Update experiment directory.

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.aero

@@ -20,6 +20,9 @@ case ${machine} in
   "WCOSS2")
     AERO_INPUTS_DIR="/lfs/h2/emc/global/noscrub/emc.global/data/gocart_emissions"
     ;;
+  "GAEA")
+    AERO_INPUTS_DIR="/gpfs/f5/epic/proj-shared/global/glopara/data/gocart_emissions"
+    ;;
   "JET")
     AERO_INPUTS_DIR="/lfs4/HFIP/hfv3gfs/glopara/data/gocart_emissions"
     ;;
@@ -30,12 +33,12 @@ case ${machine} in
 esac
 export AERO_INPUTS_DIR
 
-export AERO_DIAG_TABLE="${HOMEgfs}/parm/ufs/fv3/diag_table.aero"
-export AERO_FIELD_TABLE="${HOMEgfs}/parm/ufs/fv3/field_table.aero"
+export AERO_DIAG_TABLE="${PARMgfs}/ufs/fv3/diag_table.aero"
+export AERO_FIELD_TABLE="${PARMgfs}/ufs/fv3/field_table.aero"
 # Biomass burning emission dataset. Choose from: gbbepx, qfed, none
 export AERO_EMIS_FIRE="qfed"
 # Directory containing GOCART configuration files
-export AERO_CONFIG_DIR="${HOMEgfs}/parm/ufs/gocart"
+export AERO_CONFIG_DIR="${PARMgfs}/ufs/gocart"
 
 # Aerosol convective scavenging factors (list of string array elements)
 # Element syntax: '<tracer_name>:<factor>'. Use <tracer_name> = * to set default factor for all aerosol tracers

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.aeroanl

@@ -6,25 +6,26 @@
 echo "BEGIN: config.aeroanl"
 
 export CASE_ANL=${CASE}
-export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/aero/obs/config/
-export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/aero/obs/lists/gdas_aero_prototype.yaml
+export OBS_LIST="${PARMgfs}/gdas/aero/obs/lists/gdas_aero.yaml.j2"
 export STATICB_TYPE='identity'
-export BERROR_YAML=${HOMEgfs}/sorc/gdas.cd/parm/aero/berror/staticb_${STATICB_TYPE}.yaml
-export FIXgdas=${HOMEgfs}/fix/gdas
-export BERROR_DATA_DIR=${FIXgdas}/bump/aero/${CASE_ANL}/
+export BERROR_YAML="${PARMgfs}/gdas/aero/berror/staticb_${STATICB_TYPE}.yaml.j2"
+export BERROR_DATA_DIR="${FIXgfs}/gdas/bump/aero/${CASE_ANL}/"
 export BERROR_DATE="20160630.000000"
 
+export CRTM_FIX_YAML="${PARMgfs}/gdas/aero_crtm_coeff.yaml.j2"
+export JEDI_FIX_YAML="${PARMgfs}/gdas/aero_jedi_fix.yaml.j2"
+
 export io_layout_x=1
 export io_layout_y=1
 
-export JEDIEXE=${HOMEgfs}/exec/fv3jedi_var.x
+export JEDIEXE="${EXECgfs}/gdas.x"
 
 if [[ "${DOIAU}" == "YES" ]]; then
   export aero_bkg_times="3,6,9"
-  export AEROVARYAML=${HOMEgfs}/sorc/gdas.cd/parm/aero/variational/3dvar_fgat_gfs_aero.yaml
+  export JEDIYAML="${PARMgfs}/gdas/aero/variational/3dvar_fgat_gfs_aero.yaml.j2"
 else
   export aero_bkg_times="6"
-  export AEROVARYAML=${HOMEgfs}/sorc/gdas.cd/parm/aero/variational/3dvar_gfs_aero.yaml
+  export JEDIYAML="${PARMgfs}/gdas/aero/variational/3dvar_gfs_aero.yaml.j2"
 fi
 
 echo "END: config.aeroanl"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.aeroanlfinal

@@ -6,5 +6,5 @@
 echo "BEGIN: config.aeroanlfinal"
 
