rm -fr INPUT RESTART
if [ $NPX = 97 ]; then
  inputdir=FV3_input_data
elif [ $NPX = 49 ]; then
  inputdir=FV3_input_data48
elif [ $NPX = 193 ]; then
  inputdir=FV3_input_data192
elif [ $NPX = 385 ]; then
  inputdir=FV3_input_data384
elif [ $NPX = 769 ]; then
  inputdir=FV3_input_data768
fi
echo "inputdir=$inputdir,NPX=$NPX"

OPNREQ_TEST=${OPNREQ_TEST:-false}
SUFFIX=${RT_SUFFIX}
if [ $WARM_START = .false. ]; then
  mkdir INPUT RESTART
  cp -r @[INPUTDATA_ROOT]/${inputdir}/INPUT_L127/* ./INPUT/.
else
  mkdir INPUT RESTART

  if [[ ${OPNREQ_TEST} == true ]]; then
    SUFFIX=${BL_SUFFIX}
  fi

  # WAVE restart file for ATMW ORT tests
  if [[ $CPLWAV == .true. ]]; then
    if [[ $med_model == cmeps ]] && [[ $RUNTYPE == continue ]]; then
      # CMEPS restart and pointer files
      RFILE=ufs.atmw.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
      cp  ../${DEP_RUN}${SUFFIX}/RESTART/${RFILE} .
      ls -1 ${RFILE}>rpointer.cpl
    fi
    RFILE=ufs.atmw.ww3.r.${RESTART_FILE_SUFFIX_SECS}
    cp ../${DEP_RUN}${SUFFIX}/${RFILE} .
  fi

  if [ $MODEL_INITIALIZATION = false ]; then
    #read_inc and iau tests restart from fh=24
    CURRDIR=`pwd`
    FILEDIR=${CURRDIR}/../${DEP_RUN}${SUFFIX}/RESTART
  else
    #for warm start from initialiation time
    FILEDIR=@[INPUTDATA_ROOT]/${inputdir}/INPUT_L127_GDAS
  fi

  if [[ ${IAU_OFFSET} != 0 ]] || [[ $READ_INCREMENT = .true. ]]; then

    if [ $MODEL_INITIALIZATION = false ]; then
      cp ${FILEDIR}/../INPUT/fv3_increment.nc INPUT/.
      cp ${FILEDIR}/../INPUT/grid_spec.nc INPUT/.
      cp ${FILEDIR}/../INPUT/*_grid.tile*.nc INPUT/.
      cp ${FILEDIR}/../INPUT/oro_data.tile*.nc INPUT/.
    else
      cp ${FILEDIR}/fv_increment*.nc INPUT/.
      cp ${FILEDIR}/grid_spec.nc INPUT/.
      cp ${FILEDIR}/*_grid.tile*.nc INPUT/.
      cp ${FILEDIR}/oro_data.tile*.nc INPUT/.
    fi
    cp ${FILEDIR}/coupler.res INPUT/.
    cp ${FILEDIR}/fv_core.res.* INPUT/.
    cp ${FILEDIR}/fv_srf_wnd.res.* INPUT/.
    cp ${FILEDIR}/fv_tracer.* INPUT/.
    cp ${FILEDIR}/phy_data.* INPUT/.
    cp ${FILEDIR}/sfc_data.* INPUT/.
  else
    #restart test start from fh FHROT
    cp -r ../${DEP_RUN}${SUFFIX}/RESTART/${RESTART_FILE_PREFIX}.* ./INPUT
    rm -f INPUT/fv_core.res.*
    rm -f INPUT/fv_srf_wnd.res.*
    rm -f INPUT/fv_tracer.res.*
    rm -f INPUT/phy_data.*
    rm -f INPUT/sfc_data.*
    cp ${FILEDIR}/../INPUT/grid_spec.nc INPUT/.
    cp ${FILEDIR}/../INPUT/*_grid.tile*.nc INPUT/.
    cp ${FILEDIR}/../INPUT/oro_data*.nc INPUT/.
    for RFILE in ../${DEP_RUN}${SUFFIX}/RESTART/${RESTART_FILE_PREFIX}.*; do
      [ -e $RFILE ] || exit 1
      RFILE_OLD=$(basename $RFILE)
      RFILE_NEW="${RFILE_OLD//${RESTART_FILE_PREFIX}./}"
      cp $RFILE INPUT/${RFILE_NEW}
    done
  fi
fi

