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exglobal_forecast.sh
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#!/bin/ksh
################################################################################
# UNIX Script Documentation Block
# Script name: exglobal_forecast.sh
# Script description: Runs a global FV3GFS model forecast
#
# Author: Fanglin Yang Org: NCEP/EMC Date: 2016-11-15
# Abstract: This script runs a single GFS forecast with FV3 dynamical core.
# This script is created based on a C-shell script that GFDL wrote
# for the NGGPS Phase-II Dycore Comparison Project.
#
# Script history log:
# 2016-11-15 Fanglin Yang First Version.
# 2017-02-09 Rahul Mahajan Added warm start and restructured the code.
# 2017-03-10 Fanglin Yang Updated for running forecast on Cray.
# 2017-03-24 Fanglin Yang Updated to use NEMS FV3GFS with IPD4
# 2017-05-24 Rahul Mahajan Updated for cycling with NEMS FV3GFS
# 2017-09-13 Fanglin Yang Updated for using GFDL MP and Write Component
# 2019-03-05 Rahul Mahajan Implemented IAU
# 2019-03-21 Fanglin Yang Add restart capability for running gfs fcst from a break point.
# 2019-12-12 Henrique Alves Added wave model blocks for coupled run
# 2020-01-31 Henrique Alves Added IAU capability for wave component
# 2020-06-02 Fanglin Yang restore restart capability when IAU is turned on.
#
# $Id$
#
# Attributes:
# Language: Portable Operating System Interface (POSIX) Shell
# Machine: WCOSS-CRAY, Theia
################################################################################
# Set environment.
VERBOSE=${VERBOSE:-"YES"}
if [ $VERBOSE = "YES" ] ; then
echo $(date) EXECUTING $0 $* >&2
set -x
fi
machine=${machine:-"WCOSS_C"}
machine=$(echo $machine | tr '[a-z]' '[A-Z]')
# Cycling and forecast hour specific parameters
CDUMPwave="${CDUMP}wave"
CASE=${CASE:-C768}
CDATE=${CDATE:-2017032500}
CDUMP=${CDUMP:-gdas}
FHMIN=${FHMIN:-0}
FHMAX=${FHMAX:-9}
FHOUT=${FHOUT:-3}
FHZER=${FHZER:-6}
FHCYC=${FHCYC:-24}
FHMAX_HF=${FHMAX_HF:-0}
FHOUT_HF=${FHOUT_HF:-1}
NSOUT=${NSOUT:-"-1"}
FDIAG=$FHOUT
if [ $FHMAX_HF -gt 0 -a $FHOUT_HF -gt 0 ]; then FDIAG=$FHOUT_HF; fi
WRITE_DOPOST=${WRITE_DOPOST:-".false."}
restart_interval=${restart_interval:-0}
rst_invt1=`echo $restart_interval |cut -d " " -f 1`
PDY=$(echo $CDATE | cut -c1-8)
cyc=$(echo $CDATE | cut -c9-10)
# Directories.
pwd=$(pwd)
NWPROD=${NWPROD:-${NWROOT:-$pwd}}
HOMEgfs=${HOMEgfs:-$NWPROD}
FIX_DIR=${FIX_DIR:-$HOMEgfs/fix}
FIX_AM=${FIX_AM:-$FIX_DIR/fix_am}
FIXfv3=${FIXfv3:-$FIX_DIR/fix_fv3_gmted2010}
DATA=${DATA:-$pwd/fv3tmp$$} # temporary running directory
ROTDIR=${ROTDIR:-$pwd} # rotating archive directory
ICSDIR=${ICSDIR:-$pwd} # cold start initial conditions
DMPDIR=${DMPDIR:-$pwd} # global dumps for seaice, snow and sst analysis
# Model resolution specific parameters
DELTIM=${DELTIM:-225}
layout_x=${layout_x:-8}
layout_y=${layout_y:-16}
LEVS=${LEVS:-65}
# Utilities
NCP=${NCP:-"/bin/cp -p"}
NLN=${NLN:-"/bin/ln -sf"}
NMV=${NMV:-"/bin/mv"}
SEND=${SEND:-"YES"} #move final result to rotating directory
ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
KEEPDATA=${KEEPDATA:-"NO"}
# Other options
MEMBER=${MEMBER:-"-1"} # -1: control, 0: ensemble mean, >0: ensemble member $MEMBER
ENS_NUM=${ENS_NUM:-1} # Single executable runs multiple members (e.g. GEFS)
PREFIX_ATMINC=${PREFIX_ATMINC:-""} # allow ensemble to use recentered increment
# IAU options
DOIAU=${DOIAU:-"NO"}
IAUFHRS=${IAUFHRS:-0}
IAU_DELTHRS=${IAU_DELTHRS:-0}
IAU_OFFSET=${IAU_OFFSET:-0}
# Model specific stuff
FCSTEXECDIR=${FCSTEXECDIR:-$HOMEgfs/sorc/fv3gfs.fd/NEMS/exe}
FCSTEXEC=${FCSTEXEC:-fv3_gfs.x}
PARM_FV3DIAG=${PARM_FV3DIAG:-$HOMEgfs/parm/parm_fv3diag}
PARM_POST=${PARM_POST:-$HOMEgfs/parm/post}
# Wave coupling parameter defaults to false
cplwav=${cplwav:-.false.}
