From 5deb7a85a5f011bf77062db6fe2b30e5848ee71b Mon Sep 17 00:00:00 2001
From: "Jeff.Beck" <Jeff.Beck@noaa.gov>
Date: Wed, 10 Jun 2020 21:27:19 +0000
Subject: [PATCH 1/9] Remove all references to /lfs3 on Jet

---
 modulefiles/module-setup.csh.inc              |  2 +-
 modulefiles/module-setup.sh.inc               |  2 +-
 modulefiles/tasks/jet/make_ics.hardcoded      | 34 -------------------
 modulefiles/tasks/jet/make_ics.local          |  5 ---
 modulefiles/tasks/jet/make_lbcs.hardcoded     | 34 -------------------
 modulefiles/tasks/jet/make_lbcs.local         |  5 ---
 tests/baseline_configs/config.nco_conus.sh    |  6 ++--
 .../baseline_configs/config.nco_conus_c96.sh  |  6 ++--
 tests/baseline_configs/config.regional_006.sh |  7 ++--
 tests/baseline_configs/config.regional_009.sh |  4 +--
 ush/load_fv3gfs_modules.sh                    |  2 +-
 ush/setup.sh                                  |  2 +-
 12 files changed, 15 insertions(+), 94 deletions(-)
 delete mode 100644 modulefiles/tasks/jet/make_ics.hardcoded
 delete mode 100644 modulefiles/tasks/jet/make_ics.local
 delete mode 100644 modulefiles/tasks/jet/make_lbcs.hardcoded
 delete mode 100644 modulefiles/tasks/jet/make_lbcs.local

diff --git a/modulefiles/module-setup.csh.inc b/modulefiles/module-setup.csh.inc
index a93b21a3c..5ac893cab 100644
--- a/modulefiles/module-setup.csh.inc
+++ b/modulefiles/module-setup.csh.inc
@@ -2,7 +2,7 @@ set __ms_shell=csh
 
 eval "if ( -d / ) set __ms_shell=tcsh"
 
-if ( { test -d /lfs3 } ) then 
+if ( { test -d /lfs4 } ) then 
     if ( ! { module help >& /dev/null } ) then
             source /apps/lmod/lmod/init/$__ms_shell
     endif
diff --git a/modulefiles/module-setup.sh.inc b/modulefiles/module-setup.sh.inc
index 82a60938e..ec81c0187 100644
--- a/modulefiles/module-setup.sh.inc
+++ b/modulefiles/module-setup.sh.inc
@@ -16,7 +16,7 @@ else
     __ms_shell=sh
 fi
 
-if [[ -d /lfs3 ]] ; then
+if [[ -d /lfs4 ]] ; then
     # We are on NOAA Jet
     if ( ! eval module help > /dev/null 2>&1 ) ; then
         source /apps/lmod/lmod/init/$__ms_shell
diff --git a/modulefiles/tasks/jet/make_ics.hardcoded b/modulefiles/tasks/jet/make_ics.hardcoded
deleted file mode 100644
index 5e63864de..000000000
--- a/modulefiles/tasks/jet/make_ics.hardcoded
+++ /dev/null
@@ -1,34 +0,0 @@
-#%Module#####################################################
-## Module file for make_ics task.
-#############################################################
-
-module load intel/18.0.5.274
-module load impi/2018.4.274
-module load szip
-module load hdf5
-module load netcdf/4.2.1.1
-
-module use /mnt/lfs3/projects/hfv3gfs/gwv/ljtjet/lib/modulefiles
-module load esmflocal/ESMF_8_0_0_beta_snapshot_21
-
-module load w3nco-intel-sandybridge/2.0.6
-module load sp-intel-sandybridge/2.0.2
-module load bacio-intel-sandybridge/2.0.2
-module load sigio-intel-sandybridge/2.0.1
-module load sfcio-intel-sandybridge/1.0.0
-module load nemsio-intel-sandybridge/2.2.3
-
-export FCOMP=mpiifort
-#export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
-# for debugging
-export FFLAGS="-O0 -g -traceback -r8 -i4 -qopenmp -convert big_endian -check bounds -warn unused -assume byterecl"
-
-export WGRIB2API_LIB="/apps/wgrib2/2.0.8/intel/18.0.5.274/lib/libwgrib2_api.a"
-export WGRIB2API_INC="/apps/wgrib2/2.0.8/intel/18.0.5.274/lib"
-export WGRIB2_LIB="/apps/wgrib2/2.0.8/intel/18.0.5.274/lib/libwgrib2.a"
-export WGRIB2_DIR="/apps/wgrib2/2.0.8/intel/18.0.5.274/bin"
-module load wgrib2/2.0.8
-
-module use -a /contrib/miniconda3/modulefiles
-module load miniconda3
-conda activate regional_workflow
diff --git a/modulefiles/tasks/jet/make_ics.local b/modulefiles/tasks/jet/make_ics.local
deleted file mode 100644
index d5fa8e56b..000000000
--- a/modulefiles/tasks/jet/make_ics.local
+++ /dev/null
@@ -1,5 +0,0 @@
-module load wgrib2/2.0.8 
-
-module use -a /contrib/miniconda3/modulefiles
-module load miniconda3
-conda activate regional_workflow
diff --git a/modulefiles/tasks/jet/make_lbcs.hardcoded b/modulefiles/tasks/jet/make_lbcs.hardcoded
deleted file mode 100644
index 5e63864de..000000000
--- a/modulefiles/tasks/jet/make_lbcs.hardcoded
+++ /dev/null
@@ -1,34 +0,0 @@
-#%Module#####################################################
-## Module file for make_ics task.
-#############################################################
-
-module load intel/18.0.5.274
-module load impi/2018.4.274
-module load szip
-module load hdf5
-module load netcdf/4.2.1.1
-
-module use /mnt/lfs3/projects/hfv3gfs/gwv/ljtjet/lib/modulefiles
-module load esmflocal/ESMF_8_0_0_beta_snapshot_21
-
-module load w3nco-intel-sandybridge/2.0.6
-module load sp-intel-sandybridge/2.0.2
-module load bacio-intel-sandybridge/2.0.2
-module load sigio-intel-sandybridge/2.0.1
-module load sfcio-intel-sandybridge/1.0.0
-module load nemsio-intel-sandybridge/2.2.3
-
-export FCOMP=mpiifort
-#export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
-# for debugging
-export FFLAGS="-O0 -g -traceback -r8 -i4 -qopenmp -convert big_endian -check bounds -warn unused -assume byterecl"
-
-export WGRIB2API_LIB="/apps/wgrib2/2.0.8/intel/18.0.5.274/lib/libwgrib2_api.a"
-export WGRIB2API_INC="/apps/wgrib2/2.0.8/intel/18.0.5.274/lib"
-export WGRIB2_LIB="/apps/wgrib2/2.0.8/intel/18.0.5.274/lib/libwgrib2.a"
-export WGRIB2_DIR="/apps/wgrib2/2.0.8/intel/18.0.5.274/bin"
-module load wgrib2/2.0.8
-
-module use -a /contrib/miniconda3/modulefiles
-module load miniconda3
-conda activate regional_workflow
diff --git a/modulefiles/tasks/jet/make_lbcs.local b/modulefiles/tasks/jet/make_lbcs.local
deleted file mode 100644
index d5fa8e56b..000000000
--- a/modulefiles/tasks/jet/make_lbcs.local
+++ /dev/null
@@ -1,5 +0,0 @@
-module load wgrib2/2.0.8 
-
-module use -a /contrib/miniconda3/modulefiles
-module load miniconda3
-conda activate regional_workflow
diff --git a/tests/baseline_configs/config.nco_conus.sh b/tests/baseline_configs/config.nco_conus.sh
index 26051f68e..9da21f187 100644
--- a/tests/baseline_configs/config.nco_conus.sh
+++ b/tests/baseline_configs/config.nco_conus.sh
@@ -105,9 +105,9 @@ STMP="/scratch2/BMC/det/Gerard.Ketefian/UFS_CAM/NCO_dirs/stmp"
 PTMP="/scratch2/BMC/det/Gerard.Ketefian/UFS_CAM/NCO_dirs/ptmp"
 
 #On Jet:
-#COMINgfs="/lfs1/projects/hwrf-data/hafs-input/COMGFS"
-#STMP="/lfs3/BMC/wrfruc/beck/NCO_dirs/stmp"
-#PTMP="/lfs3/BMC/wrfruc/beck/NCO_dirs/ptmp"
+#COMINgfs="/lfs1/HFIP/hwrf-data/hafs-input/COMGFS"
+#STMP=""
+#PTMP=""
 
 #
 # In NCO mode, the user must manually (e.g. after doing the build step)
diff --git a/tests/baseline_configs/config.nco_conus_c96.sh b/tests/baseline_configs/config.nco_conus_c96.sh
index 9d01489af..ba07895a8 100644
--- a/tests/baseline_configs/config.nco_conus_c96.sh
+++ b/tests/baseline_configs/config.nco_conus_c96.sh
@@ -105,9 +105,9 @@ STMP="/scratch2/BMC/det/Gerard.Ketefian/UFS_CAM/NCO_dirs/stmp"
 PTMP="/scratch2/BMC/det/Gerard.Ketefian/UFS_CAM/NCO_dirs/ptmp"
 
 #On Jet:
-#COMINgfs="/lfs1/projects/hwrf-data/hafs-input/COMGFS"
-#STMP="/lfs3/BMC/wrfruc/beck/NCO_dirs/stmp"
-#PTMP="/lfs3/BMC/wrfruc/beck/NCO_dirs/ptmp"
+#COMINgfs="/lfs1/HFIP/hwrf-data/hafs-input/COMGFS"
+#STMP=""
+#PTMP=""
 
 #
 # In NCO mode, the user must manually (e.g. after doing the build step)
diff --git a/tests/baseline_configs/config.regional_006.sh b/tests/baseline_configs/config.regional_006.sh
index bfa1b0f8b..9ad8eb981 100644
--- a/tests/baseline_configs/config.regional_006.sh
+++ b/tests/baseline_configs/config.regional_006.sh
@@ -51,7 +51,6 @@ RUN_TASK_MAKE_SFC_CLIMO="FALSE"
 SFC_CLIMO_DIR="/scratch2/BMC/det/FV3SAR_pregen/sfc_climo/GSD_HRRR25km"
 
 #On Jet
-#GRID_DIR="/lfs3/projects/wrfruc/beck/FV3SAR_pregen/grid/GSD_HRRR25km"
-#OROG_DIR="/lfs3/projects/wrfruc/beck/FV3SAR_pregen/orog/GSD_HRRR25km"
-#SFC_CLIMO_DIR="/lfs3/projects/wrfruc/beck/FV3SAR_pregen/sfc_climo/GSD_HRRR25km"
-
+#GRID_DIR=""
+#OROG_DIR=""
+#SFC_CLIMO_DIR=""
diff --git a/tests/baseline_configs/config.regional_009.sh b/tests/baseline_configs/config.regional_009.sh
index ff4515a01..935039f60 100644
--- a/tests/baseline_configs/config.regional_009.sh
+++ b/tests/baseline_configs/config.regional_009.sh
@@ -105,8 +105,8 @@ PTMP="/scratch2/BMC/det/Gerard.Ketefian/UFS_CAM/NCO_dirs/ptmp"
 
 #On Jet:
 #COMINgfs="/lfs1/projects/hwrf-data/hafs-input/COMGFS"
-#STMP="/lfs3/BMC/wrfruc/beck/NCO_dirs/stmp"
-#PTMP="/lfs3/BMC/wrfruc/beck/NCO_dirs/ptmp"
+#STMP=""
+#PTMP=""
 
 #
 # In NCO mode, the user must manually (e.g. after doing the build step)
diff --git a/ush/load_fv3gfs_modules.sh b/ush/load_fv3gfs_modules.sh
index e48f1af47..f95b0237a 100755
--- a/ush/load_fv3gfs_modules.sh
+++ b/ush/load_fv3gfs_modules.sh
@@ -12,7 +12,7 @@ source "$HOMEgfs/modulefiles/module-setup.sh.inc"
 # Load our modules:
 module use "$HOMEgfs/modulefiles" 
 
-if [[ -d /lfs3 ]] ; then
+if [[ -d /lfs4 ]] ; then
     # We are on NOAA Jet
 	module load module_base.jet 
 elif [[ -d /scratch3 ]] ; then
diff --git a/ush/setup.sh b/ush/setup.sh
index 5d61fb9f5..5aff206f4 100755
--- a/ush/setup.sh
+++ b/ush/setup.sh
@@ -664,7 +664,7 @@ case $MACHINE in
   ;;
 
 "JET")
-  FIXgsm="/lfs3/projects/hpc-wof1/ywang/regional_fv3/fix/fix_am"
+  FIXgsm="/lfs4/HFIP/gsd-fv3-hfip/FV3/fix/fix_am"
   SFC_CLIMO_INPUT_DIR="/lfs1/HFIP/hwrf-data/git/fv3gfs/fix/fix_sfc_climo"
   ;;
 

From 43722f863b0bbff0868d26beb7ba3ec2aed697d2 Mon Sep 17 00:00:00 2001
From: "Jeff.Beck" <Jeff.Beck@noaa.gov>
Date: Wed, 10 Jun 2020 21:35:41 +0000
Subject: [PATCH 2/9] Add Ben and Ratko to the CODEOWNERS file

---
 .github/CODEOWNERS | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 633d0445b..40196de74 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -3,7 +3,7 @@
 
 # These owners will be the default owners for everything in the repo.
 #*       @defunkt
-*       @JulieSchramm @mkavulich @gsketefian @JeffBeck-NOAA
+*       @JulieSchramm @mkavulich @gsketefian @JeffBeck-NOAA @RatkoVasic-NOAA @BenjaminBlake-NOAA
 
 # Order is important. The last matching pattern has the most precedence.
 # So if a pull request only touches javascript files, only these owners

From 6f3e29428c27d502a6cd240a32b67dace460cbd1 Mon Sep 17 00:00:00 2001
From: "Jeff.Beck" <Jeff.Beck@noaa.gov>
Date: Thu, 11 Jun 2020 19:44:15 +0000
Subject: [PATCH 3/9] Replace hard-coded make_orog module file with build-level
 module file in UFS_UTILS

---
 modulefiles/tasks/jet/make_orog.hardcoded | 9 ---------
 ush/generate_FV3SAR_wflow.sh              | 5 ++---
 2 files changed, 2 insertions(+), 12 deletions(-)
 delete mode 100644 modulefiles/tasks/jet/make_orog.hardcoded

diff --git a/modulefiles/tasks/jet/make_orog.hardcoded b/modulefiles/tasks/jet/make_orog.hardcoded
deleted file mode 100644
index 128da319a..000000000
--- a/modulefiles/tasks/jet/make_orog.hardcoded
+++ /dev/null
@@ -1,9 +0,0 @@
-#%Module#####################################################
-## Module file for make_orog task.
-#############################################################
-
-module purge
-# Loading Intel Compiler Suite
-module load intel/18.0.5.274
-module load netcdf/4.7.0
-module load hdf5/1.10.5
diff --git a/ush/generate_FV3SAR_wflow.sh b/ush/generate_FV3SAR_wflow.sh
index 79b97eae8..1f59eb540 100755
--- a/ush/generate_FV3SAR_wflow.sh
+++ b/ush/generate_FV3SAR_wflow.sh
@@ -237,9 +237,8 @@ cd_vrfy "${MODULES_DIR}/tasks/$machine"
 # that is defined.  That needs to be fixed.  Until then, we have to use
 # a hard-coded module file, which may or may not be compatible with the
 # modules used in the UFS_UTILS repo to build the orog code.
-#ln_vrfy -fs "${UFS_UTILS_DIR}/modulefiles/fv3gfs/orog.$machine" \
-#            "${MAKE_OROG_TN}"
-ln_vrfy -fs "${MAKE_OROG_TN}.hardcoded" "${MAKE_OROG_TN}"
+ln_vrfy -fs "${UFS_UTILS_DIR}/modulefiles/fv3gfs/orog.$machine" \
+            "${MAKE_OROG_TN}"
 
 ln_vrfy -fs "${UFS_UTILS_DIR}/modulefiles/modulefile.sfc_climo_gen.$machine" \
             "${MAKE_SFC_CLIMO_TN}"

From bf87e023386f7afb958655f6774c256e7d0856fc Mon Sep 17 00:00:00 2001
From: "Jeff.Beck" <Jeff.Beck@noaa.gov>
Date: Thu, 11 Jun 2020 19:47:22 +0000
Subject: [PATCH 4/9] Remove hard-coded make_sfc_climo module file

---
 modulefiles/tasks/jet/make_sfc_climo.hardcoded | 12 ------------
 1 file changed, 12 deletions(-)
 delete mode 100644 modulefiles/tasks/jet/make_sfc_climo.hardcoded

diff --git a/modulefiles/tasks/jet/make_sfc_climo.hardcoded b/modulefiles/tasks/jet/make_sfc_climo.hardcoded
deleted file mode 100644
index 3e06d3e73..000000000
--- a/modulefiles/tasks/jet/make_sfc_climo.hardcoded
+++ /dev/null
@@ -1,12 +0,0 @@
-#%Module#####################################################
-## Module file for make_sfc_climo task.
-#############################################################
-
-module purge
-
-module load intel/18.0.5.274
-module load impi/2018.0.4
-
-module use -a /scratch1/NCEPDEV/global/gwv/l819/lib/modulefiles
-module load esmflocal/8_0_48b.netcdf47
-

From a5397683de0a3d6688f8674f5d11d148f023206f Mon Sep 17 00:00:00 2001
From: jeff beck <jeff.beck@noaa.gov>
Date: Tue, 18 Aug 2020 05:35:39 +0000
Subject: [PATCH 5/9] Fixes after updating fork with authoritative repo

---
 scripts/exregional_make_ics.sh  | 261 +++++++++++++-------------------
 scripts/exregional_make_lbcs.sh | 166 ++++++--------------
 ush/config_defaults.sh          |  12 +-
 3 files changed, 164 insertions(+), 275 deletions(-)

diff --git a/scripts/exregional_make_ics.sh b/scripts/exregional_make_ics.sh
index 0da673482..4dcaac7ef 100755
--- a/scripts/exregional_make_ics.sh
+++ b/scripts/exregional_make_ics.sh
@@ -42,21 +42,20 @@ print_info_msg "
 Entering script:  \"${scrfunc_fn}\"
 In directory:     \"${scrfunc_dir}\"
 
-This is the ex-script for the task that generates initial condition
-(IC), surface, and zeroth hour lateral boundary condition (LBC0) files
+This is the ex-script for the task that generates initial condition 
+(IC), surface, and zeroth hour lateral boundary condition (LBC0) files 
 for FV3 (in NetCDF format).
 ========================================================================"
 #
 #-----------------------------------------------------------------------
 #
-# Specify the set of valid argument names for this script/function.  Then
-# process the arguments provided to this script/function (which should
+# Specify the set of valid argument names for this script/function.  Then 
+# process the arguments provided to this script/function (which should 
 # consist of a set of name-value pairs of the form arg1="value1", etc).
 #
 #-----------------------------------------------------------------------
 #
 valid_args=( \
-"wgrib2_dir" \
 "ics_dir" \
 "APRUN" \
 )
@@ -71,10 +70,10 @@ process_args valid_args "$@"
 #-----------------------------------------------------------------------
 #
 print_input_args valid_args
-#
-#-----------------------------------------------------------------------
-#
-# Source the file containing definitions of variables associated with the
+#                                                                        
+#----------------------------------------------------------------------- 
+#                                                                        
+# Source the file containing definitions of variables associated with the 
 # external model for ICs.
 #
 #-----------------------------------------------------------------------
@@ -95,39 +94,30 @@ cd_vrfy $workdir
 #
 #-----------------------------------------------------------------------
 #
-# Set physics-suite-dependent variables that are needed in the FORTRAN
-# namelist file that the chgres executable will read in.
+# Set physics-suite-dependent variable mapping table needed in the FORTRAN
+# namelist file that the chgres_cube executable will read in.
 #
 #-----------------------------------------------------------------------
 #
-phys_suite=""
+varmap_file=""
 
 case "${CCPP_PHYS_SUITE}" in
 
-"FV3_GFS_2017_gfdlmp" | "FV3_GFS_2017_gfdlmp_regional" )
-  phys_suite="GFS"
+"FV3_GFS_2017_gfdlmp" | "FV3_GFS_2017_gfdlmp_regional" | "FV3_GFS_v16beta" | \
+"FV3_GFS_v15p2" )
+  varmap_file="GFSphys_var_map.txt"
   ;;
 "FV3_GSD_v0" | "FV3_GSD_SAR" | "FV3_GSD_SAR_v1" |"FV3_RRFS_v0" )
-  phys_suite="GSD"
-  ;;
-"FV3_CPT_v0")
-  phys_suite="CPT"
-  ;;
-"FV3_GFS_v15p2")
-  phys_suite="v15p2"
-  ;;
-"FV3_GFS_v16beta")
-  phys_suite="v16beta"
+  varmap_file="GSDphys_var_map.txt"
   ;;
 *)
   print_err_msg_exit "\
-Physics-suite-dependent namelist variables have not yet been specified
-for this physics suite:
+A variable mapping table has not yet been defined for this physics suite:
   CCPP_PHYS_SUITE = \"${CCPP_PHYS_SUITE}\""
   ;;
 
 esac
-#
+
 #-----------------------------------------------------------------------
 #
 # Set external-model-dependent variables that are needed in the FORTRAN
@@ -136,7 +126,7 @@ esac
 # subset of these all variables are set (since some may be irrelevant).
 #
 # external_model:
-# Name of the external model from which we are obtaining the fields
+# Name of the external model from which we are obtaining the fields 
 # needed to generate the ICs.
 #
 # fn_atm_nemsio:
@@ -150,22 +140,22 @@ esac
 # input_type:
 # The "type" of input being provided to chgres.  This contains a combi-
 # nation of information on the external model, external model file for-
-# mat, and maybe other parameters.  For clarity, it would be best to
+# mat, and maybe other parameters.  For clarity, it would be best to 
 # eliminate this variable in chgres and replace with with 2 or 3 others
 # (e.g. extrn_mdl, extrn_mdl_file_format, etc).
-#
+# 
 # tracers_input:
 # List of atmospheric tracers to read in from the external model file
 # containing these tracers.
 #
 # tracers:
-# Names to use in the output NetCDF file for the atmospheric tracers
+# Names to use in the output NetCDF file for the atmospheric tracers 
 # specified in tracers_input.  With the possible exception of GSD phys-
 # ics, the elements of this array should have a one-to-one correspond-
 # ence with the elements in tracers_input, e.g. if the third element of
 # tracers_input is the name of the O3 mixing ratio, then the third ele-
 # ment of tracers should be the name to use for the O3 mixing ratio in
-# the output file.  For GSD physics, three additional tracers -- ice,
+# the output file.  For GSD physics, three additional tracers -- ice, 
 # rain, and water number concentrations -- may be specified at the end
 # of tracers, and these will be calculated by chgres.
 #
@@ -174,27 +164,29 @@ esac
 # face model (LSM) variables available in the HRRRX grib2 files created
 # after about 2019111500.
 #
-# numsoil_out:
+# nsoill_out:
 # The number of soil layers to include in the output NetCDF file.
 #
-# replace_FIELD, where FIELD="vgtyp", "sotyp", or "vgfrc":
-# Logical variable indicating whether or not to obtain the field in
+# FIELD_from_climo, where FIELD = "vgtyp", "sotyp", "vgfrc", "lai", or 
+# "minmax_vgfrc":
+# Logical variable indicating whether or not to obtain the field in 
 # question from climatology instead of the external model.  The field in
 # question is one of vegetation type (FIELD="vgtyp"), soil type (FIELD=
-# "sotyp"), and vegetation fraction (FIELD="vgfrc").  If replace_FIELD
-# is set to ".true.", then the field is obtained from climatology (re-
-# gardless of whether or not it exists in an external model file).  If
-# it is set to ".false.", then the field is obtained from the external
-# model.  If the external model file does not provide this field, then
-# chgres prints out an error message and stops.
+# "sotyp"), vegetation fraction (FIELD="vgfrc"), leaf area index 
+# (FIELD="lai"), or min/max areal fractional coverage of annual green 
+# vegetation (FIELD="minmax_vfrr").  If FIELD_from_climo is set to 
+# ".true.", then the field is obtained from climatology (regardless of
+# whether or not it exists in an external model file).  If it is set
+# to ".false.", then the field is obtained from the external  model.
+# If "false" is chosen and the external model file does not provide
+# this field, then chgres_cube prints out an error message and stops.
 #
 # tg3_from_soil:
 # Logical variable indicating whether or not to set the tg3 soil tempe-  # Needs to be verified.
-# rature field to the temperature of the deepest soil layer.
+# rature field to the temperature of the deepest soil layer. 
 #
 #-----------------------------------------------------------------------
 #
-
 # GSK comments about chgres:
 #
 # The following are the three atmsopheric tracers that are in the atmo-
@@ -228,7 +220,6 @@ esac
 # A non-prognostic variable that appears in the field_table for GSD physics
 # is cld_amt.  Why is that in the field_table at all (since it is a non-
 # prognostic field), and how should we handle it here??
-
 # I guess this works for FV3GFS but not for the spectral GFS since these
 # variables won't exist in the spectral GFS atmanl files.
 #  tracers_input="\"sphum\",\"liq_wat\",\"ice_wat\",\"rainwat\",\"snowwat\",\"graupel\",\"o3mr\""
@@ -243,12 +234,13 @@ fn_grib2=""
 input_type=""
 tracers_input="\"\""
 tracers="\"\""
-internal_GSD=""
-numsoil_out=""
+nsoill_out=""
 geogrid_file_input_grid="\"\""
-replace_vgtyp=""
-replace_sotyp=""
-replace_vgfrc=""
+vgtyp_from_climo=""
+sotyp_from_climo=""
+vgfrc_from_climo=""
+minmax_vgfrc_from_climo=""
+lai_from_climo=""
 tg3_from_soil=""
 convert_nst=""
 
@@ -262,16 +254,17 @@ case "${EXTRN_MDL_NAME_ICS}" in
 
   fn_atm_nemsio="${EXTRN_MDL_FNS[0]}"
   fn_sfc_nemsio="${EXTRN_MDL_FNS[1]}"
-  input_type="gfs_gaussian" # For spectral GFS Gaussian grid in nemsio format.
+  input_type="gfs_gaussian_nemsio" # For spectral GFS Gaussian grid in nemsio format.
 
   tracers_input="[\"spfh\",\"clwmr\",\"o3mr\"]"
   tracers="[\"sphum\",\"liq_wat\",\"o3mr\"]"
 
-  internal_GSD=False
-  numsoil_out="4"
-  replace_vgtyp=True
-  replace_sotyp=True
-  replace_vgfrc=True
+  nsoill_out="4"
+  vgtyp_from_climo=True
+  sotyp_from_climo=True
+  vgfrc_from_climo=True
+  minmax_vgfrc_from_climo=True
+  lai_from_climo=True
   tg3_from_soil=False
   convert_nst=False
 
@@ -286,7 +279,8 @@ case "${EXTRN_MDL_NAME_ICS}" in
 
     fn_atm_nemsio="${EXTRN_MDL_FNS[0]}"
     fn_sfc_nemsio="${EXTRN_MDL_FNS[1]}"
-    input_type="gaussian"     # For FV3-GFS Gaussian grid in nemsio format.
+    input_type="gaussian_nemsio"     # For FV3-GFS Gaussian grid in nemsio format.
+    convert_nst=True
 
     tracers_input="[\"spfh\",\"clwmr\",\"o3mr\",\"icmr\",\"rwmr\",\"snmr\",\"grle\"]"
 
@@ -326,16 +320,17 @@ case "${EXTRN_MDL_NAME_ICS}" in
 
     fn_grib2="${EXTRN_MDL_FNS[0]}"
     input_type="grib2"
+    convert_nst=False
 
   fi
 
-  internal_GSD=False
-  numsoil_out="4"
-  replace_vgtyp=True
-  replace_sotyp=True
-  replace_vgfrc=True
+  nsoill_out="4"
+  vgtyp_from_climo=True
+  sotyp_from_climo=True
+  vgfrc_from_climo=True
+  minmax_vgfrc_from_climo=True
+  lai_from_climo=True
   tg3_from_soil=False
-  convert_nst=True
 
   ;;
 
@@ -347,18 +342,6 @@ case "${EXTRN_MDL_NAME_ICS}" in
   fn_grib2="${EXTRN_MDL_FNS[0]}"
   input_type="grib2"
 
-  internal_GSD=False
-  cdate_min_HRRRX="2019111500"
-  if [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_v0" -o \
-       "${CCPP_PHYS_SUITE}" = "FV3_GSD_SAR" ] && \
-     [ ${CDATE} -gt ${cdate_min_HRRRX} ]; then
-    print_info_msg "
-Setting the chgres_cube namelist setting \"internal_GSD\" to \".true.\" in
-order to read in land surface model (LSM) variables available in the
-HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
-    internal_GSD=True
-  fi
-
   if [ "${USE_CCPP}" = "TRUE" ]; then
     if [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_2017_gfdlmp" ] || \
        [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_SAR_v1" ] || \
@@ -366,10 +349,10 @@ HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
        [ "${CCPP_PHYS_SUITE}" = "FV3_CPT_v0" ] || \
        [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_v15p2" ] || \
        [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_v16beta" ]; then
-      numsoil_out="4"
+      nsoill_out="4"
     elif [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_v0" ] || \
          [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_SAR" ]; then
-      numsoil_out="9"
+      nsoill_out="9"
     fi
   fi
 #
@@ -381,9 +364,15 @@ HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
     geogrid_file_input_grid="/misc/whome/rtrr/HRRR/static/WPS/geo_em.d01.nc"
   fi
 
-  replace_vgtyp=False
-  replace_sotyp=False
-  replace_vgfrc=False
+
+  #Note that vgfrc, shdmin/shdmax (minmax_vgfrc), and lai fields are only available in HRRRX 
+  #files after mid-July 2019, and only so long as the record order didn't change afterward
+
+  vgtyp_from_climo=False
+  sotyp_from_climo=False
+  vgfrc_from_climo=False
+  minmax_vgfrc_from_climo=False
+  lai_from_climo=False
   tg3_from_soil=True
   convert_nst=False
 
@@ -396,8 +385,6 @@ HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
   fn_grib2="${EXTRN_MDL_FNS[0]}"
   input_type="grib2"
 
