NOAA-EMC · jkuang-exploro · Mar 4, 2020 · Mar 6, 2020 · Mar 6, 2020 · Mar 9, 2020
diff --git a/scripts/exglobal_fcst_nemsfv3gfs.sh b/scripts/exglobal_fcst_nemsfv3gfs.sh
@@ -1,4 +1,4 @@
-#!/bin/ksh
+#!/bin/bash
 ################################################################################
 ## UNIX Script Documentation Block
 ## Script name:         exglobal_fcst_nemsfv3gfs.sh
@@ -72,7 +72,6 @@
 ##	2. nems.configure
 ##	3. model_configure
 ##	4. input.nml
-
 #######################
 # Main body starts here
 #######################
@@ -83,29 +82,8 @@ if [ $VERBOSE = "YES" ] ; then
   set -x
 fi
 
-## Run in sandbox if no $machine defined
-## Locate mod_forecast script folder
-if [ -z $machine ]; then
-	machine='sandbox'
-	echo "MAIN: !!!Running in sandbox mode!!!"
-	unameOut="$(uname -s)"
-	case "${unameOut}" in
-    		Linux*)
-			SCRIPTDIR=$(dirname $(readlink -f "$0") )/../ush
-			echo "MAIN: Linux environment. Current Script locates in $SCRIPTDIR."
-			;;
-    		Darwin*)
-                        SCRIPTDIR=$(pwd)/../ush
-                        echo "MAIN: MacOS environment. Current Script locates in $SCRIPTDIR."
-			;;
-    		CYGWIN*)    echo CYGWIN ;;
-    		MINGW*)     echo MinGw ;;
-    		*)          echo "UNKNOWN:${unameOut}"
-    esac
-else
-	SCRIPTDIR=$(dirname $(readlink -f "$0") )/../ush
-	echo "MAIN: environment loaded for $machine platform,Current Script locates in $SCRIPTDIR."
-fi
+SCRIPTDIR=$(dirname $(readlink -f "$0") )/../ush
+echo "MAIN: environment loaded for $machine platform,Current Script locates in $SCRIPTDIR."
 
 # include all subroutines. Executions later.
 source $SCRIPTDIR/cplvalidate.sh	# validation of cpl*
@@ -114,6 +92,7 @@ source $SCRIPTDIR/forecast_det.sh  # include functions for run type determinatio
 source $SCRIPTDIR/forecast_postdet.sh	# include functions for variables after run type determination
 source $SCRIPTDIR/nems_configure.sh	# include functions for nems_configure processing
 source $SCRIPTDIR/parsing_model_configure_FV3.sh
+source $SCRIPTDIR/parsing_model_configure_DATM.sh
 
 # Compset string. For nems.configure.* template selection. Default ATM only
 confignamevarfornems=${confignamevarfornems:-'atm'}
@@ -125,15 +104,12 @@ cplwav=${cplwav:-.false.} # ? how to control 1-way/2-way?
 cplchem=${cplchem:-.false.} # Chemistry model
 cplice=${cplice:-.false.} # ICE model
 
-OCNTIM=${OCNTIM:-1800}
+OCNTIM=${OCNTIM:-3600}
 DELTIM=${DELTIM:-450}
 ICETIM=${DELTIM}
 
-CPL_SLOW=${OCNTIM}
-CPL_FAST=${ICETIM}
-# Coupling control switches, for coupling purpose, off by default
-
-[[ $machine = 'sandbox' ]] && RUN=gfs
+CPL_SLOW=${CPL_SLOW:-$OCNTIM}
+CPL_FAST=${CPL_FAST:-$ICETIM}
 
 echo "MAIN: $confignamevarfornems selected"
 echo "MAIN: Forecast script started for $confignamevarfornems on $machine"
@@ -149,7 +125,7 @@ common_predet
 
 echo $RUN
 case $RUN in
-	'data') Data_ATM_setup;;
+	'data') DATM_predet;;
 	'gfs') FV3_GFS_predet;;
 	'gdas') FV3_GFS_predet;;
 	'gefs') FV3_GEFS_predet;;
@@ -174,6 +150,7 @@ echo "MAIN: RUN Type Determined"
 echo "MAIN: Post-determination set up of run type"
 echo $RUN
 case $RUN in
+        'data') DATM_postdet;;
 	'gfs') FV3_GFS_postdet;;
 	'gdas') FV3_GFS_postdet;;
 	'gefs') FV3_GEFS_postdet;;
@@ -186,6 +163,7 @@ echo "MAIN: Post-determination set up of run type finished"
 
