#!/bin/ksh
######################################################################
# hwrf_nmm_gsi_d2.sh
####################
# April 2007 Written by Qingfu Liu
#            Modified for operations by Vijay Tallapragada
# April 2008 Modified by Qingfu Liu
#            Modified for operations by Vijay Tallapragada
# June 2009  Modified for HWRF 2009 implementation Vijay Tallapragada
# January 2010 Modified by Mingjing Tong
#              Using operational (200902) gsi executable compiled on cirrus
# NOTE:  To ensure reproducible results, must use same number of
#        MPI tasks AND nodes for each run.  blocking=unlimited
#        leads to roundoff differences in mpi_allreduce.
#####################################################################

set -u -e

set -x
if [ $GSI == NO ]; then
echo 'Initialization not requested.  GSI = $GSI This script need not be run'
sh ${utilscript}/setup.sh
err=911
err_exit "Initialization not requested.  GSI = $GSI This script need not be run"
fi

######### GET THE INPUT VARIABLLES ###############

if [ $# -eq 7 ]
then
   export storm=${1}
   export YEAR=${2}
   export MONTH=${3}
   export DATE=${4}
   export CYCLE=${5}
   export RLATC=${6}
   export RLONC=${7}

   echo 'storm  = ' ${storm}
   echo 'YEAR   = ' ${YEAR}
   echo 'MONTH  = ' ${MONTH}
   echo 'DATE   = ' ${DATE}
   echo 'CYCLE  = ' ${CYCLE}
   echo 'RLATC  = ' ${RLATC}
   echo 'RLONC  = ' ${RLONC}
else
   echo 'Usage: sh hwrf_nmm_gsi_d1.sh storm YEAR MONTH DATE '
   echo '                             CYCLE RLATC RLONC     '
   echo 'NEED SEVEN ARGUMENTS'
   echo 'SCRIPT WILL EXIT'
   sh ${utilscript}/setup.sh
   err=911
   err_exit "NEED SEVEN ARGUMENTS"
fi

####################################################

st_size=${STORM_SIZE}
st_int=${STORM_INT}
st_depth=${STORM_DEPTH}

export RRADC=1200.0
echo 'RRADC = ' ${RRADC}

export adate=$YEAR$MONTH$DATE$CYCLE
echo 'adate = ' ${adate}


# Set environment variables for NCEP IBM
export MEMORY_AFFINITY=MCM
export MP_SHARED_MEMORY=yes

# Set environment variables for threads
export AIXTHREAD_SCOPE=S
export XLSMPOPTS="parthds=1:stack=128000000"

# Recommended MPI environment variable setttings from IBM
# (Appendix E, HPC Clusters Using InfiniBand on IBM Power Systems Servers)
export LAPI_DEBUG_ENABLE_AFFINITY=YES
export MP_FIFO_MTU=4K
export MP_SYNC_QP=YES
export MP_SHM_ATTACH_THRESH=500000 # default is better sometimes
export MP_EUIDEVELOP=min
export MP_USE_BULK_XFER=yes
export MP_BULK_MIN_MSG_SIZE=64k
export MP_RC_MAX_QP=8192
export LAPI_DEBUG_RC_DREG_THRESHOLD=1000000
export LAPI_DEBUG_QP_NOTIFICATION=no
export LAPI_DEBUG_RC_INIT_SETUP=yes

# Set environment variables for user preferences
export XLFRTEOPTS="nlwidth=80"
export MP_LABELIO=yes
export MP_INFOLEVEL=1

# Variables for debugging (don't always need)
##export XLFRTEOPTS="buffering=disable_all"
##export MP_COREFILE_FORMAT=lite

# Set guess/analysis (i/o) file format.  Two
# option are available:  binary or netcdf
if [[ "$IO_FORM" == 2 ]] ; then
    io_format=netcdf
    NETCDF=.true.
    FORMAT=netcdf
else
    # Default to binary just in case $IO_FORM is unset in operations
    io_format=binary
    NETCDF=.false.
    FORMAT=binary
fi

# Set experiment name and analysis date
exp=gsi_cvs2



# Set path/file for gsi executable
gsiexec=${EXEChwrf}/hwrf_gsi

# Set resolution and other dependent parameters
export JCAP=62
export LEVS=42
export JCAP_B=62
export DELTIM=1200
export NLAT=987
export NLON=528

export gps_dtype="gps_ref"