if [ $TILEDFIX = .true. ]; then
    if [ $CPLLND == .true. ]; then
        cp    @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]/@[ATMRES]*.nc INPUT/.
    else
        cp    @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]/@[ATMRES]*.nc .
    fi
    cp    @[INPUTDATA_ROOT]/FV3_fix/global_glacier.2x2.grb .
    cp    @[INPUTDATA_ROOT]/FV3_fix/global_maxice.2x2.grb .
    cp    @[INPUTDATA_ROOT]/FV3_fix/RTGSST.1982.2012.monthly.clim.grb .
    cp    @[INPUTDATA_ROOT]/FV3_fix/global_snoclim.1.875.grb .
    cp    @[INPUTDATA_ROOT]/FV3_fix/IMS-NIC.blended.ice.monthly.clim.grb .
    cp    @[INPUTDATA_ROOT]/${inputdir}/@[FNSMCC] .
    cp    @[INPUTDATA_ROOT]/${inputdir}/@[FNMSKH_control] .
else
    cp    @[INPUTDATA_ROOT]/${inputdir}/*grb .
fi

if [ $CPLWAV = .true. ]; then
  if [ $WW3_MULTIGRID = 'true' ]; then
    cp    @[INPUTDATA_ROOT_WW3]/mod_def.pointsatmw mod_def.points
    cp    @[INPUTDATA_ROOT_WW3]/@[WW3_MODDEF] .
    cp    @[INPUTDATA_ROOT_WW3]/rmp_src* .
  else
    cp    @[INPUTDATA_ROOT_WW3]/@[WW3_MODDEF] mod_def.ww3
    cp    @[INPUTDATA_ROOT_WW3]/@[MESH_WAV] .
  fi
fi

#inline post
if [[ $POSTAPP = 'global' ]]; then
  cp    ${PATHRT}/parm/post_itag_gfs itag
  cp    ${PATHRT}/parm/postxconfig-NT-gfs.txt postxconfig-NT.txt
  cp    ${PATHRT}/parm/postxconfig-NT-gfs_FH00.txt postxconfig-NT_FH00.txt
  cp    ${PATHRT}/parm/params_grib2_tbl_new params_grib2_tbl_new
fi

#rrtmgp
if [ $DO_RRTMGP = .true. ]; then
  cp    @[INPUTDATA_ROOT]/FV3_input_data_RRTMGP/* .
fi

#merra2
if [ $USE_MERRA2 = .true. ]; then
  for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m${n}.nc aeroclim.m${n}.nc
  done
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat  optics_BC.dat
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat  optics_OC.dat
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_DU.v15_3.dat optics_DU.dat
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SS.v3_3.dat  optics_SS.dat
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SU.v1_3.dat  optics_SU.dat
fi

#rad_c_gocart
if [ $IAER = 2011 ]; then
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat  optics_BC.dat
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat  optics_OC.dat
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_DU.v15_3.dat optics_DU.dat
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SS.v3_3.dat  optics_SS.dat
  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SU.v1_3.dat  optics_SU.dat
fi
#ugwpv1
if [ $DO_UGWP_V1 = .true. ]; then
  cp    @[INPUTDATA_ROOT]/FV3_input_data/ugwp_c384_tau.nc ./ugwp_limb_tau.nc
fi

#Thompson
if [ $IMP_PHYSICS = 8 ]; then
  cp    @[INPUTDATA_ROOT]/FV3_fix/qr_acr_qsV2.dat .
  cp    @[INPUTDATA_ROOT]/FV3_fix/qr_acr_qgV2.dat .
  cp    @[INPUTDATA_ROOT]/FV3_fix/freezeH2O.dat .
  cp    @[INPUTDATA_ROOT]/FV3_fix/CCN_ACTIVATE.BIN .
fi

#prognostic aerosols
if [ $CPLCHM = .true. ]; then
  cp      ${PATHRT}/parm/gocart/*.rc .
  ln -sf  @[INPUTDATA_ROOT]/GOCART/p8/ExtData .
fi