 echo "MAIN: Writing name lists and model configuration"
 case $RUN in
+        'data') DATM_nml;;
         'gfs') FV3_GFS_nml;;
         'gdas') FV3_GFS_nml;;
         'gefs') FV3_GEFS_nml;;
@@ -194,7 +172,13 @@ esac				#no namelist for data atmosphere
 [[ $cplwav = .true. ]] && WW3_nml
 [[ $cplice = .true. ]] && CICE_nml
 [[ $cplchem = .true. ]] && GSD_nml
-Common_model_configure
+
+case $RUN in
+        'data') DATM_model_configure;;
+        'gfs') FV3_model_configure;;
+        'gdas') FV3_model_configure;;
+        'gefs') FV3_model_configure;;
+esac
 echo "MAIN: Name lists and model configuration written"
 
 echo "MAIN: Writing NEMS Configure file"
@@ -204,39 +188,26 @@ echo "MAIN: NEMS configured"
 #------------------------------------------------------------------
 # run the executable
 
-if [ $machine != 'sandbox' ]; then
-	$NCP $FCSTEXECDIR/$FCSTEXEC $DATA/.
-	export OMP_NUM_THREADS=$NTHREADS_FV3
-	$APRUN_FV3 $DATA/$FCSTEXEC 1>&1 2>&2
-	export ERR=$?
-	export err=$ERR
-	$ERRSCRIPT || exit $err
-else
-	echo "MAIN: mpirun launch here"
-fi
+$NCP $FCSTEXECDIR/$FCSTEXEC $DATA/.
+export OMP_NUM_THREADS=$NTHREADS_FV3
+$APRUN_FV3 $DATA/$FCSTEXEC 1>&1 2>&2
+export ERR=$?
+export err=$ERR
+$ERRSCRIPT || exit $err
 
-if [ $machine != 'sandbox' ]; then		
-	case $RUN in
-		'data') data_out_Data_ATM;;
-		'gfs') data_out_GFS;;
-		'gdas') data_out_GFS;;
-		'gefs') data_out_GEFS;;
-	esac
-	[[ $cplflx = .true. ]] && MOM6_out
-	[[ $cplwav = .true. ]] && WW3_out
-	[[ $cplice = .true. ]] && CICE_out
-	[[ $cplchem = .true. ]] && GSD_out
-else
-	echo "MAIN: Running on sandbox mode, no output linking"
-fi
+case $RUN in
+        'data') data_out_Data_ATM;;
+        'gfs') data_out_GFS;;
+        'gdas') data_out_GFS;;
+        'gefs') data_out_GEFS;;
+esac
+[[ $cplflx = .true. ]] && MOM6_out
+[[ $cplwav = .true. ]] && WW3_out
+[[ $cplice = .true. ]] && CICE_out
+[[ $cplchem = .true. ]] && GSD_out
 echo "MAIN: Output copied to COMROT"
 
 #------------------------------------------------------------------
-# Clean up before leaving
-if [ $mkdata = "YES" ]; then rm -rf $DATA; fi
-
-#------------------------------------------------------------------
-#set +x
 if [ $VERBOSE = "YES" ] ; then
   echo $(date) EXITING $0 with return code $err >&2
 fi
@@ -246,5 +217,6 @@ if [ $err != 0 ]; then
   exit $err
 else
   echo "MAIN: $confignamevarfornems Forecast completed at normal status"
+  if [ $mkdata = "YES" ]; then rm -rf $DATA; fi
   exit 0
 fi
diff --git a/ush/cplvalidate.sh b/ush/cplvalidate.sh
@@ -12,6 +12,7 @@ cplvalidate(){
 echo "SUB cplvalidate: validating cpl** switches for $confignamevarfornems"
 case $confignamevarfornems in
 	'atm') combination=.false..false..false..false..false.;;
+        'datm') combination=.true..true..false..false..false.;;
 	'med_atm_ocn_ice') combination=.true..true..true..false..false.;;
 	'blocked_atm_wav') combination=.true..false..false..true..false.;;
 	'leapfrog_atm_wav')combination=.true..false..false..true..false.;;

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
@@ -16,6 +16,21 @@ FV3_GEFS_postdet(){
 # soft link commands insert here
 }
 