-  internal_GSD=False
-
   if [ "${USE_CCPP}" = "TRUE" ]; then
     if [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_2017_gfdlmp" ] || \
        [ "${CCPP_PHYS_SUITE}" = "FV3_CPT_v0" ] || \
@@ -405,10 +392,10 @@ HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
        [ "${CCPP_PHYS_SUITE}" = "FV3_RRFS_v0" ] || \
        [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_v15p2" ] || \
        [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_v16beta" ]; then
-      numsoil_out="4"
+      nsoill_out="4"
     elif [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_v0" ] || \
          [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_SAR" ]; then
-      numsoil_out="9"
+      nsoill_out="9"
     fi
   fi
 #
@@ -420,9 +407,11 @@ HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
     geogrid_file_input_grid="/misc/whome/rtrr/HRRR/static/WPS/geo_em.d01.nc"
   fi
 
-  replace_vgtyp=False
-  replace_sotyp=False
-  replace_vgfrc=False
+  vgtyp_from_climo=True
+  sotyp_from_climo=False
+  vgfrc_from_climo=True
+  minmax_vgfrc_from_climo=True
+  lai_from_climo=True
   tg3_from_soil=True
   convert_nst=False
 
@@ -430,7 +419,7 @@ HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
 
 *)
   print_err_msg_exit "\
-External-model-dependent namelist variables have not yet been specified
+External-model-dependent namelist variables have not yet been specified 
 for this external model:
   EXTRN_MDL_NAME_ICS = \"${EXTRN_MDL_NAME_ICS}\""
   ;;
@@ -454,14 +443,14 @@ hh="${EXTRN_MDL_CDATE:8:2}"
 #-----------------------------------------------------------------------
 #
 exec_fn="chgres_cube.exe"
-exec_fp="$EXECDIR/${exec_fn}"
-if [ ! -f "${exec_fp}" ]; then
-  print_err_msg_exit "\
+exec_fp="$EXECDIR/${exec_fn}"                                            
+if [ ! -f "${exec_fp}" ]; then                                           
+  print_err_msg_exit "\                                                  
 The executable (exec_fp) for generating initial conditions on the FV3SAR
-native grid does not exist:
-  exec_fp = \"${exec_fp}\"
-Please ensure that you've built this executable."
-fi
+native grid does not exist:                  
+  exec_fp = \"${exec_fp}\"                                               
+Please ensure that you've built this executable."                        
+fi                                                                       
 #
 #-----------------------------------------------------------------------
 #
@@ -469,45 +458,6 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-# For GFS physics, the character arrays tracers_input(:) and tracers(:)
-# must be specified in the namelist file.  tracers_input(:) contains the
-# tracer name to look for in the external model file(s), while tracers(:)
-# contains the names to use for the tracers in the output NetCDF files
-# that chgres creates (that will be read in by FV3).  Since when FV3
-# reads these NetCDF files it looks for atmospheric traces as specified
-# in the file field_table, tracers(:) should be set to the names in
-# field_table.
-#
-# NOTE: This process should be automated where the set of elements that
-# tracers(:) should be set to is obtained from reading in field_table.
-#
-# To know how to set tracers_input(:), you have to know the names of the
-# variables in the input atmospheric nemsio file (usually this file is
-# named gfs.t00z.atmanl.nemsio).
-#
-# It is not quite clear how these should be specified.  Here are a list
-# of examples:
-#
-# [Gerard.Ketefian@tfe05] /scratch3/.../chgres_cube.fd/run (feature/chgres_grib2_gsk)
-# $ grep -n -i "tracers" * | grep theia
-# config.C1152.l91.atm.theia.nml:24: tracers="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-# config.C1152.l91.atm.theia.nml:25: tracers_input="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-# config.C48.gaussian.theia.nml:20: tracers="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-# config.C48.gaussian.theia.nml:21: tracers_input="spfh","clwmr","o3mr","icmr","rwmr","snmr","grle"
-# config.C48.gfs.gaussian.theia.nml:21: tracers="sphum","liq_wat","o3mr"
-# config.C48.gfs.gaussian.theia.nml:22: tracers_input="spfh","clwmr","o3mr"
-# config.C48.gfs.spectral.theia.nml:21: tracers_input="spfh","o3mr","clwmr"
-# config.C48.gfs.spectral.theia.nml:22: tracers="sphum","o3mr","liq_wat"
-# config.C48.theia.nml:21: tracers="sphum","liq_wat","o3mr"
-# config.C48.theia.nml:22: tracers_input="spfh","clwmr","o3mr"
-# config.C768.atm.theia.nml:24: tracers="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-# config.C768.atm.theia.nml:25: tracers_input="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-# config.C768.l91.atm.theia.nml:24: tracers="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-# config.C768.l91.atm.theia.nml:25: tracers_input="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-# config.C768.nest.atm.theia.nml:22: tracers="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-# config.C768.nest.atm.theia.nml:23: tracers_input="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
-
-
 # fix_dir_target_grid="${BASEDIR}/JP_grid_HRRR_like_fix_files_chgres_cube"
 # base_install_dir="${SORCDIR}/chgres_cube.fd"
 
@@ -520,38 +470,37 @@ fi
 #
 settings="
 'config': {
+ 'fix_dir_input_grid': ${UFS_UTILS_DIR}/fix/fix_chgres,
  'fix_dir_target_grid': ${FIXsar},
- 'mosaic_file_target_grid': ${FIXsar}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc,
+ 'mosaic_file_target_grid': ${FIXsar}/${CRES}${DOT_OR_USCORE}mosaic.halo$((10#${NH4})).nc,
  'orog_dir_target_grid': ${FIXsar},
- 'orog_files_target_grid': ${CRES}${DOT_OR_USCORE}oro_data.tile${TILE_RGNL}.halo${NH4}.nc,
+ 'orog_files_target_grid': ${CRES}${DOT_OR_USCORE}oro_data.tile${TILE_RGNL}.halo$((10#${NH4})).nc,
  'vcoord_file_target_grid': ${FIXam}/global_hyblev.l65.txt,
- 'mosaic_file_input_grid': '',
- 'orog_dir_input_grid': '',
- 'base_install_dir': ${CHGRES_DIR},
- 'wgrib2_path': ${wgrib2_dir},
+ 'varmap_file': ${UFS_UTILS_DIR}/parm/varmap_tables/${varmap_file},
  'data_dir_input_grid': ${extrn_mdl_staging_dir},
  'atm_files_input_grid': ${fn_atm_nemsio},
  'sfc_files_input_grid': ${fn_sfc_nemsio},
  'grib2_file_input_grid': \"${fn_grib2}\",
- 'cycle_mon': $((10#$mm)),
- 'cycle_day': $((10#$dd)),
- 'cycle_hour': $((10#$hh)),
+ 'cycle_mon': $((10#${mm})),
+ 'cycle_day': $((10#${dd})),
+ 'cycle_hour': $((10#${hh})),
  'convert_atm': True,
  'convert_sfc': True,
  'convert_nst': ${convert_nst},
  'regional': 1,
- 'halo_bndy': ${NH4},
+ 'halo_bndy': $((10#${NH4})),
+ 'halo_blend': $((10#${HALO_BLEND})),
  'input_type': ${input_type},
  'external_model': ${external_model},
  'tracers_input': ${tracers_input},
- 'tracers': ${tracers},
- 'phys_suite': ${phys_suite},
- 'internal_GSD': ${internal_GSD},
- 'numsoil_out': ${numsoil_out},
+ 'tracers': ${tracers}, 
+ 'nsoill_out': $((10#${nsoill_out})),
  'geogrid_file_input_grid': ${geogrid_file_input_grid},
- 'replace_vgtyp': ${replace_vgtyp},
- 'replace_sotyp': ${replace_sotyp},
- 'replace_vgfrc': ${replace_vgfrc},
+ 'vgtyp_from_climo': ${vgtyp_from_climo},
+ 'sotyp_from_climo': ${sotyp_from_climo},
+ 'vgfrc_from_climo': ${vgfrc_from_climo},
+ 'minmax_vgfrc_from_climo': ${minmax_vgfrc_from_climo},
+ 'lai_from_climo': ${lai_from_climo},
  'tg3_from_soil': ${tg3_from_soil},
 }
 "
@@ -561,8 +510,8 @@ settings="
 nml_fn="fort.41"
 ${USHDIR}/set_namelist.py -q -u "$settings" -o ${nml_fn} || \
   print_err_msg_exit "\
-Call to python script set_namelist.py to set the variables in the namelist
-file read in by the ${exec_fn} executable failed.  Parameters passed to
+Call to python script set_namelist.py to set the variables in the namelist 
+file read in by the ${exec_fn} executable failed.  Parameters passed to 
 this script are:
   Name of output namelist file:
     nml_fn = \"${nml_fn}\"
@@ -580,13 +529,13 @@ $settings"
 # Often when the chgres_cube.exe run fails, it still returns a zero re-
 # turn code, so the failure isn't picked up the the logical OR (||) be-
 # low.  That should be fixed.  This might be due to the APRUN command -
-# maybe that is returning a zero exit code even though the exit code
+# maybe that is returning a zero exit code even though the exit code 
 # of chgres_cube is nonzero.
 # A similar thing happens in the forecast task.
 #
 ${APRUN} ${exec_fp} || \
   print_err_msg_exit "\
-Call to executable (exec_fp) to generate surface and initial conditions
+Call to executable (exec_fp) to generate surface and initial conditions 
 (ICs) files for the FV3SAR failed:
   exec_fp = \"${exec_fp}\"
 The external model from which the ICs files are to be generated is:
@@ -598,7 +547,7 @@ located in the following directory:
 #-----------------------------------------------------------------------
 #
 # Move initial condition, surface, control, and 0-th hour lateral bound-
-# ary files to ICs_BCs directory.
+# ary files to ICs_BCs directory. 
 #
 #-----------------------------------------------------------------------
 #
@@ -610,7 +559,7 @@ mv_vrfy out.sfc.tile${TILE_RGNL}.nc \
 
 mv_vrfy gfs_ctrl.nc ${ics_dir}
 
-mv_vrfy gfs_bndy.nc ${ics_dir}/gfs_bndy.tile${TILE_RGNL}.000.nc
+mv_vrfy gfs.bndy.nc ${ics_dir}/gfs_bndy.tile${TILE_RGNL}.000.nc
 #
 #-----------------------------------------------------------------------
 #
diff --git a/scripts/exregional_make_lbcs.sh b/scripts/exregional_make_lbcs.sh
index d9a837439..17a5bb5a6 100755
--- a/scripts/exregional_make_lbcs.sh
+++ b/scripts/exregional_make_lbcs.sh
@@ -49,15 +49,14 @@ hour zero).
 #
 #-----------------------------------------------------------------------
 #
-# Specify the set of valid argument names for this script/function.  Then
-# process the arguments provided to this script/function (which should
+# Specify the set of valid argument names for this script/function.  Then 
+# process the arguments provided to this script/function (which should 
 # consist of a set of name-value pairs of the form arg1="value1", etc).
 #
 #-----------------------------------------------------------------------
 #
 valid_args=( \
 "lbcs_dir" \
-"wgrib2_dir" \
 "APRUN" \
 )
 process_args valid_args "$@"
@@ -95,34 +94,25 @@ cd_vrfy $workdir
 #
 #-----------------------------------------------------------------------
 #
-# Set physics-suite-dependent variables that are needed in the FORTRAN
-# namelist file that the chgres executable will read in.
+# Set physics-suite-dependent variable mapping table needed in the FORTRAN
+# namelist file that the chgres_cube executable will read in.
 #
 #-----------------------------------------------------------------------
 #
-phys_suite=""
+varmap_file=""
 
 case "${CCPP_PHYS_SUITE}" in
 
-"FV3_GFS_2017_gfdlmp" | "FV3_GFS_2017_gfdlmp_regional")
-  phys_suite="GFS"
-  ;;
-"FV3_GSD_v0" | "FV3_GSD_SAR" | "FV3_GSD_SAR_v1" | "FV3_RRFS_v0" )
-  phys_suite="GSD"
-  ;;
-"FV3_CPT_v0" )
-  phys_suite="CPT"
-  ;;
+"FV3_GFS_2017_gfdlmp" | "FV3_GFS_2017_gfdlmp_regional" | "FV3_GFS_v16beta" | \
 "FV3_GFS_v15p2" )
-  phys_suite="v15p2"
+  varmap_file="GFSphys_var_map.txt"
   ;;
-"FV3_GFS_v16beta" )
-  phys_suite="v16beta"
+"FV3_GSD_v0" | "FV3_GSD_SAR" | "FV3_GSD_SAR_v1" |"FV3_RRFS_v0" )
+  varmap_file="GSDphys_var_map.txt"
   ;;
 *)
   print_err_msg_exit "\
-Physics-suite-dependent namelist variables have not yet been specified
-for this physics suite:
+A variable mapping table has not yet been defined for this physics suite:
   CCPP_PHYS_SUITE = \"${CCPP_PHYS_SUITE}\""
   ;;
 
@@ -136,9 +126,13 @@ esac
 # subset of these all variables are set (since some may be irrelevant).
 #
 # external_model:
-# Name of the external model from which we are obtaining the fields
+# Name of the external model from which we are obtaining the fields 
 # needed to generate the LBCs.
 #
+# fn_atm_nemsio:
+# Name (not including path) of the nemsio file generated by the external
+# model that contains the atmospheric fields.
+#
 # fn_sfc_nemsio:
 # Name (not including path) of the nemsio file generated by the external
 # model that contains the surface fields.
@@ -146,7 +140,7 @@ esac
 # input_type:
 # The "type" of input being provided to chgres.  This contains a combi-
 # nation of information on the external model, external model file for-
-# mat, and maybe other parameters.  For clarity, it would be best to
+# mat, and maybe other parameters.  For clarity, it would be best to 
 # eliminate this variable in chgres and replace with with 2 or 3 others
 # (e.g. extrn_mdl, extrn_mdl_file_format, etc).
 #
@@ -165,24 +159,6 @@ esac
 # rain, and water number concentrations -- may be specified at the end
 # of tracers, and these will be calculated by chgres.
 #
-# numsoil_out:
-# The number of soil layers to include in the output NetCDF file.
-#
-# replace_FIELD, where FIELD="vgtyp", "sotyp", or "vgfrc":
-# Logical variable indicating whether or not to obtain the field in
-# question from climatology instead of the external model.  The field in
-# question is one of vegetation type (FIELD="vgtyp"), soil type (FIELD=
-# "sotyp"), and vegetation fraction (FIELD="vgfrc").  If replace_FIELD
-# is set to ".true.", then the field is obtained from climatology (re-
-# gardless of whether or not it exists in an external model file).  If
-# it is set to ".false.", then the field is obtained from the external
-# model.  If the external model file does not provide this field, then
-# chgres prints out an error message and stops.
-#
-# tg3_from_soil:
-# Logical variable indicating whether or not to set the tg3 soil tempe-  # Needs to be verified.
-# rature field to the temperature of the deepest soil layer.
-#
 #-----------------------------------------------------------------------
 #
 
@@ -235,13 +211,6 @@ fn_grib2=""
 input_type=""
 tracers_input="\"\""
 tracers="\"\""
-numsoil_out=""
-geogrid_file_input_grid="\"\""
-replace_vgtyp=""
-replace_sotyp=""
-replace_vgfrc=""
-tg3_from_soil=""
-
 
 case "${EXTRN_MDL_NAME_LBCS}" in
 
@@ -250,17 +219,11 @@ case "${EXTRN_MDL_NAME_LBCS}" in
 
   external_model="GSMGFS"
 
-  input_type="gfs_gaussian" # For spectral GFS Gaussian grid in nemsio format.
+  input_type="gfs_gaussian_nemsio" # For spectral GFS Gaussian grid in nemsio format.
 
   tracers_input="[\"spfh\",\"clwmr\",\"o3mr\"]"
   tracers="[\"sphum\",\"liq_wat\",\"o3mr\"]"
 
-  numsoil_out="4"
-  replace_vgtyp=".true."
-  replace_sotyp=".true."
-  replace_vgfrc=".true."
-  tg3_from_soil=".false."
-
   ;;
 
 
@@ -270,7 +233,7 @@ case "${EXTRN_MDL_NAME_LBCS}" in
 
     external_model="FV3GFS"
 
-    input_type="gaussian"     # For FV3-GFS Gaussian grid in nemsio format.
+    input_type="gaussian_nemsio"     # For FV3-GFS Gaussian grid in nemsio format.
 
     tracers_input="[\"spfh\",\"clwmr\",\"o3mr\",\"icmr\",\"rwmr\",\"snmr\",\"grle\"]"
 #
@@ -307,45 +270,19 @@ case "${EXTRN_MDL_NAME_LBCS}" in
 
     external_model="GFS"
 
-    input_type="grib2"
     fn_grib2="${EXTRN_MDL_FNS[0]}"
+    input_type="grib2"
 
   fi
 
-  numsoil_out="4"
-  replace_vgtyp=".true."
-  replace_sotyp=".true."
-  replace_vgfrc=".true."
-  tg3_from_soil=".false."
-
   ;;
 
 
 "RAPX")
 
   external_model="RAP"
-
   input_type="grib2"
 
-  if [ "${USE_CCPP}" = "TRUE" ]; then
-    if [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_2017_gfdlmp" ] || \
-       [ "${CCPP_PHYS_SUITE}" = "FV3_CPT_v0" ] || \
-       [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_SAR_v1" ] || \
-       [ "${CCPP_PHYS_SUITE}" = "FV3_RRFS_v0" ] || \
-       [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_v15p2" ] || \
-       [ "${CCPP_PHYS_SUITE}" = "FV3_GFS_v16beta" ]; then
-      numsoil_out="4"
-    elif [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_v0" ] || \
-         [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_SAR" ]; then
-      numsoil_out="9"
-    fi
-  fi
-
-  replace_vgtyp=".false."
-  replace_sotyp=".false."
-  replace_vgfrc=".false."
-  tg3_from_soil=".true."
-
   ;;
 
 
@@ -417,8 +354,8 @@ list file has not specified for this external model:
     ;;
   esac
 #
-# Get the starting date (year, month, and day together), month, day, and
-# hour of the the external model forecast.  Then add the forecast hour
+# Get the starting date (year, month, and day together), month, day, and 
+# hour of the the external model forecast.  Then add the forecast hour 
 # to it to get a date and time corresponding to the current forecast time.
 #
   yyyymmdd="${EXTRN_MDL_CDATE:0:8}"
@@ -428,7 +365,7 @@ list file has not specified for this external model:
 
   cdate_crnt_fhr=$( date --utc --date "${yyyymmdd} ${hh} UTC + ${fhr} hours" "+%Y%m%d%H" )
 #
-# Get the month, day, and hour corresponding to the current forecast time
+# Get the month, day, and hour corresponding to the current forecast time 
 # of the the external model.
 #
   mm="${cdate_crnt_fhr:4:2}"
@@ -437,9 +374,6 @@ list file has not specified for this external model:
 #
 # Build the FORTRAN namelist file that chgres_cube will read in.
 #
-# QUESTION:
-# Do numsoil_out, ..., tg3_from_soil need to be in this namelist (as
-# they are for the ICs namelist)?
 
 #
 # Create a multiline variable that consists of a yaml-compliant string
@@ -448,44 +382,40 @@ list file has not specified for this external model:
 # this variable will be passed to a python script that will create the
 # namelist file.
 #
-  settings="
+settings="
 'config': {
+ 'fix_dir_input_grid': ${UFS_UTILS_DIR}/fix/fix_chgres,
  'fix_dir_target_grid': ${FIXsar},
- 'mosaic_file_target_grid': ${FIXsar}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc,
+ 'mosaic_file_target_grid': ${FIXsar}/${CRES}${DOT_OR_USCORE}mosaic.halo$((10#${NH4})).nc,
  'orog_dir_target_grid': ${FIXsar},
- 'orog_files_target_grid': ${CRES}${DOT_OR_USCORE}oro_data.tile7.halo${NH4}.nc,
+ 'orog_files_target_grid': ${CRES}${DOT_OR_USCORE}oro_data.tile${TILE_RGNL}.halo$((10#${NH4})).nc,
  'vcoord_file_target_grid': ${FIXam}/global_hyblev.l65.txt,
- 'mosaic_file_input_grid': '',
- 'orog_dir_input_grid': '',
- 'base_install_dir': ${CHGRES_DIR},
- 'wgrib2_path': ${wgrib2_dir},
+ 'varmap_file': ${UFS_UTILS_DIR}/parm/varmap_tables/${varmap_file},
  'data_dir_input_grid': ${extrn_mdl_staging_dir},
  'atm_files_input_grid': ${fn_atm_nemsio},
  'sfc_files_input_grid': ${fn_sfc_nemsio},
  'grib2_file_input_grid': \"${fn_grib2}\",
- 'cycle_mon': $((10#$mm)),
- 'cycle_day': $((10#$dd)),
- 'cycle_hour': $((10#$hh)),
+ 'cycle_mon': $((10#${mm})),
+ 'cycle_day': $((10#${dd})),
+ 'cycle_hour': $((10#${hh})),
  'convert_atm': True,
- 'convert_sfc': False,
- 'convert_nst': False,
  'regional': 2,
- 'halo_bndy': ${NH4},
+ 'halo_bndy': $((10#${NH4})),
+ 'halo_blend': $((10#${HALO_BLEND})),
  'input_type': ${input_type},
  'external_model': ${external_model},
  'tracers_input': ${tracers_input},
  'tracers': ${tracers},
- 'phys_suite': ${phys_suite},
- }
+}
 "
 #
 # Call the python script to create the namelist file.
 #
-  nml_fn="fort.41"
-  ${USHDIR}/set_namelist.py -q -u "$settings" -o ${nml_fn} || \
-    print_err_msg_exit "\
-Call to python script set_namelist.py to set the variables in the namelist
-file read in by the ${exec_fn} executable failed.  Parameters passed to
+nml_fn="fort.41"
+${USHDIR}/set_namelist.py -q -u "$settings" -o ${nml_fn} || \
+  print_err_msg_exit "\
+Call to python script set_namelist.py to set the variables in the namelist 
+file read in by the ${exec_fn} executable failed.  Parameters passed to 
 this script are:
   Name of output namelist file:
     nml_fn = \"${nml_fn}\"
@@ -507,17 +437,17 @@ $settings"
 # of chgres_cube is nonzero.
 # A similar thing happens in the forecast task.
 #
-  ${APRUN} ${exec_fp} || \
-    print_err_msg_exit "\
-Call to executable (exec_fp) to generate lateral boundary conditions (LBCs)
-file for the FV3SAR for forecast hour fhr failed:
+${APRUN} ${exec_fp} || \
+  print_err_msg_exit "\
+Call to executable (exec_fp) to generate surface and initial conditions 
+(LBCs) files for the FV3SAR failed:
   exec_fp = \"${exec_fp}\"
   fhr = \"$fhr\"
-The external model from which the LBCs files are to be generated is:
-  EXTRN_MDL_NAME_LBCS = \"${EXTRN_MDL_NAME_LBCS}\"
-The external model files that are inputs to the executable (exec_fp) are
-located in the following directory:
-  extrn_mdl_staging_dir = \"${extrn_mdl_staging_dir}\""
+The external model from which the LBCs files are to be generated is:      
+  EXTRN_MDL_NAME_LBCS = \"${EXTRN_MDL_NAME_LBCS}\"                         
+The external model files that are inputs to the executable (exec_fp) are 
+located in the following directory:                                      
+  extrn_mdl_staging_dir = \"${extrn_mdl_staging_dir}\""                      
 #
 # Move LBCs file for the current lateral boundary update time to the LBCs
 # work directory.  Note that we rename the file by including in its name
@@ -525,7 +455,7 @@ located in the following directory:
 # that of the external model since their start times may be offset).
 #
   fcst_hhh_FV3SAR=$( printf "%03d" "${LBC_SPEC_FCST_HRS[$i]}" )
-  mv_vrfy gfs_bndy.nc ${lbcs_dir}/gfs_bndy.tile7.${fcst_hhh_FV3SAR}.nc
+  mv_vrfy gfs.bndy.nc ${lbcs_dir}/gfs_bndy.tile7.${fcst_hhh_FV3SAR}.nc
 
