#!/bin/sh
###############################################################################
####  UNIX Script Documentation Block                                         #
#                                                                             #
# Script name:         exofs_atl_analysis.sh.sms                              #
# Script description:                                                         #
#                                                                             #
# Author:        Dan Iredell       Org: NP23         Date: 2005-06-14         #
#                                                                             #
# Abstract: This script generates the analysis field and creates the initial  #
#           condition for the OFS_ATL Ocean model                             #
#                                                                             #
# Sub-scripts called:                                                         #
#    seasforce.sh : create the forcing field                                 #
#                                                                             #
# Script history log:                                                         #
# 2005-06-14  Dan Iredell                                                     #
#                                                                             #
###############################################################################
set -xa

export PS4='$SECONDS + '

cd $DATA

msg="OFS_ATL Analysis has begun on `hostname` at `date`"
postmsg "$jlogfile" "$msg"

# --------------------------------------------------------------------------- #
# 0.  Preparations
# --------------------------------------------------------------------------- #

# 0.a date and time stuff

  export nested=${nested:-0}
  export srtdate=`echo $PDYm1 | cut -c1-8`
  export enddate=`echo $PDY | cut -c1-8`
  export inputgrid=${inputgrid:-ncep1_12}

# --------------------------------------------------------------------------- #
# 1  Set up the start time and end time for the forecast
  sday=`sh $utilscript/date_normal2hycom.sh $srtdate$cyc`
  eday=`sh $utilscript/date_normal2hycom.sh $enddate$cyc`
  echo "  $sday $eday false false  " > limits

# 2. Copy the necessary input files for the model forecast

# 2.a Get topography (depth, grid and mask)
  ln -s -f $FIXofs/ofs_${modID}.$inputgrid.regional.depth.a regional.depth.a
  ln -s -f $FIXofs/ofs_${modID}.$inputgrid.regional.depth.b regional.depth.b 
  ln -s -f $FIXofs/ofs_${modID}.$inputgrid.regional.grid.a regional.grid.a
  ln -s -f $FIXofs/ofs_${modID}.$inputgrid.regional.grid.b regional.grid.b
  ln -s -f $FIXofs/ofs_${modID}.$inputgrid.regional.mask.a regional.mask.a
  ln -s -f $FIXofs/ofs_${modID}.$inputgrid.regional.mask.b regional.mask.b


  # Check to make sure all the topography files are copied:
  for fil in depth grid mask
  do
     for type in a b
     do
        if [ -s regional.$fil.$type ]
        then
           echo "regional.${fil}.${type} copied" 
        else
           msg="ABNORMAL EXIT NOWCAST: NO FILE for regional.${fil}.${type}"
           postmsg "$jlogfile" "$msg"
           echo $msg
           err=2;
           export err;err_chk
        fi
     done
  done


  # 2.aa Get open boundary files

  if [ $nested -eq 0 ]
  then
  ln -s -f $PARMofs/ofs_${modID}.lowfreq.input lowfreq.input 

  $USHofs/ofs_lowfreq_mean.sh

  # Check to make sure all the open boundary files are copied:
  if [ -s lowfreq.input ]   
  then                                                                    
      echo "LOWR files for open boundaries copied"                        
  else                                                                    
      msg="ABNORMAL EXIT NOWCAST: FATAL ERROR--NO LOWFREQ FILE"             
      postmsg "$jlogfile" "$msg"
      echo $msg
      err=911;                                                            
      export err;err_chk                                                  
  fi
  fi

# 2.b Get boundary conditions (relax files)

# new for atl000:

  if [ $nested -eq 0 ]
  then

    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.intf.a relax.intf.a
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.intf.b relax.intf.b
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.rmu.a relax.rmu.a 
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.rmu.b relax.rmu.b 
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.temp.a relax.temp.a 
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.temp.b relax.temp.b 
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.saln.a relax.saln.a 
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.saln.b relax.saln.b 
    filreq='intf rmu temp saln'

  else
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.rmu.a relax.rmu.a 
    ln -s -f $FIXofs/ofs_${modID}.$inputgrid.relax.rmu.b relax.rmu.b 
    filreq='rmu'