 # Get task specific resources
-. $EXPDIR/config.resources aeroanlfinal
+source "${EXPDIR}/config.resources" aeroanlfinal
 echo "END: config.aeroanlfinal"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.aeroanlinit

@@ -6,5 +6,5 @@
 echo "BEGIN: config.aeroanlinit"
 
 # Get task specific resources
-. $EXPDIR/config.resources aeroanlinit
+source "${EXPDIR}/config.resources" aeroanlinit
 echo "END: config.aeroanlinit"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.aeroanlrun

@@ -6,6 +6,6 @@
 echo "BEGIN: config.aeroanlrun"
 
 # Get task specific resources
-. $EXPDIR/config.resources aeroanlrun
+source "${EXPDIR}/config.resources" aeroanlrun
 
 echo "END: config.aeroanlrun"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.anal

@@ -12,20 +12,13 @@ if [[ ${DONST} = "YES" ]]; then
   . ${EXPDIR}/config.nsst
 fi
 
-if [[ "${CDUMP}" = "gfs" ]] ; then
+if [[ "${RUN}" == "gfs" ]] ; then
   export USE_RADSTAT="NO" # This can be only used when bias correction is not-zero.
   export GENDIAG="NO"
   export SETUP='diag_rad=.false.,diag_pcp=.false.,diag_conv=.false.,diag_ozone=.false.,write_diag(3)=.false.,niter(2)=100,'
   export DIAG_TARBALL="YES"
 fi
 
-export npe_gsi=${npe_anal}
-
-if [[ "${CDUMP}" == "gfs" ]] ; then
-  export npe_gsi=${npe_anal_gfs}
-  export nth_anal=${nth_anal_gfs}
-fi
-
 # Set parameters specific to L127
 if [[ ${LEVS} = "128" ]]; then
   export GRIDOPTS="nlayers(63)=1,nlayers(64)=1,"
@@ -45,51 +38,58 @@ export AMSR2BF=${AMSR2BF:-/dev/null}
 
 # Set default values for info files and observation error
 #  NOTE:  Remember to set PRVT in config.prep as OBERROR is set below
-export CONVINFO=${FIXgsi}/global_convinfo.txt
-export OZINFO=${FIXgsi}/global_ozinfo.txt
-export SATINFO=${FIXgsi}/global_satinfo.txt
-export OBERROR=${FIXgsi}/prepobs_errtable.global
-
+export CONVINFO=${FIXgfs}/gsi/global_convinfo.txt
+export OZINFO=${FIXgfs}/gsi/global_ozinfo.txt
+export SATINFO=${FIXgfs}/gsi/global_satinfo.txt
+export OBERROR=${FIXgfs}/gsi/prepobs_errtable.global
+
+if [[ ${GSI_SOILANAL} = "YES" ]]; then
+    export hofx_2m_sfcfile=".true."
+    export reducedgrid=".false." # not possible for sfc analysis, Jeff Whitaker says it's not useful anyway
+    export paranc=".false." # temporary until sfc io coded for parance (PR being prepared by T. Gichamo)
+    export CONVINFO=${FIXgfs}/gsi/global_convinfo_2mObs.txt
+    export ANAVINFO=${FIXgfs}/gsi/global_anavinfo_soilanal.l127.txt
+fi
 
 # Use experimental dumps in EMC GFS v16 parallels
 if [[ ${RUN_ENVIR} == "emc" ]]; then
   #   Set info files and prepobs.errtable.global for GFS v16 retrospective parallels
   if [[ "${PDY}${cyc}" -ge "2019021900" && "${PDY}${cyc}" -lt "2019110706" ]]; then
-    export CONVINFO=${FIXgsi}/gfsv16_historical/global_convinfo.txt.2019021900
-    export OBERROR=${FIXgsi}/gfsv16_historical/prepobs_errtable.global.2019021900
+    export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2019021900
+    export OBERROR=${FIXgfs}/gsi/gfsv16_historical/prepobs_errtable.global.2019021900
   fi
 
