From 8097bc1263bd1323c62aa7e3a9eb2d8fe7014090 Mon Sep 17 00:00:00 2001
From: albany-weiwilliam <swei@albany.edu>
Date: Sat, 16 May 2020 21:18:53 +0000
Subject: [PATCH 1/5] 1) additional regression test for the functionality of
 aerosol-radiance impacts. 2) bugfix in read_files for external aerosol files.

---
 regression/global_C96_fv3aerorad.sh | 388 ++++++++++++++++++++++++++++
 regression/regression_namelists.sh  | 181 +++++++++++++
 regression/regression_param.sh      |  33 +++
 regression/regression_var.sh        |  17 +-
 src/gsi/read_files.f90              |  22 +-
 5 files changed, 636 insertions(+), 5 deletions(-)
 create mode 100755 regression/global_C96_fv3aerorad.sh

diff --git a/regression/global_C96_fv3aerorad.sh b/regression/global_C96_fv3aerorad.sh
new file mode 100755
index 0000000000..37313aefae
--- /dev/null
+++ b/regression/global_C96_fv3aerorad.sh
@@ -0,0 +1,388 @@
+set -x
+# Set experiment name and analysis date
+
+exp=$jobname
+
+# Set the JCAP resolution which you want.
+# All resolutions use LEVS=64
+export LEVS=64
+
+# Set runtime and save directories
+tmpdir=$tmpdir/$tmpregdir/${exp}
+savdir=$savdir/outC96_fv3aerorad/${exp}
+
+# Specify GSI fixed field and data directories.
+fixcrtm=${fixcrtm:-$CRTM_FIX}
+
+# Set variables used in script
+#   CLEAN up $tmpdir when finished (YES=remove, NO=leave alone)
+#   ncp is cp replacement, currently keep as /bin/cp
+
+UNCOMPRESS=gunzip
+CLEAN=NO
+ncp=/bin/cp
+ncpl="ln -fs"
+
+# Given the analysis date, compute the date from which the
+# first guess comes.  Extract cycle and set prefix and suffix
+# for guess and observation data files
+PDY=`echo $global_C96_fv3aerorad_adate | cut -c1-8`
+cyc=`echo $global_C96_fv3aerorad_adate | cut -c9-10`
+gdate=`$ndate -06 $global_C96_fv3aerorad_adate`
+gPDY=`echo $gdate | cut -c1-8`
+gcyc=`echo $gdate | cut -c9-10`
+hha=`echo $global_C96_fv3aerorad_adate | cut -c9-10`
+hhg=`echo $gdate | cut -c9-10`
+prefix_obs=gfs.t${hha}z
+prefix_prep=$prefix_obs
+prefix_tbc=gdas1.t${hhg}z
+prefix_sfc=gfs.t${hhg}z
+prefix_atm=gfs.t${hhg}z
+prefix_aer=gfsC96.t${hhg}z
+suffix_obs=gfs.${global_C96_fv3aerorad_adate}
+suffix_bias=gdas.${gdate}
+suffix=tm00.bufr_d
+
+datobs=$global_C96_fv3aerorad_datobs/gfs.$PDY/$cyc
+datanl=$global_C96_fv3aerorad_datobs/gfs.$PDY/$cyc
+datges=$global_C96_fv3aerorad_datges/gfs.$gPDY/$gcyc
+
+# Set up $tmpdir
+rm -rf $tmpdir
+mkdir -p $tmpdir
+cd $tmpdir
+rm -rf core*
+
+
+# CO2 namelist and file decisions
+ICO2=${ICO2:-0}
+if [ $ICO2 -gt 0 ] ; then
+        # Copy co2 files to $tmpdir
+        co2dir=${CO2DIR:-$fixgsi}
+        yyyy=$(echo ${CDATE:-$global_C96_fv3aerorad_adate}|cut -c1-4)
+        rm ./global_co2_data.txt
+        co2=$co2dir/global_co2.gcmscl_$yyyy.txt
+        while [ ! -s $co2 ] ; do
+                ((yyyy-=1))
+                co2=$co2dir/global_co2.gcmscl_$yyyy.txt
+        done
+        if [ -s $co2 ] ; then
+                $ncp $co2 ./global_co2_data.txt
+        fi
+        if [ ! -s ./global_co2_data.txt ] ; then
+                echo "\./global_co2_data.txt" not created
+                exit 1
+   fi
+fi
+#CH4 file decision
+ICH4=${ICH4:-0}
+if [ $ICH4 -gt 0 ] ; then
+#        # Copy ch4 files to $tmpdir
+        ch4dir=${CH4DIR:-$fixgsi}
+        yyyy=$(echo ${CDATE:-$global_C96_fv3aerorad_adate}|cut -c1-4)
+        rm ./ch4globaldata.txt
+        ch4=$ch4dir/global_ch4_esrlctm_$yyyy.txt
+        while [ ! -s $ch4 ] ; do
+                ((yyyy-=1))
+                ch4=$ch4dir/global_ch4_esrlctm_$yyyy.txt
+        done
+        if [ -s $ch4 ] ; then
+                $ncp $ch4 ./ch4globaldata.txt
+        fi
+        if [ ! -s ./ch4globaldata.txt ] ; then
+                echo "\./ch4globaldata.txt" not created
+                exit 1
+   fi
+fi
+IN2O=${IN2O:-0}
+if [ $IN2O -gt 0 ] ; then
+#        # Copy ch4 files to $tmpdir
+        n2odir=${N2ODIR:-$fixgsi}
+        yyyy=$(echo ${CDATE:-$global_C96_fv3aerorad_adate}|cut -c1-4)
+        rm ./n2oglobaldata.txt
+        n2o=$n2odir/global_n2o_esrlctm_$yyyy.txt
+        while [ ! -s $n2o ] ; do
+                ((yyyy-=1))
+                n2o=$n2odir/global_n2o_esrlctm_$yyyy.txt
+        done
+        if [ -s $n2o ] ; then
+                $ncp $n2o ./n2oglobaldata.txt
+        fi
+        if [ ! -s ./n2oglobaldata.txt ] ; then
+                echo "\./n2oglobaldata.txt" not created
+                exit 1
+   fi
+fi
+ICO=${ICO:-0}
+if [ $ICO -gt 0 ] ; then
+#        # Copy CO files to $tmpdir
+        codir=${CODIR:-$fixgsi}
+        yyyy=$(echo ${CDATE:-$global_C96_fv3aerorad_adate}|cut -c1-4)
+        rm ./coglobaldata.txt
+        co=$codir/global_co_esrlctm_$yyyy.txt
+        while [ ! -s $co ] ; do
+                ((yyyy-=1))
+                co=$codir/global_co_esrlctm_$yyyy.txt
+        done
+        if [ -s $co ] ; then
+                $ncp $co ./coglobaldata.txt
+        fi
+        if [ ! -s ./coglobaldata.txt ] ; then
+                echo "\./coglobaldata.txt" not created
+                exit 1
+   fi
+fi
+
+# Make gsi namelist
+
+. $scripts/regression_nl_update.sh
+
+SETUP="$SETUP_update"
+GRIDOPTS="$GRIDOPTS_update"
+BKGVERR="$BKGVERR_update"
+ANBKGERR="$ANBKERR_update"
+JCOPTS="$JCOPTS_update"
+STRONGOPTS="$STRONGOPTS_update"