# Model config options
APRUN_FV3=${APRUN_FV3:-${APRUN_FCST:-${APRUN:-""}}}
NTHREADS_FV3=${NTHREADS_FV3:-${NTHREADS_FCST:-${nth_fv3:-1}}}
cores_per_node=${cores_per_node:-${npe_node_max:-24}}
ntiles=${ntiles:-6}
NTASKS_FV3=${NTASKS_FV3:-$npe_fv3}
TYPE=${TYPE:-"nh"} # choices: nh, hydro
MONO=${MONO:-"non-mono"} # choices: mono, non-mono
RUN_CCPP=${RUN_CCPP:-"NO"}
QUILTING=${QUILTING:-".true."}
OUTPUT_GRID=${OUTPUT_GRID:-"gaussian_grid"}
OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
WRITE_NEMSIOFLIP=${WRITE_NEMSIOFLIP:-".true."}
WRITE_FSYNCFLAG=${WRITE_FSYNCFLAG:-".true."}
affix="nemsio"
[[ "$OUTPUT_FILE" = "netcdf" ]] && affix="nc"
rCDUMP=${rCDUMP:-$CDUMP}
#------------------------------------------------------------------
# setup the runtime environment
if [ $machine = "WCOSS_C" ] ; then
HUGEPAGES=${HUGEPAGES:-hugepages4M}
. $MODULESHOME/init/sh 2>/dev/null
module load iobuf craype-$HUGEPAGES 2>/dev/null
export MPICH_GNI_COLL_OPT_OFF=${MPICH_GNI_COLL_OPT_OFF:-MPI_Alltoallv}
export MKL_CBWR=AVX2
export WRTIOBUF=${WRTIOBUF:-"4M"}
export NC_BLKSZ=${NC_BLKSZ:-"4M"}
export IOBUF_PARAMS="*nemsio:verbose:size=${WRTIOBUF},*:verbose:size=${NC_BLKSZ}"
fi
#-------------------------------------------------------
if [ ! -d $ROTDIR ]; then mkdir -p $ROTDIR; fi
mkdata=NO
if [ ! -d $DATA ]; then
mkdata=YES
mkdir -p $DATA
fi
cd $DATA || exit 8
mkdir -p $DATA/INPUT
if [ $cplwav = ".true." ]; then
if [ $CDUMP = "gdas" ]; then
RSTDIR_WAVE=$ROTDIR/${CDUMP}.${PDY}/${cyc}/wave/restart
else
RSTDIR_WAVE=${RSTDIR_WAVE:-$ROTDIR/${CDUMP}.${PDY}/${cyc}/wave/restart}
fi
if [ ! -d $RSTDIR_WAVE ]; then mkdir -p $RSTDIR_WAVE ; fi
$NLN $RSTDIR_WAVE restart_wave
fi
if [ $CDUMP = "gfs" -a $rst_invt1 -gt 0 ]; then
RSTDIR_ATM=${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART
if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
$NLN $RSTDIR_ATM RESTART
else
mkdir -p $DATA/RESTART
fi
#-------------------------------------------------------
# determine if restart IC exists to continue from a previous forecast
RERUN="NO"
filecount=$(find $RSTDIR_ATM -type f | wc -l)
if [ $CDUMP = "gfs" -a $rst_invt1 -gt 0 -a $FHMAX -gt $rst_invt1 -a $filecount -gt 10 ]; then
reverse=$(echo "${restart_interval[@]} " | tac -s ' ')
for xfh in $reverse ; do
yfh=$((xfh-(IAU_OFFSET/2)))
SDATE=$($NDATE +$yfh $CDATE)
PDYS=$(echo $SDATE | cut -c1-8)
cycs=$(echo $SDATE | cut -c9-10)
flag1=$RSTDIR_ATM/${PDYS}.${cycs}0000.coupler.res
flag2=$RSTDIR_ATM/coupler.res
if [ -s $flag1 ]; then
CDATE_RST=$SDATE
[[ $RERUN = "YES" ]] && break
mv $flag1 ${flag1}.old
if [ -s $flag2 ]; then mv $flag2 ${flag2}.old ;fi
RERUN="YES"
[[ $xfh = $rst_invt1 ]] && RERUN="NO"
fi
done
fi
#-------------------------------------------------------
# member directory
if [ $MEMBER -lt 0 ]; then
prefix=$CDUMP
rprefix=$rCDUMP
memchar=""
else
prefix=enkf$CDUMP
rprefix=enkf$rCDUMP
memchar=mem$(printf %03i $MEMBER)
fi
memdir=$ROTDIR/${prefix}.$PDY/$cyc/atmos/$memchar
if [ ! -d $memdir ]; then mkdir -p $memdir; fi
GDATE=$($NDATE -$assim_freq $CDATE)
gPDY=$(echo $GDATE | cut -c1-8)
gcyc=$(echo $GDATE | cut -c9-10)
gmemdir=$ROTDIR/${rprefix}.$gPDY/$gcyc/atmos/$memchar
sCDATE=$($NDATE -3 $CDATE)
if [[ "$DOIAU" = "YES" ]]; then
sCDATE=$($NDATE -3 $CDATE)
sPDY=$(echo $sCDATE | cut -c1-8)
scyc=$(echo $sCDATE | cut -c9-10)
tPDY=$gPDY
tcyc=$gcyc
else
sCDATE=$CDATE
sPDY=$PDY
scyc=$cyc
tPDY=$sPDY
tcyc=$cyc
fi
#-------------------------------------------------------
# initial conditions
warm_start=${warm_start:-".false."}
read_increment=${read_increment:-".false."}
res_latlon_dynamics="''"
# Determine if this is a warm start or cold start
if [ -f $gmemdir/RESTART/${sPDY}.${scyc}0000.coupler.res ]; then
export warm_start=".true."