# Set runtime and save directories
tmpdir=${DATA}/3DVAR/tmpreg_nmm_netcdf/$exp.$storm.$adate
savdir=${DATA}/3DVAR/outreg/nmm_netcdf/$exp.$storm.$adate

echo 'tmpdir = ' ${tmpdir}
echo 'savdir = ' ${savdir}

# Specify GSI fixed field and data directories.
if [[ "$PARAFLAG" == YES && "$( $USHhwrf/hwrf_port_byteorder.sh )" == littleendian ]] ; then
    BYTE_ORDER=Little_Endian
else
    BYTE_ORDER=Big_Endian
fi
fixgsi=$FIX_GSI_PATH
fixcrtm=$FIX_GSI_CRTM_PATH

datobs=$ATMOS_INPUT
datges=${DATA}/3DVAR/hwrf_rel/$storm.$adate


# Set variables used in script
#   CLEAN up $tmpdir when finished (YES=remove, NO=leave alone)
#   ndate is a date manipulation utility
#   ncp is cp replacement, currently keep as /bin/cp

CLEAN=NO
ndate=${NDATE_PATH:-${utilexec}/ndate}
ncp=${CP_PATH:-/bin/cp}


# Given the analysis date, compute the date from which the
# first guess comes.  Extract cycle and set prefix and suffix
# for guess and observation data files
gdate=`$ndate -06 $adate`
hha=`echo $adate | cut -c9-10`
hhg=`echo $gdate | cut -c9-10`
prefixa=gfs.t${hha}z
prefixg=gfs.t${hhg}z
suffix=tm00.bufr_d

echo 'gdate = ' ${gdate}
echo 'hha   = ' ${hha}
echo 'hhg   = ' ${hhg}

# Set up $tmpdir
rm -rf $tmpdir
$USHhwrf/hwrf_mkdirp.sh $tmpdir
chgrp rstprod $tmpdir || /bin/true # so that set -e can succeed
chmod 750 $tmpdir
cd $tmpdir
rm -rf core*

# Make parameters for hybrid DA

# Define parameters for hybrid ensemble option test.
#   (default is set to false, so no hybrid ensemble option test.)

export HYBENS_REGIONAL=".false."
export ENSEMBLE_SIZE_REGIONAL="80"
export HYBENS_UV_REGIONAL=".true."
export BETA1_INV_REGIONAL="0.2"
export HYBENS_HOR_SCALE_REGIONAL="300"
export HYBENS_VER_SCALE_REGIONAL="10"
export GENERATE_ENS_REGIONAL=".false."
export GEFS_IN_REGIONAL=".true."
export MERGE_TWO_GRID=".false."
export HYBENS_ANISO_REGIONAL=".false."
export NLON_ENS_REGIONAL="528"
export NLAT_ENS_REGIONAL="494"
export JCAP_ENS_REGIONAL="0"
export JCAP_ENS_TEST_REGIONAL="0"

