From 2da9604475f046ae374412e479535ef294db8d67 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Tue, 27 Sep 2022 09:44:56 +0000
Subject: [PATCH 01/13] Rename post scripts

Rename post scripts to remove the unnecessary "ncep" qualifier.
---
 ...OBAL_ATMOS_NCEPPOST => JGLOBAL_ATMOS_POST} |   2 +-
 jobs/rocoto/post.sh                           |   2 +-
 parm/config/config.post                       |   8 +-
 ...atmos_nceppost.sh => exgdas_atmos_post.sh} |   2 +-
 ..._atmos_nceppost.sh => exgfs_atmos_post.sh} |   2 +-
 sorc/link_workflow.sh                         |   4 +-
 ush/{gfs_nceppost.sh => gfs_post.sh}          |  16 +-
 ush/global_nceppost.sh                        | 476 ------------------
 8 files changed, 18 insertions(+), 494 deletions(-)
 rename jobs/{JGLOBAL_ATMOS_NCEPPOST => JGLOBAL_ATMOS_POST} (99%)
 rename scripts/{exgdas_atmos_nceppost.sh => exgdas_atmos_post.sh} (99%)
 rename scripts/{exgfs_atmos_nceppost.sh => exgfs_atmos_post.sh} (99%)
 rename ush/{gfs_nceppost.sh => gfs_post.sh} (96%)
 delete mode 100755 ush/global_nceppost.sh

diff --git a/jobs/JGLOBAL_ATMOS_NCEPPOST b/jobs/JGLOBAL_ATMOS_POST
similarity index 99%
rename from jobs/JGLOBAL_ATMOS_NCEPPOST
rename to jobs/JGLOBAL_ATMOS_POST
index 56d6ca602e5..73b8c72876b 100755
--- a/jobs/JGLOBAL_ATMOS_NCEPPOST
+++ b/jobs/JGLOBAL_ATMOS_POST
@@ -117,7 +117,7 @@ export SLEEP_INT=5
 ###############################################################
 # Run relevant exglobal script
 
-$SCRgfs/ex${RUN}_atmos_nceppost.sh
+$SCRgfs/ex${RUN}_atmos_post.sh
 status=$?
 [[ $status -ne 0 ]] && exit $status
 
diff --git a/jobs/rocoto/post.sh b/jobs/rocoto/post.sh
index b32e8c511d7..a6dfb0fbaf4 100755
--- a/jobs/rocoto/post.sh
+++ b/jobs/rocoto/post.sh
@@ -27,7 +27,7 @@ fi
 #---------------------------------------------------------------
 for fhr in $fhrlst; do
     export post_times=$fhr
-    $HOMEgfs/jobs/JGLOBAL_ATMOS_NCEPPOST
+    $HOMEgfs/jobs/JGLOBAL_ATMOS_POST
     status=$?
     [[ $status -ne 0 ]] && exit $status
 done
diff --git a/parm/config/config.post b/parm/config/config.post
index a545f0fafcf..cdea64e2a31 100755
--- a/parm/config/config.post
+++ b/parm/config/config.post
@@ -19,13 +19,13 @@ if [ $OUTPUT_FILE = "netcdf" ]; then
     export MODEL_OUT_FORM=netcdfpara
 fi
 
-# Post driver job that calls gfs_nceppost.sh and downstream jobs
-export POSTJJOBSH="$HOMEpost/jobs/JGLOBAL_NCEPPOST"
+# Post driver job that calls gfs_post.sh and downstream jobs
+export POSTJJOBSH="$HOMEpost/jobs/JGLOBAL_POST"
 export GFSDOWNSH="$HOMEpost/ush/fv3gfs_downstream_nems.sh"
 export GFSDWNSH="$HOMEpost/ush/fv3gfs_dwn_nems.sh"
 
-export POSTGPSH="$HOMEpost/ush/gfs_nceppost.sh"
-export POSTGPEXEC="$HOMEpost/exec/gfs_ncep_post"
+export POSTGPSH="$HOMEpost/ush/gfs_post.sh"
+export POSTGPEXEC="$HOMEpost/exec/upp.x"
 export GOESF=NO                              # goes image
 export FLXF=YES                               # grib2 flux file written by post
 
diff --git a/scripts/exgdas_atmos_nceppost.sh b/scripts/exgdas_atmos_post.sh
similarity index 99%
rename from scripts/exgdas_atmos_nceppost.sh
rename to scripts/exgdas_atmos_post.sh
index 005911db6ae..4de4ffaf717 100755
--- a/scripts/exgdas_atmos_nceppost.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -28,7 +28,7 @@ source "$HOMEgfs/ush/preamble.sh"
 
 cd $DATA
 
-export POSTGPSH=${POSTGPSH:-$USHgfs/gfs_nceppost.sh}
+export POSTGPSH=${POSTGPSH:-$USHgfs/gfs_post.sh}
 export GFSDOWNSH=${GFSDOWNSH:-$USHgfs/fv3gfs_downstream_nems.sh}
 export GFSDWNSH=${GFSDWNSH:-$USHgfs/fv3gfs_dwn_nems.sh}
 export TRIMRH=${TRIMRH:-$USHgfs/trim_rh.sh}
diff --git a/scripts/exgfs_atmos_nceppost.sh b/scripts/exgfs_atmos_post.sh
similarity index 99%
rename from scripts/exgfs_atmos_nceppost.sh
rename to scripts/exgfs_atmos_post.sh
index ae94472aeba..92bb8b5463a 100755
--- a/scripts/exgfs_atmos_nceppost.sh
+++ b/scripts/exgfs_atmos_post.sh
@@ -41,7 +41,7 @@ source "$HOMEgfs/ush/preamble.sh"
 cd $DATA
 
 # specify model output format type: 4 for nemsio, 3 for sigio
-export POSTGPSH=${POSTGPSH:-$USHgfs/gfs_nceppost.sh}
+export POSTGPSH=${POSTGPSH:-$USHgfs/gfs_post.sh}
 export GFSDOWNSH=${GFSDOWNSH:-$USHgfs/fv3gfs_downstream_nems.sh}
 export GFSDOWNSHF=${GFSDOWNSHF:-$USHgfs/inter_flux.sh}
 export GFSDWNSH=${GFSDWNSH:-$USHgfs/fv3gfs_dwn_nems.sh}
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 6ce9775dd2b..4656c4aaa26 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -205,8 +205,8 @@ done
 [[ -s ufs_model.x ]] && rm -f ufs_model.x
 $LINK ../sorc/ufs_model.fd/tests/ufs_model.x .
 
-[[ -s gfs_ncep_post ]] && rm -f gfs_ncep_post
-$LINK ../sorc/upp.fd/exec/upp.x gfs_ncep_post
+[[ -s upp.x ]] && rm -f upp.x
+$LINK ../sorc/upp.fd/exec/upp.x .
 
 if [ -d ${pwd}/gfs_wafs.fd ]; then
     for wafsexe in \
diff --git a/ush/gfs_nceppost.sh b/ush/gfs_post.sh
similarity index 96%
rename from ush/gfs_nceppost.sh
rename to ush/gfs_post.sh
index a8bee62d4d7..c38edfe4ec2 100755
--- a/ush/gfs_nceppost.sh
+++ b/ush/gfs_post.sh
@@ -3,7 +3,7 @@
 ################################################################################
 ####  UNIX Script Documentation Block
 #                      .                                             .
-# Script name:         gfs_nceppost.sh           
+# Script name:         gfs_post.sh           
 # Script description:  Posts the global pressure GRIB file
 #
 # Author:        Mark Iredell       Org: NP23         Date: 1999-05-01
@@ -19,8 +19,8 @@
 # 2012-06-04  Jun Wang: add grib2 option
 # 2015-03-20  Lin Gan: add Perl for Post XML performance upgrade
 # 2016-02-08  Lin Gan: Modify to use Vertical Structure
-# 2018-02-05  Wen Meng: For EE2 standard, create gfs_nceppost.sh based
-#                  global_nceppost.sh and change EXECglobal to EXECgfs;
+# 2018-02-05  Wen Meng: For EE2 standard, create gfs_post.sh based
+#                  global_post.sh and change EXECglobal to EXECgfs;
 #                  Remove legacy setting for reading non-nemsio model output
 #                  and generating grib1 data
 # 2019-06-02  Wen Meng: Remove the links of gfs fix files. 
@@ -63,7 +63,7 @@
 #		    default to to ${USHglobal}/global_chgres.sh
 #     SIGLEVEL      optional: the coordinate text file
 #		    default to to /nwprod/fix/global_hyblev.l${LEVS}.txt
-##### Chuang: Add new imported Shell Variable for ncep post
+##### Chuang: Add new imported Shell Variable for post
 #     OUTTYP        Output file type read in by post 
 #                   1: if user has a sigma file and needs post to run chgres to convert to gfs io file
 #                   2: if user already has a gfs io file
@@ -71,7 +71,7 @@
 #                   0: if user wishes to generate both gfsio and sigma files
 #                   4: if user uses post to read nemsio file directly
 #     VDATE         Verifying date 10 digits yyyymmddhh
-#     GFSOUT        Optional, output file name from chgres which is input file name to nceppost 
+#     GFSOUT        Optional, output file name from chgres which is input file name to post 
 #                   if model already runs gfs io, make sure GFSOUT is linked to the gfsio file
 #     CTLFILE       Optional, Your version of control file if not using operational one
 #     OVERPARMEXEC  Optional, the executable for changing Grib KPDS ID
@@ -106,7 +106,7 @@
 #     XC            Suffix to add to executables
 #                   defaults to none
 #     POSTGPEXEC    Global post executable
-#                   defaults to ${EXECglobal}/ncep_post
+#                   defaults to ${EXECglobal}/upp.x
 #     GRBINDEX      GRIB index maker
 #                   defaults to ${EXECUTIL}/grbindex$XC
 #     POSTGPLIST    File containing further namelist inputs
@@ -210,7 +210,7 @@ export DATA=${DATA:-$(pwd)}
 #  Filenames.
 export MP=${MP:-$([[ ${LOADL_STEP_TYPE:-SERIAL} = PARALLEL ]]&&echo "p"||echo "s")}
 export XC=${XC:-}
-export POSTGPEXEC=${POSTGPEXEC:-${EXECgfs}/gfs_ncep_post}
+export POSTGPEXEC=${POSTGPEXEC:-${EXECgfs}/upp.x}
 export OVERPARMEXEC=${OVERPARMEXEC:-${EXECgfs}/overparm_grib}
 export POSTGPLIST=${POSTGPLIST:-/dev/null}
 export INISCRIPT=${INISCRIPT:-}
@@ -340,7 +340,7 @@ export CTL=$(basename $CTLFILE)
 ln -sf griddef.out fort.110
 cp ${PARMpost}/nam_micro_lookup.dat ./eta_micro_lookup.dat
 
-echo "gfs_nceppost.sh OMP_NUM_THREADS= $OMP_NUM_THREADS"
+echo "gfs_post.sh OMP_NUM_THREADS= $OMP_NUM_THREADS"
 ${APRUN:-mpirun.lsf} $POSTGPEXEC < itag > outpost_gfs_${VDATE}_${CTL}
 
 export ERR=$?
diff --git a/ush/global_nceppost.sh b/ush/global_nceppost.sh
deleted file mode 100755
index 2c0711c57f4..00000000000
--- a/ush/global_nceppost.sh
+++ /dev/null
@@ -1,476 +0,0 @@
-#! /usr/bin/env bash
-
-################################################################################
-####  UNIX Script Documentation Block
-#                      .                                             .
-# Script name:         global_nceppost.sh           
-# Script description:  Posts the global pressure GRIB file
-#
-# Author:        Mark Iredell       Org: NP23         Date: 1999-05-01
-#
-# Abstract: This script reads a single global GFS IO file and (optionally)
-#   a global flux file and creates a global pressure GRIB file.
-#   The resolution and generating code of the output GRIB file can also
-#   be set in the argument list.
-#
-# Script history log:
-# 1999-05-01  Mark Iredell
-# 2007-04-04  Huiya Chuang: Modify the script to run unified post
-# 2012-06-04  Jun Wang: add grib2 option
-# 2015-03-20  Lin Gan: add Perl for Post XML performance upgrade
-# 2016-02-08  Lin Gan: Modify to use Vertical Structure
-#
-# Usage:  global_postgp.sh SIGINP FLXINP FLXIOUT PGBOUT PGIOUT IGEN
-#
-#   Input script positional parameters:
-#     1             Input sigma file
-#                   defaults to $SIGINP
-#     2             Input flux file
-#                   defaults to $FLXINP
-#     3             Output flux index file
-#                   defaults to $FLXIOUT
-#     4             Output pressure GRIB file
-#                   defaults to $PGBOUT
-#     5             Output pressure GRIB index file
-#                   defaults to $PGIOUT, then to none
-#     8             Model generating code,
-#                   defaults to $IGEN, then to input sigma generating code
-#
-#   Imported Shell Variables:
-#     SIGINP        Input sigma file
-#                   overridden by $1
-#     FLXINP        Input flux file
-#                   overridden by $2
-#     FLXIOUT       Output flux index file
-#                   overridden by $3
-#     PGBOUT        Output pressure GRIB file
-#                   overridden by $4. If not defined,
-#                   post will use the filename specified in
-#                   the control file
-#     PGIOUT        Output pressure GRIB index file
-#                   overridden by $5; defaults to none
-#     IGEN          Model generating code
-#                   overridden by $8; defaults to input sigma generating code
-##### Moorthi: Add new imported shell variable for running chgres
-#     CHGRESSH      optional: the script to run chgres
-#		    default to to ${USHglobal}/global_chgres.sh
-#     SIGLEVEL      optional: the coordinate text file
-#		    default to to $HOMEgfs/fix/global_hyblev.l${LEVS}.txt
-##### Chuang: Add new imported Shell Variable for ncep post
-#     OUTTYP        Output file type read in by post 
-#                   1: if user has a sigma file and needs post to run chgres to convert to gfs io file
-#                   2: if user already has a gfs io file
-#                   3: if user uses post to read sigma file directly
-#                   0: if user wishes to generate both gfsio and sigma files
-#                   4: if user uses post to read nemsio file directly
-#     VDATE         Verifying date 10 digits yyyymmddhh
-#     GFSOUT        Optional, output file name from chgres which is input file name to nceppost 
-#                   if model already runs gfs io, make sure GFSOUT is linked to the gfsio file
-#     CTLFILE       Optional, Your version of control file if not using operational one
-#     OVERPARMEXEC  Optional, the executable for changing Grib KPDS ID
-#		    default to to ${EXECglobal}/overparm_grib 
-#     CHGRESTHREAD  Optional, speed up chgres by using multiple threads 
-#		    default to 1
-#     FILTER        Optional, set to 1 to filter SLP and 500 mb height using copygb
-#     D3DINP        Optional, Inout D3D file, if not defined, post will run
-#                   without processing D3D file
-#     D3DOUT        Optional, output D3D file, if not defined, post will
-#                   use the file name specified in the control file
-#     IPVOUT        Optional, output IPV file, if not defined, post will
-#                   use the file name specified in the control file
-#    GENPSICHI      Optional, set to YES will generate psi and chi and
-#                   append it to the end of PGBOUT.  Default to NO
-#    GENPSICHIEXE   Optional, specify where executable is for generating
-#                   psi and chi.
-########################################################################       
-#     EXECglobal    Directory for global executables
-#                   defaults to $HOMEgfs/exec
-#     USHglobal     Directory for global scripts
-#                   defaults to $HOMEgfs/ush
-#     DATA          working directory
-#                   (if nonexistent will be made, used and deleted)
-#                   defaults to current working directory
-#     MP            Multi-processing type ("p" or "s")
-#                   defaults to "p", or "s" if LOADL_STEP_TYPE is not PARALLEL
-#     XC            Suffix to add to executables
-#                   defaults to none
-#     POSTGPEXEC    Global post executable
-#                   defaults to ${EXECglobal}/ncep_post
-#     GRBINDEX      GRIB index maker
-#     ANOMCATSH     Global anomaly GRIB script
-#                   defaults to ${USHglobal/global_anomcat.sh
-#     POSTGPLIST    File containing further namelist inputs
-#                   defaults to /dev/null
-#     INISCRIPT     Preprocessing script
-#                   defaults to none
-#     LOGSCRIPT     Log posting script
-#                   defaults to none
-#     ERRSCRIPT     Error processing script
-#                   defaults to 'eval [[ $err = 0 ]]'
-#     ENDSCRIPT     Postprocessing script
-#                   defaults to none
-#     POSTGPVARS    Other namelist inputs to the global post executable
-#                   such as IDRT,KO,PO,KTT,KT,PT,KZZ,ZZ,
-#                           NCPUS,MXBIT,IDS,POB,POT,MOO,MOOA,MOW,MOWA,
-#                           ICEN,ICEN2,IENST,IENSI
-#                   defaults to none set
-#     NTHREADS      Number of threads
-#                   defaults to 1
-#     NTHSTACK      Size of stack per thread
-#                   defaults to 64000000
-#     VERBOSE       Verbose flag (YES or NO)
-#                   defaults to NO
-#     PGMOUT        Executable standard output
-#                   defaults to $pgmout, then to '&1'
-#     PGMERR        Executable standard error
-#                   defaults to $pgmerr, then to '&1'
-#     pgmout        Executable standard output default
-#     pgmerr        Executable standard error default
-#     REDOUT        standard output redirect ('1>' or '1>>')
-#                   defaults to '1>', or to '1>>' to append if $PGMOUT is a file
-#     REDERR        standard error redirect ('2>' or '2>>')
-#                   defaults to '2>', or to '2>>' to append if $PGMERR is a file
-#
-#   Exported Shell Variables:
-#     PGM           Current program name
-#     pgm
-#     ERR           Last return code
-#     err
-#
-#   Modules and files referenced:
-#     scripts    : $INISCRIPT
-#                  $LOGSCRIPT
-#                  $ERRSCRIPT
-#                  $ENDSCRIPT
-#                  $ANOMCATSH
-#
-#     programs   : $POSTGPEXEC
-#                  $GRBINDEX
-#
-#     input data : $1 or $SIGINP
-#                  $2 or $SFCINP
-#                  $POSTGPLIST
-#
-#     output data: $3 or $FLXIOUT
-#                  $4 or $PGBOUT
-#                  $5 or $PGIOUT
-#                  $PGMOUT
-#                  $PGMERR
-#
-#     scratch    : ${DATA}/postgp.inp.sig
-#                  ${DATA}/postgp.inp.flx
-#                  ${DATA}/postgp.out.pgb
-#
-# Remarks:
-#
-#   Condition codes
-#      0 - no problem encountered
-#     >0 - some problem encountered
-#
-#   Control variable resolution priority
-#     1 Command line argument.
-#     2 Environment variable.
-#     3 Inline default.
-#
-# Attributes:
-#   Language: POSIX shell
-#   Machine: IBM SP
-#
-####
-################################################################################
-#  Set environment.
-source "$HOMEgfs/ush/preamble.sh"
-
-#  Command line arguments.
-export SIGINP=${1:-${SIGINP}}
-export FLXINP=${2:-${FLXINP}}
-export FLXIOUT=${3:-${FLXIOUT}}
-export PGBOUT=${4:-${PGBOUT}}
-#export PGIOUT=${5:-${PGIOUT}}
-export PGIOUT=${PGIOUT:-pgb.idx}
-export IO=${6:-${IO:-0}}
-export JO=${7:-${JO:-0}}
-export IGEN=${8:-${IGEN:-0}}
-#  Directories.
-export EXECglobal=${EXECglobal:-$HOMEgfs/exec}
-export USHglobal=${USHglobal:-$HOMEgfs/ush}
-export DATA=${DATA:-$(pwd)}
-#  Filenames.
-export MP=${MP:-$([[ $LOADL_STEP_TYPE = PARALLEL ]]&&echo "p"||echo "s")}
-export XC=${XC}
-export POSTGPEXEC=${POSTGPEXEC:-${EXECglobal}/ncep_post}
-export OVERPARMEXEC=${OVERPARMEXEC:-${EXECglobal}/overparm_grib}
-export ANOMCATSH=${ANOMCATSH:-${USHglobal}/global_anomcat.sh}
-export CHGRESSH=${CHGRESSH:-${USHglobal}/global_chgres.sh}
-export POSTGPLIST=${POSTGPLIST:-/dev/null}
-export INISCRIPT=${INISCRIPT}
-export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
-export LOGSCRIPT=${LOGSCRIPT}
-export ENDSCRIPT=${ENDSCRIPT}
-export GFSOUT=${GFSOUT:-gfsout}
-export CTLFILE=${CTLFILE:-$HOMEgfs/parm/post/postcntrl_gfs.xml}
-export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
-export GRIBVERSION=${GRIBVERSION:-'grib1'}
-#  Other variables.
-export POSTGPVARS=${POSTGPVARS}
-export NTHREADS=${NTHREADS:-1}
-export NTHSTACK=${NTHSTACK:-64000000}
-export PGMOUT=${PGMOUT:-${pgmout:-'&1'}}
-export PGMERR=${PGMERR:-${pgmerr:-'&2'}}
-export CHGRESTHREAD=${CHGRESTHREAD:-1}
-export FILTER=${FILTER:-1}
-export GENPSICHI=${GENPSICHI:-NO}
-export GENPSICHIEXE=${GENPSICHIEXE:-${EXECglobal}/genpsiandchi}
-export ens=${ens:-NO}
-#export D3DINP=${D3DINP:-/dev/null}
-l=$(echo $PGMOUT | xargs | cut -c1)
-[[ $l = '&' ]]&&a=''||a='>'
-export REDOUT=${REDOUT:-'1>'$a}
-l=$(echo $PGMERR | xargs | cut -c1)
-[[ $l = '&' ]]&&a=''||a='>'
-export REDERR=${REDERR:-'2>'$a}
-################################################################################
-
-# Chuang: Run chgres if OUTTYP=1 or 0
-
-export APRUN=${APRUNP:-${APRUN:-""}}
-
-# exit if SIGINP does not exist
-if [ ${OUTTYP} -le 3 ] ; then
-	if [ ! -s $SIGINP ] ; then
-		echo "sigma file not found, exitting"
-		exit 111
-	fi
-fi
-
-export SIGHDR=${SIGHDR:-$HOMEgfs/exec/global_sighdr}
-export IDRT=${IDRT:-4}
-
-if [ ${OUTTYP} -le 1 ] ; then
-	export JCAP=${JCAP:-$(echo jcap|$SIGHDR ${SIGINP})}
-	export LEVS=${LEVS:-$(echo levs|$SIGHDR ${SIGINP})}
-	export IDVC=${IDVC:-$(echo idvc|$SIGHDR ${SIGINP})}
-	export IDVM=${IDVM:-$(echo idvm|$SIGHDR ${SIGINP})}
-	export NVCOORD=${NVCOORD:-$(echo nvcoord|$SIGHDR ${SIGINP})}
-	export IVSSIG=${IVSSIG:-$(echo ivs|$SIGHDR ${SIGINP})}
-	export LATCH=${LATCH:-8}
-	if [ ${OUTTYP} -eq 1 ] ; then 
-		export CHGRESVARS="IDVC=$IDVC,IDVM=$IDVM,NVCOORD=$NVCOORD,IVSSIG=$IVSSIG,LATCH=$LATCH,"  
-	elif [ ${OUTTYP} -eq 0 ] ; then
-		export CHGRESVARS="LATCH=$LATCH,$CHGRESVARS"
-	fi 
-	#export SIGLEVEL=${SIGLEVEL:-""}
-	export SIGLEVEL=${SIGLEVEL:-"$HOMEgfs/fix/global_hyblev.l${LEVS}.txt"}
-	# specify threads for running chgres
-	export OMP_NUM_THREADS=$CHGRESTHREAD 
-	export NTHREADS=$OMP_NUM_THREADS
-	if [ ${JCAP} -eq 574 -a ${IDRT} -eq 4 ]; then
-		export NTHSTACK=1024000000
-	fi   
-	export XLSMPOPTS="parthds=$NTHREADS:stack=$NTHSTACK"
-
-	$CHGRESSH
-
-	export ERR=$?
-	export err=$ERR
-	$ERRSCRIPT||exit 1
-
-# run post to read sigma file directly if OUTTYP=3
-elif [ ${OUTTYP} -eq 3 ] ; then
-	export LONB=${LONB:-$(echo lonb|$SIGHDR ${SIGINP})}
-	export LATB=${LATB:-$(echo latb|$SIGHDR ${SIGINP})}
-	export MODEL_OUT_FORM=sigio
-	export GFSOUT=${SIGINP}
-
-# run post to read nemsio file if OUTTYP=4
-elif [ ${OUTTYP} -eq 4 ] ; then
-	export nemsioget=${nemsioget:-$EXECglobal/nemsio_get}
-	export LONB=${LONB:-$($nemsioget $NEMSINP dimx | awk '{print $2}')}
-	export LATB=${LATB:-$($nemsioget $NEMSINP dimy | awk '{print $2}')}
-	export JCAP=${JCAP:-$(expr $LATB - 2)}
-	# export LONB=${LONB:-$($nemsioget $NEMSINP lonf |grep -i "lonf" |awk -F"= " '{print $2}' |awk -F" " '{print $1}')}
-	# export LATB=${LATB:-$($nemsioget $NEMSINP latg |grep -i "latg" |awk -F"= " '{print $2}' |awk -F" " '{print $1}')}
-	# export JCAP=${JCAP:-$($nemsioget $NEMSINP jcap |grep -i "jcap" |awk -F"= " '{print $2}' |awk -F" " '{print $1}')}
-
-	export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
-	export GFSOUT=${NEMSINP}
-	ln -sf $FIXglobal/fix_am/global_lonsperlat.t${JCAP}.${LONB}.${LATB}.txt  ./lonsperlat.dat 
-	ln -sf $FIXglobal/fix_am/global_hyblev.l${LEVS}.txt                      ./global_hyblev.txt
-fi
-
-# allow threads to use threading in Jim's sp lib
-# but set default to 1 
-export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
-
-pwd=$(pwd)
-if [[ -d $DATA ]]; then
-	mkdata=NO
-else
-	mkdir -p $DATA
-	mkdata=YES
-fi
-cd $DATA||exit 99
-################################################################################
-#  Post GRIB
-export PGM=$POSTGPEXEC
-export pgm=$PGM
-$LOGSCRIPT
-cat <<-EOF >postgp.inp.nml$$
-	&NAMPGB
-	$POSTGPVARS
-EOF
-
-cat <<-EOF >>postgp.inp.nml$$
-	/
-EOF
-
-if [[ "$VERBOSE" = "YES" ]]; then
-	cat postgp.inp.nml$$
-fi
-
-# making the time stamp format for ncep post
-export YY=$(echo $VDATE | cut -c1-4)
-export MM=$(echo $VDATE | cut -c5-6)
-export DD=$(echo $VDATE | cut -c7-8)
-export HH=$(echo $VDATE | cut -c9-10)
-
-cat > itag <<-EOF
-	$GFSOUT
-	${MODEL_OUT_FORM}
-	${GRIBVERSION}
-	${YY}-${MM}-${DD}_${HH}:00:00
-	GFS
-	$FLXINP
-	$D3DINP
-EOF
-
-cat postgp.inp.nml$$ >> itag
-
-cat itag
-
-rm -f fort.*
-
-#ln -sf $SIGINP     postgp.inp.sig$$
-#ln -sf $FLXINP     postgp.inp.flx$$
-#ln -sf $PGBOUT     postgp.out.pgb$$
-
-# change model generating Grib number 
-if [ ${GRIBVERSION} = grib1 ]; then
-	if [ ${IGEN} -le 9 ] ; then
-		cat ${CTLFILE}|sed s:00082:0000${IGEN}:>./gfs_cntrl.parm
-	elif [ ${IGEN} -le 99 ] ; then
-		cat ${CTLFILE}|sed s:00082:000${IGEN}:>./gfs_cntrl.parm
-	elif [ ${IGEN} -le 999 ] ; then
-		cat ${CTLFILE}|sed s:00082:00${IGEN}:>./gfs_cntrl.parm
-	else
-		ln -sf ${CTLFILE} ./gfs_cntrl.parm
-	fi
-	ln -sf ./gfs_cntrl.parm fort.14
-elif [ ${GRIBVERSION} = grib2 ]; then
-	cp ${POSTGRB2TBL} .
-	cp ${PostFlatFile} ./postxconfig-NT.txt
-	if [ ${ens} = "YES" ] ; then
-		sed < ${PostFlatFile} -e "s#negatively_pert_fcst#${ens_pert_type}#" > ./postxconfig-NT.txt
-	fi
-	#  cp ${CTLFILE} postcntrl.xml
-fi
-export CTL=$(basename $CTLFILE)
-
-ln -sf griddef.out fort.110
-cp ${PARMglobal}/nam_micro_lookup.dat ./eta_micro_lookup.dat
-
-${APRUN:-mpirun.lsf} $POSTGPEXEC < itag > outpost_gfs_${VDATE}_${CTL}
-
-export ERR=$?
-export err=$ERR
-$ERRSCRIPT||exit 2
-
-if [ $FILTER = "1" ] ; then
-	# Filter SLP and 500 mb height using copygb, change GRIB ID, and then
-	# cat the filtered fields to the pressure GRIB file, from Iredell
-
-	if [ $GRIBVERSION = grib1 ]; then
-		$COPYGB -x -i'4,0,80' -k'4*-1,1,102' $PGBOUT tfile
-		ln -s -f tfile fort.11
-		ln -s -f prmsl fort.51
-		echo 0 2|$OVERPARMEXEC
-		$COPYGB -x -i'4,1,5' -k'4*-1,7,100,500' $PGBOUT tfile
-		ln -s -f tfile fort.11
-		ln -s -f h5wav fort.51
-		echo 0 222|$OVERPARMEXEC
-
-		#cat $PGBOUT prmsl h5wav >> $PGBOUT
-		cat  prmsl h5wav >> $PGBOUT
-	elif [ $GRIBVERSION = grib2 ]; then
-		if [ ${ens} = YES ] ; then
-			$COPYGB2 -x -i'4,0,80' -k'1 3 0 7*-9999 101 0 0' $PGBOUT tfile
-		else
-			$COPYGB2 -x -i'4,0,80' -k'0 3 0 7*-9999 101 0 0' $PGBOUT tfile
-		fi
-		$WGRIB2 tfile -set_byte 4 11 1 -grib prmsl
-		if [ ${ens} = YES ] ; then
-			$COPYGB2 -x -i'4,1,5' -k'1 3 5 7*-9999 100 0 50000' $PGBOUT tfile
-		else
-			$COPYGB2 -x -i'4,1,5' -k'0 3 5 7*-9999 100 0 50000' $PGBOUT tfile
-		fi
-		$WGRIB2 tfile -set_byte 4 11 193 -grib h5wav
-
-		#cat $PGBOUT prmsl h5wav >> $PGBOUT
-
-		cat  prmsl h5wav >> $PGBOUT
-	fi
-fi
-
-################################################################################
-#  Anomaly concatenation
-#  for now just do anomaly concentration for grib1
-if [ $GRIBVERSION = grib1 ]; then
-	if [[ -x $ANOMCATSH ]]; then
-		if [[ -n $PGIOUT ]]; then
-			$GRBINDEX $PGBOUT $PGIOUT
-		fi
-		export PGM=$ANOMCATSH
-		export pgm=$PGM
-		$LOGSCRIPT
-
-		eval $ANOMCATSH $PGBOUT $PGIOUT
-
-		export ERR=$?
-		export err=$ERR
-		$ERRSCRIPT||exit 3
-	fi
-fi
-################################################################################
-#  Make GRIB index file
-if [[ -n $PGIOUT ]]; then
-	if [ $GRIBVERSION = grib2 ]; then
-		# JY $GRBINDEX2 $PGBOUT $PGIOUT
-		$GRB2INDEX $PGBOUT $PGIOUT
-	else
-		$GRBINDEX $PGBOUT $PGIOUT
-	fi
-fi
-if [[ -r $FLXINP && -n $FLXIOUT && $OUTTYP -le 3 ]]; then
-	$GRBINDEX $FLXINP $FLXIOUT
-fi
-################################################################################
-# generate psi and chi
-echo "GENPSICHI= " $GENPSICHI
-if [ $GENPSICHI = YES ] ; then
-	#echo "PGBOUT PGIOUT=" $PGBOUT $PGIOUT
-	#echo "YY MM=" $YY $MM
-	export psichifile=./psichi.grb
-	$GENPSICHIEXE < postgp.inp.nml$$
-	rc=$?
-	if [[ $rc -ne 0 ]] ; then
-		echo 'Nonzero return code rc= '$rc
-		exit 3
-	fi
-	cat ./psichi.grb >> $PGBOUT
-fi
-################################################################################
-#  Postprocessing
-cd $pwd
-[[ $mkdata = YES ]]&&rmdir $DATA
-
-exit $err

From 1b8a12367a15278507f84ac7be63c6eec05e8a8d Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 15:23:44 +0000
Subject: [PATCH 02/13] Linter fixes for post rename

---
 jobs/JGLOBAL_ATMOS_POST      | 3 ++-
 scripts/exgdas_atmos_post.sh | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/jobs/JGLOBAL_ATMOS_POST b/jobs/JGLOBAL_ATMOS_POST
index 73b8c72876b..3d10b0f2507 100755
--- a/jobs/JGLOBAL_ATMOS_POST
+++ b/jobs/JGLOBAL_ATMOS_POST
@@ -11,6 +11,7 @@ configs="base post"
 export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
 config_path=${EXPDIR:-$PACKAGEROOT/gfs.${gfs_ver}/parm/config}
 for config in $configs; do
+    # shellcheck source-path=parm/config
     . $config_path/config.$config
     status=$?
     [[ $status -ne 0 ]] && exit $status
@@ -117,7 +118,7 @@ export SLEEP_INT=5
 ###############################################################
 # Run relevant exglobal script
 
-$SCRgfs/ex${RUN}_atmos_post.sh
+"${SCRgfs}/ex${RUN}_atmos_post.sh"
 status=$?
 [[ $status -ne 0 ]] && exit $status
 
diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index 4de4ffaf717..818480ff41f 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -28,7 +28,7 @@ source "$HOMEgfs/ush/preamble.sh"
 
 cd $DATA
 
-export POSTGPSH=${POSTGPSH:-$USHgfs/gfs_post.sh}
+export POSTGPSH=${POSTGPSH:-${USHgfs}/gfs_post.sh}
 export GFSDOWNSH=${GFSDOWNSH:-$USHgfs/fv3gfs_downstream_nems.sh}
 export GFSDWNSH=${GFSDWNSH:-$USHgfs/fv3gfs_dwn_nems.sh}
 export TRIMRH=${TRIMRH:-$USHgfs/trim_rh.sh}

From 6f870e2c15c38745d07a7e7a0bc6d5299b9c9d11 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 15:43:24 +0000
Subject: [PATCH 03/13] Linter corrections for post j-job

---
 jobs/JGLOBAL_ATMOS_POST | 58 +++++++++++++++++++++++------------------
 1 file changed, 32 insertions(+), 26 deletions(-)

diff --git a/jobs/JGLOBAL_ATMOS_POST b/jobs/JGLOBAL_ATMOS_POST
index 3d10b0f2507..bc6b83b6a5b 100755
--- a/jobs/JGLOBAL_ATMOS_POST
+++ b/jobs/JGLOBAL_ATMOS_POST
@@ -1,6 +1,7 @@
 #! /usr/bin/env bash
 
-source "$HOMEgfs/ush/preamble.sh"
+# shellcheck source=ush/preamble.sh
+source "${HOMEgfs:?}/ush/preamble.sh"
 
 export RUN_ENVIR=${RUN_ENVIR:-"nco"}
 
@@ -8,40 +9,43 @@ export RUN_ENVIR=${RUN_ENVIR:-"nco"}
 # Source relevant config files
 #############################
 configs="base post"
-export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
-config_path=${EXPDIR:-$PACKAGEROOT/gfs.${gfs_ver}/parm/config}
-for config in $configs; do
+export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
+config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config}
+for config in ${configs}; do
     # shellcheck source-path=parm/config
-    . $config_path/config.$config
+    . "${config_path}/config.${config}"
     status=$?
-    [[ $status -ne 0 ]] && exit $status
+    (( status != 0 )) && exit "${status}"
 done
 
 
 ##########################################
 # Source machine runtime environment
 ##########################################
-. $HOMEgfs/env/${machine}.env post
+# shellcheck source-path=env
+. ${HOMEgfs}/env/${machine}.env post
 status=$?
-[[ $status -ne 0 ]] && exit $status
+(( status != 0 )) && exit "${status}"
 
 
 ##############################################
 # Obtain unique process id (pid) and make temp directory
 ##############################################
 export pid=${pid:-$$}
-export outid=${outid:-"LL$job"}
+export outid=${outid:-"LL${job}"}
 export DATA=${DATA:-${DATAROOT}/${jobid:?}}
-mkdir -p $DATA
-cd $DATA
+mkdir -p "${DATA}"
+cd "${DATA}" || exit 1
 
 
 ##############################################
 # Run setpdy and initialize PDY variables
 ##############################################
-export cycle="t${cyc}z"
+export cycle="t${cyc:?}z"
 setpdy.sh
+# shellcheck disable=SC1091
 . ./PDY
+# shellcheck disable=
 
 
 ##############################################
@@ -69,22 +73,24 @@ export COMPONENT=${COMPONENT:-atmos}
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
-export APRUNP=${APRUN:-$APRUN_NP}
+export APRUNP=${APRUN:-${APRUN_NP}}
 export RERUN=${RERUN:-NO}
 export HOMECRTM=${HOMECRTM:-${PACKAGEROOT:?}/lib/crtm/${crtm_ver:?}}
 export FIXCRTM=${CRTM_FIX:-${HOMECRTM}/fix}
-export PARMpost=${PARMpost:-$HOMEgfs/parm/post}
+export PARMpost=${PARMpost:-${HOMEgfs}/parm/post}
 export INLINE_POST=${WRITE_DOPOST:-".false."}
 
-export COMIN=${COMIN:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
-export COMOUT=${COMOUT:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+export COMIN=${COMIN:-${ROTDIR}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
+export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
 
-[[ ! -d $COMOUT ]] && mkdir -m 775 -p $COMOUT
+# shellcheck disable=SC2174
+[[ ! -d "${COMOUT}" ]] && mkdir -m 775 -p "${COMOUT}"
+# shellcheck disable=
 
-if [ $RUN = gfs ];then
+if [ "${RUN}" = gfs ];then
   export FHOUT_PGB=${FHOUT_GFS:-3} #Output frequency of gfs pgb file at 1.0 and 0.5 deg.
 fi
-if [ $RUN = gdas ]; then
+if [ "${RUN}" = gdas ]; then
   export IGEN_GFS="gfs_avn"
   export IGEN_ANL="anal_gfs"
   export IGEN_FCST="gfs_avn"
@@ -92,7 +98,7 @@ if [ $RUN = gdas ]; then
   export FHOUT_PGB=${FHOUT:-1} #Output frequency of gfs pgb file at 1.0 and 0.5 deg.
 fi
 
-if [ $GRIBVERSION = grib2 ]; then
+if [ "${GRIBVERSION:?}" = grib2 ]; then
   export IGEN_ANL="anal_gfs"
   export IGEN_FCST="gfs_avn"
   export IGEN_GFS="gfs_avn"
@@ -101,7 +107,7 @@ fi
 #######################################
 # Specify Restart File Name to Key Off
 #######################################
-export restart_file=$COMIN/${RUN}.t${cyc}z.logf
+export restart_file=${COMIN}/${RUN}.t${cyc}z.logf
 
 ####################################
 # Specify Timeout Behavior of Post
@@ -120,7 +126,7 @@ export SLEEP_INT=5
 
 "${SCRgfs}/ex${RUN}_atmos_post.sh"
 status=$?
-[[ $status -ne 0 ]] && exit $status
+(( status != 0 )) && exit "${status}"
 
 ##############################################
 # End JOB SPECIFIC work
@@ -129,15 +135,15 @@ status=$?
 ##############################################
 # Final processing
 ##############################################
-if [ -e "$pgmout" ]; then
-  cat $pgmout
+if [ -e "${pgmout}" ]; then
+  cat "${pgmout}"
 fi
 
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd $DATAROOT
-[[ $KEEPDATA = "NO" ]] && rm -rf $DATA
+cd "${DATAROOT}" || exit 1
+[[ "${KEEPDATA:-NO}" = "NO" ]] && rm -rf "${DATA}"
 
 
 exit 0

From 8ed0dfbdf0ccb02e2444f3b9fec887c8aa0c67d9 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 16:50:24 +0000
Subject: [PATCH 04/13] Linter corrections for gdas post exscript

---
 jobs/JGLOBAL_ATMOS_POST      |   4 +-
 scripts/exgdas_atmos_post.sh | 213 ++++++++++++++++++-----------------
 2 files changed, 109 insertions(+), 108 deletions(-)

diff --git a/jobs/JGLOBAL_ATMOS_POST b/jobs/JGLOBAL_ATMOS_POST
index bc6b83b6a5b..004afd6e86f 100755
--- a/jobs/JGLOBAL_ATMOS_POST
+++ b/jobs/JGLOBAL_ATMOS_POST
@@ -23,7 +23,7 @@ done
 # Source machine runtime environment
 ##########################################
 # shellcheck source-path=env
-. ${HOMEgfs}/env/${machine}.env post
+. "${HOMEgfs}/env/${machine:?}.env" post
 status=$?
 (( status != 0 )) && exit "${status}"
 
@@ -124,7 +124,7 @@ export SLEEP_INT=5
 ###############################################################
 # Run relevant exglobal script
 
-"${SCRgfs}/ex${RUN}_atmos_post.sh"
+"${SCRgfs:?}/ex${RUN}_atmos_post.sh"
 status=$?
 (( status != 0 )) && exit "${status}"
 
diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index 818480ff41f..7f056d5bfbe 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -24,15 +24,16 @@
 # echo "-----------------------------------------------------"
 #####################################################################
 
-source "$HOMEgfs/ush/preamble.sh"
+# shellcheck source=ush/preamble.sh
+source "${HOMEgfs:?}/ush/preamble.sh"
 
-cd $DATA
+cd "${DATA:?}" || exit 1
 
 export POSTGPSH=${POSTGPSH:-${USHgfs}/gfs_post.sh}
-export GFSDOWNSH=${GFSDOWNSH:-$USHgfs/fv3gfs_downstream_nems.sh}
-export GFSDWNSH=${GFSDWNSH:-$USHgfs/fv3gfs_dwn_nems.sh}
-export TRIMRH=${TRIMRH:-$USHgfs/trim_rh.sh}
-export MODICEC=${MODICEC:-$USHgfs/mod_icec.sh}
+export GFSDOWNSH=${GFSDOWNSH:-${USHgfs}/fv3gfs_downstream_nems.sh}
+export GFSDWNSH=${GFSDWNSH:-${USHgfs}/fv3gfs_dwn_nems.sh}
+export TRIMRH=${TRIMRH:-${USHgfs}/trim_rh.sh}
+export MODICEC=${MODICEC:-${USHgfs}/mod_icec.sh}
 export INLINE_POST=${INLINE_POST:-".false."}
 
 ############################################################
@@ -52,8 +53,8 @@ export OUTTYP=${OUTTYP:-4}
 export OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
 export TCYC=${TCYC:-".t${cyc}z."}
 export PREFIX=${PREFIX:-${RUN}${TCYC}}
-if [ $OUTTYP -eq 4 ] ; then
-  if [ $OUTPUT_FILE = "netcdf" ]; then
+if (( OUTTYP == 4 )) ; then
+  if [ "${OUTPUT_FILE}" = "netcdf" ]; then
     export SUFFIX=".nc"
   else
     export SUFFIX=".nemsio"
@@ -77,19 +78,19 @@ export IDRT=${IDRT:-0} # IDRT=0 is setting for outputting grib files on lat/lon
 # Post Analysis Files before starting the Forecast Post
 ############################################################
 # Chuang: modify to process analysis when post_times is 00
-export stime=$(echo $post_times | cut -c1-3)
-if [ $OUTTYP -eq 4 ] ; then
-  export loganl=$COMIN/${PREFIX}atmanl${SUFFIX}
+export stime="$(echo ${post_times:?} | cut -c1-3)"
+if (( OUTTYP == 4 )) ; then
+  export loganl="${COMIN:?}/${PREFIX}atmanl${SUFFIX}"
 else
-  export loganl=$COMIN/${PREFIX}sanl
+  export loganl="${COMIN:?}/${PREFIX}sanl"
 fi
 
-if [ ${stime} = "anl" ]; then
-  if [ -f $loganl ]; then
+if [ "${stime}" = "anl" ]; then
+  if [ -f "${loganl}" ]; then
     # add new environmental variables for running new ncep post
     # Validation date
 
-    export VDATE=${PDY}${cyc}
+    export VDATE=${PDY:?}${cyc}
 
     # set outtyp to 1 because we need to run chgres in the post before model start running chgres
     # otherwise set to 0, then chgres will not be executed in global_nceppost.sh
@@ -100,68 +101,68 @@ if [ ${stime} = "anl" ]; then
     # if model already runs gfs io, make sure GFSOUT is linked to the gfsio file
     # new imported variable for global_nceppost.sh
 
-    export GFSOUT=${RUN}.${cycle}.gfsioanl
+    export GFSOUT=${RUN}.${cycle:?}.gfsioanl
 
     # specify smaller control file for GDAS because GDAS does not
     # produce flux file, the default will be /nwprod/parm/gfs_cntrl.parm
 
-    if [ $GRIBVERSION = 'grib2' ]; then
+    if [ "${GRIBVERSION:?}" = 'grib2' ]; then
       export POSTGRB2TBL=${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}
-      export PostFlatFile=${PostFlatFile:-$PARMpost/postxconfig-NT-GFS-ANL.txt}
-      export CTLFILE=$PARMpost/postcntrl_gfs_anl.xml
+      export PostFlatFile=${PostFlatFile:-${PARMpost}/postxconfig-NT-GFS-ANL.txt}
+      export CTLFILE=${PARMpost}/postcntrl_gfs_anl.xml
     fi
 
     [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
-    if [ $OUTTYP -eq 4 ] ; then
-      ln -fs $COMIN/${PREFIX}atmanl${SUFFIX} nemsfile
+    if (( OUTTYP == 4 )) ; then
+      ln -fs "${COMIN}/${PREFIX}atmanl${SUFFIX}" nemsfile
       export NEMSINP=nemsfile
-      ln -fs $COMIN/${PREFIX}sfcanl${SUFFIX} flxfile
+      ln -fs "${COMIN}/${PREFIX}sfcanl${SUFFIX}" flxfile
       export FLXINP=flxfile
     fi
     export PGBOUT=pgbfile
     export PGIOUT=pgifile
     export PGBOUT2=pgbfile.grib2
     export PGIOUT2=pgifile.grib2.idx
-    export IGEN=$IGEN_ANL
+    export IGEN="${IGEN_ANL:?}"
     export FILTER=0
 
     # specify fhr even for analysis because postgp uses it
     #  export fhr=00
 
-    $POSTGPSH
+    ${POSTGPSH}
     export err=$?; err_chk
 
 
-    if [ $GRIBVERSION = 'grib2' ]; then
-      mv $PGBOUT $PGBOUT2
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
+      mv "${PGBOUT}" "${PGBOUT2}"
 
       #Proces pgb files
       export FH=-1
       export downset=${downset:-1}
-      $GFSDOWNSH
+      ${GFSDOWNSH}
       export err=$?; err_chk
 
       export fhr3=anl
     fi
 
-    if [ $SENDCOM = 'YES' ]; then
+    if [ "${SENDCOM:-YES}" = 'YES' ]; then
       export fhr3=anl
-      if [ $GRIBVERSION = 'grib2' ]; then
+      if [ "${GRIBVERSION}" = 'grib2' ]; then
         MASTERANL=${PREFIX}master.grb2${fhr3}
         ##########XXW Accord to Boi, fortran index should use *if${fhr}, wgrib index use .idx
         #MASTERANLIDX=${RUN}.${cycle}.master.grb2${fhr3}.idx
         MASTERANLIDX=${PREFIX}master.grb2i${fhr3}
-        cp $PGBOUT2  $COMOUT/${MASTERANL}
-        $GRB2INDEX $PGBOUT2 $COMOUT/${MASTERANLIDX}
+        cp "${PGBOUT2}" "${COMOUT:?}/${MASTERANL}"
+        ${GRB2INDEX:?} "${PGBOUT2}" "${COMOUT}/${MASTERANLIDX}"
       fi
 
-      if [ $SENDDBN = 'YES' ]; then
-        run=$(echo $RUN | tr '[a-z]' '[A-Z]')
-        if [ $GRIBVERSION = 'grib2' ]; then
-          $DBNROOT/bin/dbn_alert MODEL ${run}_MSC_sfcanl $job $COMOUT/${PREFIX}sfc${fhr3}${SUFFIX}
-          $DBNROOT/bin/dbn_alert MODEL ${run}_SA $job $COMIN/${PREFIX}atm${fhr3}${SUFFIX}
-          $DBNROOT/bin/dbn_alert MODEL GDAS_PGA_GB2 $job $COMOUT/${PREFIX}pgrb2.1p00.${fhr3}
-          $DBNROOT/bin/dbn_alert MODEL GDAS_PGA_GB2_WIDX $job $COMOUT/${PREFIX}pgrb2.1p00.${fhr3}.idx
+      if [ "${SENDDBN:-YES}" = 'YES' ]; then
+        run=$(echo ${RUN} | tr 'a-z' 'A-Z')
+        if [ "${GRIBVERSION}" = 'grib2' ]; then
+          "${DBNROOT:?}/bin/dbn_alert" MODEL "${run}_MSC_sfcanl" "${job:?}" "${COMOUT}/${PREFIX}sfc${fhr3}${SUFFIX}"
+          "${DBNROOT:?}/bin/dbn_alert" MODEL "${run}_SA" "${job:?}" "${COMIN}/${PREFIX}atm${fhr3}${SUFFIX}"
+          "${DBNROOT:?}/bin/dbn_alert" MODEL "GDAS_PGA_GB2" "${job:?}" "${COMOUT}/${PREFIX}pgrb2.1p00.${fhr3}"
+          "${DBNROOT:?}/bin/dbn_alert" MODEL "GDAS_PGA_GB2_WIDX" "${job:?}" "${COMOUT}/${PREFIX}pgrb2.1p00.${fhr3}.idx"
         fi
       fi
     fi
@@ -173,32 +174,32 @@ if [ ${stime} = "anl" ]; then
     err_chk
   fi
 else   ## not_anl if_stimes
-  SLEEP_LOOP_MAX=$(expr $SLEEP_TIME / $SLEEP_INT)
+  SLEEP_LOOP_MAX=$(( ${SLEEP_TIME:?} / ${SLEEP_INT:?} ))
 
   ############################################################
   # Loop Through the Post Forecast Files
   ############################################################
 
-  for fhr in $post_times; do
+  for fhr in ${post_times}; do
     ###############################
     # Start Looping for the
     # existence of the restart files
     ###############################
     export pgm="postcheck"
     ic=1
-    while [ $ic -le $SLEEP_LOOP_MAX ]; do
-      if [ -f ${restart_file}${fhr}.txt ]; then
+    while (( ic <= SLEEP_LOOP_MAX )); do
+      if [ -f "${restart_file:?}${fhr}.txt" ]; then
         break
       else
-        ic=$(expr $ic + 1)
-        sleep $SLEEP_INT
+        ic=$(( ic + 1 ))
+        sleep "${SLEEP_INT}"
       fi
       ###############################
       # If we reach this point assume
       # fcst job never reached restart
       # period and error exit
       ###############################
-      if [ $ic -eq $SLEEP_LOOP_MAX ]; then
+      if (( ic == SLEEP_LOOP_MAX )); then
         echo " *** FATAL ERROR: No model output in nemsio for f${fhr} "
         export err=9
         err_chk
@@ -211,51 +212,51 @@ else   ## not_anl if_stimes
     ###############################
     [[ -f flxfile ]] && rm flxfile
     [[ -f nemsfile ]] && rm nemsfile
-    if [ $OUTTYP -eq 4 ] ; then
-      ln -sf $COMIN/${PREFIX}atmf$fhr${SUFFIX} nemsfile
+    if (( OUTTYP == 4 )) ; then
+      ln -sf "${COMIN}/${PREFIX}atmf$fhr${SUFFIX}" nemsfile
       export NEMSINP=nemsfile
-      ln -sf $COMIN/${PREFIX}sfcf$fhr${SUFFIX} flxfile
+      ln -sf "${COMIN}/${PREFIX}sfcf$fhr${SUFFIX}" flxfile
       export FLXINP=flxfile
     fi
 
-    if [ $fhr -gt 0 ]; then
-      export IGEN=$IGEN_FCST
+    if (( fhr > 0 )); then
+      export IGEN=${IGEN_FCST:?}
     else
-      export IGEN=$IGEN_ANL
+      export IGEN=${IGEN_ANL:?}
     fi
 
     # add new environmental variables for running new ncep post
     # Validation date
 
-    export VDATE=$(${NDATE} +${fhr} ${PDY}${cyc})
+    export VDATE="$(${NDATE:?} "+${fhr}" "${PDY}${cyc}")"
 
     # set to 3 to output lat/lon grid
 
     export OUTTYP=${OUTTYP:-4}
 
-    if [ $GRIBVERSION = 'grib2' ]; then
-      export POSTGRB2TBL=${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}
-      export PostFlatFile=$PARMpost/postxconfig-NT-GFS.txt
-      if [ $RUN = gfs ]; then
-        export IGEN=$IGEN_GFS
-        if [ $fhr -gt 0 ]; then export IGEN=$IGEN_FCST ; fi
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
+      export POSTGRB2TBL="${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}"
+      export PostFlatFile="${PARMpost}/postxconfig-NT-GFS.txt"
+      if [ "${RUN}" = gfs ]; then
+        export IGEN="${IGEN_GFS:?}"
+        if (( fhr > 0 )); then export IGEN="${IGEN_FCST}" ; fi
       else
-        export IGEN=$IGEN_GDAS_ANL
-        if [ $fhr -gt 0 ]; then export IGEN=$IGEN_FCST ; fi
+        export IGEN="${IGEN_GDAS_ANL:?}"
+        if (( fhr > 0 )); then export IGEN="${IGEN_FCST}" ; fi
       fi
-      if [[ $RUN = gfs ]]; then
-        if [ $fhr -eq 0 ]; then
-          export PostFlatFile=$PARMpost/postxconfig-NT-GFS-F00.txt
-          export CTLFILE=$PARMpost/postcntrl_gfs_f00.xml
+      if [[ "${RUN}" = gfs ]]; then
+        if (( fhr == 0 )); then
+          export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-F00.txt"
+          export CTLFILE="${PARMpost}/postcntrl_gfs_f00.xml"
         else
-          export CTLFILE=${CTLFILEGFS:-$PARMpost/postcntrl_gfs.xml}
+          export CTLFILE="${CTLFILEGFS:-${PARMpost}/postcntrl_gfs.xml}"
         fi
       else
-        if [ $fhr -eq 0 ]; then
-          export PostFlatFile=$PARMpost/postxconfig-NT-GFS-F00.txt
-          export CTLFILE=${CTLFILEGFS:-$PARMpost/postcntrl_gfs_f00.xml}
+        if (( fhr == 0 )); then
+          export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-F00.txt"
+          export CTLFILE="${CTLFILEGFS:-${PARMpost}/postcntrl_gfs_f00.xml}"
         else
-          export CTLFILE=${CTLFILEGFS:-$PARMpost/postcntrl_gfs.xml}
+          export CTLFILE="${CTLFILEGFS:-${PARMpost}/postcntrl_gfs.xml}"
         fi
       fi
     fi
@@ -266,77 +267,77 @@ else   ## not_anl if_stimes
     export PGBOUT2=pgbfile.grib2
     export PGIOUT2=pgifile.grib2.idx
     export FILTER=0
-    export fhr3=$fhr
-    if [ $GRIBVERSION = 'grib2' ]; then
+    export fhr3=${fhr}
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
       MASTERFHR=${PREFIX}master.grb2f${fhr}
       MASTERFHRIDX=${PREFIX}master.grb2if${fhr}
     fi
 
