From 1b5827c78e3238e4061b16a0a34eb387243dfe18 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Fri, 10 Jun 2022 18:56:01 -0400
Subject: [PATCH 01/24] Improve to run fcst (atm only)

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   jobs/rocoto/fcst.sh
	modified:   ush/forecast_det.sh
	modified:   ush/forecast_postdet.sh
	modified:   ush/forecast_predet.sh

Refs: #822
---
 jobs/rocoto/fcst.sh     |  4 +++-
 ush/forecast_det.sh     |  1 +
 ush/forecast_postdet.sh | 19 +++++++++++++++++++
 ush/forecast_predet.sh  | 36 +++++++++++++++++++++++++++++++-----
 4 files changed, 54 insertions(+), 6 deletions(-)

diff --git a/jobs/rocoto/fcst.sh b/jobs/rocoto/fcst.sh
index 199c89724a9..e142fcce795 100755
--- a/jobs/rocoto/fcst.sh
+++ b/jobs/rocoto/fcst.sh
@@ -5,7 +5,9 @@
 . $HOMEgfs/ush/load_fv3gfs_modules.sh
 status=$?
 [[ $status -ne 0 ]] && exit $status
-
+if [[ $CDUMP == "gefs" ]]; then
+    export MEMBER=`echo ${RUNMEM:-"c00"}|cut -c2-3`
+fi
 ###############################################################
 # Execute the JJOB
 $HOMEgfs/jobs/JGLOBAL_FORECAST
diff --git a/ush/forecast_det.sh b/ush/forecast_det.sh
index 5529ce8a834..30ec79015dc 100755
--- a/ush/forecast_det.sh
+++ b/ush/forecast_det.sh
@@ -66,6 +66,7 @@ FV3_GFS_det(){
 
 FV3_GEFS_det(){
   echo "SUB ${FUNCNAME[0]}: Defining variables for FV3GEFS"
+  FV3_GFS_det
 }
 
 WW3_det(){
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 5f2f152670f..1a333a13a50 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -14,6 +14,7 @@
 FV3_GEFS_postdet(){
   echo SUB ${FUNCNAME[0]}: Linking input data for FV3 $RUN
   # soft link commands insert here
+  FV3_GFS_postdet
 }
 
 DATM_postdet(){
@@ -558,6 +559,20 @@ FV3_GFS_nml(){
   echo SUB ${FUNCNAME[0]}: FV3 name lists and model configure file created
 }
 
+FV3_GEFS_nml(){
+  # namelist output for a certain component
+  echo SUB ${FUNCNAME[0]}: Creating name lists and model configure file for FV3
+  if [ $machine = 'sandbox' ]; then
+    cd $SCRIPTDIR
+    echo "MAIN: !!!Sandbox mode, writing to current directory!!!"
+  fi
+  # Call child scripts in current script directory
+  source $SCRIPTDIR/parsing_namelists_FV3.sh
+  FV3_namelists
+  echo SUB ${FUNCNAME[0]}: FV3 name lists and model configure file created
+}
+
+
 DATM_nml(){
   source $SCRIPTDIR/parsing_namelists_DATM.sh
   DATM_namelists
@@ -609,6 +624,10 @@ data_out_GFS() {
   echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
 }
 
+data_out_GEFS() {
+  data_out_GFS
+}
+
 WW3_postdet() {
   echo "SUB ${FUNCNAME[0]}: Linking input data for WW3"
   COMPONENTwave=${COMPONENTwave:-${RUN}wave}
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 2f9ed863ca7..5704bda6d8f 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -252,17 +252,35 @@ FV3_GFS_predet(){
     rprefix=$rCDUMP
     memchar=""
   else
-    prefix=enkf$CDUMP
-    rprefix=enkf$rCDUMP
-    memchar=mem$(printf %03i $MEMBER)
+    if [[ $CDUMP == "gefs" ]]; then
+        prefix=$CDUMP
+        rprefix=$rCDUMP
+        if [ $MEMBER -eq 0 ]; then
+            memchar=c$(printf %02i $MEMBER)
+        else
+            memchar=p$(printf %02i $MEMBER)
+        fi
+    else
+        prefix=enkf$CDUMP
+        rprefix=enkf$rCDUMP
+        memchar=mem$(printf %03i $MEMBER)
+    fi
+  fi
+  if [[ $CDUMP == "gefs" ]]; then
+    memdir=$ROTDIR/${prefix}.$PDY/$cyc/$memchar/atmos
+  else
+    memdir=$ROTDIR/${prefix}.$PDY/$cyc/atmos/$memchar
   fi
-  memdir=$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
+  if [[ $CDUMP == "gefs" ]]; then
+    gmemdir=$ROTDIR/${rprefix}.$gPDY/$gcyc/$memchar/atmos
+  else
+    gmemdir=$ROTDIR/${rprefix}.$gPDY/$gcyc/atmos/$memchar
+  fi
   sCDATE=$($NDATE -3 $CDATE)
 
   if [[ "$DOIAU" = "YES" ]]; then
@@ -282,6 +300,14 @@ FV3_GFS_predet(){
   echo "SUB ${FUNCNAME[0]}: pre-determination variables set"
 }
 
+FV3_GEFS_predet(){
+  echo "SUB ${FUNCNAME[0]}: Defining variables for FV3GFS"
+
+  FV3_GFS_predet
+
+  echo "SUB ${FUNCNAME[0]}: pre-determination variables set"
+}
+
 WW3_predet(){
   echo "SUB ${FUNCNAME[0]}: Defining variables for WW3"
   if [ $CDUMP = "gdas" ]; then

From 9865bf9530b9d847601db5020789f8f96ce99422 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Thu, 21 Jul 2022 11:37:42 -0400
Subject: [PATCH 02/24] Improve the script to run fcst for GEFS

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   jobs/JGLOBAL_FORECAST
	modified:   jobs/rocoto/fcst.sh
	modified:   parm/config/config.fcst
	modified:   ush/forecast_postdet.sh
	modified:   ush/forecast_predet.sh

Refs: #822
---
 jobs/JGLOBAL_FORECAST   |  2 +-
 jobs/rocoto/fcst.sh     |  3 ++
 parm/config/config.fcst | 79 +++++++++++++++++++++++++++++++++++++++++
 ush/forecast_postdet.sh |  2 ++
 ush/forecast_predet.sh  | 29 ++++++++++++++-
 5 files changed, 113 insertions(+), 2 deletions(-)

diff --git a/jobs/JGLOBAL_FORECAST b/jobs/JGLOBAL_FORECAST
index d72a07614f9..134c7072472 100755
--- a/jobs/JGLOBAL_FORECAST
+++ b/jobs/JGLOBAL_FORECAST
@@ -122,7 +122,7 @@ rCDUMP=$CDUMP
 [[ $CDUMP = "gfs" ]] && export rCDUMP="gdas"
 
 # Forecast length for GFS forecast
-if [ $CDUMP = "gfs" ]; then
+if [ $CDUMP = "gfs" ] || [ $CDUMP = "gefs" ]; then
     export FHMAX=$FHMAX_GFS
     export FHOUT=$FHOUT_GFS
     export FHMAX_HF=$FHMAX_HF_GFS
diff --git a/jobs/rocoto/fcst.sh b/jobs/rocoto/fcst.sh
index e142fcce795..90402efb9f3 100755
--- a/jobs/rocoto/fcst.sh
+++ b/jobs/rocoto/fcst.sh
@@ -7,6 +7,9 @@ status=$?
 [[ $status -ne 0 ]] && exit $status
 if [[ $CDUMP == "gefs" ]]; then
     export MEMBER=`echo ${RUNMEM:-"c00"}|cut -c2-3`
+    if [[ $RUNMEM != "c00" ]]; then
+        export PREFIX_ATMINC="r"
+    fi
 fi
 ###############################################################
 # Execute the JJOB
diff --git a/parm/config/config.fcst b/parm/config/config.fcst
index e73c35d15da..3041906a8e8 100755
--- a/parm/config/config.fcst
+++ b/parm/config/config.fcst
@@ -358,6 +358,85 @@ elif [[ "$CDUMP" == "gfs" ]] ; then # GFS cycle specific parameters
       export io_layout="1,1"
     fi
 