cat << EOF > gsiparm.anl
 &SETUP
   miter=2,niter(1)=50,niter(2)=50,
   write_diag(1)=.true.,write_diag(2)=.false.,write_diag(3)=.true.,
   gencode=78,qoption=2,
   factqmin=0.0,factqmax=0.0,deltim=$DELTIM,
   ndat=10,iguess=-1,
   oneobtest=.false.,retrieval=.false.,
   nhr_assimilation=3,l_foto=.false.,
   use_pbl=.false.,use_compress=.false.,
 /
 &GRIDOPTS
   JCAP=$JCAP,JCAP_B=$JCAP_B,NLAT=$NLAT,NLON=$NLON,nsig=$LEVS,hybrid=.true.,
   wrf_nmm_regional=.true.,wrf_mass_regional=.false.,
   diagnostic_reg=.false.,
   filled_grid=.false.,half_grid=.true.,netcdf=$NETCDF,
 /
 &BKGERR
   hzscl=0.2,0.4,0.8,
   vs=1.0,bw=0.,fstat=.true.,
 /
 &ANBKGERR
   anisotropic=.false.,an_vs=1.0,ngauss=1,
   an_flen_u=-5.,an_flen_t=3.,an_flen_z=-200.,
   ifilt_ord=2,npass=3,normal=-200,grid_ratio=4.,nord_f2a=4,
 /
 &JCOPTS
 /
 &STRONGOPTS
   jcstrong=.false.,jcstrong_option=3,nstrong=0,nvmodes_keep=20,period_max=3.,
   baldiag_full=.true.,baldiag_inc=.true.,
 /
 &OBSQC
   dfact=0.75,dfact1=3.0,noiqc=.false.,c_varqc=0.02,vadfile='prepbufr',
 /
 &OBS_INPUT
   dmesh(1)=120.0,dmesh(2)=60.0,dmesh(3)=60.0,dmesh(4)=60.0,dmesh(5)=120,time_window_max=1.5,
   dfile(01)='prepbufr',  dtype(01)='ps',        dplat(01)=' ',         dsis(01)='ps',                  dval(01)=1.0,  dthin(01)=0, dsfcalc(01)=0,
   dfile(02)='prepbufr'   dtype(02)='t',         dplat(02)=' ',         dsis(02)='t',                   dval(02)=1.0,  dthin(02)=0, dsfcalc(02)=0,
   dfile(03)='prepbufr',  dtype(03)='q',         dplat(03)=' ',         dsis(03)='q',                   dval(03)=1.0,  dthin(03)=0, dsfcalc(03)=0,
   dfile(04)='prepbufr',  dtype(04)='uv',        dplat(04)=' ',         dsis(04)='uv',                  dval(04)=1.0,  dthin(04)=0, dsfcalc(04)=0,
   dfile(05)='satwnd',  dtype(05)='uv',          dplat(05)=' ',         dsis(05)='uv',                  dval(05)=1.0,  dthin(05)=0, dsfcalc(05)=0,
   dfile(06)='prepbufr',  dtype(06)='spd',       dplat(06)=' ',         dsis(06)='spd',                 dval(06)=1.0,  dthin(06)=0, dsfcalc(06)=0,
   dfile(07)='radarbufr', dtype(07)='rw',        dplat(07)=' ',         dsis(07)='rw',                  dval(07)=1.0,  dthin(07)=0, dsfcalc(07)=0,
   dfile(08)='prepbufr',  dtype(08)='dw',        dplat(08)=' ',         dsis(08)='dw',                  dval(08)=1.0,  dthin(08)=0, dsfcalc(08)=0,
   dfile(09)='prepbufr',  dtype(09)='sst',       dplat(09)=' ',         dsis(09)='sst',                 dval(09)=1.0,  dthin(09)=0, dsfcalc(09)=0,
   dfile(10)='prepbufr',  dtype(10)='pw',        dplat(10)=' ',         dsis(10)='pw',                  dval(10)=1.0,  dthin(10)=0, dsfcalc(10)=0,
   dfile(11)='gpsrobufr', dtype(11)='$gps_dtype',   dplat(11)=' ',      dsis(11)='gps',                 dval(11)=1.0,  dthin(11)=0, dsfcalc(11)=0,
   dfile(12)='ssmirrbufr',dtype(12)='pcp_ssmi',  dplat(12)='dmsp',      dsis(12)='pcp_ssmi',            dval(12)=1.0,  dthin(12)=-1,dsfcalc(12)=0,
   dfile(13)='tmirrbufr', dtype(13)='pcp_tmi',   dplat(13)='trmm',      dsis(13)='pcp_tmi',             dval(13)=1.0,  dthin(13)=-1,dsfcalc(13)=0,
   dfile(14)='sbuvbufr',  dtype(14)='sbuv2',     dplat(14)='n16',       dsis(14)='sbuv8_n16',           dval(14)=1.0,  dthin(14)=0, dsfcalc(14)=0,
   dfile(15)='sbuvbufr',  dtype(15)='sbuv2',     dplat(15)='n17',       dsis(15)='sbuv8_n17',           dval(15)=1.0,  dthin(15)=0, dsfcalc(15)=0,
   dfile(16)='sbuvbufr',  dtype(16)='sbuv2',     dplat(16)='n18',       dsis(16)='sbuv8_n18',           dval(16)=1.0,  dthin(16)=0, dsfcalc(16)=0,
   dfile(17)='omi',       dtype(17)='omi',       dplat(17)='aura',      dsis(17)='omi_aura',            dval(17)=1.0,  dthin(17)=6, dsfcalc(17)=0,