 done
 #
diff --git a/ush/config_defaults.sh b/ush/config_defaults.sh
index 7f91c0819..bea848666 100644
--- a/ush/config_defaults.sh
+++ b/ush/config_defaults.sh
@@ -1204,4 +1204,14 @@ SKEB_TSCALE="21600" #Variable "skeb_tau" in input.nml
 SKEB_INT="3600" #Variable "skebint" in input.nml
 SKEB_VDOF="10"
 USE_ZMTNBLCK="false"
-
+#
+#-----------------------------------------------------------------------
+# 
+# HALO_BLEND:
+# Number of rows into the computational domain that should be blended 
+# with the LBCs.
+#
+#-----------------------------------------------------------------------
+#
+HALO_BLEND=10
+#

From f10d313978bebeeade26aebef14f152f14bfb7ff Mon Sep 17 00:00:00 2001
From: jeff beck <jeff.beck@noaa.gov>
Date: Fri, 11 Sep 2020 03:14:23 +0000
Subject: [PATCH 6/9] Set ad-hoc stochastic physics scheme magnitudes to -999.0
 when not used to avoid bug with do_sppt/skeb/shum namelist entries

---
 ush/generate_FV3LAM_wflow.sh | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/ush/generate_FV3LAM_wflow.sh b/ush/generate_FV3LAM_wflow.sh
index 6d9ce5798..1424463ce 100755
--- a/ush/generate_FV3LAM_wflow.sh
+++ b/ush/generate_FV3LAM_wflow.sh
@@ -657,6 +657,22 @@ Please change one or more of these parameters or provide a value for lsoil
 
 fi
 #
+# Set magnitude of stochastic ad-hoc schemes to -999.0 if they are not
+# being used. This is required at the moment, since "do_shum/sppt/skeb"
+# does not override the use of the scheme unless the magnitude is also
+# specifically set to -999.0.  If all "do_shum/sppt/skeb" are set to
+# "false," then none will run, regardless of the magnitude values. 
+#
+if [ "${DO_SHUM}" = "false" ]; then
+  SHUM_MAG=-999.0
+fi
+if [ "${DO_SKEB}" = "false" ]; then
+  SKEB_MAG=-999.0
+fi
+if [ "${DO_SPPT}" = "false" ]; then
+  SPPT_MAG=-999.0
+fi
+#
 # Create a multiline variable that consists of a yaml-compliant string
 # specifying the values that the namelist variables that are physics-
 # suite-independent need to be set to.  Below, this variable will be

From 25491ed7e322bc04db68f7ac2b98cfa70711ef31 Mon Sep 17 00:00:00 2001
From: jeff beck <jeff.beck@noaa.gov>
Date: Fri, 11 Sep 2020 03:29:13 +0000
Subject: [PATCH 7/9] Add nrows to input.nml, HALO_BLEND to config_defaults.sh,
 and apply HALO_BLEND user-defined value during generate step.

---
 ush/config_defaults.sh       | 10 ++++++++++
 ush/generate_FV3LAM_wflow.sh | 17 +----------------
 2 files changed, 11 insertions(+), 16 deletions(-)

diff --git a/ush/config_defaults.sh b/ush/config_defaults.sh
index 23254e7da..048fb6348 100644
--- a/ush/config_defaults.sh
+++ b/ush/config_defaults.sh
@@ -1219,6 +1219,16 @@ SKEB_VDOF="10"
 USE_ZMTNBLCK="false"
 #
 #-----------------------------------------------------------------------
+# 
+# HALO_BLEND:
+# Number of rows into the computational domain that should be blended 
+# with the LBCs.
+#
+#-----------------------------------------------------------------------
+#
+HALO_BLEND=10
+#
+#-----------------------------------------------------------------------
 #
 # GWD_RRFS_v1beta_BASEDIR:
 # Temporary workflow variable specifies the base directory in which to 
diff --git a/ush/generate_FV3LAM_wflow.sh b/ush/generate_FV3LAM_wflow.sh
index 1424463ce..a2cf6eea6 100755
--- a/ush/generate_FV3LAM_wflow.sh
+++ b/ush/generate_FV3LAM_wflow.sh
@@ -657,22 +657,6 @@ Please change one or more of these parameters or provide a value for lsoil
 
 fi
 #
-# Set magnitude of stochastic ad-hoc schemes to -999.0 if they are not
-# being used. This is required at the moment, since "do_shum/sppt/skeb"
-# does not override the use of the scheme unless the magnitude is also
-# specifically set to -999.0.  If all "do_shum/sppt/skeb" are set to
-# "false," then none will run, regardless of the magnitude values. 
-#
-if [ "${DO_SHUM}" = "false" ]; then
-  SHUM_MAG=-999.0
-fi
-if [ "${DO_SKEB}" = "false" ]; then
-  SKEB_MAG=-999.0
-fi
-if [ "${DO_SPPT}" = "false" ]; then
-  SPPT_MAG=-999.0
-fi
-#
 # Create a multiline variable that consists of a yaml-compliant string
 # specifying the values that the namelist variables that are physics-
 # suite-independent need to be set to.  Below, this variable will be
@@ -687,6 +671,7 @@ settings="\
 'fv_core_nml': {
     'target_lon': ${LON_CTR},
     'target_lat': ${LAT_CTR},
+    'nrows_blend': ${HALO_BLEND},
 #
 # Question:
 # For a ESGgrid type grid, what should stretch_fac be set to?  This depends

From 8a1058595e6d8f4a03c96a3ba53b596c2ed6d164 Mon Sep 17 00:00:00 2001
From: jeff beck <jeff.beck@noaa.gov>
Date: Fri, 11 Sep 2020 03:34:44 +0000
Subject: [PATCH 8/9] Add nrows_blend to the template namelist file.

---
 ush/templates/input.nml.FV3 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ush/templates/input.nml.FV3 b/ush/templates/input.nml.FV3
index aa52e07dd..75cc97c8f 100644
--- a/ush/templates/input.nml.FV3
+++ b/ush/templates/input.nml.FV3
@@ -103,6 +103,7 @@
     nord = 2
     nord_zs_filter = 4
     npz = 64
+    nrows_blend = 10
     ntiles = 1
     nudge_qv = .false.
     nwat = 6

From dc2e6a045009e62d721872266f498cb2e6bb350a Mon Sep 17 00:00:00 2001
From: jeff beck <jeff.beck@noaa.gov>
Date: Mon, 14 Sep 2020 22:59:00 +0000
Subject: [PATCH 9/9] Add comment in config_defaults.sh to set HALO_BLEND to
 zero if the user wants to shut it off.

---
 ush/config_defaults.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/config_defaults.sh b/ush/config_defaults.sh
index 048fb6348..cbdf53505 100644
--- a/ush/config_defaults.sh
+++ b/ush/config_defaults.sh
@@ -1222,7 +1222,7 @@ USE_ZMTNBLCK="false"
 # 
 # HALO_BLEND:
 # Number of rows into the computational domain that should be blended 
-# with the LBCs.
+# with the LBCs.  To shut of halo blending, this can be set to zero.
 #
 #-----------------------------------------------------------------------
 #