+OBSQC="$OBSQC_update"
+OBSINPUT="$OBSINPUT_update"
+SUPERRAD="$SUPERRAD_update"
+SINGLEOB="$SINGLEOB_update"
+
+. $scripts/regression_namelists.sh global_C96_fv3aerorad
+
+##!   l4dvar=.false.,nhr_assimilation=6,nhr_obsbin=6,
+##!   lsqrtb=.true.,lcongrad=.false.,ltlint=.true.,
+##!   idmodel=.true.,lwrtinc=.false.,
+
+cat << EOF > gsiparm.anl
+
+$gsi_namelist
+
+EOF
+
+# Set fixed files
+#   berror   = forecast model background error statistics
+#   specoef  = CRTM spectral coefficients
+#   trncoef  = CRTM transmittance coefficients
+#   emiscoef = CRTM coefficients for IR sea surface emissivity model
+#   aerocoef = CRTM coefficients for aerosol effects
+#   cldcoef  = CRTM coefficients for cloud effects
+#   satinfo  = text file with information about assimilation of brightness temperatures
+#   cloudyinfo  = text file with information about assimilation of cloudy radiance
+#   satangl  = angle dependent bias correction file (fixed in time)
+#   pcpinfo  = text file with information about assimilation of prepcipitation rates
+#   ozinfo   = text file with information about assimilation of ozone data
+#   errtable = text file with obs error for conventional data (optional)
+#   convinfo = text file with information about assimilation of conventional data
+#   bufrtable= text file ONLY needed for single obs test (oneobstest=.true.)
+#   bftab_sst= bufr table for sst ONLY needed for sst retrieval (retrieval=.true.)
+
+berror=$fixgsi/Big_Endian/global_berror.l64y194.f77
+
+emiscoef_IRwater=$fixcrtm/Nalli.IRwater.EmisCoeff.bin
+emiscoef_IRice=$fixcrtm/NPOESS.IRice.EmisCoeff.bin
+emiscoef_IRland=$fixcrtm/NPOESS.IRland.EmisCoeff.bin
+emiscoef_IRsnow=$fixcrtm/NPOESS.IRsnow.EmisCoeff.bin
+emiscoef_VISice=$fixcrtm/NPOESS.VISice.EmisCoeff.bin
+emiscoef_VISland=$fixcrtm/NPOESS.VISland.EmisCoeff.bin
+emiscoef_VISsnow=$fixcrtm/NPOESS.VISsnow.EmisCoeff.bin
+emiscoef_VISwater=$fixcrtm/NPOESS.VISwater.EmisCoeff.bin
+emiscoef_MWwater=$fixcrtm/FASTEM6.MWwater.EmisCoeff.bin
+aercoef=$fixcrtm/AerosolCoeff.bin
+cldcoef=$fixcrtm/CloudCoeff.bin
+satangl=$fixgsi/global_satangbias.txt
+scaninfo=$fixgsi/global_scaninfo.txt
+satinfo=$fixgsi/fv3aerorad_satinfo.txt
+cloudyinfo=$fixgsi/cloudy_radiance_info.txt
+convinfo=$fixgsi/global_convinfo_reg_test.txt
+anavinfo=$fixgsi/anavinfo_fv3aerorad
+aeroinfo=$fixgsi/aeroinfo_fv3aerorad
+ozinfo=$fixgsi/global_ozinfo.txt
+pcpinfo=$fixgsi/global_pcpinfo.txt
+hybens_info=$fixgsi/global_hybens_info.l64.txt
+errtable=$fixgsi/prepobs_errtable.global
+atmsbeaminfo=$fixgsi/atms_beamwidth.txt
+
+# Copy executable and fixed files to $tmpdir
+if [[ $exp == *"updat"* ]]; then
+   $ncp $gsiexec_updat  ./gsi.x
+elif [[ $exp == *"contrl"* ]]; then
+   $ncp $gsiexec_contrl ./gsi.x
+fi
+
+mkdir ./crtm_coeffs
+$ncp $berror   ./berror_stats
+$ncp $emiscoef_IRwater ./crtm_coeffs/Nalli.IRwater.EmisCoeff.bin
+$ncp $emiscoef_IRice ./crtm_coeffs/NPOESS.IRice.EmisCoeff.bin
+$ncp $emiscoef_IRsnow ./crtm_coeffs/NPOESS.IRsnow.EmisCoeff.bin
+$ncp $emiscoef_IRland ./crtm_coeffs/NPOESS.IRland.EmisCoeff.bin
+$ncp $emiscoef_VISice ./crtm_coeffs/NPOESS.VISice.EmisCoeff.bin
+$ncp $emiscoef_VISland ./crtm_coeffs/NPOESS.VISland.EmisCoeff.bin
+$ncp $emiscoef_VISsnow ./crtm_coeffs/NPOESS.VISsnow.EmisCoeff.bin
+$ncp $emiscoef_VISwater ./crtm_coeffs/NPOESS.VISwater.EmisCoeff.bin
+$ncp $emiscoef_MWwater ./crtm_coeffs/FASTEM6.MWwater.EmisCoeff.bin
+$ncp $aercoef  ./crtm_coeffs/AerosolCoeff.bin
+$ncp $cldcoef  ./crtm_coeffs/CloudCoeff.bin
+$ncp $satangl  ./satbias_angle
+$ncp $scaninfo ./scaninfo
+$ncp $satinfo  ./satinfo
+$ncp $cloudyinfo  ./cloudy_radiance_info.txt
+$ncp $pcpinfo  ./pcpinfo
+$ncp $ozinfo   ./ozinfo
+$ncp $convinfo ./convinfo
+$ncp $errtable ./errtable
+$ncp $anavinfo ./anavinfo
+$ncp $aeroinfo ./aeroinfo
+$ncp $hybens_info ./hybens_info
+$ncp $atmsbeaminfo ./atms_beamwidth.txt
+
+# Copy CRTM coefficient files
+for file in `awk '{if($1!~"!"){print $1}}' ./satinfo | sort | uniq` ;do
+    $ncp $fixcrtm/${file}.SpcCoeff.bin ./crtm_coeffs
+    $ncp $fixcrtm/${file}.TauCoeff.bin ./crtm_coeffs
+done
+
+# Copy observational data to $tmpdir
+$ncpl $datobs/${prefix_obs}.prepbufr                ./prepbufr
+$ncpl $datobs/${prefix_obs}.prepbufr.acft_profiles  ./prepbufr_profl
+$ncpl $datobs/${prefix_obs}.nsstbufr                ./nsstbufr
+$ncpl $datobs/${prefix_obs}.gpsro.${suffix}         ./gpsrobufr
+$ncpl $datobs/${prefix_obs}.satwnd.${suffix}        ./satwndbufr
+$ncpl $datobs/${prefix_obs}.spssmi.${suffix}        ./ssmirrbufr
+$ncpl $datobs/${prefix_obs}.sptrmm.${suffix}        ./tmirrbufr
+$ncpl $datobs/${prefix_obs}.osbuv8.${suffix}        ./sbuvbufr
+$ncpl $datobs/${prefix_obs}.goesfv.${suffix}        ./gsnd1bufr
+$ncpl $datobs/${prefix_obs}.1bamua.${suffix}        ./amsuabufr
+$ncpl $datobs/${prefix_obs}.1bamub.${suffix}        ./amsubbufr
+$ncpl $datobs/${prefix_obs}.1bhrs2.${suffix}        ./hirs2bufr
+$ncpl $datobs/${prefix_obs}.1bhrs3.${suffix}        ./hirs3bufr
+$ncpl $datobs/${prefix_obs}.1bhrs4.${suffix}        ./hirs4bufr
+$ncpl $datobs/${prefix_obs}.1bmhs.${suffix}         ./mhsbufr
+$ncpl $datobs/${prefix_obs}.1bmsu.${suffix}         ./msubufr
+$ncpl $datobs/${prefix_obs}.airsev.${suffix}        ./airsbufr
