From 95e66acad07bd691c29207e5ef2307fd25c9733e Mon Sep 17 00:00:00 2001
From: "Jessica.Meixner" <Jessica.Meixner@noaa.gov>
Date: Tue, 9 Feb 2021 21:56:52 +0000
Subject: [PATCH 1/4] change where DO_WAVE config is

---
 workflow/config/base.yaml | 6 ++++++
 workflow/config/fcst.yaml | 6 ------
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/workflow/config/base.yaml b/workflow/config/base.yaml
index 50aaba7729..fbb9cf625c 100644
--- a/workflow/config/base.yaml
+++ b/workflow/config/base.yaml
@@ -28,6 +28,12 @@ config_base:
     export print_esmf="{doc.settings.print_esmf}"
     export esmf_profile="{doc.settings.esmf_profile}"
 
+    if [[ $cplwav = ".true." ]]; then
+       export DO_WAVE="YES"
+    else
+       export DO_WAVE="NO"
+    fi
+
     export nems_temp="{doc.settings.nems_temp}"
     export nems_temp_cold="{doc.settings.nems_temp_cold}"
                
diff --git a/workflow/config/fcst.yaml b/workflow/config/fcst.yaml
index 68001960bb..f3e567a74e 100644
--- a/workflow/config/fcst.yaml
+++ b/workflow/config/fcst.yaml
@@ -189,12 +189,6 @@ config_fcst:
     export sppt_sfclimit=.true.
     export use_zmtnblck=.true.
 
-
-    if [[ $cplwav = ".true." ]]; then 
-       export DO_WAVE="YES"
-    else 
-       export DO_WAVE="NO"
-    fi
     #---------------------------------------------------------------------
     # Disable the use of coupler.res; get model start time from model_configure
     export USE_COUPLER_RES="NO"

From 4fa2954c7dee93539a886ebfe8dfd41449cf4688 Mon Sep 17 00:00:00 2001
From: "Jessica.Meixner" <Jessica.Meixner@noaa.gov>
Date: Wed, 10 Feb 2021 13:41:44 +0000
Subject: [PATCH 2/4] update archiving jobs for cplflx=true

---
 jobs/rocoto/arch.sh | 30 +++++++++++++++++++++++++++
 ush/hpssarch_gen.sh | 50 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 80 insertions(+)

diff --git a/jobs/rocoto/arch.sh b/jobs/rocoto/arch.sh
index ee3af795c2..1cfae3e1d5 100755
--- a/jobs/rocoto/arch.sh
+++ b/jobs/rocoto/arch.sh
@@ -27,6 +27,8 @@ for config in $configs; do
     [[ $status -ne 0 ]] && exit $status
 done
 
+set -x
+
 # ICS are restarts and always lag INC by $assim_freq hours
 ARCHINC_CYC=$ARCH_CYC
 ARCHICS_CYC=$((ARCH_CYC-assim_freq))
@@ -174,6 +176,33 @@ cd $ROTDIR
 
 if [ $CDUMP = "gfs" ]; then
 
+
+  if [ $cplflx = ".true." ]; then
+    # ocn and ice files
+    echo "current location is $ROTDIR"
+    echo `date`
+    echo "starting gzip netcdf files, this will take a while ......"
+    gzip $COMIN/../ocn_2D*nc $COMIN/../ice*nc $COMIN/../ocn_daily*nc
+    echo `date`
+    echo "gzip done !"
+    for targrp in ocn ocn_2D ocn_3D ocn_xsect ice ocn_daily log wavocn wave; do
+       htar -P -cvf $ATARDIR/$CDATE/${targrp}.tar `cat $ARCH_LIST/${targrp}.txt`
+    done
+
+    #rearrangement of atm files
+    htar -P -cvf $ATARDIR/$CDATE/gfs_pgrb2_0p25.tar `cat $ARCH_LIST/gfsa.txt`
+    htar -P -cvf $ATARDIR/$CDATE/gfs_pgrb2_1p00.tar `cat $ARCH_LIST/gfsb.txt`
+
+    for targrp in gfs_flux gfs_flux_1p00 gfs_pgrb2_1p00 gfs_pgrb2_0p25 gfs_pgrb2b_1p00 gfs_pgrb2b_0p25; do
+       htar -P -cvf $ATARDIR/$CDATE/${targrp}.tar `cat $ARCH_LIST/${targrp}.txt`
+       status=$?
+       if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
+          echo "HTAR $CDATE ${targrp}.tar failed"
+          exit $status
+       fi
+    done
+  else  #if not cplflx, normal: 
+
     #for targrp in gfsa gfsb - NOTE - do not check htar error status
     for targrp in gfsa gfsb; do
         htar -P -cvf $ATARDIR/$CDATE/${targrp}.tar `cat $ARCH_LIST/${targrp}.txt`
@@ -190,6 +219,7 @@ if [ $CDUMP = "gfs" ]; then
             fi
         done
     fi
+  fi #end if cplflx
 