-    if [ $INLINE_POST = ".false." ]; then
-      $POSTGPSH
+    if [ "${INLINE_POST}" = ".false." ]; then
+      ${POSTGPSH}
     else
-      cp $COMOUT/${MASTERFHR} $PGBOUT
+      cp "${COMOUT}/${MASTERFHR}" "${PGBOUT}"
     fi
     export err=$?; err_chk
 
-    if [ $GRIBVERSION = 'grib2' ]; then
-      mv $PGBOUT $PGBOUT2
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
+      mv "${PGBOUT}" "${PGBOUT2}"
     fi
 
     #wm Process pgb files
-    export FH=$(expr $fhr + 0)
+    export FH=$(( fhr + 0 ))
     export downset=${downset:-1}
-    $GFSDOWNSH
+    ${GFSDOWNSH}
     export err=$?; err_chk
 
-    if [ $SENDDBN = YES ]; then
-      run=$(echo $RUN | tr '[a-z]' '[A-Z]')
-      $DBNROOT/bin/dbn_alert MODEL ${run}_PGB2_0P25 $job $COMOUT/${PREFIX}pgrb2.0p25.f${fhr}
-      $DBNROOT/bin/dbn_alert MODEL ${run}_PGB2_0P25_WIDX $job $COMOUT/${PREFIX}pgrb2.0p25.f${fhr}.idx
-      $DBNROOT/bin/dbn_alert MODEL ${run}_PGB_GB2 $job $COMOUT/${PREFIX}pgrb2.1p00.f${fhr}
-      $DBNROOT/bin/dbn_alert MODEL ${run}_PGB_GB2_WIDX $job $COMOUT/${PREFIX}pgrb2.1p00.f${fhr}.idx
+    if [ "${SENDDBN}" = YES ]; then
+      run=$(echo ${RUN} | tr 'a-z' 'A-Z')
+      "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB2_0P25" "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.f${fhr}"
+      "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB2_0P25_WIDX ""${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.f${fhr}.idx"
+      "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB_GB2" "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.f${fhr}"
+      "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB_GB2_WIDX" "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.f${fhr}.idx"
     fi
 
 
-    if [ $SENDCOM = 'YES' ]; then
-      if [ $GRIBVERSION = 'grib2' ] ; then
-        if [ $INLINE_POST = ".false." ]; then
-          cp $PGBOUT2 $COMOUT/${MASTERFHR}
+    if [ "${SENDCOM}" = 'YES' ]; then
+      if [ "${GRIBVERSION}" = 'grib2' ] ; then
+        if [ "${INLINE_POST}" = ".false." ]; then
+          cp "${PGBOUT2}" "${COMOUT}/${MASTERFHR}"
         fi
-        $GRB2INDEX $PGBOUT2 $COMOUT/${MASTERFHRIDX}
+        ${GRB2INDEX} "${PGBOUT2}" "${COMOUT}/${MASTERFHRIDX}"
       fi
 
       # Model generated flux files will be in nemsio after FY17 upgrade
       # use post to generate Grib2 flux files
 
-      if [ $OUTTYP -eq 4 ] ; then
-        export NEMSINP=$COMIN/${PREFIX}atmf${fhr}${SUFFIX}
-        export FLXINP=$COMIN/${PREFIX}sfcf${fhr}${SUFFIX}
-        if [ $fhr -eq 0 ]; then
-          export PostFlatFile=$PARMpost/postxconfig-NT-GFS-FLUX-F00.txt
-          export CTLFILE=$PARMpost/postcntrl_gfs_flux_f00.xml
+      if (( OUTTYP == 4 )) ; then
+        export NEMSINP=${COMIN}/${PREFIX}atmf${fhr}${SUFFIX}
+        export FLXINP=${COMIN}/${PREFIX}sfcf${fhr}${SUFFIX}
+        if (( fhr == 0 )); then
+          export PostFlatFile=${PARMpost}/postxconfig-NT-GFS-FLUX-F00.txt
+          export CTLFILE=${PARMpost}/postcntrl_gfs_flux_f00.xml
         else
-          export PostFlatFile=$PARMpost/postxconfig-NT-GFS-FLUX.txt
-          export CTLFILE=$PARMpost/postcntrl_gfs_flux.xml
+          export PostFlatFile=${PARMpost}/postxconfig-NT-GFS-FLUX.txt
+          export CTLFILE=${PARMpost}/postcntrl_gfs_flux.xml
         fi
         export PGBOUT=fluxfile
         export FILTER=0
         FLUXFL=${PREFIX}sfluxgrbf${fhr}.grib2
         FLUXFLIDX=${PREFIX}sfluxgrbf${fhr}.grib2.idx
 
-        if [ $INLINE_POST = ".false." ]; then
-          $POSTGPSH
+        if [ "${INLINE_POST}" = ".false." ]; then
+          ${POSTGPSH}
           export err=$?; err_chk
-          mv fluxfile $COMOUT/${FLUXFL}
+          mv fluxfile "${COMOUT}/${FLUXFL}"
         fi
-        $WGRIB2 -s $COMOUT/${FLUXFL} > $COMOUT/${FLUXFLIDX}
+        ${WGRIB2:?} -s "${COMOUT}/${FLUXFL}" > "${COMOUT}/${FLUXFLIDX}"
       fi
 
-      if [ "$SENDDBN" = 'YES' -a  \( "$RUN" = 'gdas' \) -a $(expr $fhr % 3) -eq 0 ]; then
-        $DBNROOT/bin/dbn_alert MODEL ${run}_SF $job $COMOUT/${PREFIX}atmf${fhr}${SUFFIX}
-        $DBNROOT/bin/dbn_alert MODEL ${run}_BF $job $COMOUT/${PREFIX}sfcf${fhr}${SUFFIX}
-        $DBNROOT/bin/dbn_alert MODEL ${run}_SGB_GB2 $job $COMOUT/${PREFIX}sfluxgrbf${fhr}.grib2
-        $DBNROOT/bin/dbn_alert MODEL ${run}_SGB_GB2_WIDX $job $COMOUT/${PREFIX}sfluxgrbf${fhr}.grib2.idx
+      if [ "${SENDDBN}" = 'YES' ] -a [ "${RUN}" = 'gdas' ] -a (( fhr % 3 == 0 )); then
+        "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SF" "${job}" "${COMOUT}/${PREFIX}atmf${fhr}${SUFFIX}"
+        "${DBNROOT}/bin/dbn_alert" MODEL "${run}_BF" "${job}" "${COMOUT}/${PREFIX}sfcf${fhr}${SUFFIX}"
+        "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SGB_GB2" "${job}" "${COMOUT}/${PREFIX}sfluxgrbf${fhr}.grib2"
+        "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SGB_GB2_WIDX ""${job}" "${COMOUT}/${PREFIX}sfluxgrbf${fhr}.grib2.idx"
       fi
     fi
 

From 137463f74c1d85d1748aafa39a4d9fc84fdcd3d0 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 18:06:00 +0000
Subject: [PATCH 05/13] Linter corrections for gfs post exscript

---
 scripts/exgdas_atmos_post.sh |   6 +-
 scripts/exgfs_atmos_post.sh  | 359 +++++++++++++++++------------------
 2 files changed, 182 insertions(+), 183 deletions(-)

diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index 7f056d5bfbe..cb6b55a6218 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -78,7 +78,7 @@ export IDRT=${IDRT:-0} # IDRT=0 is setting for outputting grib files on lat/lon
 # Post Analysis Files before starting the Forecast Post
 ############################################################
 # Chuang: modify to process analysis when post_times is 00
-export stime="$(echo ${post_times:?} | cut -c1-3)"
+export stime="$(echo "${post_times:?}" | cut -c1-3)"
 if (( OUTTYP == 4 )) ; then
   export loganl="${COMIN:?}/${PREFIX}atmanl${SUFFIX}"
 else
@@ -300,7 +300,7 @@ else   ## not_anl if_stimes
 
 
     if [ "${SENDCOM}" = 'YES' ]; then
-      if [ "${GRIBVERSION}" = 'grib2' ] ; then
+      if [ "${GRIBVERSION}" = 'grib2' ]; then
         if [ "${INLINE_POST}" = ".false." ]; then
           cp "${PGBOUT2}" "${COMOUT}/${MASTERFHR}"
         fi
@@ -333,7 +333,7 @@ else   ## not_anl if_stimes
         ${WGRIB2:?} -s "${COMOUT}/${FLUXFL}" > "${COMOUT}/${FLUXFLIDX}"
       fi
 
-      if [ "${SENDDBN}" = 'YES' ] -a [ "${RUN}" = 'gdas' ] -a (( fhr % 3 == 0 )); then
+      if [ "${SENDDBN}" = 'YES' ] && [ "${RUN}" = 'gdas' ] && (( fhr % 3 == 0 )); then
         "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SF" "${job}" "${COMOUT}/${PREFIX}atmf${fhr}${SUFFIX}"
         "${DBNROOT}/bin/dbn_alert" MODEL "${run}_BF" "${job}" "${COMOUT}/${PREFIX}sfcf${fhr}${SUFFIX}"
         "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SGB_GB2" "${job}" "${COMOUT}/${PREFIX}sfluxgrbf${fhr}.grib2"
diff --git a/scripts/exgfs_atmos_post.sh b/scripts/exgfs_atmos_post.sh
index 92bb8b5463a..d88f2f241f3 100755
--- a/scripts/exgfs_atmos_post.sh
+++ b/scripts/exgfs_atmos_post.sh
@@ -36,17 +36,17 @@
 # echo "-----------------------------------------------------"
 #####################################################################
 
-source "$HOMEgfs/ush/preamble.sh"
+source "${HOMEgfs:?}/ush/preamble.sh"
 
-cd $DATA
+cd "${DATA:?}" || exit 1
 
 # specify model output format type: 4 for nemsio, 3 for sigio
-export POSTGPSH=${POSTGPSH:-$USHgfs/gfs_post.sh}
-export GFSDOWNSH=${GFSDOWNSH:-$USHgfs/fv3gfs_downstream_nems.sh}
-export GFSDOWNSHF=${GFSDOWNSHF:-$USHgfs/inter_flux.sh}
-export GFSDWNSH=${GFSDWNSH:-$USHgfs/fv3gfs_dwn_nems.sh}
-export TRIMRH=${TRIMRH:-$USHgfs/trim_rh.sh}
-export MODICEC=${MODICEC:-$USHgfs/mod_icec.sh}
+export POSTGPSH=${POSTGPSH:-${USHgfs}/gfs_post.sh}
+export GFSDOWNSH=${GFSDOWNSH:-${USHgfs}/fv3gfs_downstream_nems.sh}
+export GFSDOWNSHF=${GFSDOWNSHF:-${USHgfs}/inter_flux.sh}
+export GFSDWNSH=${GFSDWNSH:-${USHgfs}/fv3gfs_dwn_nems.sh}
+export TRIMRH=${TRIMRH:-${USHgfs}/trim_rh.sh}
+export MODICEC=${MODICEC:-${USHgfs}/mod_icec.sh}
 export INLINE_POST=${INLINE_POST:-".false."}
 
 ############################################################
@@ -68,8 +68,8 @@ export PGBF=${PGBF:-"YES"}
 export TCYC=${TCYC:-".t${cyc}z."}
 export OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
 export PREFIX=${PREFIX:-${RUN}${TCYC}}
-if [ $OUTTYP -eq 4 ]; then
-  if [ $OUTPUT_FILE = "netcdf" ]; then
+if (( OUTTYP == 4 )); then
+  if [ "${OUTPUT_FILE}" = "netcdf" ]; then
     export SUFFIX=".nc"
   else
     export SUFFIX=".nemsio"
@@ -77,7 +77,7 @@ if [ $OUTTYP -eq 4 ]; then
 else
   export SUFFIX=
 fi
-export machine=${machine:-WCOSS_C}
+export machine=${machine:-WCOSS2}
 
 ###########################
 # Specify Output layers
@@ -93,18 +93,18 @@ export IDRT=${IDRT:-0} # IDRT=0 is setting for outputting grib files on lat/lon
 # Post Analysis Files before starting the Forecast Post
 ############################################################
 # Process analysis when post_times is 00
-export stime=$(echo $post_times | cut -c1-3)
-if [ $OUTTYP -eq 4 ]; then
-  export loganl=$COMIN/${PREFIX}atmanl${SUFFIX}
+export stime="$(echo ${post_times:?} | cut -c1-3)"
+if (( OUTTYP == 4 )); then
+  export loganl="${COMIN:?}/${PREFIX}atmanl${SUFFIX}"
 else
-  export loganl=$COMIN/${PREFIX}sanl
+  export loganl="${COMIN:?}/${PREFIX}sanl"
 fi
 
-if [ ${stime} = "anl" ]; then
-  if [ -f $loganl ]; then
+if [ "${stime}" = "anl" ]; then
+  if [ -f "${loganl}" ]; then
     # add new environmental variables for running new ncep post
     # Validation date
-    export VDATE=${PDY}${cyc}
+    export VDATE=${PDY:?}${cyc}
     # specify output file name from chgres which is input file name to nceppost
     # if model already runs gfs io, make sure GFSOUT is linked to the gfsio file
     # new imported variable for global_nceppost.sh
@@ -112,18 +112,18 @@ if [ ${stime} = "anl" ]; then
 
     # specify smaller control file for GDAS because GDAS does not
     # produce flux file, the default will be /nwprod/parm/gfs_cntrl.parm
-    if [ $GRIBVERSION = 'grib2' ]; then
+    if [ "${GRIBVERSION:?}" = 'grib2' ]; then
       # use grib2 nomonic table in product g2tmpl directory as default 
       export POSTGRB2TBL=${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}
-      export PostFlatFile=${PostFlatFile:-$PARMpost/postxconfig-NT-GFS-ANL.txt}
-      export CTLFILE=$PARMpost/postcntrl_gfs_anl.xml
+      export PostFlatFile=${PostFlatFile:-${PARMpost}/postxconfig-NT-GFS-ANL.txt}
+      export CTLFILE=${PARMpost}/postcntrl_gfs_anl.xml
     fi
 
     [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
-    if [ $OUTTYP -eq 4 ]; then
-      ln -fs $COMIN/${PREFIX}atmanl${SUFFIX} nemsfile
+    if (( OUTTYP == 4 )); then
+      ln -fs "${COMIN}/${PREFIX}atmanl${SUFFIX}" nemsfile
       export NEMSINP=nemsfile
-      ln -fs $COMIN/${PREFIX}sfcanl${SUFFIX} flxfile
+      ln -fs "${COMIN}/${PREFIX}sfcanl${SUFFIX}" flxfile
       export FLXINP=flxfile
     fi
 
@@ -131,52 +131,51 @@ if [ ${stime} = "anl" ]; then
     export PGIOUT=pgifile
     export PGBOUT2=pgbfile.grib2
     export PGIOUT2=pgifile.grib2.idx
-    export IGEN=$IGEN_ANL
+    export IGEN=${IGEN_ANL:?}
     export FILTER=0
 
-    $POSTGPSH
+    ${POSTGPSH}
     export err=$?; err_chk
 
-    if [ $GRIBVERSION = 'grib2' ]; then
-      mv $PGBOUT $PGBOUT2
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
+      mv "${PGBOUT}" "${PGBOUT2}"
     fi
 
     #  Process pgb files
-    if [ "$PGBF" = 'YES' ]; then
+    if [ "${PGBF}" = 'YES' ]; then
       export FH=-1
       export downset=${downset:-2}
-      $GFSDOWNSH
+      ${GFSDOWNSH}
       export err=$?; err_chk
     fi
 
-    if [ "$SENDCOM" = 'YES' ]; then
+    if [ "${SENDCOM:-YES}" = 'YES' ]; then
       export fhr3=anl
-      if [ $GRIBVERSION = 'grib2' ]; then
+      if [ "${GRIBVERSION}" = 'grib2' ]; then
         MASTERANL=${PREFIX}master.grb2${fhr3}
         MASTERANLIDX=${PREFIX}master.grb2i${fhr3}
-        cp $PGBOUT2 $COMOUT/${MASTERANL}
-        $GRB2INDEX $PGBOUT2 $COMOUT/${MASTERANLIDX}
+        cp "${PGBOUT2}" "${COMOUT:?}/${MASTERANL}"
+        ${GRB2INDEX:?} "${PGBOUT2}" "${COMOUT}/${MASTERANLIDX}"
       fi
 
-      if [ "$SENDDBN" = 'YES' ]; then
-        $DBNROOT/bin/dbn_alert MODEL GFS_MSC_sfcanl $job $COMOUT/${PREFIX}sfcanl${SUFFIX}
-        $DBNROOT/bin/dbn_alert MODEL GFS_SA $job $COMOUT/${PREFIX}atmanl${SUFFIX}
-        #alert removed in v15.0       $DBNROOT/bin/dbn_alert MODEL GFS_MASTER $job $COMOUT/${MASTERANL}
+      if [ "${SENDDBN:-YES}" = 'YES' ]; then
+        "${DBNROOT}/bin/dbn_alert" MODEL GFS_MSC_sfcanl "${job}" "${COMOUT}/${PREFIX}sfcanl${SUFFIX}"
+        "${DBNROOT}/bin/dbn_alert" MODEL GFS_SA "${job}" "${COMOUT}/${PREFIX}atmanl${SUFFIX}"
         if [ "$PGBF" = 'YES' ]; then
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_0P25 $job $COMOUT/${PREFIX}pgrb2.0p25.anl
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_0P25_WIDX $job $COMOUT/${PREFIX}pgrb2.0p25.anl.idx
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_0P25 $job $COMOUT/${PREFIX}pgrb2b.0p25.anl
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_0P25_WIDX $job $COMOUT/${PREFIX}pgrb2b.0p25.anl.idx
-
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_0P5 $job $COMOUT/${PREFIX}pgrb2.0p50.anl
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_0P5_WIDX $job $COMOUT/${PREFIX}pgrb2.0p50.anl.idx
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_0P5 $job $COMOUT/${PREFIX}pgrb2b.0p50.anl
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_0P5_WIDX $job $COMOUT/${PREFIX}pgrb2b.0p50.anl.idx
-
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_1P0 $job $COMOUT/${PREFIX}pgrb2.1p00.anl
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_1P0_WIDX $job $COMOUT/${PREFIX}pgrb2.1p00.anl.idx
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_1P0 $job $COMOUT/${PREFIX}pgrb2b.1p00.anl
-          $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_1P0_WIDX $job $COMOUT/${PREFIX}pgrb2b.1p00.anl.idx
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P25 "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.anl"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P25_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.anl.idx"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P25 "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p25.anl"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P25_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p25.anl.idx"
+
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P5 "${job}" "${COMOUT}/${PREFIX}pgrb2.0p50.anl"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P5_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2.0p50.anl.idx"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P5 "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p50.anl"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P5_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p50.anl.idx"
+
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_1P0 "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.anl"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_1P0_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.anl.idx"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_1P0 "${job}" "${COMOUT}/${PREFIX}pgrb2b.1p00.anl"
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_1P0_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2b.1p00.anl.idx"
         fi
       fi
     fi
@@ -185,39 +184,39 @@ if [ ${stime} = "anl" ]; then
 
