#!/bin/sh

date
export PS4='+ $SECONDS + '
set -x

export cycle=${cycle:-t${cyc:?}z}
export storm_num=${storm_num:-1}
export stormlabel=${stormlabel:-storm$storm_num}
export hafs_ver=${hafs_ver:?}
export NET=${NET:?}
export RUN=${RUN:?}
export RUN_ENVIR=${RUN_ENVIR:?}

export SENDCOM=${SENDCOM:-YES}
export SENDDBN=${SENDDBN:-NO}
export SENDECF=${SENDECF:-NO}
export EMAIL_SDM=${EMAIL_SDM:-NO}
export SCRUBDATA=${SCRUBDATA:-YES}
# HAFS workflow jobs use shared working dir, and the CLEANUP or SCRUB job will clean up WORKhafs
#export KEEPDATA=${KEEPDATA:-YES}
export KEEPDATA=YES

export HOMEhafs=${HOMEhafs:-${OPSROOT:?}/hafs.${hafs_ver:?}}
export USHhafs=$HOMEhafs/ush
export EXEChafs=$HOMEhafs/exec
export PARMhafs=$HOMEhafs/parm
export FIXhafs=$HOMEhafs/fix

export WORKhafs=${WORKhafs:-${DATAROOT:?}/${RUN:?}${storm_num:?}_${cyc:?}_${envir:?}_${hafs_ver:?}}

if [ "${RUN_ENVIR^^}" != "NCO" ]; then
  # Detect platform and load modules if not run by NCO
  source ${USHhafs}/hafs_pre_job.sh.inc
  export machine=${WHERE_AM_I:-wcoss2}
  if [ ${machine}  = "wcoss2" ]; then
    module reset
    module use $HOMEhafs/sorc/hafs_gsi.fd/modulefiles
    module load gsi_${machine}
    module load cray-pals/1.2.2
    module load cfp/2.0.4
  fi
  if [ ${machine}  = "hera" ]; then
    module purge
    module use $HOMEhafs/sorc/hafs_gsi.fd/modulefiles
    module load gsi_${machine}.intel
  fi
  if [[ ${machine}  = "jet" ]] || [[ ${machine}  = "orion" ]] || [[ ${machine}  = "hercules" ]]; then
    module purge
    module use $HOMEhafs/sorc/hafs_gsi.fd/modulefiles
    module load gsi_${machine}
  fi
  module list
else
  # Run by NCO on WCOSS2
  export machine=${WHERE_AM_I:-wcoss2}
  # Prepend $USHhafs to python package search path
  export PYTHONPATH=$USHhafs${PYTHONPATH:+:$PYTHONPATH}
  # Initialize PDY
# setpdy.sh # only needed for the launch job
  # Get PDY
  source ${WORKhafs}/PDY
fi

source ${USHhafs}/hafs_runcmd.sh.inc

env

export COMhafs=${COMhafs:-$(compath.py ${envir}/${NET}/${hafs_ver})/${RUN}.${PDY}/${cyc}}
export CONFhafs=$COMhafs/$stormlabel.conf
export HOLDVARS=${HOLDVARS:-$COMhafs/$stormlabel.holdvars.txt}

source ${HOLDVARS}

export GSI_D01=${GSI_D01:-NO}
export GSI_D02=${GSI_D02:-NO}
export ENSDA=${ENSDA:-NO}

export CDATE=${CDATE:-${YMDH}}
yr=$(echo $CDATE | cut -c1-4)
mn=$(echo $CDATE | cut -c5-6)
dy=$(echo $CDATE | cut -c7-8)

