From bc618628c96583ef29e455d7dd50670e61e813f4 Mon Sep 17 00:00:00 2001
From: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Thu, 5 Dec 2024 11:04:05 -0500
Subject: [PATCH] Use stochastic restart patterns on rerun (#3077)

The stochastic pattern restart files were not being copied into the
input directory when restarting the model after a segment/failure. These
files are now copied in and the stochini flag set to `.true.` in the
namelist on a rerun.

The files are NOT copied in for non-rerun warm starts.

Also removes the restriction that stochastic physics cannot be run on
member 0, as this is desired down the line. Additional settings are
added to the fcst and efcs configs to retain the current behavior.

A bug was also discovered and corrected during this work. The stage,
forecast, and archive job all assumed that `ca_data` tile files are
always present, but these are only created when cellular automata is on.
Now `ca_data` files are handled if CA is on. To implement this change,
the `DO_CA` setting had to be moved from the forecast configs to base so
it is available to the stage_ic and archive jobs.

Resolves #2937
---
 .gitmodules                            |  1 -
 parm/archive/enkf_restartb_grp.yaml.j2 |  5 +-
 parm/archive/gdas_restartb.yaml.j2     |  5 +-
 parm/config/gefs/config.base           |  9 ++-
 parm/config/gefs/config.efcs           | 20 +++---
 parm/config/gefs/config.fcst           | 11 +--
 parm/config/gfs/config.base            |  3 +
 parm/config/gfs/config.fcst            | 14 ++--
 parm/stage/atmosphere_nest.yaml.j2     |  5 +-
 parm/stage/atmosphere_warm.yaml.j2     |  5 +-
 scripts/exgdas_enkf_earc.py            |  2 +-
 scripts/exglobal_archive.py            |  2 +-
 scripts/exglobal_stage_ic.py           |  2 +-
 ush/forecast_postdet.sh                | 16 ++++-
 ush/forecast_predet.sh                 | 94 +++++++++++++++-----------
 ush/parsing_namelists_FV3.sh           |  1 +
 16 files changed, 122 insertions(+), 73 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 5c9e569243..c80d24c03a 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,7 +1,6 @@
 [submodule "sorc/ufs_model.fd"]
   path = sorc/ufs_model.fd
   url = https://github.com/ufs-community/ufs-weather-model
-  ignore = dirty
 [submodule "sorc/wxflow"]
   path = sorc/wxflow
   url = https://github.com/NOAA-EMC/wxflow
diff --git a/parm/archive/enkf_restartb_grp.yaml.j2 b/parm/archive/enkf_restartb_grp.yaml.j2
index 7cd799f0a9..c7aaf6682e 100644
--- a/parm/archive/enkf_restartb_grp.yaml.j2
+++ b/parm/archive/enkf_restartb_grp.yaml.j2
@@ -27,8 +27,11 @@ enkf_restartb_grp:
         {% set r_dt = current_cycle | add_to_datetime(r_timedelta) %}
         {% set r_prefix = r_dt | to_YMD + "." + r_dt | strftime("%H") + "0000" %}
         {% for itile in range(1, 7) %}
-        {% for datatype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for datatype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.{{datatype}}.tile{{ itile }}.nc"
+        {% if DO_CA %}
+        - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.ca_data.tile{{ itile }}.nc"
+        {% endif %}
         {% endfor %}
         {% endfor %}
         - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.coupler.res"
diff --git a/parm/archive/gdas_restartb.yaml.j2 b/parm/archive/gdas_restartb.yaml.j2
index 0bbf517fb2..620e0fb988 100644
--- a/parm/archive/gdas_restartb.yaml.j2
+++ b/parm/archive/gdas_restartb.yaml.j2
@@ -30,8 +30,11 @@ gdas_restartb:
         {% set r_HH = r_dt | strftime("%H") %}
         {% set r_prefix = r_YMD + "." + r_HH + "0000" %}
         {% for itile in range(1, 7) %}
-        {% for datatype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for datatype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.{{datatype}}.tile{{ itile }}.nc"
+        {% if DO_CA %}
+        - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.ca_data.tile{{ itile }}.nc"
+        {% endif %}
         {% endfor %}
         {% endfor %}
         - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.coupler.res"
diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
index 65bca1b377..2bafde04f5 100644
--- a/parm/config/gefs/config.base
+++ b/parm/config/gefs/config.base
@@ -287,10 +287,17 @@ export DO_MERGENSST="NO"
 export NMEM_ENS=@NMEM_ENS@
 
