From a886e6a75dccd55cc4deba232332b121cad02625 Mon Sep 17 00:00:00 2001
From: George Gayno <George.Gayno@noaa.gov>
Date: Fri, 10 Feb 2023 20:41:10 +0000
Subject: [PATCH 1/5] Place copy of coldstart files in a common script.

Fixes #772.
---
 util/gdas_init/copy_coldstart_files.sh | 49 ++++++++++++++++++++++++++
 util/gdas_init/run_pre-v14.chgres.sh   | 26 +-------------
 util/gdas_init/run_v14.chgres.sh       | 26 +-------------
 util/gdas_init/run_v16.chgres.sh       | 27 +-------------
 4 files changed, 52 insertions(+), 76 deletions(-)
 create mode 100755 util/gdas_init/copy_coldstart_files.sh

diff --git a/util/gdas_init/copy_coldstart_files.sh b/util/gdas_init/copy_coldstart_files.sh
new file mode 100755
index 000000000..08d7820bf
--- /dev/null
+++ b/util/gdas_init/copy_coldstart_files.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+copy_data()
+{
+
+set -x
+
+mkdir -p $SAVEDIR
+cp gfs_ctrl.nc $SAVEDIR
+
+for tile in 'tile1' 'tile2' 'tile3' 'tile4' 'tile5' 'tile6'
+do
+  cp out.atm.${tile}.nc  ${SAVEDIR}/gfs_data.${tile}.nc
+  cp out.sfc.${tile}.nc  ${SAVEDIR}/sfc_data.${tile}.nc
+done
+}
+
+set -x
+
+MEMBER=$1
+OUTDIR=$2
+yy=$3
+mm=$4
+dd=$5
+hh=$6
+INPUT_DATA_DIR=$7
+
+echo 'in new script'
+echo $MEMBER $OUTDIR
+
+if [ ${MEMBER} == 'gdas' ] || [ ${MEMBER} == 'gfs' ]; then
+  SUBDIR=$OUTDIR/${MEMBER}.${yy}${mm}${dd}/${hh}
+  rm -fr $SUBDIR
+  SAVEDIR=$SUBDIR/atmos/INPUT
+  copy_data
+  touch $SAVEDIR/../${MEMBER}.t${hh}z.loginc.txt
+  if [ ${MEMBER} == 'gdas' ]; then
+    cp ${INPUT_DATA_DIR}/*abias* $SAVEDIR/..
+    cp ${INPUT_DATA_DIR}/*radstat $SAVEDIR/..
+  fi
+else
+  SUBDIR=$OUTDIR/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER}
+  rm -fr $SUBDIR
+  SAVEDIR=$SUBDIR/atmos/INPUT
+  copy_data
+  touch $SAVEDIR/../enkfgdas.t${hh}z.loginc.txt
+fi
+
+exit 0
diff --git a/util/gdas_init/run_pre-v14.chgres.sh b/util/gdas_init/run_pre-v14.chgres.sh
index 3d7ebd9d3..4d64d1913 100755
--- a/util/gdas_init/run_pre-v14.chgres.sh
+++ b/util/gdas_init/run_pre-v14.chgres.sh
@@ -18,8 +18,6 @@ WORKDIR=${WORKDIR:-$OUTDIR/work.${MEMBER}}
 if [ "${MEMBER}" = "gdas" ] || [ "${MEMBER}" = "gfs" ]; then
   CTAR=${CRES_HIRES}
   INPUT_DATA_DIR="${EXTRACT_DIR}/${MEMBER}.${yy}${mm}${dd}/${hh}"
-  RADSTAT_DATA_DIR="${EXTRACT_DIR}/${MEMBER}.${yy}${mm}${dd}/${hh}"
-  OUTDIR=$OUTDIR/${MEMBER}.${yy}${mm}${dd}/${hh}/atmos
   if [ "${MEMBER}" = "gdas" ]; then
     ATMFILE="gdas1.t${hh}z.sanl"
     SFCFILE="gdas1.t${hh}z.sfcanl"
@@ -30,8 +28,6 @@ if [ "${MEMBER}" = "gdas" ] || [ "${MEMBER}" = "gfs" ]; then
 else  
   CTAR=${CRES_ENKF}
   INPUT_DATA_DIR="${EXTRACT_DIR}/enkf.${yy}${mm}${dd}/${hh}/mem${MEMBER}"
-  RADSTAT_DATA_DIR="${EXTRACT_DIR}/enkf.${yy}${mm}${dd}/${hh}/mem${MEMBER}"
-  OUTDIR=$OUTDIR/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER}/atmos
   ATMFILE="siganl_${yy}${mm}${dd}${hh}_mem${MEMBER}"
   SFCFILE="sfcanl_${yy}${mm}${dd}${hh}_mem${MEMBER}"
 fi
@@ -40,10 +36,6 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-rm -fr $OUTDIR
-mkdir -p $OUTDIR
-mkdir -p $OUTDIR/INPUT
-
 cat << EOF > fort.41
 