+$ncpl $datobs/${prefix_obs}.sevcsr.${suffix}        ./seviribufr
+$ncpl $datobs/${prefix_obs}.mtiasi.${suffix}        ./iasibufr
+$ncpl $datobs/${prefix_obs}.ssmit.${suffix}         ./ssmitbufr
+$ncpl $datobs/${prefix_obs}.ssmisu.${suffix}        ./ssmisbufr
+$ncpl $datobs/${prefix_obs}.gome.${suffix}          ./gomebufr
+$ncpl $datobs/${prefix_obs}.omi.${suffix}           ./omibufr
+$ncpl $datobs/${prefix_obs}.mls.${suffix}           ./mlsbufr
+$ncpl $datobs/${prefix_obs}.eshrs3.${suffix}        ./hirs3bufrears
+$ncpl $datobs/${prefix_obs}.esamua.${suffix}        ./amsuabufrears
+$ncpl $datobs/${prefix_obs}.esamub.${suffix}        ./amsubbufrears
+$ncpl $datobs/${prefix_obs}.atms.${suffix}          ./atmsbufr
+$ncpl $datobs/${prefix_obs}.cris.${suffix}          ./crisbufr
+$ncpl $datobs/${prefix_obs}.crisf4.${suffix}        ./crisfsbufr
+$ncpl $datobs/${prefix_obs}.syndata.tcvitals.tm00   ./tcvitl
+$ncpl $datobs/${prefix_obs}.avcsam.${suffix}        ./avhambufr
+$ncpl $datobs/${prefix_obs}.avcspm.${suffix}        ./avhpmbufr
+$ncpl $datobs/${prefix_obs}.saphir.${suffix}        ./saphirbufr
+$ncpl $datobs/${prefix_obs}.gmi1cr.${suffix}        ./gmibufr
+if [ "$debug" = ".false." ]; then
+    $ncpl $datobs/${prefix_obs}.esiasi.${suffix}        ./iasibufrears
+fi
+$ncpl $datobs/${prefix_obs}.hrs3db.${suffix}        ./hirs3bufr_db
+$ncpl $datobs/${prefix_obs}.amuadb.${suffix}        ./amsuabufr_db
+$ncpl $datobs/${prefix_obs}.amubdb.${suffix}        ./amsubbufr_db
+$ncpl $datobs/${prefix_obs}.iasidb.${suffix}        ./iasibufr_db
+$ncpl $datobs/${prefix_obs}.crisdb.${suffix}        ./crisbufr_db
+$ncpl $datobs/${prefix_obs}.atmsdb.${suffix}        ./atmsbufr_db
+$ncpl $datobs/${prefix_obs}.escris.${suffix}        ./crisbufrears
+$ncpl $datobs/${prefix_obs}.esatms.${suffix}        ./atmsbufrears
+
+
+# Copy bias correction, atmospheric and surface files
+$ncpl $datges/gfs.t18z.abias           ./satbias_in
+$ncpl $datges/gfs.t18z.abias_pc        ./satbias_pc
+$ncpl $datges/gfs.t18z.abias_air               ./aircftbias_in
+#$ncpl $datges/gfs.t18z.radstat         ./radstat.gdas
+
+if [[ "$endianness" = "Big_Endian" ]]; then
+   $ncpl $datges/${prefix_aer}.sigf03            ./aerf03
+   $ncpl $datges/${prefix_aer}.sigf06            ./aerf06
+   $ncpl $datges/${prefix_aer}.sigf09            ./aerf09
+elif [[ "$endianness" = "Little_Endian" ]]; then
+   $ncpl $datges/${prefix_aer}.sigf03.le         ./aerf03
+   $ncpl $datges/${prefix_aer}.sigf06.le         ./aerf06
+   $ncpl $datges/${prefix_aer}.sigf09.le         ./aerf09
+fi
+
+if [[ "$endianness" = "Big_Endian" ]]; then
+   $ncpl $datges/${prefix_sfc}.sfcf003.${sfcsuffix}            ./sfcf03
+   $ncpl $datges/${prefix_sfc}.sfcf006.${sfcsuffix}            ./sfcf06
+   $ncpl $datges/${prefix_sfc}.sfcf009.${sfcsuffix}            ./sfcf09
+elif [[ "$endianness" = "Little_Endian" ]]; then
+   $ncpl $datges/${prefix_sfc}.sfcf03.le         ./sfcf03
+   $ncpl $datges/${prefix_sfc}.sfcf06.le         ./sfcf06
+   $ncpl $datges/${prefix_sfc}.sfcf09.le         ./sfcf09
+fi
+
+if [[ "$endianness" = "Big_Endian" ]]; then
+   $ncpl $datges/${prefix_atm}.atmf003.${atmsuffix}        ./sigf03
+   $ncpl $datges/${prefix_atm}.atmf006.${atmsuffix}        ./sigf06
+   $ncpl $datges/${prefix_atm}.atmf009.${atmsuffix}        ./sigf09
+elif [[ "$endianness" = "Little_Endian" ]]; then
+   $ncpl $datges/${prefix_atm}.sigf03.le     ./sigf03
+   $ncpl $datges/${prefix_atm}.sigf06.le     ./sigf06
+   $ncpl $datges/${prefix_atm}.sigf09.le     ./sigf09
+fi
+
+# Run GSI
+cd $tmpdir
+echo "run gsi now"
+eval "$APRUN $tmpdir/gsi.x > stdout 2>&1"
+rc=$?
+exit $rc
+
+
+# Loop over first and last outer loops to generate innovation
+# diagnostic files for indicated observation types (groups)
+#
+# NOTE:  Since we set miter=2 in GSI namelist SETUP, outer
+#        loop 03 will contain innovations with respect to 
+#        the analysis.  Creation of o-a innovation files
+#        is triggered by write_diag(3)=.true.  The setting
+#        write_diag(1)=.true. turns on creation of o-g
+#        innovation files.
+#
+
+
+echo "Time before diagnostic loop is `date` "
+cd $tmpdir
+loops="01 03"
+for loop in $loops; do
+
+case $loop in
+  01) string=ges;;
+  03) string=anl;;
+   *) string=$loop;;
+esac
+
+#  Collect diagnostic files for obs types (groups) below
+   listall="modis_aod_terra modis_aod_aqua"
+   for type in $listall; do
+      count=`ls dir.*/${type}_${loop}* | wc -l`
+      if [[ $count -gt 0 ]]; then
+         cat dir.*/${type}_${loop}* > diag_${type}_${string}.${global_T62_adate}
+         compress diag_${type}_${string}.${global_T62_adate}
+         $ncp diag_${type}_${string}.${global_T62_adate}.Z $savdir/
+      fi
+   done
+done
+echo "Time after diagnostic loop is `date` "
+
+
+
+# If requested, clean up $tmpdir
+if [[ "$CLEAN" = "YES" ]];then
+   if [[ $rc -eq 0 ]];then
+      rm -rf $tmpdir
+      cd $tmpdir
+      cd ../
+      rmdir $tmpdir
+   fi
+fi
+
+
+# End of script
+exit
diff --git a/regression/regression_namelists.sh b/regression/regression_namelists.sh
index b80672e192..57252a4f22 100755
--- a/regression/regression_namelists.sh
+++ b/regression/regression_namelists.sh
@@ -2711,6 +2711,187 @@ OBS_INPUT::
   obhourset=0.,
  /
 