 # set default member number memdir for control
-# this will be overwritten for the perturbed members
+# this will be overwridden for the perturbed members
 export ENSMEM=${ENSMEM:-"000"}
 export MEMDIR="mem${ENSMEM}"
 
+# cellular automata
+if (( ENSMEM == 0 )); then
+    export DO_CA="YES"
+else
+    export DO_CA="YES"
+fi
+
 export DOIAU="NO"  # While we are not doing IAU, we may want to warm start w/ IAU in the future
 
 # Check if cycle is warm starting with IAU
diff --git a/parm/config/gefs/config.efcs b/parm/config/gefs/config.efcs
index 6bf0ed0a18..d1f7f7f714 100644
--- a/parm/config/gefs/config.efcs
+++ b/parm/config/gefs/config.efcs
@@ -44,16 +44,18 @@ export SPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
 export SPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
 export SPPT_LOGIT=".true."
 export SPPT_SFCLIMIT=".true."
-export DO_CA="YES"
 # OCN options
-export DO_OCN_SPPT="YES"
-export OCNSPPT="0.8,0.4,0.2,0.08,0.04"
-export OCNSPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
-export OCNSPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
-export DO_OCN_PERT_EPBL="YES"
-export EPBL="0.8,0.4,0.2,0.08,0.04"
-export EPBL_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
-export EPBL_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+if (( OCNRES <= 100 )); then
+    # Ocean stochastic options not supported at 5p00
+    export DO_OCN_SPPT="YES"
+    export OCNSPPT="0.8,0.4,0.2,0.08,0.04"
+    export OCNSPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
+    export OCNSPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+    export DO_OCN_PERT_EPBL="YES"
+    export EPBL="0.8,0.4,0.2,0.08,0.04"
+    export EPBL_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
+    export EPBL_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+fi
 
 if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
     export ODA_INCUPD="True"
diff --git a/parm/config/gefs/config.fcst b/parm/config/gefs/config.fcst
index 0461c7e909..d57e7e9e92 100644
--- a/parm/config/gefs/config.fcst
+++ b/parm/config/gefs/config.fcst
@@ -225,11 +225,12 @@ case ${imp_physics} in
 esac
 
 # Stochastic physics
-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"}
+export DO_SPPT="NO"
+export DO_SKEB="NO"
+export DO_SHUM="NO"
+export DO_LAND_PERT="NO"
+export DO_OCN_SPPT="NO"
+export DO_OCN_PERT_EPBL="NO"
 
 #coupling settings
 export cplmode="ufs.frac"
diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
index 46e27b4541..8e54bc321c 100644
--- a/parm/config/gfs/config.base
+++ b/parm/config/gfs/config.base
@@ -460,6 +460,9 @@ export INCVARS_EFOLD="5"
 export netcdf_diag=".true."
 export binary_diag=".false."
 
+# Cellular automata
+export DO_CA="YES"
+
 # Verification options
 export DO_METP="@DO_METP@"   # Run METPLUS jobs - set METPLUS settings in config.metp
 export DO_FIT2OBS="YES"      # Run fit to observations package
diff --git a/parm/config/gfs/config.fcst b/parm/config/gfs/config.fcst
index b154d37114..c95f8796e5 100644
--- a/parm/config/gfs/config.fcst
+++ b/parm/config/gfs/config.fcst
@@ -245,14 +245,12 @@ case ${imp_physics} in
 esac
 
 # Stochastic physics
-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.
-fi
+export DO_SPPT="NO"
+export DO_SKEB="NO"
+export DO_SHUM="NO"
+export DO_LAND_PERT="NO"
+export DO_OCN_SPPT="NO"
+export DO_OCN_PERT_EPBL="NO"
 