 &config
@@ -74,23 +66,7 @@ if [ $rc != 0 ]; then
   exit $rc
 fi
 
-mv gfs_ctrl.nc ${OUTDIR}/INPUT
-
-for tile in 'tile1' 'tile2' 'tile3' 'tile4' 'tile5' 'tile6'
-do
-  mv out.atm.${tile}.nc  ${OUTDIR}/INPUT/gfs_data.${tile}.nc
-  mv out.sfc.${tile}.nc  ${OUTDIR}/INPUT/sfc_data.${tile}.nc 
-done
-
-if [ "${MEMBER}" = "gdas" ]; then
-  cp ${RADSTAT_DATA_DIR}/*radstat* $OUTDIR
-  cp ${RADSTAT_DATA_DIR}/*abias* $OUTDIR
-  touch $OUTDIR/gdas.t${hh}z.loginc.txt
-elif [ "${MEMBER}" = "gfs" ]; then
-  touch $OUTDIR/gfs.t${hh}z.loginc.txt
-else
-  touch $OUTDIR/enkfgdas.t${hh}z.loginc.txt
-fi
+$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
 
 rm -fr $WORKDIR
 
diff --git a/util/gdas_init/run_v14.chgres.sh b/util/gdas_init/run_v14.chgres.sh
index 6df881f8b..a41832bf2 100755
--- a/util/gdas_init/run_v14.chgres.sh
+++ b/util/gdas_init/run_v14.chgres.sh
@@ -17,16 +17,12 @@ WORKDIR=${WORKDIR:-$OUTDIR/work.${MEMBER}}
 if [ "${MEMBER}" = "gdas" ] || [ "${MEMBER}" = "gfs" ]; then
   CTAR=${CRES_HIRES}
   INPUT_DATA_DIR="${EXTRACT_DIR}/${MEMBER}.${yy}${mm}${dd}/${hh}"
-  RADSTAT_DATA_DIR="${EXTRACT_DIR}/${MEMBER}.${yy}${mm}${dd}/${hh}"
-  OUTDIR=$OUTDIR/${MEMBER}.${yy}${mm}${dd}/${hh}/atmos
   ATMFILE="${MEMBER}.t${hh}z.atmanl.nemsio"
   SFCFILE="${MEMBER}.t${hh}z.sfcanl.nemsio"
   NSTFILE="${MEMBER}.t${hh}z.nstanl.nemsio"
 else  
   CTAR=${CRES_ENKF}
   INPUT_DATA_DIR="${EXTRACT_DIR}/enkf.${yy}${mm}${dd}/${hh}/mem${MEMBER}"
-  RADSTAT_DATA_DIR="${EXTRACT_DIR}/enkf.${yy}${mm}${dd}/${hh}/mem${MEMBER}"
-  OUTDIR=$OUTDIR/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER}/atmos
   ATMFILE="gdas.t${hh}z.ratmanl.mem${MEMBER}.nemsio"
   SFCFILE="gdas.t${hh}z.sfcanl.mem${MEMBER}.nemsio"
   NSTFILE="gdas.t${hh}z.nstanl.mem${MEMBER}.nemsio"
@@ -36,10 +32,6 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-rm -fr $OUTDIR
-mkdir -p $OUTDIR
-mkdir -p $OUTDIR/INPUT
-
 cat << EOF > fort.41
 