     #for targrp in gfswave
     if [ $DO_WAVE = "YES" -a "$WAVE_CDUMP" != "gdas" ]; then
diff --git a/ush/hpssarch_gen.sh b/ush/hpssarch_gen.sh
index 1f4c8ed542..23c814f7ff 100755
--- a/ush/hpssarch_gen.sh
+++ b/ush/hpssarch_gen.sh
@@ -187,6 +187,56 @@ if [ $type = "gfs" ]; then
 
   fi
 
+
+  # for coupled model
+  if [ $cplflx = ".true." ]; then
+
+    dirpath="gfs.${PDY}/${cyc}/"
+    dirname="./${dirpath}"
+
+    head="gfs.t${cyc}z."
+
+    echo "cplflx=",$cplflx
+    rm -f gfs_pgrb2b_1p00.txt
+    rm -f gfs_pgrb2b_0p25.txt
+    rm -f gfs_flux_1p00.txt
+    rm -f ocn.txt
+    rm -f ocn_2D.txt
+    rm -f ocn_3D.txt
+    rm -f ocn_xsect.txt
+    rm -f log.txt
+    rm -f ice.txt
+    rm -f ocn_daily.txt
+    rm -f wavocn.txt
+    touch gfs_flux_1p00.txt
+    touch gfs_pgrb2b_1p00.txt
+    touch gfs_pgrb2b_0p25.txt
+    touch ocn.txt
+    touch ocn_2D.txt
+    touch ocn_3D.txt
+    touch ocn_xsect.txt
+    touch ocn_daily.txt
+    touch log.txt
+    touch ice.txt
+    touch wavocn.txt
+    echo  "${dirname}ice*nc                     " >>ice.txt
+    echo  "${dirname}ocn_2D*                    " >>ocn_2D.txt
+    echo  "${dirname}ocn_3D*                    " >>ocn_3D.txt
+    echo  "${dirname}ocn*EQ*                    " >>ocn_xsect.txt
+    echo  "${dirname}ocn_daily*                 " >>ocn_daily.txt
+    echo  "${dirname}wavocn*                    " >>wavocn.txt
+    echo  "${dirname}/atmos/input.nml           " >>log.txt
+    echo  "${dirname}ice_in                     " >>log.txt
+    echo  "${dirname}MOM_input                  " >>log.txt
+    echo  "./logs/${CDATE}/gfs*.log             " >>log.txt
+    echo  "${dirname}/atmos/${head}logf*.txt    " >>log.txt
+    echo  "${dirname}/wave/rundata/ww3_multi*   " >>log.txt
+    echo  "${dirname}ocn_ice*grb2               " >>ocn.txt
+    echo  "${dirname}${head}flux.1p00.f???      " >>gfs_flux_1p00.txt
+    echo  "${dirname}${head}flux.1p00.f???.idx  " >>gfs_flux_1p00.txt
+  fi
+
+
 #-----------------------------------------------------
 fi   ##end of gfs
 #-----------------------------------------------------

From eea02be4ba6eb6be334a7acf8657b710965db625 Mon Sep 17 00:00:00 2001
From: "Jessica.Meixner" <Jessica.Meixner@noaa.gov>
Date: Wed, 10 Feb 2021 21:58:34 +0000
Subject: [PATCH 3/4] updates for archiving job

---
 jobs/rocoto/arch.sh     |  13 ++---
 ush/forecast_postdet.sh |   2 +-
 ush/hpssarch_gen.sh     | 122 +++++++++++++++++++++++-----------------
 3 files changed, 76 insertions(+), 61 deletions(-)

diff --git a/jobs/rocoto/arch.sh b/jobs/rocoto/arch.sh
index 1cfae3e1d5..74c7ed2a2c 100755
--- a/jobs/rocoto/arch.sh
+++ b/jobs/rocoto/arch.sh
@@ -38,7 +38,8 @@ fi
 
