Add and call a function that checks for use of Thompson microphysics …

…parameterization in the SDF and if so, adjusts certain workflow arrays to contain the names and other associated values of the fixed files needed by this parameterization so that those files are automatically copied and/or linked to. (#319)

## DESCRIPTION OF CHANGES: 
Add and call a function that checks for use of Thompson microphysics parameterization in the suite definition file (SDF).  If not, do nothing.  If so, add to the appropriate workflow arrays the names and other associated values of the fixed files needed by this parameterization so that they are automatically copied and/or linked to instead of being regenerated from scratch in the run_fcst task.

## TESTS CONDUCTED: 
On hera, ran two WE2E tests, one in NCO mode (nco_RRFS_CONUS_25km_HRRRX_RAPX) and the other in community mode (suite_FV3_GSD_v0).  These use suites FV3_GSD_SAR and FV3_GSD_v0, respectively, and both of these call Thompson microphysics.  Both succeeded.

## ISSUE (optional):
This PR resolves issue #297.

scripts/exregional_run_fcst.sh

@@ -88,57 +88,63 @@ print_input_args valid_args
 #-----------------------------------------------------------------------
 #
 case $MACHINE in
-#
-"WCOSS_CRAY")
-#
-  ulimit -s unlimited
-  ulimit -a
-  APRUN="aprun -b -j1 -n${PE_MEMBER01} -N24 -d1 -cc depth"
-  ;;
-#
-"WCOSS_DELL_P3")
-  ulimit -s unlimited
-  ulimit -a
-  APRUN="mpirun -l -np ${PE_MEMBER01}"
-  ;;
-#
-"HERA")
-  ulimit -s unlimited
-  ulimit -a
-  APRUN="srun"
-  OMP_NUM_THREADS=4
-  ;;
-#
-"JET")
-  ulimit -s unlimited
-  ulimit -a
-  APRUN="srun"
-  OMP_NUM_THREADS=4
-  ;;
-#
-"ODIN")
-#
-  module list
-
-  ulimit -s unlimited
-  ulimit -a
-  APRUN="srun -n ${PE_MEMBER01}"
-  ;;
-#
-"CHEYENNE")
-#
-  module list
-  nprocs=$(( NNODES_RUN_FCST*PPN_RUN_FCST ))
-  APRUN="mpirun -np $nprocs"
-  ;;
-#
-
-"STAMPEDE")
-#
-  module list
 
-  APRUN="ibrun -np ${PE_MEMBER01}"
-  ;;
+  "WCOSS_CRAY")
+    ulimit -s unlimited
+    ulimit -a
+    APRUN="aprun -b -j1 -n${PE_MEMBER01} -N24 -d1 -cc depth"
+    ;;
+
+  "WCOSS_DELL_P3")
+    ulimit -s unlimited
+    ulimit -a
+    APRUN="mpirun -l -np ${PE_MEMBER01}"
+    ;;
+
+  "HERA")
+    ulimit -s unlimited
+    ulimit -a
+    APRUN="srun"
+    OMP_NUM_THREADS=4
+    ;;
+
+  "ORION")
+    ulimit -s unlimited
+    ulimit -a
+    APRUN="srun"
+    ;;
+
+  "JET")
+    ulimit -s unlimited
+    ulimit -a
+    APRUN="srun"
+    OMP_NUM_THREADS=4
+    ;;
+
+  "ODIN")
+    module list
+    ulimit -s unlimited
+    ulimit -a
+    APRUN="srun -n ${PE_MEMBER01}"
+    ;;
+
+  "CHEYENNE")
+    module list
+    nprocs=$(( NNODES_RUN_FCST*PPN_RUN_FCST ))
+    APRUN="mpirun -np $nprocs"
+    ;;
+
+  "STAMPEDE")
+    module list
+    APRUN="ibrun -np ${PE_MEMBER01}"
+    ;;
+
+  *)
+    print_err_msg_exit "\
+Run command has not been specified for this machine:
+  MACHINE = \"$MACHINE\"
+  APRUN = \"$APRUN\""
+    ;;
 
 esac
 #
@@ -152,13 +158,13 @@ run_dir="${cycle_dir}${slash_ensmem_subdir}"
 #
 #-----------------------------------------------------------------------
 #
-# Create links in the INPUT subdirectory of the current run directory to 
+# Create links in the INPUT subdirectory of the current run directory to
 # the grid and (filtered) orography files.
 #
 #-----------------------------------------------------------------------
 #
 print_info_msg "$VERBOSE" "
-Creating links in the INPUT subdirectory of the current run directory to 
+Creating links in the INPUT subdirectory of the current run directory to
 the grid and (filtered) orography files ..."
 
 
@@ -249,14 +255,14 @@ Cannot create symlink because target does not exist:
 fi
 #
 # If using the FV3_RRFS_v1beta physics suite, there are two files (that
-# contain statistics of the orography) that are needed by the drag 
+# contain statistics of the orography) that are needed by the drag
 # parameterization in that suite.  Below, symlinks to these are created
 # in the run directory.  Note that the symlinks must have specific names
-# that the FV3 model is hardcoded to recognize ("${CRES}_" and "halo0" 
+# that the FV3 model is hardcoded to recognize ("${CRES}_" and "halo0"
 # must be stripped from the file names).  We use those below.
 #
 if [ "${CCPP_PHYS_SUITE}" = "FV3_RRFS_v1beta" ]; then
-# Symlink to orographic statistics fields file with "${CRES}_" and "halo0" 
+# Symlink to orographic statistics fields file with "${CRES}_" and "halo0"
 # stripped from name.
   target="${FIXLAM}/${CRES}${DOT_OR_USCORE}oro_data_ls.tile${TILE_RGNL}.halo${NH0}.nc"
   symlink="oro_data_ls.nc"
@@ -312,7 +318,7 @@ fi
 #   gfs_bndy*.nc
 #   gfs_ctrl.nc
 #
-# Some of these files (gfs_ctrl.nc, gfs_bndy*.nc) already exist, but 
+# Some of these files (gfs_ctrl.nc, gfs_bndy*.nc) already exist, but
 # others do not.  Thus, create links with these names to the appropriate
 # files (in this case the initial condition and surface files only).
 #
@@ -353,17 +359,17 @@ fi
 #-----------------------------------------------------------------------
 #
 # Create links in the current run directory to fixed (i.e. static) files
-# in the FIXam directory.  These links have names that are set to the 
+# in the FIXam directory.  These links have names that are set to the
 # names of files that the forecast model expects to exist in the current
-# working directory when the forecast model executable is called (and 
+# working directory when the forecast model executable is called (and
 # that is just the run directory).
 #
 #-----------------------------------------------------------------------
 #
 cd_vrfy ${run_dir}
 
 print_info_msg "$VERBOSE" "
-Creating links in the current run directory (run_dir) to fixed (i.e. 
+Creating links in the current run directory (run_dir) to fixed (i.e.
 static) files in the FIXam directory:
   FIXam = \"${FIXam}\"
   run_dir = \"${run_dir}\""
@@ -397,8 +403,8 @@ done
 #
 #-----------------------------------------------------------------------
 #
-# If running this cycle/ensemble member combination more than once (e.g. 
-# using rocotoboot), remove any time stamp file that may exist from the 
+# If running this cycle/ensemble member combination more than once (e.g.
+# using rocotoboot), remove any time stamp file that may exist from the
 # previous attempt.
 #
 #-----------------------------------------------------------------------
@@ -409,13 +415,13 @@ rm_vrfy -f time_stamp.out
 #-----------------------------------------------------------------------
 #
 # Create links in the current run directory to cycle-independent (and
-# ensemble-member-independent) model input files in the main experiment 
+# ensemble-member-independent) model input files in the main experiment
 # directory.
 #
 #-----------------------------------------------------------------------
 #
 print_info_msg "$VERBOSE" "
-Creating links in the current run directory to cycle-independent model 
+Creating links in the current run directory to cycle-independent model
 input files in the main experiment directory..."
 
 relative_or_null=""
@@ -432,13 +438,6 @@ if [ "${DO_ENSEMBLE}" = TRUE ]; then
 else
   ln_vrfy -sf ${relative_or_null} ${FV3_NML_FP} ${run_dir}
 fi
-
-ln_vrfy -sf ${relative_or_null} ${CCPP_PHYS_SUITE_FP} ${run_dir} 
-if [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_v0" ] || \
-   [ "${CCPP_PHYS_SUITE}" = "FV3_RRFS_v1beta" ] || \
-   [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_SAR" ]; then
-  ln_vrfy -sf ${relative_or_null} $EXPTDIR/CCN_ACTIVATE.BIN ${run_dir}
-fi
 #
 #-----------------------------------------------------------------------
 #
@@ -451,17 +450,17 @@ create_model_configure_file \
   cdate="$cdate" \
   nthreads=${OMP_NUM_THREADS:-1} \
   run_dir="${run_dir}" || print_err_msg_exit "\
-Call to function to create a model configuration file for the current 
+Call to function to create a model configuration file for the current
 cycle's (cdate) run directory (run_dir) failed:
   cdate = \"${cdate}\"
   run_dir = \"${run_dir}\""
 #
 #-----------------------------------------------------------------------
 #
-# If running ensemble forecasts, create a link to the cycle-specific 
-# diagnostic tables file in the cycle directory.  Note that this link 
-# should not be made if not running ensemble forecasts because in that 
-# case, the cycle directory is the run directory (and we would be creating 
+# If running ensemble forecasts, create a link to the cycle-specific
+# diagnostic tables file in the cycle directory.  Note that this link
+# should not be made if not running ensemble forecasts because in that
+# case, the cycle directory is the run directory (and we would be creating
 # a symlink with the name of a file that already exists).
 #
 #-----------------------------------------------------------------------
@@ -486,15 +485,15 @@ export OMP_STACKSIZE=1024m
 #-----------------------------------------------------------------------
 #
 # Run the FV3-LAM model.  Note that we have to launch the forecast from
-# the current cycle's directory because the FV3 executable will look for 
-# input files in the current directory.  Since those files have been 
+# the current cycle's directory because the FV3 executable will look for
+# input files in the current directory.  Since those files have been
 # staged in the cycle directory, the current directory must be the cycle
 # directory (which it already is).
 #
 #-----------------------------------------------------------------------
 #
 $APRUN ${FV3_EXEC_FP} || print_err_msg_exit "\
-Call to executable to run FV3-LAM forecast returned with nonzero exit 
+Call to executable to run FV3-LAM forecast returned with nonzero exit
 code."
 #
 #-----------------------------------------------------------------------

ush/generate_FV3LAM_wflow.sh

@@ -518,25 +518,6 @@ print_info_msg "$VERBOSE" "
 Copying the CCPP physics suite definition XML file from its location in
 the forecast model directory sturcture to the experiment directory..."
 cp_vrfy "${CCPP_PHYS_SUITE_IN_CCPP_FP}" "${CCPP_PHYS_SUITE_FP}"
-#
-# If using a physics suite that includes the Thompson microphysics 
-# parameterization, copy the fixed file containing cloud condensation 
-# nuclei (CCN) data that is needed by that parameterization.
-#
-if [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_v0" ] || \
-   [ "${CCPP_PHYS_SUITE}" = "FV3_RRFS_v1beta" ] || \
-   [ "${CCPP_PHYS_SUITE}" = "FV3_GSD_SAR" ]; then
-  print_info_msg "$VERBOSE" "
-Copying the fixed file containing cloud condensation nuclei (CCN) data
-(needed by the Thompson microphysics parameterization) to the experiment
-directory..."
-  cp_vrfy "${FIXgsm}/CCN_ACTIVATE.BIN" "$EXPTDIR"
-fi
-
-
-
-
-
 #
 #-----------------------------------------------------------------------
 #

ush/set_ozone_param.sh

@@ -203,9 +203,9 @@ After setting the file name of the ozone production/loss file in the
 FIXgsm directory (based on the ozone parameterization specified in the
 CCPP suite definition file), the array specifying the mapping between
 the symlinks that need to be created in the cycle directories and the
-files in the FIXgsm directory is:
+files in the FIXam directory is:
 
-CYCLEDIR_LINKS_TO_FIXam_FILES_MAPPING = ( \\
+  CYCLEDIR_LINKS_TO_FIXam_FILES_MAPPING = ( \\
 "
   msg="$msg"$( printf "\"%s\" \\\\\n" "${CYCLEDIR_LINKS_TO_FIXam_FILES_MAPPING[@]}" )
   msg="$msg"$( printf "\n)" )