Rename SAR to LAM and JP to ESG, remove fix files (#268)

* Remove all references to /lfs3 on Jet

* Add Ben and Ratko to the CODEOWNERS file

* Replace hard-coded make_orog module file with build-level module file in UFS_UTILS

* Remove hard-coded make_sfc_climo module file

* Rename all FV3-SAR and SAR-FV3 to FV3-LAM, rename all JPgrid to ESGgrid.  Remove fix files in regional_workflow and source from fix_am and EMC_post.

* Add alpha/kappa parameter back in exregional_make_grid.sh

* Remove dash from FV3LAM_wflow.xml

* Change FIXam to FIXgsm to source Thompson CCN file

* Remove old, unused grid stanza from exregional_run_post.sh

* Change Jet locations of fix_am/fix_orog to EMC paths

jobs/JREGIONAL_GET_EXTRN_MDL_FILES

@@ -206,7 +206,7 @@ cd_vrfy "${extrn_mdl_staging_dir}"
 get_extrn_mdl_file_dir_info \
   extrn_mdl_name="${EXTRN_MDL_NAME}" \
   anl_or_fcst="${anl_or_fcst}" \
-  cdate_FV3SAR="${CDATE}" \
+  cdate_FV3LAM="${CDATE}" \
   time_offset_hrs="${time_offset_hrs}" \
   varname_extrn_mdl_cdate="extrn_mdl_cdate" \
   varname_extrn_mdl_lbc_spec_fhrs="extrn_mdl_lbc_spec_fhrs" \

jobs/JREGIONAL_MAKE_GRID

@@ -4,7 +4,7 @@
 #-----------------------------------------------------------------------
 #
 # This script generates grid and orography files in NetCDF format that
-# are required as inputs for running the FV3SAR model (i.e. the FV3 mo-
+# are required as inputs for running the FV3-LAM model (i.e. the FV3 mo-
 # del on a regional domain).  It in turn calls three other scripts whose
 # file names are specified in the variables grid_gen_scr, orog_gen_scr,
 # and orog_fltr_scr and then calls the executable defined in the varia-
@@ -28,7 +28,7 @@
 #       large enough such that the "shave" steps later below (which take
 #       this file as input and generate grid files with thinner halos)
 #       have a wide enough starting halo to work with.  More specifical-
-#       ly, the FV3SAR model needs as inputs two grid files: one with a
+#       ly, the FV3-LAM model needs as inputs two grid files: one with a
 #       halo that is 3 cells and another with a halo that is 4 cells 
 #       wide.  Thus, the halo in the grid file that the grid_gen_scr 
 #       script generates must be greater than 4 since otherwise, the
@@ -38,7 +38,7 @@
 #       name denotes number of cells, the "h" is used to indicate that
 #       it refers to a halo region, the "w" is used to indicate that it
 #       refers to a wide halo (i.e. wider than the 3-cell and 4-cell ha-
-#       los that the FV3SAR model requires as inputs, and the "T7" is
+#       los that the FV3-LAM model requires as inputs, and the "T7" is
 #       used to indicate that the cell count is on tile 7.
 #
 # 2) orog_gen_scr:
@@ -63,7 +63,7 @@
 #       generated by script orog_gen_scr (and the grid file generated by 
 #       grid_gen_scr).
 #
-#    b) In analogy with the input grid files, the FV3SAR model needs as
+#    b) In analogy with the input grid files, the FV3-LAM model needs as
 #       input two (filtered) orography files -- one with no halo cells
 #       and another with 3.  These are obtained later below by "shaving"
 #       off layers of halo cells from the (filtered) orography file ge-

jobs/JREGIONAL_RUN_POST

@@ -4,7 +4,7 @@
 #-----------------------------------------------------------------------
 #
 # This script runs the post-processor (UPP) on the NetCDF output files
-# of the write component of the FV3SAR model.
+# of the write component of the FV3-LAM model.
 #
 #-----------------------------------------------------------------------
 #

scripts/exregional_get_extrn_mdl_files.sh

@@ -631,7 +631,7 @@ file unzip_log_fn in that directory for details:
 # of each external model file.  If any are missing, then the corresponding 
 # files are not in the zip file and thus cannot be extracted.  In that 
 # case, print out a message and exit the script because initial condition 
-# and surface field files for the FV3SAR cannot be generated without all 
+# and surface field files for the FV3-LAM cannot be generated without all 
 # the external model files.
 #
 #-----------------------------------------------------------------------
@@ -690,7 +690,7 @@ details:
     print_info_msg "
 ========================================================================
 External model files needed for generating initial condition and surface 
-fields for the FV3SAR successfully fetched from HPSS!!!
+fields for the FV3-LAM successfully fetched from HPSS!!!
 