 #coupling settings
 export cplmode="ufs.frac"
diff --git a/parm/stage/atmosphere_nest.yaml.j2 b/parm/stage/atmosphere_nest.yaml.j2
index 13ec0ed8c5..d86942c1ba 100644
--- a/parm/stage/atmosphere_nest.yaml.j2
+++ b/parm/stage/atmosphere_nest.yaml.j2
@@ -11,8 +11,11 @@ atmosphere_nest:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
-        {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for ftype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}/{{ m_prefix }}.{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+        {% if DO_CA %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.ca_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}/{{ m_prefix }}.ca_data.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+        {% endif %}
         {% endfor %}
         {% endfor %} # mem loop
     {% else %} # cold start
diff --git a/parm/stage/atmosphere_warm.yaml.j2 b/parm/stage/atmosphere_warm.yaml.j2
index 14c8615262..44d6d78e30 100644
--- a/parm/stage/atmosphere_warm.yaml.j2
+++ b/parm/stage/atmosphere_warm.yaml.j2
@@ -15,9 +15,12 @@ atmosphere_warm:
         {% for ftype in ["coupler.res", "fv_core.res.nc"] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
         {% endfor %}
-        {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for ftype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         {% for ntile in range(1, ntiles + 1) %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
+        {% if DO_CA %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.ca_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
+        {% endif %}
         {% endfor %} # ntile
         {% endfor %} # ftype
         {% for ntile in range(1, ntiles + 1) %}
diff --git a/scripts/exgdas_enkf_earc.py b/scripts/exgdas_enkf_earc.py
index c724bdbd67..467cfa88dc 100755
--- a/scripts/exgdas_enkf_earc.py
+++ b/scripts/exgdas_enkf_earc.py
@@ -25,7 +25,7 @@ def main():
             'lobsdiag_forenkf', 'FHMIN_ENKF', 'FHMAX_ENKF_GFS',
             'FHOUT_ENKF_GFS', 'FHMAX_ENKF', 'FHOUT_ENKF', 'ENKF_SPREAD',
             'restart_interval_enkfgdas', 'restart_interval_enkfgfs',
-            'DOHYBVAR', 'DOIAU_ENKF', 'IAU_OFFSET', 'DOIAU',
+            'DOHYBVAR', 'DOIAU_ENKF', 'IAU_OFFSET', 'DOIAU', 'DO_CA',
             'DO_CALC_INCREMENT', 'assim_freq', 'ARCH_CYC',
             'ARCH_WARMICFREQ', 'ARCH_FCSTICFREQ',
             'IAUFHRS_ENKF', 'NET']
diff --git a/scripts/exglobal_archive.py b/scripts/exglobal_archive.py
index 2d3fa58313..6998831366 100755
--- a/scripts/exglobal_archive.py
+++ b/scripts/exglobal_archive.py
@@ -29,7 +29,7 @@ def main():
             'DOIAU', 'OCNRES', 'ICERES', 'NUM_SND_COLLECTIVES', 'FHOUT_WAV',
             'FHOUT_HF_WAV', 'FHMAX_WAV', 'FHMAX_HF_WAV', 'FHMAX_WAV_GFS',
             'restart_interval_gdas', 'restart_interval_gfs',
-            'DO_AERO_ANL', 'DO_AERO_FCST', 'DOIBP_WAV', 'DO_JEDIOCNVAR',
+            'DO_AERO_ANL', 'DO_AERO_FCST', 'DO_CA', 'DOIBP_WAV', 'DO_JEDIOCNVAR',
             'NMEM_ENS', 'DO_JEDIATMVAR', 'DO_VRFY_OCEANDA', 'FHMAX_FITS', 'waveGRD',
             'IAUFHRS', 'DO_FIT2OBS', 'NET', 'FHOUT_HF_GFS', 'FHMAX_HF_GFS', 'REPLAY_ICS',
             'OFFSET_START_HOUR']
diff --git a/scripts/exglobal_stage_ic.py b/scripts/exglobal_stage_ic.py
index 1a49c4f64d..9d74d227fc 100755
--- a/scripts/exglobal_stage_ic.py
+++ b/scripts/exglobal_stage_ic.py
@@ -22,7 +22,7 @@ def main():
             'assim_freq', 'current_cycle', 'previous_cycle',
             'ROTDIR', 'ICSDIR', 'STAGE_IC_YAML_TMPL', 'DO_JEDIATMVAR',
             'OCNRES', 'waveGRD', 'ntiles', 'DOIAU', 'DO_JEDIOCNVAR',
-            'REPLAY_ICS', 'DO_WAVE', 'DO_OCN', 'DO_ICE', 'DO_NEST',
+            'REPLAY_ICS', 'DO_WAVE', 'DO_OCN', 'DO_ICE', 'DO_NEST', 'DO_CA',
             'USE_ATM_ENS_PERTURB_FILES', 'USE_OCN_ENS_PERTURB_FILES']
 
     stage_dict = AttrDict()
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index aade469ddc..532e0bb883 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -47,7 +47,19 @@ FV3_postdet() {
       || ( echo "FATAL ERROR: Unable to copy FV3 IC, ABORT!"; exit 1 )
     done
 