+ &NST
+  nst_gsi=3,
+  nstinfo=4,fac_dtl=1,fac_tsl=1,zsea1=0,zsea2=0,
+ /"
+;;
+
+    global_C96_fv3aerorad)
+
+# Define namelist for global run (aerosol analysis)
+
+export gsi_namelist="
+ &SETUP
+  niter(1)=100,niter(2)=100
+  niter_no_qc(1)=50,niter_no_qc(2)=0,
+  write_diag(1)=.true.,write_diag(2)=.false.,write_diag(3)=.true.,
+  qoption=2,
+  gencode=82,factqmin=0.5,factqmax=0.005,deltim=1200,
+  iguess=-1,
+  tzr_qc=1,
+  oneobtest=.false.,retrieval=.false.,l_foto=.false.,
+  use_pbl=.false.,use_compress=.true.,nsig_ext=12,gpstop=50.,
+  use_gfs_nemsio=.true.,sfcnst_comb=.true.,
+  use_readin_anl_sfcmask=.false.,
+  lrun_subdirs=.true.,
+  crtm_coeffs_path='./crtm_coeffs/',
+  newpc4pred=.true.,adp_anglebc=.true.,angord=4,passive_bc=.true.,use_edges=.false.,
+  diag_precon=.true.,step_start=1.e-3,emiss_bc=.true.,nhr_obsbin=3,
+  cwoption=3,imp_physics=11,lupp=.true.,
+  netcdf_diag=.true.,binary_diag=.false.,
+  lobsdiag_forenkf=.false.,
+  diag_aero=.false., use_fv3_aero=.true.,offtime_data=.true.,
+  diag_rad=.true.,diag_pcp=.false.,diag_conv=.true.,diag_ozone=.false.,
+ /
+
+ &GRIDOPTS
+  JCAP_B=190,JCAP=190,NLAT=194,NLON=384,nsig=64,
+  regional=.false.,nlayers(63)=3,nlayers(64)=6,
+ /
+
+ &BKGERR
+  vs=0.7,
+  hzscl=1.7,0.8,0.5,
+  hswgt=0.45,0.3,0.25,
+  bw=0.0,norsp=4,
+  bkgv_flowdep=.true.,bkgv_rewgtfct=1.5,
+  bkgv_write=.false.,
+  cwcoveqqcov=.false.,
+ /
+
+ &ANBKGERR
+  anisotropic=.false.,
+ /
+
+ &JCOPTS
+  ljcdfi=.false.,alphajc=0.0,ljcpdry=.true.,bamp_jcpdry=5.0e7,
+ /
+
+ &STRONGOPTS
+  tlnmc_option=2,nstrong=1,nvmodes_keep=8,period_max=6.,period_width=1.5,
+ /
+
+ &OBSQC
+  dfact=0.75,dfact1=3.0,noiqc=.true.,oberrflg=.false.,c_varqc=0.02,
+  use_poq7=.true.,qc_noirjaco3_pole=.true.,vqc=.true.,
+  aircraft_t_bc=.false.,biaspredt=1000.0,upd_aircraft=.true.,cleanup_tail=.true.,
+ /
+
+ &OBS_INPUT
+  dmesh(1)=145.0,dmesh(2)=150.0,dmesh(3)=100.0,time_window_max=3.0,
+ /
+
+OBS_INPUT::
+!  dfile          dtype       dplat       dsis                dval    dthin dsfcalc
+   prepbufr       ps          null      ps                   0.0     0     0
+   prepbufr       t           null      t                    0.0     0     0
+   prepbufr       q           null      q                    0.0     0     0
+   prepbufr       pw          null      pw                   0.0     0     0
+   satwndbufr     uv          null      uv                   0.0     0     0
+   prepbufr       uv          null      uv                   0.0     0     0
+   prepbufr       spd         null      spd                  0.0     0     0
+   prepbufr       dw          null      dw                   0.0     0     0
+   radarbufr      rw          null      l3rw                 0.0     0     0
+   l2rwbufr       rw          null      l2rw                 0.0     0     0
+   nsstbufr       sst         nsst      sst                  0.0     0     0
+   gpsrobufr      $gps_dtype  null      gps                  0.0     0     0
+   ssmirrbufr     pcp_ssmi    dmsp      pcp_ssmi             0.0    -1     0
+   tmirrbufr      pcp_tmi     trmm      pcp_tmi              0.0    -1     0
+   sbuvbufr       sbuv2       n16       sbuv8_n16            0.0     0     0
+   sbuvbufr       sbuv2       n17       sbuv8_n17            0.0     0     0
+   sbuvbufr       sbuv2       n18       sbuv8_n18            0.0     0     0
+   hirs3bufr      hirs3       n17       hirs3_n17            0.0     1     1
+   hirs4bufr      hirs4       metop-a   hirs4_metop-a        0.0     1     1
+   gimgrbufr      goes_img    g11       imgr_g11             0.0     1     0
+   gimgrbufr      goes_img    g12       imgr_g12             0.0     1     0
+   airsbufr       airs        aqua      airs_aqua            0.0     1     1
+   amsuabufr      amsua       n15       amsua_n15            0.0     1     1
+   amsuabufr      amsua       n18       amsua_n18            0.0     1     1
+   amsuabufr      amsua       metop-a   amsua_metop-a        0.0     1     1
+   airsbufr       amsua       aqua      amsua_aqua           0.0     1     1
+   amsubbufr      amsub       n17       amsub_n17            0.0     1     1
+   mhsbufr        mhs         n18       mhs_n18              0.0     1     1
+   mhsbufr        mhs         metop-a   mhs_metop-a          0.0     1     1
+   ssmitbufr      ssmi        f15       ssmi_f15             0.0     1     0
+   amsrebufr      amsre_low   aqua      amsre_aqua           0.0     1     0
+   amsrebufr      amsre_mid   aqua      amsre_aqua           0.0     1     0
+   amsrebufr      amsre_hig   aqua      amsre_aqua           0.0     1     0
+   ssmisbufr      ssmis_las   f16       ssmis_f16            0.0     1     0
+   ssmisbufr      ssmis_uas   f16       ssmis_f16            0.0     1     0
+   ssmisbufr      ssmis_img   f16       ssmis_f16            0.0     1     0
+   ssmisbufr      ssmis_env   f16       ssmis_f16            0.0     1     0
+   gsnd1bufr      sndrd1      g12       sndrD1_g12           0.0     1     0
+   gsnd1bufr      sndrd2      g12       sndrD2_g12           0.0     1     0
+   gsnd1bufr      sndrd3      g12       sndrD3_g12           0.0     1     0
+   gsnd1bufr      sndrd4      g12       sndrD4_g12           0.0     1     0
+   gsnd1bufr      sndrd1      g11       sndrD1_g11           0.0     1     0
+   gsnd1bufr      sndrd2      g11       sndrD2_g11           0.0     1     0
+   gsnd1bufr      sndrd3      g11       sndrD3_g11           0.0     1     0
+   gsnd1bufr      sndrd4      g11       sndrD4_g11           0.0     1     0
+   gsnd1bufr      sndrd1      g13       sndrD1_g13           0.0     1     0
+   gsnd1bufr      sndrd2      g13       sndrD2_g13           0.0     1     0
+   gsnd1bufr      sndrd3      g13       sndrD3_g13           0.0     1     0
+   gsnd1bufr      sndrd4      g13       sndrD4_g13           0.0     1     0
+   iasibufr       iasi        metop-a   iasi_metop-a         0.0     1     1
+   gomebufr       gome        metop-a   gome_metop-a         0.0     2     0
+   omibufr        omi         aura      omi_aura             0.0     2     0
+   sbuvbufr       sbuv2       n19       sbuv8_n19            0.0     0     0
+   hirs4bufr      hirs4       n19       hirs4_n19            0.0     1     1
+   amsuabufr      amsua       n19       amsua_n19            0.0     1     1
+   mhsbufr        mhs         n19       mhs_n19              0.0     1     1
+   tcvitl         tcp         null      tcp                  0.0     0     0
+   seviribufr     seviri      m08       seviri_m08           0.0     1     0
+   seviribufr     seviri      m09       seviri_m09           0.0     1     0
+   seviribufr     seviri      m10       seviri_m10           0.0     1     0
+   seviribufr     seviri      m11       seviri_m11           0.0     1     0
+   hirs4bufr      hirs4       metop-b   hirs4_metop-b        0.0     1     0
+   amsuabufr      amsua       metop-b   amsua_metop-b        0.0     1     0
+   mhsbufr        mhs         metop-b   mhs_metop-b          0.0     1     0
+   iasibufr       iasi        metop-b   iasi_metop-b         0.0     1     0
+   gomebufr       gome        metop-b   gome_metop-b         0.0     2     0
+   atmsbufr       atms        npp       atms_npp             0.0     1     0
+   atmsbufr       atms        n20       atms_n20             0.0     1     0
+   crisbufr       cris        npp       cris_npp             0.0     1     0
+   crisfsbufr     cris-fsr    npp       cris-fsr_npp         0.0     1     0
+   crisfsbufr     cris-fsr    n20       cris-fsr_n20         0.0     1     0
+   mlsbufr        mls30       aura      mls30_aura           0.0     0     0
+   oscatbufr      uv          null      uv                   0.0     0     0
+   ompsnpbufr     ompsnp      npp       ompsnp_npp           0.0     0     0
+   ompstcbufr     ompstc8     npp       ompstc8_npp          0.0     2     0
+   abibufr        abi         g16       abi_g16              0.0     1     0
+::
+
+ &SUPEROB_RADAR
+ /
+
+ &LAG_DATA
+ /
+
+ &HYBRID_ENSEMBLE
+  l_hyb_ens=.false.,
+  generate_ens=.false.,
+  beta_s0=0.125,readin_beta=.false.,
+  s_ens_h=800.,s_ens_v=-0.8,readin_localization=.true.,
+  aniso_a_en=.false.,oz_univ_static=.false.,uv_hyb_ens=.true.,
+  ensemble_path='./ensemble_data/',
+  ens_fast_read=.true.,
+ /
+
+ &RAPIDREFRESH_CLDSURF
+  dfi_radar_latent_heat_time_period=30.0,
+ /
+
+ &CHEM
+  lread_ext_aerosol=.true.,
+ /
+
+ &SINGLEOB_TEST
+  maginnov=0.1,magoberr=0.1,oneob_type='t',
+  oblat=45.,oblon=180.,obpres=1000.,obdattim=2019061718,
+  obhourset=0.,
+ /
+
  &NST
   nst_gsi=3,
   nstinfo=4,fac_dtl=1,fac_tsl=1,zsea1=0,zsea2=0,
diff --git a/regression/regression_param.sh b/regression/regression_param.sh
index ba6aeb8917..8083020e55 100755
--- a/regression/regression_param.sh
+++ b/regression/regression_param.sh
@@ -602,6 +602,39 @@ case $regtest in
 