 &config
@@ -71,23 +63,7 @@ if [ $rc != 0 ]; then
   exit $rc
 fi
 
-mv gfs_ctrl.nc ${OUTDIR}/INPUT
-
-for tile in 'tile1' 'tile2' 'tile3' 'tile4' 'tile5' 'tile6'
-do
-  mv out.atm.${tile}.nc  ${OUTDIR}/INPUT/gfs_data.${tile}.nc
-  mv out.sfc.${tile}.nc  ${OUTDIR}/INPUT/sfc_data.${tile}.nc 
-done
-
-if [ "${MEMBER}" = "gdas" ]; then
-  cp ${RADSTAT_DATA_DIR}/*radstat* $OUTDIR
-  cp ${RADSTAT_DATA_DIR}/*abias* $OUTDIR
-  touch $OUTDIR/gdas.t${hh}z.loginc.txt
-elif [ "${MEMBER}" = "gfs" ]; then
-  touch $OUTDIR/gfs.t${hh}z.loginc.txt
-else
-  touch $OUTDIR/enkfgdas.t${hh}z.loginc.txt
-fi
+$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
 
 rm -fr $WORKDIR
 
diff --git a/util/gdas_init/run_v16.chgres.sh b/util/gdas_init/run_v16.chgres.sh
index d359b0361..7b5f12f57 100755
--- a/util/gdas_init/run_v16.chgres.sh
+++ b/util/gdas_init/run_v16.chgres.sh
@@ -1,18 +1,5 @@
 #!/bin/bash
 
-copy_data()
-{
-
-mkdir -p $SAVEDIR
-cp gfs_ctrl.nc $SAVEDIR
-
-for tile in 'tile1' 'tile2' 'tile3' 'tile4' 'tile5' 'tile6'
-do
-  cp out.atm.${tile}.nc  ${SAVEDIR}/gfs_data.${tile}.nc
-  cp out.sfc.${tile}.nc  ${SAVEDIR}/sfc_data.${tile}.nc 
-done
-}
-
 #---------------------------------------------------------------------------
 # Run chgres using v16 netcdf history data as input.  These history
 # files are part of the OPS v16 gfs/gdas/enkf tarballs, and the
@@ -89,19 +76,7 @@ if [ $rc != 0 ]; then
   exit $rc
 fi
 
-if [ ${MEMBER} == 'gdas' ] || [ ${MEMBER} == 'gfs' ]; then
-  SAVEDIR=$OUTDIR/${MEMBER}.${yy}${mm}${dd}/${hh}/atmos/INPUT
-  copy_data
-  touch $SAVEDIR/../${MEMBER}.t${hh}z.loginc.txt
-  if [ ${MEMBER} == 'gdas' ]; then
-    cp ${INPUT_DATA_DIR}/*abias* $SAVEDIR/..
-    cp ${INPUT_DATA_DIR}/*radstat $SAVEDIR/..
-  fi
-else  
-  SAVEDIR=$OUTDIR/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER}/atmos/INPUT
-  copy_data
-  touch $SAVEDIR/../enkfgdas.t${hh}z.loginc.txt
-fi
+$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
 
 rm -fr $WORKDIR
 

From 5d3b898350a0ca0efcbb2a18675da0d20bb93ae2 Mon Sep 17 00:00:00 2001
From: George Gayno <George.Gayno@noaa.gov>
Date: Mon, 13 Feb 2023 20:43:55 +0000
Subject: [PATCH 2/5] Updates required for v16 retro data and v15 data.