-    if [[ "${RERUN}" != "YES" ]]; then
+    if [[ "${RERUN}" == "YES" ]]; then
+      if [[ "${DO_SPPT:-}" == "YES" || "${DO_SKEB:-}" == "YES" || \
+            "${DO_SHUM:-}" == "YES" || "${DO_LAND_PERT:-}" == "YES" ]]; then
+        stochini=".true."
+        file_list=$(stoch_restarts)
+        echo "Copying stochastic restarts for 'RUN=${RUN}' at '${restart_date}' from '${restart_dir}'"
+        for stoch_file in $(stoch_restarts); do
+          restart_file="${restart_date:0:8}.${restart_date:8:2}0000.${stoch_file}"
+          ${NCP} "${restart_dir}/${restart_file}" "${DATA}/INPUT/${stoch_file}" \
+          || ( echo "FATAL ERROR: Unable to copy stochastic restart, ABORT!"; exit 1 )
+        done
+      fi
+    else
       # Replace sfc_data with sfcanl_data restart files from current cycle (if found)
       local nn
       for (( nn = 1; nn <= ntiles; nn++ )); do
@@ -78,7 +90,7 @@ FV3_postdet() {
                  "${DATA}/INPUT/fv_tracer.res.tile${nn}.nc"
         done
       fi # if [[ ${use_anl_aero} == "YES" ]]; then
-    fi  # if [[ "${RERUN}" != "YES" ]]; then
+    fi  # if [[ "${RERUN}" == "YES" ]]; then
 
   fi  # if [[ "${warm_start}" == ".true." ]]; then
 
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 3c3dd719ef..59afe483ea 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -57,7 +57,10 @@ FV3_restarts(){
   # Create an array of FV3 restart files
   local fv3_restart_files tile_files
   fv3_restart_files=(coupler.res fv_core.res.nc)
-  tile_files=(fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data ca_data)
+  tile_files=(fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data)
+  if [[ ${DO_CA:-"NO"} == "YES" ]]; then
+    tile_files+=(ca_data)
+  fi
   local nn tt
   for (( nn = 1; nn <= ntiles; nn++ )); do
     for tt in "${tile_files[@]}"; do
@@ -68,6 +71,22 @@ FV3_restarts(){
   IFS=, echo "${fv3_restart_files[*]}"
 }
 
+stoch_restarts(){
+  # These only get copied for reruns
+  local stoch_restart_files
+  stoch_restart_files=(  )
+
+  if [[ "${DO_SPPT:-}" == "YES" || "${DO_SKEB:-}" == "YES" || \
+        "${DO_SHUM:-}" == "YES" || "${DO_LAND_PERT:-}" == "YES" ]]; then
+    stoch_restart_files+=(atm_stoch.res.nc)
+  fi
+  if [[ "${DO_OCN:-}" == "YES" && ( "${DO_OCN_SPPT:-}" == "YES" || "${DO_OCN_PERT_EPBL}" == "YES" ) ]]; then
+    stoch_restart_files+=(ocn_stoch.res.nc)
+  fi
+  # Create a comma separated string from array using IFS
+  IFS=, echo "${stoch_restart_files[*]}"
+}
+
 # shellcheck disable=SC2034
 common_predet(){
   echo "SUB ${FUNCNAME[0]}: Defining variables for shared through model components"
@@ -377,41 +396,38 @@ FV3_predet(){
   do_sppt=".false."
   do_ca=".false."
   ISEED=0
-  if (( MEMBER > 0 )); then  # these are only applicable for ensemble members
-    local imem=${MEMBER#0}
-    local base_seed=$((current_cycle*10000 + imem*100))
-
-    if [[ "${DO_SKEB:-}" == "YES" ]]; then
-      do_skeb=".true."
-      ISEED_SKEB=$((base_seed + 1))
-    fi
+  local imem=${MEMBER#0}
+  local base_seed=$((current_cycle*10000 + imem*100))
 
-    if [[ "${DO_SHUM:-}" == "YES" ]]; then
-      do_shum=".true."
-      ISEED_SHUM=$((base_seed + 2))
-    fi
+  if [[ "${DO_SKEB:-}" == "YES" ]]; then
+    do_skeb=".true."
+    ISEED_SKEB=$((base_seed + 1))
+  fi
 
