Add support for optional arguments in ccpp physics and framework (NO…

…AA-EMC#807)

* In ccpp/data/GFS_typedefs.meta: change units 'flashes 5 min-1' to 'flashes min-1' and update long name to make clear this is per 5 minutes

* In ccpp/driver/GFS_diagnostics.F90, scale lightning threat from flashes per minute to flashes per 5 minutes to match diagnostic units

* Fix wrong long names for lightning threat indices in ccpp/data/GFS_typedefs.meta

* Remove invalid active attributes in ccpp/data/GFS_typedefs.meta

* Bug fix for GFDL-MP in CCPP: use correct allocation of variables but internally bend everything back to where it's expected (affects some, but not all variables in CCPP_typedefs.{F90,meta})

* Bug fix in ccpp/data/GFS_typedefs.meta: sncovr_ice is always allocated, remove active attribute

* Bug fix in ccpp/data/CCPP_typedefs.meta small-scale gravity wave drag variables are active for options 2,3,22,33 of gwd, not just 3,33

* Bug fix in ccpp/data/GFS_typedefs.meta: three variables are always allocated, remove active attribute

* More bug fixes for active attributes in ccpp/data/GFS_typedefs.meta

* More bug fixes for allocation dimensions in ccpp/data/CCPP_typedefs.*; optional arguments in stochastic_physics/stochastic_physics_wrapper.F90

* Set ccpp_data's thrd_cnt in ccpp/driver/CCPP_driver.F90

* No default in OMP pragmas in ccpp/driver/CCPP_driver.F90

ccpp/data/CCPP_typedefs.F90

@@ -452,10 +452,18 @@ module CCPP_typedefs
      integer                             :: ie
      integer                             :: isd
      integer                             :: ied
+     integer                             :: isc1
+     integer                             :: iec1
+     integer                             :: isc2
+     integer                             :: iec2
      integer                             :: js
      integer                             :: je
      integer                             :: jsd
      integer                             :: jed
+     integer                             :: jsc1
+     integer                             :: jec1
+     integer                             :: jsc2
+     integer                             :: jec2
      integer                             :: ng
      integer                             :: npz
      integer                             :: npzp1
@@ -1557,6 +1565,18 @@ subroutine gfdl_interstitial_create (Interstitial, is, ie, isd, ied, js, je, jsd
     integer,        intent(in)           :: mpirank
     integer,        intent(in)           :: mpiroot
     !
+    integer :: isc1, jsc1, iec1, jec1
+    integer :: isc2, jsc2, iec2, jec2
+    !
+    isc1 = lbound(delp, dim=1)
+    jsc1 = lbound(delp, dim=2)
+    iec1 = ubound(delp, dim=1)
+    jec1 = ubound(delp, dim=2)
+    isc2 = lbound(delz, dim=1)
+    jsc2 = lbound(delz, dim=2)
+    iec2 = ubound(delz, dim=1)
+    jec2 = ubound(delz, dim=2)
+    !
 #ifdef MOIST_CAPPA
     Interstitial%npzcappa = npz
     allocate (Interstitial%cappa  (isd:ied, jsd:jed, 1:npz) )
@@ -1594,13 +1614,22 @@ subroutine gfdl_interstitial_create (Interstitial, is, ie, isd, ied, js, je, jsd
     Interstitial%ie         =  ie
     Interstitial%isd        =  isd
     Interstitial%ied        =  ied
+    Interstitial%isc1       =  isc1
+    Interstitial%iec1       =  iec1
+    Interstitial%isc2       =  isc2
+    Interstitial%iec2       =  iec2
     Interstitial%js         =  js
     Interstitial%je         =  je
     Interstitial%jsd        =  jsd
     Interstitial%jed        =  jed
+    Interstitial%jsc1       =  jsc1
+    Interstitial%jec1       =  jec1
+    Interstitial%jsc2       =  jsc2
+    Interstitial%jec2       =  jec2
     Interstitial%ng         =  ng
     Interstitial%npz        =  npz
     Interstitial%npzp1      =  npz+1
+    !
     ! Set up links from GFDL_interstitial DDT to ATM DDT
     Interstitial%delp       => delp
     Interstitial%delz       => delz
@@ -1617,6 +1646,7 @@ subroutine gfdl_interstitial_create (Interstitial, is, ie, isd, ied, js, je, jsd
     if (do_qs) Interstitial%qs => qs
     if (do_qg) Interstitial%qg => qg
     if (do_qa) Interstitial%qc => qc
+    !
 #ifdef USE_COND
     Interstitial%npzq_con = npz
 #else