   dfile(18)='hirs2bufr', dtype(18)='hirs2',     dplat(18)='n14',       dsis(18)='hirs2_n14',           dval(18)=6.0,  dthin(18)=1, dsfcalc(18)=1,
   dfile(19)='hirs3bufr', dtype(19)='hirs3',     dplat(19)='n16',       dsis(19)='hirs3_n16',           dval(19)=0.0,  dthin(19)=1, dsfcalc(19)=1,
   dfile(20)='hirs3bufr', dtype(20)='hirs3',     dplat(20)='n17',       dsis(20)='hirs3_n17',           dval(20)=0.0,  dthin(20)=1, dsfcalc(20)=1,
   dfile(21)='hirs4bufr', dtype(21)='hirs4',     dplat(21)='n18',       dsis(21)='hirs4_n18',           dval(21)=0.0,  dthin(21)=1, dsfcalc(21)=1,
   dfile(22)='hirs4bufr', dtype(22)='hirs4',     dplat(22)='metop-a',   dsis(22)='hirs4_metop-a',       dval(22)=6.0,  dthin(22)=1, dsfcalc(22)=1,
   dfile(23)='gsndrbufr', dtype(23)='sndr',      dplat(23)='g11',       dsis(23)='sndr_g11',            dval(23)=0.0,  dthin(23)=1, dsfcalc(23)=0,
   dfile(24)='gsndrbufr', dtype(24)='sndr',      dplat(24)='g12',       dsis(24)='sndr_g12',            dval(24)=0.0,  dthin(24)=1, dsfcalc(24)=0,
   dfile(25)='gimgrbufr', dtype(25)='goes_img',  dplat(25)='g11',       dsis(25)='imgr_g11',            dval(25)=0.0,  dthin(25)=1, dsfcalc(25)=0,
   dfile(26)='gimgrbufr', dtype(26)='goes_img',  dplat(26)='g12',       dsis(26)='imgr_g12',            dval(26)=0.0,  dthin(26)=1, dsfcalc(26)=0,
   dfile(27)='airsbufr',  dtype(27)='airs',      dplat(27)='aqua',      dsis(27)='airs281SUBSET_aqua',  dval(27)=20.0, dthin(27)=1, dsfcalc(27)=1,
   dfile(28)='msubufr',   dtype(28)='msu',       dplat(28)='n14',       dsis(28)='msu_n14',             dval(28)=2.0,  dthin(28)=2, dsfcalc(28)=1,
   dfile(29)='amsuabufr', dtype(29)='amsua',     dplat(29)='n15',       dsis(29)='amsua_n15',           dval(29)=10.0, dthin(29)=2, dsfcalc(29)=1,
   dfile(30)='amsuabufr', dtype(30)='amsua',     dplat(30)='n16',       dsis(30)='amsua_n16',           dval(30)=0.0,  dthin(30)=2, dsfcalc(30)=1,
   dfile(31)='amsuabufr', dtype(31)='amsua',     dplat(31)='n17',       dsis(31)='amsua_n17',           dval(31)=0.0,  dthin(31)=2, dsfcalc(31)=1,
   dfile(32)='amsuabufr', dtype(32)='amsua',     dplat(32)='n18',       dsis(32)='amsua_n18',           dval(32)=10.0, dthin(32)=2, dsfcalc(32)=1,
   dfile(33)='amsuabufr', dtype(33)='amsua',     dplat(33)='metop-a',   dsis(33)='amsua_metop-a',       dval(33)=10.0, dthin(33)=2, dsfcalc(33)=1,
   dfile(34)='airsbufr',  dtype(34)='amsua',     dplat(34)='aqua',      dsis(34)='amsua_aqua',          dval(34)=5.0,  dthin(34)=2, dsfcalc(34)=1,
   dfile(35)='amsubbufr', dtype(35)='amsub',     dplat(35)='n15',       dsis(35)='amsub_n15',           dval(35)=3.0,  dthin(35)=3, dsfcalc(35)=1,
   dfile(36)='amsubbufr', dtype(36)='amsub',     dplat(36)='n16',       dsis(36)='amsub_n16',           dval(36)=3.0,  dthin(36)=3, dsfcalc(36)=1,
   dfile(37)='amsubbufr', dtype(37)='amsub',     dplat(37)='n17',       dsis(37)='amsub_n17',           dval(37)=3.0,  dthin(37)=3, dsfcalc(37)=1,
   dfile(38)='mhsbufr',   dtype(38)='mhs',       dplat(38)='n18',       dsis(38)='mhs_n18',             dval(38)=3.0,  dthin(38)=3, dsfcalc(38)=1,
   dfile(39)='mhsbufr',   dtype(39)='mhs',       dplat(39)='metop-a',   dsis(39)='mhs_metop-a',         dval(39)=3.0,  dthin(39)=3, dsfcalc(39)=1,
   dfile(40)='ssmitbufr', dtype(40)='ssmi',      dplat(40)='f13',       dsis(40)='ssmi_f13',            dval(40)=0.0,  dthin(40)=4, dsfcalc(40)=0,
   dfile(41)='ssmitbufr', dtype(41)='ssmi',      dplat(41)='f14',       dsis(41)='ssmi_f14',            dval(41)=0.0,  dthin(41)=4, dsfcalc(41)=0,
   dfile(42)='ssmitbufr', dtype(42)='ssmi',      dplat(42)='f15',       dsis(42)='ssmi_f15',            dval(42)=0.0,  dthin(42)=4, dsfcalc(42)=0,
