Forgot to upd geopotential var names in some yaml files

src/Applications/GEOSdas_App/jedi/etc/convertana_geos.yaml

@@ -33,7 +33,7 @@ states:
     - rain_water
     - snow_water
     - mole_fraction_of_ozone_in_air
-    - geopotential_height_times_gravity_at_surface
+    - geopotential_at_surface
     - initial_mass_fraction_of_large_scale_cloud_condensate
     - initial_mass_fraction_of_convective_cloud_condensate
     - convective_cloud_area_fraction
@@ -72,7 +72,7 @@ states:
       rain_water: qr
       snow_water: qs
       mole_fraction_of_ozone_in_air: o3ppmv
-      geopotential_height_times_gravity_at_surface: phis
+      geopotential_at_surface: phis
       initial_mass_fraction_of_large_scale_cloud_condensate: qls
       initial_mass_fraction_of_convective_cloud_condensate: qcn
       convective_cloud_area_fraction: cfcn

src/Applications/GEOSdas_App/jedi/etc/diffstates_geos.yaml

@@ -35,9 +35,12 @@ state1:
   - rain_water
   - snow_water
   - mole_fraction_of_ozone_in_air
-  - geopotential_height_times_gravity_at_surface
+  - geopotential_at_surface
   - air_pressure_levels
   - air_pressure_at_surface
+  - fraction_of_ocean
+  - fraction_of_lake
+  - fraction_of_ice
   - skin_temperature_at_surface
   field io names: &field_io_names
     eastward_wind: ua
@@ -49,9 +52,12 @@ state1:
     rain_water: qr
     snow_water: qs
     mole_fraction_of_ozone_in_air: o3ppmv
-    geopotential_height_times_gravity_at_surface: phis
+    geopotential_at_surface: phis
     air_pressure_levels: pe
     air_pressure_at_surface: ps
+    fraction_of_ocean: frocean
+    fraction_of_lake: frlake
+    fraction_of_ice: frseaice
     skin_temperature_at_surface: ts
 state2:
   datetime: $ISO_STATES_DATE

src/Applications/GEOSdas_App/jedi/jedi_run.csh

@@ -73,6 +73,7 @@ set mmb      = `echo $nymdb | cut -c5-6`
 set ddb      = `echo $nymdb | cut -c7-8`
 set hhb      = `echo $nhmsb | cut -c1-2`
 set yyyymmddhh = ${nymdb}${hhb}
+setenv BYYYYYMMDDTHH0000Z  ${nymdb}T${hhb}0000Z
 
 set anadate  = `tick $nymdb $nhmsb $JEDI_VAROFFSET`
 set nymda    = $anadate[1]
@@ -209,6 +210,11 @@ if ( ! -e $FVWORK/.DONE_jedi_run_ana.csh.$yyyymmddhh) then
            endif
         endif
      endif
+     set ichk = `grep NaN $FVWORK/$JEDIVARLOG | wc`
+     if ( $ichk[1] > 0 ) then
+         echo " ${MYNAME}: NaNs found in JEDI, failed in VAR, aborting ..."
+         exit (1)
+     endif
      set lstinc = `ls *inc*nc4`
      if ( ! $status ) /bin/mv *inc*nc4 ./inc # somehow datapath setting in yaml is not effective at inc part
    endif
@@ -346,7 +352,13 @@ cd -
 # -------------
 touch $JEDIETC/VBC.BOOTSTRAP.DONE
 cd $JEDIWRK/vbc
-tar cvf $FVWORK/$EXPID.jedi_vbc.${nymdb}_${hhb}z.tar *satbias*nc4 *aircraft*csv
+/bin/cp $JEDIWRK/obs/*tlapse.txt .
+foreach fn (`ls *tlapse.txt`)
+  set pfx = `echo $fn | cut -d. -f1`
+  /bin/mv $fn $pfx.$BYYYYYMMDDTHH0000Z.tlapse.txt # time tag as current as
+                                                  # if JEDI output these
+end
+tar cvf $FVWORK/$EXPID.jedi_vbc.${nymdb}_${hhb}z.tar *satbias*nc4 *aircraft*csv *.txt
 cd -
 
 # If here, likely successful

src/Applications/GEOSdas_App/jedi/jedi_set.csh

@@ -183,8 +183,8 @@ end
 # If so, retrieve IODA files from existig ru
 # In adjoint case, IODA files are from same exp
 if ( $JEDI_RUN_ANASA || $JEDI_RUN_ADANA || $JEDI_OBS_OPT == 1 ) then
-  setenv NYMDB  $nymdb # initial date of current cycle
-  setenv NHMSB  $nhmsb # initial time of current cycle
+  setenv NYMD  $nymdb # initial date of current cycle
+  setenv NHMS  $nhmsb # initial time of current cycle
   setenv ACQWORK $FVWORK
   vED -env $FVHOME/run/jedi/jedi_acquire_ioda.j -o jedi_acquire_ioda.j
   if ( $BATCH_SUBCMD == "sbatch" ) then

src/Applications/GEOSdas_App/jedi/jedi_upd4geos.csh

@@ -42,7 +42,15 @@ if ( -d $JEDIWORK/iau ) then
    cd $FVWORK
 #  set cost = `grep "cost type" $JEDIWORK/Config/geosvar.yaml | cut -d: -f2 | cut -d- -f1`
 #  if ( $cost == "3D" ) then
-     foreach fn ( `ls $JEDIWORK/iau/*.agcm_import_rst.*nc4` )
+     set alliau = `ls $JEDIWORK/iau/*.agcm_import_rst.*nc4`
+     if ($status) then 
+         echo " ${MYNAME}: JEDI IAU increments not found, no overwrite taken place. "
+         if ( $JEDI_IAU_OVERWRITE ) then
+            echo " ${MYNAME}: Aborting(1) ..."
+            exit (1)
+         endif
+     endif
+     foreach fn ( $alliau )
        set bname   = `basename $fn`
        set noexpid = `echo $bname | cut -d. -f2-`
        echo /bin/ln -sf $fn $noexpid
@@ -66,7 +74,7 @@ if ( -d $JEDIWORK/iau ) then
 else
    echo " ${MYNAME}: JEDI IAU increments not found, no overwrite taken place. "
    if ( $JEDI_IAU_OVERWRITE ) then
-      echo " ${MYNAME}: Aborting ..."
+      echo " ${MYNAME}: Aborting(2) ..."
       exit (1)
    endif
 endif