     ;;
 
+   global_C96_fv3aerorad)
+
+        if [[ "$machine" = "Hera" ]]; then
+            topts[1]="0:45:00" ; popts[1]="20/8/" ; ropts[1]="/1"
+            topts[2]="0:45:00" ; popts[2]="20/8/" ; ropts[2]="/2"
+        elif [[ "$machine" = "Cheyenne" ]]; then
+            topts[1]="0:15:00" ; popts[1]="16/2/" ; ropts[1]="/1"
+            topts[2]="0:15:00" ; popts[2]="16/4/" ; ropts[2]="/2"
+        elif [[ "$machine" = "WCOSS" ]]; then
+            topts[1]="0:15:00" ; popts[1]="16/2/" ; ropts[1]="/1"
+            topts[2]="0:15:00" ; popts[2]="16/4/" ; ropts[2]="/2"
+        elif [[ "$machine" = "WCOSS_C" ]]; then
+            topts[1]="0:15:00" ; popts[1]="36/4/" ; ropts[1]="1024/1"  # sub_wcoss_c popts are "#tasks/#nodes/"
+            topts[2]="0:15:00" ; popts[2]="72/8/" ; ropts[2]="1024/2"
+        elif [[ "$machine" = "WCOSS_D" ]]; then
+           topts[1]="0:15:00" ; popts[1]="28/2/" ; ropts[1]="/1"
+           topts[2]="0:15:00" ; popts[2]="28/4/" ; ropts[2]="/2"
+        elif [[ "$machine" = "Discover" ]]; then
+           topts[1]="0:30:00" ; popts[1]="20/4"  ; ropts[1]="/1"
+           topts[2]="0:30:00" ; popts[2]="40/2"  ; ropts[2]="/2"
+        elif [[ "$machine" = "s4" ]]; then
+           topts[1]="0:25:00" ; popts[1]="36/2/" ; ropts[1]="/1"
+           topts[2]="0:25:00" ; popts[2]="72/3/" ; ropts[2]="/2"
+        fi
+
+        if [ "$debug" = ".true." ] ; then
+           topts[1]="1:00:00"
+        fi
+
+        scaling[1]=10; scaling[2]=8; scaling[3]=4
+
+    ;;
+
     *) # EXIT out for unresolved regtest
 
         echo "unknown $regtest"
diff --git a/regression/regression_var.sh b/regression/regression_var.sh
index 1017fb4e9a..db6a09bef0 100755
--- a/regression/regression_var.sh
+++ b/regression/regression_var.sh
@@ -111,6 +111,8 @@ case $machine in
      export noscrub="/scratch1/NCEPDEV/global/$LOGNAME/noscrub"
     elif [ -d /scratch2/BMC/gsienkf/$LOGNAME ]; then
      export noscrub="/scratch2/BMC/gsienkf/$LOGNAME"
+   elif [ -d /scratch1/BMC/gsd-fv3-dev/$LOGNAME ]; then
+     export noscrub="/scratch1/BMC/gsd-fv3-dev/$LOGNAME/DTCVisitor/noscrub"
    fi
    export group="global"
    export queue="batch"
@@ -118,15 +120,18 @@ case $machine in
      export basedir="/scratch1/NCEPDEV/da/$LOGNAME/git/gsi"
    fi 
 
-   export ptmp="/scratch1/NCEPDEV/stmp2/$LOGNAME/$ptmpName"
+   #export ptmp="/scratch1/NCEPDEV/stmp2/$LOGNAME/$ptmpName"
+   export ptmp="/scratch1/BMC/gsd-fv3-dev/Shih-wei.Wei/DTCVisitor/$ptmpName"
 
    export fixcrtm="/scratch1/NCEPDEV/da/Michael.Lueken/CRTM_REL-2.2.3/crtm_v2.2.3/fix_update"
-   export casesdir="/scratch1/NCEPDEV/da/Michael.Lueken/noscrub/CASES"
-   export ndate=$NDATE
+   #export casesdir="/scratch1/NCEPDEV/da/Michael.Lueken/noscrub/CASES"
+   export casesdir="/scratch1/BMC/gsd-fv3-dev/Shih-wei.Wei/DTCVisitor/casedir"
+   export ndate=${NDATE:-/scratch2/NCEPDEV/nwprod/NCEPLIBS/utils/prod_util.v1.1.0/exec/ndate}
 
    export check_resource="no"
 
-   export accnt="da-cpu"
+   #export accnt="da-cpu"
+   export accnt="gsd-fv3-dev"
 
    #  On Hera, there are no scrubbers to remove old contents from stmp* directories.
    #  After completion of regression tests, will remove the regression test subdirecories
@@ -232,6 +237,7 @@ export rtma_adate="2020022420"
 export hwrf_nmm_adate="2012102812"
 export fv3_netcdf_adate="2017030100"
 export global_C96_fv3aero_adate="2019062200"
+export global_C96_fv3aerorad_adate="2019062200"
 
 # Paths for canned case data.
 export global_T62_obs="$casesdir/global/sigmap/$global_T62_adate"
@@ -268,6 +274,8 @@ export fv3_netcdf_obs="$casesdir/regional/fv3_netcdf/$fv3_netcdf_adate"
 export fv3_netcdf_ges="$casesdir/regional/fv3_netcdf/$fv3_netcdf_adate"
 export global_C96_fv3aero_obs="$casesdir/global/fv3/$global_C96_fv3aero_adate"
 export global_C96_fv3aero_ges="$casesdir/global/fv3/$global_C96_fv3aero_adate"
+export global_C96_fv3aerorad_obs="$casesdir/global/fv3/$global_C96_fv3aerorad_adate"
+export global_C96_fv3aerorad_ges="$casesdir/global/fv3/$global_C96_fv3aerorad_adate"
 
 # Define type of GPSRO data to be assimilated (refractivity or bending angle)
 export gps_dtype="gps_bnd"
@@ -276,6 +284,7 @@ export gps_dtype="gps_bnd"
 export regression_vfydir="$noscrub/regression"
 
 # Define debug variable - If you want to run the debug tests, set this variable to .true.  Default is .false.
+#export debug=".true."
 export debug=".false."
 