 # CURRENT CYCLE
 APREFIX="${CDUMP}.t${cyc}z."
-ASUFFIX=${ASUFFIX:-$SUFFIX}
+AASUFFIX=${SUFFIX:-".nc"}
+ASUFFIX=${ASUFFIX:-$AASUFFIX}
 
 if [ $ASUFFIX = ".nc" ]; then
    format="netcdf"
@@ -179,13 +180,7 @@ if [ $CDUMP = "gfs" ]; then
 
   if [ $cplflx = ".true." ]; then
     # ocn and ice files
-    echo "current location is $ROTDIR"
-    echo `date`
-    echo "starting gzip netcdf files, this will take a while ......"
-    gzip $COMIN/../ocn_2D*nc $COMIN/../ice*nc $COMIN/../ocn_daily*nc
-    echo `date`
-    echo "gzip done !"
-    for targrp in ocn ocn_2D ocn_3D ocn_xsect ice ocn_daily log wavocn wave; do
+    for targrp in ocn_ice_grib2_0p5 ocn_ice_grib2_0p25  ocn_2D ocn_3D ocn_xsect ice ocn_daily log wavocn wave; do
        htar -P -cvf $ATARDIR/$CDATE/${targrp}.tar `cat $ARCH_LIST/${targrp}.txt`
     done
 
@@ -193,7 +188,7 @@ if [ $CDUMP = "gfs" ]; then
     htar -P -cvf $ATARDIR/$CDATE/gfs_pgrb2_0p25.tar `cat $ARCH_LIST/gfsa.txt`
     htar -P -cvf $ATARDIR/$CDATE/gfs_pgrb2_1p00.tar `cat $ARCH_LIST/gfsb.txt`
 
-    for targrp in gfs_flux gfs_flux_1p00 gfs_pgrb2_1p00 gfs_pgrb2_0p25 gfs_pgrb2b_1p00 gfs_pgrb2b_0p25; do
+    for targrp in gfs_flux gfs_${format}a gfs_sfc_${format}b gfs_atm_${format}b gfs_flux_1p00 gfs_pgrb2_1p00 gfs_pgrb2_0p25 gfs_pgrb2b_1p00 gfs_pgrb2b_0p25; do
        htar -P -cvf $ATARDIR/$CDATE/${targrp}.tar `cat $ARCH_LIST/${targrp}.txt`
        status=$?
        if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 3345bfcaf7..73f3350c44 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -535,7 +535,7 @@ if [ $SEND = "YES" ]; then
   fi
 fi
         
-$NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/
+$NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/
 
 echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
 }
diff --git a/ush/hpssarch_gen.sh b/ush/hpssarch_gen.sh
index 23c814f7ff..97b891cce0 100755
--- a/ush/hpssarch_gen.sh
+++ b/ush/hpssarch_gen.sh
@@ -57,6 +57,60 @@ if [ $type = "gfs" ]; then
     touch gfs_downstream.txt
   fi
 
