Initial commit of Li's branch with Judy's changes for running under …

…Rocky

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "sorc/ufs_model.fd"]
 	path = sorc/ufs_model.fd
 	url = https://github.com/zhanglikate/ufs-weather-model
-        branch = ufs-catchem
+        branch = thom-cat
 	ignore = dirty
 [submodule "sorc/wxflow"]
   path = sorc/wxflow

FV3GFSwfm/jkh/config.aero

@@ -0,0 +1,46 @@
+#! /usr/bin/env bash
+
+# UFS-Aerosols settings
+
+# Turn off warnings about unused variables
+# shellcheck disable=SC2034
+
+
+# Path to the input data tree
+case ${machine} in
+  "HERA")
+    AERO_INPUTS_DIR="/scratch1/NCEPDEV/global/glopara/data/gocart_emissions"
+    ;;
+  "ORION" | "HERCULES")
+    AERO_INPUTS_DIR="/work2/noaa/global/wkolczyn/noscrub/global-workflow/gocart_emissions"
+    ;;
+  "S4")
+    AERO_INPUTS_DIR="/data/prod/glopara/gocart_emissions"
+    ;;
+  "WCOSS2")
+    AERO_INPUTS_DIR="/lfs/h2/emc/global/noscrub/emc.global/data/gocart_emissions"
+    ;;
+  "JET")
+    AERO_INPUTS_DIR="/lfs4/HFIP/hfv3gfs/glopara/data/gocart_emissions"
+    ;;
+  *)
+    echo "FATAL ERROR: Machine ${machine} unsupported for aerosols"
+    exit 2
+    ;;
+esac
+export AERO_INPUTS_DIR
+
+export AERO_DIAG_TABLE="${PARMgfs}/ufs/fv3/diag_table.aero"
+export AERO_FIELD_TABLE="${PARMgfs}/ufs/fv3/field_table.aero"
+# Biomass burning emission dataset. Choose from: gbbepx, qfed, none
+export AERO_EMIS_FIRE="qfed"
+# Directory containing GOCART configuration files
+export AERO_CONFIG_DIR="${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
+# Scavenging factors are set to 0 (no scavenging) if unset
+export fscav_aero="'*:0.3','so2:0.0','msa:0.0','dms:0.0','nh3:0.4','nh4:0.6','bc1:0.6','bc2:0.6','oc1:0.4','oc2:0.4','dust1:0.6','dust2:0.6', 'dust3:0.6','dust4:0.6','dust5:0.6','seas1:0.5','seas2:0.5','seas3:0.5','seas4:0.5','seas5:0.5'"
+#
+# Number of diagnostic aerosol tracers (default: 0)
+export dnats_aero=2

FV3GFSwfm/jkh/config.aeroanl

@@ -0,0 +1,31 @@
+#!/bin/bash -x
+
+########## config.aeroanl ##########
+# configuration common to all aero analysis tasks
+
+echo "BEGIN: config.aeroanl"
+
+export CASE_ANL=${CASE}
+export OBS_LIST="${PARMgfs}/gdas/aero/obs/lists/gdas_aero.yaml.j2"
+export STATICB_TYPE='identity'
+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="${EXECgfs}/fv3jedi_var.x"
+
+if [[ "${DOIAU}" == "YES" ]]; then
+  export aero_bkg_times="3,6,9"
+  export JEDIYAML="${PARMgfs}/gdas/aero/variational/3dvar_fgat_gfs_aero.yaml.j2"
+else
+  export aero_bkg_times="6"
+  export JEDIYAML="${PARMgfs}/gdas/aero/variational/3dvar_gfs_aero.yaml.j2"
+fi
+
+echo "END: config.aeroanl"

FV3GFSwfm/jkh/config.aeroanlfinal

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.aeroanlfinal ##########
+# Post Aero Analysis specific
+
+echo "BEGIN: config.aeroanlfinal"
+
+# Get task specific resources
+source "${EXPDIR}/config.resources" aeroanlfinal
+echo "END: config.aeroanlfinal"