 # Define parameters for global_T62_3d4dvar and global_T62_4dvar
diff --git a/src/gsi/read_files.f90 b/src/gsi/read_files.f90
index 5722ede1ad..1595800c28 100644
--- a/src/gsi/read_files.f90
+++ b/src/gsi/read_files.f90
@@ -153,6 +153,7 @@ subroutine read_files(mype)
   nfldsig=0
   nfldsfc=0
   nfldnst=0
+  nfldaer=0
   iamana=0
 
 ! Check for non-zero length atm, sfc, aer, and nst files on single task
@@ -212,6 +213,24 @@ subroutine read_files(mype)
         allocate(time_nst(nfldnst,2))
      end if
 
+     if(lread_ext_aerosol) then
+!    Check for aer files with non-zero length
+        do i=0,max_file-1
+           write(filename,'(''aerf'',i2.2)')i
+           call gsi_inquire(lenbytes,fexist,filename,mype)
+           if(fexist .and. lenbytes>0) then
+              nfldaer=nfldaer+1
+              irec(nfldaer,4) = i
+           end if
+        enddo
+        if(nfldaer==0) then
+           write(6,*)'READ_FILES: ***ERROR*** NO aer fields; aborting'
+           call stop2(170)
+        end if
+
+        allocate(time_aer(nfldaer,2))
+     end if
+
 ! Let a single task query the guess files.
 
 !    Convert analysis time to minutes relative to fixed date
@@ -434,6 +453,7 @@ subroutine read_files(mype)
 !    for external aerosol files only
 !    Check for consistency of times from aer guess files.
      if ( lread_ext_aerosol ) then
+        write(6,*) 'READ_FILES: nfldaer ', nfldaer
         iwan=0
         do i=1,nfldaer
            write(filename,'(''aerf'',i2.2)')irec(i,4)
@@ -468,7 +488,7 @@ subroutine read_files(mype)
            idate5(3)=idateg(3); idate5(4)=idateg(1); idate5(5)=0
            call w3fs21(idate5,nmings)
            nming2=nmings+60*hourg
-           write(6,*)'READ_FILES:  aer guess file, hourg, idateg, nming2 ',hourg,idateg,nming2
+           write(6,*)'READ_FILES:  aer guess file',filename,hourg,idateg,nming2
            t4dv=real((nming2-iwinbgn),r_kind)*r60inv
            if (l4dvar.or.l4densvar) then
               if (t4dv<zero .OR. t4dv>winlen) cycle

From 701e1c3b0065c849e6715b9aaa35d6a7ce89c8f1 Mon Sep 17 00:00:00 2001
From: albany-weiwilliam <swei@albany.edu>
Date: Wed, 1 Jul 2020 19:27:41 +0000
Subject: [PATCH 2/5] Update for rgtest:fv3aerorad: anavinfo and satinfo, shell
 scripts under regression

---
 fix                                 |   2 +-
 regression/global_C96_fv3aerorad.sh | 100 ++++++++--------------------
 regression/regression_namelists.sh  |  66 +-----------------
 3 files changed, 30 insertions(+), 138 deletions(-)

diff --git a/fix b/fix
index 6c7d9f470f..53812885c0 160000
--- a/fix
+++ b/fix
@@ -1 +1 @@
-Subproject commit 6c7d9f470fba03cfc77850b9a5e49295ceb2f4b7
+Subproject commit 53812885c084fd2de26e53f3eeb482cc3c87bcd2
diff --git a/regression/global_C96_fv3aerorad.sh b/regression/global_C96_fv3aerorad.sh
index 37313aefae..c2149067c4 100755
--- a/regression/global_C96_fv3aerorad.sh
+++ b/regression/global_C96_fv3aerorad.sh
@@ -36,16 +36,14 @@ hhg=`echo $gdate | cut -c9-10`
 prefix_obs=gfs.t${hha}z
 prefix_prep=$prefix_obs
 prefix_tbc=gdas1.t${hhg}z
-prefix_sfc=gfs.t${hhg}z
-prefix_atm=gfs.t${hhg}z
+prefix_sfc=gfsC96.t${hhg}z
+prefix_atm=gfsC96.t${hhg}z
 prefix_aer=gfsC96.t${hhg}z
-suffix_obs=gfs.${global_C96_fv3aerorad_adate}
-suffix_bias=gdas.${gdate}
-suffix=tm00.bufr_d
+suffix_obs=tm00.bufr_d
 
-datobs=$global_C96_fv3aerorad_datobs/gfs.$PDY/$cyc
-datanl=$global_C96_fv3aerorad_datobs/gfs.$PDY/$cyc
-datges=$global_C96_fv3aerorad_datges/gfs.$gPDY/$gcyc
+datobs=$global_C96_fv3aerorad_obs/gfs.$PDY/$cyc
+datanl=$global_C96_fv3aerorad_obs/gfs.$PDY/$cyc
+datges=$global_C96_fv3aerorad_ges/gfs.$gPDY/$gcyc
 
 # Set up $tmpdir
 rm -rf $tmpdir
@@ -196,7 +194,6 @@ satinfo=$fixgsi/fv3aerorad_satinfo.txt
 cloudyinfo=$fixgsi/cloudy_radiance_info.txt
 convinfo=$fixgsi/global_convinfo_reg_test.txt
 anavinfo=$fixgsi/anavinfo_fv3aerorad
-aeroinfo=$fixgsi/aeroinfo_fv3aerorad
 ozinfo=$fixgsi/global_ozinfo.txt
 pcpinfo=$fixgsi/global_pcpinfo.txt
 hybens_info=$fixgsi/global_hybens_info.l64.txt
@@ -246,85 +243,44 @@ done
 $ncpl $datobs/${prefix_obs}.prepbufr                ./prepbufr
 $ncpl $datobs/${prefix_obs}.prepbufr.acft_profiles  ./prepbufr_profl
 $ncpl $datobs/${prefix_obs}.nsstbufr                ./nsstbufr
-$ncpl $datobs/${prefix_obs}.gpsro.${suffix}         ./gpsrobufr
-$ncpl $datobs/${prefix_obs}.satwnd.${suffix}        ./satwndbufr
-$ncpl $datobs/${prefix_obs}.spssmi.${suffix}        ./ssmirrbufr
-$ncpl $datobs/${prefix_obs}.sptrmm.${suffix}        ./tmirrbufr
-$ncpl $datobs/${prefix_obs}.osbuv8.${suffix}        ./sbuvbufr
-$ncpl $datobs/${prefix_obs}.goesfv.${suffix}        ./gsnd1bufr
-$ncpl $datobs/${prefix_obs}.1bamua.${suffix}        ./amsuabufr
-$ncpl $datobs/${prefix_obs}.1bamub.${suffix}        ./amsubbufr
-$ncpl $datobs/${prefix_obs}.1bhrs2.${suffix}        ./hirs2bufr
-$ncpl $datobs/${prefix_obs}.1bhrs3.${suffix}        ./hirs3bufr
-$ncpl $datobs/${prefix_obs}.1bhrs4.${suffix}        ./hirs4bufr
-$ncpl $datobs/${prefix_obs}.1bmhs.${suffix}         ./mhsbufr
-$ncpl $datobs/${prefix_obs}.1bmsu.${suffix}         ./msubufr
-$ncpl $datobs/${prefix_obs}.airsev.${suffix}        ./airsbufr
-$ncpl $datobs/${prefix_obs}.sevcsr.${suffix}        ./seviribufr
-$ncpl $datobs/${prefix_obs}.mtiasi.${suffix}        ./iasibufr
-$ncpl $datobs/${prefix_obs}.ssmit.${suffix}         ./ssmitbufr
-$ncpl $datobs/${prefix_obs}.ssmisu.${suffix}        ./ssmisbufr
-$ncpl $datobs/${prefix_obs}.gome.${suffix}          ./gomebufr
-$ncpl $datobs/${prefix_obs}.omi.${suffix}           ./omibufr
-$ncpl $datobs/${prefix_obs}.mls.${suffix}           ./mlsbufr
-$ncpl $datobs/${prefix_obs}.eshrs3.${suffix}        ./hirs3bufrears
-$ncpl $datobs/${prefix_obs}.esamua.${suffix}        ./amsuabufrears
-$ncpl $datobs/${prefix_obs}.esamub.${suffix}        ./amsubbufrears
-$ncpl $datobs/${prefix_obs}.atms.${suffix}          ./atmsbufr
-$ncpl $datobs/${prefix_obs}.cris.${suffix}          ./crisbufr
-$ncpl $datobs/${prefix_obs}.crisf4.${suffix}        ./crisfsbufr
-$ncpl $datobs/${prefix_obs}.syndata.tcvitals.tm00   ./tcvitl
-$ncpl $datobs/${prefix_obs}.avcsam.${suffix}        ./avhambufr
-$ncpl $datobs/${prefix_obs}.avcspm.${suffix}        ./avhpmbufr
-$ncpl $datobs/${prefix_obs}.saphir.${suffix}        ./saphirbufr
-$ncpl $datobs/${prefix_obs}.gmi1cr.${suffix}        ./gmibufr
-if [ "$debug" = ".false." ]; then
-    $ncpl $datobs/${prefix_obs}.esiasi.${suffix}        ./iasibufrears
-fi
-$ncpl $datobs/${prefix_obs}.hrs3db.${suffix}        ./hirs3bufr_db
-$ncpl $datobs/${prefix_obs}.amuadb.${suffix}        ./amsuabufr_db
-$ncpl $datobs/${prefix_obs}.amubdb.${suffix}        ./amsubbufr_db
-$ncpl $datobs/${prefix_obs}.iasidb.${suffix}        ./iasibufr_db
-$ncpl $datobs/${prefix_obs}.crisdb.${suffix}        ./crisbufr_db
-$ncpl $datobs/${prefix_obs}.atmsdb.${suffix}        ./atmsbufr_db
-$ncpl $datobs/${prefix_obs}.escris.${suffix}        ./crisbufrears
-$ncpl $datobs/${prefix_obs}.esatms.${suffix}        ./atmsbufrears
-
+$ncpl $datobs/${prefix_obs}.airsev.${suffix_obs}        ./airsbufr
+$ncpl $datobs/${prefix_obs}.mtiasi.${suffix_obs}        ./iasibufr
+$ncpl $datobs/${prefix_obs}.cris.${suffix_obs}          ./crisbufr
 
