From af31d2fcc0431fe991ef339c33faab106fb99b9a Mon Sep 17 00:00:00 2001
From: "Eric.Sinsky" <eric.sinsky@noaa.gov>
Date: Thu, 15 Aug 2024 13:11:55 +0000
Subject: [PATCH 1/7] Fix bug in variable check

Fix a bug in a variable check in the extractvars task where parenthesis in the variable name will prompt a false warning message.
---
 ush/extractvars_tools.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/extractvars_tools.sh b/ush/extractvars_tools.sh
index daf61a3d2e4..de5a014ebe5 100644
--- a/ush/extractvars_tools.sh
+++ b/ush/extractvars_tools.sh
@@ -17,7 +17,7 @@ check_atmos() {
   done
   mapfile -t requestedvar_in_allgrb2file_arr < "${requestedvar_in_allgrb2file}"
   while read -r vari; do
-    if [[ ! ${requestedvar_in_allgrb2file_arr[*]} =~ ${vari} ]] ;then
+    if [[ ! ${requestedvar_in_allgrb2file_arr[*]} =~ "${vari}" ]] ;then
       echo "WARNING: PARM VARIABLE (${vari}) is not available in pgrb and pgrb2b for f${fnhl}."
     fi
   done <"${varlistl}"

From cec7b81d42941747c8a85b0ec4ccaf1973e2f07b Mon Sep 17 00:00:00 2001
From: "Eric.Sinsky" <eric.sinsky@noaa.gov>
Date: Thu, 15 Aug 2024 13:52:47 +0000
Subject: [PATCH 2/7] Add more settings to GEFS replay CI test

---
 ci/cases/yamls/gefs_replay_ci.yaml  | 6 ++++++
 parm/config/gefs/config.base        | 6 +++---
 parm/config/gefs/yaml/defaults.yaml | 3 +++
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/ci/cases/yamls/gefs_replay_ci.yaml b/ci/cases/yamls/gefs_replay_ci.yaml
index 6f9037d9eef..6c5b06700f4 100644
--- a/ci/cases/yamls/gefs_replay_ci.yaml
+++ b/ci/cases/yamls/gefs_replay_ci.yaml
@@ -3,5 +3,11 @@ defaults:
 base:
   REPLAY_ICS: "YES"
   FCST_BREAKPOINTS: ""
+  FHMAX_GFS: 48
+  FHMAX_HF_GFS: 24
+  DO_EXTRACTVARS: "YES"
+  FHOUT_HF_GFS: 3
+  FHOUT_OCN_GFS: 24
+  FHOUT_ICE_GFS: 24
   BASE_CPLIC: {{ 'TOPICDIR' | getenv }}/REPLAY_ICs/CI
 
diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
index d4996e10119..0989a398746 100644
--- a/parm/config/gefs/config.base
+++ b/parm/config/gefs/config.base
@@ -245,9 +245,9 @@ export FCST_SEGMENTS="${FHMIN_GFS},${breakpnts:+${breakpnts},}${FHMAX_GFS}"
 
 export FHOUT_GFS=6
 export FHMAX_HF_GFS=@FHMAX_HF_GFS@
-export FHOUT_HF_GFS=1
-export FHOUT_OCN_GFS=6
-export FHOUT_ICE_GFS=6
+export FHOUT_HF_GFS=@FHOUT_HF_GFS@
+export FHOUT_OCN_GFS=@FHOUT_OCN_GFS@
+export FHOUT_ICE_GFS=@FHOUT_ICE_GFS@
 export FHMIN_WAV=${OFFSET_START_HOUR:-0}
 export FHOUT_WAV=3
 export FHMAX_HF_WAV=120
diff --git a/parm/config/gefs/yaml/defaults.yaml b/parm/config/gefs/yaml/defaults.yaml
index e4666d1aba3..e17026d3a61 100644
--- a/parm/config/gefs/yaml/defaults.yaml
+++ b/parm/config/gefs/yaml/defaults.yaml
@@ -11,6 +11,9 @@ base:
   DO_EXTRACTVARS: "NO"
   FHMAX_GFS: 120
   FHMAX_HF_GFS: 0
+  FHOUT_HF_GFS: 1
   FCST_BREAKPOINTS: "48"
   REPLAY_ICS: "NO"
   USE_OCN_PERTURB_FILES: "false"
+  FHOUT_OCN_GFS: 6
+  FHOUT_ICE_GFS: 6

