###testb
# lines between ###testb and ###teste not needed for production
###teste
################################################################################
#   Script:	gefs_init_pair.sh
#
#   Author:	Mark Iredell
#   Date:	1997 January 08
#
#   Steward:	Richard Wobus
#   Center:	Environmental Modeling Center
#   Phone:	(301) 763-8000 x7712
#
#   Abstract:	Creates initial conditions for the global ensemble
#       	by perturbing the analysis with growing modes
#               extracted from the previous day's ensemble forecasts.
#       	This script is called for a single pair from the
#               script exenstr.sh.sms.
#
#   Modified:   12/11/98	replace hardwired globampl with fixed file
#                               save growth rate output file
#   Modified:   06/08/99	dummy script made to hold over on IBM until real
#                               exenstr.sh.sms script is ready
#   Modified:   09/09/99	modified for IBM SP
#   Modified:   04/17/00	increase to 5 pairs at 12z
#   Modified:   05/19/00	create perturbation at any two resolutions,
#                               currently set to create 5 pairs and a 
#                               low-resolution control run at T126
#   Modified:   04/30/01	generalize to run with create any number of
#                               levels and any number of tracer variables
#   Modified:   05/xx/01	separate into outer and inner (single pair)
#                               scripts 
#   Modified:   06/07/05        add tropical cyclone relocation and fix energy
#   Modified:   09/09/05        add 2-sided breeding with 1-sided names
#
################################################################################

set +xa
echo " ------------------------------------------------------------"
echo "  "
echo "            GLOBAL ENSEMBLE INITIALIZATION "
echo "  "
echo "                `date`     "
echo "  "
echo "                   JOB  $job  "
echo "  "
echo "  "
echo "               FORECAST cycle TIME is $cycle"
echo "  "
echo " ------------------------------------------------------------"
echo "          processing info for this execution"
echo " Home directory is ............................ $HOMEGLOBAL"
echo " Processing directory for files.. ............. $DATA"
echo "  "
echo " Executable file directory is ................. $EXECGLOBAL"
echo " Fixed field directory is ..................... $FIXGLOBAL"
echo " Unix control language file is ................ $USHGLOBAL"
echo "  "
echo " Network id is ................................ $NET"
echo " Run id for $com processing is ................ $RUN"
echo "  "
echo " standard output in file ...................... $pgmout"
echo " unique processing id for run ................. $pid"
echo " YES SENDCOM means save com files ............. $SENDCOM"
echo " ------------------------------------------------------------"
echo " Argument list:"
echo "   1  ipair=number of this instance .............. $1"
echo "   2  npair=number of pairs ...................... $2"
echo "   3  nhrpair=number of high-resolution pairs .... $3"
echo "   4  jcap=horizontal truncation ................. $4"
echo "   5  levs=number of vertical levels ............. $5"
echo "   6  latb=number of gaussian latitudes .......... $6"
echo "   7  lonb=number of gaussian longitudes ......... $7"
echo "   8  ntrac=number of tracer variables ........... $8"
echo "   9  fhrp=preferred input forecast length ....... $9"
echo "  10  inflag=(1=n,2=p,3=both,4=both n,5=both p) .. ${10}"
echo "  11  outflag=(1=n,2=p,3=both,4=both n,5=both p) . ${11}"
echo "  12  relocfact=relocation fraction .............. ${12}"
echo " ------------------------------------------------------------"
set -xa

cd $DATA
  
################################################################################

echo
echo `date` separate begin ipair=$1
echo
if (( $# < 12 )); then
  echo $0 needs 12 arguments
  exit
fi

ipairi=$1
npairi=$2
nhrpair=$3
jcap=$4
levs=$5
latb=$6
lonb=$7
ntrac=$8
fhrp=$9
inflag=${10}
outflag=${11}
relocfact=${12}

echo ipairi=$ipairi
echo npairi=$npairi
echo
(( npairc = npairi / 4 ))
echo npairc=$npairc
if (( ipairi <= npairc )); then
  ipair=ipairi
  cyc_fcst=00
elif (( ipairi <= 2 * npairc )); then
  (( ipair = ipairi - npairc ))
  cyc_fcst=06
elif (( ipairi <= 3 * npairc )); then
  (( ipair = ipairi - 2 * npairc ))
  cyc_fcst=12
else
  (( ipair = ipairi - 3 * npairc ))
  cyc_fcst=18
fi
(( ipair = ipair + 0 ))
if (( ipair < 10 )); then
  ipair=0$ipair
fi
echo ipair=$ipair
echo cyc_fcst=$cyc_fcst
echo cyc=$cyc