fi
# turn IAU off for cold start
DOIAU_coldstart=${DOIAU_coldstart:-"NO"}
if [ $DOIAU = "YES" -a $warm_start = ".false." ] || [ $DOIAU_coldstart = "YES" -a $warm_start = ".true." ]; then
export DOIAU="NO"
echo "turning off IAU"
DOIAU_coldstart="YES"
IAU_OFFSET=0
sCDATE=$CDATE
sPDY=$PDY
scyc=$cyc
tPDY=$sPDY
tcyc=$cyc
fi
#-------------------------------------------------------
if [ $warm_start = ".true." -o $RERUN = "YES" ]; then
#-------------------------------------------------------
#.............................
if [ $RERUN = "NO" ]; then
#.............................
# Link all (except sfc_data) restart files from $gmemdir
for file in $(ls $gmemdir/RESTART/${sPDY}.${scyc}0000.*.nc); do
file2=$(echo $(basename $file))
file2=$(echo $file2 | cut -d. -f3-) # remove the date from file
fsuf=$(echo $file2 | cut -d. -f1)
if [ $fsuf != "sfc_data" ]; then
$NLN $file $DATA/INPUT/$file2
fi
done
# Link sfcanl_data restart files from $memdir
for file in $(ls $memdir/RESTART/${sPDY}.${scyc}0000.*.nc); do
file2=$(echo $(basename $file))
file2=$(echo $file2 | cut -d. -f3-) # remove the date from file
fsufanl=$(echo $file2 | cut -d. -f1)
if [ $fsufanl = "sfcanl_data" ]; then
file2=$(echo $file2 | sed -e "s/sfcanl_data/sfc_data/g")
$NLN $file $DATA/INPUT/$file2
fi
done
# Need a coupler.res when doing IAU
if [ $DOIAU = "YES" ]; then
rm -f $DATA/INPUT/coupler.res
cat >> $DATA/INPUT/coupler.res << EOF
2 (Calendar: no_calendar=0, thirty_day_months=1, julian=2, gregorian=3, noleap=4)
${gPDY:0:4} ${gPDY:4:2} ${gPDY:6:2} ${gcyc} 0 0 Model start time: year, month, day, hour, minute, second
${sPDY:0:4} ${sPDY:4:2} ${sPDY:6:2} ${scyc} 0 0 Current model time: year, month, day, hour, minute, second
EOF
fi
# Link increments
if [ $DOIAU = "YES" ]; then
for i in $(echo $IAUFHRS | sed "s/,/ /g" | rev); do
incfhr=$(printf %03i $i)
if [ $incfhr = "006" ]; then
increment_file=$memdir/${CDUMP}.t${cyc}z.${PREFIX_ATMINC}atminc.nc
else
increment_file=$memdir/${CDUMP}.t${cyc}z.${PREFIX_ATMINC}atmi${incfhr}.nc
fi
if [ ! -f $increment_file ]; then
echo "ERROR: DOIAU = $DOIAU, but missing increment file for fhr $incfhr at $increment_file"
echo "Abort!"
exit 1
fi
$NLN $increment_file $DATA/INPUT/fv_increment$i.nc
IAU_INC_FILES="'fv_increment$i.nc',$IAU_INC_FILES"
done
read_increment=".false."
res_latlon_dynamics=""
else
increment_file=$memdir/${CDUMP}.t${cyc}z.${PREFIX_INC}atminc.nc
if [ -f $increment_file ]; then
$NLN $increment_file $DATA/INPUT/fv_increment.nc
read_increment=".true."
res_latlon_dynamics="fv_increment.nc"
fi
fi
#.............................
else ##RERUN
export warm_start=".true."
PDYT=$(echo $CDATE_RST | cut -c1-8)
cyct=$(echo $CDATE_RST | cut -c9-10)
for file in $(ls $RSTDIR_ATM/${PDYT}.${cyct}0000.*); do
file2=$(echo $(basename $file))
file2=$(echo $file2 | cut -d. -f3-)
$NLN $file $DATA/INPUT/$file2
done
hour_rst=`$NHOUR $CDATE_RST $CDATE`
IAU_FHROT=$((IAU_OFFSET+hour_rst))
if [ $DOIAU = "YES" ]; then
IAUFHRS=-1
IAU_DELTHRS=0
IAU_INC_FILES="''"
fi
rst_list_rerun=""
xfh=$restart_interval_gfs
while [ $xfh -le $FHMAX_GFS ]; do
rst_list_rerun="$rst_list_rerun $xfh"
xfh=$((xfh+restart_interval_gfs))
done
restart_interval="$rst_list_rerun"
fi
#.............................
else ## cold start
for file in $(ls $memdir/INPUT/*.nc); do
file2=$(echo $(basename $file))
fsuf=$(echo $file2 | cut -c1-3)
if [ $fsuf = "gfs" -o $fsuf = "sfc" ]; then
$NLN $file $DATA/INPUT/$file2
fi
done
#-------------------------------------------------------
fi
#-------------------------------------------------------
nfiles=$(ls -1 $DATA/INPUT/* | wc -l)
if [ $nfiles -le 0 ]; then
echo "Initial conditions must exist in $DATA/INPUT, ABORT!"
msg="Initial conditions must exist in $DATA/INPUT, ABORT!"