   #   Place GOES-15 AMVs in monitor, assimilate GOES-17 AMVs, assimilate KOMPSAT-5 gps
   if [[ "${PDY}${cyc}" -ge "2019110706" && "${PDY}${cyc}" -lt "2020040718" ]]; then
-    export CONVINFO=${FIXgsi}/gfsv16_historical/global_convinfo.txt.2019110706
-    export OBERROR=${FIXgsi}/gfsv16_historical/prepobs_errtable.global.2019110706
+    export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2019110706
+    export OBERROR=${FIXgfs}/gsi/gfsv16_historical/prepobs_errtable.global.2019110706
   fi
 
   #   Assimilate 135 (T) & 235 (uv) Canadian AMDAR observations
   if [[ "${PDY}${cyc}" -ge "2020040718" && "${PDY}${cyc}" -lt "2020052612" ]]; then
-    export CONVINFO=${FIXgsi}/gfsv16_historical/global_convinfo.txt.2020040718
-    export OBERROR=${FIXgsi}/gfsv16_historical/prepobs_errtable.global.2020040718
+    export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2020040718
+    export OBERROR=${FIXgfs}/gsi/gfsv16_historical/prepobs_errtable.global.2020040718
   fi
 
   #   Assimilate COSMIC-2
   if [[ "${PDY}${cyc}" -ge "2020052612" && "${PDY}${cyc}" -lt "2020082412" ]]; then
-    export CONVINFO=${FIXgsi}/gfsv16_historical/global_convinfo.txt.2020052612
-    export OBERROR=${FIXgsi}/gfsv16_historical/prepobs_errtable.global.2020040718
+    export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2020052612
+    export OBERROR=${FIXgfs}/gsi/gfsv16_historical/prepobs_errtable.global.2020040718
   fi
 
   #   Assimilate HDOB
   if [[ "${PDY}${cyc}" -ge "2020082412" && "${PDY}${cyc}" -lt "2020091612" ]]; then
-    export CONVINFO=${FIXgsi}/gfsv16_historical/global_convinfo.txt.2020082412
+    export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2020082412
   fi
 
   #   Assimilate Metop-C GNSSRO
   if [[ "${PDY}${cyc}" -ge "2020091612" && "${PDY}${cyc}" -lt "2021031712" ]]; then
-    export CONVINFO=${FIXgsi}/gfsv16_historical/global_convinfo.txt.2020091612
+    export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2020091612
   fi
 
   #   Assimilate DO-2 GeoOptics
   if [[ "${PDY}${cyc}" -ge "2021031712" && "${PDY}${cyc}" -lt "2021091612" ]]; then
-    export CONVINFO=${FIXgsi}/gfsv16_historical/global_convinfo.txt.2021031712
+    export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2021031712
   fi
 
   #   NOTE:
@@ -98,38 +98,38 @@ if [[ ${RUN_ENVIR} == "emc" ]]; then
   #   needed at this time.
   #   Assimilate COSMIC-2 GPS
   #   if [[ "${PDY}${cyc}" -ge "2021110312" && "${PDY}${cyc}" -lt "YYYYMMDDHH" ]]; then
-  #   export CONVINFO=$FIXgsi/gfsv16_historical/global_convinfo.txt.2021110312
+  #   export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2021110312
   #   fi
 
   #   Turn off assmilation of OMPS during period of bad data
   if [[ "${PDY}${cyc}" -ge "2020011600" && "${PDY}${cyc}" -lt "2020011806" ]]; then
-    export OZINFO=${FIXgsi}/gfsv16_historical/global_ozinfo.txt.2020011600
+    export OZINFO=${FIXgfs}/gsi/gfsv16_historical/global_ozinfo.txt.2020011600
   fi
 
 
   #   Set satinfo for start of GFS v16 parallels
   if [[ "${PDY}${cyc}" -ge "2019021900" && "${PDY}${cyc}" -lt "2019110706" ]]; then
-    export SATINFO=${FIXgsi}/gfsv16_historical/global_satinfo.txt.2019021900
+    export SATINFO=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2019021900
   fi
 