export cycle_fcst=t${cyc_fcst}z
echo cycle_fcst=$cycle_fcst

if (( cyc == cyc_fcst )); then
  export cycsuffix=false
  export fcstlong=true
  export cfsuffix=""
else
  export cycsuffix=true
  export fcstlong=false
  export cfsuffix=".cycfs$cyc_fcst"
fi
echo cycsuffix=$cycsuffix
echo fcstlong=$fcstlong
echo cfsuffix=$cfsuffix

echo two digit ipair=$ipair
#ipai=`echo $ipair|cut -c2,2`
#echo one digit ipai=$ipai
echo inflag=$inflag outflag=$outflag
if (( inflag > 3 )) || (( outflag > 3 )); then
  (( ipairp = 2 * ipair ))
  (( ipairn = ipairp - 1 ))
  if (( ipairp < 10 )); then
    ipairp=0$ipairp
  fi
  if (( ipairn < 10 )); then
    ipairn=0$ipairn
  fi
  echo two digit ipairn=$ipairn ipairp=$ipairp 
fi

# cfsuffix identifies long forecast cycle 
# associated with this breeding job

# cfsuffixp identifies long forecast cycle
# associated with the previous forecast cycle
# from which tracking information will be used

echo cfsuffix=$cfsuffix
echo ensshort=$ensshort
echo cfsuffixp=$cfsuffixp
echo ensshortp=$ensshortp
echo cyc_fcst=$cyc_fcst
echo cycle_fcst=$cycle_fcst

echo inflag=$inflag
echo outflag=$outflag

# these variables specify the resolution of perturbation output
JCAP=$jcap
LEVS=$levs
LONB=$lonb
LATB=$latb
NTRAC=$ntrac

# make the local work directory

echo DATA=$DATA
DATALOCAL=$DATA/pair.$ipairi
mkdir -p $DATALOCAL
cd $DATALOCAL
pwd
# this is done for the benefit of operational scripts that use DATA
DATAPARENT=$DATA
DATA=$DATALOCAL
echo DATALOCAL=$DATALOCAL
echo DATA=$DATA
echo DATAPARENT=$DATAPARENT

sh $utilscript/setup.sh

# check for cold start
coldstartflag=0
for coldstartcycle in $coldstartcycles
do
  echo $PDY$cyc | grep $coldstartcycle >/dev/null 2>&1
  rc=$?
  if (( rc == 0 )); then
    coldstartflag=1
    echo cold start specified by $coldstartcycle
  fi
done

if (( coldstartflag == 0 )); then
#  find the previous forecasts
cyc=`echo $cycle|cut -c2-3`
haveinput=no
inflaguse=0

inflagt=$inflag

(( fhr = fhrp ))
while (( fhr <= 96 ))
do
  if (( fhr < 10 )); then
    fhr=0$fhr
  fi
  echo begin loop for nflagt=$inflagt fhr=$fhr
  if [[ $haveinput = no ]]; then
    (( cycstart = cyc - fhr ))
    comfcstin=$COMIN
    comfcstinm1=$COMINm1
    comfcstinm2=$COMINm2
    comfcstinm3=$COMINm3
    comfcstinm4=$COMINm4
    pdyin=$PDY
    pdyinm1=$PDYm1
    pdyinm2=$PDYm2
    pdyinm3=$PDYm3
    pdyinm4=$PDYm4
    while (( cycstart < 0 ))
    do
      (( cycstart=cycstart+24))
      comfcstin=$comfcstinm1
      comfcstinm1=$comfcstinm2
      comfcstinm2=$comfcstinm3
      comfcstinm3=$comfcstinm4
      comfcstinm4=null
      pdyin=$pdyinm1
      pdyinm1=$pdyinm2
      pdyinm2=$pdyinm3
      pdyinm3=$pdyinm4
      pdyinm4=00000000
    done
    if (( cycstart < 10 )); then
      cycstart="0$cycstart"
    fi
    cyclestart=t${cycstart}z
    datein=$pdyin$cycstart