+  # for coupled model
+  if [ $cplflx = ".true." ]; then
+
+    dirpath="gfs.${PDY}/${cyc}/"
+    dirname="./${dirpath}"
+
+    head="gfs.t${cyc}z."
+
+    rm -f gfs_pgrb2b_1p00.txt
+    rm -f gfs_pgrb2b_0p25.txt
+    rm -f gfs_flux_1p00.txt
+    rm -f ocn_ice_grib2_0p5.txt 
+    rm -f ocn_ice_grib2_0p25.txt
+    rm -f ocn_2D.txt
+    rm -f ocn_3D.txt
+    rm -f ocn_xsect.txt
+    rm -f log.txt
+    rm -f ice.txt
+    rm -f ocn_daily.txt
+    rm -f wavocn.txt
+    rm -f gfs_atm_${format}b.txt
+    rm -f gfs_sfc_${format}b.txt
+    touch gfs_flux_1p00.txt
+    touch gfs_pgrb2b_1p00.txt
+    touch gfs_pgrb2b_0p25.txt
+    touch ocn_ice_grib2_0p5.txt
+    touch ocn_ice_grib2_0p25.txt
+    touch ocn_2D.txt
+    touch ocn_3D.txt
+    touch ocn_xsect.txt
+    touch ocn_daily.txt
+    touch log.txt
+    touch ice.txt
+    touch wavocn.txt
+    touch gfs_atm_${format}b.txt
+    touch gfs_sfc_${format}b.txt
+    echo  "${dirname}ice*nc                     " >>ice.txt
+    echo  "${dirname}ocn_2D*                    " >>ocn_2D.txt
+    echo  "${dirname}ocn_3D*                    " >>ocn_3D.txt
+    echo  "${dirname}ocn*EQ*                    " >>ocn_xsect.txt
+    echo  "${dirname}ocn_daily*                 " >>ocn_daily.txt
+    echo  "${dirname}wavocn*                    " >>wavocn.txt
+    echo  "${dirname}/atmos/input.nml           " >>log.txt
+    echo  "${dirname}ice_in                     " >>log.txt
+    echo  "${dirname}MOM_input                  " >>log.txt
+    echo  "./logs/${CDATE}/gfs*.log             " >>log.txt
+    echo  "${dirname}/atmos/${head}logf*.txt    " >>log.txt
+    echo  "${dirname}/wave/rundata/ww3_multi*   " >>log.txt
+    echo  "${dirname}ocn_ice*0p5x0p5.grb2       " >>ocn_ice_grib2_0p5.txt
+    echo  "${dirname}ocn_ice*0p25x0p25.grb2     " >>ocn_ice_grib2_0p25.txt
+    echo  "${dirname}${head}flux.1p00.f???      " >>gfs_flux_1p00.txt
+    echo  "${dirname}${head}flux.1p00.f???.idx  " >>gfs_flux_1p00.txt
+  fi
+
   dirpath="gfs.${PDY}/${cyc}/atmos/"
   dirname="./${dirpath}"
 
@@ -67,8 +121,9 @@ if [ $type = "gfs" ]; then
   echo  "${dirname}${head}pgrb2b.0p25.anl.idx              " >>gfs_pgrb2b.txt
   echo  "${dirname}${head}pgrb2b.0p50.anl                  " >>gfs_pgrb2b.txt
   echo  "${dirname}${head}pgrb2b.0p50.anl.idx              " >>gfs_pgrb2b.txt
-
-  echo  "./logs/${CDATE}/gfs*.log                          " >>gfsa.txt
+  if [ $cplflx = ".false." ]; then
+    echo  "./logs/${CDATE}/gfs*.log                          " >>gfsa.txt
+  fi
   echo  "${dirname}${head}gsistat                          " >>gfsa.txt
   echo  "${dirname}${head}nsstbufr                         " >>gfsa.txt
   echo  "${dirname}${head}prepbufr                         " >>gfsa.txt
@@ -119,12 +174,25 @@ if [ $type = "gfs" ]; then
        echo  "${dirname}${head}pgrb2b.0p50.f${fhr}.idx     " >>gfs_pgrb2b.txt
     fi
 
+    if [ $cplflx = ".true." ]; then
+      echo  "${dirname}${head}pgrb2b.0p25.f${fhr}           " >>gfs_pgrb2b_0p25.txt
+      echo  "${dirname}${head}pgrb2b.0p25.f${fhr}.idx       " >>gfs_pgrb2b_0p25.txt
+      echo  "${dirname}${head}pgrb2b.1p00.f${fhr}           " >>gfs_pgrb2b_1p00.txt
+      echo  "${dirname}${head}pgrb2b.1p00.f${fhr}.idx       " >>gfs_pgrb2b_1p00.txt
+      echo  "${dirname}${head}flux.1p00.f${fhr}             " >>gfs_flux_1p00.txt
+      echo  "${dirname}${head}flux.1p00.f${fhr}.idx         " >>gfs_flux_1p00.txt
+      echo  "${dirname}${head}atmf${fhr}${SUFFIX}           " >>gfs_atm_${format}b.txt
+      echo  "${dirname}${head}sfcf${fhr}${SUFFIX}           " >>gfs_sfc_${format}b.txt
+    fi
+
     echo  "${dirname}${head}sfluxgrbf${fhr}.grib2           " >>gfs_flux.txt
     echo  "${dirname}${head}sfluxgrbf${fhr}.grib2.idx       " >>gfs_flux.txt
 
     echo  "${dirname}${head}pgrb2.0p25.f${fhr}              " >>gfsa.txt
     echo  "${dirname}${head}pgrb2.0p25.f${fhr}.idx          " >>gfsa.txt
-    echo  "${dirname}${head}logf${fhr}.txt                  " >>gfsa.txt
+    if [ $cplflx = ".false." ]; then
+      echo  "${dirname}${head}logf${fhr}.txt                " >>gfsa.txt
+    fi
 
     if [ -s $ROTDIR/${dirpath}${head}pgrb2.0p50.f${fhr} ]; then
        echo  "${dirname}${head}pgrb2.0p50.f${fhr}          " >>gfsb.txt
@@ -188,54 +256,6 @@ if [ $type = "gfs" ]; then
   fi
 
 
-  # for coupled model
-  if [ $cplflx = ".true." ]; then
-
-    dirpath="gfs.${PDY}/${cyc}/"
-    dirname="./${dirpath}"
-
-    head="gfs.t${cyc}z."
-
-    echo "cplflx=",$cplflx
-    rm -f gfs_pgrb2b_1p00.txt
-    rm -f gfs_pgrb2b_0p25.txt
-    rm -f gfs_flux_1p00.txt
-    rm -f ocn.txt
-    rm -f ocn_2D.txt
-    rm -f ocn_3D.txt
-    rm -f ocn_xsect.txt
-    rm -f log.txt
-    rm -f ice.txt
-    rm -f ocn_daily.txt
-    rm -f wavocn.txt
-    touch gfs_flux_1p00.txt
-    touch gfs_pgrb2b_1p00.txt
-    touch gfs_pgrb2b_0p25.txt
-    touch ocn.txt
-    touch ocn_2D.txt
-    touch ocn_3D.txt
-    touch ocn_xsect.txt
-    touch ocn_daily.txt
-    touch log.txt
-    touch ice.txt
-    touch wavocn.txt
-    echo  "${dirname}ice*nc                     " >>ice.txt
-    echo  "${dirname}ocn_2D*                    " >>ocn_2D.txt
-    echo  "${dirname}ocn_3D*                    " >>ocn_3D.txt
-    echo  "${dirname}ocn*EQ*                    " >>ocn_xsect.txt
-    echo  "${dirname}ocn_daily*                 " >>ocn_daily.txt
-    echo  "${dirname}wavocn*                    " >>wavocn.txt
-    echo  "${dirname}/atmos/input.nml           " >>log.txt
-    echo  "${dirname}ice_in                     " >>log.txt
-    echo  "${dirname}MOM_input                  " >>log.txt
-    echo  "./logs/${CDATE}/gfs*.log             " >>log.txt
-    echo  "${dirname}/atmos/${head}logf*.txt    " >>log.txt
-    echo  "${dirname}/wave/rundata/ww3_multi*   " >>log.txt
-    echo  "${dirname}ocn_ice*grb2               " >>ocn.txt
-    echo  "${dirname}${head}flux.1p00.f???      " >>gfs_flux_1p00.txt
-    echo  "${dirname}${head}flux.1p00.f???.idx  " >>gfs_flux_1p00.txt
-  fi
-
 
 #-----------------------------------------------------
 fi   ##end of gfs

From fe94164cffbb85cd1d2df3ee35d5f9022434b6fd Mon Sep 17 00:00:00 2001
From: "Jessica.Meixner" <Jessica.Meixner@noaa.gov>
Date: Thu, 11 Feb 2021 13:59:48 +0000
Subject: [PATCH 4/4] remove debug

---
 jobs/rocoto/arch.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/jobs/rocoto/arch.sh b/jobs/rocoto/arch.sh
index 74c7ed2a2c..b1cef21dc9 100755
--- a/jobs/rocoto/arch.sh
+++ b/jobs/rocoto/arch.sh
@@ -27,8 +27,6 @@ for config in $configs; do
     [[ $status -ne 0 ]] && exit $status
 done
 
-set -x
-
 # ICS are restarts and always lag INC by $assim_freq hours
 ARCHINC_CYC=$ARCH_CYC
 ARCHICS_CYC=$((ARCH_CYC-assim_freq))