Fixes #772.
---
 util/gdas_init/copy_coldstart_files.sh | 21 +++++++++++++++-
 util/gdas_init/run_v15.chgres.gfs.sh   | 15 +-----------
 util/gdas_init/run_v15.chgres.sh       | 21 +---------------
 util/gdas_init/run_v16retro.chgres.sh  | 34 +-------------------------
 4 files changed, 23 insertions(+), 68 deletions(-)

diff --git a/util/gdas_init/copy_coldstart_files.sh b/util/gdas_init/copy_coldstart_files.sh
index 08d7820bf..523c9caf6 100755
--- a/util/gdas_init/copy_coldstart_files.sh
+++ b/util/gdas_init/copy_coldstart_files.sh
@@ -25,6 +25,10 @@ dd=$5
 hh=$6
 INPUT_DATA_DIR=$7
 
+if [ ${MEMBER} == 'hires' ]; then
+  MEMBER='gdas'
+fi
+
 echo 'in new script'
 echo $MEMBER $OUTDIR
 
@@ -33,11 +37,26 @@ if [ ${MEMBER} == 'gdas' ] || [ ${MEMBER} == 'gfs' ]; then
   rm -fr $SUBDIR
   SAVEDIR=$SUBDIR/atmos/INPUT
   copy_data
-  touch $SAVEDIR/../${MEMBER}.t${hh}z.loginc.txt
   if [ ${MEMBER} == 'gdas' ]; then
     cp ${INPUT_DATA_DIR}/*abias* $SAVEDIR/..
     cp ${INPUT_DATA_DIR}/*radstat $SAVEDIR/..
   fi
+  touch $SAVEDIR/../${MEMBER}.t${hh}z.loginc.txt
+elif [ ${MEMBER} == 'enkf' ]; then  # v16 retro data only.
+  MEMBER=1
+  while [ $MEMBER -le 80 ]; do
+    if [ $MEMBER -lt 10 ]; then
+      MEMBER_CH="00${MEMBER}"
+    else
+      MEMBER_CH="0${MEMBER}"
+    fi
+    SUBDIR=$OUTDIR/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER_CH}
+    rm -fr $SUBDIR
+    SAVEDIR=$SUBDIR/atmos/INPUT
+    copy_data
+    touch $SAVEDIR/../enkfgdas.t${hh}z.loginc.txt
+    MEMBER=$(( $MEMBER + 1 ))
+  done
 else
   SUBDIR=$OUTDIR/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER}
   rm -fr $SUBDIR
diff --git a/util/gdas_init/run_v15.chgres.gfs.sh b/util/gdas_init/run_v15.chgres.gfs.sh
index dfc35c2f7..ef3a6fcfa 100755
--- a/util/gdas_init/run_v15.chgres.gfs.sh
+++ b/util/gdas_init/run_v15.chgres.gfs.sh
@@ -15,7 +15,6 @@ WORKDIR=${WORKDIR:-$OUTDIR/work.gfs}
 
 CTAR=${CRES_HIRES}
 INPUT_DATA_DIR="${EXTRACT_DIR}/gfs.${yy}${mm}${dd}/${hh}"
-OUTDIR=$OUTDIR/gfs.${yy}${mm}${dd}/${hh}/atmos
 ATMFILE="gfs.t${hh}z.atmanl.nemsio"
 SFCFILE="gfs.t${hh}z.sfcanl.nemsio"
 
@@ -23,10 +22,6 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-rm -fr $OUTDIR
-mkdir -p $OUTDIR
-mkdir -p $OUTDIR/INPUT
-
 cat << EOF > fort.41
 
 &config
@@ -57,15 +52,7 @@ if [ $rc != 0 ]; then
   exit $rc
 fi
 
-mv gfs_ctrl.nc ${OUTDIR}/INPUT
-
-for tile in 'tile1' 'tile2' 'tile3' 'tile4' 'tile5' 'tile6'
-do
-  mv out.atm.${tile}.nc  ${OUTDIR}/INPUT/gfs_data.${tile}.nc
-  mv out.sfc.${tile}.nc  ${OUTDIR}/INPUT/sfc_data.${tile}.nc 
-done
-
-touch $OUTDIR/gfs.t${hh}z.loginc.txt
+$UFS_DIR/util/gdas_init/copy_coldstart_files.sh gfs $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
 
 rm -fr $WORKDIR
 
diff --git a/util/gdas_init/run_v15.chgres.sh b/util/gdas_init/run_v15.chgres.sh
index 5d59fadc9..501205e27 100755
--- a/util/gdas_init/run_v15.chgres.sh
+++ b/util/gdas_init/run_v15.chgres.sh
@@ -27,23 +27,17 @@ if [ ${MEMBER} == 'gdas' ]; then
   CTAR=${CRES_HIRES}
   INPUT_DATA_DIR="${EXTRACT_DIR}/gdas.${yy_d}${mm_d}${dd_d}/${hh_d}/RESTART"
   RADSTAT_DATA_DIR="${EXTRACT_DIR}/gdas.${yy}${mm}${dd}/${hh}"
-  OUTDIR=$OUTDIR/gdas.${yy}${mm}${dd}/${hh}/atmos
 else  
   CINP=${CINP:-"C384"}
   CTAR=${CRES_ENKF}
   INPUT_DATA_DIR="${EXTRACT_DIR}/enkfgdas.${yy_d}${mm_d}${dd_d}/${hh_d}/mem${MEMBER}/RESTART"
   RADSTAT_DATA_DIR="${EXTRACT_DIR}/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER}"
-  OUTDIR=$OUTDIR/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER}/atmos
 fi
 
 rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-rm -fr $OUTDIR
-mkdir -p $OUTDIR
-mkdir -p $OUTDIR/INPUT
-
 cat << EOF > fort.41
 
 &config
@@ -77,20 +71,7 @@ if [ $rc != 0 ]; then
   exit $rc
 fi
 
-mv gfs_ctrl.nc ${OUTDIR}/INPUT
-
-for tile in 'tile1' 'tile2' 'tile3' 'tile4' 'tile5' 'tile6'
-do
-  mv out.atm.${tile}.nc  ${OUTDIR}/INPUT/gfs_data.${tile}.nc
-  mv out.sfc.${tile}.nc  ${OUTDIR}/INPUT/sfc_data.${tile}.nc 
-done
-
-if [ ${MEMBER} == 'gdas' ]; then
-  cp ${RADSTAT_DATA_DIR}/* $OUTDIR
-  touch $OUTDIR/gdas.t${hh}z.loginc.txt
-else
-  touch $OUTDIR/enkfgdas.t${hh}z.loginc.txt
-fi
+$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $RADSTAT_DATA_DIR
 
 rm -fr $WORKDIR
 
diff --git a/util/gdas_init/run_v16retro.chgres.sh b/util/gdas_init/run_v16retro.chgres.sh
index d8b49c796..119f67217 100755
--- a/util/gdas_init/run_v16retro.chgres.sh
+++ b/util/gdas_init/run_v16retro.chgres.sh
@@ -1,18 +1,5 @@
 #!/bin/bash
 