    # cfsuffixstart identifies long forecast cycle
    # associated with previous forecast used in
    # breeding which may be 6 or more hours previous

    if (( cycstart == cyc_fcst )); then
      cfsuffixstart=""
    else
      cfsuffixstart=".cycfs$cyc_fcst"
    fi
    echo fhr=$fhr cyc=$cyc cycstart=$cycstart cyclestart=$cyclestart datein=$datein
    echo cfsuffixstart=$cfsuffixstart
    found=false
    if (( inflagt == 1 )) || (( inflagt == 2 )) || (( inflagt == 3 )) || (( inflagt == 4 )) || (( inflagt == 5 )) ; then
      found=true
    fi
#   check for existence and correct headers of input files
    if (( inflagt == 1 )) || (( inflagt == 3 )); then
      fcstinn=$comfcstin/$cycstart/sfcsig/gen${ipair}.$cyclestart.sf$fhr$cfsuffixstart
    elif (( inflagt == 4 )); then
      fcstinn=$comfcstin/$cycstart/sfcsig/gen${ipairn}.$cyclestart.sf$fhr$cfsuffixstart
    elif (( inflagt == 5 )); then
      fcstinn=$comfcstin/$cycstart/sfcsig/gep${ipairn}.$cyclestart.sf$fhr$cfsuffixstart
    else
      fcstinn=$comfcstin/$cycstart/sfcsig/gec00.$cyclestart.sf$fhr$cfsuffixstart
    fi
    if [[ -e $fcstinn ]]; then
      echo fcstinn=$fcstinn found
      onifhr=`$sighdrexec $fcstinn ifhr`
      rc=$?
      echo rc=$rc onifhr=$onifhr
      if (( rc == 0 )); then
	if (( onifhr == fhr )); then
	  onidate=`$sighdrexec $fcstinn idate`
	  rc=$?
	  echo rc=$rc onidate=$onidate
	  if (( rc == 0 )); then
	    if (( onidate == datein )); then
	      echo fcstinn=$fcstinn appears to be usable
	      fcstinnuse=$fcstinn
	    else
	      found=false
	    fi
	  else
	    found=false
	  fi
	else
	  found=false
	fi
      else
	found=false
      fi
    else
      echo fcstinn=$fcstinn not found
      found=false
    fi
    echo found=$found
    if (( inflagt == 2 )) || (( inflagt == 3 )); then
      fcstinp=$comfcstin/$cycstart/sfcsig/gep${ipair}.$cyclestart.sf$fhr$cfsuffixstart
    elif (( inflagt == 4 )); then
      fcstinp=$comfcstin/$cycstart/sfcsig/gen${ipairp}.$cyclestart.sf$fhr$cfsuffixstart
    elif (( inflagt == 5 )); then
      fcstinp=$comfcstin/$cycstart/sfcsig/gep${ipairp}.$cyclestart.sf$fhr$cfsuffixstart
    else
      fcstinp=$comfcstin/$cycstart/sfcsig/gec00.$cyclestart.sf$fhr$cfsuffixstart
    fi
    if [[ -e $fcstinp ]]; then
      echo fcstinp=$fcstinp found
      opifhr=`$sighdrexec $fcstinp ifhr`
      rc=$?
      echo opifhr=$opifhr
      if (( rc == 0 )); then
	if (( opifhr == fhr )); then
	  opidate=`$sighdrexec $fcstinp idate`
	  rc=$?
	  echo rc=$rc opidate=$opidate
	  if (( rc == 0 )); then
	    if (( opidate == datein )); then
	      echo fcstinp=$fcstinp appears to be usable
	      fcstinpuse=$fcstinp
	    else
	      found=false
	    fi
	  else
	    found=false
	  fi
	else
	  found=false
	fi
      else
	found=false
      fi
    else
      echo fcstinp=$fcstinp not found
      found=false
    fi
    echo found=$found
    if [[ $found = true ]]; then
      ifhruse=$fhr
      echo all forecasts found for ifhruse=$ifhruse
      if (( inflagt == 1 )) || (( inflagt == 3 )) || (( inflagt == 4 )) || (( inflagt == 5 )); then
	fcstinnuse=$fcstinn
	comfcstinuse=$comfcstin
      fi
      if (( inflagt == 2 )) || (( inflagt == 3 )) || (( inflagt == 4 )) || (( inflagt == 5 )); then
	fcstinpuse=$fcstinp
	comfcstinuse=$comfcstin
      fi
      haveinput=yes
      inflaguse=$inflagt
      if (( inflaguse > 3 )); then
	inflaguse=3
      fi
    else
      echo some forecasts missing for fhr=$fhr
    fi
  fi
  echo end loop for fhr=$fhr
  (( fhr = fhr + fhrp ))
done

wait
else
haveinput=no
fi

# change the resolution of input files as necessary

if [[ $haveinput = yes ]]; then
  echo we have chosen ifhruse=$ifhruse com=$comfcstinuse
  if (( inflaguse == 1 )) || (( inflaguse == 3 )); then
    ojcap=`$sighdrexec $fcstinn jcap` 
    olevs=`$sighdrexec $fcstinn levs` 
    ontrac=`$sighdrexec $fcstinn ntrac` 
    oidvc=`$sighdrexec $fcstinn idvc` 
    export JCAP=$jcap
    export LEVS=$levs
    export LONB=$lonb
    export LATB=$latb
    export NTRAC=$ntrac
    export IDVC=$IDVC
    export NVCOORD=$IDVC
    export CHGRESVARS="NTRAC=$NTRAC,NVCOORD=$NVCOORD"
    if (( IDVC == 1 )); then
      export SIGLEVEL=$FIXGLOBAL/global_siglevel.l${LEVS}.txt
    fi
    if (( IDVC == 2 )); then
      export SIGLEVEL=$FIXGLOBAL/global_hyblev.l${LEVS}.txt
    fi
    export SIGINP=$fcstinnuse
    export SFCINP=NULL
    export SIGOUT=$DATALOCAL/finn
    export SFCOUT=sfcout
    runchgres=yes
    if (( JCAP == ojcap )); then
      if (( LEVS == olevs )); then
	if (( NTRAC == ontrac )); then
	  if (( IDVC == oidvc )); then
	    runchgres=no
	  fi
	fi
      fi
    fi
    if [[ $runchgres = yes ]]; then
#     if [[ $IDVC = 2 ]]; then
#	if [[ $oidvc != 2 ]] || [[ LEVS != olevs ]]; then
#	  export SIGLEVEL=$siglevelfile
#	  export NVCOORD=2
#	fi
#     fi
###testb
echo
echo `date` env before chgres begin
env | sort
echo `date` env before chgres end
echo
###teste
      $chgresush >>$pgmout
    else
      cp -fp $SIGINP $SIGOUT
    fi
  else
    touch $DATALOCAL/finn
  fi
  if (( inflaguse == 2 )) || (( inflaguse == 3 )); then
    ojcap=`$sighdrexec $fcstinp jcap` 
    olevs=`$sighdrexec $fcstinp levs` 
    ontrac=`$sighdrexec $fcstinp ntrac` 
    oidvc=`$sighdrexec $fcstinp idvc` 
    export JCAP=$jcap
    export LEVS=$levs
    export LONB=$lonb
    export LATB=$latb
    export NTRAC=$ntrac
    export IDVC=$IDVC
    export NVCOORD=$IDVC
    export CHGRESVARS="NTRAC=$NTRAC,NVCOORD=$NVCOORD"
    if (( IDVC == 1 )); then
      export SIGLEVEL=$FIXGLOBAL/global_siglevel.l${LEVS}.txt
    fi
    if (( IDVC == 2 )); then
      export SIGLEVEL=$FIXGLOBAL/global_hyblev.l${LEVS}.txt
    fi
    export SIGINP=$fcstinpuse
    export SFCINP=NULL
    export SIGOUT=$DATALOCAL/finp
    export SFCOUT=sfcout
    runchgres=yes
    if (( JCAP == ojcap )); then
      if (( LEVS == olevs )); then
	if (( NTRAC == ontrac )); then
	  if (( IDVC == oidvc )); then
	    runchgres=no
	  fi
	fi
      fi
    fi
    if [[ $runchgres = yes ]]; then
#     if [[ $IDVC = 2 ]]; then
#	if [[ $oidvc != 2 ]] || [[ LEVS != olevs ]]; then
#	  export SIGLEVEL=$siglevelfile
#	  export NVCOORD=2
#	fi
#     fi
###testb
echo
echo `date` env before chgres begin
env | sort
echo `date` env before chgres end
echo
###teste
      $chgresush >>$pgmout
    else
      cp -fp $SIGINP $SIGOUT
    fi
  else
    touch $DATALOCAL/finp
  fi
else
  echo data was not found, use null files
  ifhruse=$fhrp
  echo ifhruse=$ifhruse
  touch $DATALOCAL/finn
  touch $DATALOCAL/finp
  echo turn relocation off
  export relocpertflag=0
fi