 # Copy bias correction, atmospheric and surface files
 $ncpl $datges/gfs.t18z.abias           ./satbias_in
 $ncpl $datges/gfs.t18z.abias_pc        ./satbias_pc
-$ncpl $datges/gfs.t18z.abias_air               ./aircftbias_in
+$ncpl $datges/gfs.t18z.abias_air       ./aircftbias_in
 #$ncpl $datges/gfs.t18z.radstat         ./radstat.gdas
 
 if [[ "$endianness" = "Big_Endian" ]]; then
-   $ncpl $datges/${prefix_aer}.sigf03            ./aerf03
-   $ncpl $datges/${prefix_aer}.sigf06            ./aerf06
-   $ncpl $datges/${prefix_aer}.sigf09            ./aerf09
+   ln -s -f $datges/${prefix_sfc}.sfcf03            ./sfcf03
+   ln -s -f $datges/${prefix_sfc}.sfcf06            ./sfcf06
+   ln -s -f $datges/${prefix_sfc}.sfcf09            ./sfcf09
 elif [[ "$endianness" = "Little_Endian" ]]; then
-   $ncpl $datges/${prefix_aer}.sigf03.le         ./aerf03
-   $ncpl $datges/${prefix_aer}.sigf06.le         ./aerf06
-   $ncpl $datges/${prefix_aer}.sigf09.le         ./aerf09
+   ln -s -f $datges/${prefix_sfc}.sfcf03.le         ./sfcf03
+   ln -s -f $datges/${prefix_sfc}.sfcf06.le         ./sfcf06
+   ln -s -f $datges/${prefix_sfc}.sfcf09.le         ./sfcf09
 fi
 
 if [[ "$endianness" = "Big_Endian" ]]; then
-   $ncpl $datges/${prefix_sfc}.sfcf003.${sfcsuffix}            ./sfcf03
-   $ncpl $datges/${prefix_sfc}.sfcf006.${sfcsuffix}            ./sfcf06
-   $ncpl $datges/${prefix_sfc}.sfcf009.${sfcsuffix}            ./sfcf09
+   ln -s -f $datges/${prefix_atm}.sigf03        ./sigf03
+   ln -s -f $datges/${prefix_atm}.sigf06        ./sigf06
+   ln -s -f $datges/${prefix_atm}.sigf09        ./sigf09
 elif [[ "$endianness" = "Little_Endian" ]]; then
-   $ncpl $datges/${prefix_sfc}.sfcf03.le         ./sfcf03
-   $ncpl $datges/${prefix_sfc}.sfcf06.le         ./sfcf06
-   $ncpl $datges/${prefix_sfc}.sfcf09.le         ./sfcf09
+   ln -s -f $datges/${prefix_atm}.sigf03.le     ./sigf03
+   ln -s -f $datges/${prefix_atm}.sigf06.le     ./sigf06
+   ln -s -f $datges/${prefix_atm}.sigf09.le     ./sigf09
 fi
 
 if [[ "$endianness" = "Big_Endian" ]]; then
-   $ncpl $datges/${prefix_atm}.atmf003.${atmsuffix}        ./sigf03
-   $ncpl $datges/${prefix_atm}.atmf006.${atmsuffix}        ./sigf06
-   $ncpl $datges/${prefix_atm}.atmf009.${atmsuffix}        ./sigf09
+   $ncpl $datges/${prefix_aer}.sigf03            ./aerf03
+   $ncpl $datges/${prefix_aer}.sigf06            ./aerf06
+   $ncpl $datges/${prefix_aer}.sigf09            ./aerf09
 elif [[ "$endianness" = "Little_Endian" ]]; then
-   $ncpl $datges/${prefix_atm}.sigf03.le     ./sigf03
-   $ncpl $datges/${prefix_atm}.sigf06.le     ./sigf06
-   $ncpl $datges/${prefix_atm}.sigf09.le     ./sigf09
+   $ncpl $datges/${prefix_aer}.sigf03.le         ./aerf03
+   $ncpl $datges/${prefix_aer}.sigf06.le         ./aerf06
+   $ncpl $datges/${prefix_aer}.sigf09.le         ./aerf09
 fi
 
