The HAFS related developments for the write_grid_component (#10)

* output nested domain on cubed sphere grid

* output native cubed sphere grid for regional fv3 and nested fv3

* add HWRF PBL and surface drag for HAFS (sfc_diff.f, moninedmf.f, GFS_typedefs.F90, GFS_physics_driver.F90 modified)

* add back HWRF PBL and sfc drag after master revert fractional land/sea mask

* Enable outputing a grid from the write grid component, which is larger than the native computation grid of the nested/regional domain.
a. Remove the limitation of the output grid being completely inside the model native compuation grid.
b. Mask out the output grid points outside the computation grid with missing values.

* update HAFS with HWRF PBL/sfc drag

* add option to switch GWD on/off

* support/HAFS: Clean up before merging features back the develop branch.

* support/HAFS: Change the missing value in FV3GFS_io to default real type.

fv3_cap.F90

@@ -32,7 +32,7 @@ module fv3gfs_cap_mod
                                     cplprint_flag,output_1st_tstep_rst,      &
                                     first_kdt                            
 
-  use module_fv3_io_def,      only: num_pes_fcst,write_groups,               &
+  use module_fv3_io_def,      only: num_pes_fcst,write_groups,app_domain,    &
                                     num_files, filename_base,                &
                                     wrttasks_per_group, n_group,             &
                                     lead_wrttask, last_wrttask,              &
@@ -322,6 +322,10 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
                                    label ='write_tasks_per_group:',rc=rc)
       if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return
 
+      CALL ESMF_ConfigGetAttribute(config=CF,value=app_domain, default="global", &
+                                   label ='app_domain:',rc=rc)
+      if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return
+
       if(mype == 0) print *,'af nems config,restart_interval=',restart_interval, &
       'quilting=',quilting,'write_groups=',write_groups,wrttasks_per_group,      &
       'calendar=',trim(calendar),'calendar_type=',calendar_type
@@ -692,6 +696,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
             isrctermprocessing = 1
             call ESMF_FieldBundleRegridStore(fcstFB(j), wrtFB(j,i),                                    &
                                              regridMethod=regridmethod, routehandle=routehandle(j,i),  &
+                                             unmappedaction=ESMF_UNMAPPEDACTION_IGNORE,                &
                                              srcTermProcessing=isrctermprocessing, rc=rc)
 
 !           if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return

io/FV3GFS_io.F90

@@ -101,8 +101,7 @@ module FV3GFS_io_mod
   logical                    :: uwork_set = .false.
   character(128)             :: uwindname
   integer, parameter, public :: DIAG_SIZE = 500
-! real(kind=kind_phys), parameter :: missing_value = 1.d30
-  real(kind=kind_phys), parameter :: missing_value = 9.99e20
+  real, parameter :: missing_value = 9.99e20
   real, parameter:: stndrd_atmos_ps = 101325.
   real, parameter:: stndrd_atmos_lapse = 0.0065
 

io/module_fv3_io_def.F90

@@ -15,6 +15,7 @@ module module_fv3_io_def
   logical           :: write_nemsioflip
   logical           :: write_fsyncflag
   integer           :: num_files
+  character(255)    :: app_domain
   character(255)    :: output_grid
   character(255)    :: output_file
   integer           :: imo,jmo