From 5cf91e9aebda7fb6de587c5d325568c929065ba4 Mon Sep 17 00:00:00 2001
From: NeilBarton-NOAA <neil.barton@noaa.gov>
Date: Thu, 29 Feb 2024 18:17:59 +0000
Subject: [PATCH 1/5] GEFS stage ICs for C384 and with ocean perturbations

---
 parm/config/gefs/config.stage_ic | 6 ++++++
 scripts/exglobal_stage_ic.sh     | 9 +++++++++
 2 files changed, 15 insertions(+)

diff --git a/parm/config/gefs/config.stage_ic b/parm/config/gefs/config.stage_ic
index e2bb0af2b8..95fa9fcb89 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 "${CASE}" in
+  "C348")
+    export CPL_ATMIC=""
+    export CPL_ICEIC=""
+    export CPL_OCNIC=""
+    export CPL_WAVIC=""
+    ;;
   "C48")
     export CPL_ATMIC="gefs_test"
     export CPL_ICEIC="gefs_test"
diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
index 58b37f3114..7af4bbb45c 100755
--- a/scripts/exglobal_stage_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -104,6 +104,15 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
         ;;
     esac
 
+    # Ocean Perturbation Files
+    if [[ "${MEMDIR}" != "mem000" ]]; then
+        src="${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}"
+    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

From 1c670b05287f3460bb3cd29f9adf2476c8e4f33f Mon Sep 17 00:00:00 2001
From: NeilBarton-NOAA <neil.barton@noaa.gov>
Date: Thu, 29 Feb 2024 21:34:14 +0000
Subject: [PATCH 2/5] edits for option to stage ocean perturbation files

---
 parm/config/gefs/config.base.emc.dyn | 4 ++++
 parm/config/gefs/config.stage_ic     | 2 +-
 scripts/exglobal_stage_ic.sh         | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

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 [[ "${EXP_WARM_START}" = ".false." ]]; then
diff --git a/parm/config/gefs/config.stage_ic b/parm/config/gefs/config.stage_ic
index 95fa9fcb89..b332ee1826 100644
--- a/parm/config/gefs/config.stage_ic
+++ b/parm/config/gefs/config.stage_ic
@@ -8,7 +8,7 @@ echo "BEGIN: config.stage_ic"
 source "${EXPDIR}/config.resources" stage_ic
 
 case "${CASE}" in
-  "C348")
+  "C384")
     export CPL_ATMIC=""
     export CPL_ICEIC=""
     export CPL_OCNIC=""
diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
index 7af4bbb45c..dade95314f 100755
--- a/scripts/exglobal_stage_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -105,7 +105,7 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
     esac
 
     # Ocean Perturbation Files
-    if [[ "${MEMDIR}" != "mem000" ]]; then
+    if [[ "${MEMDIR}" != "mem000" ]] && [[ "${OCN_ENS_PERTURB_FILES}" == "true" ]]; then
         src="${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}"

From cb09d614ea12213414e3469fa95770212a8b992a Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu, 29 Feb 2024 16:56:12 -0500
Subject: [PATCH 3/5] Update exglobal_stage_ic.sh

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

diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
index dade95314f..e961c4423f 100755
--- a/scripts/exglobal_stage_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -105,7 +105,7 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
     esac
 
     # Ocean Perturbation Files
-    if [[ "${MEMDIR}" != "mem000" ]] && [[ "${OCN_ENS_PERTURB_FILES}" == "true" ]]; then
+    if [[ "${MEMDIR}" != "mem000" ]] && [[ "${OCN_ENS_PERTURB_FILES:-}" == "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}"

From a975e7938fd4136f3632cedee51e3528eb3e770c Mon Sep 17 00:00:00 2001
From: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Fri, 1 Mar 2024 11:01:26 -0500
Subject: [PATCH 4/5] Update scripts/exglobal_stage_ic.sh

Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
---
 scripts/exglobal_stage_ic.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
index e961c4423f..7240d48ed4 100755
--- a/scripts/exglobal_stage_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -105,7 +105,8 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
     esac
 
     # Ocean Perturbation Files
-    if [[ "${MEMDIR}" != "mem000" ]] && [[ "${OCN_ENS_PERTURB_FILES:-}" == "true" ]]; then
+    # 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}"

From 03ed0ca643166ce82f9c87f05219efe0159efb9d Mon Sep 17 00:00:00 2001
From: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Fri, 1 Mar 2024 11:01:35 -0500
Subject: [PATCH 5/5] Update scripts/exglobal_stage_ic.sh

Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
---
 scripts/exglobal_stage_ic.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
index 7240d48ed4..c12eaa84e0 100755
--- a/scripts/exglobal_stage_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -112,6 +112,7 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
         ${NCP} "${src}" "${tgt}"
         rc=${?}
         ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
+        err=$((err + rc))
     fi
 
     # TODO: Do mediator restarts exists in a ATMW configuration?