   dfile(43)='amsrebufr', dtype(43)='amsre_low', dplat(43)='aqua',      dsis(43)='amsre_aqua',          dval(43)=0.0,  dthin(43)=4, dsfcalc(43)=1,
   dfile(44)='amsrebufr', dtype(44)='amsre_mid', dplat(44)='aqua',      dsis(44)='amsre_aqua',          dval(44)=0.0,  dthin(44)=4, dsfcalc(44)=1,
   dfile(45)='amsrebufr', dtype(45)='amsre_hig', dplat(45)='aqua',      dsis(45)='amsre_aqua',          dval(45)=0.0,  dthin(45)=4, dsfcalc(45)=1,
   dfile(46)='ssmisbufr', dtype(46)='ssmis',     dplat(46)='f16',       dsis(46)='ssmis_f16',           dval(46)=0.0,  dthin(46)=4, dsfcalc(46)=1,
   dfile(47)='gsnd1bufr', dtype(47)='sndrd1',    dplat(47)='g12',       dsis(47)='sndrD1_g12',          dval(47)=1.5,  dthin(47)=5, dsfcalc(47)=0,
   dfile(48)='gsnd1bufr', dtype(48)='sndrd2',    dplat(48)='g12',       dsis(48)='sndrD2_g12',          dval(48)=1.5,  dthin(48)=5, dsfcalc(48)=0,
   dfile(49)='gsnd1bufr', dtype(49)='sndrd3',    dplat(49)='g12',       dsis(49)='sndrD3_g12',          dval(49)=1.5,  dthin(49)=5, dsfcalc(49)=0,
   dfile(50)='gsnd1bufr', dtype(50)='sndrd4',    dplat(50)='g12',       dsis(50)='sndrD4_g12',          dval(50)=1.5,  dthin(50)=5, dsfcalc(50)=0,
   dfile(51)='gsnd1bufr', dtype(51)='sndrd1',    dplat(51)='g11',       dsis(51)='sndrD1_g11',          dval(51)=1.5,  dthin(51)=5, dsfcalc(51)=0,
   dfile(52)='gsnd1bufr', dtype(52)='sndrd2',    dplat(52)='g11',       dsis(52)='sndrD2_g11',          dval(52)=1.5,  dthin(52)=5, dsfcalc(52)=0,
   dfile(53)='gsnd1bufr', dtype(53)='sndrd3',    dplat(53)='g11',       dsis(53)='sndrD3_g11',          dval(53)=1.5,  dthin(53)=5, dsfcalc(53)=0,
   dfile(54)='gsnd1bufr', dtype(54)='sndrd4',    dplat(54)='g11',       dsis(54)='sndrD4_g11',          dval(54)=1.5,  dthin(54)=5, dsfcalc(54)=0,
   dfile(55)='gsnd1bufr', dtype(55)='sndrd1',    dplat(55)='g13',       dsis(55)='sndrD1_g13',          dval(55)=1.5,  dthin(55)=5, dsfcalc(55)=0,
   dfile(56)='gsnd1bufr', dtype(56)='sndrd2',    dplat(56)='g13',       dsis(56)='sndrD2_g13',          dval(56)=1.5,  dthin(56)=5, dsfcalc(56)=0,
   dfile(57)='gsnd1bufr', dtype(57)='sndrd3',    dplat(57)='g13',       dsis(57)='sndrD3_g13',          dval(57)=1.5,  dthin(57)=5, dsfcalc(57)=0,
   dfile(58)='gsnd1bufr', dtype(58)='sndrd4',    dplat(58)='g13',       dsis(58)='sndrD4_g13',          dval(58)=1.5,  dthin(58)=5, dsfcalc(58)=0,
   dfile(59)='iasibufr',  dtype(59)='iasi',      dplat(59)='metop-a',   dsis(59)='iasi616_metop-a',     dval(59)=20.0, dthin(59)=1, dsfcalc(59)=1,
   dfile(60)='gomebufr',  dtype(60)='gome',      dplat(60)='metop-a',   dsis(60)='gome_metop-a',        dval(60)=1.0,  dthin(60)=6, dsfcalc(60)=0,
   dfile(61)='mlsbufr',   dtype(61)='mls',       dplat(61)='aura',      dsis(61)='mls_aura',            dval(61)=1.0,  dthin(61)=0, dsfcalc(61)=0,
 /
 &SUPEROB_RADAR
   del_azimuth=5.,del_elev=.25,del_range=5000.,del_time=.5,elev_angle_max=5.,minnum=50,range_max=100000.,
   l2superob_only=.false.,
 /
 &LAG_DATA
 /
 &HYBRID_ENSEMBLE
   l_hyb_ens=${HYBENS_REGIONAL},
   n_ens=${ENSEMBLE_SIZE_REGIONAL},
   uv_hyb_ens=${HYBENS_UV_REGIONAL},
   beta1_inv=${BETA1_INV_REGIONAL},
   s_ens_h=${HYBENS_HOR_SCALE_REGIONAL},
   s_ens_v=${HYBENS_VER_SCALE_REGIONAL},
   generate_ens=${GENERATE_ENS_REGIONAL},
   aniso_a_en=${HYBENS_ANISO_REGIONAL},
   nlon_ens=${NLON_ENS_REGIONAL},
   nlat_ens=${NLAT_ENS_REGIONAL},
   jcap_ens=${JCAP_ENS_REGIONAL},
   jcap_ens_test=${JCAP_ENS_TEST_REGIONAL},
 /
 &RAPIDREFRESH_CLDSURF
   dfi_radar_latent_heat_time_period=30.0,
 /
 &CHEM
 /
 &SINGLEOB_TEST
   maginnov=1.0,magoberr=0.8,oneob_type='t',
   oblat=38.,oblon=279.,obpres=500.,obdattim=${adate},
   obhourset=0.,
 /