     ##########################  WAFS U/V/T analysis start ##########################
     # U/V/T on ICAO standard atmospheric pressure levels for WAFS verification
-    if [ $WAFSF = "YES" ]; then
-      if [[ $RUN = gfs && $GRIBVERSION = 'grib2' ]]; then
+    if [ "${WAFSF}" = "YES" ]; then
+      if [[ "${RUN}" = gfs && "${GRIBVERSION}" = 'grib2' ]]; then
         export OUTTYP=${OUTTYP:-4}
 
-        export PostFlatFile=$PARMpost/postxconfig-NT-GFS-WAFS-ANL.txt
-        export CTLFILE=$PARMpost/postcntrl_gfs_wafs_anl.xml
+        export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-WAFS-ANL.txt"
+        export CTLFILE="${PARMpost}/postcntrl_gfs_wafs_anl.xml"
 
         export PGBOUT=wafsfile
         export PGIOUT=wafsifile
 
         $POSTGPSH
         export err=$?
-        if [ $err -ne 0 ]; then
+        if (( err != 0 )); then
           echo " *** GFS POST WARNING: WAFS output failed for analysis, err=$err"
         else
           # WAFS package doesn't process this part.
           # Need to be saved for WAFS U/V/T verification, 
           # resolution higher than WAFS 1.25 deg for future compatibility
           wafsgrid="latlon 0:1440:0.25 90:721:-0.25"
-          $WGRIB2 $PGBOUT -set_grib_type same -new_grid_winds earth \
+          ${WGRIB2:?} "${PGBOUT}" -set_grib_type same -new_grid_winds earth \
           -new_grid_interpolation bilinear -set_bitmap 1 \
-          -new_grid $wafsgrid ${PGBOUT}.tmp
+          -new_grid "${wafsgrid}" "${PGBOUT}.tmp"
 
-          if [ $SENDCOM = "YES" ]; then
-            cp ${PGBOUT}.tmp $COMOUT/${PREFIX}wafs.0p25.anl
-            $WGRIB2 -s ${PGBOUT}.tmp > $COMOUT/${PREFIX}wafs.0p25.anl.idx
+          if [ "${SENDCOM}" = "YES" ]; then
+            cp "${PGBOUT}.tmp" "${COMOUT}/${PREFIX}wafs.0p25.anl"
+            ${WGRIB2} -s "${PGBOUT}.tmp" > "${COMOUT}/${PREFIX}wafs.0p25.anl.idx"
 
             # if [ $SENDDBN = YES ]; then
             #    $DBNROOT/bin/dbn_alert MODEL GFS_WAFS_GB2 $job $COMOUT/${PREFIX}wafs.0p25.anl
             #    $DBNROOT/bin/dbn_alert MODEL GFS_WAFS_GB2__WIDX $job $COMOUT/${PREFIX}wafs.0p25.anl.idx
             # fi
           fi
-          rm $PGBOUT ${PGBOUT}.tmp
+          rm "${PGBOUT}" "${PGBOUT}.tmp"
         fi
       fi
     fi
@@ -229,33 +228,33 @@ if [ ${stime} = "anl" ]; then
     err_chk
   fi
 else   ## not_anl if_stime
-  SLEEP_LOOP_MAX=$(expr $SLEEP_TIME / $SLEEP_INT)
+  SLEEP_LOOP_MAX=$(( ${SLEEP_TIME:?} / ${SLEEP_INT:?} ))
 
   ############################################################
   # Loop Through the Post Forecast Files 
   ############################################################
 
-  for fhr in $post_times; do
-    echo 'Start processing fhr='$post_times
+  for fhr in ${post_times}; do
+    echo "Start processing fhr=${post_times}"
     ###############################
     # Start Looping for the 
     # existence of the restart files
     ###############################
     export pgm="postcheck"
     ic=1
-    while [ $ic -le $SLEEP_LOOP_MAX ]; do
-      if [ -f $restart_file${fhr}.txt ]; then
+    while (( ic <= SLEEP_LOOP_MAX )); do
+      if [ -f "${restart_file:?}${fhr}.txt" ]; then
         break
       else
-        ic=$(expr $ic + 1)
-        sleep $SLEEP_INT
+        ic=$(( ic + 1 ))
+        sleep ${SLEEP_INT}
       fi
       ###############################
       # If we reach this point assume
       # fcst job never reached restart 
       # period and error exit
       ###############################
-      if [ $ic -eq $SLEEP_LOOP_MAX ]; then
+      if (( ic == SLEEP_LOOP_MAX )); then
         echo " *** FATAL ERROR: No model output in nemsio for f${fhr} "
         export err=9
         err_chk
@@ -267,47 +266,47 @@ else   ## not_anl if_stime
     # for backup to start Model Fcst
     ###############################
     [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
-    if [ $OUTTYP -eq 4 ]; then
-      ln -fs $COMIN/${PREFIX}atmf${fhr}${SUFFIX} nemsfile
+    if (( OUTTYP == 4 )); then
+      ln -fs "${COMIN}/${PREFIX}atmf${fhr}${SUFFIX}" nemsfile
       export NEMSINP=nemsfile
-      ln -fs $COMIN/${PREFIX}sfcf${fhr}${SUFFIX} flxfile
+      ln -fs "${COMIN}/${PREFIX}sfcf${fhr}${SUFFIX}" flxfile
       export FLXINP=flxfile
     fi
 
-    if [ $fhr -gt 0 ]; then
-      export IGEN=$IGEN_FCST
+    if (( fhr > 0 )); then
+      export IGEN=${IGEN_FCST:?}
     else
-      export IGEN=$IGEN_ANL
+      export IGEN=${IGEN_ANL}
     fi
 
-    export VDATE=$(${NDATE} +${fhr} ${PDY}${cyc})
+    export VDATE=$(${NDATE:?} +${fhr} "${PDY}${cyc}")
     export OUTTYP=${OUTTYP:-4}
-    export GFSOUT=${PREFIX}gfsio${fhr}
+    export GFSOUT="${PREFIX}gfsio${fhr}"
 
     if [ $GRIBVERSION = 'grib2' ]; then
-      export POSTGRB2TBL=${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}
-      export PostFlatFile=${PostFlatFile:-$PARMpost/postxconfig-NT-GFS.txt}
+      export POSTGRB2TBL="${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}"
+      export PostFlatFile="${PostFlatFile:-${PARMpost}/postxconfig-NT-GFS.txt}"
 
-      if [ $RUN = gfs ]; then
-        export IGEN=$IGEN_GFS
-        if [ $fhr -gt 0 ]; then export IGEN=$IGEN_FCST ; fi
+      if [ "${RUN}" = "gfs" ]; then
+        export IGEN=${IGEN_GFS:?}
+        if (( fhr > 0 )); then export IGEN=${IGEN_FCST} ; fi
       else
-        export IGEN=$IGEN_GDAS_ANL
-        if [ $fhr -gt 0 ]; then export IGEN=$IGEN_FCST ; fi
+        export IGEN=${IGEN_GDAS_ANL:?}
+        if (( fhr > 0 )); then export IGEN=${IGEN_FCST} ; fi
       fi
-      if [[ $RUN = gfs ]]; then
-        if [ $fhr -eq 0 ]; then
-          export PostFlatFile=$PARMpost/postxconfig-NT-GFS-F00.txt
-          export CTLFILE=$PARMpost/postcntrl_gfs_f00.xml
+      if [[ "${RUN}" = "gfs" ]]; then
+        if (( fhr == 0 )); then
+          export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-F00.txt"
+          export CTLFILE="${PARMpost}/postcntrl_gfs_f00.xml"
         else
-          export CTLFILE=${CTLFILEGFS:-$PARMpost/postcntrl_gfs.xml}
+          export CTLFILE="${CTLFILEGFS:-${PARMpost}/postcntrl_gfs.xml}"
         fi
       else
-        if [ $fhr -eq 0 ]; then
-          export PostFlatFile=$PARMpost/postxconfig-NT-GFS-F00.txt
-          export CTLFILE=${CTLFILEGFS:-$PARMpost/postcntrl_gfs_f00.xml}
+        if (( fhr == 0 )); then
+          export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-F00.txt"
+          export CTLFILE="${CTLFILEGFS:-${PARMpost}/postcntrl_gfs_f00.xml}"
         else
-          export CTLFILE=${CTLFILEGFS:-$PARMpost/postcntrl_gfs.xml}
+          export CTLFILE="${CTLFILEGFS:-${PARMpost}/postcntrl_gfs.xml}"
         fi
       fi
     fi
@@ -318,78 +317,78 @@ else   ## not_anl if_stime
     export PGBOUT2=pgbfile.grib2
     export PGIOUT2=pgifile.grib2.idx
     export FILTER=0 
-    if [ $GRIBVERSION = 'grib2' ]; then
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
       MASTERFL=${PREFIX}master.grb2f${fhr}
       MASTERFLIDX=${PREFIX}master.grb2if${fhr}
     fi
 
-    if [ $INLINE_POST = ".false." ]; then
-      $POSTGPSH
+    if [ "${INLINE_POST}" = ".false." ]; then
+      ${POSTGPSH}
     else
-      cp -p $COMOUT/${MASTERFL} $PGBOUT 
+      cp -p "${COMOUT}/${MASTERFL}" "${PGBOUT}" 
     fi
     export err=$?; err_chk
 
-    if [ $GRIBVERSION = 'grib2' ]; then
-      mv $PGBOUT $PGBOUT2
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
+      mv "${PGBOUT}" "${PGBOUT2}"
     fi
 
     #  Process pgb files
-    if [ "$PGBF" = 'YES' ]; then
-      export FH=$(expr $fhr + 0)
+    if [ "${PGBF}" = 'YES' ]; then
+      export FH=$(( fhr + 0 ))
       export downset=${downset:-2}
-      $GFSDOWNSH
+      ${GFSDOWNSH}
       export err=$?; err_chk
     fi
 
-    if [ $SENDCOM = "YES" ]; then
-      if [ $GRIBVERSION = 'grib2' ]; then
-        if [ $INLINE_POST = ".false." ]; then 
-          cp $PGBOUT2 $COMOUT/${MASTERFL} 
+    if [ "${SENDCOM}" = "YES" ]; then
+      if [ "${GRIBVERSION}" = 'grib2' ]; then
+        if [ "${INLINE_POST}" = ".false." ]; then 
+          cp "${PGBOUT2}" "${COMOUT}/${MASTERFL}"
         fi
-        $GRB2INDEX $PGBOUT2  $COMOUT/${MASTERFLIDX}
+        ${GRB2INDEX} "${PGBOUT2}" "${COMOUT}/${MASTERFLIDX}"
       fi
 
-      if [ "$SENDDBN" = 'YES' ]; then
-        if [ $GRIBVERSION = 'grib2' ]; then
-          if [ "$PGBF" = 'YES' ]; then
-            $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_0P25 $job $COMOUT/${PREFIX}pgrb2.0p25.f${fhr}
-            $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_0P25_WIDX $job $COMOUT/${PREFIX}pgrb2.0p25.f${fhr}.idx
-            $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_0P25 $job $COMOUT/${PREFIX}pgrb2b.0p25.f${fhr}
-            $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_0P25_WIDX $job $COMOUT/${PREFIX}pgrb2b.0p25.f${fhr}.idx
-
-            if [ -s $COMOUT/${PREFIX}pgrb2.0p50.f${fhr} ]; then
-              $DBNROOT/bin/dbn_alert  MODEL GFS_PGB2_0P5 $job $COMOUT/${PREFIX}pgrb2.0p50.f${fhr}
-              $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_0P5_WIDX $job $COMOUT/${PREFIX}pgrb2.0p50.f${fhr}.idx
-              $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_0P5 $job $COMOUT/${PREFIX}pgrb2b.0p50.f${fhr}
-              $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_0P5_WIDX $job $COMOUT/${PREFIX}pgrb2b.0p50.f${fhr}.idx
+      if [ "${SENDDBN}" = 'YES' ]; then
+        if [ "${GRIBVERSION}" = 'grib2' ]; then
+          if [ "${PGBF}" = 'YES' ]; then
+            "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P25 "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.f${fhr}"
+            "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P25_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.f${fhr}.idx"
+            "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P25 "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p25.f${fhr}"
+            "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P25_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p25.f${fhr}.idx"
+
+            if [ -s "${COMOUT}/${PREFIX}pgrb2.0p50.f${fhr}" ]; then
+              "${DBNROOT}/bin/dbn_alert"  MODEL GFS_PGB2_0P5 "${job}" "${COMOUT}/${PREFIX}pgrb2.0p50.f${fhr}"
+              "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P5_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2.0p50.f${fhr}.idx"
+              "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P5 "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p50.f${fhr}"
+              "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P5_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p50.f${fhr}.idx"
             fi
 
-            if [ -s $COMOUT/${PREFIX}pgrb2.1p00.f${fhr} ]; then
-              $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_1P0 $job $COMOUT/${PREFIX}pgrb2.1p00.f${fhr}
-              $DBNROOT/bin/dbn_alert MODEL GFS_PGB2_1P0_WIDX $job $COMOUT/${PREFIX}pgrb2.1p00.f${fhr}.idx
-              $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_1P0 $job $COMOUT/${PREFIX}pgrb2b.1p00.f${fhr}
-              $DBNROOT/bin/dbn_alert MODEL GFS_PGB2B_1P0_WIDX $job $COMOUT/${PREFIX}pgrb2b.1p00.f${fhr}.idx
+            if [ -s "${COMOUT}/${PREFIX}pgrb2.1p00.f${fhr}" ]; then
+              "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_1P0 "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.f${fhr}"
+              "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_1P0_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.f${fhr}.idx"
+              "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_1P0 "${job}" "${COMOUT}/${PREFIX}pgrb2b.1p00.f${fhr}"
+              "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_1P0_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2b.1p00.f${fhr}.idx"
             fi
           fi
         fi 
       fi
 
       export fhr
-      $USHgfs/gfs_transfer.sh
+      "${USHgfs}/gfs_transfer.sh"
     fi
     [[ -f pgbfile.grib2 ]] && rm pgbfile.grib2
 
 
     # use post to generate GFS Grib2 Flux file as model generated Flux file
     # will be in nemsio format after FY17 upgrade.
-    if [ $OUTTYP -eq 4 -a $FLXF = "YES" ]; then
-      if [ $fhr -eq 0 ]; then
-        export PostFlatFile=$PARMpost/postxconfig-NT-GFS-FLUX-F00.txt
-        export CTLFILE=$PARMpost/postcntrl_gfs_flux_f00.xml
+    if (( OUTTYP == 4 )) && [[ "${FLXF}" == "YES" ]]; then
+      if (( fhr == 0 )); then
+        export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-FLUX-F00.txt"
+        export CTLFILE="${PARMpost}/postcntrl_gfs_flux_f00.xml"
       else
-        export PostFlatFile=$PARMpost/postxconfig-NT-GFS-FLUX.txt
-        export CTLFILE=$PARMpost/postcntrl_gfs_flux.xml
+        export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-FLUX.txt"
+        export CTLFILE="${PARMpost}/postcntrl_gfs_flux.xml"
       fi
       export PGBOUT=fluxfile
       export FILTER=0
@@ -398,43 +397,43 @@ else   ## not_anl if_stime
 
       #Add extra flux.1p00 file for coupled
       if [ "$FLXGF" = 'YES' ]; then                    
-        export FH=$(expr $fhr + 0)     
-        $GFSDOWNSHF                  
+        export FH=$(( fhr + 0 ))
+        ${GFSDOWNSHF}
         export err=$?; err_chk
       fi   
 
-      if [ $INLINE_POST = ".false." ]; then
-        $POSTGPSH
+      if [ "${INLINE_POST}" = ".false." ]; then
+        ${POSTGPSH}
         export err=$?; err_chk
-        mv fluxfile $COMOUT/${FLUXFL}
+        mv fluxfile "${COMOUT}/${FLUXFL}"
       fi
-      $WGRIB2 -s $COMOUT/${FLUXFL} > $COMOUT/${FLUXFLIDX}
+      ${WGRIB2} -s "${COMOUT}/${FLUXFL}" > "${COMOUT}/${FLUXFLIDX}"
 
-      if [ "$SENDDBN" = 'YES' ]; then
-        $DBNROOT/bin/dbn_alert MODEL GFS_SGB_GB2 $job $COMOUT/${FLUXFL}
-        $DBNROOT/bin/dbn_alert MODEL GFS_SGB_GB2_WIDX $job $COMOUT/${FLUXFLIDX}
+      if [ "${SENDDBN}" = 'YES' ]; then
+        "${DBNROOT}/bin/dbn_alert" MODEL GFS_SGB_GB2 "${job}" "${COMOUT}/${FLUXFL}"
+        "${DBNROOT}/bin/dbn_alert" MODEL GFS_SGB_GB2_WIDX "${job}" "${COMOUT}/${FLUXFLIDX}"
       fi
     fi
 
     # process satellite look alike separately so that master pgb gets out in time    
     # set outtyp to 2 because master post already generates gfs io files
-    if [ $GOESF = "YES" ]; then
-      export OUTTYP=${OUTTYP:-4}     
+    if [ "${GOESF}" = "YES" ]; then
+      export OUTTYP=${OUTTYP:-4}
 
       # specify output file name from chgres which is input file name to nceppost 
       # if model already runs gfs io, make sure GFSOUT is linked to the gfsio file
-      # new imported variable for global_nceppost.sh
+      # new imported variable for global_post.sh
 
       export GFSOUT=${PREFIX}gfsio${fhr}     
 
       # link satellite coefficients files, use hwrf version as ops crtm 2.0.5
       # does not new coefficient files used by post
       export FIXCRTM=${FIXCRTM:-${CRTM_FIX}}
-      $USHgfs/link_crtm_fix.sh $FIXCRTM
+      "${USHgfs}/link_crtm_fix.sh" ${FIXCRTM}
 