# need 48 hours of archive files for nesting.. 
# OLDWAY
#    ln -s $COMIN/../nest/ ./nest 
# NEWWAY
     mkdir -p nest
     yyyyddd=`$utilscript/date2jday.sh $PDY`
     yyyy=`echo $yyyyddd | cut -c1-4`
     ddd=`echo $yyyyddd | cut -c5-7`
     let dddm1=ddd-1
     let dddm2=ddd-2
# 1st 23 hours
     for hour in 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23
     do
        cp $COMINm1/${RUN}_${modID}.t${cyc}z.${yyyy}_${dddm2}_${hour}.a ./nest/archv_${yyyy}_${dddm2}_${hour}.a
        cp $COMINm1/${RUN}_${modID}.t${cyc}z.${yyyy}_${dddm2}_${hour}.b ./nest/archv_${yyyy}_${dddm2}_${hour}.b
     done
# next 24 hours
     for hour in 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23
     do
        cp $COMINm1/${RUN}_${modID}.t${cyc}z.${yyyy}_${dddm1}_${hour}.a ./nest/archv_${yyyy}_${dddm1}_${hour}.a
        cp $COMINm1/${RUN}_${modID}.t${cyc}z.${yyyy}_${dddm1}_${hour}.b ./nest/archv_${yyyy}_${dddm1}_${hour}.b
     done
# next 1
     cp $COMINm1/${RUN}_${modID}.t${cyc}z.${yyyy}_${ddd}_00.a ./nest/archv_${yyyy}_${ddd}_00.a
     cp $COMINm1/${RUN}_${modID}.t${cyc}z.${yyyy}_${ddd}_00.b ./nest/archv_${yyyy}_${ddd}_00.b

  fi


  for fil in $filreq
  do
     for type in a b
     do
        if [ -s relax.${fil}.${type} ]
        then
           echo "relax.${fil}.${type} copied" 
        else
           msg="ABNORMAL EXIT NOWCAST: NO FILE for relax.${fil}.${type}"
           postmsg "$jlogfile" "$msg"
           echo $msg
           err=2;
           export err;err_chk
        fi
     done
  done


# 2.c Get initialization files 
  if [ $nested -eq 0 ]
  then
  cp $PARMofs/ofs_${modID}.anal.blkdat.input blkdat.input
  cp $PARMofs/ofs_${modID}.ports.input ports.input
  cp $PARMofs/ofs_${modID}.$inputgrid.patch.input.$NPROCS patch.input
  cp $PARMofs/ofs_${modID}.angle.input angle.input
  cp $PARMofs/ofs_${modID}.tidalports_p.input tidalports_p.input
  cp $PARMofs/ofs_${modID}.tidalports_vel.input tidalports_vel.input
  filreq='blkdat ports patch angle tidalports_p tidalports_vel'
  else
  cp $PARMofs/ofs_${modID}.anal.blkdat.input blkdat.input
  cp $PARMofs/ofs_${modID}.ports.input ports.input
  cp $PARMofs/ofs_${modID}.$inputgrid.patch.input.$NPROCS patch.input
  cp $PARMofs/ofs_${modID}.angle.input angle.input
  filreq='blkdat ports patch angle'
  fi 

  for fil in $filreq
  do
     if [ -s ${fil}.input ]
     then
        echo "${fil}.input copied" 
     else
        msg="ABNORMAL EXIT NOWCAST: NO FILE for ${fil}.input"
        postmsg "$jlogfile" "$msg"
        echo $msg
        err=2;
        export err;err_chk
     fi
  done

# 2.d Get initial conditions (restart files)
  if [ $cyc -eq 00 ]
  then
       yesterday_dir=$COMINm1
       today_dir=$COMIN
  else
       yesterday_dir=$COMIN
       today_dir=$COMIN
  fi

  if [ -s ${today_dir}/ofs_${modID}.t${cyc}z.updated_restart.a -a \
       -s ${today_dir}/ofs_${modID}.t${cyc}z.updated_restart.b ] 
  then
    echo "Restarts after assimilation are found."
    echo "Restarts after assimilation are found." >> \
      $COMOUT/${RUN}_${modID}.restart_status
    ln -s -f ${today_dir}/ofs_${modID}.t${cyc}z.updated_restart.a restart_in.a
    ln -s -f ${today_dir}/ofs_${modID}.t${cyc}z.updated_restart.b restart_in.b
  else
    echo "WARNING: IMPORTANT !!! Restarts after assimilation are not found !!!!"    
    echo "WARNING: IMPORTANT !!! Restarts after assimilation are not found !!!!" >> \
      $COMOUT/${RUN}_${modID}.restart_status
    if [ -s $yesterday_dir/ofs_${modID}.t${cyc}z.next_restart.a  -a \
         -s $yesterday_dir/ofs_${modID}.t${cyc}z.next_restart.b  ]
    then
      ln -s -f $yesterday_dir/ofs_${modID}.t${cyc}z.next_restart.a restart_in.a
      ln -s -f $yesterday_dir/ofs_${modID}.t${cyc}z.next_restart.b restart_in.b
      echo "Initial restart files copied"
      echo "Initial restart files copied" >> \
      $COMOUT/${RUN}_${modID}.restart_status
    else
      echo "Missing Restart File" >> $COMOUT/${RUN}_${modID}.restart_status
      msg="ABNORMAL EXIT NOWCAST: FATAL ERROR--NO RESTART FILE"
      postmsg "$jlogfile" "$msg"
      err=911;
      export err;err_chk
  fi
 fi
  

