/RSL/RSL
mkdir external/RSL/RSL
ln -sf $WRFSRC/WRFV2/external/RSL/RSL/* external/RSL/RSL/
mkdir external/io_esmf
ln -sf $WRFSRC/WRFV2/external/io_esmf/* external/io_esmf/
mkdir external/io_mcel
ln -sf $WRFSRC/WRFV2/external/io_mcel/* external/io_mcel/
echo ${laphysiq}
if [[ "${laphysiq}" == *"void"* ]]
then

  ## case with no physics
  rm -f physics.sed
  touch physics.sed

else
  ## case with physics
  echo $laphysiq
  mkdir $laphysiq
  mkdir $laphysiq/libf
  mkdir $laphysiq/libf/grid
  ln -sf $WRFSRC/WRFV2/$laphysiq/libf/grid/* $laphysiq/libf/grid/
  mkdir $laphysiq/libf/dyn3d
  ln -sf $WRFSRC/WRFV2/$laphysiq/libf/dyn3d/* $laphysiq/libf/dyn3d/
  mkdir $laphysiq/libf/bibio
  ln -sf $WRFSRC/WRFV2/$laphysiq/libf/bibio/* $laphysiq/libf/bibio/
  if [[ "${laphysiq}" == *"mars"* ]]
  then
    ln -sf $WRFSRC/WRFV2/$laphysiq/makegcm* $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/meso_dimphys.h* $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/create_make_gcm $laphysiq/
    #ln -sf $WRFSRC/WRFV2/$laphysiq/makefile $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/duplicate* $laphysiq/libf/
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/generate* $laphysiq/libf/
    mkdir $laphysiq/libf/aeronomars
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/aeronomars/* $laphysiq/libf/aeronomars/
    mkdir $laphysiq/libf/phymars
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/phymars/* $laphysiq/libf/phymars/
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/phy_common/* $laphysiq/libf/phymars/
    ###
    \rm $laphysiq/libf/phymars/dimphys.h
  elif [[ "${laphysiq}" == *"venus"* ]]
  then
    ln -sf $WRFSRC/WRFV2/$laphysiq/makelmdz $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/deftank $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/arch* $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/tmp* $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf_gcm $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/makefile $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/make_dir $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/create_make_gcm $laphysiq/
    ln -sf $WRFSRC/WRFV2/$laphysiq/Tools $laphysiq/
    mkdir $laphysiq/ioipsl
    ln -sf $WRFSRC/WRFV2/$laphysiq/ioipsl/modipsl/lib/* $laphysiq/ioipsl/
    mkdir $laphysiq/libf/phyvenus
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/phyvenus/* $laphysiq/libf/phyvenus/
    mkdir $laphysiq/libf/phy_common
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/phy_common/* $laphysiq/libf/phy_common/
    mkdir $laphysiq/libf/misc
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/misc/* $laphysiq/libf/misc/
    mkdir $laphysiq/libf/filtrez
    ln -sf $WRFSRC/WRFV2/$laphysiq/libf/filtrez/* $laphysiq/libf/filtrez/
  fi
  mkdir $laphysiq/libo
  #touch $laphysiq/makefile

  sed s+"YORGLYORGL"+"$laphysiq"+g $WRFSRC/WRFV2/physics.sed > physics.sed
fi

mkdir test
mkdir test/em_real
mkdir test/em_quarter_ss
ln -sf $WRFSRC/WRFV2/test/em_real/* test/em_real/

echo '*** end'