FV3GFSwfm/jkh/config.aeroanlinit

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.aeroanlinit ##########
+# Pre Aero Analysis specific
+
+echo "BEGIN: config.aeroanlinit"
+
+# Get task specific resources
+source "${EXPDIR}/config.resources" aeroanlinit
+echo "END: config.aeroanlinit"

FV3GFSwfm/jkh/config.aeroanlrun

@@ -0,0 +1,11 @@
+#!/bin/bash -x
+
+########## config.aeroanlrun ##########
+# Aerosol Analysis specific
+
+echo "BEGIN: config.aeroanlrun"
+
+# Get task specific resources
+source "${EXPDIR}/config.resources" aeroanlrun
+
+echo "END: config.aeroanlrun"

FV3GFSwfm/jkh/config.aerosol_init

@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+
+########## config.aerosol_init ##########
+
+echo "BEGIN: config.aerosol_init"
+
+# Get task specific resources
+source $EXPDIR/config.resources aerosol_init
+
+echo "END: config.aerosol_init"

FV3GFSwfm/jkh/config.anal

@@ -0,0 +1,153 @@
+#! /usr/bin/env bash
+
+########## config.anal ##########
+# Analysis specific
+
+echo "BEGIN: config.anal"
+
+# Get task specific resources
+. ${EXPDIR}/config.resources anal
+
+if [[ ${DONST} = "YES" ]]; then
+  . ${EXPDIR}/config.nsst
+fi
+
+if [[ "${CDUMP}" = "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 [[ ${LEVS} = "128" ]]; then
+  export GRIDOPTS="nlayers(63)=1,nlayers(64)=1,"
+  export SETUP="gpstop=55,nsig_ext=45,${SETUP:-}"
+fi
+
+# Set namelist option for LETKF
+export lobsdiag_forenkf=".false."  # anal does not need to write out jacobians
+                   # set to .true. in config.eobs and config.eupd
+
+# Do not process the following datasets
+export GSNDBF=${GSNDBF:-/dev/null}
+export AMSREBF=${AMSREBF:-/dev/null}
+export SSMITBF=${SSMITBF:-/dev/null}
+export AMSR2BF=${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=${FIXgfs}/gsi/global_convinfo.txt
+export OZINFO=${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}${cyc}" -lt "2019110706" ]]; then
+    export CONVINFO=${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}${cyc}" -lt "2020040718" ]]; then
+    export CONVINFO=${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}${cyc}" -lt "2020052612" ]]; then
+    export CONVINFO=${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}${cyc}" -lt "2020082412" ]]; then
+    export CONVINFO=${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}${cyc}" -lt "2020091612" ]]; then
+    export CONVINFO=${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=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2020091612
+  fi
+
+  #   Assimilate DO-2 GeoOptics
+  if [[ "${PDY}${cyc}" -ge "2021031712" && "${PDY}${cyc}" -lt "2021091612" ]]; then
+    export CONVINFO=${FIXgfs}/gsi/gfsv16_historical/global_convinfo.txt.2021031712
+  fi
+
+  #   NOTE:
+  #   As of 2021110312, gfsv16_historical/global_convinfo.txt.2021110312 is
+  #   identical to ../global_convinfo.txt.  Thus, the logic below is not
+  #   needed at this time.
+  #   Assimilate COSMIC-2 GPS
+  #   if [[ "${PDY}${cyc}" -ge "2021110312" && "${PDY}${cyc}" -lt "YYYYMMDDHH" ]]; then
+  #   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}${cyc}" -lt "2020011806" ]]; then
+    export OZINFO=${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=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2019021900
+  fi
+
+  #   Turn on assimilation of Metop-C AMSUA and MHS
+  if [[ "${PDY}${cyc}" -ge "2019110706" && "${PDY}${cyc}" -lt "2020022012" ]]; then
+    export SATINFO=${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=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2020022012
+  fi
+
+  #   Turn off assimilation of S-NPP CrIS
+  if [[ "${PDY}${cyc}" -ge "2021052118" && "${PDY}${cyc}" -lt "2021092206" ]]; then
+    export SATINFO=${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=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2021092206
+  fi
+
+  #   NOTE:
+  #   As of 2021110312, gfsv16_historical/global_satinfo.txt.2021110312 is
+  #   identical to ../global_satinfo.txt.  Thus, the logic below is not
+  #   needed at this time
+  #
+  #   Turn off assmilation of all Metop-A MHS
+  #   if [[ "${PDY}${cyc}" -ge "2021110312" && "${PDY}${cyc}" -lt "YYYYMMDDHH" ]]; then
+  #     export SATINFO=${FIXgfs}/gsi/gfsv16_historical/global_satinfo.txt.2021110312
+  #   fi
+fi
+
+echo "END: config.anal"