+elif [[ "$CDUMP" == "gefs" ]] ; then # GEFS cycle specific parameters
+
+    if [[ $RUNMEM == "c00" ]]; then
+        # Write more variables to output
+        if [ $QUILTING = ".true." -a $OUTPUT_GRID = "gaussian_grid" ]; then
+            export DIAG_TABLE="$HOMEgfs/parm/parm_fv3diag/diag_table"
+        else
+            export DIAG_TABLE="$HOMEgfs/parm/parm_fv3diag/diag_table_orig"
+        fi
+
+        # Write gfs restart files to rerun fcst from any break point
+        export restart_interval_gfs=${restart_interval_gfs:-0}
+        if [ $restart_interval_gfs -le 0 ]; then
+            export restart_interval="$FHMAX_GFS"
+        else
+            rst_list=""
+            IAU_OFFSET=${IAU_OFFSET:-0}
+            [[ $DOIAU = "NO" ]] && export IAU_OFFSET=0
+            xfh=$((restart_interval_gfs+(IAU_OFFSET/2)))
+            while [ $xfh -le $FHMAX_GFS ]; do
+                rst_list="$rst_list $xfh"
+                xfh=$((xfh+restart_interval_gfs))
+            done
+            export restart_interval="$rst_list"
+        fi
+
+        if [ $DO_AERO = "YES" ]; then
+            # Make sure a restart file is written at the cadence time
+            if [[ ! "${restart_interval[*]}" =~ "$STEP_GFS"  ]]; then
+                export restart_interval="$STEP_GFS $restart_interval"
+            fi
+        fi
+
+        # Choose coupling with wave
+        if [ $DO_WAVE = "YES" -a "$WAVE_CDUMP" != "gdas" ]; then
+            export cplwav=".true."
+        fi
+
+        # Turn off dry mass adjustment in GFS
+        export adjust_dry_mass=".false."
+
+        # Write each restart file in 16 small files to save time
+        if [ $CASE = C768 ]; then
+            export io_layout="4,4"
+        else
+            export io_layout="1,1"
+        fi
+
+    else
+        # Variables used in DA cycling
+        if [ $QUILTING = ".true." -a $OUTPUT_GRID = "gaussian_grid" ]; then
+            export DIAG_TABLE="$HOMEgfs/parm/parm_fv3diag/diag_table_da"
+        else
+            export DIAG_TABLE="$HOMEgfs/parm/parm_fv3diag/diag_table_da_orig"
+        fi
+
+        # Write restart files, where $number is current model start time.
+        # restart_interval:        $number
+        #    number=0, writes out restart files at the end of forecast.
+        #    number>0, writes out restart files at the frequency of $number and at the end of forecast.
+        # restart_interval:        "$number -1"
+        #    writes out restart files only once at $number forecast hour.
+        # restart_interval:        "$number1 $number2 $number3 ..."
+        #    writes out restart file at the specified forecast hours
+        export restart_interval=${restart_interval:-6}
+
+        # For IAU, write restarts at beginning of window also
+        if [ $DOIAU = "YES" ]; then
+            export restart_interval="3 6"
+        fi
+
+        # Choose coupling with wave
+        if [ $DO_WAVE = "YES" ]; then export cplwav=".true." ; fi
+
+        # Turn on dry mass adjustment in GDAS
+        export adjust_dry_mass=".true."
+
+    fi
+
 fi
 
 if [[ $DO_COUPLED = "YES" ]] ; then # coupled model
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index a67e6f4df65..85b502f453d 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -618,6 +618,8 @@ data_out_GFS() {
       fi
     elif [ $CDUMP = "gfs" ]; then
       $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/
+    elif [ $CDUMP = "gefs" ]; then
+      $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/$RUNMEM/atmos/
     fi
   fi
 
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 3ebd3605790..833b5c89a9f 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -127,7 +127,11 @@ FV3_GFS_predet(){
   if [ $MEMBER -lt 0 ]; then
     NTASKS_TOT=${NTASKS_TOT:-$npe_fcst_gfs}
   else
-    NTASKS_TOT=${NTASKS_TOT:-$npe_efcs}
+    if [[ $CDUMP == gefs ]]; then
+      NTASKS_TOT=${NTASKS_TOT:-$npe_fcst_gfs}
+    else
+      NTASKS_TOT=${NTASKS_TOT:-$npe_efcs}
+    fi
   fi
 
   TYPE=${TYPE:-"nh"}                  # choices:  nh, hydro
@@ -241,6 +245,29 @@ FV3_GFS_predet(){
     for file in $files; do
       $NLN $RSTDIR_ATM/$file $RSTDIR_ATM/${vPDY}.${vcyc}0000.$file
     done
+  elif [ $CDUMP = "gefs" -a $rst_invt1 -gt 0 ]; then
+    if [ $MEMBER -eq 0 ]; then
+      memchar=c$(printf %02i $MEMBER)
+    else
+      memchar=p$(printf %02i $MEMBER)
+    fi
+    RSTDIR_ATM=${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/${memchar}/atmos/RERUN_RESTART
+    if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
+    $NLN $RSTDIR_ATM RESTART
+    # The final restart written at the end doesn't include the valid date
+    # Create links that keep the same name pattern for these files
+    VDATE=$($NDATE +$FHMAX_GFS $CDATE)
+    vPDY=$(echo $VDATE | cut -c1-8)
+    vcyc=$(echo $VDATE | cut -c9-10)
+    files="coupler.res fv_core.res.nc"
+    for tile in {1..6}; do
+      for base in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data; do
+        files="${files} ${base}.tile${tile}.nc"
+      done
+    done
+    for file in $files; do
+      $NLN $RSTDIR_ATM/$file $RSTDIR_ATM/${vPDY}.${vcyc}0000.$file
+    done
   else
     mkdir -p $DATA/RESTART
   fi

From 9f57a1f3d101af742a5dda04fe68e41c733d7905 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Sun, 11 Dec 2022 16:05:18 -0500
Subject: [PATCH 03/24] Modify to run atm fcst for GEFS

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   ush/forecast_postdet.sh
	modified:   ush/forecast_predet.sh

Refs: #822
---
 ush/forecast_postdet.sh | 17 +++++++----
 ush/forecast_predet.sh  | 63 ++++++-----------------------------------
 2 files changed, 21 insertions(+), 59 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index e0eba828e42..28aaf7e4233 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -308,8 +308,13 @@ EOF
   # 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
+    if [[ $RUN == "gefs" ]]; then
+      $NLN $PARM_POST/postxconfig-NT-GEFS.txt         $DATA/postxconfig-NT.txt
+      $NLN $PARM_POST/postxconfig-NT-GEFS-F00.txt     $DATA/postxconfig-NT_FH00.txt
+    else
+      $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
+    fi
     $NLN $PARM_POST/params_grib2_tbl_new            $DATA/params_grib2_tbl_new
   fi
 
@@ -615,9 +620,11 @@ data_out_GFS() {
         done
       fi
     elif [ $CDUMP = "gfs" ]; then
-      $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/
-    elif [ $CDUMP = "gefs" ]; then
-      $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/$RUNMEM/atmos/
+      if [ $RUN = "gefs" ]; then
+        $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/$RUNMEM/atmos/
+      else
+        $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/
+      fi
     fi
   fi
 
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 13524119bf5..3ea97929025 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -125,11 +125,7 @@ FV3_GFS_predet(){
   if [ $MEMBER -lt 0 ]; then
     NTASKS_TOT=${NTASKS_TOT:-${npe_fcst_gfs:-0}}
   else
-    if [[ $CDUMP == gefs ]]; then
-      NTASKS_TOT=${NTASKS_TOT:-${npe_fcst_gfs:-0}}
-    else
-      NTASKS_TOT=${NTASKS_TOT:-${npe_efcs:-0}}
-    fi
+    NTASKS_TOT=${NTASKS_TOT:-${npe_efcs:-0}}
   fi
 
   TYPE=${TYPE:-"nh"}                  # choices:  nh, hydro
@@ -212,31 +208,8 @@ FV3_GFS_predet(){
   print_freq=${print_freq:-6}
 
   #-------------------------------------------------------
-  if [ $CDUMP = "gfs" ] && [ $rst_invt1 -gt 0 ] && [ $MEMBER -lt 0 ]; then
-    RSTDIR_ATM=${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART
-    if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
-    $NLN $RSTDIR_ATM RESTART
-    # The final restart written at the end doesn't include the valid date
-    # Create links that keep the same name pattern for these files
-    VDATE=$($NDATE +$FHMAX_GFS $CDATE)
-    vPDY=$(echo $VDATE | cut -c1-8)
-    vcyc=$(echo $VDATE | cut -c9-10)
-    files="coupler.res fv_core.res.nc"
-    for tile in {1..6}; do
-      for base in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data; do
-        files="${files} ${base}.tile${tile}.nc"
-      done
-    done
-    for file in $files; do
-      $NLN $RSTDIR_ATM/$file $RSTDIR_ATM/${vPDY}.${vcyc}0000.$file
-    done
-  elif [ $CDUMP = "gefs" -a $rst_invt1 -gt 0 ]; then
-    if [ $MEMBER -eq 0 ]; then
-      memchar=c$(printf %02i $MEMBER)
-    else
-      memchar=p$(printf %02i $MEMBER)
-    fi
-    RSTDIR_ATM=${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/${memchar}/atmos/RERUN_RESTART
+  if [ $CDUMP = "gfs" || $RUN = "gefs" ] && [ $rst_invt1 -gt 0 ] && [ $MEMBER -lt 0 ]; then
+    RSTDIR_ATM=${RSTDIR_ATM:-${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART}
     if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
     $NLN $RSTDIR_ATM RESTART
     # The final restart written at the end doesn't include the valid date
@@ -259,40 +232,22 @@ FV3_GFS_predet(){
 
   #-------------------------------------------------------
   # member directory
-  if [ $MEMBER -lt 0 ]; then
+  if [ $MEMBER -lt 0 || $RUN = "gefs" ]; then
     prefix=$CDUMP
     rprefix=$rCDUMP
     memchar=""
   else
-    if [[ $CDUMP == "gefs" ]]; then
-        prefix=$CDUMP
-        rprefix=$rCDUMP
-        if [ $MEMBER -eq 0 ]; then
-            memchar=c$(printf %02i $MEMBER)
-        else
-            memchar=p$(printf %02i $MEMBER)
-        fi
-    else
-        prefix=enkf$CDUMP
-        rprefix=enkf$rCDUMP
-        memchar=mem$(printf %03i $MEMBER)
-    fi
-  fi
-  if [[ $CDUMP == "gefs" ]]; then
-    memdir=$ROTDIR/${prefix}.$PDY/$cyc/$memchar/atmos
-  else
-    memdir=$ROTDIR/${prefix}.$PDY/$cyc/atmos/$memchar
+    prefix=enkf$CDUMP
+    rprefix=enkf$rCDUMP
+    memchar=mem$(printf %03i $MEMBER)
   fi
+  memdir=${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)
-  if [[ $CDUMP == "gefs" ]]; then
-    gmemdir=$ROTDIR/${rprefix}.$gPDY/$gcyc/$memchar/atmos
-  else
-    gmemdir=$ROTDIR/${rprefix}.$gPDY/$gcyc/atmos/$memchar
-  fi
+  gmemdir=${gmemdir:-$ROTDIR/${rprefix}.$gPDY/$gcyc/atmos/$memchar}
 
   if [[ "$DOIAU" = "YES" ]]; then
     sCDATE=$($NDATE -3 $CDATE)

From c905b74a0f6e6e99fac6cda7a64ed85e032d1535 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Sun, 11 Dec 2022 23:27:30 -0500
Subject: [PATCH 04/24] Fix bugs for condition statements

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   ush/forecast_predet.sh

Refs: #822
---
 ush/forecast_predet.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 3ea97929025..b6ba2dc43e8 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -208,7 +208,7 @@ FV3_GFS_predet(){
   print_freq=${print_freq:-6}
 
   #-------------------------------------------------------
-  if [ $CDUMP = "gfs" || $RUN = "gefs" ] && [ $rst_invt1 -gt 0 ] && [ $MEMBER -lt 0 ]; then
+  if [[ $CDUMP = "gfs" || $RUN = "gefs" ]] && [ $rst_invt1 -gt 0 ] && [ $MEMBER -lt 0 ]; then
     RSTDIR_ATM=${RSTDIR_ATM:-${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART}
     if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
     $NLN $RSTDIR_ATM RESTART
@@ -232,7 +232,7 @@ FV3_GFS_predet(){
 
   #-------------------------------------------------------
   # member directory
-  if [ $MEMBER -lt 0 || $RUN = "gefs" ]; then
+  if [[ $MEMBER -lt 0 || $RUN = "gefs" ]]; then
     prefix=$CDUMP
     rprefix=$rCDUMP
     memchar=""

From af7dc51316fb2b0280c93b3541e143d1d8cbd51d Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Fri, 23 Dec 2022 14:33:14 -0500
Subject: [PATCH 05/24] Introduce FHOUT_ENKF_GFS for gfsefcs jobs     and
 increase alltime of efcs jobs

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   parm/config/config.base.emc.dyn
	modified:   parm/config/config.resources
	modified:   scripts/exgdas_enkf_fcst.sh

Refs: #822
---
 parm/config/config.base.emc.dyn | 1 +
 parm/config/config.resources    | 2 +-
 scripts/exgdas_enkf_fcst.sh     | 4 +++-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index 5519b6a3bb4..b0ed66769e3 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -340,6 +340,7 @@ if [ $DOHYBVAR = "YES" ]; then
     export FHMIN_ENKF=3
     export FHMAX_ENKF=9
     export FHMAX_ENKF_GFS=120
+    export FHOUT_ENKF_GFS=3
     if [ $l4densvar = ".true." ]; then
         export FHOUT=1
         export FHOUT_ENKF=1
diff --git a/parm/config/config.resources b/parm/config/config.resources
index cbd45561aa3..3862f0a5f63 100755
--- a/parm/config/config.resources
+++ b/parm/config/config.resources
@@ -737,7 +737,7 @@ elif [ ${step} = "esfc" ]; then
 elif [ ${step} = "efcs" ]; then
 
     if [ ${CASE} = "C768" ]; then
-      export wtime_efcs="01:20:00"
+      export wtime_efcs="06:00:00"
     else
       export wtime_efcs="00:40:00"
     fi
diff --git a/scripts/exgdas_enkf_fcst.sh b/scripts/exgdas_enkf_fcst.sh
index 5b002430127..5a26d12c3da 100755
--- a/scripts/exgdas_enkf_fcst.sh
+++ b/scripts/exgdas_enkf_fcst.sh
@@ -108,7 +108,9 @@ export LEVS=${LEVS_ENKF:-${LEVS:-64}}
 
 # nggps_diag_nml
 export FHOUT=${FHOUT_ENKF:-3}
-
+if [[ $CDUMP == "gfs" ]]; then
+    export FHOUT=${FHOUT_ENKF_GFS:-${FHOUT_ENKF:${FHOUT:-3}}}
+fi
 # model_configure
 export DELTIM=${DELTIM_ENKF:-${DELTIM:-225}}
 export FHMAX=${FHMAX_ENKF:-9}

From 052ad495738b09e0c6b8868d48ed0010af2baccd Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Fri, 30 Dec 2022 11:08:47 -0500
Subject: [PATCH 06/24] Add FHOUT_ENKF_GFS to calculate epos group

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   workflow/rocoto/workflow_tasks.py

Refs: #822
---
 workflow/rocoto/workflow_tasks.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/workflow/rocoto/workflow_tasks.py b/workflow/rocoto/workflow_tasks.py
index c31397dd264..83850e44c18 100644
--- a/workflow/rocoto/workflow_tasks.py
+++ b/workflow/rocoto/workflow_tasks.py
@@ -1259,9 +1259,10 @@ def epos(self):
         def _get_eposgroups(epos):
             fhmin = epos['FHMIN_ENKF']
             fhmax = epos['FHMAX_ENKF']
+            fhout = epos['FHOUT_ENKF']
             if self.cdump == "gfs":
                 fhmax = epos['FHMAX_ENKF_GFS']
-            fhout = epos['FHOUT_ENKF']
+                fhout = epos['FHOUT_ENKF_GFS']
             fhrs = range(fhmin, fhmax + fhout, fhout)
 
             neposgrp = epos['NEPOSGRP']

From f0aaaf0593a7664362bd157c8f9049e9a7404103 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Fri, 30 Dec 2022 11:20:13 -0500
Subject: [PATCH 07/24] Add GEFS functions with new COM to fcst ush scripts  On
 branch feature/gefs_v13_822_add_atm_fcst  Changes to be committed: 
 modified:   ush/forecast_det.sh 	modified:   ush/forecast_postdet.sh 
 modified:   ush/forecast_predet.sh

Refs: #822
---
 ush/forecast_det.sh     |  2 +-
 ush/forecast_postdet.sh | 44 ++++++++++++++++++++++++++---------------
 ush/forecast_predet.sh  |  6 ++++++
 3 files changed, 35 insertions(+), 17 deletions(-)

diff --git a/ush/forecast_det.sh b/ush/forecast_det.sh
index c3a49360768..cb0cd875520 100755
--- a/ush/forecast_det.sh
+++ b/ush/forecast_det.sh
@@ -41,7 +41,7 @@ FV3_GFS_det(){
   # determine if restart IC exists to continue from a previous forecast
   RERUN="NO"
   filecount=$(find "${RSTDIR_ATM:-/dev/null}" -type f | wc -l)
-  if [ ${CDUMP} = "gfs" -a ${rst_invt1} -gt 0 -a ${FHMAX} -gt ${rst_invt1} -a ${filecount} -gt 10 ]; then
+  if [[ ( ${CDUMP} = "gfs" || ( $RUN = "gefs" && $CDATE_RST = "" )) && ${rst_invt1} -gt 0 && ${FHMAX} -gt ${rst_invt1} && ${filecount} -gt 10 ]]; then
     reverse=$(echo "${restart_interval[@]} " | tac -s ' ')
     for xfh in ${reverse} ; do
       yfh=$((xfh-(IAU_OFFSET/2)))
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 28aaf7e4233..1012eeb0c3f 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -525,11 +525,19 @@ EOF
       logi=logf${FH3}
       pgbi=GFSPRS.GrbF${FH2}
       flxi=GFSFLX.GrbF${FH2}
-      atmo=$memdir/${CDUMP}.t${cyc}z.atmf${FH3}.$affix
-      sfco=$memdir/${CDUMP}.t${cyc}z.sfcf${FH3}.$affix
-      logo=$memdir/${CDUMP}.t${cyc}z.logf${FH3}.txt
-      pgbo=$memdir/${CDUMP}.t${cyc}z.master.grb2f${FH3}
-      flxo=$memdir/${CDUMP}.t${cyc}z.sfluxgrbf${FH3}.grib2
+      if [[ $RUN == "gefs" ]]; then
+        atmo=$memdir/history/${CDUMP}.t${cyc}z.atmf${FH3}.$affix
+        sfco=$memdir/history/${CDUMP}.t${cyc}z.sfcf${FH3}.$affix
+        logo=$memdir/history/${CDUMP}.t${cyc}z.logf${FH3}.txt
+        pgbo=$memdir/master/${CDUMP}.t${cyc}z.master.grb2f${FH3}
+        flxo=$memdir/master/${CDUMP}.t${cyc}z.sfluxgrbf${FH3}.grib2
+      else
+        atmo=$memdir/${CDUMP}.t${cyc}z.atmf${FH3}.$affix
+        sfco=$memdir/${CDUMP}.t${cyc}z.sfcf${FH3}.$affix
+        logo=$memdir/${CDUMP}.t${cyc}z.logf${FH3}.txt
+        pgbo=$memdir/${CDUMP}.t${cyc}z.master.grb2f${FH3}
+        flxo=$memdir/${CDUMP}.t${cyc}z.sfluxgrbf${FH3}.grib2
+      fi
       eval $NLN $atmo $atmi
       eval $NLN $sfco $sfci
       eval $NLN $logo $logi
@@ -540,11 +548,19 @@ EOF
     done
   else
     for n in $(seq 1 $ntiles); do
-      eval $NLN nggps2d.tile${n}.nc       $memdir/nggps2d.tile${n}.nc
-      eval $NLN nggps3d.tile${n}.nc       $memdir/nggps3d.tile${n}.nc
-      eval $NLN grid_spec.tile${n}.nc     $memdir/grid_spec.tile${n}.nc
-      eval $NLN atmos_static.tile${n}.nc  $memdir/atmos_static.tile${n}.nc
-      eval $NLN atmos_4xdaily.tile${n}.nc $memdir/atmos_4xdaily.tile${n}.nc
+      if [[ $RUN == "gefs" ]]; then
+        eval $NLN nggps2d.tile${n}.nc       $memdir/history/nggps2d.tile${n}.nc
+        eval $NLN nggps3d.tile${n}.nc       $memdir/history/nggps3d.tile${n}.nc
+        eval $NLN grid_spec.tile${n}.nc     $memdir/history/grid_spec.tile${n}.nc
+        eval $NLN atmos_static.tile${n}.nc  $memdir/history/atmos_static.tile${n}.nc
+        eval $NLN atmos_4xdaily.tile${n}.nc $memdir/history/atmos_4xdaily.tile${n}.nc
+      else
+        eval $NLN nggps2d.tile${n}.nc       $memdir/nggps2d.tile${n}.nc
+        eval $NLN nggps3d.tile${n}.nc       $memdir/nggps3d.tile${n}.nc
+        eval $NLN grid_spec.tile${n}.nc     $memdir/grid_spec.tile${n}.nc
+        eval $NLN atmos_static.tile${n}.nc  $memdir/atmos_static.tile${n}.nc
+        eval $NLN atmos_4xdaily.tile${n}.nc $memdir/atmos_4xdaily.tile${n}.nc
+      fi
     done
   fi
 }
@@ -619,12 +635,8 @@ data_out_GFS() {
           $NCP $file $memdir/RESTART/$file
         done
       fi
-    elif [ $CDUMP = "gfs" ]; then
-      if [ $RUN = "gefs" ]; then
-        $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/$RUNMEM/atmos/
-      else
-        $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/
-      fi
+    elif [ $CDUMP = "gfs" ] || [ ${RUN} = "gefs" ]; then
+      $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/${RUNMEM:-""}/atmos/
     fi
   fi
 
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index b6ba2dc43e8..38a490d14f6 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -243,6 +243,12 @@ FV3_GFS_predet(){
   fi
   memdir=${memdir:-$ROTDIR/${prefix}.$PDY/$cyc/atmos/$memchar}
   if [ ! -d $memdir ]; then mkdir -p $memdir; fi
+  if [[ $RUN == "gefs" ]]; then
+    if [ ! -d ${memdir}/history ]; then mkdir -p ${memdir}/history; fi
+    if [ $WRITE_DOPOST = ".true." ]; then
+      if [ ! -d ${memdir}/master ]; then mkdir -p ${memdir}/master; fi
+    fi
+  fi
 
   GDATE=$($NDATE -$assim_freq $CDATE)
   gPDY=$(echo $GDATE | cut -c1-8)

From a56b707cc7888333115846f2b3d44addde4b9e8b Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Mon, 2 Jan 2023 00:30:32 -0500
Subject: [PATCH 08/24] Remove unused statements for gefs

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   parm/config/config.fcst

Refs: #822
---
 parm/config/config.fcst | 79 -----------------------------------------
 1 file changed, 79 deletions(-)

diff --git a/parm/config/config.fcst b/parm/config/config.fcst
index e23dd059de9..6a57a804a5a 100755
--- a/parm/config/config.fcst
+++ b/parm/config/config.fcst
@@ -357,85 +357,6 @@ elif [[ "$CDUMP" == "gfs" ]] ; then # GFS cycle specific parameters
       export io_layout="1,1"
     fi
 
-elif [[ "$CDUMP" == "gefs" ]] ; then # GEFS cycle specific parameters
-
-    if [[ $RUNMEM == "c00" ]]; then
-        # Write more variables to output
-        if [ $QUILTING = ".true." -a $OUTPUT_GRID = "gaussian_grid" ]; then
-            export DIAG_TABLE="$HOMEgfs/parm/parm_fv3diag/diag_table"
-        else
-            export DIAG_TABLE="$HOMEgfs/parm/parm_fv3diag/diag_table_orig"
-        fi
-
-        # Write gfs restart files to rerun fcst from any break point
-        export restart_interval_gfs=${restart_interval_gfs:-0}
-        if [ $restart_interval_gfs -le 0 ]; then
-            export restart_interval="$FHMAX_GFS"
-        else
-            rst_list=""
-            IAU_OFFSET=${IAU_OFFSET:-0}
-            [[ $DOIAU = "NO" ]] && export IAU_OFFSET=0
-            xfh=$((restart_interval_gfs+(IAU_OFFSET/2)))
-            while [ $xfh -le $FHMAX_GFS ]; do
-                rst_list="$rst_list $xfh"
-                xfh=$((xfh+restart_interval_gfs))
-            done
-            export restart_interval="$rst_list"
-        fi
-
-        if [ $DO_AERO = "YES" ]; then
-            # Make sure a restart file is written at the cadence time
-            if [[ ! "${restart_interval[*]}" =~ "$STEP_GFS"  ]]; then
-                export restart_interval="$STEP_GFS $restart_interval"
-            fi
-        fi
-
-        # Choose coupling with wave
-        if [ $DO_WAVE = "YES" -a "$WAVE_CDUMP" != "gdas" ]; then
-            export cplwav=".true."
-        fi
-
-        # Turn off dry mass adjustment in GFS
-        export adjust_dry_mass=".false."
-
-        # Write each restart file in 16 small files to save time
-        if [ $CASE = C768 ]; then
-            export io_layout="4,4"
-        else
-            export io_layout="1,1"
-        fi
-
-    else
-        # Variables used in DA cycling
-        if [ $QUILTING = ".true." -a $OUTPUT_GRID = "gaussian_grid" ]; then
-            export DIAG_TABLE="$HOMEgfs/parm/parm_fv3diag/diag_table_da"
-        else
-            export DIAG_TABLE="$HOMEgfs/parm/parm_fv3diag/diag_table_da_orig"
-        fi
-
-        # Write restart files, where $number is current model start time.
-        # restart_interval:        $number
-        #    number=0, writes out restart files at the end of forecast.
-        #    number>0, writes out restart files at the frequency of $number and at the end of forecast.
-        # restart_interval:        "$number -1"
-        #    writes out restart files only once at $number forecast hour.
-        # restart_interval:        "$number1 $number2 $number3 ..."
-        #    writes out restart file at the specified forecast hours
-        export restart_interval=${restart_interval:-6}
-
-        # For IAU, write restarts at beginning of window also
-        if [ $DOIAU = "YES" ]; then
-            export restart_interval="3 6"
-        fi
-
-        # Choose coupling with wave
-        if [ $DO_WAVE = "YES" ]; then export cplwav=".true." ; fi
-
-        # Turn on dry mass adjustment in GDAS
-        export adjust_dry_mass=".true."
-
-    fi
-
 fi
 
 if [[ "$DO_COUPLED" = "YES" ]] ; then # coupled model

From 61f44aaff68dd6914c32ba237f73c8f29aaa9bb4 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Mon, 2 Jan 2023 00:36:17 -0500
Subject: [PATCH 09/24] Add FLTFILEGFS[F00] & POSTGRB2TBL to pass values

from external packages such as GEFS

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   ush/forecast_postdet.sh

Refs: #822
---
 ush/forecast_postdet.sh | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 1012eeb0c3f..2782ce2fefd 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -308,14 +308,9 @@ EOF
   # inline post fix files
   if [ $WRITE_DOPOST = ".true." ]; then
     $NLN $PARM_POST/post_tag_gfs${LEVS}             $DATA/itag
-    if [[ $RUN == "gefs" ]]; then
-      $NLN $PARM_POST/postxconfig-NT-GEFS.txt         $DATA/postxconfig-NT.txt
-      $NLN $PARM_POST/postxconfig-NT-GEFS-F00.txt     $DATA/postxconfig-NT_FH00.txt
-    else
-      $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
-    fi
-    $NLN $PARM_POST/params_grib2_tbl_new            $DATA/params_grib2_tbl_new
+    $NLN ${FLTFILEGFS:-$PARM_POST/postxconfig-NT-GFS-TWO.txt}           $DATA/postxconfig-NT.txt
+    $NLN ${FLTFILEGFSF00:-$PARM_POST/postxconfig-NT-GFS-F00-TWO.txt}    $DATA/postxconfig-NT_FH00.txt
+    $NLN ${POSTGRB2TBL:-$PARM_POST/params_grib2_tbl_new}                $DATA/params_grib2_tbl_new
   fi
 
   #------------------------------------------------------------------
@@ -636,7 +631,11 @@ data_out_GFS() {
         done
       fi
     elif [ $CDUMP = "gfs" ] || [ ${RUN} = "gefs" ]; then
-      $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/${RUNMEM:-""}/atmos/
+      if [ ${RUN} = "gefs" ]; then
+        $NCP $DATA/input.nml ${ROTDIR}/${RUN}.${PDY}/$cyc/${mem}/atmos/history/
+      else
+        $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/
+      fi
     fi
   fi
 

From 4ef0d93267a71fdda2c6dd85a1d78c89c2657f51 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Wed, 4 Jan 2023 14:09:46 -0500
Subject: [PATCH 10/24] Add braces around variables to fix the lint warning

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
\	modified:   ush/forecast_det.sh

Refs: #822
---
 ush/forecast_det.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/forecast_det.sh b/ush/forecast_det.sh
index cb0cd875520..1337413030f 100755
--- a/ush/forecast_det.sh
+++ b/ush/forecast_det.sh
@@ -41,7 +41,7 @@ FV3_GFS_det(){
   # determine if restart IC exists to continue from a previous forecast
   RERUN="NO"
   filecount=$(find "${RSTDIR_ATM:-/dev/null}" -type f | wc -l)
-  if [[ ( ${CDUMP} = "gfs" || ( $RUN = "gefs" && $CDATE_RST = "" )) && ${rst_invt1} -gt 0 && ${FHMAX} -gt ${rst_invt1} && ${filecount} -gt 10 ]]; then
+  if [[ ( ${CDUMP} = "gfs" || ( ${RUN} = "gefs" && ${CDATE_RST} = "" )) && ${rst_invt1} -gt 0 && ${FHMAX} -gt ${rst_invt1} && ${filecount} -gt 10 ]]; then
     reverse=$(echo "${restart_interval[@]} " | tac -s ' ')
     for xfh in ${reverse} ; do
       yfh=$((xfh-(IAU_OFFSET/2)))

From bf053c167a8ef3ecafc7705198495022206ed307 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Wed, 4 Jan 2023 14:44:40 -0500
Subject: [PATCH 11/24] Remove FV3_GEFS_nml and use FV3_GFS_nml for GEFS

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   scripts/exglobal_forecast.sh
	modified:   ush/forecast_postdet.sh

Refs: #822
---
 scripts/exglobal_forecast.sh |  2 +-
 ush/forecast_postdet.sh      | 14 --------------
 2 files changed, 1 insertion(+), 15 deletions(-)

diff --git a/scripts/exglobal_forecast.sh b/scripts/exglobal_forecast.sh
index 3f2ad87cafd..65e2cc50f5e 100755
--- a/scripts/exglobal_forecast.sh
+++ b/scripts/exglobal_forecast.sh
@@ -161,7 +161,7 @@ case $RUN in
   'data') DATM_nml;;
   'gfs') FV3_GFS_nml;;
   'gdas') FV3_GFS_nml;;
-  'gefs') FV3_GEFS_nml;;
+  'gefs') FV3_GFS_nml;;
 esac				#no namelist for data atmosphere
 [[ $cplflx = .true. ]] && MOM6_nml
 [[ $cplwav = .true. ]] && WW3_nml
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 2782ce2fefd..332397db27b 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -573,20 +573,6 @@ FV3_GFS_nml(){
   echo SUB ${FUNCNAME[0]}: FV3 name lists and model configure file created
 }
 
-FV3_GEFS_nml(){
-  # namelist output for a certain component
-  echo SUB ${FUNCNAME[0]}: Creating name lists and model configure file for FV3
-  if [ $machine = 'sandbox' ]; then
-    cd $SCRIPTDIR
-    echo "MAIN: !!!Sandbox mode, writing to current directory!!!"
-  fi
-  # Call child scripts in current script directory
-  source $SCRIPTDIR/parsing_namelists_FV3.sh
-  FV3_namelists
-  echo SUB ${FUNCNAME[0]}: FV3 name lists and model configure file created
-}
-
-
 DATM_nml(){
   source $SCRIPTDIR/parsing_namelists_DATM.sh
   DATM_namelists

From 4346c8c53ee99f76143e5db6b1b947e5e7cea25b Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Wed, 4 Jan 2023 15:35:55 -0500
Subject: [PATCH 12/24] Remove the new COM dirs

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   ush/forecast_postdet.sh

Refs: #822
---
 ush/forecast_postdet.sh | 42 +++++++++++------------------------------
 1 file changed, 11 insertions(+), 31 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 332397db27b..9c0f3b8ee82 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -520,19 +520,11 @@ EOF
       logi=logf${FH3}
       pgbi=GFSPRS.GrbF${FH2}
       flxi=GFSFLX.GrbF${FH2}
-      if [[ $RUN == "gefs" ]]; then
-        atmo=$memdir/history/${CDUMP}.t${cyc}z.atmf${FH3}.$affix
-        sfco=$memdir/history/${CDUMP}.t${cyc}z.sfcf${FH3}.$affix
-        logo=$memdir/history/${CDUMP}.t${cyc}z.logf${FH3}.txt
-        pgbo=$memdir/master/${CDUMP}.t${cyc}z.master.grb2f${FH3}
-        flxo=$memdir/master/${CDUMP}.t${cyc}z.sfluxgrbf${FH3}.grib2
-      else
-        atmo=$memdir/${CDUMP}.t${cyc}z.atmf${FH3}.$affix
-        sfco=$memdir/${CDUMP}.t${cyc}z.sfcf${FH3}.$affix
-        logo=$memdir/${CDUMP}.t${cyc}z.logf${FH3}.txt
-        pgbo=$memdir/${CDUMP}.t${cyc}z.master.grb2f${FH3}
-        flxo=$memdir/${CDUMP}.t${cyc}z.sfluxgrbf${FH3}.grib2
-      fi
+      atmo=$memdir/${CDUMP}.t${cyc}z.atmf${FH3}.$affix
+      sfco=$memdir/${CDUMP}.t${cyc}z.sfcf${FH3}.$affix
+      logo=$memdir/${CDUMP}.t${cyc}z.logf${FH3}.txt
+      pgbo=$memdir/${CDUMP}.t${cyc}z.master.grb2f${FH3}
+      flxo=$memdir/${CDUMP}.t${cyc}z.sfluxgrbf${FH3}.grib2
       eval $NLN $atmo $atmi
       eval $NLN $sfco $sfci
       eval $NLN $logo $logi
@@ -543,19 +535,11 @@ EOF
     done
   else
     for n in $(seq 1 $ntiles); do
-      if [[ $RUN == "gefs" ]]; then
-        eval $NLN nggps2d.tile${n}.nc       $memdir/history/nggps2d.tile${n}.nc
-        eval $NLN nggps3d.tile${n}.nc       $memdir/history/nggps3d.tile${n}.nc
-        eval $NLN grid_spec.tile${n}.nc     $memdir/history/grid_spec.tile${n}.nc
-        eval $NLN atmos_static.tile${n}.nc  $memdir/history/atmos_static.tile${n}.nc
-        eval $NLN atmos_4xdaily.tile${n}.nc $memdir/history/atmos_4xdaily.tile${n}.nc
-      else
-        eval $NLN nggps2d.tile${n}.nc       $memdir/nggps2d.tile${n}.nc
-        eval $NLN nggps3d.tile${n}.nc       $memdir/nggps3d.tile${n}.nc
-        eval $NLN grid_spec.tile${n}.nc     $memdir/grid_spec.tile${n}.nc
-        eval $NLN atmos_static.tile${n}.nc  $memdir/atmos_static.tile${n}.nc
-        eval $NLN atmos_4xdaily.tile${n}.nc $memdir/atmos_4xdaily.tile${n}.nc
-      fi
+      eval $NLN nggps2d.tile${n}.nc       $memdir/nggps2d.tile${n}.nc
+      eval $NLN nggps3d.tile${n}.nc       $memdir/nggps3d.tile${n}.nc
+      eval $NLN grid_spec.tile${n}.nc     $memdir/grid_spec.tile${n}.nc
+      eval $NLN atmos_static.tile${n}.nc  $memdir/atmos_static.tile${n}.nc
+      eval $NLN atmos_4xdaily.tile${n}.nc $memdir/atmos_4xdaily.tile${n}.nc
     done
   fi
 }
@@ -617,11 +601,7 @@ data_out_GFS() {
         done
       fi
     elif [ $CDUMP = "gfs" ] || [ ${RUN} = "gefs" ]; then
-      if [ ${RUN} = "gefs" ]; then
-        $NCP $DATA/input.nml ${ROTDIR}/${RUN}.${PDY}/$cyc/${mem}/atmos/history/
-      else
-        $NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/
-      fi
+      $NCP $DATA/input.nml ${ROTDIR}/${RUN}.${PDY}/$cyc/${mem:-""}/atmos/
     fi
   fi
 

From e1f83055bfaac325907c587108f0a61aabb32275 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Wed, 4 Jan 2023 17:15:22 -0500
Subject: [PATCH 13/24] Correct a typo

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   ush/forecast_predet.sh

Refs: #822
---
 ush/forecast_predet.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 38a490d14f6..e9132fa7a8c 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -273,7 +273,7 @@ FV3_GFS_predet(){
 }
 
 FV3_GEFS_predet(){
-  echo "SUB ${FUNCNAME[0]}: Defining variables for FV3GFS"
+  echo "SUB ${FUNCNAME[0]}: Defining variables for FV3GEFS"
 
   FV3_GFS_predet
 

From ec701f5363ac823af3d6d079d5bce51b6048561a Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Wed, 4 Jan 2023 17:19:05 -0500
Subject: [PATCH 14/24] Delete the unused statements

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   ush/forecast_predet.sh

Refs: #822
---
 ush/forecast_predet.sh | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index e9132fa7a8c..fc105f456ea 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -243,12 +243,6 @@ FV3_GFS_predet(){
   fi
   memdir=${memdir:-$ROTDIR/${prefix}.$PDY/$cyc/atmos/$memchar}
   if [ ! -d $memdir ]; then mkdir -p $memdir; fi
-  if [[ $RUN == "gefs" ]]; then
-    if [ ! -d ${memdir}/history ]; then mkdir -p ${memdir}/history; fi
-    if [ $WRITE_DOPOST = ".true." ]; then
-      if [ ! -d ${memdir}/master ]; then mkdir -p ${memdir}/master; fi
-    fi
-  fi
 
   GDATE=$($NDATE -$assim_freq $CDATE)
   gPDY=$(echo $GDATE | cut -c1-8)

From 4299561fc2cebeaa519057befea5a00bf6d0661d Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Fri, 6 Jan 2023 23:16:48 -0500
Subject: [PATCH 15/24] Modify to save RESTART files for both gfs and gefs

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   ush/forecast_predet.sh

Refs: #822
---
 ush/forecast_predet.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index fc105f456ea..2d5f1050726 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -208,7 +208,7 @@ FV3_GFS_predet(){
   print_freq=${print_freq:-6}
 
   #-------------------------------------------------------
-  if [[ $CDUMP = "gfs" || $RUN = "gefs" ]] && [ $rst_invt1 -gt 0 ] && [ $MEMBER -lt 0 ]; then
+  if [[ $CDUMP = "gfs" || $RUN = "gefs" ]] && [ $rst_invt1 -gt 0 ]; then
     RSTDIR_ATM=${RSTDIR_ATM:-${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART}
     if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
     $NLN $RSTDIR_ATM RESTART

From fd325acba7c9075be88ce88536d1a2170e62388e Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Wed, 11 Jan 2023 10:46:37 -0500
Subject: [PATCH 16/24] Make RERUN receive value from out of the script

This is mostly for GEFS forecast_d16_35 job

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   ush/forecast_det.sh

Refs: #822
---
 ush/forecast_det.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/forecast_det.sh b/ush/forecast_det.sh
index 1337413030f..257f0e13ff9 100755
--- a/ush/forecast_det.sh
+++ b/ush/forecast_det.sh
@@ -39,7 +39,7 @@ FV3_GFS_det(){
 
   #-------------------------------------------------------
   # determine if restart IC exists to continue from a previous forecast
-  RERUN="NO"
+  RERUN=${RERUN:-"NO"}
   filecount=$(find "${RSTDIR_ATM:-/dev/null}" -type f | wc -l)
   if [[ ( ${CDUMP} = "gfs" || ( ${RUN} = "gefs" && ${CDATE_RST} = "" )) && ${rst_invt1} -gt 0 && ${FHMAX} -gt ${rst_invt1} && ${filecount} -gt 10 ]]; then
     reverse=$(echo "${restart_interval[@]} " | tac -s ' ')

From 33b4d90f76835309dba5f865c37a8ff13b8ef798 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Thu, 12 Jan 2023 12:56:40 -0500
Subject: [PATCH 17/24] Delete the GEFS functions to reuse GFS functions  On
 branch feature/gefs_v13_822_add_atm_fcst 	modified:  
 scripts/exglobal_forecast.sh 	modified:   ush/forecast_det.sh 
 modified:   ush/forecast_postdet.sh 	modified:   ush/forecast_predet.sh

Refs: #822
---
 scripts/exglobal_forecast.sh | 8 ++++----
 ush/forecast_det.sh          | 5 -----
 ush/forecast_postdet.sh      | 9 ---------
 ush/forecast_predet.sh       | 8 --------
 4 files changed, 4 insertions(+), 26 deletions(-)

diff --git a/scripts/exglobal_forecast.sh b/scripts/exglobal_forecast.sh
index 65e2cc50f5e..87c96833a56 100755
--- a/scripts/exglobal_forecast.sh
+++ b/scripts/exglobal_forecast.sh
@@ -125,7 +125,7 @@ case $RUN in
   'data') DATM_predet;;
   'gfs') FV3_GFS_predet;;
   'gdas') FV3_GFS_predet;;
-  'gefs') FV3_GEFS_predet;;
+  'gefs') FV3_GFS_predet;;
 esac
 [[ $cplflx = .true. ]] && MOM6_predet
 [[ $cplwav = .true. ]] && WW3_predet
@@ -134,7 +134,7 @@ esac
 case $RUN in
   'gfs') FV3_GFS_det;;
   'gdas') FV3_GFS_det;;
-  'gefs') FV3_GEFS_det;;
+  'gefs') FV3_GFS_det;;
 esac				#no run type determination for data atmosphere
 [[ $cplflx = .true. ]] && MOM6_det
 [[ $cplwav = .true. ]] && WW3_det
@@ -148,7 +148,7 @@ case $RUN in
   'data') DATM_postdet;;
   'gfs') FV3_GFS_postdet;;
   'gdas') FV3_GFS_postdet;;
-  'gefs') FV3_GEFS_postdet;;
+  'gefs') FV3_GFS_postdet;;
 esac				#no post determination set up for data atmosphere
 [[ $cplflx = .true. ]] && MOM6_postdet
 [[ $cplwav = .true. ]] && WW3_postdet
@@ -204,7 +204,7 @@ if [ $machine != 'sandbox' ]; then
     'data') data_out_Data_ATM;;
     'gfs') data_out_GFS;;
     'gdas') data_out_GFS;;
-    'gefs') data_out_GEFS;;
+    'gefs') data_out_GFS;;
   esac
   [[ $cplflx = .true. ]] && MOM6_out
   [[ $cplwav = .true. ]] && WW3_out
diff --git a/ush/forecast_det.sh b/ush/forecast_det.sh
index 257f0e13ff9..575f35696ab 100755
--- a/ush/forecast_det.sh
+++ b/ush/forecast_det.sh
@@ -74,11 +74,6 @@ FV3_GFS_det(){
   #-------------------------------------------------------
 }
 
-FV3_GEFS_det(){
-  echo "SUB ${FUNCNAME[0]}: Defining variables for FV3GEFS"
-  FV3_GFS_det
-}
-
 WW3_det(){
   echo "SUB ${FUNCNAME[0]}: Run type determination for WW3"
 }
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 9c0f3b8ee82..1be06620228 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -11,12 +11,6 @@
 ## for execution.
 #####
 
-FV3_GEFS_postdet(){
-  echo SUB ${FUNCNAME[0]}: Linking input data for FV3 $RUN
-  # soft link commands insert here
-  FV3_GFS_postdet
-}
-
 DATM_postdet(){
   ######################################################################
   # Link DATM  inputs (ie forcing files)                           #
@@ -608,9 +602,6 @@ data_out_GFS() {
   echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
 }
 
-data_out_GEFS() {
-  data_out_GFS
-}
 
 WW3_postdet() {
   echo "SUB ${FUNCNAME[0]}: Linking input data for WW3"
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index c2c0f019bf2..e46b9fac92b 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -266,14 +266,6 @@ FV3_GFS_predet(){
   echo "SUB ${FUNCNAME[0]}: pre-determination variables set"
 }
 
-FV3_GEFS_predet(){
-  echo "SUB ${FUNCNAME[0]}: Defining variables for FV3GEFS"
-
-  FV3_GFS_predet
-
-  echo "SUB ${FUNCNAME[0]}: pre-determination variables set"
-}
-
 WW3_predet(){
   echo "SUB ${FUNCNAME[0]}: Defining variables for WW3"
   if [ $CDUMP = "gdas" ]; then

From 119e5b7aca00302bfe578cbeec390475d14051d7 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Tue, 17 Jan 2023 17:55:47 -0500
Subject: [PATCH 18/24] Add { } to variables

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   scripts/exgdas_enkf_fcst.sh
	modified:   ush/forecast_predet.sh

Refs: #822
---
 scripts/exgdas_enkf_fcst.sh | 2 +-
 ush/forecast_predet.sh      | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/scripts/exgdas_enkf_fcst.sh b/scripts/exgdas_enkf_fcst.sh
index cd21704ca99..32221f96ec1 100755
--- a/scripts/exgdas_enkf_fcst.sh
+++ b/scripts/exgdas_enkf_fcst.sh
@@ -108,7 +108,7 @@ export LEVS=${LEVS_ENKF:-${LEVS:-64}}
 
 # nggps_diag_nml
 export FHOUT=${FHOUT_ENKF:-3}
-if [[ $CDUMP == "gfs" ]]; then
+if [[ ${CDUMP} == "gfs" ]]; then
     export FHOUT=${FHOUT_ENKF_GFS:-${FHOUT_ENKF:${FHOUT:-3}}}
 fi
 # model_configure
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index e46b9fac92b..536c33cb378 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -208,7 +208,7 @@ FV3_GFS_predet(){
   print_freq=${print_freq:-6}
 
   #-------------------------------------------------------
-  if [[ $CDUMP = "gfs" || $RUN = "gefs" ]] && [ $rst_invt1 -gt 0 ]; then
+  if [[ ${CDUMP} = "gfs" || ${RUN} = "gefs" ]] && [ ${rst_invt1} -gt 0 ]; then
     RSTDIR_ATM=${RSTDIR_ATM:-${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART}
     if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
     $NLN $RSTDIR_ATM RESTART
@@ -232,7 +232,7 @@ FV3_GFS_predet(){
 
   #-------------------------------------------------------
   # member directory
-  if [[ $MEMBER -lt 0 || $RUN = "gefs" ]]; then
+  if [[ ${MEMBER} -lt 0 || ${RUN} = "gefs" ]]; then
     prefix=$CDUMP
     rprefix=$rCDUMP
     memchar=""
@@ -241,13 +241,13 @@ FV3_GFS_predet(){
     rprefix=enkf$rCDUMP
     memchar=mem$(printf %03i $MEMBER)
   fi
-  memdir=${memdir:-$ROTDIR/${prefix}.$PDY/$cyc/$memchar/atmos}
+  memdir=${memdir:-${ROTDIR}/${prefix}.${PDY}/${cyc}/${memchar}/atmos}
   if [ ! -d $memdir ]; then mkdir -p $memdir; fi
 
   GDATE=$($NDATE -$assim_freq $CDATE)
   gPDY=$(echo $GDATE | cut -c1-8)
   gcyc=$(echo $GDATE | cut -c9-10)
-  gmemdir=${gmemdir:-$ROTDIR/${rprefix}.$gPDY/$gcyc/$memchar/atmos}
+  gmemdir=${gmemdir:-${ROTDIR}/${rprefix}.${gPDY}/${gcyc}/${memchar}/atmos}
 
   if [[ "$DOIAU" = "YES" ]]; then
     sCDATE=$($NDATE -3 $CDATE)

From 5c95d7ab913f4f95c55b1740c478d4f0c18ac89b Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Thu, 19 Jan 2023 12:09:13 -0500
Subject: [PATCH 19/24] Remove unused RSTDIR  On branch
 feature/gefs_v13_822_add_atm_fcst  Changes to be committed: 	modified:  
 ush/forecast_predet.sh

Refs: #822
---
 ush/forecast_predet.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 536c33cb378..6e5c317a689 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -209,7 +209,7 @@ FV3_GFS_predet(){
 
   #-------------------------------------------------------
   if [[ ${CDUMP} = "gfs" || ${RUN} = "gefs" ]] && [ ${rst_invt1} -gt 0 ]; then
-    RSTDIR_ATM=${RSTDIR_ATM:-${RSTDIR:-$ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART}
+    RSTDIR_ATM=${RSTDIR_ATM:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART}
     if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
     $NLN $RSTDIR_ATM RESTART
     # The final restart written at the end doesn't include the valid date

From 1be0572989bc123ca6b9ba29c3337d01d450955d Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Sun, 22 Jan 2023 17:57:24 -0500
Subject: [PATCH 20/24] Create links for final restart written files only  
 when FHMAX_GFS%restart_interval_gfs=0

These changes will avoid to create invalid links for the final
  restart writting files

 On branch feature/gefs_v13_822_add_atm_fcst
 Changes to be committed:
	modified:   ush/forecast_predet.sh

Refs: #822
---
 ush/forecast_predet.sh | 28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 6e5c317a689..3292d29947c 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -212,20 +212,22 @@ FV3_GFS_predet(){
     RSTDIR_ATM=${RSTDIR_ATM:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos/RERUN_RESTART}
     if [ ! -d $RSTDIR_ATM ]; then mkdir -p $RSTDIR_ATM ; fi
     $NLN $RSTDIR_ATM RESTART
-    # The final restart written at the end doesn't include the valid date
-    # Create links that keep the same name pattern for these files
-    VDATE=$($NDATE +$FHMAX_GFS $CDATE)
-    vPDY=$(echo $VDATE | cut -c1-8)
-    vcyc=$(echo $VDATE | cut -c9-10)
-    files="coupler.res fv_core.res.nc"
-    for tile in {1..6}; do
-      for base in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data; do
-        files="${files} ${base}.tile${tile}.nc"
+    if [[ $(( ${FHMAX_GFS} % ${restart_interval_gfs} )) == 0 ]]; then
+      # The final restart written at the end doesn't include the valid date
+      # Create links that keep the same name pattern for these files
+      VDATE=$($NDATE +$FHMAX_GFS $CDATE)
+      vPDY=$(echo $VDATE | cut -c1-8)
+      vcyc=$(echo $VDATE | cut -c9-10)
+      files="coupler.res fv_core.res.nc"
+      for tile in {1..6}; do
+        for base in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data; do
+          files="${files} ${base}.tile${tile}.nc"
+        done
       done
-    done
-    for file in $files; do
-      $NLN $RSTDIR_ATM/$file $RSTDIR_ATM/${vPDY}.${vcyc}0000.$file
-    done
+      for file in $files; do
+        $NLN $RSTDIR_ATM/$file $RSTDIR_ATM/${vPDY}.${vcyc}0000.$file
+      done
+    fi
   else
     mkdir -p $DATA/RESTART
   fi

From 7ee08e292e92a07f60058bbd1ec8a930f1c45643 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Mon, 23 Jan 2023 20:56:43 -0500
Subject: [PATCH 21/24] Change memdir/INPUT using ICSDIR to use dif ICSDIR

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   ush/forecast_postdet.sh

Refs: #822
---
 ush/forecast_postdet.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 1be06620228..0bbbd4b4e3e 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -129,7 +129,8 @@ EOF
     #.............................
 
   else ## cold start
-    for file in $(ls $memdir/INPUT/*.nc); do
+    ICSDIR=${ICSDIR:-${memdir}/INPUT}         # cold start initial conditions
+    for file in $(ls ${ICSDIR}/*.nc); do
       file2=$(echo $(basename $file))
       fsuf=$(echo $file2 | cut -c1-3)
       if [ $fsuf = "gfs" -o $fsuf = "sfc" ]; then
@@ -594,7 +595,7 @@ data_out_GFS() {
           $NCP $file $memdir/RESTART/$file
         done
       fi
-    elif [ $CDUMP = "gfs" ] || [ ${RUN} = "gefs" ]; then
+    elif [ $CDUMP = "gfs" ]; then
       $NCP $DATA/input.nml ${ROTDIR}/${RUN}.${PDY}/$cyc/${mem:-""}/atmos/
     fi
   fi

From b686fe7fdb415bdf4f3efd4b2a617d5c1421b4e3 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Mon, 23 Jan 2023 21:01:50 -0500
Subject: [PATCH 22/24] Remove unused function

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   ush/forecast_postdet.sh

Refs: #822
---
 ush/forecast_postdet.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 0bbbd4b4e3e..70498fe610e 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -596,7 +596,7 @@ data_out_GFS() {
         done
       fi
     elif [ $CDUMP = "gfs" ]; then
-      $NCP $DATA/input.nml ${ROTDIR}/${RUN}.${PDY}/$cyc/${mem:-""}/atmos/
+      $NCP $DATA/input.nml ${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos/
     fi
   fi
 

From 1ac2957369e707db2b24368deaf051eb329abfb9 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Wed, 25 Jan 2023 15:22:22 -0500
Subject: [PATCH 23/24] Remove the ICSDIR in the forecast_postdef.sh

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   ush/forecast_postdet.sh

Refs: #822
---
 ush/forecast_postdet.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index e58add682ae..824a0946ce4 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -129,8 +129,7 @@ EOF
     #.............................
 
   else ## cold start
-    ICSDIR=${ICSDIR:-${memdir}/INPUT}         # cold start initial conditions
-    for file in $(ls ${ICSDIR}/*.nc); do
+    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

From c6e082c70fb2359d6752c8e7ea07e70d9d0c6fb3 Mon Sep 17 00:00:00 2001
From: "Xianwu.Xue" <Xianwu.Xue@noaa.gov>
Date: Wed, 25 Jan 2023 16:53:21 -0500
Subject: [PATCH 24/24] Optimize case statements in the script

 On branch feature/gefs_v13_822_add_atm_fcst
	modified:   scripts/exglobal_forecast.sh

Refs: #822
---
 scripts/exglobal_forecast.sh | 24 ++++++------------------
 1 file changed, 6 insertions(+), 18 deletions(-)

diff --git a/scripts/exglobal_forecast.sh b/scripts/exglobal_forecast.sh
index 87c96833a56..5130b6602ed 100755
--- a/scripts/exglobal_forecast.sh
+++ b/scripts/exglobal_forecast.sh
@@ -123,18 +123,14 @@ common_predet
 echo $RUN
 case $RUN in
   'data') DATM_predet;;
-  'gfs') FV3_GFS_predet;;
-  'gdas') FV3_GFS_predet;;
-  'gefs') FV3_GFS_predet;;
+  'gfs' | 'gdas' | 'gefs') FV3_GFS_predet;;
 esac
 [[ $cplflx = .true. ]] && MOM6_predet
 [[ $cplwav = .true. ]] && WW3_predet
 [[ $cplice = .true. ]] && CICE_predet
 
 case $RUN in
-  'gfs') FV3_GFS_det;;
-  'gdas') FV3_GFS_det;;
-  'gefs') FV3_GFS_det;;
+  'gfs' | 'gdas' | 'gefs') FV3_GFS_det;;
 esac				#no run type determination for data atmosphere
 [[ $cplflx = .true. ]] && MOM6_det
 [[ $cplwav = .true. ]] && WW3_det
@@ -146,9 +142,7 @@ 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_GFS_postdet;;
+  'gfs' | 'gdas' | 'gefs') FV3_GFS_postdet;;
 esac				#no post determination set up for data atmosphere
 [[ $cplflx = .true. ]] && MOM6_postdet
 [[ $cplwav = .true. ]] && WW3_postdet
@@ -159,9 +153,7 @@ 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_GFS_nml;;
+  'gfs' | 'gdas' | 'gefs') FV3_GFS_nml;;
 esac				#no namelist for data atmosphere
 [[ $cplflx = .true. ]] && MOM6_nml
 [[ $cplwav = .true. ]] && WW3_nml
@@ -170,9 +162,7 @@ esac				#no namelist for data atmosphere
 
 case $RUN in
   'data') DATM_model_configure;;
-  'gfs') FV3_model_configure;;
-  'gdas') FV3_model_configure;;
-  'gefs') FV3_model_configure;;
+  'gfs' | 'gdas' | 'gefs') FV3_model_configure;;
 esac
 echo "MAIN: Name lists and model configuration written"
 
@@ -202,9 +192,7 @@ fi
 if [ $machine != 'sandbox' ]; then
   case $RUN in
     'data') data_out_Data_ATM;;
-    'gfs') data_out_GFS;;
-    'gdas') data_out_GFS;;
-    'gefs') data_out_GFS;;
+    'gfs' | 'gdas' | 'gefs') data_out_GFS;;
   esac
   [[ $cplflx = .true. ]] && MOM6_out
   [[ $cplwav = .true. ]] && WW3_out