-      if [ $GRIBVERSION = 'grib2' ]; then 
-        export PostFlatFile=$PARMpost/postxconfig-NT-GFS-GOES.txt      
-        export CTLFILE=$PARMpost/postcntrl_gfs_goes.xml
+      if [ "${GRIBVERSION}" = 'grib2' ]; then 
+        export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-GOES.txt   "   
+        export CTLFILE="${PARMpost}/postcntrl_gfs_goes.xml"
       fi
       export FLXINP=flxfile
       export FLXIOUT=flxifile
@@ -445,25 +444,25 @@ else   ## not_anl if_stime
       export JO=0
       export IGEN=0
 
-      if [ $NET = gfs ]; then
-        $POSTGPSH
+      if [ "${NET:?}" = "gfs" ]; then
+        ${POSTGPSH}
         export err=$?; err_chk
       fi
 
-      if [ $GRIBVERSION = 'grib2' ]; then
-        SPECIALFL=${PREFIX}special.grb2
-        SPECIALFLIDX=${PREFIX}special.grb2i
+      if [ "${GRIBVERSION}" = 'grib2' ]; then
+        SPECIALFL="${PREFIX}special.grb2"
+        SPECIALFLIDX="${PREFIX}special.grb2i"
       fi
-      fhr3=$fhr
+      fhr3=${fhr}
 
-      if [ $SENDCOM = "YES" ]; then
+      if [ "${SENDCOM}" = "YES" ]; then
         #       echo "$PDY$cyc$pad$fhr" > $COMOUT/${RUN}.t${cyc}z.master.control
 
-        mv goesfile $COMOUT/${SPECIALFL}f$fhr
-        mv goesifile $COMOUT/${SPECIALFLIDX}f$fhr
+        mv goesfile "${COMOUT}/${SPECIALFL}f${fhr}"
+        mv goesifile "${COMOUT}/${SPECIALFLIDX}f${fhr}"
 
-        if [ $SENDDBN = YES ]; then
-          $DBNROOT/bin/dbn_alert MODEL GFS_SPECIAL_GB2 $job $COMOUT/${SPECIALFL}f$fhr
+        if [ "${SENDDBN}" = "YES" ]; then
+          "${DBNROOT}/bin/dbn_alert" MODEL GFS_SPECIAL_GB2 "${job}" "${COMOUT}/${SPECIALFL}f${fhr}"
         fi
       fi
     fi
@@ -472,17 +471,17 @@ else   ## not_anl if_stime
     ##########################  WAFS start ##########################
     # Generate WAFS products on ICAO standard level.
     # Do not need to be sent out to public, WAFS package will process the data.
-    if [[ $WAFSF = "YES"  && 10#$fhr -le 120 ]]; then
-      if [[ $RUN = gfs && $GRIBVERSION = 'grib2' ]]; then
+    if [[ "${WAFSF}" = "YES" ]] && (( 10#${fhr} <= 120 )); then
+      if [[ "${RUN}" = gfs && "${GRIBVERSION}" = 'grib2' ]]; then
         export OUTTYP=${OUTTYP:-4}
 
         # Extend WAFS icing and gtg up to 120 hours
-        export PostFlatFile=$PARMpost/postxconfig-NT-GFS-WAFS.txt
-        export CTLFILE=$PARMpost/postcntrl_gfs_wafs.xml
+        export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-WAFS.txt"
+        export CTLFILE="${PARMpost}/postcntrl_gfs_wafs.xml"
 
         # gtg has its own configurations
-        cp $PARMpost/gtg.config.gfs gtg.config
-        cp $PARMpost/gtg_imprintings.txt gtg_imprintings.txt
+        cp "${PARMpost}/gtg.config.gfs" gtg.config
+        cp "${PARMpost}/gtg_imprintings.txt" gtg_imprintings.txt
 
         export PGBOUT=wafsfile
         export PGIOUT=wafsifile
@@ -491,24 +490,24 @@ else   ## not_anl if_stime
         #   hourly if fhr<=24
         #   every 3 forecast hour if 24<fhr<=48
         #   every 6 forecast hour if 48<fhr<=120
-        if [  $fhr -le 24  ]; then
-          $POSTGPSH
-        elif [  $fhr -le 48  ]; then
-          if [  $((10#$fhr%3)) -eq 0  ]; then
-            $POSTGPSH
+        if (( $fhr <= 24 )); then
+          ${POSTGPSH}
+        elif (( $fhr <= 48 )); then
+          if (( 10#${fhr}%3 == 0 )); then
+            ${POSTGPSH}
           fi
-        elif [  $((10#$fhr%6)) -eq 0  ]; then
-          $POSTGPSH
+        elif (( 10#${fhr}%6 == 0 )); then
+          ${POSTGPSH}
         fi
 
         export err=$?; err_chk
-        if [ $err -ne 0 ]; then
-          echo " *** GFS POST WARNING: WAFS output failed for f${fhr}, err=$err"
+        if (( err != 0 )); then
+          echo " *** GFS POST WARNING: WAFS output failed for f${fhr}, err=${err}"
         else
-          if [ -e $PGBOUT ]; then
-            if [ $SENDCOM = "YES" ]; then
-              cp $PGBOUT $COMOUT/${PREFIX}wafs.grb2f$fhr
-              cp $PGIOUT $COMOUT/${PREFIX}wafs.grb2if$fhr
+          if [ -e ${PGBOUT} ]; then
+            if [ "${SENDCOM}" = "YES" ]; then
+              cp "${PGBOUT}" "${COMOUT}/${PREFIX}wafs.grb2f${fhr}"
+              cp "${PGIOUT}" "${COMOUT}/${PREFIX}wafs.grb2if${fhr}"
             fi
           fi
         fi

From 5877e7d4093a619bb4b995bc9b7f34ea5b0abbfd Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 19:01:00 +0000
Subject: [PATCH 06/13] Disable variable assigned but not defined shellcheck

Disables SC2154 (variable assigned but not defined).
---
 .shellcheckrc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.shellcheckrc b/.shellcheckrc
index 1c80a97072f..a34e63a71a8 100644
--- a/.shellcheckrc
+++ b/.shellcheckrc
@@ -1,2 +1,3 @@
 # Global settings for Spellcheck (https://github.com/koalaman/shellcheck)
 enable=all
+disable=SC2154

From 6153acfeaf02839f3e4a7991462b3bb363cf4e31 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 19:24:40 +0000
Subject: [PATCH 07/13] Remove excess default variable setting

With SC2154 turned off, the excessive usage of :? can be removed.
---
 jobs/JGLOBAL_ATMOS_POST      | 14 ++++----
 scripts/exgdas_atmos_post.sh | 62 +++++++++++++++++++-----------------
 scripts/exgfs_atmos_post.sh  | 62 +++++++++++++++++++-----------------
 3 files changed, 71 insertions(+), 67 deletions(-)

diff --git a/jobs/JGLOBAL_ATMOS_POST b/jobs/JGLOBAL_ATMOS_POST
index 004afd6e86f..1a19a72bfff 100755
--- a/jobs/JGLOBAL_ATMOS_POST
+++ b/jobs/JGLOBAL_ATMOS_POST
@@ -1,7 +1,7 @@
 #! /usr/bin/env bash
 
 # shellcheck source=ush/preamble.sh
-source "${HOMEgfs:?}/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
 export RUN_ENVIR=${RUN_ENVIR:-"nco"}
 
@@ -23,7 +23,7 @@ done
 # Source machine runtime environment
 ##########################################
 # shellcheck source-path=env
-. "${HOMEgfs}/env/${machine:?}.env" post
+. "${HOMEgfs}/env/${machine}.env" post
 status=$?
 (( status != 0 )) && exit "${status}"
 
@@ -33,7 +33,7 @@ status=$?
 ##############################################
 export pid=${pid:-$$}
 export outid=${outid:-"LL${job}"}
-export DATA=${DATA:-${DATAROOT}/${jobid:?}}
+export DATA=${DATA:-${DATAROOT}/${jobid}}
 mkdir -p "${DATA}"
 cd "${DATA}" || exit 1
 
@@ -41,7 +41,7 @@ cd "${DATA}" || exit 1
 ##############################################
 # Run setpdy and initialize PDY variables
 ##############################################
-export cycle="t${cyc:?}z"
+export cycle="t${cyc}z"
 setpdy.sh
 # shellcheck disable=SC1091
 . ./PDY
@@ -75,7 +75,7 @@ export COMPONENT=${COMPONENT:-atmos}
 ##############################################
 export APRUNP=${APRUN:-${APRUN_NP}}
 export RERUN=${RERUN:-NO}
-export HOMECRTM=${HOMECRTM:-${PACKAGEROOT:?}/lib/crtm/${crtm_ver:?}}
+export HOMECRTM=${HOMECRTM:-${PACKAGEROOT}/lib/crtm/${crtm_ver}}
 export FIXCRTM=${CRTM_FIX:-${HOMECRTM}/fix}
 export PARMpost=${PARMpost:-${HOMEgfs}/parm/post}
 export INLINE_POST=${WRITE_DOPOST:-".false."}
@@ -98,7 +98,7 @@ if [ "${RUN}" = gdas ]; then
   export FHOUT_PGB=${FHOUT:-1} #Output frequency of gfs pgb file at 1.0 and 0.5 deg.
 fi
 
-if [ "${GRIBVERSION:?}" = grib2 ]; then
+if [ "${GRIBVERSION}" = grib2 ]; then
   export IGEN_ANL="anal_gfs"
   export IGEN_FCST="gfs_avn"
   export IGEN_GFS="gfs_avn"
@@ -124,7 +124,7 @@ export SLEEP_INT=5
 ###############################################################
 # Run relevant exglobal script
 
-"${SCRgfs:?}/ex${RUN}_atmos_post.sh"
+"${SCRgfs}/ex${RUN}_atmos_post.sh"
 status=$?
 (( status != 0 )) && exit "${status}"
 
diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index cb6b55a6218..b4d960d01b8 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -25,9 +25,9 @@
 #####################################################################
 
 # shellcheck source=ush/preamble.sh
-source "${HOMEgfs:?}/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
-cd "${DATA:?}" || exit 1
+cd "${DATA}" || exit 1
 
 export POSTGPSH=${POSTGPSH:-${USHgfs}/gfs_post.sh}
 export GFSDOWNSH=${GFSDOWNSH:-${USHgfs}/fv3gfs_downstream_nems.sh}
@@ -78,11 +78,12 @@ export IDRT=${IDRT:-0} # IDRT=0 is setting for outputting grib files on lat/lon
 # Post Analysis Files before starting the Forecast Post
 ############################################################
 # Chuang: modify to process analysis when post_times is 00
-export stime="$(echo "${post_times:?}" | cut -c1-3)"
+stime="$(echo "${post_times}" | cut -c1-3)"
+export stime
 if (( OUTTYP == 4 )) ; then
-  export loganl="${COMIN:?}/${PREFIX}atmanl${SUFFIX}"
+  export loganl="${COMIN}/${PREFIX}atmanl${SUFFIX}"
 else
-  export loganl="${COMIN:?}/${PREFIX}sanl"
+  export loganl="${COMIN}/${PREFIX}sanl"
 fi
 
 if [ "${stime}" = "anl" ]; then
@@ -90,7 +91,7 @@ if [ "${stime}" = "anl" ]; then
     # add new environmental variables for running new ncep post
     # Validation date
 
-    export VDATE=${PDY:?}${cyc}
+    export VDATE=${PDY}${cyc}
 
     # set outtyp to 1 because we need to run chgres in the post before model start running chgres
     # otherwise set to 0, then chgres will not be executed in global_nceppost.sh
@@ -101,12 +102,12 @@ if [ "${stime}" = "anl" ]; then
     # if model already runs gfs io, make sure GFSOUT is linked to the gfsio file
     # new imported variable for global_nceppost.sh
 
-    export GFSOUT=${RUN}.${cycle:?}.gfsioanl
+    export GFSOUT=${RUN}.${cycle}.gfsioanl
 
     # specify smaller control file for GDAS because GDAS does not
     # produce flux file, the default will be /nwprod/parm/gfs_cntrl.parm
 
-    if [ "${GRIBVERSION:?}" = 'grib2' ]; then
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
       export POSTGRB2TBL=${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}
       export PostFlatFile=${PostFlatFile:-${PARMpost}/postxconfig-NT-GFS-ANL.txt}
       export CTLFILE=${PARMpost}/postcntrl_gfs_anl.xml
@@ -123,7 +124,7 @@ if [ "${stime}" = "anl" ]; then
     export PGIOUT=pgifile
     export PGBOUT2=pgbfile.grib2
     export PGIOUT2=pgifile.grib2.idx
-    export IGEN="${IGEN_ANL:?}"
+    export IGEN="${IGEN_ANL}"
     export FILTER=0
 
     # specify fhr even for analysis because postgp uses it
@@ -145,24 +146,24 @@ if [ "${stime}" = "anl" ]; then
       export fhr3=anl
     fi
 
-    if [ "${SENDCOM:-YES}" = 'YES' ]; then
+    if [ "${SENDCOM}" = 'YES' ]; then
       export fhr3=anl
       if [ "${GRIBVERSION}" = 'grib2' ]; then
         MASTERANL=${PREFIX}master.grb2${fhr3}
         ##########XXW Accord to Boi, fortran index should use *if${fhr}, wgrib index use .idx
         #MASTERANLIDX=${RUN}.${cycle}.master.grb2${fhr3}.idx
         MASTERANLIDX=${PREFIX}master.grb2i${fhr3}
-        cp "${PGBOUT2}" "${COMOUT:?}/${MASTERANL}"
-        ${GRB2INDEX:?} "${PGBOUT2}" "${COMOUT}/${MASTERANLIDX}"
+        cp "${PGBOUT2}" "${COMOUT}/${MASTERANL}"
+        ${GRB2INDEX} "${PGBOUT2}" "${COMOUT}/${MASTERANLIDX}"
       fi
 
-      if [ "${SENDDBN:-YES}" = 'YES' ]; then
-        run=$(echo ${RUN} | tr 'a-z' 'A-Z')
+      if [ "${SENDDBN}" = 'YES' ]; then
+        run="$(echo ${RUN} | tr '[:lower:]' '[:upper:]')"
         if [ "${GRIBVERSION}" = 'grib2' ]; then
-          "${DBNROOT:?}/bin/dbn_alert" MODEL "${run}_MSC_sfcanl" "${job:?}" "${COMOUT}/${PREFIX}sfc${fhr3}${SUFFIX}"
-          "${DBNROOT:?}/bin/dbn_alert" MODEL "${run}_SA" "${job:?}" "${COMIN}/${PREFIX}atm${fhr3}${SUFFIX}"
-          "${DBNROOT:?}/bin/dbn_alert" MODEL "GDAS_PGA_GB2" "${job:?}" "${COMOUT}/${PREFIX}pgrb2.1p00.${fhr3}"
-          "${DBNROOT:?}/bin/dbn_alert" MODEL "GDAS_PGA_GB2_WIDX" "${job:?}" "${COMOUT}/${PREFIX}pgrb2.1p00.${fhr3}.idx"
+          "${DBNROOT}/bin/dbn_alert" MODEL "${run}_MSC_sfcanl" "${job}" "${COMOUT}/${PREFIX}sfc${fhr3}${SUFFIX}"
+          "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SA" "${job}" "${COMIN}/${PREFIX}atm${fhr3}${SUFFIX}"
+          "${DBNROOT}/bin/dbn_alert" MODEL "GDAS_PGA_GB2" "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.${fhr3}"
+          "${DBNROOT}/bin/dbn_alert" MODEL "GDAS_PGA_GB2_WIDX" "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.${fhr3}.idx"
         fi
       fi
     fi
@@ -174,7 +175,7 @@ if [ "${stime}" = "anl" ]; then
     err_chk
   fi
 else   ## not_anl if_stimes
-  SLEEP_LOOP_MAX=$(( ${SLEEP_TIME:?} / ${SLEEP_INT:?} ))
+  SLEEP_LOOP_MAX=$(( SLEEP_TIME / SLEEP_INT ))
 
   ############################################################
   # Loop Through the Post Forecast Files
@@ -188,7 +189,7 @@ else   ## not_anl if_stimes
     export pgm="postcheck"
     ic=1
     while (( ic <= SLEEP_LOOP_MAX )); do
-      if [ -f "${restart_file:?}${fhr}.txt" ]; then
+      if [ -f "${restart_file}${fhr}.txt" ]; then
         break
       else
         ic=$(( ic + 1 ))
@@ -213,22 +214,23 @@ else   ## not_anl if_stimes
     [[ -f flxfile ]] && rm flxfile
     [[ -f nemsfile ]] && rm nemsfile
     if (( OUTTYP == 4 )) ; then
-      ln -sf "${COMIN}/${PREFIX}atmf$fhr${SUFFIX}" nemsfile
+      ln -sf "${COMIN}/${PREFIX}atmf${fhr}${SUFFIX}" nemsfile
       export NEMSINP=nemsfile
-      ln -sf "${COMIN}/${PREFIX}sfcf$fhr${SUFFIX}" flxfile
+      ln -sf "${COMIN}/${PREFIX}sfcf${fhr}${SUFFIX}" flxfile
       export FLXINP=flxfile
     fi
 
     if (( fhr > 0 )); then
-      export IGEN=${IGEN_FCST:?}
+      export IGEN=${IGEN_FCST}
     else
-      export IGEN=${IGEN_ANL:?}
+      export IGEN=${IGEN_ANL}
     fi
 
     # add new environmental variables for running new ncep post
     # Validation date
 
-    export VDATE="$(${NDATE:?} "+${fhr}" "${PDY}${cyc}")"
+    VDATE="$(${NDATE} "+${fhr}" "${PDY}${cyc}")"
+    export VDATE
 
     # set to 3 to output lat/lon grid
 
@@ -238,10 +240,10 @@ else   ## not_anl if_stimes
       export POSTGRB2TBL="${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}"
       export PostFlatFile="${PARMpost}/postxconfig-NT-GFS.txt"
       if [ "${RUN}" = gfs ]; then
-        export IGEN="${IGEN_GFS:?}"
+        export IGEN="${IGEN_GFS}"
         if (( fhr > 0 )); then export IGEN="${IGEN_FCST}" ; fi
       else
-        export IGEN="${IGEN_GDAS_ANL:?}"
+        export IGEN="${IGEN_GDAS_ANL}"
         if (( fhr > 0 )); then export IGEN="${IGEN_FCST}" ; fi
       fi
       if [[ "${RUN}" = gfs ]]; then
@@ -290,8 +292,8 @@ else   ## not_anl if_stimes
     ${GFSDOWNSH}
     export err=$?; err_chk
 