-    if [[ "${DO_SPPT:-}" == "YES" ]]; then
-      do_sppt=".true."
-      ISEED_SPPT=$((base_seed + 3)),$((base_seed + 4)),$((base_seed + 5)),$((base_seed + 6)),$((base_seed + 7))
-    fi
+  if [[ "${DO_SHUM:-}" == "YES" ]]; then
+    do_shum=".true."
+    ISEED_SHUM=$((base_seed + 2))
+  fi
 
-    if [[ "${DO_CA:-}" == "YES" ]]; then
-      do_ca=".true."
-      ISEED_CA=$(( (base_seed + 18) % 2147483647 ))
-    fi
+  if [[ "${DO_SPPT:-}" == "YES" ]]; then
+    do_sppt=".true."
+    ISEED_SPPT=$((base_seed + 3)),$((base_seed + 4)),$((base_seed + 5)),$((base_seed + 6)),$((base_seed + 7))
+  fi
 
-    if [[ "${DO_LAND_PERT:-}" == "YES" ]]; then
-      lndp_type=${lndp_type:-2}
-      ISEED_LNDP=$(( (base_seed + 5) % 2147483647 ))
-      LNDP_TAU=${LNDP_TAU:-21600}
-      LNDP_SCALE=${LNDP_SCALE:-500000}
-      lndp_var_list=${lndp_var_list:-"'smc', 'vgf',"}
-      lndp_prt_list=${lndp_prt_list:-"0.2,0.1"}
-      n_var_lndp=$(echo "${lndp_var_list}" | wc -w)
-    fi
+  if [[ "${DO_CA:-}" == "YES" ]]; then
+    do_ca=".true."
+    ISEED_CA=$(( (base_seed + 18) % 2147483647 ))
+  fi
 
-  fi  # end of ensemble member specific options
+  if [[ "${DO_LAND_PERT:-}" == "YES" ]]; then
+    lndp_type=${lndp_type:-2}
+    ISEED_LNDP=$(( (base_seed + 5) % 2147483647 ))
+    LNDP_TAU=${LNDP_TAU:-21600}
+    LNDP_SCALE=${LNDP_SCALE:-500000}
+    lndp_var_list=${lndp_var_list:-"'smc', 'vgf',"}
+    lndp_prt_list=${lndp_prt_list:-"0.2,0.1"}
+    n_var_lndp=$(echo "${lndp_var_list}" | wc -w)
+  fi
 
   #--------------------------------------------------------------------------
 
@@ -680,17 +696,15 @@ MOM6_predet(){
 
   # If using stochastic parameterizations, create a seed that does not exceed the
   # largest signed integer
-  if (( MEMBER > 0 )); then  # these are only applicable for ensemble members
-    local imem=${MEMBER#0}
-    local base_seed=$((current_cycle*10000 + imem*100))
+  local imem=${MEMBER#0}
+  local base_seed=$((current_cycle*10000 + imem*100))
 
-    if [[ "${DO_OCN_SPPT:-}" == "YES" ]]; then
-      ISEED_OCNSPPT=$((base_seed + 8)),$((base_seed + 9)),$((base_seed + 10)),$((base_seed + 11)),$((base_seed + 12))
-    fi
+  if [[ "${DO_OCN_SPPT:-}" == "YES" ]]; then
+    ISEED_OCNSPPT=$((base_seed + 8)),$((base_seed + 9)),$((base_seed + 10)),$((base_seed + 11)),$((base_seed + 12))
+  fi
 
-    if [[ "${DO_OCN_PERT_EPBL:-}" == "YES" ]]; then
-      ISEED_EPBL=$((base_seed + 13)),$((base_seed + 14)),$((base_seed + 15)),$((base_seed + 16)),$((base_seed + 17))
-    fi
+  if [[ "${DO_OCN_PERT_EPBL:-}" == "YES" ]]; then
+    ISEED_EPBL=$((base_seed + 13)),$((base_seed + 14)),$((base_seed + 15)),$((base_seed + 16)),$((base_seed + 17))
   fi
 
   # Fix files
diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
index 9279b284f8..bb6a204cc8 100755
--- a/ush/parsing_namelists_FV3.sh
+++ b/ush/parsing_namelists_FV3.sh
@@ -656,6 +656,7 @@ if [[ "${DO_SPPT}" = "YES" || "${DO_SHUM}" = "YES" || "${DO_SKEB}" = "YES" || "$
 
     cat >> input.nml << EOF
 &nam_stochy
+  stochini=${stochini:-".false."}
 EOF
 
   if [[ ${DO_SKEB} = "YES" ]]; then