postmsg "$jlogfile" "$msg"
exit 1
fi
# If doing IAU, change forecast hours
if [[ "$DOIAU" = "YES" ]]; then
FHMAX=$((FHMAX+6))
if [ $FHMAX_HF -gt 0 ]; then
FHMAX_HF=$((FHMAX_HF+6))
fi
fi
#--------------------------------------------------------------------------
# Grid and orography data
for n in $(seq 1 $ntiles); do
$NLN $FIXfv3/$CASE/${CASE}_grid.tile${n}.nc $DATA/INPUT/${CASE}_grid.tile${n}.nc
$NLN $FIXfv3/$CASE/${CASE}_oro_data.tile${n}.nc $DATA/INPUT/oro_data.tile${n}.nc
done
$NLN $FIXfv3/$CASE/${CASE}_mosaic.nc $DATA/INPUT/grid_spec.nc
# GFS standard input data
IAER=${IAER:-111}
ICO2=${ICO2:-2}
if [ ${new_o3forc:-YES} = YES ]; then
O3FORC=ozprdlos_2015_new_sbuvO3_tclm15_nuchem.f77
else
O3FORC=global_o3prdlos.f77
fi
H2OFORC=${H2OFORC:-"global_h2o_pltc.f77"}
$NLN $FIX_AM/${O3FORC} $DATA/global_o3prdlos.f77
$NLN $FIX_AM/${H2OFORC} $DATA/global_h2oprdlos.f77
$NLN $FIX_AM/global_solarconstant_noaa_an.txt $DATA/solarconstant_noaa_an.txt
$NLN $FIX_AM/global_sfc_emissivity_idx.txt $DATA/sfc_emissivity_idx.txt
$NLN $FIX_AM/global_co2historicaldata_glob.txt $DATA/co2historicaldata_glob.txt
$NLN $FIX_AM/co2monthlycyc.txt $DATA/co2monthlycyc.txt
if [ $ICO2 -gt 0 ]; then
for file in $(ls $FIX_AM/fix_co2_proj/global_co2historicaldata*) ; do
$NLN $file $DATA/$(echo $(basename $file) | sed -e "s/global_//g")
done
fi
$NLN $FIX_AM/global_climaeropac_global.txt $DATA/aerosol.dat
if [ $IAER -gt 0 ] ; then
for file in $(ls $FIX_AM/global_volcanic_aerosols*) ; do
$NLN $file $DATA/$(echo $(basename $file) | sed -e "s/global_//g")
done
fi
#-------------wavewave----------------------
if [ $cplwav = ".true." ]; then
for file in $(ls $COMINwave/rundata/rmp_src_to_dst_conserv_*) ; do
$NLN $file $DATA/
done
$NLN $COMINwave/rundata/ww3_multi.${CDUMPwave}${WAV_MEMBER}.${cycle}.inp $DATA/ww3_multi.inp
array=($WAVECUR_FID $WAVEICE_FID $WAVEWND_FID $waveuoutpGRD $waveGRD $waveesmfGRD $wavesbsGRD $wavepostGRD $waveinterpGRD)
grdALL=`printf "%s\n" "${array[@]}" | sort -u | tr '\n' ' '`
for wavGRD in ${grdALL}; do
$NLN $COMINwave/rundata/${CDUMPwave}.mod_def.$wavGRD $DATA/mod_def.$wavGRD
done
export WAVHCYC=${WAVHCYC:-6}
export WRDATE=`$NDATE -${WAVHCYC} $CDATE`
export WRPDY=`echo $WRDATE | cut -c1-8`
export WRcyc=`echo $WRDATE | cut -c9-10`
export WRDIR=${ROTDIR}/${CDUMPRSTwave}.${WRPDY}/${WRcyc}/wave/restart
export datwave=$COMOUTwave/rundata
export wavprfx=${CDUMPwave}${WAV_MEMBER}
for wavGRD in $waveGRD ; do
if [ $RERUN = "NO" ]; then
if [ ! -f ${WRDIR}/${sPDY}.${scyc}0000.restart.${wavGRD} ]; then
echo "WARNING: NON-FATAL ERROR wave IC is missing, will start from rest"
fi
$NLN ${WRDIR}/${sPDY}.${scyc}0000.restart.${wavGRD} $DATA/restart.${wavGRD}
else
if [ ! -f ${RSTDIR_WAVE}/${PDYT}.${cyct}0000.restart.${wavGRD} ]; then
echo "WARNING: NON-FATAL ERROR wave IC is missing, will start from rest"
fi
$NLN ${RSTDIR_WAVE}/${PDYT}.${cyct}0000.restart.${wavGRD} $DATA/restart.${wavGRD}
fi
eval $NLN $datwave/${wavprfx}.log.${wavGRD}.${PDY}${cyc} log.${wavGRD}
done
if [ "$WW3ICEINP" = "YES" ]; then
wavicefile=$COMINwave/rundata/${CDUMPwave}.${WAVEICE_FID}.${cycle}.ice
if [ ! -f $wavicefile ]; then
echo "ERROR: WW3ICEINP = ${WW3ICEINP}, but missing ice file"
echo "Abort!"
exit 1
fi
$NLN ${wavicefile} $DATA/ice.${WAVEICE_FID}
fi
if [ "$WW3CURINP" = "YES" ]; then
wavcurfile=$COMINwave/rundata/${CDUMPwave}.${WAVECUR_FID}.${cycle}.cur
if [ ! -f $wavcurfile ]; then
echo "ERROR: WW3CURINP = ${WW3CURINP}, but missing current file"
echo "Abort!"
exit 1
fi
$NLN $wavcurfile $DATA/current.${WAVECUR_FID}
fi
# Link output files
cd $DATA
eval $NLN $datwave/${wavprfx}.log.mww3.${PDY}${cyc} log.mww3
# Loop for gridded output (uses FHINC)
fhr=$FHMIN_WAV
while [ $fhr -le $FHMAX_WAV ]; do
YMDH=`$NDATE $fhr $CDATE`
YMD=$(echo $YMDH | cut -c1-8)
HMS="$(echo $YMDH | cut -c9-10)0000"
for wavGRD in ${waveGRD} ; do
eval $NLN $datwave/${wavprfx}.out_grd.${wavGRD}.${YMD}.${HMS} ${YMD}.${HMS}.out_grd.${wavGRD}
done
FHINC=$FHOUT_WAV
if [ $FHMAX_HF_WAV -gt 0 -a $FHOUT_HF_WAV -gt 0 -a $fhr -lt $FHMAX_HF_WAV ]; then
FHINC=$FHOUT_HF_WAV
fi
fhr=$((fhr+FHINC))
done
# Loop for point output (uses DTPNT)
fhr=$FHMIN_WAV
while [ $fhr -le $FHMAX_WAV ]; do
YMDH=`$NDATE $fhr $CDATE`
YMD=$(echo $YMDH | cut -c1-8)
HMS="$(echo $YMDH | cut -c9-10)0000"
eval $NLN $datwave/${wavprfx}.out_pnt.${waveuoutpGRD}.${YMD}.${HMS} ${YMD}.${HMS}.out_pnt.${waveuoutpGRD}
FHINC=$FHINCP_WAV
fhr=$((fhr+FHINC))
done
fi #cplwav=true
#-------------wavewave----------------------
# inline post fix files
if [ $WRITE_DOPOST = ".true." ]; then
$NLN $PARM_POST/post_tag_gfs${LEVS} $DATA/itag
$NLN $PARM_POST/postxconfig-NT-GFS-TWO.txt $DATA/postxconfig-NT.txt
$NLN $PARM_POST/postxconfig-NT-GFS-F00-TWO.txt $DATA/postxconfig-NT_FH00.txt
$NLN $PARM_POST/params_grib2_tbl_new $DATA/params_grib2_tbl_new
fi
#------------------------------------------------------------------
# changeable parameters
# dycore definitions
res=$(echo $CASE |cut -c2-5)
resp=$((res+1))
npx=$resp
npy=$resp
npz=$((LEVS-1))
io_layout=${io_layout:-"1,1"}
#ncols=$(( (${npx}-1)*(${npy}-1)*3/2 ))
# spectral truncation and regular grid resolution based on FV3 resolution
JCAP_CASE=$((2*res-2))
LONB_CASE=$((4*res))
LATB_CASE=$((2*res))
JCAP=${JCAP:-$JCAP_CASE}
LONB=${LONB:-$LONB_CASE}
LATB=${LATB:-$LATB_CASE}
LONB_IMO=${LONB_IMO:-$LONB_CASE}
LATB_JMO=${LATB_JMO:-$LATB_CASE}
# Fix files
FNGLAC=${FNGLAC:-"$FIX_AM/global_glacier.2x2.grb"}
FNMXIC=${FNMXIC:-"$FIX_AM/global_maxice.2x2.grb"}
FNTSFC=${FNTSFC:-"$FIX_AM/RTGSST.1982.2012.monthly.clim.grb"}
FNSNOC=${FNSNOC:-"$FIX_AM/global_snoclim.1.875.grb"}
FNZORC=${FNZORC:-"igbp"}
FNALBC2=${FNALBC2:-"$FIX_AM/global_albedo4.1x1.grb"}
FNAISC=${FNAISC:-"$FIX_AM/CFSR.SEAICE.1982.2012.monthly.clim.grb"}
FNTG3C=${FNTG3C:-"$FIX_AM/global_tg3clim.2.6x1.5.grb"}
FNVEGC=${FNVEGC:-"$FIX_AM/global_vegfrac.0.144.decpercent.grb"}
FNMSKH=${FNMSKH:-"$FIX_AM/global_slmask.t1534.3072.1536.grb"}
FNVMNC=${FNVMNC:-"$FIX_AM/global_shdmin.0.144x0.144.grb"}
FNVMXC=${FNVMXC:-"$FIX_AM/global_shdmax.0.144x0.144.grb"}
FNSLPC=${FNSLPC:-"$FIX_AM/global_slope.1x1.grb"}
FNALBC=${FNALBC:-"$FIX_AM/global_snowfree_albedo.bosu.t${JCAP}.${LONB}.${LATB}.rg.grb"}
FNVETC=${FNVETC:-"$FIX_AM/global_vegtype.igbp.t${JCAP}.${LONB}.${LATB}.rg.grb"}
FNSOTC=${FNSOTC:-"$FIX_AM/global_soiltype.statsgo.t${JCAP}.${LONB}.${LATB}.rg.grb"}
FNABSC=${FNABSC:-"$FIX_AM/global_mxsnoalb.uariz.t${JCAP}.${LONB}.${LATB}.rg.grb"}
FNSMCC=${FNSMCC:-"$FIX_AM/global_soilmgldas.statsgo.t${JCAP}.${LONB}.${LATB}.grb"}
# If the appropriate resolution fix file is not present, use the highest resolution available (T1534)
[[ ! -f $FNALBC ]] && FNALBC="$FIX_AM/global_snowfree_albedo.bosu.t1534.3072.1536.rg.grb"
[[ ! -f $FNVETC ]] && FNVETC="$FIX_AM/global_vegtype.igbp.t1534.3072.1536.rg.grb"
[[ ! -f $FNSOTC ]] && FNSOTC="$FIX_AM/global_soiltype.statsgo.t1534.3072.1536.rg.grb"
[[ ! -f $FNABSC ]] && FNABSC="$FIX_AM/global_mxsnoalb.uariz.t1534.3072.1536.rg.grb"
[[ ! -f $FNSMCC ]] && FNSMCC="$FIX_AM/global_soilmgldas.statsgo.t1534.3072.1536.grb"
# NSST Options
# nstf_name contains the NSST related parameters
# nstf_name(1) : NST_MODEL (NSST Model) : 0 = OFF, 1 = ON but uncoupled, 2 = ON and coupled
# nstf_name(2) : NST_SPINUP : 0 = OFF, 1 = ON,
# nstf_name(3) : NST_RESV (Reserved, NSST Analysis) : 0 = OFF, 1 = ON
# nstf_name(4) : ZSEA1 (in mm) : 0
# nstf_name(5) : ZSEA2 (in mm) : 0
# nst_anl : .true. or .false., NSST analysis over lake
NST_MODEL=${NST_MODEL:-0}
NST_SPINUP=${NST_SPINUP:-0}
NST_RESV=${NST_RESV-0}
ZSEA1=${ZSEA1:-0}
ZSEA2=${ZSEA2:-0}
nstf_name=${nstf_name:-"$NST_MODEL,$NST_SPINUP,$NST_RESV,$ZSEA1,$ZSEA2"}
nst_anl=${nst_anl:-".false."}
# blocking factor used for threading and general physics performance
#nyblocks=`expr \( $npy - 1 \) \/ $layout_y `
#nxblocks=`expr \( $npx - 1 \) \/ $layout_x \/ 32`
#if [ $nxblocks -le 0 ]; then nxblocks=1 ; fi
blocksize=${blocksize:-32}
# the pre-conditioning of the solution
# =0 implies no pre-conditioning
# >0 means new adiabatic pre-conditioning
# <0 means older adiabatic pre-conditioning
na_init=${na_init:-1}
[[ $warm_start = ".true." ]] && na_init=0
# variables for controlling initialization of NCEP/NGGPS ICs
filtered_terrain=${filtered_terrain:-".true."}
gfs_dwinds=${gfs_dwinds:-".true."}
# various debug options
no_dycore=${no_dycore:-".false."}
dycore_only=${adiabatic:-".false."}
chksum_debug=${chksum_debug:-".false."}
print_freq=${print_freq:-6}
if [ ${TYPE} = "nh" ]; then # non-hydrostatic options
hydrostatic=".false."
phys_hydrostatic=".false." # enable heating in hydrostatic balance in non-hydrostatic simulation
use_hydro_pressure=".false." # use hydrostatic pressure for physics
if [ $warm_start = ".true." ]; then
make_nh=".false." # restarts contain non-hydrostatic state
else
make_nh=".true." # re-initialize non-hydrostatic state
fi
else # hydrostatic options
hydrostatic=".true."
phys_hydrostatic=".false." # ignored when hydrostatic = T
use_hydro_pressure=".false." # ignored when hydrostatic = T
make_nh=".false." # running in hydrostatic mode
fi
# Conserve total energy as heat globally
consv_te=${consv_te:-1.} # range 0.-1., 1. will restore energy to orig. val. before physics
# time step parameters in FV3
k_split=${k_split:-2}
n_split=${n_split:-6}
if [ $(echo $MONO | cut -c-4) = "mono" ]; then # monotonic options
d_con=${d_con_mono:-"0."}
do_vort_damp=".false."
if [ ${TYPE} = "nh" ]; then # non-hydrostatic
hord_mt=${hord_mt_nh_mono:-"10"}
hord_xx=${hord_xx_nh_mono:-"10"}
else # hydrostatic
hord_mt=${hord_mt_hydro_mono:-"10"}
hord_xx=${hord_xx_hydro_mono:-"10"}
fi
else # non-monotonic options
d_con=${d_con_nonmono:-"1."}
do_vort_damp=".true."
if [ ${TYPE} = "nh" ]; then # non-hydrostatic
hord_mt=${hord_mt_nh_nonmono:-"5"}
hord_xx=${hord_xx_nh_nonmono:-"5"}
else # hydrostatic
hord_mt=${hord_mt_hydro_nonmono:-"10"}
hord_xx=${hord_xx_hydro_nonmono:-"10"}
fi
fi
if [ $(echo $MONO | cut -c-4) != "mono" -a $TYPE = "nh" ]; then
vtdm4=${vtdm4_nh_nonmono:-"0.06"}
else
vtdm4=${vtdm4:-"0.05"}
fi
if [ $warm_start = ".true." ]; then # warm start from restart file
nggps_ic=".false."
ncep_ic=".false."
external_ic=".false."
mountain=".true."
if [ $read_increment = ".true." ]; then # add increment on the fly to the restarts
res_latlon_dynamics="fv_increment.nc"
else
res_latlon_dynamics='""'
fi
else # CHGRES'd GFS analyses
nggps_ic=${nggps_ic:-".true."}
ncep_ic=${ncep_ic:-".false."}
external_ic=".true."
mountain=".false."
read_increment=".false."
res_latlon_dynamics='""'
fi
# Stochastic Physics Options
if [ ${SET_STP_SEED:-"YES"} = "YES" ]; then
ISEED_SKEB=$((CDATE*1000 + MEMBER*10 + 1))
ISEED_SHUM=$((CDATE*1000 + MEMBER*10 + 2))
ISEED_SPPT=$((CDATE*1000 + MEMBER*10 + 3))
else
ISEED=${ISEED:-0}
fi
DO_SKEB=${DO_SKEB:-"NO"}
DO_SPPT=${DO_SPPT:-"NO"}
DO_SHUM=${DO_SHUM:-"NO"}
if [ $DO_SKEB = "YES" ]; then
do_skeb=".true."
fi
if [ $DO_SHUM = "YES" ]; then
do_shum=".true."
fi
if [ $DO_SPPT = "YES" ]; then
do_sppt=".true."
fi
# copy over the tables
DIAG_TABLE=${DIAG_TABLE:-$PARM_FV3DIAG/diag_table}
DATA_TABLE=${DATA_TABLE:-$PARM_FV3DIAG/data_table}
FIELD_TABLE=${FIELD_TABLE:-$PARM_FV3DIAG/field_table}
# build the diag_table with the experiment name and date stamp
if [ $DOIAU = "YES" ]; then
cat > diag_table << EOF
FV3 Forecast
${gPDY:0:4} ${gPDY:4:2} ${gPDY:6:2} ${gcyc} 0 0
EOF
cat $DIAG_TABLE >> diag_table
else
cat > diag_table << EOF
FV3 Forecast
${sPDY:0:4} ${sPDY:4:2} ${sPDY:6:2} ${scyc} 0 0
EOF
cat $DIAG_TABLE >> diag_table
fi
$NCP $DATA_TABLE data_table
$NCP $FIELD_TABLE field_table
# copy CCN_ACTIVATE.BIN for Thompson microphysics
if [ $RUN_CCPP = "YES" ]; then
if [ "$CCPP_SUITE" = 'FV3_GSD_v0' -o "$CCPP_SUITE" = 'FV3_GSD_noah' ]; then
$NLN $FIX_AM/CCN_ACTIVATE.BIN CCN_ACTIVATE.BIN
$NLN $FIX_AM/freezeH2O.dat freezeH2O.dat
$NLN $FIX_AM/qr_acr_qg.dat qr_acr_qg.dat
$NLN $FIX_AM/qr_acr_qs.dat qr_acr_qs.dat
fi
fi
#------------------------------------------------------------------
rm -f nems.configure
if [ $cplwav = ".true." ]; then
#### ww3 version of nems.configure
# Switch on cpl flag
cpl=.true.
NTASKS_FV3m1=$((NTASKS_FV3-1))
atm_petlist_bounds=" 0 $((NTASKS_FV3-1))"
wav_petlist_bounds=" $((NTASKS_FV3)) $((NTASKS_FV3m1+npe_wav))"
### atm_petlist_bounds=" 0 1511"
### atm_petlist_bounds=$atm_petlist_bounds
### wav_petlist_bounds="1512 1691"
### wav_petlist_bounds=$wav_petlist_bounds
coupling_interval_sec=${coupling_interval_sec:-1800}
rm -f nems.configure
cat > nems.configure <<EOF
EARTH_component_list: ATM WAV
EARTH_attributes::
Verbosity = high
HierarchyProtocol = off
::
ATM_model: fv3
ATM_petlist_bounds: ${atm_petlist_bounds}
ATM_attributes::
Verbosity = 0
DumpFields = false
::
WAV_model: ww3
WAV_petlist_bounds: ${wav_petlist_bounds}
WAV_attributes::
Verbosity = high
::
runSeq::
@${coupling_interval_sec}
ATM
ATM -> WAV :SrcTermProcessing=0:TermOrder=SrcSeq
WAV
@
::
EOF
else
#### fv3 standalone version of nems.configure
cat > nems.configure <<EOF
EARTH_component_list: ATM
ATM_model: fv3
runSeq::
ATM
::
EOF
fi
# Set NTASKS_CFG to reflect cplwav
NTASKS_CFG=$NTASKS_FV3
if [ $cplwav = ".true." ]; then
NTASKS_CFG=$((NTASKS_FV3 + npe_wav))
fi
rm -f model_configure
cat > model_configure <<EOF
total_member: $ENS_NUM
print_esmf: ${print_esmf:-.false.}
PE_MEMBER01: $NTASKS_CFG
start_year: ${tPDY:0:4}
start_month: ${tPDY:4:2}
start_day: ${tPDY:6:2}
start_hour: ${tcyc}
start_minute: 0
start_second: 0
fhrot: ${IAU_FHROT:-0}
nhours_fcst: $FHMAX
RUN_CONTINUE: ${RUN_CONTINUE:-".false."}
ENS_SPS: ${ENS_SPS:-".false."}
dt_atmos: $DELTIM
output_1st_tstep_rst: .false.
calendar: ${calendar:-'julian'}
cpl: ${cpl:-".false."}
memuse_verbose: ${memuse_verbose:-".false."}
atmos_nthreads: $NTHREADS_FV3
use_hyper_thread: ${hyperthread:-".false."}
ncores_per_node: $cores_per_node
restart_interval: $restart_interval
quilting: $QUILTING
write_groups: ${WRITE_GROUP:-1}
write_tasks_per_group: ${WRTTASK_PER_GROUP:-24}
output_history: ${OUTPUT_HISTORY:-".true."}
write_dopost: ${WRITE_DOPOST:-".false."}
num_files: ${NUM_FILES:-2}
filename_base: 'atm' 'sfc'
output_grid: $OUTPUT_GRID
output_file: $OUTPUT_FILETYPES
ichunk2d: ${ichunk2d:-0}
jchunk2d: ${jchunk2d:-0}
ichunk3d: ${ichunk3d:-0}
jchunk3d: ${jchunk3d:-0}
kchunk3d: ${kchunk3d:-0}
ideflate: ${ideflate:-1}
nbits: ${nbits:-14}
write_nemsioflip: $WRITE_NEMSIOFLIP
write_fsyncflag: $WRITE_FSYNCFLAG
imo: $LONB_IMO
jmo: $LATB_JMO
nfhout: $FHOUT
nfhmax_hf: $FHMAX_HF
nfhout_hf: $FHOUT_HF
nsout: $NSOUT
iau_offset: ${IAU_OFFSET}
EOF
#&coupler_nml
# months = ${months:-0}
# days = ${days:-$((FHMAX/24))}
# hours = ${hours:-$((FHMAX-24*(FHMAX/24)))}
# dt_atmos = $DELTIM
# dt_ocean = $DELTIM
# current_date = $curr_date
# calendar = 'julian'
# memuse_verbose = .false.
# atmos_nthreads = $NTHREADS_FV3
# use_hyper_thread = ${hyperthread:-".false."}
# ncores_per_node = $cores_per_node
# restart_secs = $restart_secs
# $coupler_nml
#/
atmos_model_nml=""
if [ $RUN_CCPP = "YES" ]; then
atmos_model_nml="ccpp_suite = $CCPP_SUITE"
fi
cat > input.nml <<EOF
&amip_interp_nml
interp_oi_sst = .true.
use_ncep_sst = .true.
use_ncep_ice = .false.
no_anom_sst = .false.
data_set = 'reynolds_oi'
date_out_of_range = 'climo'
$amip_interp_nml
/
&atmos_model_nml
blocksize = $blocksize
chksum_debug = $chksum_debug
dycore_only = $dycore_only
fdiag = $FDIAG
fhmax = $FHMAX
fhout = $FHOUT
fhmaxhf = $FHMAX_HF
fhouthf = $FHOUT_HF
$atmos_model_nml
/
&diag_manager_nml
prepend_date = .false.
$diag_manager_nml
/
&fms_io_nml
checksum_required = .false.
max_files_r = 100
max_files_w = 100
$fms_io_nml
/
&mpp_io_nml
shuffle=${shuffle:-1}
deflate_level=${deflate_level:-1}
/
&fms_nml
clock_grain = 'ROUTINE'
domains_stack_size = ${domains_stack_size:-3000000}
print_memory_usage = ${print_memory_usage:-".false."}
$fms_nml
/
&fv_core_nml
layout = $layout_x,$layout_y
io_layout = $io_layout
npx = $npx
npy = $npy
ntiles = $ntiles
npz = $npz
grid_type = -1
make_nh = $make_nh
fv_debug = ${fv_debug:-".false."}
range_warn = ${range_warn:-".false."}
reset_eta = .false.
n_sponge = ${n_sponge:-"10"}
nudge_qv = ${nudge_qv:-".true."}
nudge_dz = ${nudge_dz:-".false."}
tau = ${tau:-10.}
rf_cutoff = ${rf_cutoff:-"7.5e2"}
d2_bg_k1 = ${d2_bg_k1:-"0.15"}
d2_bg_k2 = ${d2_bg_k2:-"0.02"}
kord_tm = ${kord_tm:-"-9"}
kord_mt = ${kord_mt:-"9"}
kord_wz = ${kord_wz:-"9"}
kord_tr = ${kord_tr:-"9"}
hydrostatic = $hydrostatic
phys_hydrostatic = $phys_hydrostatic
use_hydro_pressure = $use_hydro_pressure
beta = 0.
a_imp = 1.
p_fac = 0.1
k_split = $k_split
n_split = $n_split
nwat = ${nwat:-2}
na_init = $na_init
d_ext = 0.
dnats = ${dnats:-0}
fv_sg_adj = ${fv_sg_adj:-"450"}
d2_bg = 0.
nord = ${nord:-3}
dddmp = ${dddmp:-0.2}
d4_bg = ${d4_bg:-0.15}
vtdm4 = $vtdm4
delt_max = ${delt_max:-"0.002"}
ke_bg = 0.
do_vort_damp = $do_vort_damp
external_ic = $external_ic
external_eta = ${external_eta:-.true.}
gfs_phil = ${gfs_phil:-".false."}
nggps_ic = $nggps_ic
mountain = $mountain
ncep_ic = $ncep_ic
d_con = $d_con
hord_mt = $hord_mt
hord_vt = $hord_xx
hord_tm = $hord_xx
hord_dp = -$hord_xx
hord_tr = ${hord_tr:-"8"}
adjust_dry_mass = ${adjust_dry_mass:-".true."}
dry_mass=${dry_mass:-98320.0}
consv_te = $consv_te
do_sat_adj = ${do_sat_adj:-".false."}
consv_am = .false.
fill = .true.
dwind_2d = .false.
print_freq = $print_freq
warm_start = $warm_start
no_dycore = $no_dycore
z_tracer = .true.
agrid_vel_rst = ${agrid_vel_rst:-".true."}
read_increment = $read_increment