From b5dd23b16a2e4a3ae561a69414b38437c21d4ab0 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Thu, 25 Apr 2024 13:40:54 -0600
Subject: [PATCH 01/15] Add the global nesting capability

---
 parm/config/gfs/config.base        |   7 ++
 parm/config/gfs/config.fcst        |   6 +-
 parm/config/gfs/config.resources   |   7 ++
 parm/config/gfs/config.stage_ic    |   4 +
 parm/config/gfs/config.ufs         | 102 +++++++++++++++++-
 scripts/exglobal_stage_ic.sh       |  13 ++-
 ush/forecast_postdet.sh            |  11 +-
 ush/forecast_predet.sh             |  19 +++-
 ush/parsing_model_configure_FV3.sh |  21 ++++
 ush/parsing_namelists_FV3.sh       | 163 +++++++++++++++++++++--------
 10 files changed, 301 insertions(+), 52 deletions(-)

diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
index 5a58c75220e..ab35f717cbf 100644
--- a/parm/config/gfs/config.base
+++ b/parm/config/gfs/config.base
@@ -184,6 +184,13 @@ export DO_AERO="NO"
 export WAVE_CDUMP="" # When to include wave suite: gdas, gfs, or both
 export DOBNDPNT_WAVE="NO"
 export FRAC_GRID=".true."
+export DO_NEST="NO" # Whether to run a global-nested domain
+if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
+  export ntiles=7
+  export NEST_OUTPUT_GRID="regional_latlon"
+else
+  export ntiles=6
+fi
 
 # Set operational resolution
 export OPS_RES="C768" # Do not change # TODO: Why is this needed and where is it used?
diff --git a/parm/config/gfs/config.fcst b/parm/config/gfs/config.fcst
index 14621307f59..ddca84306b5 100644
--- a/parm/config/gfs/config.fcst
+++ b/parm/config/gfs/config.fcst
@@ -253,7 +253,11 @@ export DO_SPPT=${DO_SPPT:-"NO"}
 export DO_SKEB=${DO_SKEB:-"NO"}
 export DO_SHUM=${DO_SHUM:-"NO"}
 export DO_LAND_PERT=${DO_LAND_PERT:-"NO"}
-export DO_CA=${DO_CA:-"YES"}
+if [[ "${DO_NEST:-NO}" == YES ]] ; then
+  export DO_CA="NO" #CA does not work with nesting. 
+else
+  export DO_CA=${DO_CA:-"YES"}
+fi
 
 #coupling settings
 export cplmode="ufs.frac"
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index 9e229de11af..63b57b15b4e 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -600,6 +600,13 @@ case ${step} in
         [[ "${DO_ICE}" == "YES" ]] && nthreads_cice6=1
       fi
 
+      if [[ ${ntiles} -gt 6 ]] ; then
+        export layout_x_nest=${layout_x_nest:-10}
+        export layout_y_nest=${layout_y_nest:-10}
+        export npx_nest=${npx_nest:-1441}
+        export npy_nest=${npy_nest:-961}
+      fi
+
       # PETS for the atmosphere dycore
       (( FV3PETS = ntasks_fv3 * nthreads_fv3 ))
       echo "FV3 using (nthreads, PETS) = (${nthreads_fv3}, ${FV3PETS})"
diff --git a/parm/config/gfs/config.stage_ic b/parm/config/gfs/config.stage_ic
index 63d0e4a5cf3..51e57c33dd3 100644
--- a/parm/config/gfs/config.stage_ic
+++ b/parm/config/gfs/config.stage_ic
@@ -38,4 +38,8 @@ case "${CASE}" in
     ;;
 esac
 
+if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
+  export CPL_ATMIC=GLOBAL-NEST_${CASE}
+fi
+
 echo "END: config.stage_ic"
diff --git a/parm/config/gfs/config.ufs b/parm/config/gfs/config.ufs
index 7cec5a08220..6aabe3c268b 100644
--- a/parm/config/gfs/config.ufs
+++ b/parm/config/gfs/config.ufs
@@ -68,6 +68,21 @@ if [[ "${skip_mom6}" == "false" ]] || [[ "${skip_cice6}" == "false" ]] || [[ "${
   skip_mediator=false
 fi
 
+if [[ "${DO_NEST:-NO}" == YES ]] ; then
+    export grid_type=0
+    export target_lat=32.5
+    export target_lon=-135.0
+    export stretch_fac=1.0001
+    export NEST_LON1=-195.000000
+    export NEST_LAT1=-7.500000
+    export NEST_LON2=-75.000000
+    export NEST_LAT2=72.500000
+    export twowaynest=${twowaynest:-.true.}
+else
+    # No nest.
+    export grid_type=-1
+fi
+
 # (Standard) Model resolution dependent variables
 case "${fv3_res}" in
     "C48")
@@ -105,6 +120,24 @@ case "${fv3_res}" in
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=1
         export WRITE_GROUP_GFS=1
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=1
+        if [[ ${DO_NEST:-NO} == YES ]] ; then
+            export DELTIM=450
+            export layout_x_gfs=4
+            export layout_y_gfs=4
+            export layout_x_nest=12
+            export layout_y_nest=10
+            export nest_refine=4
+            export nest_ioffset=4
+            export nest_joffset=9
+            export npx_nest=361
+            export npy_nest=241
+            export NEST_DLON=0.25
+            export NEST_DLAT=0.25
+            export WRITE_GROUP=2
+            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=2
+            export WRITE_GROUP_GFS=2
+            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=2
+        fi
         ;;
     "C192")
         export DELTIM=450
@@ -123,6 +156,24 @@ case "${fv3_res}" in
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
         export WRITE_GROUP_GFS=2
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=5
+        if [[ ${DO_NEST:-NO} == YES ]] ; then
+            export DELTIM=225
+            export layout_x_gfs=5
+            export layout_y_gfs=6
+            export layout_x_nest=15
+            export layout_y_nest=25
+            export nest_refine=4
+            export nest_ioffset=7
+            export nest_joffset=19
+            export npx_nest=721
+            export npy_nest=481
+            export NEST_DLON=0.125
+            export NEST_DLAT=0.125
+            export WRITE_GROUP=2
+            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=15
+            export WRITE_GROUP_GFS=2
+            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=15
+        fi
         ;;
     "C384")
         export DELTIM=300
@@ -141,6 +192,26 @@ case "${fv3_res}" in
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
         export WRITE_GROUP_GFS=4
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=10
+        if [[ ${DO_NEST:-NO} == YES ]] ; then
+            export DELTIM=150
+            export layout_x=8
+            export layout_y=8
+            export layout_x_gfs=8
+            export layout_y_gfs=8
+            export layout_x_nest=34
+            export layout_y_nest=24
+            export nest_refine=4
+            export nest_ioffset=13
+            export nest_joffset=37
+            export npx_nest=1441
+            export npy_nest=961
+            export NEST_DLON=0.0625
+            export NEST_DLAT=0.0625
+            export WRITE_GROUP=2
+            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=20
+            export WRITE_GROUP_GFS=2
+            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20
+        fi
         ;;
     "C768")
         export DELTIM=150
@@ -159,6 +230,28 @@ case "${fv3_res}" in
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
         export WRITE_GROUP_GFS=4
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20 #Note this should be 10 for WCOSS2
+        if [[ ${DO_NEST:-NO} == YES ]] ; then
+            export DELTIM=75
+            export layout_x=16
+            export layout_y=10
+            export layout_x_gfs=16
+            export layout_y_gfs=10
+            export layout_x_nest=48
+            export layout_y_nest=45
+            export nthreads_fv3=2
+            export nthreads_fv3_gfs=2
+            export nest_refine=4
+            export nest_ioffset=24
+            export nest_joffset=72
+            export npx_nest=2881
+            export npy_nest=1921
+            export NEST_DLON=0.0325
+            export NEST_DLAT=0.0325
+            export WRITE_GROUP=2
+            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=90
+            export WRITE_GROUP_GFS=2
+            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=90
+        fi
         ;;
     "C1152")
         export DELTIM=120
@@ -209,6 +302,9 @@ export WRTTASK_PER_GROUP_PER_THREAD_GFS
 
 (( ntasks_fv3 = layout_x * layout_y * 6 ))
 (( ntasks_fv3_gfs = layout_x_gfs * layout_y_gfs * 6 ))
+if [[ "${DO_NEST:-NO}" == YES ]] ; then
+  (( ntasks_fv3_gfs += layout_x_nest * layout_y_nest ))
+fi
 export ntasks_fv3
 export ntasks_fv3_gfs
 
@@ -241,7 +337,11 @@ export cplice=".false."
 export cplchm=".false."
 export cplwav=".false."
 export cplwav2atm=".false."
-export CCPP_SUITE="${CCPP_SUITE:-FV3_GFS_v17_p8_ugwpv1}"
+if [[ "${DO_NEST:-NO}" == YES ]] ; then
+  export CCPP_SUITE="${CCPP_SUITE:-FV3_global_nest_v1}"
+else
+  export CCPP_SUITE="${CCPP_SUITE:-FV3_GFS_v17_p8_ugwpv1}"
+fi
 model_list="atm"
 
 # Mediator specific settings
diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
index 1a15ceb465d..d941fa10b48 100755
--- a/scripts/exglobal_stage_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -42,9 +42,13 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
       err=$((err + rc))
     done
     for ftype in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data; do
-      for ((tt = 1; tt <= 6; tt++)); do
+      for ((tt = 1; tt <= ntiles; tt++)); do
         src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
-        tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
+        if (( tt > 6 )) ; then
+            tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}.nest0$((tt-5)).tile${tt}.nc"
+        else
+            tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
+        fi
         ${NCP} "${src}" "${tgt}"
         rc=$?
         ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
@@ -62,7 +66,7 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
     ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
     err=$((err + rc))
     for ftype in gfs_data sfc_data; do
-      for ((tt = 1; tt <= 6; tt++)); do
+      for ((tt = 1; tt <= ntiles; tt++)); do
         src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${ftype}.tile${tt}.nc"
         tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
         ${NCP} "${src}" "${tgt}"
@@ -70,6 +74,9 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
         ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
         err=$((err + rc))
       done
+      if (( ntiles > 6 )); then
+        ${NLN} "${COM_ATMOS_INPUT}/${ftype}.tile7.nc" "${COM_ATMOS_INPUT}/${ftype}.nest02.tile7.nc"
+      fi
     done
   fi
 
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 1c0c50de206..36df6c30aa4 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -175,6 +175,10 @@ EOF
       if [[ "${WRITE_DOPOST}" == ".true." ]]; then
         ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.master.grb2f${FH3}" "GFSPRS.GrbF${FH2}"
         ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}"
+        if [[ "${DO_NEST:-NO}" == YES ]] ; then
+            ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.grb2f${FH3}" "GFSPRS.GrbF${FH2}.nest02"
+            ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}.nest02"
+        fi
       fi
     done
   else  # TODO: Is this even valid anymore?
@@ -196,7 +200,12 @@ FV3_nml() {
   source "${USHgfs}/parsing_namelists_FV3.sh"
   source "${USHgfs}/parsing_model_configure_FV3.sh"
 
-  FV3_namelists
+  if [[ "${DO_NEST:-NO}" == YES ]] ; then
+      FV3_namelists global_with_nest
+      FV3_namelists nest
+  else
+      FV3_namelists #default to global without nest
+  fi
   FV3_model_configure
 
   echo "SUB ${FUNCNAME[0]}: FV3 name lists and model configure file created"
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 6605a9fa95e..212257c3239 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -107,9 +107,6 @@ FV3_predet(){
   IAUFHRS=${IAUFHRS:-0}
   IAU_DELTHRS=${IAU_DELTHRS:-0}
 
-  # Model config options
-  ntiles=6
-
   #------------------------------------------------------------------
   # changeable parameters
   # dycore definitions
@@ -232,9 +229,16 @@ FV3_predet(){
 
   # Conserve total energy as heat globally
   consv_te=${consv_te:-1.} # range 0.-1., 1. will restore energy to orig. val. before physics
+  if [[ "${DO_NEST:-NO}" == YES ]] ; then
+    consv_te=0
+    k_split=${k_split:-1}
+    k_split_nest=${k_split_nest:-4}
+  else
+    consv_te=${consv_te:-1.} # range 0.-1., 1. will restore energy to orig. val. before physics
+    k_split=${k_split:-2}
+  fi
 
   # time step parameters in FV3
-  k_split=${k_split:-2}
   n_split=${n_split:-5}
 
   if [[ "${MONO:0:4}" == "mono" ]]; then  # monotonic options
@@ -360,6 +364,13 @@ FV3_predet(){
     ${NCP} "${FIXgfs}/ugwd/${CASE}/${CASE}_oro_data_ls.tile${tt}.nc"          "${DATA}/INPUT/oro_data_ls.tile${tt}.nc"
     ${NCP} "${FIXgfs}/ugwd/${CASE}/${CASE}_oro_data_ss.tile${tt}.nc"          "${DATA}/INPUT/oro_data_ss.tile${tt}.nc"
   done
+  if [[ "${DO_NEST:-NO}" == YES ]] ; then
+    ${NLN} "${DATA}/INPUT/oro_data.tile7.nc" "${DATA}/INPUT/oro_data.nest02.tile7.nc"
+    ${NLN} "${DATA}/INPUT/${CASE}_grid.tile7.nc"     "${DATA}/INPUT/${CASE}_grid.nest02.tile7.nc"
+    ${NLN} "${DATA}/INPUT/${CASE}_grid.tile7.nc"     "${DATA}/INPUT/grid.nest02.tile7.nc"
+    ${NLN} "${DATA}/INPUT/oro_data_ls.tile7.nc" "${DATA}/INPUT/oro_data_ls.nest02.tile7.nc"
+    ${NLN} "${DATA}/INPUT/oro_data_ss.tile7.nc" "${DATA}/INPUT/oro_data_ss.nest02.tile7.nc"
+  fi
 
   # NoahMP table
   local noahmptablefile="${PARMgfs}/ufs/noahmptable.tbl"
diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh
index 62d023a369a..e10107a49b7 100755
--- a/ush/parsing_model_configure_FV3.sh
+++ b/ush/parsing_model_configure_FV3.sh
@@ -59,6 +59,27 @@ if [[ ! -f ${template} ]]; then
 fi
 rm -f "${DATA}/model_configure"
 atparse < "${template}" >> "${DATA}/model_configure"
+
+if [[ "${DO_NEST:-NO}" == YES ]] ; then
+    cat >> model_configure <<EOF
+
+# Output settings for the nest.
+<output_grid_02>
+output_grid:             ${NEST_OUTPUT_GRID}
+imo:                     ${npx_nest}
+jmo:                     ${npy_nest}
+cen_lon:                 ${target_lon}
+cen_lat:                 ${target_lat}
+lon1:                    ${NEST_LON1}
+lat1:                    ${NEST_LAT1}
+lon2:                    ${NEST_LON2}
+lat2:                    ${NEST_LAT2}
+dlon:                    ${NEST_DLON}
+dlat:                    ${NEST_DLAT}
+</output_grid_02>
+EOF
+fi
+
 echo "Rendered model_configure"
 cat "${DATA}/model_configure"
 
diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
index 9e6e67f9cc7..664174f6e32 100755
--- a/ush/parsing_namelists_FV3.sh
+++ b/ush/parsing_namelists_FV3.sh
@@ -6,6 +6,20 @@
 # shellcheck disable=SC2034
 FV3_namelists(){
 
+# First argument tells us which namelist we're writing:
+#   global_no_nest  = writing input.nml for global-only (no nest)
+#   global_with_nest = writing input.nml for running global with a nest
+#   nest             = writing input_nest02.nml for running the nest
+namelist_mode="${1:-global_no_nest}"
+
+if [[ ${namelist_mode} == nest ]] ; then
+    nml_file=input_nest02.nml
+    only_input_nml="YES"
+else
+    nml_file=input.nml
+    only_input_nml="NO"
+fi
+
 # setup the tables
 DIAG_TABLE=${DIAG_TABLE:-${PARMgfs}/ufs/fv3/diag_table}
 DIAG_TABLE_APPEND=${DIAG_TABLE_APPEND:-${PARMgfs}/ufs/fv3/diag_table_aod}
@@ -20,6 +34,7 @@ fi
 # ensure non-prognostic tracers are set
 dnats=${dnats:-0}
 
+if [[ "${only_input_nml:-NO}" == "NO" ]] ; then
 # build the diag_table
 {
 echo "UFS_Weather_Model_Forecast"
@@ -67,8 +82,28 @@ if [[ -n "${AERO_FIELD_TABLE:-}" ]]; then
 else
   ${NCP} "${FIELD_TABLE}" field_table
 fi
+fi # only_input_nml
+
+if [[ ${namelist_mode} =~ global ]] ; then
+    layout_x_here=${layout_x}
+    layout_y_here=${layout_y}
+    ntiles_here=6
+    npx_here=${npx}
+    npy_here=${npy}
+    k_split_here=${k_split}
+else
+    layout_x_here=${layout_x_nest}
+    layout_y_here=${layout_y_nest}
+    ntiles_here=1
+    nested_here=.true.
+    twowaynest_here=${twowaynest:-.true.}
+    nestupdate_here=${nestupdate:-7}
+    npx_here=${npx_nest}
+    npy_here=${npy_nest}
+    k_split_here=${k_split_nest}
+fi
 
-cat > input.nml <<EOF
+cat > "${nml_file}" <<EOF
 &atmos_model_nml
   blocksize = ${blocksize}
   chksum_debug = ${chksum_debug}
@@ -95,15 +130,18 @@ cat > input.nml <<EOF
 /
 
 &fv_core_nml
-  layout = ${layout_x},${layout_y}
+  layout = ${layout_x_here},${layout_y_here}
   io_layout = ${io_layout}
-  npx = ${npx}
-  npy = ${npy}
-  ntiles = ${ntiles}
+  npx = ${npx_here}
+  npy = ${npy_here}
+  ntiles = ${ntiles_here}
+  ${nested_here:+nested = $nested_here}
+  ${twowaynest_here:+twowaynest = $twowaynest_here}
+  ${nestupdate_here:+nestupdate = $nestupdate_here}
   npz = ${npz}
   dz_min =  ${dz_min:-"6"}
   psm_bc = ${psm_bc:-"0"}
-  grid_type = -1
+  grid_type = ${grid_type:--1}
   make_nh = ${make_nh}
   fv_debug = ${fv_debug:-".false."}
   range_warn = ${range_warn:-".true."}
@@ -125,7 +163,7 @@ cat > input.nml <<EOF
   beta = 0.
   a_imp = 1.
   p_fac = 0.1
-  k_split = ${k_split}
+  k_split = ${k_split_here}
   n_split = ${n_split}
   nwat = ${nwat:-2}
   na_init = ${na_init}
@@ -168,6 +206,26 @@ cat > input.nml <<EOF
   read_increment = ${read_increment}
   res_latlon_dynamics = ${res_latlon_dynamics}
   ${fv_core_nml-}
+EOF
+
+if [[ "${DO_NEST:-NO}" == YES && ${namelist_mode} =~ global ]] ; then
+  cat >> "${nml_file}" <<EOF
+  do_schmidt = .true.
+  target_lat = ${target_lat}
+  target_lon = ${target_lon}
+  stretch_fac = ${stretch_fac}
+EOF
+fi
+
+if [[ "${DO_NEST:-NO}" == YES && ${namelist_mode} == nest ]] ; then
+  cat >> "${nml_file}" <<EOF
+  nested = .true.
+  twowaynest = ${twowaynest:-.true.} ! .true.
+  nestupdate = 7
+EOF
+fi
+
+cat >> "${nml_file}" <<EOF
 /
 
 &external_ic_nml
@@ -193,13 +251,13 @@ EOF
 
 case "${CCPP_SUITE:-}" in
   "FV3_GFS_v15p2_coupled")
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   oz_phys      = .false.
   oz_phys_2015 = .true.
 EOF
   ;;
   "FV3_GSD_v0")
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -219,7 +277,7 @@ EOF
 EOF
   ;;
   FV3_GFS_v16_coupled*)
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -237,7 +295,7 @@ EOF
 EOF
   ;;
   FV3_GFS_v16*)
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -257,7 +315,7 @@ EOF
   ;;
   FV3_GFS_v17*)
   local default_dt_inner=$(( DELTIM/2 ))
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".true."}
@@ -292,7 +350,7 @@ EOF
   ;;
   FV3_global_nest*)
   local default_dt_inner=$(( DELTIM/2 ))
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   lcnorm       = ${lcnorm:-".false."}
   ltaerosol    = ${ltaerosol:-".false."}
@@ -327,13 +385,13 @@ EOF
 EOF
   ;;
   *)
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
 EOF
   ;;
 esac
 
-cat >> input.nml <<EOF
+cat >> "${nml_file}" <<EOF
   pdfcld       = ${pdfcld:-".false."}
   fhswr        = ${FHSWR:-"3600."}
   fhlwr        = ${FHLWR:-"3600."}
@@ -411,12 +469,12 @@ cat >> input.nml <<EOF
 EOF
 
 if [[ ${cplchm} = ".true." ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   fscav_aero = ${fscav_aero:-'*:0.0'}
 EOF
 fi
 
-cat >> input.nml <<EOF
+cat >> "${nml_file}" <<EOF
   do_sppt      = ${do_sppt:-".false."}
   do_shum      = ${do_shum:-".false."}
   do_skeb      = ${do_skeb:-".false."}
@@ -429,7 +487,7 @@ cat >> input.nml <<EOF
 EOF
 
 if [[ ${DO_SPPT} = "YES" ]]; then
-cat >> input.nml <<EOF
+cat >> "${nml_file}" <<EOF
   pert_mp = .false.
   pert_radtend = .false.
   pert_clds = .true.
@@ -438,7 +496,7 @@ fi
 
 # Add namelist for IAU
 if [[ ${DOIAU} = "YES" ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iaufhrs      = ${IAUFHRS}
   iau_delthrs  = ${IAU_DELTHRS}
   iau_inc_files= ${IAU_INC_FILES}
@@ -448,7 +506,7 @@ EOF
 fi
 
 if [[ ${DO_CA:-"NO"} = "YES" ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   do_ca      = .true.
   ca_global  = ${ca_global:-".false."}
   ca_sgs     = ${ca_sgs:-".true."}
@@ -465,19 +523,33 @@ EOF
 fi
 
 if [[ "${DO_LAND_PERT:-NO}" == "YES" ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   lndp_type = ${lndp_type:-2}
   n_var_lndp = ${n_var_lndp:-0}
 EOF
 fi
 
 # Close &gfs_physics_nml section
-cat >> input.nml << EOF
+cat >> "${nml_file}" << EOF
+/
+EOF
+
+if [[ ${namelist_mode} == "global_with_nest" ]] ; then
+  cat >> "${nml_file}" << EOF
+&fv_nest_nml
+  grid_pes = $(( layout_x * layout_y * 6 )),$(( layout_x_nest * layout_y_nest ))
+  tile_coarse = 0,6
+  num_tile_top = 6
+  p_split = 1
+  nest_refine = 0,${nest_refine}
+  nest_ioffsets = 0,${nest_ioffset}
+  nest_joffsets = 0,${nest_joffset}
 /
 EOF
+fi
 
 if [[ ${knob_ugwp_version} -eq 0 ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
 &cires_ugwp_nml
   knob_ugwp_solver  = ${knob_ugwp_solver:-2}
   knob_ugwp_source  = ${knob_ugwp_source:-1,1,0,0}
@@ -496,7 +568,7 @@ EOF
 fi
 
 if [[ ${knob_ugwp_version} -eq 1 ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
 &cires_ugwp_nml
   knob_ugwp_solver  = ${knob_ugwp_solver:-2}
   knob_ugwp_source  = ${knob_ugwp_source:-1,1,0,0}
@@ -522,9 +594,9 @@ if [[ ${knob_ugwp_version} -eq 1 ]]; then
 EOF
 fi
 
-echo "" >> input.nml
+echo "" >> "${nml_file}"
 
-cat >> input.nml <<EOF
+cat >> "${nml_file}" <<EOF
 &gfdl_cloud_microphysics_nml
   sedi_transport = .true.
   do_sedi_heat = .false.
@@ -628,22 +700,29 @@ cat >> input.nml <<EOF
 /
 
 &fv_grid_nml
+EOF
+if [[ "${DO_NEST:-NO}" == NO ]] ; then
+    cat >> "${nml_file}" <<EOF
   grid_file = 'INPUT/grid_spec.nc'
+EOF
+fi
+
+cat >> "${nml_file}" <<EOF
   ${fv_grid_nml:-}
 /
 EOF
 
 # Add namelist for stochastic physics options
-echo "" >> input.nml
+echo "" >> "${nml_file}"
 #if [ $MEMBER -gt 0 ]; then
 if [[ "${DO_SPPT}" = "YES" || "${DO_SHUM}" = "YES" || "${DO_SKEB}" = "YES" || "${DO_LAND_PERT}" = "YES" ]]; then
 
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
 &nam_stochy
 EOF
 
   if [[ ${DO_SKEB} = "YES" ]]; then
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
   skeb = ${SKEB}
   iseed_skeb = ${ISEED_SKEB:-${ISEED}}
   skeb_tau = ${SKEB_TAU:-"-999."}
@@ -655,7 +734,7 @@ EOF
   fi
 
   if [[ ${DO_SHUM} = "YES" ]]; then
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
   shum = ${SHUM}
   iseed_shum = ${ISEED_SHUM:-${ISEED}}
   shum_tau = ${SHUM_TAU:-"-999."}
@@ -664,7 +743,7 @@ EOF
   fi
 
   if [[ ${DO_SPPT} = "YES" ]]; then
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
   sppt = ${SPPT}
   iseed_sppt = ${ISEED_SPPT:-${ISEED}}
   sppt_tau = ${SPPT_TAU:-"-999."}
@@ -677,7 +756,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_SPPT:-NO}" == "YES" ]]; then
-    cat >> input.nml <<EOF
+    cat >> "${nml_file}" <<EOF
   OCNSPPT=${OCNSPPT}
   OCNSPPT_LSCALE=${OCNSPPT_LSCALE}
   OCNSPPT_TAU=${OCNSPPT_TAU}
@@ -686,7 +765,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_PERT_EPBL:-NO}" == "YES" ]]; then
-    cat >> input.nml <<EOF
+    cat >> "${nml_file}" <<EOF
   EPBL=${EPBL}
   EPBL_LSCALE=${EPBL_LSCALE}
   EPBL_TAU=${EPBL_TAU}
@@ -695,7 +774,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_SPPT:-NO}" == "YES" ]]; then
-    cat >> input.nml <<EOF
+    cat >> "${nml_file}" <<EOF
   OCNSPPT=${OCNSPPT}
   OCNSPPT_LSCALE=${OCNSPPT_LSCALE}
   OCNSPPT_TAU=${OCNSPPT_TAU}
@@ -704,7 +783,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_PERT_EPBL:-NO}" == "YES" ]]; then
-    cat >> input.nml <<EOF
+    cat >> "${nml_file}" <<EOF
   EPBL=${EPBL}
   EPBL_LSCALE=${EPBL_LSCALE}
   EPBL_TAU=${EPBL_TAU}
@@ -712,12 +791,12 @@ EOF
 EOF
   fi
 
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
 /
 EOF
 
   if [[ ${DO_LAND_PERT} = "YES" ]]; then
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
 &nam_sfcperts
   lndp_type = ${lndp_type}
   LNDP_TAU = ${LNDP_TAU}
@@ -728,7 +807,7 @@ EOF
 /
 EOF
   else
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
 &nam_sfcperts
 /
 EOF
@@ -736,7 +815,7 @@ EOF
 
 else
 
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
 &nam_stochy
 /
 &nam_sfcperts
@@ -745,9 +824,9 @@ EOF
 
 fi
 
-# Echo out formatted "input.nml"
+# Echo out formatted ""${nml_file}""
 echo "===================================="
-echo "FV3_namelists(): 'input.nml'"
-cat input.nml
+echo "FV3_namelists(): '${nml_file}'"
+cat "${nml_file}"
 echo "===================================="
 }

From b1ad53dddcdcda115b1086dc4be40c0f4d28e4e0 Mon Sep 17 00:00:00 2001
From: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Thu, 25 Apr 2024 16:45:55 -0600
Subject: [PATCH 02/15] Apply suggestions from code review

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 parm/config/gfs/config.fcst      | 7 +++----
 parm/config/gfs/config.resources | 2 +-
 parm/config/gfs/config.stage_ic  | 2 +-
 parm/config/gfs/config.ufs       | 3 ++-
 ush/forecast_postdet.sh          | 3 ++-
 5 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/parm/config/gfs/config.fcst b/parm/config/gfs/config.fcst
index ddca84306b5..63273e0fe4c 100644
--- a/parm/config/gfs/config.fcst
+++ b/parm/config/gfs/config.fcst
@@ -253,10 +253,9 @@ export DO_SPPT=${DO_SPPT:-"NO"}
 export DO_SKEB=${DO_SKEB:-"NO"}
 export DO_SHUM=${DO_SHUM:-"NO"}
 export DO_LAND_PERT=${DO_LAND_PERT:-"NO"}
-if [[ "${DO_NEST:-NO}" == YES ]] ; then
-  export DO_CA="NO" #CA does not work with nesting. 
-else
-  export DO_CA=${DO_CA:-"YES"}
+export DO_CA=${DO_CA:-"YES"}
+if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
+  export DO_CA="NO"  # CA does not work with nesting.
 fi
 
 #coupling settings
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index 63b57b15b4e..62a3e17bdb9 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -600,7 +600,7 @@ case ${step} in
         [[ "${DO_ICE}" == "YES" ]] && nthreads_cice6=1
       fi
 
-      if [[ ${ntiles} -gt 6 ]] ; then
+      if (( ntiles > 6 )); then
         export layout_x_nest=${layout_x_nest:-10}
         export layout_y_nest=${layout_y_nest:-10}
         export npx_nest=${npx_nest:-1441}
diff --git a/parm/config/gfs/config.stage_ic b/parm/config/gfs/config.stage_ic
index 51e57c33dd3..9956e8af6a0 100644
--- a/parm/config/gfs/config.stage_ic
+++ b/parm/config/gfs/config.stage_ic
@@ -39,7 +39,7 @@ case "${CASE}" in
 esac
 
 if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
-  export CPL_ATMIC=GLOBAL-NEST_${CASE}
+  export CPL_ATMIC="GLOBAL-NEST_${CASE}"
 fi
 
 echo "END: config.stage_ic"
diff --git a/parm/config/gfs/config.ufs b/parm/config/gfs/config.ufs
index 6aabe3c268b..abbdbb6d1c9 100644
--- a/parm/config/gfs/config.ufs
+++ b/parm/config/gfs/config.ufs
@@ -68,7 +68,8 @@ if [[ "${skip_mom6}" == "false" ]] || [[ "${skip_cice6}" == "false" ]] || [[ "${
   skip_mediator=false
 fi
 
-if [[ "${DO_NEST:-NO}" == YES ]] ; then
+if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
+    # Describe nest location, interaction with parent, etc.
     export grid_type=0
     export target_lat=32.5
     export target_lon=-135.0
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 36df6c30aa4..b3f0ff5817a 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -200,11 +200,12 @@ FV3_nml() {
   source "${USHgfs}/parsing_namelists_FV3.sh"
   source "${USHgfs}/parsing_model_configure_FV3.sh"
 
+  # Call the appropriate namelist functions
   if [[ "${DO_NEST:-NO}" == YES ]] ; then
       FV3_namelists global_with_nest
       FV3_namelists nest
   else
-      FV3_namelists #default to global without nest
+      FV3_namelists
   fi
   FV3_model_configure
 

From efce25953606beff021f41b1f7e8a59f2d16d228 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Thu, 25 Apr 2024 19:41:12 -0600
Subject: [PATCH 03/15] Apply suggestions from code review

---
 parm/config/gefs/config.base       |   7 +
 parm/config/gfs/config.ufs         | 296 +++++++++++++++--------------
 sorc/link_workflow.sh              |   2 +-
 ush/forecast_postdet.sh            |  10 +-
 ush/parsing_model_configure_FV3.sh |  27 +--
 ush/parsing_namelists_FV3.sh       |   6 +-
 6 files changed, 171 insertions(+), 177 deletions(-)

diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
index 07664f15ff2..bc37c5abbc5 100644
--- a/parm/config/gefs/config.base
+++ b/parm/config/gefs/config.base
@@ -137,6 +137,13 @@ export DO_AERO="NO"
 export WAVE_CDUMP="" # When to include wave suite: gdas, gfs, or both
 export DOBNDPNT_WAVE="NO" # The GEFS buoys file does not currently have any boundary points
 export FRAC_GRID=".true."
+export DO_NEST="NO" # Whether to run a global-nested domain
+if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
+  export ntiles=7
+  export NEST_OUTPUT_GRID="regional_latlon"
+else
+  export ntiles=6
+fi
 
 # Set operational resolution
 export OPS_RES="C768" # Do not change
diff --git a/parm/config/gfs/config.ufs b/parm/config/gfs/config.ufs
index abbdbb6d1c9..ad306277a71 100644
--- a/parm/config/gfs/config.ufs
+++ b/parm/config/gfs/config.ufs
@@ -69,19 +69,19 @@ if [[ "${skip_mom6}" == "false" ]] || [[ "${skip_cice6}" == "false" ]] || [[ "${
 fi
 
 if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
-    # Describe nest location, interaction with parent, etc.
-    export grid_type=0
-    export target_lat=32.5
-    export target_lon=-135.0
-    export stretch_fac=1.0001
-    export NEST_LON1=-195.000000
-    export NEST_LAT1=-7.500000
-    export NEST_LON2=-75.000000
-    export NEST_LAT2=72.500000
-    export twowaynest=${twowaynest:-.true.}
+  # Describe nest location, interaction with parent, etc.
+  export grid_type=0
+  export target_lat=32.5
+  export target_lon=-135.0
+  export stretch_fac=1.0001
+  export NEST_LON1=-195.000000
+  export NEST_LAT1=-7.500000
+  export NEST_LON2=-75.000000
+  export NEST_LAT2=72.500000
+  export twowaynest=${twowaynest:-.true.}
 else
-    # No nest.
-    export grid_type=-1
+  # No nest.
+  export grid_type=-1
 fi
 
 # (Standard) Model resolution dependent variables
@@ -105,153 +105,157 @@ case "${fv3_res}" in
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=1
         ;;
     "C96")
-        export DELTIM=600
-        export layout_x=2
-        export layout_y=2
-        export layout_x_gfs=2
-        export layout_y_gfs=2
-        export nthreads_fv3=1
-        export nthreads_fv3_gfs=1
-        export nthreads_ufs=1
-        export nthreads_ufs_gfs=1
-        export cdmbgwd="0.14,1.8,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
-        export cdmbgwd_gsl="20.0,2.5,1.0,1.0"   # settings for GSL drag suite
-        export knob_ugwp_tauamp=3.0e-3      # setting for UGWPv1 non-stationary GWD
-        export WRITE_GROUP=1
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=1
-        export WRITE_GROUP_GFS=1
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=1
         if [[ ${DO_NEST:-NO} == YES ]] ; then
-            export DELTIM=450
-            export layout_x_gfs=4
-            export layout_y_gfs=4
-            export layout_x_nest=12
-            export layout_y_nest=10
-            export nest_refine=4
-            export nest_ioffset=4
-            export nest_joffset=9
-            export npx_nest=361
-            export npy_nest=241
-            export NEST_DLON=0.25
-            export NEST_DLAT=0.25
-            export WRITE_GROUP=2
-            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=2
-            export WRITE_GROUP_GFS=2
-            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=2
+          export DELTIM=450
+          export layout_x_gfs=4
+          export layout_y_gfs=4
+          export layout_x_nest=12
+          export layout_y_nest=10
+          export nest_refine=4
+          export nest_ioffset=4
+          export nest_joffset=9
+          export npx_nest=361
+          export npy_nest=241
+          export NEST_DLON=0.25
+          export NEST_DLAT=0.25
+          export WRITE_GROUP=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=2
+          export WRITE_GROUP_GFS=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=2
+        else
+          export DELTIM=600
+          export layout_x=2
+          export layout_y=2
+          export layout_x_gfs=2
+          export layout_y_gfs=2
+          export nthreads_fv3=1
+          export nthreads_fv3_gfs=1
+          export nthreads_ufs=1
+          export nthreads_ufs_gfs=1
+          export cdmbgwd="0.14,1.8,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
+          export cdmbgwd_gsl="20.0,2.5,1.0,1.0"   # settings for GSL drag suite
+          export knob_ugwp_tauamp=3.0e-3      # setting for UGWPv1 non-stationary GWD
+          export WRITE_GROUP=1
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=1
+          export WRITE_GROUP_GFS=1
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=1
         fi
         ;;
     "C192")
-        export DELTIM=450
-        export layout_x=4
-        export layout_y=6
-        export layout_x_gfs=4
-        export layout_y_gfs=6
-        export nthreads_fv3=1
-        export nthreads_fv3_gfs=2
-        export nthreads_ufs=1
-        export nthreads_ufs_gfs=2
-        export cdmbgwd="0.23,1.5,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
-        export cdmbgwd_gsl="10.0,3.5,1.0,1.0"   # settings for GSL drag suite
-        export knob_ugwp_tauamp=1.5e-3      # setting for UGWPv1 non-stationary GWD
-        export WRITE_GROUP=1
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
-        export WRITE_GROUP_GFS=2
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=5
         if [[ ${DO_NEST:-NO} == YES ]] ; then
-            export DELTIM=225
-            export layout_x_gfs=5
-            export layout_y_gfs=6
-            export layout_x_nest=15
-            export layout_y_nest=25
-            export nest_refine=4
-            export nest_ioffset=7
-            export nest_joffset=19
-            export npx_nest=721
-            export npy_nest=481
-            export NEST_DLON=0.125
-            export NEST_DLAT=0.125
-            export WRITE_GROUP=2
-            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=15
-            export WRITE_GROUP_GFS=2
-            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=15
+          export DELTIM=225
+          export layout_x_gfs=5
+          export layout_y_gfs=6
+          export layout_x_nest=15
+          export layout_y_nest=25
+          export nest_refine=4
+          export nest_ioffset=7
+          export nest_joffset=19
+          export npx_nest=721
+          export npy_nest=481
+          export NEST_DLON=0.125
+          export NEST_DLAT=0.125
+          export WRITE_GROUP=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=15
+          export WRITE_GROUP_GFS=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=15
+        else
+          export DELTIM=450
+          export layout_x=4
+          export layout_y=6
+          export layout_x_gfs=4
+          export layout_y_gfs=6
+          export nthreads_fv3=1
+          export nthreads_fv3_gfs=2
+          export nthreads_ufs=1
+          export nthreads_ufs_gfs=2
+          export cdmbgwd="0.23,1.5,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
+          export cdmbgwd_gsl="10.0,3.5,1.0,1.0"   # settings for GSL drag suite
+          export knob_ugwp_tauamp=1.5e-3      # setting for UGWPv1 non-stationary GWD
+          export WRITE_GROUP=1
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
+          export WRITE_GROUP_GFS=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=5
         fi
         ;;
     "C384")
-        export DELTIM=300
-        export layout_x=8
-        export layout_y=8
-        export layout_x_gfs=8
-        export layout_y_gfs=8
-        export nthreads_fv3=2
-        export nthreads_fv3_gfs=2
-        export nthreads_ufs=2
-        export nthreads_ufs_gfs=2
-        export cdmbgwd="1.1,0.72,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
-        export cdmbgwd_gsl="5.0,5.0,1.0,1.0"   # settings for GSL drag suite
-        export knob_ugwp_tauamp=0.8e-3      # setting for UGWPv1 non-stationary GWD
-        export WRITE_GROUP=4
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
-        export WRITE_GROUP_GFS=4
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=10
         if [[ ${DO_NEST:-NO} == YES ]] ; then
-            export DELTIM=150
-            export layout_x=8
-            export layout_y=8
-            export layout_x_gfs=8
-            export layout_y_gfs=8
-            export layout_x_nest=34
-            export layout_y_nest=24
-            export nest_refine=4
-            export nest_ioffset=13
-            export nest_joffset=37
-            export npx_nest=1441
-            export npy_nest=961
-            export NEST_DLON=0.0625
-            export NEST_DLAT=0.0625
-            export WRITE_GROUP=2
-            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=20
-            export WRITE_GROUP_GFS=2
-            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20
+          export DELTIM=150
+          export layout_x=8
+          export layout_y=8
+          export layout_x_gfs=8
+          export layout_y_gfs=8
+          export layout_x_nest=34
+          export layout_y_nest=24
+          export nest_refine=4
+          export nest_ioffset=13
+          export nest_joffset=37
+          export npx_nest=1441
+          export npy_nest=961
+          export NEST_DLON=0.0625
+          export NEST_DLAT=0.0625
+          export WRITE_GROUP=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=20
+          export WRITE_GROUP_GFS=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20
+        else
+          export DELTIM=300
+          export layout_x=8
+          export layout_y=8
+          export layout_x_gfs=8
+          export layout_y_gfs=8
+          export nthreads_fv3=2
+          export nthreads_fv3_gfs=2
+          export nthreads_ufs=2
+          export nthreads_ufs_gfs=2
+          export cdmbgwd="1.1,0.72,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
+          export cdmbgwd_gsl="5.0,5.0,1.0,1.0"   # settings for GSL drag suite
+          export knob_ugwp_tauamp=0.8e-3      # setting for UGWPv1 non-stationary GWD
+          export WRITE_GROUP=4
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
+          export WRITE_GROUP_GFS=4
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=10
         fi
         ;;
     "C768")
-        export DELTIM=150
-        export layout_x=8
-        export layout_y=12
-        export layout_x_gfs=12
-        export layout_y_gfs=16
-        export nthreads_fv3=4
-        export nthreads_fv3_gfs=4
-        export nthreads_ufs=4
-        export nthreads_ufs_gfs=4
-        export cdmbgwd="4.0,0.15,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
-        export cdmbgwd_gsl="2.5,7.5,1.0,1.0"   # settings for GSL drag suite
-        export knob_ugwp_tauamp=0.5e-3      # setting for UGWPv1 non-stationary GWD
-        export WRITE_GROUP=2
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
-        export WRITE_GROUP_GFS=4
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20 #Note this should be 10 for WCOSS2
         if [[ ${DO_NEST:-NO} == YES ]] ; then
-            export DELTIM=75
-            export layout_x=16
-            export layout_y=10
-            export layout_x_gfs=16
-            export layout_y_gfs=10
-            export layout_x_nest=48
-            export layout_y_nest=45
-            export nthreads_fv3=2
-            export nthreads_fv3_gfs=2
-            export nest_refine=4
-            export nest_ioffset=24
-            export nest_joffset=72
-            export npx_nest=2881
-            export npy_nest=1921
-            export NEST_DLON=0.0325
-            export NEST_DLAT=0.0325
-            export WRITE_GROUP=2
-            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=90
-            export WRITE_GROUP_GFS=2
-            export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=90
+          export DELTIM=75
+          export layout_x=16
+          export layout_y=10
+          export layout_x_gfs=16
+          export layout_y_gfs=10
+          export layout_x_nest=48
+          export layout_y_nest=45
+          export nthreads_fv3=2
+          export nthreads_fv3_gfs=2
+          export nest_refine=4
+          export nest_ioffset=24
+          export nest_joffset=72
+          export npx_nest=2881
+          export npy_nest=1921
+          export NEST_DLON=0.0325
+          export NEST_DLAT=0.0325
+          export WRITE_GROUP=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=90
+          export WRITE_GROUP_GFS=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=90
+        else
+          export DELTIM=150
+          export layout_x=8
+          export layout_y=12
+          export layout_x_gfs=12
+          export layout_y_gfs=16
+          export nthreads_fv3=4
+          export nthreads_fv3_gfs=4
+          export nthreads_ufs=4
+          export nthreads_ufs_gfs=4
+          export cdmbgwd="4.0,0.15,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
+          export cdmbgwd_gsl="2.5,7.5,1.0,1.0"   # settings for GSL drag suite
+          export knob_ugwp_tauamp=0.5e-3      # setting for UGWPv1 non-stationary GWD
+          export WRITE_GROUP=2
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
+          export WRITE_GROUP_GFS=4
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20 #Note this should be 10 for WCOSS2
         fi
         ;;
     "C1152")
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index b3512d14d91..5420de89755 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -169,7 +169,7 @@ done
 
 # Link these templates from ufs-weather-model
 cd "${HOMEgfs}/parm/ufs" || exit 1
-declare -a ufs_templates=("model_configure.IN" \
+declare -a ufs_templates=("model_configure.IN" "model_configure.nest.IN"\
                           "MOM_input_025.IN" "MOM_input_050.IN" "MOM_input_100.IN" "MOM_input_500.IN" \
                           "MOM6_data_table.IN" \
                           "ice_in.IN" \
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index b3f0ff5817a..34c313a9056 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -176,8 +176,8 @@ EOF
         ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.master.grb2f${FH3}" "GFSPRS.GrbF${FH2}"
         ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}"
         if [[ "${DO_NEST:-NO}" == YES ]] ; then
-            ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.grb2f${FH3}" "GFSPRS.GrbF${FH2}.nest02"
-            ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}.nest02"
+          ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.grb2f${FH3}" "GFSPRS.GrbF${FH2}.nest02"
+          ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}.nest02"
         fi
       fi
     done
@@ -202,10 +202,10 @@ FV3_nml() {
 
   # Call the appropriate namelist functions
   if [[ "${DO_NEST:-NO}" == YES ]] ; then
-      FV3_namelists global_with_nest
-      FV3_namelists nest
+    FV3_namelists global_with_nest
+    FV3_namelists nest
   else
-      FV3_namelists
+    FV3_namelists
   fi
   FV3_model_configure
 
diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh
index e10107a49b7..3793b8c6bfa 100755
--- a/ush/parsing_model_configure_FV3.sh
+++ b/ush/parsing_model_configure_FV3.sh
@@ -52,34 +52,17 @@ local OUTPUT_FH=${FV3_OUTPUT_FH}
 local IAU_OFFSET=${IAU_OFFSET:-0}
 