EOF

# Set fixed files
#   berror   = forecast model background error statistics
#   specoef  = CRTM spectral coefficients
#   trncoef  = CRTM transmittance coefficients
#   emiscoef = CRTM coefficients for IR sea surface emissivity model
#   aerocoef = CRTM coefficients for aerosol effects
#   cldcoef  = CRTM coefficients for cloud effects
#   satinfo  = text file with information about assimilation of brightness temperatures
#   satangl  = angle dependent bias correction file (fixed in time)
#   pcpinfo  = text file with information about assimilation of prepcipitation rates
#   ozinfo   = text file with information about assimilation of ozone data
#   errtable = text file with obs error for conventional data (regional only)
#   convinfo = text file with information about assimilation of conventional data
#   bufrtable= text file ONLY needed for single obs test (oneobstest=.true.)
#   bftab_sst= bufr table for sst ONLY needed for sst retrieval (retrieval=.true.)

anavinfo=$fixgsi/anavinfo_hwrf
if [[ "$BYTE_ORDER" == Little_Endian ]] ; then
   berror=$fixgsi/nam_glb_berror.f77.gcv_Little_Endian
else
   berror=$fixgsi/nam_glb_berror.f77.gcv
fi
emiscoef=$fixcrtm/EmisCoeff/${BYTE_ORDER}/EmisCoeff.bin
aercoef=$fixcrtm/AerosolCoeff/${BYTE_ORDER}/AerosolCoeff.bin
cldcoef=$fixcrtm/CloudCoeff/${BYTE_ORDER}/CloudCoeff.bin
satinfo=$fixgsi/nam_regional_satinfo.txt
scaninfo=$fixgsi/global_scaninfo.txt
satangl=$fixgsi/nam_global_satangbias.txt
pcpinfo=$fixgsi/nam_global_pcpinfo.txt
ozinfo=$fixgsi/nam_global_ozinfo.txt
errtable=$fixgsi/nam_errtable.r3dv
convinfo=$fixgsi/nam_regional_convinfo.txt

# Only need this file for single obs test
bufrtable=$FIX_GSI_PATH/prepobs_prep.bufrtable

# Only need this file for sst retrieval
bftab_sst=$FIX_GSI_PATH/bufrtab.012


# Copy executable and fixed files to $tmpdir
$ncp $gsiexec ./gsi.x

# NOTE: GSI now run for all storm depths.

$ncp $anavinfo ./anavinfo
$ncp $berror   ./berror_stats
$ncp $emiscoef ./EmisCoeff.bin
$ncp $aercoef  ./AerosolCoeff.bin
$ncp $cldcoef  ./CloudCoeff.bin
$ncp $satangl  ./satbias_angle
$ncp $satinfo  ./satinfo
$ncp $scaninfo ./scaninfo
$ncp $pcpinfo  ./pcpinfo
$ncp $ozinfo   ./ozinfo
$ncp $convinfo ./convinfo
$ncp $errtable ./errtable

$ncp $bufrtable ./prepobs_prep.bufrtable
$ncp $bftab_sst ./bftab_sstphr

# Copy CRTM coefficient files based on entries in satinfo file
for satsen in $( cat $satinfo | grep -vE '^!' | cut -f 2 -d" " | sort -u ) ; do
    spccoeff=${satsen}.SpcCoeff.bin
    if  [[ ! -s $spccoeff ]]; then
        $ncp $fixcrtm/SpcCoeff/${BYTE_ORDER}/$spccoeff ./
        $ncp $fixcrtm/TauCoeff/${BYTE_ORDER}/${satsen}.TauCoeff.bin ./
    fi
done

# Copy observational data to $tmpdir

if [[ $YEAR -gt 2004 ]]; then

    # Due to NOAA's inability to figure out how to safely store
    # restricted access data on Jet, we will not be using restricted
    # access data in 2012 HWRF.

