Merge branch 'main' of https://github.com/NCAR/DART into quantile_met…

…hods

CHANGELOG.rst

@@ -22,6 +22,32 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**September 18 2023 :: Fluxnet observation converter and obs_def_rttov13_mod.f90 bug-fixes. Tag v10.8.4**
+
+Fluxnet obs converter:
+
+- Generates a new observation converter (Fluxnetfull_to_obs) for eddy 
+  covariance flux tower data (carbon, water energy fluxes)
+- Documentation changes made to the older, deprecated ameriflux 
+  converter (level4_to_obs) and the broken links have been fixed
+- New flux tower observation types added to accomodate the forward 
+  operator approach for time aggregated fluxes (daily through monthly)
+
+obs_def_rttov13_mod.f90 bug-fixes:
+
+- Added public get_channel to obs_def_rttov13_mod.f90 to compile WRF 
+  successfully with rttov13.
+- Removed cloud_overlap (integer) from the function: get_rttov_option_logical
+
+**August 21 2023 :: CAM-FV shell scripts. Tag v10.8.3**
+
+Performance improvements for CAM-FV shell scripts:
+
+- Avoid listing files if the CAM_PHIS file already exists.
+- Avoid using /var/tmp
+- RUNDIR defined after CIME_OUTPUT_ROOT change.
+- Warn if no inflation files found.
+
 **August 8 2023 :: MPAS-ATM constants and readthedocs fix. Tag v10.8.2**
 
 - MPAS-ATM constants updated to MPAS v5+

conf.py

@@ -21,7 +21,7 @@
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '10.8.2'
+release = '10.8.4'
 root_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

guide/important-capabilities-dart.rst

@@ -76,7 +76,9 @@ is as follows:
 +------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
 | `Aviso <https://www.aviso.altimetry.fr/en/home.html>`__: satellite derived sea surface height        | Aviso             | netCDF                            |
 +------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
-| Level 4 Flux Tower data from `AmeriFlux <http://ameriflux.lbl.gov/>`__                               | Ameriflux         | Comma-separated text              |
+| Level 4 Flux Tower data                                                                              | Ameriflux         | Comma-separated text              |
++------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
+| Ameriflux Fullset Flux Tower data from `AmeriFlux <https://ameriflux.lbl.gov/data/download-data>`__  | Ameriflux         | Comma-separated text              |
 +------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
 | Level 2 soil moisture from `COSMOS <http://cosmos.hwr.arizona.edu/>`__                               | COSMOS            | Fixed-width text                  |
 +------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
@@ -104,6 +106,8 @@ is as follows:
 +------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
 | Sea surface temperature                                                                              | SST               | netCDF                            |
 +------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
+| Solar-Induced Fluorescence                                                                           | SIF               | netCDF                            |
++------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
 | Special Sensor Ultraviolet Spectrographic Imager `(SSUSI) <https://ssusi.jhuapl.edu/>`__ retrievals  | SSUSI             | netCDF                            |
 +------------------------------------------------------------------------------------------------------+-------------------+-----------------------------------+
 | World Ocean Database `(WOD) <http://www.nodc.noaa.gov/OC5/WOD09/pr_wod09.html>`__                    | WOD               | World Ocean Database packed ASCII |

models/cam-fv/shell_scripts/cesm2_1/assimilate.csh.template

@@ -530,13 +530,14 @@ ${REMOVE} ${CAMINPUT}
 ${LINK} ${CASE}.cam_0001.i.${ATM_DATE_EXT}.nc ${CAMINPUT} || exit 90
 
 # All of the .h0. files contain the same PHIS field, so we can link to any of them.
-
-set hists = `${LIST} ${CASE}.cam_0001.h0.*.nc`
 set MYSTRING = `grep cam_phis_filename input.nml`
 set MYSTRING = `echo $MYSTRING | sed -e "s#[=,']# #g"`
 set CAM_PHIS = $MYSTRING[2]
-${REMOVE} ${CAM_PHIS}
-${LINK} $hists[1] ${CAM_PHIS} || exit 100
+# Listings are slow in productions runs; only do it if necessary
+if (! -f ${CAM_PHIS}) then
+   set hists = `${LIST} ${CASE}.cam_0001.h0.*.nc`
+   ${COPY} $hists[1] ${CAM_PHIS} || exit 100
+endif
 
 # Now, actually check the inflation settings
 

models/cam-fv/shell_scripts/cesm2_1/setup_advanced

@@ -42,6 +42,13 @@
 #PBS  -o Test_0.bld1
 #PBS  -j oe 
 #
+if ($?PBS_O_WORKDIR) then
+   # This avoids using /var/tmp, which can be purged by other jobs while this
+   # share queue job is running, which kills it.
+   setenv TMPDIR /glade/scratch/$USER/temp
+   mkdir -p $TMPDIR
+endif
+
 # ---------------------
 # Purpose
 # ---------------------
@@ -516,7 +523,6 @@ setenv COMP_GLC           `./xmlquery COMP_GLC           --value`
 setenv COMP_ROF           `./xmlquery COMP_ROF           --value`
 setenv CIMEROOT           `./xmlquery CIMEROOT           --value`
 setenv EXEROOT            `./xmlquery EXEROOT            --value`
-setenv RUNDIR             `./xmlquery RUNDIR             --value`
 setenv CAM_CONFIG_OPTS    `./xmlquery CAM_CONFIG_OPTS    --value`
 
 set    max_tasks_per_node = `./xmlquery    MAX_TASKS_PER_NODE --value`
@@ -672,6 +678,8 @@ echo "After xmlchanges for ROOTPEs ..."
 ./xmlchange GET_REFCASE=FALSE
 
 ./xmlchange CIME_OUTPUT_ROOT=${cime_output}
+# Changing CIME_OUTPUT_ROOT changes RUNDIR in CESM, so change it here too.
+setenv RUNDIR  `./xmlquery RUNDIR --value`
 
 ./xmlchange SSTICE_DATA_FILENAME=$sst_dataset
 ./xmlchange SSTICE_GRID_FILENAME=$sst_grid
@@ -895,7 +903,7 @@ while ($inst <= $num_instances)
    # echo " mfilt         = 1 "                             >> ${fname}
 
    echo $CAM_CONFIG_OPTS | grep 'cam4'
-   if ($status == 0) echo " fv_div24del2_flag = 4 "       >> ${fname}
+   if ($status == 0) echo " fv_div24del2flag = 4 "       >> ${fname}
 
    # Settings that differ between regular CAM and the WACCM version:
 
@@ -1236,6 +1244,16 @@ else     # CONTINUE_RUN == FALSE
    echo "All files set to run the FIRST experiment step using (ref)time" $init_time
 
 endif
+
+ls *inf*\${restart_time}* >& /dev/null
+if (\$status != 0) then 
+   echo ""
+   echo '==========================================================='
+   echo "WARNING:  no inflation files were found for \$restart_time"
+   echo '==========================================================='
+   echo ""
+endif
+
 exit 0
 
 EndOfText

models/cam-fv/shell_scripts/cesm2_1/setup_hybrid

@@ -42,6 +42,13 @@
 #PBS  -o Test_0.bld1
 #PBS  -j oe 
 #
+if ($?PBS_O_WORKDIR) then
+   # This avoids using /var/tmp, which can be purged by other jobs while this
+   # share queue job is running, which kills it.
+   setenv TMPDIR /glade/scratch/$USER/temp
+   mkdir -p $TMPDIR
+endif
+
 # ---------------------
 # Purpose
 # ---------------------
@@ -484,7 +491,6 @@ setenv COMP_GLC           `./xmlquery COMP_GLC           --value`
 setenv COMP_ROF           `./xmlquery COMP_ROF           --value`
 setenv CIMEROOT           `./xmlquery CIMEROOT           --value`
 setenv EXEROOT            `./xmlquery EXEROOT            --value`
-setenv RUNDIR             `./xmlquery RUNDIR             --value`
 setenv CAM_CONFIG_OPTS    `./xmlquery CAM_CONFIG_OPTS    --value`
 
 set    max_tasks_per_node = `./xmlquery    MAX_TASKS_PER_NODE --value`
@@ -640,6 +646,8 @@ echo "After xmlchanges for ROOTPEs ..."
 ./xmlchange GET_REFCASE=FALSE
 
 ./xmlchange CIME_OUTPUT_ROOT=${cime_output}
+# Changing CIME_OUTPUT_ROOT changes RUNDIR in CESM, so change it here too.
+setenv RUNDIR  `./xmlquery RUNDIR --value`
 
 ./xmlchange SSTICE_DATA_FILENAME=$sst_dataset
 ./xmlchange SSTICE_GRID_FILENAME=$sst_grid
@@ -860,7 +868,7 @@ while ($inst <= $num_instances)
    # echo " mfilt         = 1 "                             >> ${fname}
 
    echo $CAM_CONFIG_OPTS | grep 'cam4'
-   if ($status == 0) echo " fv_div24del2_flag = 4 "       >> ${fname}
+   if ($status == 0) echo " fv_div24del2flag = 4 "       >> ${fname}
 
    # Settings that differ between regular CAM and the WACCM version:
 
@@ -1128,6 +1136,16 @@ else     # CONTINUE_RUN == FALSE
    echo "All files set to run the FIRST experiment step using (ref)time" $init_time
 
 endif
+
+ls *inf*\${restart_time}* >& /dev/null
+if (\$status != 0) then 
+   echo ""
+   echo '==========================================================='
+   echo "WARNING:  no inflation files were found for \$restart_time"
+   echo '==========================================================='
+   echo ""
+endif
+
 exit 0
 
 EndOfText

observations/forward_operators/obs_def_rttov13_mod.f90

@@ -397,7 +397,8 @@ module obs_def_rttov_mod
                 write_rttov_metadata, &
           interactive_rttov_metadata, &
                get_expected_radiance, &
-            get_rttov_option_logical
+            get_rttov_option_logical, &
+                         get_channel
 
 ! The rttov_test.f90 program uses these, but no one else should.
 
@@ -4238,8 +4239,6 @@ function get_rttov_option_logical(field_name) result(p)
          p = USER_CLD_OPT_PARAM
       case('GRID_BOX_AVG_CLOUD')
          p = GRID_BOX_AVG_CLOUD
-      case('CLOUD_OVERLAP')
-         p = cloud_overlap
       case('ADDPC')
          p = ADDPC
       case('ADDRADREC')