 # Ensure the template exists
-template="${PARMgfs}/ufs/model_configure.IN"
+if [[ "${DO_NEST:-NO}" == YES ]] ; then
+  template="${PARMgfs}/ufs/model_configure.nest.IN"
+else
+  template="${PARMgfs}/ufs/model_configure.IN"
+fi
 if [[ ! -f ${template} ]]; then
   echo "FATAL ERROR: template '${template}' does not exist, ABORT!"
   exit 1
 fi
 rm -f "${DATA}/model_configure"
 atparse < "${template}" >> "${DATA}/model_configure"
-
-if [[ "${DO_NEST:-NO}" == YES ]] ; then
-    cat >> model_configure <<EOF
-
-# Output settings for the nest.
-<output_grid_02>
-output_grid:             ${NEST_OUTPUT_GRID}
-imo:                     ${npx_nest}
-jmo:                     ${npy_nest}
-cen_lon:                 ${target_lon}
-cen_lat:                 ${target_lat}
-lon1:                    ${NEST_LON1}
-lat1:                    ${NEST_LAT1}
-lon2:                    ${NEST_LON2}
-lat2:                    ${NEST_LAT2}
-dlon:                    ${NEST_DLON}
-dlat:                    ${NEST_DLAT}
-</output_grid_02>
-EOF
-fi
-
 echo "Rendered model_configure"
 cat "${DATA}/model_configure"
 
diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
index 664174f6e32..e6065abc15b 100755
--- a/ush/parsing_namelists_FV3.sh
+++ b/ush/parsing_namelists_FV3.sh
@@ -135,9 +135,9 @@ cat > "${nml_file}" <<EOF
   npx = ${npx_here}
   npy = ${npy_here}
   ntiles = ${ntiles_here}
-  ${nested_here:+nested = $nested_here}
-  ${twowaynest_here:+twowaynest = $twowaynest_here}
-  ${nestupdate_here:+nestupdate = $nestupdate_here}
+  ${nested_here:+nested = ${nested_here}}
+  ${twowaynest_here:+twowaynest = ${twowaynest_herei}}
+  ${nestupdate_here:+nestupdate = ${nestupdate_here}}
   npz = ${npz}
   dz_min =  ${dz_min:-"6"}
   psm_bc = ${psm_bc:-"0"}

From f22ca05ad3d8cc9130205d77983de3487b15ea83 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Thu, 25 Apr 2024 19:46:45 -0600
Subject: [PATCH 04/15] minor fix

---
 sorc/link_workflow.sh              | 2 +-
 ush/parsing_model_configure_FV3.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 5420de89755..53d0a4d249f 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -169,7 +169,7 @@ done
 
 # Link these templates from ufs-weather-model
 cd "${HOMEgfs}/parm/ufs" || exit 1
-declare -a ufs_templates=("model_configure.IN" "model_configure.nest.IN"\
+declare -a ufs_templates=("model_configure.IN" "model_configure_nest.IN"\
                           "MOM_input_025.IN" "MOM_input_050.IN" "MOM_input_100.IN" "MOM_input_500.IN" \
                           "MOM6_data_table.IN" \
                           "ice_in.IN" \
diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh
index 3793b8c6bfa..9c02dfa69b5 100755
--- a/ush/parsing_model_configure_FV3.sh
+++ b/ush/parsing_model_configure_FV3.sh
@@ -53,7 +53,7 @@ local IAU_OFFSET=${IAU_OFFSET:-0}
 
 # Ensure the template exists
 if [[ "${DO_NEST:-NO}" == YES ]] ; then
-  template="${PARMgfs}/ufs/model_configure.nest.IN"
+  template="${PARMgfs}/ufs/model_configure_nest.IN"
 else
   template="${PARMgfs}/ufs/model_configure.IN"
 fi

From b5b2809a1b9402f3189d715b3fe63a099f7de5f0 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Thu, 25 Apr 2024 21:18:14 -0600
Subject: [PATCH 05/15] minor changes

---
 parm/config/gfs/config.ufs         | 4 ++--
 ush/parsing_model_configure_FV3.sh | 2 ++
 ush/parsing_namelists_FV3.sh       | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/parm/config/gfs/config.ufs b/parm/config/gfs/config.ufs
index ad306277a71..d6719f04f01 100644
--- a/parm/config/gfs/config.ufs
+++ b/parm/config/gfs/config.ufs
@@ -71,9 +71,9 @@ fi
 if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
   # Describe nest location, interaction with parent, etc.
   export grid_type=0
-  export target_lat=32.5
-  export target_lon=-135.0
   export stretch_fac=1.0001
+  export TARGET_LAT=32.5
+  export TARGET_LON=-135.0
   export NEST_LON1=-195.000000
   export NEST_LAT1=-7.500000
   export NEST_LON2=-75.000000
diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh
index 9c02dfa69b5..6654bbcf4ca 100755
--- a/ush/parsing_model_configure_FV3.sh
+++ b/ush/parsing_model_configure_FV3.sh
@@ -53,6 +53,8 @@ local IAU_OFFSET=${IAU_OFFSET:-0}
 
 # Ensure the template exists
 if [[ "${DO_NEST:-NO}" == YES ]] ; then
+  local NEST_IMO=${npx_nest}
+  local NEST_JMO=${npy_nest}
   template="${PARMgfs}/ufs/model_configure_nest.IN"
 else
   template="${PARMgfs}/ufs/model_configure.IN"
diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
index e6065abc15b..f55d03f3d8b 100755
--- a/ush/parsing_namelists_FV3.sh
+++ b/ush/parsing_namelists_FV3.sh
@@ -211,8 +211,8 @@ EOF
 if [[ "${DO_NEST:-NO}" == YES && ${namelist_mode} =~ global ]] ; then
   cat >> "${nml_file}" <<EOF
   do_schmidt = .true.
-  target_lat = ${target_lat}
-  target_lon = ${target_lon}
+  target_lat = ${TARGET_LAT}
+  target_lon = ${TARGET_LON}
   stretch_fac = ${stretch_fac}
 EOF
 fi

From 4f04afce063451d08e223d8baf3396b707235265 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 14:57:48 -0600
Subject: [PATCH 06/15] remove self.config.ntiles=6 in analysis.py

---
 ush/python/pygfs/task/analysis.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/ush/python/pygfs/task/analysis.py b/ush/python/pygfs/task/analysis.py
index 078e013e7f8..02011423b75 100644
--- a/ush/python/pygfs/task/analysis.py
+++ b/ush/python/pygfs/task/analysis.py
@@ -25,7 +25,6 @@ class Analysis(Task):
 
     def __init__(self, config: Dict[str, Any]) -> None:
         super().__init__(config)
-        self.config.ntiles = 6
         # Store location of GDASApp jinja2 templates
         self.gdasapp_j2tmpl_dir = os.path.join(self.config.PARMgfs, 'gdas')
 

From 1029271ed71d25579120ec254aae415d7fb05627 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:03:23 -0600
Subject: [PATCH 07/15] revert changes in parsing_namelists_FV3.sh

---
 ush/parsing_namelists_FV3.sh | 163 +++++++++--------------------------
 1 file changed, 42 insertions(+), 121 deletions(-)

diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
index f55d03f3d8b..9e6e67f9cc7 100755
--- a/ush/parsing_namelists_FV3.sh
+++ b/ush/parsing_namelists_FV3.sh
@@ -6,20 +6,6 @@
 # shellcheck disable=SC2034
 FV3_namelists(){
 
-# First argument tells us which namelist we're writing:
-#   global_no_nest  = writing input.nml for global-only (no nest)
-#   global_with_nest = writing input.nml for running global with a nest
-#   nest             = writing input_nest02.nml for running the nest
-namelist_mode="${1:-global_no_nest}"
-
-if [[ ${namelist_mode} == nest ]] ; then
-    nml_file=input_nest02.nml
-    only_input_nml="YES"
-else
-    nml_file=input.nml
-    only_input_nml="NO"
-fi
-
 # setup the tables
 DIAG_TABLE=${DIAG_TABLE:-${PARMgfs}/ufs/fv3/diag_table}
 DIAG_TABLE_APPEND=${DIAG_TABLE_APPEND:-${PARMgfs}/ufs/fv3/diag_table_aod}
@@ -34,7 +20,6 @@ fi
 # ensure non-prognostic tracers are set
 dnats=${dnats:-0}
 
-if [[ "${only_input_nml:-NO}" == "NO" ]] ; then
 # build the diag_table
 {
 echo "UFS_Weather_Model_Forecast"
@@ -82,28 +67,8 @@ if [[ -n "${AERO_FIELD_TABLE:-}" ]]; then
 else
   ${NCP} "${FIELD_TABLE}" field_table
 fi
-fi # only_input_nml
-
-if [[ ${namelist_mode} =~ global ]] ; then
-    layout_x_here=${layout_x}
-    layout_y_here=${layout_y}
-    ntiles_here=6
-    npx_here=${npx}
-    npy_here=${npy}
-    k_split_here=${k_split}
-else
-    layout_x_here=${layout_x_nest}
-    layout_y_here=${layout_y_nest}
-    ntiles_here=1
-    nested_here=.true.
-    twowaynest_here=${twowaynest:-.true.}
-    nestupdate_here=${nestupdate:-7}
-    npx_here=${npx_nest}
-    npy_here=${npy_nest}
-    k_split_here=${k_split_nest}
-fi
 
-cat > "${nml_file}" <<EOF
+cat > input.nml <<EOF
 &atmos_model_nml
   blocksize = ${blocksize}
   chksum_debug = ${chksum_debug}
@@ -130,18 +95,15 @@ cat > "${nml_file}" <<EOF
 /
 
 &fv_core_nml
-  layout = ${layout_x_here},${layout_y_here}
+  layout = ${layout_x},${layout_y}
   io_layout = ${io_layout}
-  npx = ${npx_here}
-  npy = ${npy_here}
-  ntiles = ${ntiles_here}
-  ${nested_here:+nested = ${nested_here}}
-  ${twowaynest_here:+twowaynest = ${twowaynest_herei}}
-  ${nestupdate_here:+nestupdate = ${nestupdate_here}}
+  npx = ${npx}
+  npy = ${npy}
+  ntiles = ${ntiles}
   npz = ${npz}
   dz_min =  ${dz_min:-"6"}
   psm_bc = ${psm_bc:-"0"}
-  grid_type = ${grid_type:--1}
+  grid_type = -1
   make_nh = ${make_nh}
   fv_debug = ${fv_debug:-".false."}
   range_warn = ${range_warn:-".true."}
@@ -163,7 +125,7 @@ cat > "${nml_file}" <<EOF
   beta = 0.
   a_imp = 1.
   p_fac = 0.1
-  k_split = ${k_split_here}
+  k_split = ${k_split}
   n_split = ${n_split}
   nwat = ${nwat:-2}
   na_init = ${na_init}
@@ -206,26 +168,6 @@ cat > "${nml_file}" <<EOF
   read_increment = ${read_increment}
   res_latlon_dynamics = ${res_latlon_dynamics}
   ${fv_core_nml-}
-EOF
-
-if [[ "${DO_NEST:-NO}" == YES && ${namelist_mode} =~ global ]] ; then
-  cat >> "${nml_file}" <<EOF
-  do_schmidt = .true.
-  target_lat = ${TARGET_LAT}
-  target_lon = ${TARGET_LON}
-  stretch_fac = ${stretch_fac}
-EOF
-fi
-
-if [[ "${DO_NEST:-NO}" == YES && ${namelist_mode} == nest ]] ; then
-  cat >> "${nml_file}" <<EOF
-  nested = .true.
-  twowaynest = ${twowaynest:-.true.} ! .true.
-  nestupdate = 7
-EOF
-fi
-
-cat >> "${nml_file}" <<EOF
 /
 
 &external_ic_nml
@@ -251,13 +193,13 @@ EOF
 
 case "${CCPP_SUITE:-}" in
   "FV3_GFS_v15p2_coupled")
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   oz_phys      = .false.
   oz_phys_2015 = .true.
 EOF
   ;;
   "FV3_GSD_v0")
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -277,7 +219,7 @@ EOF
 EOF
   ;;
   FV3_GFS_v16_coupled*)
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -295,7 +237,7 @@ EOF
 EOF
   ;;
   FV3_GFS_v16*)
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -315,7 +257,7 @@ EOF
   ;;
   FV3_GFS_v17*)
   local default_dt_inner=$(( DELTIM/2 ))
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".true."}
@@ -350,7 +292,7 @@ EOF
   ;;
   FV3_global_nest*)
   local default_dt_inner=$(( DELTIM/2 ))
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   iovr         = ${iovr:-"3"}
   lcnorm       = ${lcnorm:-".false."}
   ltaerosol    = ${ltaerosol:-".false."}
@@ -385,13 +327,13 @@ EOF
 EOF
   ;;
   *)
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   iovr         = ${iovr:-"3"}
 EOF
   ;;
 esac
 
-cat >> "${nml_file}" <<EOF
+cat >> input.nml <<EOF
   pdfcld       = ${pdfcld:-".false."}
   fhswr        = ${FHSWR:-"3600."}
   fhlwr        = ${FHLWR:-"3600."}
@@ -469,12 +411,12 @@ cat >> "${nml_file}" <<EOF
 EOF
 
 if [[ ${cplchm} = ".true." ]]; then
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   fscav_aero = ${fscav_aero:-'*:0.0'}
 EOF
 fi
 
-cat >> "${nml_file}" <<EOF
+cat >> input.nml <<EOF
   do_sppt      = ${do_sppt:-".false."}
   do_shum      = ${do_shum:-".false."}
   do_skeb      = ${do_skeb:-".false."}
@@ -487,7 +429,7 @@ cat >> "${nml_file}" <<EOF
 EOF
 
 if [[ ${DO_SPPT} = "YES" ]]; then
-cat >> "${nml_file}" <<EOF
+cat >> input.nml <<EOF
   pert_mp = .false.
   pert_radtend = .false.
   pert_clds = .true.
@@ -496,7 +438,7 @@ fi
 
 # Add namelist for IAU
 if [[ ${DOIAU} = "YES" ]]; then
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   iaufhrs      = ${IAUFHRS}
   iau_delthrs  = ${IAU_DELTHRS}
   iau_inc_files= ${IAU_INC_FILES}
@@ -506,7 +448,7 @@ EOF
 fi
 
 if [[ ${DO_CA:-"NO"} = "YES" ]]; then
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   do_ca      = .true.
   ca_global  = ${ca_global:-".false."}
   ca_sgs     = ${ca_sgs:-".true."}
@@ -523,33 +465,19 @@ EOF
 fi
 
 if [[ "${DO_LAND_PERT:-NO}" == "YES" ]]; then
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
   lndp_type = ${lndp_type:-2}
   n_var_lndp = ${n_var_lndp:-0}
 EOF
 fi
 
 # Close &gfs_physics_nml section
-cat >> "${nml_file}" << EOF
-/
-EOF
-
-if [[ ${namelist_mode} == "global_with_nest" ]] ; then
-  cat >> "${nml_file}" << EOF
-&fv_nest_nml
-  grid_pes = $(( layout_x * layout_y * 6 )),$(( layout_x_nest * layout_y_nest ))
-  tile_coarse = 0,6
-  num_tile_top = 6
-  p_split = 1
-  nest_refine = 0,${nest_refine}
-  nest_ioffsets = 0,${nest_ioffset}
-  nest_joffsets = 0,${nest_joffset}
+cat >> input.nml << EOF
 /
 EOF
-fi
 
 if [[ ${knob_ugwp_version} -eq 0 ]]; then
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
 &cires_ugwp_nml
   knob_ugwp_solver  = ${knob_ugwp_solver:-2}
   knob_ugwp_source  = ${knob_ugwp_source:-1,1,0,0}
@@ -568,7 +496,7 @@ EOF
 fi
 
 if [[ ${knob_ugwp_version} -eq 1 ]]; then
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
 &cires_ugwp_nml
   knob_ugwp_solver  = ${knob_ugwp_solver:-2}
   knob_ugwp_source  = ${knob_ugwp_source:-1,1,0,0}
@@ -594,9 +522,9 @@ if [[ ${knob_ugwp_version} -eq 1 ]]; then
 EOF
 fi
 
-echo "" >> "${nml_file}"
+echo "" >> input.nml
 
-cat >> "${nml_file}" <<EOF
+cat >> input.nml <<EOF
 &gfdl_cloud_microphysics_nml
   sedi_transport = .true.
   do_sedi_heat = .false.
@@ -700,29 +628,22 @@ cat >> "${nml_file}" <<EOF
 /
 
 &fv_grid_nml
-EOF
-if [[ "${DO_NEST:-NO}" == NO ]] ; then
-    cat >> "${nml_file}" <<EOF
   grid_file = 'INPUT/grid_spec.nc'
-EOF
-fi
-
-cat >> "${nml_file}" <<EOF
   ${fv_grid_nml:-}
 /
 EOF
 