   #   Turn on assimilation of Metop-C AMSUA and MHS
   if [[ "${PDY}${cyc}" -ge "2019110706" && "${PDY}${cyc}" -lt "2020022012" ]]; then
-    export SATINFO=${FIXgsi}/gfsv16_historical/global_satinfo.txt.2019110706
+    export SATINFO=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2019110706
   fi
 
   #   Turn off assimilation of Metop-A MHS
   if [[ "${PDY}${cyc}" -ge "2020022012" && "${PDY}${cyc}" -lt "2021052118" ]]; then
-    export SATINFO=${FIXgsi}/gfsv16_historical/global_satinfo.txt.2020022012
+    export SATINFO=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2020022012
   fi
 
   #   Turn off assimilation of S-NPP CrIS
   if [[ "${PDY}${cyc}" -ge "2021052118" && "${PDY}${cyc}" -lt "2021092206" ]]; then
-    export SATINFO=${FIXgsi}/gfsv16_historical/global_satinfo.txt.2021052118
+    export SATINFO=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2021052118
   fi
 
   #   Turn off assimilation of MetOp-A IASI
   if [[ "${PDY}${cyc}" -ge "2021092206" && "${PDY}${cyc}" -lt "2021102612" ]]; then
-    export SATINFO=${FIXgsi}/gfsv16_historical/global_satinfo.txt.2021092206
+    export SATINFO=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2021092206
   fi
 
   #   NOTE:
@@ -139,8 +139,14 @@ if [[ ${RUN_ENVIR} == "emc" ]]; then
   #
   #   Turn off assmilation of all Metop-A MHS
   #   if [[ "${PDY}${cyc}" -ge "2021110312" && "${PDY}${cyc}" -lt "YYYYMMDDHH" ]]; then
-  #     export SATINFO=$FIXgsi/gfsv16_historical/global_satinfo.txt.2021110312
+  #     export SATINFO=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2021110312
   #   fi
 fi
 
+# Flag to turn on (.true.) or off (.false.) the infrared cloud and aerosol detection software
+# for AIRS, CrIS, and IASI.  Default is .false.
+export AIRS_CADS=".false."
+export CRIS_CADS=".false."
+export IASI_CADS=".false."
+
 echo "END: config.anal"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.analcalc

@@ -6,10 +6,6 @@
 echo "BEGIN: config.analcalc"
 
 # Get task specific resources
-. $EXPDIR/config.resources analcalc
-
-if [[ "$CDUMP" == "gfs" ]]; then
-   export nth_echgres=$nth_echgres_gfs
-fi
+. ${EXPDIR}/config.resources analcalc
 
 echo "END: config.analcalc"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.atmanl

@@ -5,17 +5,34 @@
 
 echo "BEGIN: config.atmanl"
 
-export CASE_ANL=${CASE}
-export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/config/
-export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/lists/gdas_prototype_3d.yaml
-export ATMVARYAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/variational/3dvar_dripcg.yaml
-export STATICB_TYPE="gsibec"
-export BERROR_YAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/berror/staticb_${STATICB_TYPE}.yaml
+export JCB_BASE_YAML="${PARMgfs}/gdas/atm/jcb-base.yaml.j2"
+export JCB_ALGO_YAML=${PARMgfs}/gdas/atm/jcb-prototype_3dvar.yaml.j2
+
+export STATICB_TYPE=gsibec
+export LOCALIZATION_TYPE="bump"
 export INTERP_METHOD='barycentric'
 
+if [[ ${DOHYBVAR} = "YES" ]]; then
+    # shellcheck disable=SC2153
+    export CASE_ANL=${CASE_ENS}
+    export BERROR_YAML="atmosphere_background_error_hybrid_${STATICB_TYPE}_${LOCALIZATION_TYPE}"
+else
+    export CASE_ANL=${CASE}
+    export BERROR_YAML="atmosphere_background_error_static_${STATICB_TYPE}"
+fi
+
+export CRTM_FIX_YAML="${PARMgfs}/gdas/atm_crtm_coeff.yaml.j2"
+export JEDI_FIX_YAML="${PARMgfs}/gdas/atm_jedi_fix.yaml.j2"
+export VAR_BKG_STAGING_YAML="${PARMgfs}/gdas/staging/atm_var_bkg.yaml.j2"
+export BERROR_STAGING_YAML="${PARMgfs}/gdas/staging/atm_berror_${STATICB_TYPE}.yaml.j2"
+export FV3ENS_STAGING_YAML="${PARMgfs}/gdas/staging/atm_var_fv3ens.yaml.j2"
+
+export layout_x_atmanl=8
+export layout_y_atmanl=8
+
 export io_layout_x=1
 export io_layout_y=1
 
