Merge pull request #32 from weiwilliam/master

GitHub Issue #28.  regression test for aerosol impacts on radiance.

CMakeLists.txt

@@ -309,10 +309,10 @@ project(GSI)
     if(USE_WRF)
       file(WRITE "${PROJECT_BINARY_DIR}/regression_var.out" "${CMAKE_SOURCE_DIR}/regression/regression_var.sh ${host} ${CMAKE_SOURCE_DIR}/.. ${PROJECT_BINARY_DIR} ${CMAKE_SOURCE_DIR} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${GSIEXEC} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${ENKFEXEC} ${GSICONTROL} ${ENKFCONTROL} ${BASELINE_FLAG} ")
       set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_4denvar_T126;global_fv3_4denvar_T126;;global_fv3_4denvar_C192;global_lanczos_T62;arw_netcdf;
-          arw_binary;nmm_binary;nmm_netcdf;nmmb_nems_4denvar;hwrf_nmm_d2;hwrf_nmm_d3;rtma;global_enkf_T62;netcdf_fv3_regional;global_C96_fv3aero")
+          arw_binary;nmm_binary;nmm_netcdf;nmmb_nems_4denvar;hwrf_nmm_d2;hwrf_nmm_d3;rtma;global_enkf_T62;netcdf_fv3_regional;global_C96_fv3aero;global_C96_fv3aerorad")
     else()
       file(WRITE "${PROJECT_BINARY_DIR}/regression_var.out" "${CMAKE_SOURCE_DIR}/regression/regression_var.sh ${host} ${CMAKE_SOURCE_DIR}/.. ${PROJECT_BINARY_DIR} ${CMAKE_SOURCE_DIR} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${GSIEXEC} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${ENKFEXEC} ${GSICONTROL} ${ENKFCONTROL} ${BASELINE_FLAG} ")
-      set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_lanczos_T62;global_nemsio_T62;global_C96_fv3aero")
+      set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_lanczos_T62;global_nemsio_T62;global_C96_fv3aero;global_C96_fv3aerorad")
     endif()
     foreach( REG_TEST ${REG_TEST_NAMES} )
       add_test(NAME ${REG_TEST} WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/regression COMMAND regression_driver.sh ${REG_TEST} ${PROJECT_BINARY_DIR})

regression/global_C96_fv3aero.sh

@@ -27,7 +27,11 @@ ncp=/bin/cp
 # 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_fv3aero_adate | cut -c1-8`
+cyc=`echo $global_C96_fv3aero_adate | cut -c9-10`
 gdate=`$ndate -06 $global_C96_fv3aero_adate`
+gPDY=`echo $gdate | cut -c1-8`
+gcyc=`echo $gdate | cut -c9-10`
 hha=`echo $global_C96_fv3aero_adate | cut -c9-10`
 hhg=`echo $gdate | cut -c9-10`
 prefix_obs=gfs.t${hha}z.
@@ -38,6 +42,10 @@ prefix_atm=gfsC96.t${hhg}z
 suffix_obs=gdas.${global_C96_fv3aero_adate}
 suffix_bias=gdas.${gdate}
 
+datobs=$global_C96_fv3aero_obs/gfs.$PDY/$cyc
+datanl=$global_C96_fv3aero_obs/gfs.$PDY/$cyc
+datges=$global_C96_fv3aero_ges/gfs.$gPDY/$gcyc
+
 
 # Set up $tmpdir
 rm -rf $tmpdir
@@ -235,32 +243,32 @@ $ncp $fixcrtm/v.modis_terra.SpcCoeff.bin ./crtm_coeffs/v.modis_terra.SpcCoeff.bi
 $ncp $fixcrtm/v.modis_terra.TauCoeff.bin ./crtm_coeffs/v.modis_terra.TauCoeff.bin
 
 # Copy observational data to $tmpdir
-ln -s -f $global_C96_fv3aero_obs/${prefix_obs}modisaod.tm00.bufr ./modisaodbufr
+ln -s -f $datobs/${prefix_obs}modisaod.tm00.bufr ./modisaodbufr
 
 
 # Copy bias correction, atmospheric and surface files
-ln -s -f $global_C96_fv3aero_ges/gfs.t18z.abias           ./satbias_in
-ln -s -f $global_C96_fv3aero_ges/gfs.t18z.abias_pc        ./satbias_pc
-#ln -s -f $global_C96_fv3aero_ges/gfs.t18z.radstat         ./radstat.gdas
+ln -s -f $datges/gfs.t18z.abias           ./satbias_in
+ln -s -f $datges/gfs.t18z.abias_pc        ./satbias_pc
+#ln -s -f $datges/gfs.t18z.radstat         ./radstat.gdas
 
 if [[ "$endianness" = "Big_Endian" ]]; then
-   ln -s -f $global_C96_fv3aero_ges/${prefix_sfc}.sfcf03            ./sfcf03
-   ln -s -f $global_C96_fv3aero_ges/${prefix_sfc}.sfcf06            ./sfcf06
-   ln -s -f $global_C96_fv3aero_ges/${prefix_sfc}.sfcf09            ./sfcf09
+   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
-   ln -s -f $global_C96_fv3aero_ges/${prefix_sfc}.sfcf03.le         ./sfcf03
-   ln -s -f $global_C96_fv3aero_ges/${prefix_sfc}.sfcf06.le         ./sfcf06
-   ln -s -f $global_C96_fv3aero_ges/${prefix_sfc}.sfcf09.le         ./sfcf09
+   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
-   ln -s -f $global_C96_fv3aero_ges/${prefix_atm}.sigf03        ./sigf03
-   ln -s -f $global_C96_fv3aero_ges/${prefix_atm}.sigf06        ./sigf06
-   ln -s -f $global_C96_fv3aero_ges/${prefix_atm}.sigf09        ./sigf09
+   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
-   ln -s -f $global_C96_fv3aero_ges/${prefix_atm}.sigf03.le     ./sigf03
-   ln -s -f $global_C96_fv3aero_ges/${prefix_atm}.sigf06.le     ./sigf06
-   ln -s -f $global_C96_fv3aero_ges/${prefix_atm}.sigf09.le     ./sigf09
+   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
 
 # Run GSI

regression/global_C96_fv3aerorad.sh

@@ -0,0 +1,305 @@
+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=gfsC96.t${hhg}z
+prefix_atm=gfsC96.t${hhg}z
+prefix_aer=gfsC96.t${hhg}z
+suffix_obs=tm00.bufr_d
+
+datobs=$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
+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
+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}.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 $datges/gfs.t18z.radstat         ./radstat.gdas
+
+if [[ "$endianness" = "Big_Endian" ]]; then
+   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
+   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
+   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
+   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_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
+
+# Run GSI
+cd $tmpdir
+echo "run gsi now"
+eval "$APRUN $tmpdir/gsi.x > stdout 2>&1"
+rc=$?
+exit $rc
+
+# 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