From 4aaca9ac06e9072206eb98c4ad50ff8b9642957e Mon Sep 17 00:00:00 2001
From: "Eric.Sinsky" <eric.sinsky@noaa.gov>
Date: Thu, 15 Aug 2024 15:24:27 +0000
Subject: [PATCH 3/7] Add atmos variables requested for reforeacst

---
 parm/product/gefs.0p25.fFFF.paramlist.b.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/parm/product/gefs.0p25.fFFF.paramlist.b.txt b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
index f7fdb73ddf3..b62d403b8e8 100644
--- a/parm/product/gefs.0p25.fFFF.paramlist.b.txt
+++ b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
@@ -65,6 +65,7 @@
 :CWORK:entire atmosphere (considered as a single layer):
 :DPT:30-0 mb above ground:
 :DUVB:surface:
+:FDNSSTMP:surface:
 :FLDCP:surface:
 :FRICV:surface:
 :GFLUX:surface:
@@ -276,6 +277,7 @@
 :TCDC:475 mb:
 :TCDC:boundary layer cloud layer:
 :TCDC:convective cloud layer:
+:TCDC:entire atmosphere (considered as a single layer):
 :TCDC:high cloud layer:
 :TCDC:low cloud layer:
 :TCDC:middle cloud layer:
@@ -345,6 +347,7 @@
 :TMP:PV=5e-07 (Km^2/kg/s) surface:
 :TMP:surface:
 :TMP:tropopause:
+:TSNOWP:surface:
 :TOZNE:entire atmosphere (considered as a single layer):
 :TSOIL:0.1-0.4 m below ground:
 :TSOIL:0.4-1 m below ground:

From 11e1957d2b911eebcd1989a442dab0f47e58d72e Mon Sep 17 00:00:00 2001
From: "Eric.Sinsky" <eric.sinsky@noaa.gov>
Date: Thu, 15 Aug 2024 15:27:24 +0000
Subject: [PATCH 4/7] Reorganize TSNOWP in paramlist

---
 parm/product/gefs.0p25.fFFF.paramlist.b.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/product/gefs.0p25.fFFF.paramlist.b.txt b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
index b62d403b8e8..bae2778ca11 100644
--- a/parm/product/gefs.0p25.fFFF.paramlist.b.txt
+++ b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
@@ -347,8 +347,8 @@
 :TMP:PV=5e-07 (Km^2/kg/s) surface:
 :TMP:surface:
 :TMP:tropopause:
-:TSNOWP:surface:
 :TOZNE:entire atmosphere (considered as a single layer):
+:TSNOWP:surface:
 :TSOIL:0.1-0.4 m below ground:
 :TSOIL:0.4-1 m below ground:
 :TSOIL:1-2 m below ground:

From a005e5fe4cac42e3c6a7af2fa1d74366bab6da08 Mon Sep 17 00:00:00 2001
From: "Eric.Sinsky" <eric.sinsky@noaa.gov>
Date: Thu, 15 Aug 2024 15:58:40 +0000
Subject: [PATCH 5/7] Extract ice variables from history file instead