-export JEDIEXE=${HOMEgfs}/exec/fv3jedi_var.x
+export JEDIEXE=${EXECgfs}/gdas.x
 
 echo "END: config.atmanl"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.atmanlfv3inc

@@ -0,0 +1,14 @@
+#! /usr/bin/env bash
+
+########## config.atmanlfv3inc ##########
+# Atm Var Analysis specific
+
+echo "BEGIN: config.atmanlfv3inc"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" atmanlfv3inc
+
+export JCB_ALGO=fv3jedi_fv3inc_variational
+export JEDIEXE=${EXECgfs}/fv3jedi_fv3inc.x
+
+echo "END: config.atmanlfv3inc"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.atmanlinit

@@ -7,4 +7,5 @@ echo "BEGIN: config.atmanlinit"
 
 # Get task specific resources
 . "${EXPDIR}/config.resources" atmanlinit
+
 echo "END: config.atmanlinit"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.atmanlvar

@@ -0,0 +1,11 @@
+#! /usr/bin/env bash
+
+########## config.atmanlvar ##########
+# Atm Var Analysis specific
+
+echo "BEGIN: config.atmanlvar"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" atmanlvar
+
+echo "END: config.atmanlvar"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.atmensanl

@@ -5,14 +5,21 @@
 
 echo "BEGIN: config.atmensanl"
 
-export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/config/
-export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/lists/lgetkf_prototype.yaml
-export ATMENSYAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/lgetkf/lgetkf.yaml
+export JCB_BASE_YAML="${PARMgfs}/gdas/atm/jcb-base.yaml.j2"
+export JCB_ALGO_YAML=${PARMgfs}/gdas/atm/jcb-prototype_lgetkf.yaml.j2
+
 export INTERP_METHOD='barycentric'
 
+export CRTM_FIX_YAML="${PARMgfs}/gdas/atm_crtm_coeff.yaml.j2"
+export JEDI_FIX_YAML="${PARMgfs}/gdas/atm_jedi_fix.yaml.j2"
+export LGETKF_BKG_STAGING_YAML="${PARMgfs}/gdas/staging/atm_lgetkf_bkg.yaml.j2"
+
+export layout_x_atmensanl=8
+export layout_y_atmensanl=8
+
 export io_layout_x=1
 export io_layout_y=1
 
-export JEDIEXE=${HOMEgfs}/exec/fv3jedi_letkf.x
+export JEDIEXE=${EXECgfs}/gdas.x
 
 echo "END: config.atmensanl"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.atmensanlfv3inc

@@ -0,0 +1,14 @@
+#! /usr/bin/env bash
+
+########## config.atmensanlfv3inc ##########
+# Atm Var Analysis specific
+
+echo "BEGIN: config.atmensanlfv3inc"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" atmensanlfv3inc
+
+export JCB_ALGO=fv3jedi_fv3inc_lgetkf
+export JEDIEXE=${EXECgfs}/fv3jedi_fv3inc.x
+
+echo "END: config.atmensanlfv3inc"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.atmensanlinit

@@ -7,4 +7,5 @@ echo "BEGIN: config.atmensanlinit"
 
 # Get task specific resources
 . "${EXPDIR}/config.resources" atmensanlinit
+
 echo "END: config.atmensanlinit"

FV3GFSwfm/rt_v17p8_ugwpv1_mynn/config.atmensanlletkf

@@ -0,0 +1,11 @@
+#! /usr/bin/env bash
+
+########## config.atmensanlletkf ##########
+# Atm Ens Analysis specific
+
+echo "BEGIN: config.atmensanlletkf"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" atmensanlletkf
+
+echo "END: config.atmensanlletkf"