-    if [ "${SENDDBN}" = YES ]; then
-      run=$(echo ${RUN} | tr 'a-z' 'A-Z')
+    if [ "${SENDDBN}" = "YES" ]; then
+      run="$(echo ${RUN} | tr '[:lower:]' '[:upper:]')"
       "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB2_0P25" "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.f${fhr}"
       "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB2_0P25_WIDX ""${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.f${fhr}.idx"
       "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB_GB2" "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.f${fhr}"
@@ -330,7 +332,7 @@ else   ## not_anl if_stimes
           export err=$?; err_chk
           mv fluxfile "${COMOUT}/${FLUXFL}"
         fi
-        ${WGRIB2:?} -s "${COMOUT}/${FLUXFL}" > "${COMOUT}/${FLUXFLIDX}"
+        ${WGRIB2} -s "${COMOUT}/${FLUXFL}" > "${COMOUT}/${FLUXFLIDX}"
       fi
 
       if [ "${SENDDBN}" = 'YES' ] && [ "${RUN}" = 'gdas' ] && (( fhr % 3 == 0 )); then
diff --git a/scripts/exgfs_atmos_post.sh b/scripts/exgfs_atmos_post.sh
index d88f2f241f3..8daf328d963 100755
--- a/scripts/exgfs_atmos_post.sh
+++ b/scripts/exgfs_atmos_post.sh
@@ -36,9 +36,9 @@
 # echo "-----------------------------------------------------"
 #####################################################################
 
-source "${HOMEgfs:?}/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
-cd "${DATA:?}" || exit 1
+cd "${DATA}" || exit 1
 
 # specify model output format type: 4 for nemsio, 3 for sigio
 export POSTGPSH=${POSTGPSH:-${USHgfs}/gfs_post.sh}
@@ -93,18 +93,19 @@ export IDRT=${IDRT:-0} # IDRT=0 is setting for outputting grib files on lat/lon
 # Post Analysis Files before starting the Forecast Post
 ############################################################
 # Process analysis when post_times is 00
-export stime="$(echo ${post_times:?} | cut -c1-3)"
+stime="$(echo ${post_times} | cut -c1-3)"
+export stime
 if (( OUTTYP == 4 )); then
-  export loganl="${COMIN:?}/${PREFIX}atmanl${SUFFIX}"
+  export loganl="${COMIN}/${PREFIX}atmanl${SUFFIX}"
 else
-  export loganl="${COMIN:?}/${PREFIX}sanl"
+  export loganl="${COMIN}/${PREFIX}sanl"
 fi
 
 if [ "${stime}" = "anl" ]; then
   if [ -f "${loganl}" ]; then
     # add new environmental variables for running new ncep post
     # Validation date
-    export VDATE=${PDY:?}${cyc}
+    export VDATE=${PDY}${cyc}
     # specify output file name from chgres which is input file name to nceppost
     # if model already runs gfs io, make sure GFSOUT is linked to the gfsio file
     # new imported variable for global_nceppost.sh
@@ -112,7 +113,7 @@ if [ "${stime}" = "anl" ]; then
 
     # specify smaller control file for GDAS because GDAS does not
     # produce flux file, the default will be /nwprod/parm/gfs_cntrl.parm
-    if [ "${GRIBVERSION:?}" = 'grib2' ]; then
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
       # use grib2 nomonic table in product g2tmpl directory as default 
       export POSTGRB2TBL=${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}
       export PostFlatFile=${PostFlatFile:-${PARMpost}/postxconfig-NT-GFS-ANL.txt}
@@ -131,7 +132,7 @@ if [ "${stime}" = "anl" ]; then
     export PGIOUT=pgifile
     export PGBOUT2=pgbfile.grib2
     export PGIOUT2=pgifile.grib2.idx
-    export IGEN=${IGEN_ANL:?}
+    export IGEN=${IGEN_ANL}
     export FILTER=0
 
     ${POSTGPSH}
@@ -149,19 +150,19 @@ if [ "${stime}" = "anl" ]; then
       export err=$?; err_chk
     fi
 
-    if [ "${SENDCOM:-YES}" = 'YES' ]; then
+    if [ "${SENDCOM}" = 'YES' ]; then
       export fhr3=anl
       if [ "${GRIBVERSION}" = 'grib2' ]; then
         MASTERANL=${PREFIX}master.grb2${fhr3}
         MASTERANLIDX=${PREFIX}master.grb2i${fhr3}
-        cp "${PGBOUT2}" "${COMOUT:?}/${MASTERANL}"
-        ${GRB2INDEX:?} "${PGBOUT2}" "${COMOUT}/${MASTERANLIDX}"
+        cp "${PGBOUT2}" "${COMOUT}/${MASTERANL}"
+        ${GRB2INDEX} "${PGBOUT2}" "${COMOUT}/${MASTERANLIDX}"
       fi
 
-      if [ "${SENDDBN:-YES}" = 'YES' ]; then
+      if [ "${SENDDBN}" = 'YES' ]; then
         "${DBNROOT}/bin/dbn_alert" MODEL GFS_MSC_sfcanl "${job}" "${COMOUT}/${PREFIX}sfcanl${SUFFIX}"
         "${DBNROOT}/bin/dbn_alert" MODEL GFS_SA "${job}" "${COMOUT}/${PREFIX}atmanl${SUFFIX}"
-        if [ "$PGBF" = 'YES' ]; then
+        if [ "${PGBF}" = 'YES' ]; then
           "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P25 "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.anl"
           "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P25_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.anl.idx"
           "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2B_0P25 "${job}" "${COMOUT}/${PREFIX}pgrb2b.0p25.anl"
@@ -185,7 +186,7 @@ if [ "${stime}" = "anl" ]; then
     ##########################  WAFS U/V/T analysis start ##########################
     # U/V/T on ICAO standard atmospheric pressure levels for WAFS verification
     if [ "${WAFSF}" = "YES" ]; then
-      if [[ "${RUN}" = gfs && "${GRIBVERSION}" = 'grib2' ]]; then
+      if [[ "${RUN}" = "gfs" && "${GRIBVERSION}" = 'grib2' ]]; then
         export OUTTYP=${OUTTYP:-4}
 
         export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-WAFS-ANL.txt"
@@ -194,16 +195,16 @@ if [ "${stime}" = "anl" ]; then
         export PGBOUT=wafsfile
         export PGIOUT=wafsifile
 
-        $POSTGPSH
+        ${POSTGPSH}
         export err=$?
         if (( err != 0 )); then
-          echo " *** GFS POST WARNING: WAFS output failed for analysis, err=$err"
+          echo " *** GFS POST WARNING: WAFS output failed for analysis, err=${err}"
         else
           # WAFS package doesn't process this part.
           # Need to be saved for WAFS U/V/T verification, 
           # resolution higher than WAFS 1.25 deg for future compatibility
           wafsgrid="latlon 0:1440:0.25 90:721:-0.25"
-          ${WGRIB2:?} "${PGBOUT}" -set_grib_type same -new_grid_winds earth \
+          ${WGRIB2} "${PGBOUT}" -set_grib_type same -new_grid_winds earth \
           -new_grid_interpolation bilinear -set_bitmap 1 \
           -new_grid "${wafsgrid}" "${PGBOUT}.tmp"
 
@@ -228,7 +229,7 @@ if [ "${stime}" = "anl" ]; then
     err_chk
   fi
 else   ## not_anl if_stime
-  SLEEP_LOOP_MAX=$(( ${SLEEP_TIME:?} / ${SLEEP_INT:?} ))
+  SLEEP_LOOP_MAX=$(( ${SLEEP_TIME} / ${SLEEP_INT} ))
 
   ############################################################
   # Loop Through the Post Forecast Files 
@@ -243,7 +244,7 @@ else   ## not_anl if_stime
     export pgm="postcheck"
     ic=1
     while (( ic <= SLEEP_LOOP_MAX )); do
-      if [ -f "${restart_file:?}${fhr}.txt" ]; then
+      if [ -f "${restart_file}${fhr}.txt" ]; then
         break
       else
         ic=$(( ic + 1 ))
@@ -274,24 +275,25 @@ else   ## not_anl if_stime
     fi
 
     if (( fhr > 0 )); then
-      export IGEN=${IGEN_FCST:?}
+      export IGEN=${IGEN_FCST}
     else
       export IGEN=${IGEN_ANL}
     fi
 
-    export VDATE=$(${NDATE:?} +${fhr} "${PDY}${cyc}")
+    VDATE="$(${NDATE} +${fhr} "${PDY}${cyc}")"
+    export VDATE
     export OUTTYP=${OUTTYP:-4}
     export GFSOUT="${PREFIX}gfsio${fhr}"
 
-    if [ $GRIBVERSION = 'grib2' ]; then
+    if [ "${GRIBVERSION}" = 'grib2' ]; then
       export POSTGRB2TBL="${POSTGRB2TBL:-${g2tmpl_ROOT}/share/params_grib2_tbl_new}"
       export PostFlatFile="${PostFlatFile:-${PARMpost}/postxconfig-NT-GFS.txt}"
 
       if [ "${RUN}" = "gfs" ]; then
-        export IGEN=${IGEN_GFS:?}
+        export IGEN=${IGEN_GFS}
         if (( fhr > 0 )); then export IGEN=${IGEN_FCST} ; fi
       else
-        export IGEN=${IGEN_GDAS_ANL:?}
+        export IGEN=${IGEN_GDAS_ANL}
         if (( fhr > 0 )); then export IGEN=${IGEN_FCST} ; fi
       fi
       if [[ "${RUN}" = "gfs" ]]; then
@@ -396,7 +398,7 @@ else   ## not_anl if_stime
       FLUXFLIDX=${PREFIX}sfluxgrbf${fhr}.grib2.idx
 
       #Add extra flux.1p00 file for coupled
-      if [ "$FLXGF" = 'YES' ]; then                    
+      if [ "${FLXGF}" = 'YES' ]; then                    
         export FH=$(( fhr + 0 ))
         ${GFSDOWNSHF}
         export err=$?; err_chk
@@ -428,7 +430,7 @@ else   ## not_anl if_stime
 
       # link satellite coefficients files, use hwrf version as ops crtm 2.0.5
       # does not new coefficient files used by post
-      export FIXCRTM=${FIXCRTM:-${CRTM_FIX}}
+      export FIXCRTM="${FIXCRTM:-${CRTM_FIX}}"
       "${USHgfs}/link_crtm_fix.sh" ${FIXCRTM}
 
       if [ "${GRIBVERSION}" = 'grib2' ]; then 
@@ -444,7 +446,7 @@ else   ## not_anl if_stime
       export JO=0
       export IGEN=0
 
-      if [ "${NET:?}" = "gfs" ]; then
+      if [ "${NET}" = "gfs" ]; then
         ${POSTGPSH}
         export err=$?; err_chk
       fi
@@ -490,9 +492,9 @@ else   ## not_anl if_stime
         #   hourly if fhr<=24
         #   every 3 forecast hour if 24<fhr<=48
         #   every 6 forecast hour if 48<fhr<=120
-        if (( $fhr <= 24 )); then
+        if (( fhr <= 24 )); then
           ${POSTGPSH}
-        elif (( $fhr <= 48 )); then
+        elif (( fhr <= 48 )); then
           if (( 10#${fhr}%3 == 0 )); then
             ${POSTGPSH}
           fi
@@ -504,7 +506,7 @@ else   ## not_anl if_stime
         if (( err != 0 )); then
           echo " *** GFS POST WARNING: WAFS output failed for f${fhr}, err=${err}"
         else
-          if [ -e ${PGBOUT} ]; then
+          if [ -e "${PGBOUT}" ]; then
             if [ "${SENDCOM}" = "YES" ]; then
               cp "${PGBOUT}" "${COMOUT}/${PREFIX}wafs.grb2f${fhr}"
               cp "${PGIOUT}" "${COMOUT}/${PREFIX}wafs.grb2if${fhr}"

From 234fe63974e24322172c4498ab7fa09eac56277a Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 19:56:41 +0000
Subject: [PATCH 08/13] Linter corrections for gfs_pos

---
 .shellcheckrc                |   4 +
 scripts/exgdas_atmos_post.sh |   4 +-
 scripts/exgfs_atmos_post.sh  |   8 +-
 ush/gfs_post.sh              | 143 ++++++++++++++++++-----------------
 4 files changed, 83 insertions(+), 76 deletions(-)

diff --git a/.shellcheckrc b/.shellcheckrc
index a34e63a71a8..3628e97e586 100644
--- a/.shellcheckrc
+++ b/.shellcheckrc
@@ -1,3 +1,7 @@
 # Global settings for Spellcheck (https://github.com/koalaman/shellcheck)
 enable=all
+
+# Disable variable referenced but not assigned
 disable=SC2154
+
+
diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index b4d960d01b8..aa3f7989905 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -158,7 +158,7 @@ if [ "${stime}" = "anl" ]; then
       fi
 
       if [ "${SENDDBN}" = 'YES' ]; then
-        run="$(echo ${RUN} | tr '[:lower:]' '[:upper:]')"
+        run="$(echo "${RUN}" | tr '[:lower:]' '[:upper:]')"
         if [ "${GRIBVERSION}" = 'grib2' ]; then
           "${DBNROOT}/bin/dbn_alert" MODEL "${run}_MSC_sfcanl" "${job}" "${COMOUT}/${PREFIX}sfc${fhr3}${SUFFIX}"
           "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SA" "${job}" "${COMIN}/${PREFIX}atm${fhr3}${SUFFIX}"
@@ -293,7 +293,7 @@ else   ## not_anl if_stimes
     export err=$?; err_chk
 
     if [ "${SENDDBN}" = "YES" ]; then
-      run="$(echo ${RUN} | tr '[:lower:]' '[:upper:]')"
+      run="$(echo "${RUN}" | tr '[:lower:]' '[:upper:]')"
       "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB2_0P25" "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.f${fhr}"
       "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB2_0P25_WIDX ""${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.f${fhr}.idx"
       "${DBNROOT}/bin/dbn_alert" MODEL "${run}_PGB_GB2" "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.f${fhr}"
diff --git a/scripts/exgfs_atmos_post.sh b/scripts/exgfs_atmos_post.sh
index 8daf328d963..e9772b396a8 100755
--- a/scripts/exgfs_atmos_post.sh
+++ b/scripts/exgfs_atmos_post.sh
@@ -93,7 +93,7 @@ export IDRT=${IDRT:-0} # IDRT=0 is setting for outputting grib files on lat/lon
 # Post Analysis Files before starting the Forecast Post
 ############################################################
 # Process analysis when post_times is 00
-stime="$(echo ${post_times} | cut -c1-3)"
+stime="$(echo "${post_times}" | cut -c1-3)"
 export stime
 if (( OUTTYP == 4 )); then
   export loganl="${COMIN}/${PREFIX}atmanl${SUFFIX}"
@@ -229,7 +229,7 @@ if [ "${stime}" = "anl" ]; then
     err_chk
   fi
 else   ## not_anl if_stime
-  SLEEP_LOOP_MAX=$(( ${SLEEP_TIME} / ${SLEEP_INT} ))
+  SLEEP_LOOP_MAX=$(( SLEEP_TIME / SLEEP_INT ))
 
   ############################################################
   # Loop Through the Post Forecast Files 
@@ -248,7 +248,7 @@ else   ## not_anl if_stime
         break
       else
         ic=$(( ic + 1 ))
-        sleep ${SLEEP_INT}
+        sleep "${SLEEP_INT}"
       fi
       ###############################
       # If we reach this point assume
@@ -431,7 +431,7 @@ else   ## not_anl if_stime
       # link satellite coefficients files, use hwrf version as ops crtm 2.0.5
       # does not new coefficient files used by post
       export FIXCRTM="${FIXCRTM:-${CRTM_FIX}}"
-      "${USHgfs}/link_crtm_fix.sh" ${FIXCRTM}
+      "${USHgfs}/link_crtm_fix.sh" "${FIXCRTM}"
 
       if [ "${GRIBVERSION}" = 'grib2' ]; then 
         export PostFlatFile="${PARMpost}/postxconfig-NT-GFS-GOES.txt   "   
diff --git a/ush/gfs_post.sh b/ush/gfs_post.sh
index c38edfe4ec2..e36276a3868 100755
--- a/ush/gfs_post.sh
+++ b/ush/gfs_post.sh
@@ -188,7 +188,7 @@
 ####
 ################################################################################
 #  Set environment.
-source "$HOMEgfs/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
 #  Command line arguments.
 export SIGINP=${1:-${SIGINP:-}}
@@ -202,10 +202,10 @@ export JO=${7:-${JO:-0}}
 export IGEN=${8:-${IGEN:-0}}
 #  Directories.
 export NWPROD=${NWPROD:-/nwprod}
-#export EXECUTIL=${EXECUTIL:-$NWPROD/util/exec}
-export USHUTIL=${USHUTIL:-$NWPROD/util/ush}
-export EXECgfs=${EXECgfs:-$NWPROD/exec}
-export USHgfs=${USHgfs:-$NWPROD/ush}
+#export EXECUTIL=${EXECUTIL:-${NWPROD}/util/exec}
+export USHUTIL=${USHUTIL:-${NWPROD}/util/ush}
+export EXECgfs=${EXECgfs:-${NWPROD}/exec}
+export USHgfs=${USHgfs:-${NWPROD}/ush}
 export DATA=${DATA:-$(pwd)}
 #  Filenames.
 export MP=${MP:-$([[ ${LOADL_STEP_TYPE:-SERIAL} = PARALLEL ]]&&echo "p"||echo "s")}
@@ -214,11 +214,13 @@ export POSTGPEXEC=${POSTGPEXEC:-${EXECgfs}/upp.x}
 export OVERPARMEXEC=${OVERPARMEXEC:-${EXECgfs}/overparm_grib}
 export POSTGPLIST=${POSTGPLIST:-/dev/null}
 export INISCRIPT=${INISCRIPT:-}
-export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
+# shellcheck disable=SC2016
+export ERRSCRIPT=${ERRSCRIPT:-'eval (( err == 0 ))'}
+# shellcheck disable=
 export LOGSCRIPT=${LOGSCRIPT:-}
 export ENDSCRIPT=${ENDSCRIPT:-}
 export GFSOUT=${GFSOUT:-gfsout}
-export CTLFILE=${CTLFILE:-$NWPROD/parm/gfs_cntrl.parm}
+export CTLFILE=${CTLFILE:-${NWPROD}/parm/gfs_cntrl.parm}
 #export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
 export OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
 export GRIBVERSION=${GRIBVERSION:-'grib1'}
@@ -234,12 +236,12 @@ export GENPSICHI=${GENPSICHI:-NO}
 export GENPSICHIEXE=${GENPSICHIEXE:-${EXECgfs}/genpsiandchi}
 export ens=${ens:-NO}
 #export D3DINP=${D3DINP:-/dev/null}
-l=$(echo $PGMOUT | xargs | cut -c1)
-[[ $l = '&' ]]&&a=''||a='>'
-export REDOUT=${REDOUT:-'1>'$a}
-l=$(echo $PGMERR | xargs | cut -c1)
-[[ $l = '&' ]]&&a=''||a='>'
-export REDERR=${REDERR:-'2>'$a}
+l="$(echo "${PGMOUT}" | xargs | cut -c1)"
+[[ ${l} = '&' ]]&&a=''||a='>'
+export REDOUT=${REDOUT:-'1>'${a}}
+l="$(echo "${PGMERR}" | xargs | cut -c1)"
+[[ ${l} = '&' ]]&&a=''||a='>'
+export REDERR=${REDERR:-'2>'${a}}
 ################################################################################
 