wait

if (( ifhruse == fhrp )); then
  echo we are cycling at the preferred forecast length $ifhruse
else
  echo we are cycling at a different forecast length $ifhruse
  echo turn relocation off
  export relocpertflag=0
fi

ln -sf finn sig_zvdi
if [[ "$sigzvd" = "yes" ]]; then
  ln -sf finn sig_zvdo
else
  ln -sf /dev/null sig_zvdo
fi
echo ifinn$ipair > sig_zvdl
$EXECGLOBAL/global_sigzvd
ret_sigzvd=$?

ln -sf finp sig_zvdi
if [[ "$sigzvd" = "yes" ]]; then
  ln -sf finp sig_zvdo
else
  ln -sf /dev/null sig_zvdo
fi
echo ifinp$ipair > sig_zvdl
$EXECGLOBAL/global_sigzvd
ret_sigzvd=$?

#
#  Separate the storm and environment forecast fields
#
echo `date` relocflag=$relocflag relocpertflag=$relocpertflag
execseparate=${execseparate:-$EXECgefs/gefs_vortex_separate}

if (( relocpertflag == 1 )); then
  echo `date` Separate the storm and environment forecast fields for n$ipair begin

  yy=`echo $PDY|cut -c3-4`
  echo yy=$yy

# this file is created once for all in the exenstr script

  ln -s -f ../tcvitals.as fort.11

  ln -s -f $FIXGLOBAL/global_slmask.t126.grb    fort.12


  ln -s -f ../tracks.atcfunix.$cyc_fcst      fort.40
  ln -s -f finn               fort.24

  ln -s -f finn_env              fort.54
  ln -s -f finn_strm              fort.74

  export gesfhr=$ifhruse
  export ensm=p${ipairn}

  echo `date` $execseparate before
  echo $gesfhr $ensm | $execseparate
  filtrccn=$?
  echo `date` $execseparate after

# substitute files and continue only if separation succeeded 
  export relocpertflag=0
  if (( filtrccn == 0 )); then
    if [[ -s finn_env ]]; then
      if [[ -s finn_strm ]]; then
	mv -f finn finn_presep
	cp -f finn_env finn
	export relocpertflag=1
      fi
    fi
  else
    echo filtrccn=$filtrccn
  fi

  echo `date` Separate the storm and environment forecast fields for n$ipair end
fi
if (( relocpertflag == 1 )); then
  echo `date` Separate the storm and environment forecast fields for p$ipair begin

  ln -s -f ../tcvitals.as fort.11

  ln -s -f $FIXGLOBAL/global_slmask.t126.grb    fort.12

  ln -s -f ../tracks.atcfunix.$cyc_fcst      fort.40
  ln -s -f finp               fort.24

  ln -s -f finp_env              fort.54
  ln -s -f finp_strm              fort.74

  export gesfhr=$ifhruse
  export ensm=p${ipairp}

  echo `date` $execseparate before
  echo $gesfhr $ensm | $execseparate
  filtrccp=$?
  echo `date` $execseparate after