 # Run GSI
diff --git a/regression/regression_namelists.sh b/regression/regression_namelists.sh
index 57252a4f22..91108e322b 100755
--- a/regression/regression_namelists.sh
+++ b/regression/regression_namelists.sh
@@ -2788,78 +2788,14 @@ OBS_INPUT::
    prepbufr       t           null      t                    0.0     0     0
    prepbufr       q           null      q                    0.0     0     0
    prepbufr       pw          null      pw                   0.0     0     0
-   satwndbufr     uv          null      uv                   0.0     0     0
    prepbufr       uv          null      uv                   0.0     0     0
    prepbufr       spd         null      spd                  0.0     0     0
    prepbufr       dw          null      dw                   0.0     0     0
-   radarbufr      rw          null      l3rw                 0.0     0     0
-   l2rwbufr       rw          null      l2rw                 0.0     0     0
-   nsstbufr       sst         nsst      sst                  0.0     0     0
-   gpsrobufr      $gps_dtype  null      gps                  0.0     0     0
-   ssmirrbufr     pcp_ssmi    dmsp      pcp_ssmi             0.0    -1     0
-   tmirrbufr      pcp_tmi     trmm      pcp_tmi              0.0    -1     0
-   sbuvbufr       sbuv2       n16       sbuv8_n16            0.0     0     0
-   sbuvbufr       sbuv2       n17       sbuv8_n17            0.0     0     0
-   sbuvbufr       sbuv2       n18       sbuv8_n18            0.0     0     0
-   hirs3bufr      hirs3       n17       hirs3_n17            0.0     1     1
-   hirs4bufr      hirs4       metop-a   hirs4_metop-a        0.0     1     1
-   gimgrbufr      goes_img    g11       imgr_g11             0.0     1     0
-   gimgrbufr      goes_img    g12       imgr_g12             0.0     1     0
    airsbufr       airs        aqua      airs_aqua            0.0     1     1
-   amsuabufr      amsua       n15       amsua_n15            0.0     1     1
-   amsuabufr      amsua       n18       amsua_n18            0.0     1     1
-   amsuabufr      amsua       metop-a   amsua_metop-a        0.0     1     1
-   airsbufr       amsua       aqua      amsua_aqua           0.0     1     1
-   amsubbufr      amsub       n17       amsub_n17            0.0     1     1
-   mhsbufr        mhs         n18       mhs_n18              0.0     1     1
-   mhsbufr        mhs         metop-a   mhs_metop-a          0.0     1     1
-   ssmitbufr      ssmi        f15       ssmi_f15             0.0     1     0
-   amsrebufr      amsre_low   aqua      amsre_aqua           0.0     1     0
-   amsrebufr      amsre_mid   aqua      amsre_aqua           0.0     1     0
-   amsrebufr      amsre_hig   aqua      amsre_aqua           0.0     1     0
-   ssmisbufr      ssmis_las   f16       ssmis_f16            0.0     1     0
-   ssmisbufr      ssmis_uas   f16       ssmis_f16            0.0     1     0
-   ssmisbufr      ssmis_img   f16       ssmis_f16            0.0     1     0
-   ssmisbufr      ssmis_env   f16       ssmis_f16            0.0     1     0
-   gsnd1bufr      sndrd1      g12       sndrD1_g12           0.0     1     0
-   gsnd1bufr      sndrd2      g12       sndrD2_g12           0.0     1     0
-   gsnd1bufr      sndrd3      g12       sndrD3_g12           0.0     1     0
-   gsnd1bufr      sndrd4      g12       sndrD4_g12           0.0     1     0
-   gsnd1bufr      sndrd1      g11       sndrD1_g11           0.0     1     0
-   gsnd1bufr      sndrd2      g11       sndrD2_g11           0.0     1     0
-   gsnd1bufr      sndrd3      g11       sndrD3_g11           0.0     1     0
-   gsnd1bufr      sndrd4      g11       sndrD4_g11           0.0     1     0
-   gsnd1bufr      sndrd1      g13       sndrD1_g13           0.0     1     0
-   gsnd1bufr      sndrd2      g13       sndrD2_g13           0.0     1     0
-   gsnd1bufr      sndrd3      g13       sndrD3_g13           0.0     1     0
-   gsnd1bufr      sndrd4      g13       sndrD4_g13           0.0     1     0
    iasibufr       iasi        metop-a   iasi_metop-a         0.0     1     1
-   gomebufr       gome        metop-a   gome_metop-a         0.0     2     0
-   omibufr        omi         aura      omi_aura             0.0     2     0
-   sbuvbufr       sbuv2       n19       sbuv8_n19            0.0     0     0
-   hirs4bufr      hirs4       n19       hirs4_n19            0.0     1     1
-   amsuabufr      amsua       n19       amsua_n19            0.0     1     1
-   mhsbufr        mhs         n19       mhs_n19              0.0     1     1
-   tcvitl         tcp         null      tcp                  0.0     0     0
-   seviribufr     seviri      m08       seviri_m08           0.0     1     0
-   seviribufr     seviri      m09       seviri_m09           0.0     1     0
-   seviribufr     seviri      m10       seviri_m10           0.0     1     0
-   seviribufr     seviri      m11       seviri_m11           0.0     1     0
-   hirs4bufr      hirs4       metop-b   hirs4_metop-b        0.0     1     0
-   amsuabufr      amsua       metop-b   amsua_metop-b        0.0     1     0
-   mhsbufr        mhs         metop-b   mhs_metop-b          0.0     1     0
    iasibufr       iasi        metop-b   iasi_metop-b         0.0     1     0
-   gomebufr       gome        metop-b   gome_metop-b         0.0     2     0
-   atmsbufr       atms        npp       atms_npp             0.0     1     0
-   atmsbufr       atms        n20       atms_n20             0.0     1     0
    crisbufr       cris        npp       cris_npp             0.0     1     0
-   crisfsbufr     cris-fsr    npp       cris-fsr_npp         0.0     1     0
-   crisfsbufr     cris-fsr    n20       cris-fsr_n20         0.0     1     0
-   mlsbufr        mls30       aura      mls30_aura           0.0     0     0
-   oscatbufr      uv          null      uv                   0.0     0     0
-   ompsnpbufr     ompsnp      npp       ompsnp_npp           0.0     0     0
-   ompstcbufr     ompstc8     npp       ompstc8_npp          0.0     2     0
-   abibufr        abi         g16       abi_g16              0.0     1     0
+   nsstbufr       sst         nsst        sst                0.0     0     0
 ::
 
  &SUPEROB_RADAR

From ebc0ca78abd2df8c7f416ef1d00cd271969432a8 Mon Sep 17 00:00:00 2001
From: albany-weiwilliam <swei@albany.edu>
Date: Wed, 1 Jul 2020 19:58:07 +0000
Subject: [PATCH 3/5] Test to update submodule:fix

---
 fix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fix b/fix
index 53812885c0..02cade59b8 160000
--- a/fix
+++ b/fix
@@ -1 +1 @@
-Subproject commit 53812885c084fd2de26e53f3eeb482cc3c87bcd2
+Subproject commit 02cade59b87be390dca4545e4f336b033025f574

From 0007ccf179dfff72b92557dc4dc274999f801ef4 Mon Sep 17 00:00:00 2001
From: albany-weiwilliam <swei@albany.edu>
Date: Mon, 6 Jul 2020 21:31:17 +0000
Subject: [PATCH 4/5] swei_fv3aerorad: ref

---
 fix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fix b/fix
index 02cade59b8..b59fa6fc63 160000
--- a/fix
+++ b/fix
@@ -1 +1 @@
-Subproject commit 02cade59b87be390dca4545e4f336b033025f574
+Subproject commit b59fa6fc63b5a2cc3f1425f171e720329692e775

From d5dacd159b8be4af2f6b0701fc416064965b13ca Mon Sep 17 00:00:00 2001
From: albany-weiwilliam <swei@albany.edu>
Date: Mon, 6 Jul 2020 23:06:29 +0000
Subject: [PATCH 5/5] tiny change of regression_var.sh which is identical to
 the one used for test

---
 regression/regression_var.sh | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/regression/regression_var.sh b/regression/regression_var.sh
index db6a09bef0..33e2b8c195 100755
--- a/regression/regression_var.sh
+++ b/regression/regression_var.sh
@@ -111,17 +111,19 @@ case $machine in
      export noscrub="/scratch1/NCEPDEV/global/$LOGNAME/noscrub"
     elif [ -d /scratch2/BMC/gsienkf/$LOGNAME ]; then
      export noscrub="/scratch2/BMC/gsienkf/$LOGNAME"
-   elif [ -d /scratch1/BMC/gsd-fv3-dev/$LOGNAME ]; then
-     export noscrub="/scratch1/BMC/gsd-fv3-dev/$LOGNAME/DTCVisitor/noscrub"
    fi
+ 
+   export noscrub="/scratch1/BMC/gsd-fv3-dev/Shih-wei.Wei/DTCVisitor/rgtest_Jul1/noscrub"
+
    export group="global"
    export queue="batch"
    if [[ "$cmaketest" = "false" ]]; then
-     export basedir="/scratch1/NCEPDEV/da/$LOGNAME/git/gsi"
+     #export basedir="/scratch1/NCEPDEV/da/$LOGNAME/git/gsi"
+     export basedir="/scratch1/BMC/gsd-fv3-dev/Shih-wei.Wei/DTCVisitor/rgtest_Jul1/control"
    fi 
 
    #export ptmp="/scratch1/NCEPDEV/stmp2/$LOGNAME/$ptmpName"
-   export ptmp="/scratch1/BMC/gsd-fv3-dev/Shih-wei.Wei/DTCVisitor/$ptmpName"
+   export ptmp="/scratch1/BMC/gsd-fv3-dev/Shih-wei.Wei/DTCVisitor/rgtest_Jul1/ptmp"
 
    export fixcrtm="/scratch1/NCEPDEV/da/Michael.Lueken/CRTM_REL-2.2.3/crtm_v2.2.3/fix_update"
    #export casesdir="/scratch1/NCEPDEV/da/Michael.Lueken/noscrub/CASES"