 # Chuang: Run chgres if OUTTYP=1 or 0
@@ -247,21 +249,21 @@ export REDERR=${REDERR:-'2>'$a}
 export APRUN=${APRUNP:-${APRUN:-""}}
 
 # exit if NEMSINP does not exist
-if [ ${OUTTYP} -eq 4 ] ; then
-	if [ ! -s $NEMSINP -o ! -s $FLXINP  ] ; then
+if (( OUTTYP == 4 )) ; then
+	if [ ! -s "${NEMSINP}" ] || [ ! -s "${FLXINP}"  ] ; then
 		echo "model files not found, exitting"
 		exit 111
 	fi
 fi
 
-export SIGHDR=${SIGHDR:-$NWPROD/exec/global_sighdr} 
+export SIGHDR=${SIGHDR:-${NWPROD}/exec/global_sighdr} 
 export IDRT=${IDRT:-4}
 
 # run post to read nemsio file if OUTTYP=4
-if [ ${OUTTYP} -eq 4 ] ; then
-	if [ ${OUTPUT_FILE} = "netcdf" ]; then
+if (( OUTTYP == 4 )) ; then
+	if [ "${OUTPUT_FILE}" = "netcdf" ]; then
 		export MODEL_OUT_FORM=${MODEL_OUT_FORM:-netcdfpara}
-	elif [ ${OUTPUT_FILE} = "nemsio" ]; then
+	elif [ "${OUTPUT_FILE}" = "nemsio" ]; then
 		export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
 	else
 		export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
@@ -274,36 +276,37 @@ fi
 export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
 
 pwd=$(pwd)
-if [[ -d $DATA ]]; then
+if [[ -d "${DATA}" ]]; then
 	mkdata=NO
 else
-	mkdir -p $DATA
+	mkdir -p "${DATA}"
 	mkdata=YES
 fi
-cd $DATA||exit 99
+cd "${DATA}" || exit 99
 ################################################################################
 #  Post GRIB
-export PGM=$POSTGPEXEC
-export pgm=$PGM
-$LOGSCRIPT
+export PGM=${POSTGPEXEC}
+export pgm=${PGM}
+${LOGSCRIPT}
 cat <<-EOF >postgp.inp.nml$$
 	&NAMPGB
-	$POSTGPVARS
+	${POSTGPVARS}
 EOF
 
 cat <<-EOF >>postgp.inp.nml$$
 	/
 EOF
 
-if [[ "$VERBOSE" = "YES" ]]; then
+if [[ "${VERBOSE}" = "YES" ]]; then
 	cat postgp.inp.nml$$
 fi
 
 # making the time stamp format for ncep post
-export YY=$(echo $VDATE | cut -c1-4)
-export MM=$(echo $VDATE | cut -c5-6)
-export DD=$(echo $VDATE | cut -c7-8)
-export HH=$(echo $VDATE | cut -c9-10)
+YY=$(echo "${VDATE}" | cut -c1-4)
+MM=$(echo "${VDATE}" | cut -c5-6)
+DD=$(echo "${VDATE}" | cut -c7-8)
+HH=$(echo "${VDATE}" | cut -c9-10)
+export YY MM DD HH
 
 cat > itag <<-EOF
 	&model_inputs
@@ -327,54 +330,55 @@ rm -f fort.*
 #ln -sf $PGBOUT     postgp.out.pgb$$
 
 # change model generating Grib number 
-if [ ${GRIBVERSION} = grib2 ]; then
-	cp ${POSTGRB2TBL} .
-	cp ${PostFlatFile} ./postxconfig-NT.txt
-	if [ ${ens} = "YES" ] ; then
-		sed < ${PostFlatFile} -e "s#negatively_pert_fcst#${ens_pert_type}#" > ./postxconfig-NT.txt
+if [ "${GRIBVERSION}" = "grib2" ]; then
+	cp "${POSTGRB2TBL}" .
+	cp "${PostFlatFile}" ./postxconfig-NT.txt
+	if [ "${ens}" = "YES" ] ; then
+		sed < "${PostFlatFile}" -e "s#negatively_pert_fcst#${ens_pert_type}#" > ./postxconfig-NT.txt
 	fi
 	#  cp ${CTLFILE} postcntrl.xml
 fi
-export CTL=$(basename $CTLFILE)
+CTL=$(basename "${CTLFILE}")
+export CTL
 
 ln -sf griddef.out fort.110
-cp ${PARMpost}/nam_micro_lookup.dat ./eta_micro_lookup.dat
+cp "${PARMpost}/nam_micro_lookup.dat" ./eta_micro_lookup.dat
 
-echo "gfs_post.sh OMP_NUM_THREADS= $OMP_NUM_THREADS"
-${APRUN:-mpirun.lsf} $POSTGPEXEC < itag > outpost_gfs_${VDATE}_${CTL}
+echo "gfs_post.sh OMP_NUM_THREADS= ${OMP_NUM_THREADS}"
+${APRUN:-mpirun.lsf} "${POSTGPEXEC}" < itag > "outpost_gfs_${VDATE}_${CTL}"
 
 export ERR=$?
-export err=$ERR
+export err=${ERR}
 
-if [ $err -ne 0 ] ; then
-	if [ $PGBOUT = "wafsfile" ] ; then
-		exit $err
+if (( err != 0 )) ; then
+	if [ "${PGBOUT}" = "wafsfile" ] ; then
+		exit "${err}"
 	fi
 fi
-$ERRSCRIPT||exit 2
+${ERRSCRIPT} || exit 2
 
-if [ $FILTER = "1" ] ; then
+if [ "${FILTER}" = "1" ] ; then
 	# Filter SLP and 500 mb height using copygb, change GRIB ID, and then
 	# cat the filtered fields to the pressure GRIB file, from Iredell
 
-	if [ $GRIBVERSION = grib2 ]; then
-		if [ ${ens} = YES ] ; then
-			$COPYGB2 -x -i'4,0,80' -k'1 3 0 7*-9999 101 0 0' $PGBOUT tfile
+	if [ "${GRIBVERSION}" = "grib2" ]; then
+		if [ "${ens}" = "YES" ] ; then
+			"${COPYGB2}" -x -i'4,0,80' -k'1 3 0 7*-9999 101 0 0' "${PGBOUT}" tfile
 			export err=$?; err_chk
 		else
-			$COPYGB2 -x -i'4,0,80' -k'0 3 0 7*-9999 101 0 0' $PGBOUT tfile
+			"${COPYGB2}" -x -i'4,0,80' -k'0 3 0 7*-9999 101 0 0' "${PGBOUT}" tfile
 			export err=$?; err_chk
 		fi
-		$WGRIB2 tfile -set_byte 4 11 1 -grib prmsl
+		${WGRIB2} tfile -set_byte 4 11 1 -grib prmsl
 		export err=$?; err_chk
-		if [ ${ens} = YES ] ; then
-			$COPYGB2 -x -i'4,1,5' -k'1 3 5 7*-9999 100 0 50000' $PGBOUT tfile
+		if [ "${ens}" = "YES" ] ; then
+			"${COPYGB2}" -x -i'4,1,5' -k'1 3 5 7*-9999 100 0 50000' "${PGBOUT}" tfile
 			export err=$?; err_chk
 		else
-			$COPYGB2 -x -i'4,1,5' -k'0 3 5 7*-9999 100 0 50000' $PGBOUT tfile
+			"${COPYGB2}" -x -i'4,1,5' -k'0 3 5 7*-9999 100 0 50000' "${PGBOUT}" tfile
 			export err=$?; err_chk
 		fi
-		$WGRIB2 tfile -set_byte 4 11 193 -grib h5wav
+		${WGRIB2} tfile -set_byte 4 11 193 -grib h5wav
 		export err=$?; err_chk
 
 		#cat $PGBOUT prmsl h5wav >> $PGBOUT
@@ -388,33 +392,32 @@ fi
 
 ################################################################################
 #  Make GRIB index file
-if [[ -n $PGIOUT ]]; then
-	if [ $GRIBVERSION = grib2 ]; then
-		# JY $GRBINDEX2 $PGBOUT $PGIOUT
-		$GRB2INDEX $PGBOUT $PGIOUT
+if [[ -n "${PGIOUT}" ]]; then
+	if [ "${GRIBVERSION}" = "grib2" ]; then
+		${GRB2INDEX} "${PGBOUT}" "${PGIOUT}"
 	fi
 fi
-if [[ -r $FLXINP && -n $FLXIOUT && $OUTTYP -le 3 ]]; then
-	$GRBINDEX $FLXINP $FLXIOUT
+if [[ -r ${FLXINP} && -n ${FLXIOUT} && ${OUTTYP} -le 3 ]]; then
+	${GRBINDEX} "${FLXINP}" "${FLXIOUT}"
 fi
 ################################################################################
 # generate psi and chi
-echo "GENPSICHI= " $GENPSICHI
-if [ $GENPSICHI = YES ] ; then
+echo "GENPSICHI = ${GENPSICHI}"
+if [ "${GENPSICHI}" = "YES" ] ; then
 	#echo "PGBOUT PGIOUT=" $PGBOUT $PGIOUT
 	#echo "YY MM=" $YY $MM
 	export psichifile=./psichi.grb
-	$GENPSICHIEXE < postgp.inp.nml$$
+	${GENPSICHIEXE} < postgp.inp.nml$$
 	rc=$?
-	if [[ $rc -ne 0 ]] ; then
-		echo 'Nonzero return code rc= '$rc
+	if (( rc != 0 )); then
+		echo "Nonzero return code rc=${rc}"
 		exit 3
 	fi
-	cat ./psichi.grb >> $PGBOUT
+	cat ./psichi.grb >> "${PGBOUT}"
 fi
 ################################################################################
 #  Postprocessing
-cd $pwd
-[[ $mkdata = YES ]]&&rmdir $DATA
+cd "${pwd}" || exit 2
+[[ "${mkdata}" = "YES" ]] && rmdir "${DATA}"
 
-exit $err
+exit "${err}"

From d2ac3e38d9af5e78ebfe80d47324b623a9f560cd Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 20:03:19 +0000
Subject: [PATCH 09/13] Last linter cleanup for post rename

---
 scripts/exgfs_atmos_post.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/exgfs_atmos_post.sh b/scripts/exgfs_atmos_post.sh
index e9772b396a8..ab0a84ba097 100755
--- a/scripts/exgfs_atmos_post.sh
+++ b/scripts/exgfs_atmos_post.sh
@@ -280,7 +280,7 @@ else   ## not_anl if_stime
       export IGEN=${IGEN_ANL}
     fi
 
-    VDATE="$(${NDATE} +${fhr} "${PDY}${cyc}")"
+    VDATE="$(${NDATE} "+${fhr}" "${PDY}${cyc}")"
     export VDATE
     export OUTTYP=${OUTTYP:-4}
     export GFSOUT="${PREFIX}gfsio${fhr}"

From 9c199afa4b9700e7122e7590c33d79be7bd01962 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 20:10:54 +0000
Subject: [PATCH 10/13] Disable shellcheck on sourced scripts

Turns off shellcheck parsing sourced scripts and removes some shellcheck
directives that are no longer necessary.
---
 .shellcheckrc                | 4 ++--
 jobs/JGLOBAL_ATMOS_POST      | 5 -----
 scripts/exgdas_atmos_post.sh | 1 -
 ush/gfs_post.sh              | 1 +
 4 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/.shellcheckrc b/.shellcheckrc
index 3628e97e586..1a4c5fdd63f 100644
--- a/.shellcheckrc
+++ b/.shellcheckrc
@@ -1,7 +1,7 @@
 # Global settings for Spellcheck (https://github.com/koalaman/shellcheck)
 enable=all
 
+external-sources=false
+
 # Disable variable referenced but not assigned
 disable=SC2154
-
-
diff --git a/jobs/JGLOBAL_ATMOS_POST b/jobs/JGLOBAL_ATMOS_POST
index 1a19a72bfff..ab75918aa63 100755
--- a/jobs/JGLOBAL_ATMOS_POST
+++ b/jobs/JGLOBAL_ATMOS_POST
@@ -1,6 +1,5 @@
 #! /usr/bin/env bash
 
-# shellcheck source=ush/preamble.sh
 source "${HOMEgfs}/ush/preamble.sh"
 
 export RUN_ENVIR=${RUN_ENVIR:-"nco"}
@@ -12,7 +11,6 @@ configs="base post"
 export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
 config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config}
 for config in ${configs}; do
-    # shellcheck source-path=parm/config
     . "${config_path}/config.${config}"
     status=$?
     (( status != 0 )) && exit "${status}"
@@ -22,7 +20,6 @@ done
 ##########################################
 # Source machine runtime environment
 ##########################################
-# shellcheck source-path=env
 . "${HOMEgfs}/env/${machine}.env" post
 status=$?
 (( status != 0 )) && exit "${status}"
@@ -43,9 +40,7 @@ cd "${DATA}" || exit 1
 ##############################################
 export cycle="t${cyc}z"
 setpdy.sh
-# shellcheck disable=SC1091
 . ./PDY
-# shellcheck disable=
 
 
 ##############################################
diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index aa3f7989905..a1753b7fe85 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -24,7 +24,6 @@
 # echo "-----------------------------------------------------"
 #####################################################################
 
-# shellcheck source=ush/preamble.sh
 source "${HOMEgfs}/ush/preamble.sh"
 
 cd "${DATA}" || exit 1
diff --git a/ush/gfs_post.sh b/ush/gfs_post.sh
index e36276a3868..7fbb19bb707 100755
--- a/ush/gfs_post.sh
+++ b/ush/gfs_post.sh
@@ -214,6 +214,7 @@ export POSTGPEXEC=${POSTGPEXEC:-${EXECgfs}/upp.x}
 export OVERPARMEXEC=${OVERPARMEXEC:-${EXECgfs}/overparm_grib}
 export POSTGPLIST=${POSTGPLIST:-/dev/null}
 export INISCRIPT=${INISCRIPT:-}
+# Ignore warning about single quote not subtituting now
 # shellcheck disable=SC2016
 export ERRSCRIPT=${ERRSCRIPT:-'eval (( err == 0 ))'}
 # shellcheck disable=

From a0bb6cb11a01983b31a45aae571134f4bff1e657 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 20:16:17 +0000
Subject: [PATCH 11/13] Disable more shellcheck errors

---
 .shellcheckrc | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.shellcheckrc b/.shellcheckrc
index 1a4c5fdd63f..45e13c2e048 100644
--- a/.shellcheckrc
+++ b/.shellcheckrc
@@ -5,3 +5,9 @@ external-sources=false
 
 # Disable variable referenced but not assigned
 disable=SC2154
+
+# Disable following non-constant source
+disable=SC1090
+
+# Disable non-existent binary
+disable=SC1091

From f6bd60a36fcd86a294fd93842487ab430cdcfa4f Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 29 Sep 2022 20:24:36 +0000
Subject: [PATCH 12/13] Suppress possible typo warning on NDATE

---
 scripts/exgdas_atmos_post.sh | 3 +++
 scripts/exgfs_atmos_post.sh  | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index a1753b7fe85..d7533b1ae7e 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -228,7 +228,10 @@ else   ## not_anl if_stimes
     # add new environmental variables for running new ncep post
     # Validation date
 
+    # No shellcheck, NDATE is not a typo
+    # shellcheck disable=SC2153
     VDATE="$(${NDATE} "+${fhr}" "${PDY}${cyc}")"
+    # shellcheck disable=
     export VDATE
 
     # set to 3 to output lat/lon grid
diff --git a/scripts/exgfs_atmos_post.sh b/scripts/exgfs_atmos_post.sh
index ab0a84ba097..3975da594dc 100755
--- a/scripts/exgfs_atmos_post.sh
+++ b/scripts/exgfs_atmos_post.sh
@@ -280,7 +280,10 @@ else   ## not_anl if_stime
       export IGEN=${IGEN_ANL}
     fi
 
+    # No shellcheck, NDATE is not a typo
+    # shellcheck disable=SC2153
     VDATE="$(${NDATE} "+${fhr}" "${PDY}${cyc}")"
+    # shellcheck disable=
     export VDATE
     export OUTTYP=${OUTTYP:-4}
     export GFSOUT="${PREFIX}gfsio${fhr}"

From bdfa1497d8f57a1df95ffe50eb07023d806e768a Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Mon, 3 Oct 2022 01:39:34 +0000
Subject: [PATCH 13/13] Fix decimal treated as octal issue in post

After linter modifications, a variable was being treated as an octal, resulting
in the wrong result when adding.
---
 scripts/exgdas_atmos_post.sh | 2 +-
 scripts/exgfs_atmos_post.sh  | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index d7533b1ae7e..98f109c29a8 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -289,7 +289,7 @@ else   ## not_anl if_stimes
     fi
 
     #wm Process pgb files
-    export FH=$(( fhr + 0 ))
+    export FH=$(( 10#${fhr} + 0 ))
     export downset=${downset:-1}
     ${GFSDOWNSH}
     export err=$?; err_chk
diff --git a/scripts/exgfs_atmos_post.sh b/scripts/exgfs_atmos_post.sh
index 3975da594dc..6777b1a3801 100755
--- a/scripts/exgfs_atmos_post.sh
+++ b/scripts/exgfs_atmos_post.sh
@@ -340,7 +340,7 @@ else   ## not_anl if_stime
 
     #  Process pgb files
     if [ "${PGBF}" = 'YES' ]; then
-      export FH=$(( fhr + 0 ))
+      export FH=$(( 10#${fhr} + 0 ))
       export downset=${downset:-2}
       ${GFSDOWNSH}
       export err=$?; err_chk
@@ -402,7 +402,7 @@ else   ## not_anl if_stime
 
       #Add extra flux.1p00 file for coupled
       if [ "${FLXGF}" = 'YES' ]; then                    
-        export FH=$(( fhr + 0 ))
+        export FH=$(( 10#${fhr} + 0 ))
         ${GFSDOWNSHF}
         export err=$?; err_chk
       fi