Add GEFS Ocean Perturbation Options

parm/config/gefs/config.base

@@ -74,7 +74,7 @@ export NCP="/bin/cp -p"
 export NMV="/bin/mv"
 export NLN="/bin/ln -sf"
 export VERBOSE="YES"
-export KEEPDATA="NO"
+export KEEPDATA="@KEEPDATA@"
 export DEBUG_POSTSCRIPT="NO" # PBS only; sets debug=true
 export CHGRP_RSTPROD="@CHGRP_RSTPROD@"
 export CHGRP_CMD="@CHGRP_CMD@"
@@ -262,7 +262,7 @@ 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 USE_OCN_PERTURB_FILES=@STAGE_OCN_PERTURB_FILES@
 
 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

parm/config/gefs/config.efcs

@@ -60,7 +60,27 @@ export SPPT_TAU=21600.
 export SPPT_LSCALE=500000.
 export SPPT_LOGIT=".true."
 export SPPT_SFCLIMIT=".true."
+# 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 [[ "${USE_OCN_PERTURB_FILES:-false}" == "true" ]]; then
+    export ODA_INCUPD="True"
+    export ODA_TEMPINC_VAR='t_pert'
+    export ODA_SALTINC_VAR='s_pert'
+    export ODA_THK_VAR='h_anl'
+    export ODA_UINC_VAR='u_pert'
+    export ODA_VINC_VAR='v_pert'
+    export ODA_INCUPD_NHOURS=0.0
+else
+    export ODA_INCUPD="False"
+fi
 export restart_interval="${restart_interval_gfs}"
 
 echo "END: config.efcs"

parm/config/gefs/yaml/defaults.yaml

@@ -4,4 +4,9 @@ base:
   DO_JEDIOCNVAR: "NO"
   DO_JEDISNOWDA: "NO"
   DO_MERGENSST: "NO"
+  KEEPDATA: "NO" 
   FHMAX_GFS: 120
+
+stage_ic:
+  USE_OCN_PERTURB_FILES: "false"
+

scripts/exglobal_stage_ic.sh

@@ -106,7 +106,7 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
 
     # 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
+    if (( 0${MEMDIR:3} > 0 )) && [[ "${USE_OCN_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}"

ush/forecast_postdet.sh

@@ -251,8 +251,15 @@ EOF
 
   ${NLN} "${FIXgfs}/am/global_co2historicaldata_glob.txt" "${DATA}/co2historicaldata_glob.txt"
   ${NLN} "${FIXgfs}/am/co2monthlycyc.txt"                 "${DATA}/co2monthlycyc.txt"
-  if [[ ${ICO2} -gt 0 ]]; then
-    for file in $(ls "${FIXgfs}/am/fix_co2_proj/global_co2historicaldata"*) ; do
+  # Set historical CO2 values based on whether this is a reforecast run or not
+  # Ref. issue 2403
+  local co2dir
+  co2dir="fix_co2_proj"
+  if [[ ${reforecast:-"NO"} == "YES" ]]; then
+    co2dir="co2dat_4a"
+  fi
+  if (( ICO2 > 0 )); then
+    for file in $(ls "${FIXgfs}/am/${co2dir}/global_co2historicaldata"*) ; do
       ${NLN} "${file}" "${DATA}/$(basename "${file//global_}")"
     done
   fi
@@ -695,6 +702,13 @@ MOM6_postdet() {
       ${NLN} "${COM_OCEAN_ANALYSIS}/${RUN}.t${cyc}z.ocninc.nc" "${DATA}/INPUT/mom6_increment.nc"
   fi
 
+  # GEFS perturbations
+  # TODO if [[ $RUN} == "gefs" ]] block maybe be needed
+  #     to ensure it does not interfere with the GFS
+  if (( MEMBER > 0 )) && [[ "${ODA_INCUPD:-False}" == "True" ]]; then
+     ${NLN} "${COM_OCEAN_RESTART_PREV}/${sPDY}.${scyc}0000.mom6_increment.nc" "${DATA}/INPUT/mom6_increment.nc"
+  fi
+
   # Copy MOM6 fixed files
   ${NCP} "${FIXgfs}/mom6/${OCNRES}/"* "${DATA}/INPUT/"  # TODO: These need to be explicit
 