FV3GFSwfm/jkh/config.analcalc

@@ -0,0 +1,15 @@
+#! /usr/bin/env bash
+
+########## config.analcalc ##########
+# GFS post-anal specific (non-diag)
+
+echo "BEGIN: config.analcalc"
+
+# Get task specific resources
+. $EXPDIR/config.resources analcalc
+
+if [[ "$CDUMP" == "gfs" ]]; then
+   export nth_echgres=$nth_echgres_gfs
+fi
+
+echo "END: config.analcalc"

FV3GFSwfm/jkh/config.analdiag

@@ -0,0 +1,11 @@
+#! /usr/bin/env bash
+
+########## config.analdiag ##########
+# GFS post-anal specific (diag)
+
+echo "BEGIN: config.analdiag"
+
+# Get task specific resources
+. $EXPDIR/config.resources analdiag
+
+echo "END: config.analdiag"

FV3GFSwfm/jkh/config.arch

@@ -0,0 +1,15 @@
+#! /usr/bin/env bash
+
+########## config.arch ##########
+# Archive specific
+
+echo "BEGIN: config.arch"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" arch
+
+export ARCH_GAUSSIAN="YES"
+export ARCH_GAUSSIAN_FHMAX=${FHMAX_GFS}
+export ARCH_GAUSSIAN_FHINC=${FHOUT_GFS}
+
+echo "END: config.arch"

FV3GFSwfm/jkh/config.atmanl

@@ -0,0 +1,33 @@
+#! /usr/bin/env bash
+
+########## config.atmanl ##########
+# configuration common to all atm var analysis tasks
+
+echo "BEGIN: config.atmanl"
+
+export OBS_LIST="${PARMgfs}/gdas/atm/obs/lists/gdas_prototype_3d.yaml.j2"
+export JEDIYAML="${PARMgfs}/gdas/atm/variational/3dvar_drpcg.yaml.j2"
+export STATICB_TYPE="gsibec"
+export INTERP_METHOD='barycentric'
+
+if [[ ${DOHYBVAR} = "YES" ]]; then
+    # shellcheck disable=SC2153
+    export CASE_ANL=${CASE_ENS}
+    export BERROR_YAML="${PARMgfs}/gdas/atm/berror/hybvar_${STATICB_TYPE}.yaml.j2"
+else
+    export CASE_ANL=${CASE}
+    export BERROR_YAML="${PARMgfs}/gdas/atm/berror/staticb_${STATICB_TYPE}.yaml.j2"
+fi
+
+export CRTM_FIX_YAML="${PARMgfs}/gdas/atm_crtm_coeff.yaml.j2"
+export JEDI_FIX_YAML="${PARMgfs}/gdas/atm_jedi_fix.yaml.j2"
+
+export layout_x_atmanl=8
+export layout_y_atmanl=8
+
+export io_layout_x=1
+export io_layout_y=1
+
+export JEDIEXE=${EXECgfs}/fv3jedi_var.x
+
+echo "END: config.atmanl"

FV3GFSwfm/jkh/config.atmanlfinal

@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+
+########## config.atmanlfinal ##########
+# Post Atm Var Analysis specific
+
+echo "BEGIN: config.atmanlfinal"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" atmanlfinal
+echo "END: config.atmanlfinal"

FV3GFSwfm/jkh/config.atmanlinit

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