-copy_data()
-{
-
-mkdir -p $SAVEDIR
-cp gfs_ctrl.nc $SAVEDIR
-
-for tile in 'tile1' 'tile2' 'tile3' 'tile4' 'tile5' 'tile6'
-do
-  cp out.atm.${tile}.nc  ${SAVEDIR}/gfs_data.${tile}.nc
-  cp out.sfc.${tile}.nc  ${SAVEDIR}/sfc_data.${tile}.nc 
-done
-}
-
 #---------------------------------------------------------------------------
 # Run chgres for gdas/enkf members using v16 parallel data as input.
 # The enkf data is not saved.  So the coldstart files for all
@@ -102,26 +89,7 @@ if [ $rc != 0 ]; then
   exit $rc
 fi
 
-if [ ${MEMBER} == 'hires' ]; then
-  SAVEDIR=$OUTDIR/gdas.${yy}${mm}${dd}/${hh}/atmos/INPUT
-  copy_data
-  cp $RADSTAT_DATA_DIR/*abias* $SAVEDIR/..
-  cp $RADSTAT_DATA_DIR/*radstat $SAVEDIR/..
-  touch $SAVEDIR/../gdas.t${hh}z.loginc.txt
-else  
-  MEMBER=1
-  while [ $MEMBER -le 80 ]; do
-  if [ $MEMBER -lt 10 ]; then
-    MEMBER_CH="00${MEMBER}"
-  else
-    MEMBER_CH="0${MEMBER}"
-  fi
-  SAVEDIR=$OUTDIR/enkfgdas.${yy}${mm}${dd}/${hh}/mem${MEMBER_CH}/atmos/INPUT
-  copy_data
-  touch $SAVEDIR/../enkfgdas.t${hh}z.loginc.txt
-  MEMBER=$(( $MEMBER + 1 ))
-  done
-fi
+$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $RADSTAT_DATA_DIR
 
 rm -fr $WORKDIR
 

From 721de59b6be6a1f7c134d58087ff8c63c6601e6d Mon Sep 17 00:00:00 2001
From: George Gayno <George.Gayno@noaa.gov>
Date: Wed, 15 Feb 2023 14:54:04 +0000
Subject: [PATCH 3/5] Remove some diagnostic print from new copy script.

Fixes #772.
---
 util/gdas_init/copy_coldstart_files.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/util/gdas_init/copy_coldstart_files.sh b/util/gdas_init/copy_coldstart_files.sh
index 523c9caf6..06b69cfdd 100755
--- a/util/gdas_init/copy_coldstart_files.sh
+++ b/util/gdas_init/copy_coldstart_files.sh
@@ -29,8 +29,9 @@ if [ ${MEMBER} == 'hires' ]; then
   MEMBER='gdas'
 fi
 
-echo 'in new script'
-echo $MEMBER $OUTDIR
+set +x
+echo 'COPY DATA TO OUTPUT DIRECTORY'
+set -x
 
 if [ ${MEMBER} == 'gdas' ] || [ ${MEMBER} == 'gfs' ]; then
   SUBDIR=$OUTDIR/${MEMBER}.${yy}${mm}${dd}/${hh}

From c9b2d94e7d1304b18eb88640460137527887faf2 Mon Sep 17 00:00:00 2001
From: George Gayno <George.Gayno@noaa.gov>
Date: Tue, 28 Feb 2023 21:02:17 +0000
Subject: [PATCH 4/5] Add new path variables.

Fixes #772.
---
 util/gdas_init/config                 | 6 +++++-
 util/gdas_init/run_v15.chgres.gfs.sh  | 6 +++---
 util/gdas_init/run_v15.chgres.sh      | 6 +++---
 util/gdas_init/run_v16retro.chgres.sh | 6 +++---
 4 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/util/gdas_init/config b/util/gdas_init/config
index 5bfe25a81..628e59c0d 100644
--- a/util/gdas_init/config
+++ b/util/gdas_init/config
@@ -79,6 +79,10 @@ OUTDIR=/lfs/h2/emc/stmp/$USER/gdas.init/output
 #---------------------------------------------------------
 # Dont touch anything below here.
 #---------------------------------------------------------
+
+GDAS_INIT_DIR=$UFS_DIR/util/gdas_init
+EXEC_DIR=$UFS_DIR/exec
+
 if [ "$use_v16retro" = "yes" ]; then
 
   gfs_ver=v16retro
@@ -113,4 +117,4 @@ else
 fi
 
 export EXTRACT_DIR yy mm dd hh UFS_DIR OUTDIR CRES_HIRES CRES_ENKF FRAC_ORO
-export LEVS gfs_ver
+export LEVS gfs_ver EXEC_DIR GDAS_INIT_DIR
diff --git a/util/gdas_init/run_v15.chgres.gfs.sh b/util/gdas_init/run_v15.chgres.gfs.sh
index 7e25b3be5..7cead7181 100755
--- a/util/gdas_init/run_v15.chgres.gfs.sh
+++ b/util/gdas_init/run_v15.chgres.gfs.sh
@@ -22,7 +22,7 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-source $UFS_DIR/util/gdas_init/set_fixed_files.sh
+source $GDAS_INIT_DIR/set_fixed_files.sh
 
 cat << EOF > fort.41
 
@@ -47,14 +47,14 @@ cat << EOF > fort.41
 /
 EOF
 
-$APRUN $UFS_DIR/exec/chgres_cube
+$APRUN $EXEC_DIR/chgres_cube
 rc=$?
 
 if [ $rc != 0 ]; then
   exit $rc
 fi
 
-$UFS_DIR/util/gdas_init/copy_coldstart_files.sh gfs $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
+$GDAS_INIT_DIR/copy_coldstart_files.sh gfs $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
 
 rm -fr $WORKDIR
 
diff --git a/util/gdas_init/run_v15.chgres.sh b/util/gdas_init/run_v15.chgres.sh
index bf8e9dc3b..ab2dfe530 100755
--- a/util/gdas_init/run_v15.chgres.sh
+++ b/util/gdas_init/run_v15.chgres.sh
@@ -38,7 +38,7 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-source $UFS_DIR/util/gdas_init/set_fixed_files.sh
+source $GDAS_INIT_DIR/set_fixed_files.sh
 
 cat << EOF > fort.41
 
@@ -66,14 +66,14 @@ cat << EOF > fort.41
 /
 EOF
 
-$APRUN $UFS_DIR/exec/chgres_cube
+$APRUN $EXEC_DIR/chgres_cube
 rc=$?
 
 if [ $rc != 0 ]; then
   exit $rc
 fi
 
-$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $RADSTAT_DATA_DIR
+$GDAS_INIT_DIR/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $RADSTAT_DATA_DIR
 
 rm -fr $WORKDIR
 
diff --git a/util/gdas_init/run_v16retro.chgres.sh b/util/gdas_init/run_v16retro.chgres.sh
index 7deae51f5..37b75728d 100755
--- a/util/gdas_init/run_v16retro.chgres.sh
+++ b/util/gdas_init/run_v16retro.chgres.sh
@@ -56,7 +56,7 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-source $UFS_DIR/util/gdas_init/set_fixed_files.sh
+source $GDAS_INIT_DIR/set_fixed_files.sh
 
 cat << EOF > fort.41
 
@@ -84,14 +84,14 @@ cat << EOF > fort.41
 /
 EOF
 
-$APRUN $UFS_DIR/exec/chgres_cube
+$APRUN $EXEC_DIR/chgres_cube
 rc=$?
 
 if [ $rc != 0 ]; then
   exit $rc
 fi
 
-$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $RADSTAT_DATA_DIR
+$GDAS_INIT_DIR/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $RADSTAT_DATA_DIR
 
 rm -fr $WORKDIR
 

From 7b9506866b3f1cdec2ad8ddd14dcec1ede96c2aa Mon Sep 17 00:00:00 2001
From: George Gayno <George.Gayno@noaa.gov>
Date: Wed, 1 Mar 2023 15:55:32 +0000
Subject: [PATCH 5/5] Add new path variables to remaining run scripts.

Fixes #772.
---
 util/gdas_init/copy_coldstart_files.sh | 3 +++
 util/gdas_init/run_pre-v14.chgres.sh   | 6 +++---
 util/gdas_init/run_v14.chgres.sh       | 6 +++---
 util/gdas_init/run_v16.chgres.sh       | 6 +++---
 4 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/util/gdas_init/copy_coldstart_files.sh b/util/gdas_init/copy_coldstart_files.sh
index 06b69cfdd..deeb0a29a 100755
--- a/util/gdas_init/copy_coldstart_files.sh
+++ b/util/gdas_init/copy_coldstart_files.sh
@@ -1,5 +1,8 @@
 #!/bin/bash
 
+# Copy files from the working directory to the
+# output directory.
+
 copy_data()
 {
 
diff --git a/util/gdas_init/run_pre-v14.chgres.sh b/util/gdas_init/run_pre-v14.chgres.sh
index f09a497df..51290203e 100755
--- a/util/gdas_init/run_pre-v14.chgres.sh
+++ b/util/gdas_init/run_pre-v14.chgres.sh
@@ -36,7 +36,7 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-source $UFS_DIR/util/gdas_init/set_fixed_files.sh
+source $GDAS_INIT_DIR/set_fixed_files.sh
 
 cat << EOF > fort.41
 
@@ -61,14 +61,14 @@ cat << EOF > fort.41
 /
 EOF
 
-$APRUN $UFS_DIR/exec/chgres_cube
+$APRUN $EXEC_DIR/chgres_cube
 rc=$?
 
 if [ $rc != 0 ]; then
   exit $rc
 fi
 
-$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
+$GDAS_INIT_DIR/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
 
 rm -fr $WORKDIR
 
diff --git a/util/gdas_init/run_v14.chgres.sh b/util/gdas_init/run_v14.chgres.sh
index 13fcade9a..c1598a7d5 100755
--- a/util/gdas_init/run_v14.chgres.sh
+++ b/util/gdas_init/run_v14.chgres.sh
@@ -32,7 +32,7 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-source $UFS_DIR/util/gdas_init/set_fixed_files.sh
+source $GDAS_INIT_DIR/set_fixed_files.sh
 
 cat << EOF > fort.41
 
@@ -58,14 +58,14 @@ cat << EOF > fort.41
 /
 EOF
 
-$APRUN $UFS_DIR/exec/chgres_cube
+$APRUN $EXEC_DIR/chgres_cube
 rc=$?
 
 if [ $rc != 0 ]; then
   exit $rc
 fi
 
-$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
+$GDAS_INIT_DIR/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
 
 rm -fr $WORKDIR
 
diff --git a/util/gdas_init/run_v16.chgres.sh b/util/gdas_init/run_v16.chgres.sh
index 38f8f3c2f..5525afdcb 100755
--- a/util/gdas_init/run_v16.chgres.sh
+++ b/util/gdas_init/run_v16.chgres.sh
@@ -46,7 +46,7 @@ rm -fr $WORKDIR
 mkdir -p $WORKDIR
 cd $WORKDIR
 
-source $UFS_DIR/util/gdas_init/set_fixed_files.sh
+source $GDAS_INIT_DIR/set_fixed_files.sh
 
 cat << EOF > fort.41
 
@@ -71,14 +71,14 @@ cat << EOF > fort.41
 /
 EOF
 
-$APRUN $UFS_DIR/exec/chgres_cube
+$APRUN $EXEC_DIR/chgres_cube
 rc=$?
 
 if [ $rc != 0 ]; then
   exit $rc
 fi
 
-$UFS_DIR/util/gdas_init/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
+$GDAS_INIT_DIR/copy_coldstart_files.sh $MEMBER $OUTDIR $yy $mm $dd $hh $INPUT_DATA_DIR
 
 rm -fr $WORKDIR