 # Add namelist for stochastic physics options
-echo "" >> "${nml_file}"
+echo "" >> input.nml
 #if [ $MEMBER -gt 0 ]; then
 if [[ "${DO_SPPT}" = "YES" || "${DO_SHUM}" = "YES" || "${DO_SKEB}" = "YES" || "${DO_LAND_PERT}" = "YES" ]]; then
 
-    cat >> "${nml_file}" << EOF
+    cat >> input.nml << EOF
 &nam_stochy
 EOF
 
   if [[ ${DO_SKEB} = "YES" ]]; then
-    cat >> "${nml_file}" << EOF
+    cat >> input.nml << EOF
   skeb = ${SKEB}
   iseed_skeb = ${ISEED_SKEB:-${ISEED}}
   skeb_tau = ${SKEB_TAU:-"-999."}
@@ -734,7 +655,7 @@ EOF
   fi
 
   if [[ ${DO_SHUM} = "YES" ]]; then
-    cat >> "${nml_file}" << EOF
+    cat >> input.nml << EOF
   shum = ${SHUM}
   iseed_shum = ${ISEED_SHUM:-${ISEED}}
   shum_tau = ${SHUM_TAU:-"-999."}
@@ -743,7 +664,7 @@ EOF
   fi
 
   if [[ ${DO_SPPT} = "YES" ]]; then
-    cat >> "${nml_file}" << EOF
+    cat >> input.nml << EOF
   sppt = ${SPPT}
   iseed_sppt = ${ISEED_SPPT:-${ISEED}}
   sppt_tau = ${SPPT_TAU:-"-999."}
@@ -756,7 +677,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_SPPT:-NO}" == "YES" ]]; then
-    cat >> "${nml_file}" <<EOF
+    cat >> input.nml <<EOF
   OCNSPPT=${OCNSPPT}
   OCNSPPT_LSCALE=${OCNSPPT_LSCALE}
   OCNSPPT_TAU=${OCNSPPT_TAU}
@@ -765,7 +686,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_PERT_EPBL:-NO}" == "YES" ]]; then
-    cat >> "${nml_file}" <<EOF
+    cat >> input.nml <<EOF
   EPBL=${EPBL}
   EPBL_LSCALE=${EPBL_LSCALE}
   EPBL_TAU=${EPBL_TAU}
@@ -774,7 +695,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_SPPT:-NO}" == "YES" ]]; then
-    cat >> "${nml_file}" <<EOF
+    cat >> input.nml <<EOF
   OCNSPPT=${OCNSPPT}
   OCNSPPT_LSCALE=${OCNSPPT_LSCALE}
   OCNSPPT_TAU=${OCNSPPT_TAU}
@@ -783,7 +704,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_PERT_EPBL:-NO}" == "YES" ]]; then
-    cat >> "${nml_file}" <<EOF
+    cat >> input.nml <<EOF
   EPBL=${EPBL}
   EPBL_LSCALE=${EPBL_LSCALE}
   EPBL_TAU=${EPBL_TAU}
@@ -791,12 +712,12 @@ EOF
 EOF
   fi
 
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
 /
 EOF
 
   if [[ ${DO_LAND_PERT} = "YES" ]]; then
-    cat >> "${nml_file}" << EOF
+    cat >> input.nml << EOF
 &nam_sfcperts
   lndp_type = ${lndp_type}
   LNDP_TAU = ${LNDP_TAU}
@@ -807,7 +728,7 @@ EOF
 /
 EOF
   else
-    cat >> "${nml_file}" << EOF
+    cat >> input.nml << EOF
 &nam_sfcperts
 /
 EOF
@@ -815,7 +736,7 @@ EOF
 
 else
 
-  cat >> "${nml_file}" << EOF
+  cat >> input.nml << EOF
 &nam_stochy
 /
 &nam_sfcperts
@@ -824,9 +745,9 @@ EOF
 
 fi
 
-# Echo out formatted ""${nml_file}""
+# Echo out formatted "input.nml"
 echo "===================================="
-echo "FV3_namelists(): '${nml_file}'"
-cat "${nml_file}"
+echo "FV3_namelists(): 'input.nml'"
+cat input.nml
 echo "===================================="
 }

From 9b509d18e751ad662db633fedf6db4bf33c92876 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:25:58 -0600
Subject: [PATCH 08/15] add a new file - parsing_namelists_FV3_nest.sh

---
 ush/parsing_namelists_FV3_nest.sh | 753 ++++++++++++++++++++++++++++++
 1 file changed, 753 insertions(+)
 create mode 100755 ush/parsing_namelists_FV3_nest.sh

diff --git a/ush/parsing_namelists_FV3_nest.sh b/ush/parsing_namelists_FV3_nest.sh
new file mode 100755
index 00000000000..9e6e67f9cc7
--- /dev/null
+++ b/ush/parsing_namelists_FV3_nest.sh
@@ -0,0 +1,753 @@
+#! /usr/bin/env bash
+
+# parsing namelist of FV3, diag_table, etc.
+
+# Disable variable not used warnings
+# shellcheck disable=SC2034
+FV3_namelists(){
+
+# setup the tables
+DIAG_TABLE=${DIAG_TABLE:-${PARMgfs}/ufs/fv3/diag_table}
+DIAG_TABLE_APPEND=${DIAG_TABLE_APPEND:-${PARMgfs}/ufs/fv3/diag_table_aod}
+DATA_TABLE=${DATA_TABLE:-${PARMgfs}/ufs/MOM6_data_table.IN}
+FIELD_TABLE=${FIELD_TABLE:-${PARMgfs}/ufs/fv3/field_table}
+
+# set cdmbgwd
+if (( gwd_opt == 2 )) && [[ ${do_gsl_drag_ls_bl} == ".true." ]]; then
+  cdmbgwd=${cdmbgwd_gsl}
+fi
+
+# ensure non-prognostic tracers are set
+dnats=${dnats:-0}
+
+# build the diag_table
+{
+echo "UFS_Weather_Model_Forecast"
+if [[ "${DOIAU}" = "YES" ]]; then
+  echo "${previous_cycle:0:4} ${previous_cycle:4:2} ${previous_cycle:6:2} ${previous_cycle:8:2} 0 0"
+else
+  echo "${current_cycle:0:4} ${current_cycle:4:2} ${current_cycle:6:2} ${current_cycle:8:2} 0 0"
+fi
+cat "${DIAG_TABLE}"
+if [[ -n "${AERO_DIAG_TABLE:-}" ]]; then
+  cat "${AERO_DIAG_TABLE}"
+fi
+cat "${DIAG_TABLE_APPEND}"
+} >> diag_table_template
+
+local template=diag_table_template
+local SYEAR=${current_cycle:0:4}
+local SMONTH=${current_cycle:4:2}
+local SDAY=${current_cycle:6:2}
+local CHOUR=${current_cycle:8:2}
+local MOM6_OUTPUT_DIR="./MOM6_OUTPUT"
+
+atparse < "${template}" >> "diag_table"
+
+
+# copy data table
+${NCP} "${DATA_TABLE}" data_table
+
+# build field_table
+if [[ -n "${AERO_FIELD_TABLE:-}" ]]; then
+  nrec=$(wc -l < "${FIELD_TABLE}")
+  prec=${nrec}
+  if (( dnats > 0 )); then
+    prec=$( grep -F -n TRACER "${FIELD_TABLE}" 2> /dev/null | tail -n "${dnats}" | head -1 | cut -d: -f1 )
+    prec=${prec:-0}
+    prec=$(( prec > 0 ? prec - 1 : prec ))
+  fi
+  { \
+    head -n "${prec}" "${FIELD_TABLE}" ; \
+    cat "${AERO_FIELD_TABLE}" ; \
+    tail -n $(( nrec - prec )) "${FIELD_TABLE}" ; \
+  } > field_table
+  # add non-prognostic tracers from additional table
+  dnats=$(( dnats + dnats_aero ))
+else
+  ${NCP} "${FIELD_TABLE}" field_table
+fi
+
+cat > input.nml <<EOF
+&atmos_model_nml
+  blocksize = ${blocksize}
+  chksum_debug = ${chksum_debug}
+  dycore_only = ${dycore_only}
+  ccpp_suite = ${CCPP_SUITE}
+  ${atmos_model_nml:-}
+/
+
+&diag_manager_nml
+  prepend_date = .false.
+  max_output_fields = 300
+  ${diag_manager_nml:-}
+/
+
+&fms_nml
+  clock_grain = 'ROUTINE'
+  domains_stack_size = ${domains_stack_size:-3000000}
+  print_memory_usage = ${print_memory_usage:-".false."}
+  ${fms_nml:-}
+/
+
+&fms2_io_nml
+  netcdf_default_format = "netcdf4"
+/
+
+&fv_core_nml
+  layout = ${layout_x},${layout_y}
+  io_layout = ${io_layout}
+  npx = ${npx}
+  npy = ${npy}
+  ntiles = ${ntiles}
+  npz = ${npz}
+  dz_min =  ${dz_min:-"6"}
+  psm_bc = ${psm_bc:-"0"}
+  grid_type = -1
+  make_nh = ${make_nh}
+  fv_debug = ${fv_debug:-".false."}
+  range_warn = ${range_warn:-".true."}
+  reset_eta = .false.
+  n_sponge = ${n_sponge:-"10"}
+  nudge_qv = ${nudge_qv:-".false."}
+  nudge_dz = ${nudge_dz:-".false."}
+  tau = ${tau:-10.}
+  rf_cutoff = ${rf_cutoff:-"7.5e2"}
+  d2_bg_k1 = ${d2_bg_k1:-"0.15"}
+  d2_bg_k2 = ${d2_bg_k2:-"0.02"}
+  kord_tm = ${kord_tm:-"-9"}
+  kord_mt = ${kord_mt:-"9"}
+  kord_wz = ${kord_wz:-"9"}
+  kord_tr = ${kord_tr:-"9"}
+  hydrostatic = ${hydrostatic}
+  phys_hydrostatic = ${phys_hydrostatic}
+  use_hydro_pressure = ${use_hydro_pressure}
+  beta = 0.
+  a_imp = 1.
+  p_fac = 0.1
+  k_split = ${k_split}
+  n_split = ${n_split}
+  nwat = ${nwat:-2}
+  na_init = ${na_init}
+  d_ext = 0.
+  dnats = ${dnats}
+  fv_sg_adj = ${fv_sg_adj:-"450"}
+  d2_bg = 0.
+  nord = ${nord:-3}
+  dddmp = ${dddmp:-0.1}
+  d4_bg = ${d4_bg:-0.15}
+  vtdm4 = ${vtdm4}
+  delt_max = ${delt_max:-"0.002"}
+  ke_bg = 0.
+  do_vort_damp = ${do_vort_damp}
+  external_ic = ${external_ic}
+  external_eta = ${external_eta:-.true.}
+  gfs_phil = ${gfs_phil:-".false."}
+  nggps_ic = ${nggps_ic}
+  mountain = ${mountain}
+  ncep_ic = ${ncep_ic}
+  d_con = ${d_con}
+  hord_mt = ${hord_mt}
+  hord_vt = ${hord_xx}
+  hord_tm = ${hord_xx}
+  hord_dp = -${hord_xx}
+  hord_tr = ${hord_tr:-"8"}
+  adjust_dry_mass = ${adjust_dry_mass:-".true."}
+  dry_mass=${dry_mass:-98320.0}
+  consv_te = ${consv_te}
+  do_sat_adj = ${do_sat_adj:-".false."}
+  fast_tau_w_sec = ${fast_tau_w_sec:-"0.2"}
+  consv_am = .false.
+  fill = .true.
+  dwind_2d = .false.
+  print_freq = ${print_freq}
+  warm_start = ${warm_start}
+  no_dycore = ${no_dycore}
+  z_tracer = .true.
+  agrid_vel_rst = ${agrid_vel_rst:-".true."}
+  read_increment = ${read_increment}
+  res_latlon_dynamics = ${res_latlon_dynamics}
+  ${fv_core_nml-}
+/
+
+&external_ic_nml
+  filtered_terrain = ${filtered_terrain}
+  levp = ${LEVS}
+  gfs_dwinds = ${gfs_dwinds}
+  checker_tr = .false.
+  nt_checker = 0
+  ${external_ic_nml-}
+/
+
+&gfs_physics_nml
+  fhzero       = ${FHZER}
+  h2o_phys     = ${h2o_phys:-".true."}
+  ldiag3d      = ${ldiag3d:-".false."}
+  qdiag3d      = ${qdiag3d:-".false."}
+  print_diff_pgr = ${print_diff_pgr:-".false."}
+  fhcyc        = ${FHCYC}
+  use_ufo      = ${use_ufo:-".true."}
+  pre_rad      = ${pre_rad:-".false."}
+  imp_physics  = ${imp_physics:-"99"}
+EOF
+
+case "${CCPP_SUITE:-}" in
+  "FV3_GFS_v15p2_coupled")
+  cat >> input.nml << EOF
+  oz_phys      = .false.
+  oz_phys_2015 = .true.
+EOF
+  ;;
+  "FV3_GSD_v0")
+  cat >> input.nml << EOF
+  iovr         = ${iovr:-"3"}
+  ltaerosol    = ${ltaerosol:-".false."}
+  lradar       = ${lradar:-".false."}
+  ttendlim     = ${ttendlim:-0.005}
+  oz_phys      = ${oz_phys:-".false."}
+  oz_phys_2015 = ${oz_phys_2015:-".true."}
+  lsoil_lsm    = ${lsoil_lsm:-"4"}
+  do_mynnedmf  = ${do_mynnedmf:-".false."}
+  do_mynnsfclay = ${do_mynnsfclay:-".false."}
+  icloud_bl    = ${icloud_bl:-"1"}
+  bl_mynn_edmf = ${bl_mynn_edmf:-"1"}
+  bl_mynn_tkeadvect=${bl_mynn_tkeadvect:-".true."}
+  bl_mynn_edmf_mom=${bl_mynn_edmf_mom:-"1"}
+  min_lakeice  = ${min_lakeice:-"0.15"}
+  min_seaice   = ${min_seaice:-"0.15"}
+  use_cice_alb = ${use_cice_alb:-".false."}
+EOF
+  ;;
+  FV3_GFS_v16_coupled*)
+  cat >> input.nml << EOF
+  iovr         = ${iovr:-"3"}
+  ltaerosol    = ${ltaerosol:-".false."}
+  lradar       = ${lradar:-".false."}
+  ttendlim     = ${ttendlim:-"0.005"}
+  oz_phys      = ${oz_phys:-".false."}
+  oz_phys_2015 = ${oz_phys_2015:-".true."}
+  do_mynnedmf  = ${do_mynnedmf:-".false."}
+  do_mynnsfclay = ${do_mynnsfclay:-".false."}
+  icloud_bl    = ${icloud_bl:-"1"}
+  bl_mynn_edmf = ${bl_mynn_edmf:-"1"}
+  bl_mynn_tkeadvect = ${bl_mynn_tkeadvect:-".true."}
+  bl_mynn_edmf_mom = ${bl_mynn_edmf_mom:-"1"}
+  min_lakeice  = ${min_lakeice:-"0.15"}
+  min_seaice   = ${min_seaice:-"0.15"}
+EOF
+  ;;
+  FV3_GFS_v16*)
+  cat >> input.nml << EOF
+  iovr         = ${iovr:-"3"}
+  ltaerosol    = ${ltaerosol:-".false."}
+  lradar       = ${lradar:-".false."}
+  ttendlim     = ${ttendlim:-"0.005"}
+  oz_phys      = ${oz_phys:-".false."}
+  oz_phys_2015 = ${oz_phys_2015:-".true."}
+  lsoil_lsm    = ${lsoil_lsm:-"4"}
+  do_mynnedmf  = ${do_mynnedmf:-".false."}
+  do_mynnsfclay = ${do_mynnsfclay:-".false."}
+  icloud_bl    = ${icloud_bl:-"1"}
+  bl_mynn_edmf = ${bl_mynn_edmf:-"1"}
+  bl_mynn_tkeadvect = ${bl_mynn_tkeadvect:-".true."}
+  bl_mynn_edmf_mom = ${bl_mynn_edmf_mom:-"1"}
+  min_lakeice  = ${min_lakeice:-"0.15"}
+  min_seaice   = ${min_seaice:-"0.15"}
+EOF
+  ;;
+  FV3_GFS_v17*)
+  local default_dt_inner=$(( DELTIM/2 ))
+  cat >> input.nml << EOF
+  iovr         = ${iovr:-"3"}
+  ltaerosol    = ${ltaerosol:-".false."}
+  lradar       = ${lradar:-".true."}
+  ttendlim     = ${ttendlim:-"-999"}
+  dt_inner     = ${dt_inner:-"${default_dt_inner}"}
+  sedi_semi    = ${sedi_semi:-".true."}
+  decfl        = ${decfl:-"10"}
+  oz_phys      = ${oz_phys:-".false."}
+  oz_phys_2015 = ${oz_phys_2015:-".true."}
+  lsoil_lsm    = ${lsoil_lsm:-"4"}
+  do_mynnedmf  = ${do_mynnedmf:-".false."}
+  do_mynnsfclay = ${do_mynnsfclay:-".false."}
+  icloud_bl    = ${icloud_bl:-"1"}
+  bl_mynn_edmf = ${bl_mynn_edmf:-"1"}
+  bl_mynn_tkeadvect = ${bl_mynn_tkeadvect:-".true."}
+  bl_mynn_edmf_mom = ${bl_mynn_edmf_mom:-"1"}
+  do_ugwp      = ${do_ugwp:-".false."}
+  do_tofd      = ${do_tofd:-".false."}
+  gwd_opt      = ${gwd_opt:-"2"}
+  do_ugwp_v0   = ${do_ugwp_v0:-".false."}
+  do_ugwp_v1   = ${do_ugwp_v1:-".true."}
+  do_ugwp_v0_orog_only = ${do_ugwp_v0_orog_only:-".false."}
+  do_ugwp_v0_nst_only  = ${do_ugwp_v0_nst_only:-".false."}
+  do_gsl_drag_ls_bl    = ${do_gsl_drag_ls_bl:-".true."}
+  do_gsl_drag_ss       = ${do_gsl_drag_ss:-".true."}
+  do_gsl_drag_tofd     = ${do_gsl_drag_tofd:-".true."}
+  do_ugwp_v1_orog_only = ${do_ugwp_v1_orog_only:-".false."}
+  min_lakeice  = ${min_lakeice:-"0.15"}
+  min_seaice   = ${min_seaice:-"0.15"}
+  use_cice_alb = ${use_cice_alb:-".false."}
+EOF
+  ;;
+  FV3_global_nest*)
+  local default_dt_inner=$(( DELTIM/2 ))
+  cat >> input.nml << EOF
+  iovr         = ${iovr:-"3"}
+  lcnorm       = ${lcnorm:-".false."}
+  ltaerosol    = ${ltaerosol:-".false."}
+  lradar       = ${lradar:-".true."}
+  ttendlim     = ${ttendlim:-"-999"}
+  dt_inner     = ${dt_inner:-"${default_dt_inner}"}
+  sedi_semi    = ${sedi_semi:-".true."}
+  decfl        = ${decfl:-"10"}
+  oz_phys      = ${oz_phys:-".false."}
+  oz_phys_2015 = ${oz_phys_2015:-".true."}
+  lsoil_lsm    = ${lsoil_lsm:-"4"}
+  do_mynnedmf  = ${do_mynnedmf:-".false."}
+  do_mynnsfclay = ${do_mynnsfclay:-".false."}
+  icloud_bl    = ${icloud_bl:-"1"}
+  bl_mynn_edmf = ${bl_mynn_edmf:-"1"}
+  bl_mynn_tkeadvect = ${bl_mynn_tkeadvect:-".true."}
+  bl_mynn_edmf_mom = ${bl_mynn_edmf_mom:-"1"}
+  do_ugwp      = ${do_ugwp:-".false."}
+  do_tofd      = ${do_tofd:-".false."}
+  gwd_opt      = ${gwd_opt:-"2"}
+  do_ugwp_v0   = ${do_ugwp_v0:-".false."}
+  do_ugwp_v1   = ${do_ugwp_v1:-".true."}
+  do_ugwp_v0_orog_only = ${do_ugwp_v0_orog_only:-".false."}
+  do_ugwp_v0_nst_only  = ${do_ugwp_v0_nst_only:-".false."}
+  do_gsl_drag_ls_bl    = ${do_gsl_drag_ls_bl:-".true."}
+  do_gsl_drag_ss       = ${do_gsl_drag_ss:-".true."}
+  do_gsl_drag_tofd     = ${do_gsl_drag_tofd:-".true."}
+  do_ugwp_v1_orog_only = ${do_ugwp_v1_orog_only:-".false."}
+  min_lakeice  = ${min_lakeice:-"0.15"}
+  min_seaice   = ${min_seaice:-"0.15"}
+  use_cice_alb = ${use_cice_alb:-".false."}
+EOF
+  ;;
+  *)
+  cat >> input.nml << EOF
+  iovr         = ${iovr:-"3"}
+EOF
+  ;;
+esac
+
+cat >> input.nml <<EOF
+  pdfcld       = ${pdfcld:-".false."}
+  fhswr        = ${FHSWR:-"3600."}
+  fhlwr        = ${FHLWR:-"3600."}
+  ialb         = ${IALB:-"1"}
+  iems         = ${IEMS:-"1"}
+  iaer         = ${IAER}
+  icliq_sw     = ${icliq_sw:-"2"}
+  ico2         = ${ICO2}
+  isubc_sw     = ${isubc_sw:-"2"}
+  isubc_lw     = ${isubc_lw:-"2"}
+  isol         = ${ISOL:-"2"}
+  lwhtr        = ${lwhtr:-".true."}
+  swhtr        = ${swhtr:-".true."}
+  cnvgwd       = ${cnvgwd:-".true."}
+  shal_cnv     = ${shal_cnv:-".true."}
+  cal_pre      = ${cal_pre:-".true."}
+  redrag       = ${redrag:-".true."}
+  dspheat      = ${dspheat:-".true."}
+  hybedmf      = ${hybedmf:-".false."}
+  satmedmf     = ${satmedmf-".true."}
+  isatmedmf    = ${isatmedmf-"1"}
+  lheatstrg    = ${lheatstrg-".false."}
+  lseaspray    = ${lseaspray:-".true."}
+  random_clds  = ${random_clds:-".true."}
+  trans_trac   = ${trans_trac:-".true."}
+  cnvcld       = ${cnvcld:-".true."}
+  imfshalcnv   = ${imfshalcnv:-"2"}
+  imfdeepcnv   = ${imfdeepcnv:-"2"}
+  progsigma    = ${progsigma:-".true."}
+  betascu      = ${betascu:-"8.0"}
+  betamcu      = ${betamcu:-"1.0"}
+  betadcu      = ${betadcu:-"2.0"}
+  ras          = ${ras:-".false."}
+  cdmbgwd      = ${cdmbgwd:-"3.5,0.25"}
+  prslrd0      = ${prslrd0:-"0."}
+  ivegsrc      = ${ivegsrc:-"1"}
+  isot         = ${isot:-"1"}
+  lsoil        = ${lsoil:-"4"}
+  lsm          = ${lsm:-"2"}
+  iopt_dveg    = ${iopt_dveg:-"1"}
+  iopt_crs     = ${iopt_crs:-"1"}
+  iopt_btr     = ${iopt_btr:-"1"}
+  iopt_run     = ${iopt_run:-"1"}
+  iopt_sfc     = ${iopt_sfc:-"1"}
+  iopt_frz     = ${iopt_frz:-"1"}
+  iopt_inf     = ${iopt_inf:-"1"}
+  iopt_rad     = ${iopt_rad:-"1"}
+  iopt_alb     = ${iopt_alb:-"2"}
+  iopt_snf     = ${iopt_snf:-"4"}
+  iopt_tbot    = ${iopt_tbot:-"2"}
+  iopt_stc     = ${iopt_stc:-"1"}
+  iopt_trs     = ${iopt_trs:-"2"}
+  iopt_diag    = ${iopt_diag:-"1"}
+  debug        = ${gfs_phys_debug:-".false."}
+  nstf_name    = ${nstf_name}
+  nst_anl      = ${nst_anl}
+  psautco      = ${psautco:-"0.0008,0.0005"}
+  prautco      = ${prautco:-"0.00015,0.00015"}
+  lgfdlmprad   = ${lgfdlmprad:-".false."}
+  effr_in      = ${effr_in:-".false."}
+  ldiag_ugwp   = ${ldiag_ugwp:-".false."}
+  do_RRTMGP          = ${do_RRTMGP:-".false."}
+  active_gases       = ${active_gases:-'h2o_co2_o3_n2o_ch4_o2'}
+  ngases             = ${ngases:-"6"}
+  lw_file_gas        = ${lw_file_gas:-'rrtmgp-data-lw-g128-210809.nc'}
+  lw_file_clouds     = ${lw_file_clouds:-'rrtmgp-cloud-optics-coeffs-lw.nc'}
+  sw_file_gas        = ${sw_file_gas:-'rrtmgp-data-sw-g112-210809.nc'}
+  sw_file_clouds     = ${sw_file_clouds:-'rrtmgp-cloud-optics-coeffs-sw.nc'}
+  rrtmgp_nGptsSW     = ${rrtmgp_nGptsSW:-"112"}
+  rrtmgp_nGptsLW     = ${rrtmgp_nGptsLW:-"128"}
+  rrtmgp_nBandsLW    = ${rrtmgp_nBandsLW:-"16"}
+  rrtmgp_nBandsSW    = ${rrtmgp_nBandsSW:-"14"}
+  doGP_cldoptics_LUT = ${doGP_cldoptics_LUT:-".false."}
+  doGP_lwscat        = ${doGP_lwscat:-".false."}
+EOF
+
+if [[ ${cplchm} = ".true." ]]; then
+  cat >> input.nml << EOF
+  fscav_aero = ${fscav_aero:-'*:0.0'}
+EOF
+fi
+
+cat >> input.nml <<EOF
+  do_sppt      = ${do_sppt:-".false."}
+  do_shum      = ${do_shum:-".false."}
+  do_skeb      = ${do_skeb:-".false."}
+  frac_grid    = ${FRAC_GRID:-".true."}
+  cplchm       = ${cplchm:-".false."}
+  cplflx       = ${cplflx:-".false."}
+  cplice       = ${cplice:-".false."}
+  cplwav       = ${cplwav:-".false."}
+  cplwav2atm   = ${cplwav2atm:-".false."}
+EOF
+
+if [[ ${DO_SPPT} = "YES" ]]; then
+cat >> input.nml <<EOF
+  pert_mp = .false.
+  pert_radtend = .false.
+  pert_clds = .true.
+EOF
+fi
+
+# Add namelist for IAU
+if [[ ${DOIAU} = "YES" ]]; then
+  cat >> input.nml << EOF
+  iaufhrs      = ${IAUFHRS}
+  iau_delthrs  = ${IAU_DELTHRS}
+  iau_inc_files= ${IAU_INC_FILES}
+  iau_drymassfixer = .false.
+  iau_filter_increments = ${IAU_FILTER_INCREMENTS:-".false."}
+EOF
+fi
+
+if [[ ${DO_CA:-"NO"} = "YES" ]]; then
+  cat >> input.nml << EOF
+  do_ca      = .true.
+  ca_global  = ${ca_global:-".false."}
+  ca_sgs     = ${ca_sgs:-".true."}
+  nca        = ${nca:-"1"}
+  ncells     = ${ncells:-"5"}
+  nlives     = ${nlives:-"12"}
+  nseed      = ${nseed:-"1"}
+  nfracseed  = ${nfracseed:-"0.5"}
+  nthresh    = ${nthresh:-"18"}
+  ca_trigger = ${ca_trigger:-".true."}
+  nspinup    = ${nspinup:-"1"}
+  iseed_ca   = ${ISEED_CA:-"12345"}
+EOF
+fi
+
+if [[ "${DO_LAND_PERT:-NO}" == "YES" ]]; then
+  cat >> input.nml << EOF
+  lndp_type = ${lndp_type:-2}
+  n_var_lndp = ${n_var_lndp:-0}
+EOF
+fi
+
+# Close &gfs_physics_nml section
+cat >> input.nml << EOF
+/
+EOF
+
+if [[ ${knob_ugwp_version} -eq 0 ]]; then
+  cat >> input.nml << EOF
+&cires_ugwp_nml
+  knob_ugwp_solver  = ${knob_ugwp_solver:-2}
+  knob_ugwp_source  = ${knob_ugwp_source:-1,1,0,0}
+  knob_ugwp_wvspec  = ${knob_ugwp_wvspec:-1,25,25,25}
+  knob_ugwp_azdir   = ${knob_ugwp_azdir:-2,4,4,4}
+  knob_ugwp_stoch   = ${knob_ugwp_stoch:-0,0,0,0}
+  knob_ugwp_effac   = ${knob_ugwp_effac:-1,1,1,1}
+  knob_ugwp_doaxyz  = ${knob_ugwp_doaxyz:-1}
+  knob_ugwp_doheat  = ${knob_ugwp_doheat:-1}
+  knob_ugwp_dokdis  = ${knob_ugwp_dokdis:-1}
+  knob_ugwp_ndx4lh  = ${knob_ugwp_ndx4lh:-1}
+  knob_ugwp_version = ${knob_ugwp_version:-0}
+  launch_level      = ${launch_level:-54}
+/
+EOF
+fi
+
+if [[ ${knob_ugwp_version} -eq 1 ]]; then
+  cat >> input.nml << EOF
+&cires_ugwp_nml
+  knob_ugwp_solver  = ${knob_ugwp_solver:-2}
+  knob_ugwp_source  = ${knob_ugwp_source:-1,1,0,0}
+  knob_ugwp_wvspec  = ${knob_ugwp_wvspec:-1,25,25,25}
+  knob_ugwp_azdir   = ${knob_ugwp_azdir:-2,4,4,4}
+  knob_ugwp_stoch   = ${knob_ugwp_stoch:-0,0,0,0}
+  knob_ugwp_effac   = ${knob_ugwp_effac:-1,1,1,1}
+  knob_ugwp_doaxyz  = ${knob_ugwp_doaxyz:-1}
+  knob_ugwp_doheat  = ${knob_ugwp_doheat:-1}
+  knob_ugwp_dokdis  = ${knob_ugwp_dokdis:-2}
+  knob_ugwp_ndx4lh  = ${knob_ugwp_ndx4lh:-4}
+  knob_ugwp_version = ${knob_ugwp_version:-1}
+  knob_ugwp_palaunch = ${knob_ugwp_palaunch:-275.0e2}
+  knob_ugwp_nslope   = ${knob_ugwp_nslope:-1}
+  knob_ugwp_lzmax    = ${knob_ugwp_lzmax:-15.750e3}
+  knob_ugwp_lzmin    = ${knob_ugwp_lzmin:-0.75e3}
+  knob_ugwp_lzstar   = ${knob_ugwp_lzstar:-2.0e3}
+  knob_ugwp_taumin   = ${knob_ugwp_taumin:-0.25e-3}
+  knob_ugwp_tauamp   = ${knob_ugwp_tauamp:-3.0e-3}
+  knob_ugwp_lhmet    = ${knob_ugwp_lhmet:-200.0e3}
+  knob_ugwp_orosolv  = ${knob_ugwp_orosolv:-'pss-1986'}
+/
+EOF
+fi
+
+echo "" >> input.nml
+
+cat >> input.nml <<EOF
+&gfdl_cloud_microphysics_nml
+  sedi_transport = .true.
+  do_sedi_heat = .false.
+  rad_snow = .true.
+  rad_graupel = .true.
+  rad_rain = .true.
+  const_vi = .false.
+  const_vs = .false.
+  const_vg = .false.
+  const_vr = .false.
+  vi_max = 1.
+  vs_max = 2.
+  vg_max = 12.
+  vr_max = 12.
+  qi_lim = 1.
+  prog_ccn = .false.
+  do_qa = .true.
+  fast_sat_adj = .true.
+  tau_l2v = 225.
+  tau_v2l = 150.
+  tau_g2v = 900.
+  rthresh = 10.e-6  ! This is a key parameter for cloud water
+  dw_land  = 0.16
+  dw_ocean = 0.10
+  ql_gen = 1.0e-3
+  ql_mlt = 1.0e-3
+  qi0_crt = 8.0E-5
+  qs0_crt = 1.0e-3
+  tau_i2s = 1000.
+  c_psaci = 0.05
+  c_pgacs = 0.01
+  rh_inc = 0.30
+  rh_inr = 0.30
+  rh_ins = 0.30
+  ccn_l = 300.
+  ccn_o = 100.
+  c_paut = 0.5
+  c_cracw = 0.8
+  use_ppm = .false.
+  use_ccn = .true.
+  mono_prof = .true.
+  z_slope_liq  = .true.
+  z_slope_ice  = .true.
+  de_ice = .false.
+  fix_negative = .true.
+  icloud_f = 1
+  mp_time = 150.
+  reiflag = ${reiflag:-"2"}
+
+  ${gfdl_cloud_microphysics_nml:-}
+/
+
+&interpolator_nml
+  interp_method = 'conserve_great_circle'
+  ${interpolator_nml:-}
+/
+
+&namsfc
+  FNGLAC   = '${FNGLAC}'
+  FNMXIC   = '${FNMXIC}'
+  FNTSFC   = '${FNTSFC}'
+  FNSNOC   = '${FNSNOC}'
+  FNZORC   = '${FNZORC}'
+  FNALBC   = '${FNALBC}'
+  FNALBC2  = '${FNALBC2}'
+  FNAISC   = '${FNAISC}'
+  FNTG3C   = '${FNTG3C}'
+  FNVEGC   = '${FNVEGC}'
+  FNVETC   = '${FNVETC}'
+  FNSOTC   = '${FNSOTC}'
+  FNSOCC   = '${FNSOCC}'
+  FNSMCC   = '${FNSMCC}'
+  FNMSKH   = '${FNMSKH}'
+  FNTSFA   = '${FNTSFA}'
+  FNACNA   = '${FNACNA:-}'
+  FNSNOA   = '${FNSNOA:-}'
+  FNVMNC   = '${FNVMNC:-}'
+  FNVMXC   = '${FNVMXC:-}'
+  FNSLPC   = '${FNSLPC:-}'
+  FNABSC   = '${FNABSC:-}'
+  LDEBUG = ${LDEBUG:-".false."}
+  FSMCL(2) = ${FSMCL2:-99999}
+  FSMCL(3) = ${FSMCL3:-99999}
+  FSMCL(4) = ${FSMCL4:-99999}
+  LANDICE  = ${landice:-".true."}
+  FTSFS = ${FTSFS:-90}
+  FAISL = ${FAISL:-99999}
+  FAISS = ${FAISS:-99999}
+  FSNOL = ${FSNOL:-99999}
+  FSNOS = ${FSNOS:-99999}
+  FSICL = ${FSICL:-99999}
+  FSICS = ${FSICS:-99999}
+  FTSFL = ${FTSFL:-99999}
+  FVETL = ${FVETL:-99999}
+  FSOTL = ${FSOTL:-99999}
+  FvmnL = ${FvmnL:-99999}
+  FvmxL = ${FvmxL:-99999}
+  FSLPL = ${FSLPL:-99999}
+  FABSL = ${FABSL:-99999}
+  ${namsfc_nml:-}
+/
+
+&fv_grid_nml
+  grid_file = 'INPUT/grid_spec.nc'
+  ${fv_grid_nml:-}
+/
+EOF
+
+# Add namelist for stochastic physics options
+echo "" >> input.nml
+#if [ $MEMBER -gt 0 ]; then
+if [[ "${DO_SPPT}" = "YES" || "${DO_SHUM}" = "YES" || "${DO_SKEB}" = "YES" || "${DO_LAND_PERT}" = "YES" ]]; then
+
+    cat >> input.nml << EOF
+&nam_stochy
+EOF
+
+  if [[ ${DO_SKEB} = "YES" ]]; then
+    cat >> input.nml << EOF
+  skeb = ${SKEB}
+  iseed_skeb = ${ISEED_SKEB:-${ISEED}}
+  skeb_tau = ${SKEB_TAU:-"-999."}
+  skeb_lscale = ${SKEB_LSCALE:-"-999."}
+  skebnorm = ${SKEBNORM:-"1"}
+  skeb_npass = ${SKEB_NPASS:-"30"}
+  skeb_vdof = ${SKEB_VDOF:-"5"}
+EOF
+  fi
+
+  if [[ ${DO_SHUM} = "YES" ]]; then
+    cat >> input.nml << EOF
+  shum = ${SHUM}
+  iseed_shum = ${ISEED_SHUM:-${ISEED}}
+  shum_tau = ${SHUM_TAU:-"-999."}
+  shum_lscale = ${SHUM_LSCALE:-"-999."}
+EOF
+  fi
+
+  if [[ ${DO_SPPT} = "YES" ]]; then
+    cat >> input.nml << EOF
+  sppt = ${SPPT}
+  iseed_sppt = ${ISEED_SPPT:-${ISEED}}
+  sppt_tau = ${SPPT_TAU:-"-999."}
+  sppt_lscale = ${SPPT_LSCALE:-"-999."}
+  sppt_logit = ${SPPT_LOGIT:-".true."}
+  sppt_sfclimit = ${SPPT_SFCLIMIT:-".true."}
+  use_zmtnblck = ${use_zmtnblck:-".true."}
+  pbl_taper = ${pbl_taper:-"0,0,0,0.125,0.25,0.5,0.75"}
+EOF
+  fi
+
+  if [[ "${DO_OCN_SPPT:-NO}" == "YES" ]]; then
+    cat >> input.nml <<EOF
+  OCNSPPT=${OCNSPPT}
+  OCNSPPT_LSCALE=${OCNSPPT_LSCALE}
+  OCNSPPT_TAU=${OCNSPPT_TAU}
+  ISEED_OCNSPPT=${ISEED_OCNSPPT:-${ISEED}}
+EOF
+  fi
+
+  if [[ "${DO_OCN_PERT_EPBL:-NO}" == "YES" ]]; then
+    cat >> input.nml <<EOF
+  EPBL=${EPBL}
+  EPBL_LSCALE=${EPBL_LSCALE}
+  EPBL_TAU=${EPBL_TAU}
+  ISEED_EPBL=${ISEED_EPBL:-${ISEED}}
+EOF
+  fi
+
+  if [[ "${DO_OCN_SPPT:-NO}" == "YES" ]]; then
+    cat >> input.nml <<EOF
+  OCNSPPT=${OCNSPPT}
+  OCNSPPT_LSCALE=${OCNSPPT_LSCALE}
+  OCNSPPT_TAU=${OCNSPPT_TAU}
+  ISEED_OCNSPPT=${ISEED_OCNSPPT:-${ISEED}}
+EOF
+  fi
+
+  if [[ "${DO_OCN_PERT_EPBL:-NO}" == "YES" ]]; then
+    cat >> input.nml <<EOF
+  EPBL=${EPBL}
+  EPBL_LSCALE=${EPBL_LSCALE}
+  EPBL_TAU=${EPBL_TAU}
+  ISEED_EPBL=${ISEED_EPBL:-${ISEED}}
+EOF
+  fi
+
+  cat >> input.nml << EOF
+/
+EOF
+
+  if [[ ${DO_LAND_PERT} = "YES" ]]; then
+    cat >> input.nml << EOF
+&nam_sfcperts
+  lndp_type = ${lndp_type}
+  LNDP_TAU = ${LNDP_TAU}
+  LNDP_SCALE = ${LNDP_SCALE}
+  ISEED_LNDP = ${ISEED_LNDP:-${ISEED}}
+  lndp_var_list = ${lndp_var_list}
+  lndp_prt_list = ${lndp_prt_list}
+/
+EOF
+  else
+    cat >> input.nml << EOF
+&nam_sfcperts
+/
+EOF
+  fi
+
+else
+
+  cat >> input.nml << EOF
+&nam_stochy
+/
+&nam_sfcperts
+/
+EOF
+
+fi
+
+# Echo out formatted "input.nml"
+echo "===================================="
+echo "FV3_namelists(): 'input.nml'"
+cat input.nml
+echo "===================================="
+}

From 1dc95ae413b5cfe1f5fe89caea25f2a515f3a6a2 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:28:22 -0600
Subject: [PATCH 09/15] update parsing_namelists_FV3_nest.sh for global nest

---
 ush/parsing_namelists_FV3_nest.sh | 162 ++++++++++++++++++++++--------
 1 file changed, 120 insertions(+), 42 deletions(-)

diff --git a/ush/parsing_namelists_FV3_nest.sh b/ush/parsing_namelists_FV3_nest.sh
index 9e6e67f9cc7..ba7376585fe 100755
--- a/ush/parsing_namelists_FV3_nest.sh
+++ b/ush/parsing_namelists_FV3_nest.sh
@@ -6,6 +6,19 @@
 # shellcheck disable=SC2034
 FV3_namelists(){
 
+# First argument tells us which namelist we're writing:
+#   global = writing input.nml for running global with a nest
+#   nest   = writing input_nest02.nml for running the nest
+namelist_mode="${1:-global}"
+
+if [[ "${namelist_mode}" == "nest" ]] ; then
+  nml_file=input_nest02.nml
+  only_input_nml="YES"
+else
+  nml_file=input.nml
+  only_input_nml="NO"
+fi
+
 # setup the tables
 DIAG_TABLE=${DIAG_TABLE:-${PARMgfs}/ufs/fv3/diag_table}
 DIAG_TABLE_APPEND=${DIAG_TABLE_APPEND:-${PARMgfs}/ufs/fv3/diag_table_aod}
@@ -20,6 +33,7 @@ fi
 # ensure non-prognostic tracers are set
 dnats=${dnats:-0}
 
+if [[ "${only_input_nml:-NO}" == "NO" ]] ; then
 # build the diag_table
 {
 echo "UFS_Weather_Model_Forecast"
@@ -67,8 +81,28 @@ if [[ -n "${AERO_FIELD_TABLE:-}" ]]; then
 else
   ${NCP} "${FIELD_TABLE}" field_table
 fi
+fi # only_input_nml
+
+if [[ "${namelist_mode}" == "global" ]] ; then
+    layout_x_here=${layout_x}
+    layout_y_here=${layout_y}
+    ntiles_here=6
+    npx_here=${npx}
+    npy_here=${npy}
+    k_split_here=${k_split}
+else
+    layout_x_here=${layout_x_nest}
+    layout_y_here=${layout_y_nest}
+    ntiles_here=1
+    nested_here=.true.
+    twowaynest_here=${twowaynest:-.true.}
+    nestupdate_here=${nestupdate:-7}
+    npx_here=${npx_nest}
+    npy_here=${npy_nest}
+    k_split_here=${k_split_nest}
+fi
 
-cat > input.nml <<EOF
+cat > "${nml_file}" <<EOF
 &atmos_model_nml
   blocksize = ${blocksize}
   chksum_debug = ${chksum_debug}
@@ -95,15 +129,18 @@ cat > input.nml <<EOF
 /
 
 &fv_core_nml
-  layout = ${layout_x},${layout_y}
+  layout = ${layout_x_here},${layout_y_here}
   io_layout = ${io_layout}
-  npx = ${npx}
-  npy = ${npy}
-  ntiles = ${ntiles}
+  npx = ${npx_here}
+  npy = ${npy_here}
+  ntiles = ${ntiles_here}
+  ${nested_here:+nested = ${nested_here}}
+  ${twowaynest_here:+twowaynest = ${twowaynest_herei}}
+  ${nestupdate_here:+nestupdate = ${nestupdate_here}}
   npz = ${npz}
   dz_min =  ${dz_min:-"6"}
   psm_bc = ${psm_bc:-"0"}
-  grid_type = -1
+  grid_type = ${grid_type:-"-1"}
   make_nh = ${make_nh}
   fv_debug = ${fv_debug:-".false."}
   range_warn = ${range_warn:-".true."}
@@ -125,7 +162,7 @@ cat > input.nml <<EOF
   beta = 0.
   a_imp = 1.
   p_fac = 0.1
-  k_split = ${k_split}
+  k_split = ${k_split_here}
   n_split = ${n_split}
   nwat = ${nwat:-2}
   na_init = ${na_init}
@@ -168,6 +205,26 @@ cat > input.nml <<EOF
   read_increment = ${read_increment}
   res_latlon_dynamics = ${res_latlon_dynamics}
   ${fv_core_nml-}
+EOF
+
+if [[ "${DO_NEST:-NO}" == "YES" && "${namelist_mode}" == "global" ]] ; then
+  cat >> "${nml_file}" <<EOF
+  do_schmidt = .true.
+  target_lat = ${TARGET_LAT}
+  target_lon = ${TARGET_LON}
+  stretch_fac = ${stretch_fac}
+EOF
+fi
+
+if [[ "${DO_NEST:-NO}" == "YES" && "${namelist_mode}" == "nest" ]] ; then
+  cat >> "${nml_file}" <<EOF
+  nested = .true.
+  twowaynest = ${twowaynest:-.true.} ! .true.
+  nestupdate = 7
+EOF
+fi
+
+cat >> "${nml_file}" <<EOF
 /
 
 &external_ic_nml
@@ -193,13 +250,13 @@ EOF
 
 case "${CCPP_SUITE:-}" in
   "FV3_GFS_v15p2_coupled")
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   oz_phys      = .false.
   oz_phys_2015 = .true.
 EOF
   ;;
   "FV3_GSD_v0")
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -219,7 +276,7 @@ EOF
 EOF
   ;;
   FV3_GFS_v16_coupled*)
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -237,7 +294,7 @@ EOF
 EOF
   ;;
   FV3_GFS_v16*)
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".false."}
@@ -257,7 +314,7 @@ EOF
   ;;
   FV3_GFS_v17*)
   local default_dt_inner=$(( DELTIM/2 ))
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   ltaerosol    = ${ltaerosol:-".false."}
   lradar       = ${lradar:-".true."}
@@ -292,7 +349,7 @@ EOF
   ;;
   FV3_global_nest*)
   local default_dt_inner=$(( DELTIM/2 ))
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
   lcnorm       = ${lcnorm:-".false."}
   ltaerosol    = ${ltaerosol:-".false."}
@@ -327,13 +384,13 @@ EOF
 EOF
   ;;
   *)
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iovr         = ${iovr:-"3"}
 EOF
   ;;
 esac
 
-cat >> input.nml <<EOF
+cat >> "${nml_file}" <<EOF
   pdfcld       = ${pdfcld:-".false."}
   fhswr        = ${FHSWR:-"3600."}
   fhlwr        = ${FHLWR:-"3600."}
@@ -411,12 +468,12 @@ cat >> input.nml <<EOF
 EOF
 
 if [[ ${cplchm} = ".true." ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   fscav_aero = ${fscav_aero:-'*:0.0'}
 EOF
 fi
 
-cat >> input.nml <<EOF
+cat >> "${nml_file}" <<EOF
   do_sppt      = ${do_sppt:-".false."}
   do_shum      = ${do_shum:-".false."}
   do_skeb      = ${do_skeb:-".false."}
@@ -429,7 +486,7 @@ cat >> input.nml <<EOF
 EOF
 
 if [[ ${DO_SPPT} = "YES" ]]; then
-cat >> input.nml <<EOF
+cat >> "${nml_file}" <<EOF
   pert_mp = .false.
   pert_radtend = .false.
   pert_clds = .true.
@@ -438,7 +495,7 @@ fi
 