# substitute files and continue only if separation succeeded 
  export relocpertflag=0
  if (( filtrccp == 0 )); then
    if [[ -s finp_env ]]; then
      if [[ -s finp_strm ]]; then
	mv -f finp finp_presep
	cp -f finp_env finp
	export relocpertflag=1
      fi
    fi
  else
    echo filtrccp=$filtrccp
  fi


  echo `date` Separate the storm and environment forecast fields for p$ipair end
fi
wait
echo `date` relocflag=$relocflag relocpertflag=$relocpertflag
#
# end relocation splitting section
#

ln -sf finn sig_zvdi
if [[ "$sigzvd" = "yes" ]]; then
  ln -sf finn sig_zvdo
else
  ln -sf /dev/null sig_zvdo
fi
echo sfinn$ipair > sig_zvdl
$EXECGLOBAL/global_sigzvd
ret_sigzvd=$?

ln -sf finp sig_zvdi
if [[ "$sigzvd" = "yes" ]]; then
  ln -sf finp sig_zvdo
else
  ln -sf /dev/null sig_zvdo
fi
echo sfinp$ipair > sig_zvdl
$EXECGLOBAL/global_sigzvd
ret_sigzvd=$?

if (( ipair > nhrpair )); then
  export SIGINP=../sanl.lr.in
  export SFCINP=../sfcanl.lr.in
else
  export SIGINP=../sanl.hr.in
  export SFCINP=../sfcanl.hr.in
fi

export SIGOUT=$DATALOCAL/sanl.in
export SFCOUT=$DATALOCAL/sfcanl.in

cp -fp $SIGINP $SIGOUT
cp -fp $SFCINP $SFCOUT

wait

unset SFCINP
unset SFCOUT

for meml in n p
do
  export JCAP=$jcap
  export LEVS=$levs
  export LONB=$lonb
  export LATB=$latb
  export NTRAC=$ntrac
  export IDVC=$IDVC
  export NVCOORD=$IDVC
  export CHGRESVARS="NTRAC=$NTRAC,NVCOORD=$NVCOORD"
  if (( IDVC == 1 )); then
    export SIGLEVEL=$FIXGLOBAL/global_siglevel.l${LEVS}.txt
  fi
  if (( IDVC == 2 )); then
    export SIGLEVEL=$FIXGLOBAL/global_hyblev.l${LEVS}.txt
  fi
  export SIGINP=$FIXgefs/gefs.pertback.$cycle_fcst.${meml}${ipair}
  export SFCINP=NULL
  export SIGOUT=$DATALOCAL/gefs.pertback.$cycle_fcst.${meml}${ipair}
  export SFCOUT=sfcout
  ojcap=`$sighdrexec $SIGINP jcap` 
  olevs=`$sighdrexec $SIGINP levs` 
  ontrac=`$sighdrexec $SIGINP ntrac` 
  oidvc=`$sighdrexec $SIGINP idvc` 
  runchgres=yes
  if (( JCAP == ojcap )); then
    if (( LEVS == olevs )); then
      if (( NTRAC == ontrac )); then
	if (( IDVC == oidvc )); then
	  runchgres=no
	fi
      fi
    fi
  fi
  if [[ $runchgres = yes ]]; then
#   if [[ $IDVC = 2 ]]; then
#     if [[ $oidvc != 2 ]] || [[ LEVS != olevs ]]; then
#	export SIGLEVEL=$siglevelfile
#	export NVCOORD=2
#     fi
#   fi
###testb
echo
echo `date` env before chgres begin
env | sort
echo `date` env before chgres end
echo
###teste
    $chgresush >>$pgmout
  else
    cp -fp $SIGINP $SIGOUT
  fi
done

wait

echo
echo `date` save from 1st to 2nd ush script begin
echo
echo $relocpertflag>save.relocpertflag
echo $inflaguse>save.inflaguse
echo $ifhruse>save.ifhruse
for file in finn finp finn_env finp_env finn_strm finp_strm finn_presep finp_presep gefs.pertback.$cycle_fcst.n${ipair} gefs.pertback.$cycle_fcst.p${ipair} sanl.in sfcanl.in save.relocpertflag save.inflaguse save.ifhruse
do
  fils=../$file.pair$ipairi
  echo file=$file fils=$fils
  if [[ -f $file ]]; then
    ls -al $file
    mv -f $file $fils
    ls -al $fils
  else
    echo file=$file DOES NOT EXIST
  fi
done
echo
echo `date` save from 1st to 2nd ush script end
echo
echo
echo `date` separate end ipair=$ipairi
echo