# 2.e copy interpolator data

# determine flavor of intp_pars.dat file based on intvl

  intvl=${intvl:-1}
  psource=${psource:-1} # if =1, use master file for surface pressure, if =0, then pgrb file
  if [ $intvl -eq 3 ]
  then
    cp $FIXofs/ofs_${modID}.intp_pars.dat intp_pars.dat
  else

cat > intp_pars.dat << EOF
&intp_pars
avstep = 1.,      ! averaging fluxes (in hours)
mrffreq = 1.,     ! frequency of MRF fluxes (in hours)  = mrffreq for no averaging
flxflg = 5,       ! Type of HYCOM input (=4 => nhycom=7 and =5 => nhycom=8)
dbgn = 1,         ! debugging =0 - no dbg; =1,2,3 - add output
avg3 = 2,         ! if avg3 = 1, then averaged fluxes are converted to instantaneous fields
wslocal = 1       ! if  wslocal = 1, then wind stress are computed from wind velcoities
/
EOF

  fi

  if [[ -s intp_pars.dat ]]
  then
      echo "interpolator data copied"
  else
      msg="ABNORMAL EXIT NOWCAST: NO FILE for intp_pars.dat"
      postmsg "$jlogfile" "$msg"
      echo $msg
      err=2;
      export err;err_chk
  fi

# 2.f Get parameter data for seasforce

  cp $FIXofs/ofs_${modID}.ismus_msk384x190.dat ismus_msk384x190.dat  
  cp $FIXofs/ofs_${modID}.ismus_msk512x256.dat ismus_msk512x256.dat  
  cp $FIXofs/ofs_${modID}.ismus_msk768x384.dat ismus_msk768x384.dat  
  cp $FIXofs/ofs_${modID}.ismus_msk1152x576.dat ismus_msk1152x576.dat 
  cp $FIXofs/ofs_${modID}.ismus_msk1760x880.dat ismus_msk1760x880.dat

  for rel in 384x190 512x256 768x384 1152x576 1760x880
  do
     if [ -s ismus_msk${rel}.dat ]
     then
        echo "File ismus_msk${rel}.dat copied"
     else
        msg="ABNORMAL EXIT NOWCAST: NO FILE for ismus_msk${rel}.dat"
        postmsg "$jlogfile" "$msg"
        echo $msg
        err=2;
        export err;err_chk
     fi
  done

# 2.g Get river forcing files

###   export gridlabel=A12
  export TANK=${TANK:-${DCOMROOT}/us007003}
  $USHofs/ofs_create_river.sh

  if [ -s forcing.rivers.a -a forcing.rivers.b ]                             
  then
      echo "River Forcing Files copied"
  else
      msg="ABNORMAL EXIT NOWCAST: NO FILE for forcing.rivers.a or .b "
      postmsg "$jlogfile" "$msg"
      echo $msg
      err=911;
      export err;err_chk
  fi

# 3. Create Forcing files

# 3.a call seasforce3 to get the forcing files 

  export mode=anal
  $USHofs/ofs_seasforce3.sh $srtdate$cyc $enddate$cyc ### $intvl $psource

# 3.b correct air temperature over ice.

  $USHofs/ofs_correct_forcing.sh 


# 4. Copy the SST ASSIM file here

# Notes:
#  if runsst set to 0 then
#  1) no assim.surtmp needed 
#  2) set value of asiflg=0

  if [ $runsst -eq 1 ] ; then
  ln -s -f $COMIN/${RUN}_${modID}.t${cyc}z.sstanl.a assim.surtmp.a 
  ln -s -f $COMIN/${RUN}_${modID}.t${cyc}z.sstanl.b assim.surtmp.b

  if [ -s assim.surtmp.a -a assim.surtmp.b ]
  then
     echo "4.b   assim.surtmp copied $COMIN/assim.surtmp.[ab] "
  else
     msg="4.b ABNORMAL EXIT NOWCAST PRE : NO FILE assim.surtmp:  $COMIN"
     postmsg "$jlogfile" "$msg"
     err=2;
     export err;err_chk
  fi
  else
    # whoops, have wrong blkdat.in file, so change value asiflg to 0
    asiflgline=`grep asiflg blkdat.input`
    sed -e "/^$asiflgline/s/1/0/" blkdat.input >blkdat.input.new
    rm -f blkdat.input
    mv blkdat.input.new blkdat.input
  fi
    

# 5. Prepare for the analysis run


  export OMP_NUM_THREADS=2
  export XLSMPOPTS=spins=0:yields=0
  
  touch ok
  rm -f ok
  date >> TRACK

  cmdtype='poe'

  export MP_LABELIO=YES
  export MP_STDOUTMODE=ordered
  export MEMORY_AFFINITY=MCM

  export MP_COREFILE_FORMAT=txt

 poe $EXECofs/ofs_forecast -procs $NPROCS >> $pgmout 2>errfile

  export err=$?; err_chk

  date >> TRACK

# --------------------------------------------------------------------------- #
# 5.c  Check for errors

if [ -e ok ]; then
   modelstatus=0
else
   modelstatus=1
fi

# --------------------------------------------------------------------------- #
# 6.  Ending output

if [ $modelstatus = 0 ]
then
   if [ $SENDCOM = YES ]
   then
       yyyyddd=`$utilscript/date2jday.sh $enddate`
       yyyy=`echo $yyyyddd | cut -c -1-4`
       ddd=`echo $yyyyddd | cut -c -5-7`

      # Copy diagnostic outputs to /com:
      # for file in `ls archv.*`
      # do
      #    newfile=`echo $file |sed -e "s/archv/${RUN}_${modID}.t${cyc}z/g"`
      #    cp $file $COMOUT/$newfile
      # done

      # Copy the restart files to /com:
       cp restart_out.a $COMOUT/${RUN}_${modID}.t${cyc}z.next_restart.a
       cp restart_out.b $COMOUT/${RUN}_${modID}.t${cyc}z.next_restart.b

      # Copy probes to /com
       for prb in `ls probe_out_*`
       do
         cp $prb $COMOUT/${RUN}_${modID}.t${cyc}z.${prb}
       done

      # copy lowfreq.out to /com
       cp lowfreq.out $COMOUT/${RUN}_${modID}.t${cyc}z.anal.lowfreq.out
       cp lowfreq.input $COMOUT/${RUN}_${modID}.t${cyc}z.anal.lowfreq.input       
       cp lowfreq_mean.txt $COMOUT/${RUN}_${modID}.t${cyc}z.anal.lowfreq_mean.txt              

      # copy list of forcing files to /com
       cp -p  listflx.dat $COMOUT/${RUN}_${modID}.t${cyc}z.anal.listflx.dat

       echo "done" >$COMOUT/${RUN}_${modID}.t${cyc}z.log
       msg="6. Analysis job completed normally"
       postmsg "$jlogfile" "$msg"
       exit 0
   fi
else
# failed .. if by neg dp then can reduce baclin to get run through
# suggest new number....
    baclin=`grep \'baclin\' blkdat.input|cut -f1 -d"'"`
    batrop=`grep \'batrop\' blkdat.input|cut -f1 -d"'"`
    baclini=`echo $baclin|cut -d. -f1`
    case $baclini in
     240) newbaclin=120.0;;
      80) newbaclin=60.0;;
      60) newbaclin=40.0;;
      40) newbaclin=30.0;;
      30) newbaclin=20.0;;
      *) newbaclin="a lower number";;
    esac
    msg="ABNORMAL EXIT NOWCAST: Try modifying baclin from $baclin to ${newbaclin} and rerunning "
    postmsg "$jlogfile" "$msg"
    echo $msg
    err=13;
    export err;err_chk
fi

#################################################
msg="THE OFS_ATL_ANALYSIS JOB HAS ENDED NORMALLY."
postmsg "$jlogfile" "$msg"
################## END OF SCRIPT #######################