 Exiting script:  \"${scrfunc_fn}\"
 In directory:    \"${scrfunc_dir}\"
@@ -701,7 +701,7 @@ In directory:    \"${scrfunc_dir}\"
     print_info_msg "
 ========================================================================
 External model files needed for generating lateral boundary conditions
-on the halo of the FV3SAR's regional grid successfully fetched from 
+on the halo of the FV3-LAM's regional grid successfully fetched from 
 HPSS!!!
 
 Exiting script:  \"${scrfunc_fn}\"

scripts/exregional_make_grid.sh

@@ -189,7 +189,7 @@ mkdir_vrfy -p "$tmpdir"
 # GRID_DIR.  Note that the file for tile 7 will include a halo of width
 # NHW cells.
 #
-# Since tiles 1 through 6 are not needed to run the FV3SAR model and are
+# Since tiles 1 through 6 are not needed to run the FV3-LAM model and are
 # not used later on in any other preprocessing steps, it is not clear
 # why they are generated.  It might be because it is not possible to di-
 # rectly generate a standalone regional grid using the make_hgrid uti-
@@ -283,7 +283,7 @@ mkdir_vrfy -p "$tmpdir"
 #
 if [ "${GRID_GEN_METHOD}" = "GFDLgrid" ]; then
   exec_fn="make_hgrid"
-elif [ "${GRID_GEN_METHOD}" = "JPgrid" ]; then
+elif [ "${GRID_GEN_METHOD}" = "ESGgrid" ]; then
   exec_fn="regional_grid"
 fi
 
@@ -343,11 +343,11 @@ nonzero exit code.
 #
   grid_fn="${grid_name}.tile${TILE_RGNL}.nc"
 #
-# Generate a JPgrid-type of grid.
+# Generate a ESGgrid-type of grid.
 #
-elif [ "${GRID_GEN_METHOD}" = "JPgrid" ]; then
+elif [ "${GRID_GEN_METHOD}" = "ESGgrid" ]; then
 #
-# Create the namelist file read in by the JPgrid-type grid generation
+# Create the namelist file read in by the ESGgrid-type grid generation
 # code in the temporary subdirectory.
 #
   rgnl_grid_nml_fp="$tmpdir/${RGNL_GRID_NML_FN}"
@@ -372,9 +372,9 @@ generation executable (exec_fp):
     'dely': ${DEL_ANGLE_Y_SG},
     'lx': ${NEG_NX_OF_DOM_WITH_WIDE_HALO},
     'ly': ${NEG_NY_OF_DOM_WITH_WIDE_HALO},
-    'a': ${JPgrid_ALPHA_PARAM},
-    'k': ${JPgrid_KAPPA_PARAM},
- }
+    'a': ${ESGgrid_ALPHA_PARAM},
+    'k': ${ESGgrid_KAPPA_PARAM},
+}
 "
 #
 # Call the python script to create the namelist file.
@@ -393,7 +393,7 @@ $settings"
 #
   $APRUN ${exec_fp} ${rgnl_grid_nml_fp} || \
     print_err_msg_exit "\
-Call to executable (exec_fp) that generates a JPgrid-type regional grid
+Call to executable (exec_fp) that generates a ESGgrid-type regional grid
 returned with nonzero exit code:
   exec_fp = \"${exec_fp}\"" 
 #
@@ -461,7 +461,7 @@ if [ "${GRID_GEN_METHOD}" = "GFDLgrid" ]; then
   else
     CRES="C${res_equiv}"
   fi
-elif [ "${GRID_GEN_METHOD}" = "JPgrid" ]; then
+elif [ "${GRID_GEN_METHOD}" = "ESGgrid" ]; then
   CRES="C${res_equiv}"
 fi
 set_file_param "${GLOBAL_VAR_DEFNS_FP}" "CRES" "\"$CRES\""
@@ -482,22 +482,22 @@ mv_vrfy "${grid_fp_orig}" "${grid_fp}"
 #
 # If there are pre-existing orography or climatology files that we will
 # be using (i.e. if RUN_TASK_MAKE_OROG or RUN_TASK_MAKE_SURF_CLIMO is set
-# to "FALSE", in which case RES_IN_FIXSAR_FILENAMES will not be set to a
+# to "FALSE", in which case RES_IN_FIXLAM_FILENAMES will not be set to a
 # null string), check that the grid resolution contained in the variable
 # CRES set above matches the resolution appearing in the names of the 
 # preexisting orography and/or surface climatology files.
 #
 #-----------------------------------------------------------------------
 #
-if [ ! -z "${RES_IN_FIXSAR_FILENAMES}" ]; then
+if [ ! -z "${RES_IN_FIXLAM_FILENAMES}" ]; then
   res="${CRES:1}"
-  if [ "$res" -ne "${RES_IN_FIXSAR_FILENAMES}" ]; then
+  if [ "$res" -ne "${RES_IN_FIXLAM_FILENAMES}" ]; then
     print_err_msg_exit "\
 The resolution (res) calculated for the grid does not match the resolution 
-(RES_IN_FIXSAR_FILENAMES) appearing in the names of the orography and/or
+(RES_IN_FIXLAM_FILENAMES) appearing in the names of the orography and/or
 surface climatology files:
   res = \"$res\"
-  RES_IN_FIXSAR_FILENAMES = \"${RES_IN_FIXSAR_FILENAMES}\""
+  RES_IN_FIXLAM_FILENAMES = \"${RES_IN_FIXLAM_FILENAMES}\""
   fi
 fi
 #
@@ -635,7 +635,7 @@ halo failed."
 #
 #-----------------------------------------------------------------------
 #
-# Create symlinks in the FIXsar directory to the grid and mosaic files 
+# Create symlinks in the FIXLAM directory to the grid and mosaic files 
 # generated above in the GRID_DIR directory.
 #
 #-----------------------------------------------------------------------
@@ -654,7 +654,7 @@ failed."
 # paths to the surface climatology files.  These files will either already 
 # be avaialable in a user-specified directory (SFC_CLIMO_DIR) or will be
 # generated by the MAKE_SFC_CLIMO_TN task.  They (or symlinks to them) 
-# will be placed (or wll already exist) in the FIXsar directory.
+# will be placed (or wll already exist) in the FIXLAM directory.
 #
 # Also, if running ensemble forecasts, call a function (set_FV3nml_stoch_params) 
 # to create a new FV3 namelist file for each ensemble member that contains 

scripts/exregional_make_ics.sh

@@ -376,7 +376,7 @@ HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
 # These geogrid files need to be moved to more permanent locations.
 #
   if [ "${MACHINE}" = "HERA" ]; then
-    geogrid_file_input_grid="/scratch2/BMC/det/beck/FV3-SAR/geo_em.d01.nc_HRRRX"
+    geogrid_file_input_grid="/scratch2/BMC/det/beck/FV3-LAM/geo_em.d01.nc_HRRRX"
   elif [ "${MACHINE}" = "JET" ]; then
     geogrid_file_input_grid="/misc/whome/rtrr/HRRR/static/WPS/geo_em.d01.nc"
   fi
@@ -415,7 +415,7 @@ HRRRX grib2 files created after about \"${cdate_min_HRRRX}\"..."
 # These geogrid files need to be moved to more permanent locations.
 #
   if [ "${MACHINE}" = "HERA" ]; then
-    geogrid_file_input_grid="/scratch2/BMC/det/beck/FV3-SAR/geo_em.d01.nc_RAPX"
+    geogrid_file_input_grid="/scratch2/BMC/det/beck/FV3-LAM/geo_em.d01.nc_RAPX"
   elif [ "${MACHINE}" = "JET" ]; then
     geogrid_file_input_grid="/misc/whome/rtrr/HRRR/static/WPS/geo_em.d01.nc"
   fi
@@ -457,7 +457,7 @@ exec_fn="chgres_cube.exe"
 exec_fp="$EXECDIR/${exec_fn}"
 if [ ! -f "${exec_fp}" ]; then
   print_err_msg_exit "\
-The executable (exec_fp) for generating initial conditions on the FV3SAR
+The executable (exec_fp) for generating initial conditions on the FV3-LAM
 native grid does not exist:
   exec_fp = \"${exec_fp}\"
 Please ensure that you've built this executable."
@@ -508,7 +508,7 @@ fi
 # config.C768.nest.atm.theia.nml:23: tracers_input="sphum","liq_wat","o3mr","ice_wat","rainwat","snowwat","graupel"
 
 
-# fix_dir_target_grid="${BASEDIR}/JP_grid_HRRR_like_fix_files_chgres_cube"
+# fix_dir_target_grid="${BASEDIR}/ESG_grid_HRRR_like_fix_files_chgres_cube"
 # base_install_dir="${SORCDIR}/chgres_cube.fd"
 
 #
@@ -520,9 +520,9 @@ fi
 #
 settings="
 'config': {
- 'fix_dir_target_grid': ${FIXsar},
- 'mosaic_file_target_grid': ${FIXsar}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc,
- 'orog_dir_target_grid': ${FIXsar},
+ 'fix_dir_target_grid': ${FIXLAM},
+ 'mosaic_file_target_grid': ${FIXLAM}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc,
+ 'orog_dir_target_grid': ${FIXLAM},
  'orog_files_target_grid': ${CRES}${DOT_OR_USCORE}oro_data.tile${TILE_RGNL}.halo${NH4}.nc,
  'vcoord_file_target_grid': ${FIXam}/global_hyblev.l65.txt,
  'mosaic_file_input_grid': '',
@@ -587,7 +587,7 @@ $settings"
 ${APRUN} ${exec_fp} || \
   print_err_msg_exit "\
 Call to executable (exec_fp) to generate surface and initial conditions
-(ICs) files for the FV3SAR failed:
+(ICs) files for the FV3-LAM failed:
   exec_fp = \"${exec_fp}\"
 The external model from which the ICs files are to be generated is:
   EXTRN_MDL_NAME_ICS = \"${EXTRN_MDL_NAME_ICS}\"

scripts/exregional_make_lbcs.sh

@@ -369,7 +369,7 @@ exec_fn="chgres_cube.exe"
 exec_fp="$EXECDIR/${exec_fn}"
 if [ ! -f "${exec_fp}" ]; then
   print_err_msg_exit "\
-The executable (exec_fp) for generating initial conditions on the FV3SAR
+The executable (exec_fp) for generating initial conditions on the FV3-LAM
 native grid does not exist:
   exec_fp = \"${exec_fp}\"
 Please ensure that you've built this executable."
@@ -378,7 +378,7 @@ fi
 #-----------------------------------------------------------------------
 #
 # Loop through the LBC update times and run chgres for each such time to
-# obtain an LBC file for each that can be used as input to the FV3SAR.
+# obtain an LBC file for each that can be used as input to the FV3-LAM.
 #
 #-----------------------------------------------------------------------
 #
@@ -450,9 +450,9 @@ list file has not specified for this external model:
 #
   settings="
 'config': {
- 'fix_dir_target_grid': ${FIXsar},
- 'mosaic_file_target_grid': ${FIXsar}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc,
- 'orog_dir_target_grid': ${FIXsar},
+ 'fix_dir_target_grid': ${FIXLAM},
+ 'mosaic_file_target_grid': ${FIXLAM}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc,
+ 'orog_dir_target_grid': ${FIXLAM},
  'orog_files_target_grid': ${CRES}${DOT_OR_USCORE}oro_data.tile7.halo${NH4}.nc,
  'vcoord_file_target_grid': ${FIXam}/global_hyblev.l65.txt,
  'mosaic_file_input_grid': '',
@@ -510,7 +510,7 @@ $settings"
   ${APRUN} ${exec_fp} || \
     print_err_msg_exit "\
 Call to executable (exec_fp) to generate lateral boundary conditions (LBCs)
-file for the FV3SAR for forecast hour fhr failed:
+file for the FV3-LAM for forecast hour fhr failed:
   exec_fp = \"${exec_fp}\"
   fhr = \"$fhr\"
 The external model from which the LBCs files are to be generated is:
@@ -521,11 +521,11 @@ located in the following directory:
 #
 # Move LBCs file for the current lateral boundary update time to the LBCs
 # work directory.  Note that we rename the file by including in its name
-# the forecast hour of the FV3SAR (which is not necessarily the same as
+# the forecast hour of the FV3-LAM (which is not necessarily the same as
 # that of the external model since their start times may be offset).
 #
-  fcst_hhh_FV3SAR=$( printf "%03d" "${LBC_SPEC_FCST_HRS[$i]}" )
-  mv_vrfy gfs_bndy.nc ${lbcs_dir}/gfs_bndy.tile7.${fcst_hhh_FV3SAR}.nc
+  fcst_hhh_FV3LAM=$( printf "%03d" "${LBC_SPEC_FCST_HRS[$i]}" )
+  mv_vrfy gfs_bndy.nc ${lbcs_dir}/gfs_bndy.tile7.${fcst_hhh_FV3LAM}.nc
 
 done
 #

scripts/exregional_make_orog.sh

@@ -219,10 +219,10 @@ cp_vrfy ${TOPO_DIR}/gmted2010.30sec.int fort.235
 #-----------------------------------------------------------------------
 #
 mosaic_fn="${CRES}${DOT_OR_USCORE}mosaic.halo${NHW}.nc"
-mosaic_fp="$FIXsar/${mosaic_fn}"
+mosaic_fp="$FIXLAM/${mosaic_fn}"
 
 grid_fn=$( get_charvar_from_netcdf "${mosaic_fp}" "gridfiles" )
-grid_fp="${FIXsar}/${grid_fn}"
+grid_fp="${FIXLAM}/${grid_fn}"
 #
 #-----------------------------------------------------------------------
 #
@@ -300,7 +300,7 @@ case $MACHINE in
 ${ufs_utils_ushdir}/${orog_gen_scr} \
 $res \
 ${TILE_RGNL} \
-${FIXsar} \
+${FIXLAM} \
 ${raw_dir} \
 ${UFS_UTILS_DIR} \
 ${TOPO_DIR} \
@@ -348,7 +348,7 @@ Orography file generation complete."
 #-----------------------------------------------------------------------
 #
 # Note that the orography filtering code assumes that the regional grid
-# is a GFDLgrid type of grid; it is not designed to handle JPgrid type
+# is a GFDLgrid type of grid; it is not designed to handle ESGgrid type
 # regional grids.  If the flag "regional" in the orography filtering 
 # namelist file is set to .TRUE. (which it always is will be here; see
 # below), then filtering code will first calculate a resolution (i.e. 
@@ -370,7 +370,7 @@ Orography file generation complete."
 # resolution of res_regional.  These interpolated/extrapolated values are
 # then used to perform the orography filtering.
 #
-# The above approach works for a GFDLgrid type of grid.  To handle JPgrid
+# The above approach works for a GFDLgrid type of grid.  To handle ESGgrid
 # type grids, we set res in the namelist to the orography filtering code
 # the equivalent global uniform cubed-sphere resolution of the regional
 # grid, we set stretch_fac to 1 (since the equivalent resolution assumes
@@ -398,7 +398,7 @@ if [ "${GRID_GEN_METHOD}" = "GFDLgrid" ]; then
 #  stretch_fac="${GFDLgrid_STRETCH_FAC}"
   refine_ratio="${GFDLgrid_REFINE_RATIO}"
 
-elif [ "${GRID_GEN_METHOD}" = "JPgrid" ]; then
+elif [ "${GRID_GEN_METHOD}" = "ESGgrid" ]; then
 
   res="${CRES:1}"
 #  stretch_fac="${STRETCH_FAC}"

scripts/exregional_make_sfc_climo.sh

@@ -110,8 +110,8 @@ input_slope_type_file="${SFC_CLIMO_INPUT_DIR}/slope_type.1.0.nc"
 input_soil_type_file="${SFC_CLIMO_INPUT_DIR}/soil_type.statsgo.0.05.nc"
 input_vegetation_type_file="${SFC_CLIMO_INPUT_DIR}/vegetation_type.igbp.0.05.nc"
 input_vegetation_greenness_file="${SFC_CLIMO_INPUT_DIR}/vegetation_greenness.0.144.nc"
-mosaic_file_mdl="${FIXsar}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc"
-orog_dir_mdl="${FIXsar}"
+mosaic_file_mdl="${FIXLAM}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc"
+orog_dir_mdl="${FIXLAM}"
 orog_files_mdl=${CRES}${DOT_OR_USCORE}oro_data.tile${TILE_RGNL}.halo${NH4}.nc
 halo=${NH4}
 maximum_snow_albedo_method="bilinear"