#      if [[ -s "$datobs/${prefixa}.prepbufr" && -r "$datobs/${prefixa}.prepbufr" ]] ; then
#          $ncp $datobs/${prefixa}.prepbufr           ./prepbufr
#      else
          $ncp $datobs/${prefixa}.prepbufr.nr        ./prepbufr
#      fi
     set +e
#     $ncp -f $datobs/${prefixa}.satwnd.$suffix     ./satwnd
#     $ncp -f $datobs/${prefixa}.goesfv.${suffix}   ./gsnd1bufr
#     $ncp -f $datobs/${prefixa}.1bamua.${suffix}   ./amsuabufr
#     $ncp -f $datobs/${prefixa}.1bamub.${suffix}   ./amsubbufr
#     $ncp -f $datobs/${prefixa}.1bhrs3.${suffix}   ./hirs3bufr
#     $ncp -f $datobs/${prefixa}.1bhrs4.${suffix}   ./hirs4bufr
#     $ncp -f $datobs/${prefixa}.1bmhs.${suffix}    ./mhsbufr
#     $ncp -f $datobs/${prefixa}.airsev.${suffix}   ./airsbufr
##   $ncp -f $datobs/${prefixo}.gpsro.$suffix   ./gpsrobufr
     set -e
   $ncp $datobs/gfs.t${CYCLE}z.abias              ./satbias_in
   $ncp $datobs/gfs.t${CYCLE}z.satang             ./satbias_angle
  
else
     set +e
     $ncp -f $datobs/gblav.t${CYCLE}z.1bamua.${suffix}   ./amsuabufr
     $ncp -f $datobs/gblav.t${CYCLE}z.1bamub.${suffix}   ./amsubbufr
     $ncp -f $datobs/gblav.t${CYCLE}z.1bhrs2.${suffix}   ./hirs2bufr
     $ncp -f $datobs/gblav.t${CYCLE}z.1bhrs3.${suffix}   ./hirs3bufr
     $ncp -f $datobs/gblav.t${CYCLE}z.1bmsu.${suffix}    ./msubufr
     set -e
   $ncp $datobs/gblav.t${CYCLE}z.abias              ./satbias_in
   $ncp $datobs/gblav.t${CYCLE}z.satang             ./satbias_angle

fi

###convert prepbufr file from big_endian to little_endian if needed
if [[ "$BYTE_ORDER" == Little_Endian ]] ; then
   $USHhwrf/hwrf_maybe_byteswap.sh ./prepbufr ./satwnd ./gsnd1bufr ./amsuabufr ./amsubbufr ./hirs3bufr ./hirs4bufr ./mhsbufr ./airsbufr
fi
### end of conversion

mv ./prepbufr               ./prepbufr.ALL
ln -sf prepbufr.ALL                 ./fort.21
ln -sf prepbufr                     ./fort.51

cp ${EXEChwrf}/hwrf_data_remv  ./data_remv.x
# run the executable data_remv.x
sh ${utilscript}/setup.sh
export pgm=data_remv.x
set +u +e
. prep_step
startmsg
set -u -e
./data_remv.x
export err=$?; err_chk
echo "executable data_remv.x return code err = ${err}"

ls -lt ./prepbufr.ALL ./prepbufr

if [[ $YEAR -gt 2006 ]]; then

stormlower=`echo ${storm} | tr '[A-Z]' '[a-z]'`
nid=${stormlower}${stormid}

else

cp ${FIXhwrf}/hwrf_global_satinfo.txt ./satinfo


# run the executable hwrf_reformat_abias
sh ${utilscript}/setup.sh
export pgm=hwrf_reformat_tb
set +u +e
. prep_step
startmsg
set -u -e
${EXEChwrf}/hwrf_reformat_tb
export err=$?;err_chk
echo "executable hwrf_reformat_tb return code err = ${err}"

mv   ./biascr_out        ./satbias_in
mv   ./satang_out        ./satbias_angle

fi

biascr_d2=${HISTDATA}/$stormid.$gdate.gsi_cvs2.biascr

if [ ! -f $biascr_d2 ]; then
  echo "Previous bias correction file not located at $biascr_d2"
  echo "either cold start or storm_n is greater than 30"
else
  /bin/cp -f $biascr_d2 ./satbias_in
fi