Ice variables are extracted from the history files instead of the product files. This is necessary because there are certain ice variables that are needed that are only available in the history files and not the product files.
---
 ush/ocnice_extractvars.sh | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/ush/ocnice_extractvars.sh b/ush/ocnice_extractvars.sh
index 51276172b91..789625649b6 100755
--- a/ush/ocnice_extractvars.sh
+++ b/ush/ocnice_extractvars.sh
@@ -25,11 +25,19 @@ for (( nh = FHMIN_GFS; nh <= FHMAX_GFS; nh = nh + fhout_ocnice )); do
   fnh=$(printf "%3.3d" "${nh}")
 
   if [[ ${component_name} == "ocn" ]]; then
-    infile=${COMIN_OCEAN_NETCDF}/${datares}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc
+    if [[ "${datares}" == "native" ]]; then
+      infile=${COMIN_OCN_HISTORY}/${RUN}.ocean.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc
+    else
+      infile=${COMIN_OCEAN_NETCDF}/${datares}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc
+    fi
     # For ocean products, add an argument to extract a subset of levels
     otherargs=(-d "${depthvar_name},""${zmin},""${zmax}")
   elif [[ ${component_name} == "ice" ]]; then
-    infile=${COMIN_ICE_NETCDF}/${datares}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc
+    if [[ "${datares}" == "native" ]]; then
+      infile=${COMIN_ICE_HISTORY}/${RUN}.ice.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc
+    else
+      infile=${COMIN_ICE_NETCDF}/${datares}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc
+    fi
     otherargs=()
   fi
   outfile=${subdata}/${RUN}.${component_name}.t${cyc}z.${datares}.f${fnh}.nc

From 2dd9a7e8d999c60ac42c8983647bcfc75778e1cb Mon Sep 17 00:00:00 2001
From: "Eric.Sinsky" <eric.sinsky@noaa.gov>
Date: Thu, 15 Aug 2024 16:08:47 +0000
Subject: [PATCH 6/7] Fix typo

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

diff --git a/ush/ocnice_extractvars.sh b/ush/ocnice_extractvars.sh
index 789625649b6..43e69ebe9ba 100755
--- a/ush/ocnice_extractvars.sh
+++ b/ush/ocnice_extractvars.sh
@@ -26,7 +26,7 @@ for (( nh = FHMIN_GFS; nh <= FHMAX_GFS; nh = nh + fhout_ocnice )); do
 
   if [[ ${component_name} == "ocn" ]]; then
     if [[ "${datares}" == "native" ]]; then
-      infile=${COMIN_OCN_HISTORY}/${RUN}.ocean.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc
+      infile=${COMIN_OCEAN_HISTORY}/${RUN}.ocean.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc
     else
       infile=${COMIN_OCEAN_NETCDF}/${datares}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc
     fi

From b132408d1b170cf4d5d9a00ffe2e6c122d2f2041 Mon Sep 17 00:00:00 2001
From: "Eric.Sinsky" <eric.sinsky@noaa.gov>
Date: Thu, 15 Aug 2024 16:22:00 +0000
Subject: [PATCH 7/7] Update TCDC variable to correct name

---
 parm/product/gefs.0p25.fFFF.paramlist.a.txt | 2 +-
 parm/product/gefs.0p25.fFFF.paramlist.b.txt | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/parm/product/gefs.0p25.fFFF.paramlist.a.txt b/parm/product/gefs.0p25.fFFF.paramlist.a.txt
index a4a3ace3855..a9775aca6b6 100644
--- a/parm/product/gefs.0p25.fFFF.paramlist.a.txt
+++ b/parm/product/gefs.0p25.fFFF.paramlist.a.txt
@@ -18,7 +18,7 @@
 :CIN:180-0 mb above ground:
 :CIN:surface:
 :HLCY:3000-0 m above ground:
-:TCDC:entire atmosphere:
+:TCDC:entire atmosphere (considered as a single layer):
 :WEASD:surface:
 :SNOD:surface:
 :ULWRF:top of atmosphere:
diff --git a/parm/product/gefs.0p25.fFFF.paramlist.b.txt b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
index bae2778ca11..2da9187fabd 100644
--- a/parm/product/gefs.0p25.fFFF.paramlist.b.txt
+++ b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
@@ -277,7 +277,6 @@
 :TCDC:475 mb:
 :TCDC:boundary layer cloud layer:
 :TCDC:convective cloud layer:
-:TCDC:entire atmosphere (considered as a single layer):
 :TCDC:high cloud layer:
 :TCDC:low cloud layer:
 :TCDC:middle cloud layer: