Add PM2.5 DA for RRFS-SD

fix/gsi/anavinfo.rrfs_sd

@@ -0,0 +1,65 @@
+met_guess::
+!var     level    crtm_use    desc              orig_name
+  ps        1      -1         surface_pressure     ps
+  z         1      -1         geopotential_height  phis
+  u        65       2         zonal_wind           u
+  v        65       2         meridional_wind      v
+  tv       65       2         virtual_temperature  tv
+  q        65       2         specific_humidity    sphu
+  oz       65       2         ozone                ozone
+  delp     65      -1         fv3 del pressure     delp
+::
+
+state_derivatives::
+!var  level  src
+ ps   1      met_guess
+ u    65     met_guess
+ v    65     met_guess
+ tv   65     met_guess
+ q    65     met_guess
+ oz   65     met_guess
+ cw   65     met_guess
+ prse 66     met_guess
+::
+
+state_tendencies::
+!var  levels  source
+ u    65      met_guess
+ v    65      met_guess
+ tv   65      met_guess
+ q    65      met_guess
+ oz   65      met_guess
+ prse 66      met_guess
+::
+
+state_vector::  
+!var     level  itracer source     funcof
+ u        65      0     met_guess    u
+ v        65      0     met_guess    v
+ tv       65      0     met_guess    tv
+ tsen     65      0     met_guess    tv,q
+ q        65      1     met_guess    q
+ oz       65      1     met_guess    oz
+ prse     66      0     met_guess    prse
+ ps        1      0     met_guess    prse
+ smoke    65      1     chem_guess   smoke
+ dust     65      1     chem_guess   dust
+::
+
+control_vector::
+!var     level  itracer as/tsfc_sdv  an_amp0   source  funcof
+ sf       65      0       0.90        -1.0     state    u,v
+ vp       65      0       0.90        -1.0     state    u,v
+ ps        1      0       1.00        -1.0     state    prse
+ t        65      0       1.40        -1.0     state    tv
+ q        65      1       0.80        -1.0     state    q
+ smoke    65      1       1.00        -1.0     state    smoke
+ dust     65      1       1.00        -1.0     state    dust
+::
+
+chem_guess::
+!var     level  itracer crtm_use   type    orig_name
+ smoke    65      1       12     smoke     smoke
+ dust     65      1       12     dust      dust
+ pm2_5    65      1       10     pm2_5     pm2_5
+::

fix/gsi/gsiparm.anl.sh

@@ -47,6 +47,7 @@ gsi_namelist="
  /
 OBS_INPUT::
 !  dfile          dtype       dplat     dsis                 dval    dthin dsfcalc
+   pm25bufr       pm2_5       null      TEOM                 1.0     0     0
    dbzobs.nc      dbz         null      dbz                  1.0     0     0
    prepbufr       ps          null      ps                   1.0     0     0
    prepbufr       t           null      t                    1.0     0     0
@@ -188,8 +189,8 @@ OBS_INPUT::
    build_cloud_frac_p=0.50,
    clear_cloud_frac_p=0.10,
    iclean_hydro_withRef_allcol=1,
-   i_use_2mQ4B=2,
-   i_use_2mT4B=1,
+   i_use_2mQ4B=${ii_use_2mq4b},
+   i_use_2mT4B=${ii_use_2mt4b},
    i_gsdcldanal_type=0,
    i_gsdsfc_uselist=1,
    i_lightpcp=1,
@@ -198,6 +199,8 @@ OBS_INPUT::
    i_gsdqc=2,
  /
  &CHEM
+  laeroana_fv3smoke=.true.,
+  berror_fv3_cmaq_regional = .true.,
  /
  &NST
  /

scripts/exregional_run_analysis.sh

@@ -333,6 +333,8 @@ niter2=50
 lread_obs_save=.false.
 lread_obs_skip=.false.
 if_model_dbz=.false.
+ii_use_2mq4b=2
+ii_use_2mt4b=1
 
 # Determine if hybrid option is available
 memname='atmf009'
@@ -484,6 +486,12 @@ else
 
   fi
 
+
+  if [ ${ob_type} == "AERO" ]; then
+    obs_files_source[0]=${OBSPATH_PM}/${YYYYMMDD}/pm25.airnow.${YYYYMMDD}${HH}.bufr
+    obs_files_target[0]=pm25bufr
+  fi
+
 fi
 
 #
@@ -616,6 +624,25 @@ HYBENSINFO=${FIX_GSI}/${HYBENSINFO_FN}
 OBERROR=${FIX_GSI}/${OBERROR_FN}
 BERROR=${FIX_GSI}/${BERROR_FN}
 
+
+if [[ ${gsi_type} == "ANALYSIS" && ${ob_type} == "AERO" ]]; then
+  ANAVINFO=${FIX_GSI}/${ANAVINFO_SD_FN}
+  CONVINFO=${FIX_GSI}/${CONVINFO_SD_FN}
+  BERROR=${FIX_GSI}/${BERROR_SD_FN}
+  miter=1
+  niter1=100
+  niter2=0
+  ifhyb=.false.
+  ifsd_da=.true.
+  l_hyb_ens=.false.
+  nummem=0
+  beta1_inv=0.0
+  ii_use_2mq4b=0
+  ii_use_2mt4b=0
+  netcdf_diag=.true.
+  binary_diag=.false.
+fi
+
 SATINFO=${FIX_GSI}/global_satinfo.txt
 OZINFO=${FIX_GSI}/global_ozinfo.txt
 PCPINFO=${FIX_GSI}/global_pcpinfo.txt
@@ -805,6 +832,14 @@ cat << EOF > gsiparm.anl
 $gsi_namelist
 EOF
 
+if [[ ${gsi_type} == "ANALYSIS" && ${ob_type} != "AERO" ]]; then
+# base_e GSI can't handle the below two parameter for RRFS-SD DA. So delete them.
+  mv gsiparm.anl gsiparm.anl.sd
+  sed '/laeroana_fv3smoke/d' gsiparm.anl.sd > gsiparm.anl.1
+  sed '/berror_fv3_cmaq_regional/d' gsiparm.anl.1 > gsiparm.anl
+  rm -fr gsiparm.anl.sd gsiparm.anl.1
+fi
+
 #
 #-----------------------------------------------------------------------
 #
@@ -814,6 +849,11 @@ EOF
 #
 gsi_exec="${EXECDIR}/gsi.x"
 
+if [[ ${gsi_type} == "ANALYSIS" && ${ob_type} == "AERO" ]]; then
+  gsi_exec="${EXECDIR}/gsi.x.sd"
+fi
+
+
 if [ -f $gsi_exec ]; then
   print_info_msg "$VERBOSE" "
 Copying the GSI executable to the run directory..."
@@ -842,6 +882,40 @@ fi
 #-----------------------------------------------------------------------
 #
 # comment out for testing
+if [[ ${gsi_type} == "ANALYSIS" && ${ob_type} == "AERO" ]]; then
+
+if [ ${BKTYPE} -eq 1 ]; then
+ print_info_msg "$VERBOSE" "
+ Coldstart skip GSI SD DA"
+else
+# backup background 
+  if [ "${IO_LAYOUT_Y}" == "1" ]; then
+    cp -fr ${bkpath}/fv_tracer.res.tile1.nc ${bkpath}/fv_tracer.res.tile1.nc.org
+  else
+    for ii in ${list_iolayout}
+    do
+      iii=`printf %4.4i $ii`
+      cp -fr  ${bkpath}/fv_tracer.res.tile1.nc.${iii} ${bkpath}/fv_tracer.res.tile1.nc.${iii}.org
+    done
+  fi
+
+  $APRUN ./gsi.x < gsiparm.anl > stdout 2>&1 || print_err_msg_exit "\
+  Call to executable to run GSI returned with nonzero exit code."
+
+# copy updated fv3_tracer back to  restart
+  if [ "${IO_LAYOUT_Y}" == "1" ]; then
+    cp -fr  fv3_tracer ${bkpath}/fv_tracer.res.tile1.nc
+  else
+    for ii in ${list_iolayout}
+    do
+      iii=`printf %4.4i $ii`
+      cp -fr   fv3_tracer.${iii} ${bkpath}/fv_tracer.res.tile1.nc.${iii}
+    done
+  fi
+fi
+
+else
+
 $APRUN ./gsi.x < gsiparm.anl > stdout 2>&1 || print_err_msg_exit "\
 Call to executable to run GSI returned with nonzero exit code."
 
@@ -855,6 +929,7 @@ sed -e 's/   asm all/rw asm 900/; s/   rej all/rw rej 900/; s/   mon all/rw mon
 
 cat fit_p1 fit_w1 fit_t1 fit_q1 fit_pw1 fit_rad1 fit_rw1 > $comout/rrfs_a.t${HH}z.fits.tm00
 cat fort.208 fort.210 fort.211 fort.212 fort.213 fort.220 > $comout/rrfs_a.t${HH}z.fits2.tm00
+fi
 #
 #-----------------------------------------------------------------------
 #