Implements CCPP-ized tropopause_find (#293)

Companion PR: ESCOMP/atmospheric_physics#112

Note: I think I brought in more changes than necessary in `ncar_ccpp`
due to the my `atmospheric_physics` branch being based off `development`
rather than the released used in CAM-SIMA. I can do a rebase if
necessary...

## Changes made to support CCPP-ized tropopause_find
* Copied utility module `interpolate_data.F90` from CAM
* Added utility module `tropopause_read_file.F90` to provide
climatological tropopause data to tropopause_find from CAM-SIMA
* `&tropopause_nl tropopause_climo_file` is read from
`tropopause_read_file.F90` inside SIMA and not in the parameterization,
to avoid passing this file name back and forth between the
parameterization to CAM-SIMA
* Adds `get_curr_calday()` result to new standard name variable
`fractional_calendar_days_on_end_of_current_timestep`
* Submodule update (possibly need a rebase?)

I recommend manually merging in the history PR for testing. It might be
easier to merge my branch (`jimmielin:hplin/tropopause_find`) into
`peverwhee:history_court`.

.gitmodules

@@ -14,7 +14,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
         url           = https://github.com/ESCOMP/atmospheric_physics
-        fxtag         = 098585940ad763be58ebab849bb8eaf325fda42a
+        fxtag         = atmos_phys0_05_000
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

cime_config/namelist_definition_cam.xml

@@ -333,6 +333,19 @@
     </values>
   </entry>
 
+<!-- Tropopause -->
+  <entry id="tropopause_climo_file">
+    <type>char*256</type>
+    <category>tropopause</category>
+    <group>tropopause_nl</group>
+    <desc>
+      Full pathname of boundary dataset for tropopause climatology.
+    </desc>
+    <values>
+      <value>${DIN_LOC_ROOT}/atm/cam/chem/trop_mozart/ub/clim_p_trop.nc</value>
+    </values>
+  </entry>
+
 <!-- Vertical Coordinate -->
 
   <entry id="pver">
@@ -364,7 +377,7 @@
     <group>cam_logfile_nl</group>
     <valid_values>0,1,2,3</valid_values>
     <desc>
-      Include exra checks and logging output.
+      Include extra checks and logging output.
       0: No extra checks or output
       1: Extra informational output
       2: Level 1 plus extra checks and informational output

src/control/cam_comp.F90

@@ -23,10 +23,12 @@ module cam_comp
    use time_manager,              only: timemgr_init, get_step_size
    use time_manager,              only: get_nstep
    use time_manager,              only: is_first_step, is_first_restart_step
+   use time_manager,              only: get_curr_calday
 
    use camsrfexch,                only: cam_out_t, cam_in_t
    use physics_types,             only: phys_state, phys_tend
    use physics_types,             only: dtime_phys
+   use physics_types,             only: calday
    use dyn_comp,                  only: dyn_import_t, dyn_export_t
 
    use perf_mod,                  only: t_barrierf, t_startf, t_stopf
@@ -98,6 +100,7 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
       use physics_grid,         only: columns_on_task
       use vert_coord,           only: pver
       use phys_vars_init_check, only: mark_as_initialized
+      use tropopause_climo_read, only: tropopause_climo_read_file
 
       ! Arguments
       character(len=cl), intent(in) :: caseid                ! case ID
@@ -163,11 +166,16 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
 
       call cam_ctrl_set_orbit(eccen, obliqr, lambm0, mvelpp)
 
+
       call timemgr_init(                                                      &
            dtime, calendar, start_ymd, start_tod, ref_ymd,                    &
            ref_tod, stop_ymd, stop_tod, curr_ymd, curr_tod,                   &
            perpetual_run, perpetual_ymd, initial_run_in)
 
+      ! Get current fractional calendar day. Needs to be updated at every timestep.
+      calday = get_curr_calday()
+      call mark_as_initialized('fractional_calendar_days_on_end_of_current_timestep')
+
       ! Read CAM namelists.
       filein = "atm_in" // trim(inst_suffix)
       call read_namelist(filein, single_column, scmlat, scmlon)
@@ -224,6 +232,9 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
 !!XXgoldyXX: ^ need to import this
       end if
 
+      ! Read tropopause climatology
+      call tropopause_climo_read_file()
+
       call phys_init()
 
 !!XXgoldyXX: v need to import this
@@ -270,6 +281,9 @@ subroutine cam_timestep_init()
       !
       call phys_timestep_init()
 
+      ! Update current fractional calendar day. Needs to be updated at every timestep.
+      calday = get_curr_calday()
+
    end subroutine cam_timestep_init
    !
    !-----------------------------------------------------------------------

src/control/runtime_opts.F90

@@ -44,6 +44,8 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
 !      use cam_diagnostics,     only: diag_readnl
       use inic_analytic_utils, only: analytic_ic_readnl
 
+      use tropopause_climo_read, only: tropopause_climo_readnl
+
 !      use tracers,             only: tracers_readnl
 !      use nudging,             only: nudging_readnl
 
@@ -99,6 +101,7 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
 !      call diag_readnl(nlfilename)
 !      call check_energy_readnl(nlfilename)
       call analytic_ic_readnl(nlfilename)
+      call tropopause_climo_readnl(nlfilename)
 !      call scam_readnl(nlfilename, single_column, scmlat, scmlon)
 !      call nudging_readnl(nlfilename)
 

src/data/generate_registry_data.py

@@ -26,6 +26,7 @@
     sys.path.append(__SPINSCRIPTS)
 # end if
 _ALL_STRINGS_REGEX = re.compile(r'[A-Za-z][A-Za-z_0-9]+')
+_FORTRAN_NUMERIC_REGEX = re.compile(r'^[+-]?(\d+\.?\d*|\.\d+)([eE][+-]?\d+)?(_kind_phys)?$')
 
 # CCPP framework imports
 # pylint: disable=wrong-import-position
@@ -940,9 +941,9 @@ def add_variable(self, newvar):
         all_strings = _ALL_STRINGS_REGEX.findall(newvar.initial_value)
         init_val_vars = set()
         excluded_initializations = {'null', 'nan', 'false', 'true'}
-        # Exclude NULL and nan variables
+        # Exclude NULL and nan variables and valid Fortran numeric values that pass the string regex (e.g. 1.e36, -3.2e5)
         for var in all_strings:
-            if var.lower() not in excluded_initializations:
+            if var.lower() not in excluded_initializations and not _FORTRAN_NUMERIC_REGEX.match(newvar.initial_value):
                 init_val_vars.add(var)
             # end if
         # end if

src/data/registry.xml

@@ -10,6 +10,7 @@
   <metadata_file>$SRCROOT/src/data/physconst.meta</metadata_file>
   <metadata_file>$SRCROOT/src/physics/utils/physics_grid.meta</metadata_file>
   <metadata_file>$SRCROOT/src/physics/utils/cam_constituents.meta</metadata_file>
+  <metadata_file>$SRCROOT/src/physics/utils/tropopause_climo_read.meta</metadata_file>
   <metadata_file>$SRCROOT/src/data/air_composition.meta</metadata_file>
   <metadata_file>$SRCROOT/src/data/cam_thermo.meta</metadata_file>
   <metadata_file>$SRCROOT/src/data/ref_pres.meta</metadata_file>
@@ -348,6 +349,12 @@
       <long_name>current timestep number</long_name>
       <initial_value>0</initial_value>
     </variable>
+    <!-- Date and time variables -->
+    <variable local_name="calday"
+              standard_name="fractional_calendar_days_on_end_of_current_timestep"
+              units="1" type="real" kind="kind_phys">
+      <long_name>fractional calendar day at end of current timestep</long_name>
+    </variable>
     <!-- Error handling variables -->
     <variable local_name="errcode"
               standard_name="ccpp_error_code"
@@ -361,6 +368,14 @@
       <long_name>ccpp error message</long_name>
       <initial_value>''</initial_value>
     </variable>
+    <!-- SIMA History (diagnostic output) variables -->
+    <variable local_name="fillvalue"
+              standard_name="fill_value_for_diagnostic_output"
+              units="1" type="real" kind="kind_phys"
+              allocatable="parameter">
+      <long_name>Fill value for diagnostic/history outputs</long_name>
+      <initial_value>1.e36_kind_phys</initial_value>
+    </variable>
     <!-- Composition-dependent Variables -->
     <variable local_name="cpairv"
               standard_name="composition_dependent_specific_heat_of_dry_air_at_constant_pressure"