# Copy bias correction, sigma, and surface files
#
#  *** NOTE:  The regional gsi analysis is written to (over)
#             the input guess field file (wrf_inout)
#

if [ ${INIT} == YES ]; then
cp  $datges/wrfghost_d02           ./wrf_inout
else 
cp ${DATA}/$storm.$adate/ATMOS/ghost_d02_0000-00-00_00:00:00 ./wrf_inout
fi

sh ${utilscript}/setup.sh

"$USHhwrf/hwrf_port_cachesync.sh" -p

# Run gsi under Parallel Operating Environment (poe) on NCEP IBM
$USHhwrf/hwrf_run.sh $tmpdir/gsi.x < gsiparm.anl > stdout
rc=$?
export err=$rc
if [ $rc -ne 0 ]; then
err_exit "GSI failed"
fi

# Save output
$USHhwrf/hwrf_mkdirp.sh $savdir
chgrp rstprod $savdir || /bin/true # so that set -e can succeed
chmod 750 $savdir

cat stdout fort.2* > $savdir/stdout.anl.${adate}
$ncp wrf_inout       $savdir/wrfanl.${adate}
$ncp satbias_out     $savdir/biascr.${adate}
$ncp satbias_out     ${COMOUT}/${stormid}.${adate}.gsi_cvs2.biascr

# If desired, copy guess file to unique filename in $savdir
if [ $INIT == YES ]; then
cp $datges/wrfghost_d02  $savdir/wrfges.${adate}
fi

# Loop over first and last outer loops to generate innovation
# diagnostic files for indicated observation types (groups)
#
# NOTE:  Since we set miter=2 in GSI namelist SETUP, outer
#        loop 03 will contain innovations with respect to
#        the analysis.  Creation of o-a innovation files
#        is triggered by write_diag(3)=.true.  The setting
#        write_diag(1)=.true. turns on creation of o-g
#        innovation files.
#

cd $tmpdir
loops="01 03"
for loop in $loops; do

case $loop in
  01) string=ges;;
  03) string=anl;;
   *) string=$loop;;
esac

# Collect diagnostic files for obs types (groups) below
   listall="hirs2_n14 msu_n14 sndr_g08 sndr_g10 sndr_g12 sndr_g08_prep sndr_g10_prep sndr_g12_prep sndrd1_g08 sndrd2_g08 sndrd3_g08 sndrd4_g08 sndrd1_g10 sndrd2_g10 sndrd3_g10 sndrd4_g10 sndrd1_g12 sndrd2_g12 sndrd3_g12 sndrd4_g12 sndrd1_g11 sndrd2_g11 sndrd3_g11 sndrd4_g11 sndrd1_g13 sndrd2_g13 sndrd3_g13 sndrd4_g13 hirs3_n15 hirs3_n16 hirs3_n17 amsua_n15 amsua_n16 amsua_n17 amsub_n15 amsub_n16 amsub_n17 hsb_aqua airs_aqua amsua_aqua imgr_g08 imgr_g10 imgr_g12 pcp_ssmi_dmsp pcp_tmi_trmm conv sbuv2_n16 sbuv2_n17 sbuv2_n18 omi_aura ssmi_f13 ssmi_f14 ssmi_f15 hirs4_n18 amsua_n18 mhs_n18 amsre_low_aqua amsre_mid_aqua amsre_hig_aqua ssmis_las_f16 ssmis_uas_f16 ssmis_img_f16 ssmis_env_f16 iasi_metop-a"
   for type in $listall; do
      if [[ "$IO_FORM" == 2 ]] ; then
         count=`ls pe*.${type}_${loop}* | wc -l`
      else
         count=`ls dir.*/${type}_${loop}* | wc -l`
      fi
      if [[ $count -gt 0 ]]; then
         if [[ "$IO_FORM" == 2 ]] ; then
            cat pe*.${type}_${loop}* > diag_${type}_${string}.${adate}
         else
            cat dir.*/${type}_${loop}* > diag_${type}_${string}.${adate}
         fi
         gzip diag_${type}_${string}.${adate}
         $ncp diag_${type}_${string}.${adate}.gz $savdir/
      fi
   done
done

# If requested, clean up $tmpdir
if [[ "$CLEAN" = "YES" ]];then
   if [[ $rc -eq 0 ]];then
      rm -rf $tmpdir
      cd $tmpdir
      cd ../
      rmdir $tmpdir
   fi
fi


# End of script