 # Add namelist for IAU
 if [[ ${DOIAU} = "YES" ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   iaufhrs      = ${IAUFHRS}
   iau_delthrs  = ${IAU_DELTHRS}
   iau_inc_files= ${IAU_INC_FILES}
@@ -448,7 +505,7 @@ EOF
 fi
 
 if [[ ${DO_CA:-"NO"} = "YES" ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   do_ca      = .true.
   ca_global  = ${ca_global:-".false."}
   ca_sgs     = ${ca_sgs:-".true."}
@@ -465,19 +522,33 @@ EOF
 fi
 
 if [[ "${DO_LAND_PERT:-NO}" == "YES" ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
   lndp_type = ${lndp_type:-2}
   n_var_lndp = ${n_var_lndp:-0}
 EOF
 fi
 
 # Close &gfs_physics_nml section
-cat >> input.nml << EOF
+cat >> "${nml_file}" << EOF
+/
+EOF
+
+if [[ "${namelist_mode}" == "global" ]] ; then
+  cat >> "${nml_file}" << EOF
+&fv_nest_nml
+  grid_pes = $(( layout_x * layout_y * 6 )),$(( layout_x_nest * layout_y_nest ))
+  tile_coarse = 0,6
+  num_tile_top = 6
+  p_split = 1
+  nest_refine = 0,${nest_refine}
+  nest_ioffsets = 0,${nest_ioffset}
+  nest_joffsets = 0,${nest_joffset}
 /
 EOF
+fi
 
 if [[ ${knob_ugwp_version} -eq 0 ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
 &cires_ugwp_nml
   knob_ugwp_solver  = ${knob_ugwp_solver:-2}
   knob_ugwp_source  = ${knob_ugwp_source:-1,1,0,0}
@@ -496,7 +567,7 @@ EOF
 fi
 
 if [[ ${knob_ugwp_version} -eq 1 ]]; then
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
 &cires_ugwp_nml
   knob_ugwp_solver  = ${knob_ugwp_solver:-2}
   knob_ugwp_source  = ${knob_ugwp_source:-1,1,0,0}
@@ -522,9 +593,9 @@ if [[ ${knob_ugwp_version} -eq 1 ]]; then
 EOF
 fi
 
-echo "" >> input.nml
+echo "" >> "${nml_file}"
 
-cat >> input.nml <<EOF
+cat >> "${nml_file}" <<EOF
 &gfdl_cloud_microphysics_nml
   sedi_transport = .true.
   do_sedi_heat = .false.
@@ -628,22 +699,29 @@ cat >> input.nml <<EOF
 /
 
 &fv_grid_nml
+EOF
+if [[ "${DO_NEST:-NO}" == "NO" ]] ; then
+    cat >> "${nml_file}" <<EOF
   grid_file = 'INPUT/grid_spec.nc'
+EOF
+fi
+
+cat >> "${nml_file}" <<EOF
   ${fv_grid_nml:-}
 /
 EOF
 
 # Add namelist for stochastic physics options
-echo "" >> input.nml
+echo "" >> "${nml_file}"
 #if [ $MEMBER -gt 0 ]; then
 if [[ "${DO_SPPT}" = "YES" || "${DO_SHUM}" = "YES" || "${DO_SKEB}" = "YES" || "${DO_LAND_PERT}" = "YES" ]]; then
 
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
 &nam_stochy
 EOF
 
   if [[ ${DO_SKEB} = "YES" ]]; then
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
   skeb = ${SKEB}
   iseed_skeb = ${ISEED_SKEB:-${ISEED}}
   skeb_tau = ${SKEB_TAU:-"-999."}
@@ -655,7 +733,7 @@ EOF
   fi
 
   if [[ ${DO_SHUM} = "YES" ]]; then
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
   shum = ${SHUM}
   iseed_shum = ${ISEED_SHUM:-${ISEED}}
   shum_tau = ${SHUM_TAU:-"-999."}
@@ -664,7 +742,7 @@ EOF
   fi
 
   if [[ ${DO_SPPT} = "YES" ]]; then
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
   sppt = ${SPPT}
   iseed_sppt = ${ISEED_SPPT:-${ISEED}}
   sppt_tau = ${SPPT_TAU:-"-999."}
@@ -677,7 +755,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_SPPT:-NO}" == "YES" ]]; then
-    cat >> input.nml <<EOF
+    cat >> "${nml_file}" <<EOF
   OCNSPPT=${OCNSPPT}
   OCNSPPT_LSCALE=${OCNSPPT_LSCALE}
   OCNSPPT_TAU=${OCNSPPT_TAU}
@@ -686,7 +764,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_PERT_EPBL:-NO}" == "YES" ]]; then
-    cat >> input.nml <<EOF
+    cat >> "${nml_file}" <<EOF
   EPBL=${EPBL}
   EPBL_LSCALE=${EPBL_LSCALE}
   EPBL_TAU=${EPBL_TAU}
@@ -695,7 +773,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_SPPT:-NO}" == "YES" ]]; then
-    cat >> input.nml <<EOF
+    cat >> "${nml_file}" <<EOF
   OCNSPPT=${OCNSPPT}
   OCNSPPT_LSCALE=${OCNSPPT_LSCALE}
   OCNSPPT_TAU=${OCNSPPT_TAU}
@@ -704,7 +782,7 @@ EOF
   fi
 
   if [[ "${DO_OCN_PERT_EPBL:-NO}" == "YES" ]]; then
-    cat >> input.nml <<EOF
+    cat >> "${nml_file}" <<EOF
   EPBL=${EPBL}
   EPBL_LSCALE=${EPBL_LSCALE}
   EPBL_TAU=${EPBL_TAU}
@@ -712,12 +790,12 @@ EOF
 EOF
   fi
 
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
 /
 EOF
 
   if [[ ${DO_LAND_PERT} = "YES" ]]; then
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
 &nam_sfcperts
   lndp_type = ${lndp_type}
   LNDP_TAU = ${LNDP_TAU}
@@ -728,7 +806,7 @@ EOF
 /
 EOF
   else
-    cat >> input.nml << EOF
+    cat >> "${nml_file}" << EOF
 &nam_sfcperts
 /
 EOF
@@ -736,7 +814,7 @@ EOF
 
 else
 
-  cat >> input.nml << EOF
+  cat >> "${nml_file}" << EOF
 &nam_stochy
 /
 &nam_sfcperts
@@ -745,9 +823,9 @@ EOF
 
 fi
 
-# Echo out formatted "input.nml"
+# Echo out formatted ""${nml_file}""
 echo "===================================="
-echo "FV3_namelists(): 'input.nml'"
-cat input.nml
+echo "FV3_namelists(): '${nml_file}'"
+cat "${nml_file}"
 echo "===================================="
 }

From 383f463089facb58caff2051e2c936c20f07bbcb Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:30:10 -0600
Subject: [PATCH 10/15] update config.ufs

---
 parm/config/gfs/config.ufs | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/parm/config/gfs/config.ufs b/parm/config/gfs/config.ufs
index d6719f04f01..e37e46cf700 100644
--- a/parm/config/gfs/config.ufs
+++ b/parm/config/gfs/config.ufs
@@ -105,7 +105,7 @@ case "${fv3_res}" in
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=1
         ;;
     "C96")
-        if [[ ${DO_NEST:-NO} == YES ]] ; then
+        if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
           export DELTIM=450
           export layout_x_gfs=4
           export layout_y_gfs=4
@@ -142,7 +142,7 @@ case "${fv3_res}" in
         fi
         ;;
     "C192")
-        if [[ ${DO_NEST:-NO} == YES ]] ; then
+        if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
           export DELTIM=225
           export layout_x_gfs=5
           export layout_y_gfs=6
@@ -179,7 +179,7 @@ case "${fv3_res}" in
         fi
         ;;
     "C384")
-        if [[ ${DO_NEST:-NO} == YES ]] ; then
+        if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
           export DELTIM=150
           export layout_x=8
           export layout_y=8
@@ -218,7 +218,7 @@ case "${fv3_res}" in
         fi
         ;;
     "C768")
-        if [[ ${DO_NEST:-NO} == YES ]] ; then
+        if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
           export DELTIM=75
           export layout_x=16
           export layout_y=10
@@ -307,7 +307,7 @@ export WRTTASK_PER_GROUP_PER_THREAD_GFS
 
 (( ntasks_fv3 = layout_x * layout_y * 6 ))
 (( ntasks_fv3_gfs = layout_x_gfs * layout_y_gfs * 6 ))
-if [[ "${DO_NEST:-NO}" == YES ]] ; then
+if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
   (( ntasks_fv3_gfs += layout_x_nest * layout_y_nest ))
 fi
 export ntasks_fv3
@@ -342,7 +342,7 @@ export cplice=".false."
 export cplchm=".false."
 export cplwav=".false."
 export cplwav2atm=".false."
-if [[ "${DO_NEST:-NO}" == YES ]] ; then
+if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
   export CCPP_SUITE="${CCPP_SUITE:-FV3_global_nest_v1}"
 else
   export CCPP_SUITE="${CCPP_SUITE:-FV3_GFS_v17_p8_ugwpv1}"

From 6db19cf53e755b134982d30d587189096adf93c0 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:33:20 -0600
Subject: [PATCH 11/15] update parsing_namelists_FV3_nest.sh

---
 ush/parsing_namelists_FV3_nest.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ush/parsing_namelists_FV3_nest.sh b/ush/parsing_namelists_FV3_nest.sh
index ba7376585fe..46d1050b2f2 100755
--- a/ush/parsing_namelists_FV3_nest.sh
+++ b/ush/parsing_namelists_FV3_nest.sh
@@ -4,7 +4,7 @@
 
 # Disable variable not used warnings
 # shellcheck disable=SC2034
-FV3_namelists(){
+FV3_namelists_nest(){
 
 # First argument tells us which namelist we're writing:
 #   global = writing input.nml for running global with a nest
@@ -825,7 +825,7 @@ fi
 
 # Echo out formatted ""${nml_file}""
 echo "===================================="
-echo "FV3_namelists(): '${nml_file}'"
+echo "FV3_namelists_nest(): '${nml_file}'"
 cat "${nml_file}"
 echo "===================================="
 }

From 759fa302acc5d68b3e4c45c021e120cbb5977884 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:35:02 -0600
Subject: [PATCH 12/15] update forecast_postdet.sh

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

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 34c313a9056..5f6318f6e10 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -202,8 +202,9 @@ FV3_nml() {
 
   # Call the appropriate namelist functions
   if [[ "${DO_NEST:-NO}" == YES ]] ; then
-    FV3_namelists global_with_nest
-    FV3_namelists nest
+    source "${USHgfs}/parsing_namelists_FV3_nest.sh"
+    FV3_namelists_nest global
+    FV3_namelists_nest nest
   else
     FV3_namelists
   fi

From 66406beed392db3ed691a6d449ec061e934550f8 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:41:37 -0600
Subject: [PATCH 13/15] add quotation mark to 'YES'

---
 ush/forecast_postdet.sh            | 4 ++--
 ush/forecast_predet.sh             | 4 ++--
 ush/parsing_model_configure_FV3.sh | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 5f6318f6e10..e11c20fdc39 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -175,7 +175,7 @@ EOF
       if [[ "${WRITE_DOPOST}" == ".true." ]]; then
         ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.master.grb2f${FH3}" "GFSPRS.GrbF${FH2}"
         ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}"
-        if [[ "${DO_NEST:-NO}" == YES ]] ; then
+        if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
           ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.grb2f${FH3}" "GFSPRS.GrbF${FH2}.nest02"
           ${NLN} "${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}.nest02"
         fi
@@ -201,7 +201,7 @@ FV3_nml() {
   source "${USHgfs}/parsing_model_configure_FV3.sh"
 
   # Call the appropriate namelist functions
-  if [[ "${DO_NEST:-NO}" == YES ]] ; then
+  if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
     source "${USHgfs}/parsing_namelists_FV3_nest.sh"
     FV3_namelists_nest global
     FV3_namelists_nest nest
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 212257c3239..2b44e1dd797 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -229,7 +229,7 @@ FV3_predet(){
 
   # Conserve total energy as heat globally
   consv_te=${consv_te:-1.} # range 0.-1., 1. will restore energy to orig. val. before physics
-  if [[ "${DO_NEST:-NO}" == YES ]] ; then
+  if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
     consv_te=0
     k_split=${k_split:-1}
     k_split_nest=${k_split_nest:-4}
@@ -364,7 +364,7 @@ FV3_predet(){
     ${NCP} "${FIXgfs}/ugwd/${CASE}/${CASE}_oro_data_ls.tile${tt}.nc"          "${DATA}/INPUT/oro_data_ls.tile${tt}.nc"
     ${NCP} "${FIXgfs}/ugwd/${CASE}/${CASE}_oro_data_ss.tile${tt}.nc"          "${DATA}/INPUT/oro_data_ss.tile${tt}.nc"
   done
-  if [[ "${DO_NEST:-NO}" == YES ]] ; then
+  if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
     ${NLN} "${DATA}/INPUT/oro_data.tile7.nc" "${DATA}/INPUT/oro_data.nest02.tile7.nc"
     ${NLN} "${DATA}/INPUT/${CASE}_grid.tile7.nc"     "${DATA}/INPUT/${CASE}_grid.nest02.tile7.nc"
     ${NLN} "${DATA}/INPUT/${CASE}_grid.tile7.nc"     "${DATA}/INPUT/grid.nest02.tile7.nc"
diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh
index 6654bbcf4ca..f9fa54a1ff8 100755
--- a/ush/parsing_model_configure_FV3.sh
+++ b/ush/parsing_model_configure_FV3.sh
@@ -52,7 +52,7 @@ local OUTPUT_FH=${FV3_OUTPUT_FH}
 local IAU_OFFSET=${IAU_OFFSET:-0}
 
 # Ensure the template exists
-if [[ "${DO_NEST:-NO}" == YES ]] ; then
+if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
   local NEST_IMO=${npx_nest}
   local NEST_JMO=${npy_nest}
   template="${PARMgfs}/ufs/model_configure_nest.IN"

From 9c9e2b5d30de253852934d6016d9b487d348828e Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:49:18 -0600
Subject: [PATCH 14/15] disable 'masking return value' warnings

---
 ush/parsing_namelists_FV3_nest.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ush/parsing_namelists_FV3_nest.sh b/ush/parsing_namelists_FV3_nest.sh
index 46d1050b2f2..1072d05c954 100755
--- a/ush/parsing_namelists_FV3_nest.sh
+++ b/ush/parsing_namelists_FV3_nest.sh
@@ -2,8 +2,9 @@
 
 # parsing namelist of FV3, diag_table, etc.
 
-# Disable variable not used warnings
+# Disable variable not used warnings and 'masking return value' warnings
 # shellcheck disable=SC2034
+# shellcheck disable=SC2155
 FV3_namelists_nest(){
 
 # First argument tells us which namelist we're writing:

From 19f448d9b44ddd402a2c0e2c72dd59564dcd4ea9 Mon Sep 17 00:00:00 2001
From: "guoqing.ge" <Guoqing.Ge@noaa.gov>
Date: Fri, 26 Apr 2024 15:53:03 -0600
Subject: [PATCH 15/15] shellcheck disable=SC2312

---
 ush/parsing_namelists_FV3_nest.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/parsing_namelists_FV3_nest.sh b/ush/parsing_namelists_FV3_nest.sh
index 1072d05c954..2f99a1cdf56 100755
--- a/ush/parsing_namelists_FV3_nest.sh
+++ b/ush/parsing_namelists_FV3_nest.sh
@@ -4,7 +4,7 @@
 
 # Disable variable not used warnings and 'masking return value' warnings
 # shellcheck disable=SC2034
-# shellcheck disable=SC2155
+# shellcheck disable=SC2312
 FV3_namelists_nest(){
 
 # First argument tells us which namelist we're writing: