#!/bin/ksh
#
# Construct NEMO namelist
# 
# original : 03-06 (Kristian)
#            16-07 (Magda) mods for restarts and other namelist arguments

#
# Document command line options
#
usage="Usage:\n$0 -r <working directory> -o <output directory> -d <namelists masters directory> -e expver -m asmmod -t timestep -D date0 -E dateend -s startday -y runnumber -R restart -N nrstdt  -v obsver -I obsins -s sst -l [SLA switch] -O othervar -c -p -a "
#
# Set defaults for command line options
#
#
clista=no
obs=no
asmmod=none
nmldir=unknown
ndate0=unknown
ndatend=unknown
nit000=unknown
nitend=unknown
expver=unknown
outdir=unknown
rundir=unknown
timestep=unknown
ncyc=unknown
restart=unknown
nrstdt=unknown
outfreq=15
othervar=""
sst=no
sla=no
obsver=v1c
obsins=EN3
blk=no
icemod=0
#
errflg=0

#
# Set error trapping on
#
set -euvx

set +e
#
# Get command line options
#
while getopts a:cd:D:e:E:i:n:N:o:v:I:O:pr:R:t:f:y:slB:L: option
do
  case $option in
    a) asmmod=$OPTARG;;
    c) clista=yes;;
    d) nmldir=$OPTARG;;
    D) ndate0=$OPTARG;;
    E) ndatend=$OPTARG;;
    e) nitend=$OPTARG;;
    f) outfreq=$OPTARG;;
    i) nit000=$OPTARG;;
    n) expver=$OPTARG;;
    o) outdir=$OPTARG;;
    v) obsver=$OPTARG;;
    I) obsins=$OPTARG;;    
    O) othervar="$OPTARG";;
    p) obs=yes;;
    r) rundir=$OPTARG;;
    t) timestep=$OPTARG;;
    y) ncyc=$OPTARG;;
    R) restart=$OPTARG;;
    N) nrstdt="$OPTARG";;
    s) sst=yes;;
    l) sla=yes;;
    B) blk=$OPTARG;;
    L) icemod=$OPTARG;;
    \?) errflg=1;;
  esac
done
#
# Check for errors
#
if [[ $errflg -ne 0 || $nmldir = unknown || $ndate0 = unknown || $ndatend = unknown || $nitend = unknown || $nit000 = unknown || $expver = unknown || $outdir = unknown || $rundir = unknown || $timestep = unknown || $ncyc = unknown ]] ; then
  print $usage
  exit 1
fi
#
CHECK_DIR $outdir
CHECK_DIR $rundir
#
cd $rundir
#
if [[ $clista = yes ]]
then
  echo "Ignoring restart and nrstdt from namelist"
  echo "Setting RESTART=false and NRSTDT=0"
  restart_string="RESTART=.false. NRSTDT=0"
else
  if [[ $restart = unknown ]] ;then 
    restart=.true.
  fi
  if [[ $nrstdt = unknown ]] ;then
    nrstdt=1  
  fi
  restart_string="RESTART=.$restart. NRSTDT=$nrstdt"
fi
#
# Observations
#
function list_to_namelist {
  nolines=0
  {
    while read -r line
    do
      lines[$nolines]=$line
      ((nolines=nolines+1))
    done
  } < $1
  i=0
  namelist_list=""
  if ((nolines==0))
  then
    namelist_list="''"
  else
    while((i<nolines))
    do
      if ((i==0)) then
        namelist_list="'${lines[$i]}'"
      else
        namelist_list="$namelist_list,'${lines[$i]}'"
      fi
      ((i=i+1))
    done
  fi
}

if [[ $obs = yes ]]
then
  obsopt="LOBS=.true."
  
else
  obsopt="LOBS=.false."
fi
if [[ $sst = yes ]]
then
  sstopt="LSST=.true."
else
  sstopt="LSST=.false."
fi
if [[ $sla = yes ]]
then
  slaopt="LSLA=.true."
else
  slaopt="LSLA=.false."
fi

case $asmmod in 
  bkg)
    bkgwri="LBKGWRI=.TRUE."
    asmdin="LASMDIN=.FALSE."
    asmiau="LASMIAU=.FALSE."
    trainc="LTRAINC=.FALSE."
    dyninc="LDYNINC=.FALSE."
    sshinc="LSSHINC=.FALSE.";;
  din)
    bkgwri="LBKGWRI=.FALSE."
    asmdin="LASMDIN=.TRUE."
    asmiau="LASMIAU=.FALSE."
    trainc="LTRAINC=.TRUE."
    dyninc="LDYNINC=.TRUE."
    sshinc="LSSHINC=.TRUE.";;
  IAU)
    bkgwri="LBKGWRI=.FALSE."
    asmdin="LASMDIN=.FALSE."
    asmiau="LASMIAU=.TRUE."
    trainc="LTRAINC=.TRUE."
    dyninc="LDYNINC=.TRUE."
    sshinc="LSSHINC=.TRUE.";;
  none)
    bkgwri="LBKGWRI=.FALSE."
    asmdin="LASMDIN=.FALSE."
    asmiau="LASMIAU=.FALSE."
    trainc="LTRAINC=.FALSE."
    dyninc="LDYNINC=.FALSE."
    sshinc="LSSHINC=.FALSE.";;
  \?)
  echo 'Unknown assim mode'
  exit 1 ;;
esac

#
# copy the namelist updating some values
#
if [[ -n ${DAYSTP:=""} ]]      ;then
  daystp_string="DAYSTP=$DAYSTP"
elif [[ -n ${NTIMESTEP:=""} ]] ; then
  daystp=$((86400/$NTIMESTEP))
  daystp_string="DAYSTP=$daystp"
fi
if [[ ${NSSHGLOBAL:=clim} = clim ]] ;then
 sshfile="'ssh', -1,'ssh',.true.,.true.,'yearly','',''"
 if (( ${NR_SSH} == 2 )) ;then
    sshfile="'grace_gz_bp', -1,'sobp',.true.,.true.,'yearly','',''"
 fi
elif [[ ${NSSHGLOBAL:=clim} = yearly ]] ;then
 sshfile="'aviso_ssh',-1,'ssh',.true.,.false.,'yearly','',''"
elif [[ ${NSSHGLOBAL:=clim} = monthly ]] ;then
 sshfile="'aviso_ssh',24,'ssh',.false.,.false.,'monthly','',''"
fi

if [[ $blk = @(ref|ecdrag) ]]; then
  if [[ ${USEALGOBLK:-no} = yes ]]; then
    lnalgo=.true.
    lnblk=.false.
  else
    lnalgo=.false.
    lnblk=.true.
  fi
fi

if [[ $blk = no ]]; then
  blkvar="NAM_NN_SSTR=1 NAM_LN_FLX=.true. NAM_LN_BLK=.false. NAM_LN_BLK_ALGO=.false. NAM_LN_CDEC=.false."
elif [[ $blk = ref ]]; then
  blkvar="NAM_NN_SSTR=1 NAM_LN_FLX=.false. NAM_LN_BLK=$lnblk NAM_LN_BLK_ALGO=$lnalgo NAM_LN_CDEC=.false."
elif [[ $blk = ecdrag ]]; then
  blkvar="NAM_NN_SSTR=1 NAM_LN_FLX=.false. NAM_LN_BLK=$lnblk NAM_LN_BLK_ALGO=$lnalgo NAM_LN_CDEC=.true."
elif [[ $blk = coup ]]; then
  blkvar="NAM_NN_SSTR=0 NAM_LN_FLX=.false. NAM_LN_BLK=.false. NAM_LN_BLK_ALGO=.false. NAM_LN_CDEC=.false."
else
  print "Unknown blk=$blk option"
  exit 1
fi

if [[ $icemod = 2 ]]; then
  ice="NAM_NN_ICE=2"
elif [[ $icemod = 3 ]]; then
  ice="NAM_NN_ICE=3"
else
  ice="NAM_NN_ICE=1"
fi

nitiaufin=$((nitend-nit000+1))
othervar=$othervar' NN_FWB='$NN_FWB' NAM_HDMP='$NAM_HDMP,' NAM_ZDMP='$NAM_ZDMP
othervar=$othervar' DQDT0='$DQDT0' DEDS0='$DEDS0
othervar=$othervar' LN_BIAS='${LN_BIAS}
othervar=$othervar' OFLBIAS='${LN_BIAS_OFL}
othervar=$othervar' NN_INERTIAL='$NN_INERTIAL
othervar=$othervar' NR_SSH='${NR_SSH}
othervar=$othervar' NAM_SDMP='${NAM_SDMP}
othervar=$othervar' NAM_BDMP='${NAM_BDMP}
othervar=$othervar' BIASTIMEUNITASM='${BIASTIMEUNITASM}
othervar=$othervar' LRST_BIASR='${LRST_BIASR}
othervar=$othervar' LFWBR='${LFWBR}
othervar=$othervar' NSLIMRST='${NSLIMRST}
othervar=$othervar' SSHFILE='"$sshfile"

change_namelist $nmldir/namelist.nemo $outdir/namelist EXPVER=$expver NIT000=$nit000 \
NITEND=$nitend NITIAUFIN=$nitiaufin NDATE0=$ndate0 NDATEND=$ndatend NTIMESTEP=$timestep \
OUTFREQ=$outfreq $restart_string NO=$ncyc $obsopt $slaopt $sstopt $bkgwri \
$asmdin $asmiau $trainc $dyninc $sshinc $daystp_string $othervar $blkvar $ice
#