From 23c25527ad2a62275cd9105bd103b8520a28e573 Mon Sep 17 00:00:00 2001
From: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Fri, 1 Mar 2024 13:45:39 -0500
Subject: [PATCH] Update stage IC to handle ocean perturbations (#2364)

This PR adds the option to stage ocean perturbation files for ensemble
forecasts. These perturbation files are used in GEFS forecasts.
A new variable is introduced in config.base to use the ocean
perturbation files.
This PR does not include using these perturbation files. A future PR
will address this.
---
 parm/config/gefs/config.base.emc.dyn |  4 ++++
 parm/config/gefs/config.stage_ic     |  6 ++++++
 scripts/exglobal_stage_ic.sh         | 11 +++++++++++
 3 files changed, 21 insertions(+)

diff --git a/parm/config/gefs/config.base.emc.dyn b/parm/config/gefs/config.base.emc.dyn
index 0062aed163..5ae47e3948 100644
--- a/parm/config/gefs/config.base.emc.dyn
+++ b/parm/config/gefs/config.base.emc.dyn
@@ -259,6 +259,10 @@ export NMEM_ENS=@NMEM_ENS@
 export ENSMEM=${ENSMEM:-"000"}
 export MEMDIR="mem${ENSMEM}"
 
+# initialize ocean ensemble members with perturbations
+#   if true, only occurs for members greater than zero
+export OCN_ENS_PERTURB_FILES=false
+
 export DOIAU="NO"  # While we are not doing IAU, we may want to warm start w/ IAU in the future
 # Check if cycle is cold starting
 if [[ "${EXP_WARM_START}" = ".false." ]]; then
diff --git a/parm/config/gefs/config.stage_ic b/parm/config/gefs/config.stage_ic
index e2bb0af2b8..b332ee1826 100644
--- a/parm/config/gefs/config.stage_ic
+++ b/parm/config/gefs/config.stage_ic
@@ -8,6 +8,12 @@ echo "BEGIN: config.stage_ic"
 source "${EXPDIR}/config.resources" stage_ic
 
 case "${CASE}" in
+  "C384")
+    export CPL_ATMIC=""
+    export CPL_ICEIC=""
+    export CPL_OCNIC=""
+    export CPL_WAVIC=""
+    ;;
   "C48")
     export CPL_ATMIC="gefs_test"
     export CPL_ICEIC="gefs_test"
diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
index 58b37f3114..c12eaa84e0 100755
--- a/scripts/exglobal_stage_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -104,6 +104,17 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
         ;;
     esac
 
+    # Ocean Perturbation Files
+    # Extra zero on MEMDIR ensure we have a number even if the string is empty
+    if (( 0${MEMDIR:3} > 0 )) && [[ "${OCN_ENS_PERTURB_FILES:-false}" == "true" ]]; then
+        src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.mom6_increment.nc"
+        tgt="${COM_OCEAN_RESTART_PREV}/${PDY}.${cyc}0000.mom6_increment.nc"
+        ${NCP} "${src}" "${tgt}"
+        rc=${?}
+        ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
+        err=$((err + rc))
+    fi
+
     # TODO: Do mediator restarts exists in a ATMW configuration?
     # TODO: No mediator is presumably involved in an ATMA configuration
     if [[ ${EXP_WARM_START:-".false."} = ".true." ]]; then