+DATM_postdet(){
+######################################################################
+# 3.1 Link DATM  inputs (ie forcing files)                           #
+######################################################################
+
+#TODO: This should be some loop through CDATE-> CDATE+ FORECAST length 
+#and get input from either CFSR or GEFS or Whatever... 
+#Currently assumes you only need the month of DATM input for IC date
+
+# DATM forcing file name convention is ${DATM_FILENAME_BASE}.$YYYYMMDDHH.nc 
+echo "Link DATM forcing files"
+DATMINPUTDIR="/scratch2/NCEPDEV/marineda/DATM_INPUT/CFSR/${SYEAR}${SMONTH}"
+ln -sf ${DATMINPUTDIR}/${DATM_FILENAME_BASE}*.nc $DATA/DATM_INPUT/
+}
+
 FV3_GFS_postdet(){
 
 	echo "SUB ${FUNCNAME[0]}: $RERUN and $warm_start determined for $RUN"
@@ -180,6 +195,16 @@ EOF
 	    O3FORC=global_o3prdlos.f77
 	fi
 	H2OFORC=${H2OFORC:-"global_h2o_pltc.f77"}
+        ####
+        # copy CCN_ACTIVATE.BIN for Thompson microphysics
+        if [ $imp_physics -eq 8 ]; then
+        $NCP $FV3INP/CCN_ACTIVATE.BIN  CCN_ACTIVATE.BIN
+        ####
+        $NCP /scratch1/NCEPDEV/stmp2/Lin.Gan/RUNDIRS/gsdsuite-NEW/2019100900/gfs/fcst.383441/freezeH2O.dat  freezeH2O.dat
+        $NCP /scratch1/NCEPDEV/stmp2/Lin.Gan/RUNDIRS/gsdsuite-NEW/2019100900/gfs/fcst.383441/qr_acr_qg.dat  qr_acr_qg.dat
+        $NCP /scratch1/NCEPDEV/stmp2/Lin.Gan/RUNDIRS/gsdsuite-NEW/2019100900/gfs/fcst.383441/qr_acr_qs.dat  qr_acr_qs.dat
+        sleep 60
+        fi
 	$NLN $FIX_AM/${O3FORC}                         $DATA/global_o3prdlos.f77
 	$NLN $FIX_AM/${H2OFORC}                        $DATA/global_h2oprdlos.f77
 	$NLN $FIX_AM/global_solarconstant_noaa_an.txt  $DATA/solarconstant_noaa_an.txt
@@ -362,9 +387,9 @@ EOF
 	else
 	  ISEED=${ISEED:-0}
 	fi
-	DO_SKEB=${DO_SKEB:-"NO"}
-	DO_SPPT=${DO_SPPT:-"NO"}
-	DO_SHUM=${DO_SHUM:-"NO"}
+	DO_SKEB=${DO_SKEB:-".false."}
+	DO_SPPT=${DO_SPPT:-".false."}
+	DO_SHUM=${DO_SHUM:-".false."}
 	JCAP_STP=${JCAP_STP:-$JCAP_CASE}
 	LONB_STP=${LONB_STP:-$LONB_CASE}
 	LATB_STP=${LATB_STP:-$LATB_CASE}
@@ -415,6 +440,12 @@ FV3_GFS_nml(){
 	echo SUB ${FUNCNAME[0]}: FV3 name lists and model configure file created
 }
 
+DATM_nml(){
+        source $SCRIPTDIR/parsing_namelists_DATM.sh
+        DATM_namelists
+        echo SUB ${FUNCNAME[0]}: DATM name lists and model configure file created
+}
+
 data_out_GFS()
 {
 # data in take for FV3GFS
@@ -581,37 +612,57 @@ MOM6_out()
 CICE_postdet()
 {
 	echo "SUB ${FUNCNAME[0]}: CICE after run type determination"
+
+        year=$(echo $CDATE|cut -c 1-4)
+        #BL2018
+        stepsperhr=$((3600/$DT_CICE))
+        #BL2018
+        nhours=$(${NHOUR} ${CDATE} ${SYEAR}010100)
+        istep0=$((nhours*stepsperhr))
+        npt=$((FHMAX*$stepsperhr))      # Need this in order for dump_last to work
+
+        histfreq_n=${histfreq_n:-6}
+        restart_interval=${restart_interval:-1296000}    # restart write interval in seconds, default 15 days
+        dumpfreq_n=$restart_interval                     # restart write interval in seconds
+
+        #BL2018
+        #dumpfreq='d'
+        #dumpfreq='s'
+        if [ -d $ROTDIR/../NEXT_IC ]; then
+          #continuing run "hot start" 
+          RUNTYPE='continue'
+          USE_RESTART_TIME='.true.'
+          restart_pond_lvl=${restart_pond_lvl:-".true."}
+        else
+          #using cold start IC
+          RUNTYPE='initial'
+          USE_RESTART_TIME='.false.'
+          restart_pond_lvl=${restart_pond_lvl:-".false."}
+        fi
+
+        dumpfreq_n=${dumpfreq_n:-"${restart_interval}"}
+        dumpfreq=${dumpfreq:-"s"} #  "s" or "d" or "m" for restarts at intervals of "seconds", "days" or "months"
+
+        iceres=${iceres:-"mx025"}
+        ice_grid_file=${ice_grid_file:-"grid_cice_NEMS_${iceres}.nc"}
+        ice_kmt_file=${ice_kmt_file:-"kmtu_cice_NEMS_${iceres}.nc"}
+
+        #TODO iceic name... this might need to be update? 
+        iceic="cice5_model.res_$CDATE.nc"
+
 	# Copy CICE5 IC - pre-generated from CFSv2
-        cp -p $ICSDIR/$CDATE/cice5_model_0.25.res_$CDATE.nc $DATA/cice5_model.res_$CDATE.nc
+        cp -p $ICSDIR/$CDATE/cice5_model_0.25.res_$CDATE.nc $DATA/$iceic
 	#cp -p $ICSDIR/$CDATE/cpc/cice5_model_0.25.res_$CDATE.nc ./cice5_model.res_$CDATE.nc
 
-        # Copy CICE5 fixed files, and namelists
-        cp -p $FIXcice/kmtu_cice_NEMS_mx025.nc $DATA/
-        cp -p $FIXcice/grid_cice_NEMS_mx025.nc $DATA/
+        echo "Link CICE fixed files"
+        ln -sf $FIXcice/${ice_grid_file} $DATA/
+        ln -sf $FIXcice/${ice_kmt_file} $DATA/
 
         # Copy grid_spec and mosaic files
         cp -pf $FIXgrid/$CASE/${CASE}_mosaic* $DATA/INPUT/
         cp -pf $FIXgrid/$CASE/grid_spec.nc $DATA/INPUT/
         cp -pf $FIXgrid/$CASE/ocean_mask.nc $DATA/INPUT/
         cp -pf $FIXgrid/$CASE/land_mask* $DATA/INPUT/
-
-	iceic=cice5_model.res_$CDATE.nc
-	year=$(echo $CDATE|cut -c 1-4)
-	#BL2018
-	stepsperhr=$((3600/$ICETIM))
-	#BL2018
-	nhours=$($NHOUR $CDATE ${year}010100)
-	steps=$((nhours*stepsperhr))
-	npt=$((FHMAX*$stepsperhr))      # Need this in order for dump_last to work
-
-	histfreq_n=${histfreq_n:-6}
-	restart_interval=${restart_interval:-1296000}    # restart write interval in seconds, default 15 days
-	dumpfreq_n=$restart_interval                     # restart write interval in seconds
-
-	#BL2018
-	#dumpfreq='d'
-	#dumpfreq='s'
-
 }
 
 CICE_nml()
@@ -683,3 +734,6 @@ GSD_out()
 	echo "SUB ${FUNCNAME[0]}: Copying output data for GSD"
 	# soft link commands insert here
 }
+
+
+
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
@@ -21,6 +21,20 @@ common_predet(){
 	ICSDIR=${ICSDIR:-$pwd}         # cold start initial conditions
 }
 
+DATM_predet(){
+        SYEAR=$(echo  $CDATE | cut -c1-4)
+        SMONTH=$(echo $CDATE | cut -c5-6)
+        SDAY=$(echo   $CDATE | cut -c7-8)
+        SHOUR=$(echo  $CDATE | cut -c9-10)
+        # directory set up
+        if [ ! -d $DATA ]; then mkdir -p $DATA; fi
+        if [ ! -d $DATA/DATM_INPUT ]; then mkdir -p $DATA/DATM_INPUT; fi
+        FHMAX=${FHMAX:-9}
+# Go to Run Directory (DATA)         
+cd $DATA
+
+}
+
 FV3_GFS_predet(){
 	echo "SUB ${FUNCNAME[0]}: Defining variables for FV3GFS"
 	CDUMP=${CDUMP:-gdas}
@@ -83,7 +97,11 @@ FV3_GFS_predet(){
 	NTHREADS_FV3=${NTHREADS_FV3:-${NTHREADS_FCST:-${nth_fv3:-1}}}
 	cores_per_node=${cores_per_node:-${npe_node_max:-24}}
 	ntiles=${ntiles:-6}
-	NTASKS_TOT=${NTASKS_TOT:-$npe_fcst}
+        if [ $MEMBER -lt 0 ]; then
+                NTASKS_TOT=${NTASKS_TOT:-$npe_fcst}
+        else
+                NTASKS_TOT=${NTASKS_TOT:-$npe_efcs}
+        fi
 
 	TYPE=${TYPE:-"nh"}                  # choices:  nh, hydro
 	MONO=${MONO:-"non-mono"}            # choices:  mono, non-mono