@@ -709,13 +723,11 @@ MOM6_postdet() {
 
   # If using stochatic parameterizations, create a seed that does not exceed the
   # largest signed integer
-  if [[ "${DO_OCN_SPPT}" = "YES" ]] || [[ "${DO_OCN_PERT_EPBL}" = "YES" ]]; then
-    if [[ ${SET_STP_SEED:-"YES"} = "YES" ]]; then
-      ISEED_OCNSPPT=$(( (current_cycle*1000 + MEMBER*10 + 6) % 2147483647 ))
-      ISEED_EPBL=$(( (current_cycle*1000 + MEMBER*10 + 7) % 2147483647 ))
-    else
-      ISEED=${ISEED:-0}
-    fi
+  if [[ ${DO_OCN_SPPT} = "YES" ]]; then
+    ISEED_OCNSPPT=$((current_cycle*10000 + ${MEMBER#0}*100 + 8)),$((current_cycle*10000 + ${MEMBER#0}*100 + 9)),$((current_cycle*10000 + ${MEMBER#0}*100 + 10)),$((current_cycle*10000 + ${MEMBER#0}*100 + 11)),$((current_cycle*10000 + ${MEMBER#0}*100 + 12))
+  fi
+  if [[ ${DO_OCN_PERT_EPBL} = "YES" ]]; then
+    ISEED_EPBL=$((current_cycle*10000 + ${MEMBER#0}*100 + 13)),$((current_cycle*10000 + ${MEMBER#0}*100 + 14)),$((current_cycle*10000 + ${MEMBER#0}*100 + 15)),$((current_cycle*10000 + ${MEMBER#0}*100 + 16)),$((current_cycle*10000 + ${MEMBER#0}*100 + 17))
   fi
 
   # Link output files

ush/parsing_namelists_FV3.sh

@@ -631,6 +631,24 @@ EOF
   use_zmtnblck = ${use_zmtnblck:-".true."}
 EOF
   fi
+
+  if [[ "${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
   ${nam_stochy_nml:-}

ush/parsing_namelists_MOM6.sh

@@ -25,24 +25,6 @@ EOF
 #  new_lscale=.true.
 #EOF
 
-if [[ "${DO_OCN_SPPT}" == "YES" ]]; then
-  cat >> input.nml <<EOF
-  OCNSPPT=${OCNSPPT:-1.0}
-  OCNSPPT_LSCALE=${OCNSPPT_LSCALE:-500e3}
-  OCNSPPT_TAU=${OCNSPPT_TAU:-21600}
-  ISEED_OCNSPPT=${ISEED_OCNSPPT:-${ISEED}}
-EOF
-fi
-
-if [[ "${DO_OCN_PERT_EPBL}" == "YES" ]]; then
-  cat >> input.nml <<EOF
-  EPBL=${EPBL:-1.0}
-  EPBL_LSCALE=${EPBL_LSCALE:-500e3}
-  EPBL_TAU=${EPBL_TAU:-21600}
-  ISEED_EPBL=${ISEED_EPBL:-${ISEED}}
-EOF
-fi
-
 #cat >> input.nml <<EOF
 #/
 #
@@ -85,12 +67,12 @@ else
   local MOM6_USE_WAVES="False"
 fi
 # == MOM_oda_incupd section ==
-local ODA_TEMPINC_VAR="Temp"
-local ODA_SALTINC_VAR="Salt"
-local ODA_THK_VAR="h"
+local ODA_TEMPINC_VAR=${ODA_TEMPINC_VAR:-"Temp"}
+local ODA_SALTINC_VAR=${ODA_SALTINC_VAR:-"Salt"}
+local ODA_THK_VAR=${ODA_THK_VAR:-"h"}
 local ODA_INCUPD_UV="True"
-local ODA_UINC_VAR="u"
-local ODA_VINC_VAR="v"
+local ODA_UINC_VAR=${ODA_UINC_VAR:-"u"}
+local ODA_VINC_VAR=${ODA_VINC_VAR:-"v"}
 # ODA_INCUPD
 # ODA_INCUPD_NHOURS
 # == MOM_surface_forcing section ==