if [ ${RUN_ATM_VI_FGAT} = "YES" ]; then
  RESTARTinp_fgat06=${WORKhafs}/intercom/RESTART_vi_fgat06
elif [ ${RUN_ATM_MERGE_FGAT} = "YES" ]; then
  RESTARTinp_fgat06=${WORKhafs}/intercom/RESTART_merge_fgat06
elif [ ${RUN_ATM_INIT_FGAT} = "YES" ]; then
  RESTARTinp_fgat06=${WORKhafs}/intercom/RESTART_init_fgat06
else
  if [ ${RUN_ATM_VI} = "YES" ]; then
    RESTARTinp_fgat06=${WORKhafs}/intercom/RESTART_vi
  elif [ ${RUN_ATM_MERGE} = "YES" ]; then
    RESTARTinp_fgat06=${WORKhafs}/intercom/RESTART_merge
  elif [ ${RUN_ATM_INIT} = "YES" ]; then
    RESTARTinp_fgat06=${WORKhafs}/intercom/RESTART_init
  else
    RESTARTinp_fgat06=${COMOLD}/RESTART
  fi
fi
RESTARTinp=${RESTARTinp_fgat06}

#===============================================================================
# Run analysis for d01 if needed
if [ ${GSI_D01} = YES ]; then

export gridstr=$(echo ${out_gridnames} | cut -d, -f 1)
export neststr=${neststr:-""}
export tilestr=${tilestr:-".tile1"}
export nesttilestr=${nesttilestr:-""}
export DATA=${WORKhafs}/analysis

if [ "${SCRUBDATA:-YES}" = YES ]; then
  rm -rf $DATA
fi
mkdir -p $DATA
cd $DATA

# Execute ex-script
${HOMEhafs}/scripts/exhafs_analysis.sh
export err=$?; err_chk

# Cleanup DATA dir
cd ${WORKhafs}
if [ "${KEEPDATA:-YES}" != "YES" ]; then
  rm -rf $DATA
fi

else # Pass over the need files for downstream jobs

export neststr=${neststr:-""}
export tilestr=${tilestr:-".tile1"}
export nesttilestr=${nesttilestr:-""}
export RESTARTanl=${RESTARTanl:-${WORKhafs}/intercom/RESTART_analysis}
mkdir -p ${RESTARTanl}

if [ -s ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res${neststr}${tilestr}.nc ]; then

${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.coupler.res ${RESTARTanl}/${PDY}.${cyc}0000.coupler.res
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res${neststr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_core.res${neststr}.nc
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.sfc_data${nesttilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.sfc_data${nesttilestr}.nc
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_srf_wnd.res${neststr}${tilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_srf_wnd.res${neststr}${tilestr}.nc
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res${neststr}${tilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_core.res${neststr}${tilestr}.nc
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res${neststr}${tilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_tracer.res${neststr}${tilestr}.nc
${NCP} ${RESTARTinp}/oro_data${nesttilestr}.nc ${RESTARTanl}/oro_data${nesttilestr}.nc
${NCP} ${RESTARTinp}/atmos_static${nesttilestr}.nc ${RESTARTanl}/atmos_static${nesttilestr}.nc
${NCP} ${RESTARTinp}/grid_spec${nesttilestr}.nc ${RESTARTanl}/grid_spec${nesttilestr}.nc
# pass over phy_data as well
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.phy_data${nesttilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.phy_data${nesttilestr}.nc
if [[ ! -z "$neststr" ]] && [ -e ${RESTARTinp}/${PDY}.${cyc}0000.fv_BC_ne.res${neststr}.nc ]; then
  ${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_BC_ne.res${neststr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_BC_ne.res${neststr}.nc
  ${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_BC_sw.res${neststr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_BC_sw.res${neststr}.nc
fi
# Pass over the grid_mspec files for moving nest
if [[ "${is_moving_nest:-".false."}" = *".true."* ]] || [[ "${is_moving_nest:-".false."}" = *".T."* ]]; then
  if [[ -z "$neststr" ]] && [[ $tilestr = ".tile1" ]]; then
    # "grid_mspec_${yr}_${mn}_${dy}_${cyc}.nc" for domain 02
    ${NCP} -p ${RESTARTinp}/grid_mspec_${yr}_${mn}_${dy}_${cyc}.nc ${RESTARTanl}/
  else
    # "grid_mspec.nest02_${yr}_${mn}_${dy}_${cyc}.tile2.nc" for domain 02
    ${NCP} -p ${RESTARTinp}/grid_mspec${neststr}_${yr}_${mn}_${dy}_${cyc}${tilestr}.nc ${RESTARTanl}/
  fi
fi

fi #end if [ -s ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res${neststr}${tilestr}.nc ]; then

fi #end if [ ${GSI_D01} = YES ]; then

#===============================================================================
# Run analysis for d02 if needed
if [ ${GSI_D02} = YES ] && [[ $nest_grids -ge 2 ]]; then

export gridstr=$(echo ${out_gridnames} | cut -d, -f 2)
export neststr=".nest02"
export tilestr=".tile2"
export nesttilestr=".nest02.tile2"
export DATA=${WORKhafs}/analysis_d02

if [ "${SCRUBDATA:-YES}" = YES ]; then
  rm -rf $DATA
fi
mkdir -p $DATA
cd $DATA

# Execute ex-script
${HOMEhafs}/scripts/exhafs_analysis.sh
export err=$?; err_chk

# Cleanup DATA dir
cd ${WORKhafs}
if [ "${KEEPDATA:-YES}" != "YES" ]; then
  rm -rf $DATA
fi

elif [ ${GSI_D02} != YES ] && [[ $nest_grids -ge 2 ]]; then

export neststr=".nest02"
export tilestr=".tile2"
export nesttilestr=".nest02.tile2"
export RESTARTanl=${RESTARTanl:-${WORKhafs}/intercom/RESTART_analysis}
mkdir -p ${RESTARTanl}

if [ -s ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res${neststr}${tilestr}.nc ]; then

${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.coupler.res ${RESTARTanl}/${PDY}.${cyc}0000.coupler.res
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res${neststr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_core.res${neststr}.nc
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.sfc_data${nesttilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.sfc_data${nesttilestr}.nc
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_srf_wnd.res${neststr}${tilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_srf_wnd.res${neststr}${tilestr}.nc
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res${neststr}${tilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_core.res${neststr}${tilestr}.nc
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res${neststr}${tilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_tracer.res${neststr}${tilestr}.nc
${NCP} ${RESTARTinp}/oro_data${nesttilestr}.nc ${RESTARTanl}/oro_data${nesttilestr}.nc
${NCP} ${RESTARTinp}/atmos_static${nesttilestr}.nc ${RESTARTanl}/atmos_static${nesttilestr}.nc
${NCP} ${RESTARTinp}/grid_spec${nesttilestr}.nc ${RESTARTanl}/grid_spec${nesttilestr}.nc
# pass over phy_data as well
${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.phy_data${nesttilestr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.phy_data${nesttilestr}.nc
if [[ ! -z "$neststr" ]] && [ -e ${RESTARTinp}/${PDY}.${cyc}0000.fv_BC_ne.res${neststr}.nc ]; then
  ${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_BC_ne.res${neststr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_BC_ne.res${neststr}.nc
  ${NCP} ${RESTARTinp}/${PDY}.${cyc}0000.fv_BC_sw.res${neststr}.nc ${RESTARTanl}/${PDY}.${cyc}0000.fv_BC_sw.res${neststr}.nc
fi
# Pass over the grid_mspec files for moving nest
if [[ "${is_moving_nest:-".false."}" = *".true."* ]] || [[ "${is_moving_nest:-".false."}" = *".T."* ]]; then
  if [[ -z "$neststr" ]] && [[ $tilestr = ".tile1" ]]; then
    # "grid_mspec_${yr}_${mn}_${dy}_${cyc}.nc" for domain 02
    ${NCP} -p ${RESTARTinp}/grid_mspec_${yr}_${mn}_${dy}_${cyc}.nc ${RESTARTanl}/
  else
    # "grid_mspec.nest02_${yr}_${mn}_${dy}_${cyc}.tile2.nc" for domain 02
    ${NCP} -p ${RESTARTinp}/grid_mspec${neststr}_${yr}_${mn}_${dy}_${cyc}${tilestr}.nc ${RESTARTanl}/
  fi
fi

fi #end if [ -s ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res${neststr}${tilestr}.nc ]; then

fi #end if [ ${GSI_D02} = YES ] && [[ $nest_grids -ge 2 ]]; then

#===============================================================================
date