ccpp/data/CCPP_typedefs.meta

@@ -344,7 +344,7 @@
   dimensions = (horizontal_loop_extent,4)
   type = real
   kind = kind_phys
-  active = (control_for_drag_suite_gravity_wave_drag == 3 .or. control_for_drag_suite_gravity_wave_drag == 33)
+  active = (control_for_drag_suite_gravity_wave_drag == 2 .or. control_for_drag_suite_gravity_wave_drag == 3 .or. control_for_drag_suite_gravity_wave_drag == 22 .or. control_for_drag_suite_gravity_wave_drag == 33)
 [cmm_water]
   standard_name = surface_drag_wind_speed_for_momentum_in_air_over_water
   long_name = momentum exchange coefficient over water
@@ -1526,15 +1526,15 @@
   dimensions = (horizontal_loop_extent)
   type = real
   kind = kind_phys
-  active = (control_for_drag_suite_gravity_wave_drag == 3 .or. control_for_drag_suite_gravity_wave_drag == 33)
+  active = (control_for_drag_suite_gravity_wave_drag == 2 .or. control_for_drag_suite_gravity_wave_drag == 3 .or. control_for_drag_suite_gravity_wave_drag == 22 .or. control_for_drag_suite_gravity_wave_drag == 33)
 [oa4ss]
   standard_name = asymmetry_of_subgrid_orography_small_scale
   long_name = asymmetry of subgrid height_above_mean_sea_level small scale
   units = none
   dimensions = (horizontal_loop_extent,4)
   type = real
   kind = kind_phys
-  active = (control_for_drag_suite_gravity_wave_drag == 3 .or. control_for_drag_suite_gravity_wave_drag == 33)
+  active = (control_for_drag_suite_gravity_wave_drag == 2 .or. control_for_drag_suite_gravity_wave_drag == 3 .or. control_for_drag_suite_gravity_wave_drag == 22 .or. control_for_drag_suite_gravity_wave_drag == 33)
 [oc]
   standard_name = convexity_of_subgrid_orography
   long_name = convexity of subgrid height_above_mean_sea_level
@@ -1549,7 +1549,7 @@
   dimensions = (horizontal_loop_extent)
   type = real
   kind = kind_phys
-  active = (control_for_drag_suite_gravity_wave_drag == 3 .or. control_for_drag_suite_gravity_wave_drag == 33)
+  active = (control_for_drag_suite_gravity_wave_drag == 2 .or. control_for_drag_suite_gravity_wave_drag == 3 .or. control_for_drag_suite_gravity_wave_drag == 22 .or. control_for_drag_suite_gravity_wave_drag == 33)
 [olyr]
   standard_name = ozone_concentration_at_layer_for_radiation
   long_name = ozone concentration layer
@@ -2964,6 +2964,30 @@
   units = count
   dimensions = ()
   type = integer
+[isc1]
+  standard_name = starting_x_direction_index_alloc1
+  long_name = starting X direction index for allocation
+  units = count
+  dimensions = ()
+  type = integer
+[iec1]
+  standard_name = ending_x_direction_index_alloc1
+  long_name = ending X direction index for allocation
+  units = count
+  dimensions = ()
+  type = integer
+[isc2]
+  standard_name = starting_x_direction_index_alloc2
+  long_name = starting X direction index for allocation
+  units = count
+  dimensions = ()
+  type = integer
+[iec2]
+  standard_name = ending_x_direction_index_alloc2
+  long_name = ending X direction index for allocation
+  units = count
+  dimensions = ()
+  type = integer
 [js]
   standard_name = starting_y_direction_index
   long_name = starting Y direction index
@@ -2988,25 +3012,49 @@
   units = count
   dimensions = ()
   type = integer
+[jsc1]
+  standard_name = starting_y_direction_index_alloc1
+  long_name = starting X direction index for allocation
+  units = count
+  dimensions = ()
+  type = integer
+[jec1]
+  standard_name = ending_y_direction_index_alloc1
+  long_name = ending X direction index for allocation
+  units = count
+  dimensions = ()
+  type = integer
+[jsc2]
+  standard_name = starting_y_direction_index_alloc2
+  long_name = starting X direction index for allocation
+  units = count
+  dimensions = ()
+  type = integer
+[jec2]
+  standard_name = ending_y_direction_index_alloc2
+  long_name = ending X direction index for allocation
+  units = count
+  dimensions = ()
+  type = integer
 [delp]
   standard_name = pressure_thickness_at_Lagrangian_surface
   long_name = pressure thickness at Lagrangian surface
   units = Pa
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [delz]
   standard_name = thickness_at_Lagrangian_surface
   long_name = thickness at Lagrangian_surface
   units = m
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_thickness_at_Lagrangian_surface)
+  dimensions = (starting_x_direction_index_alloc2:ending_x_direction_index_alloc2,starting_y_direction_index_alloc2:ending_y_direction_index_alloc2,1:vertical_dimension_for_thickness_at_Lagrangian_surface)
   type = real
   kind = kind_dyn
 [area]
   standard_name = cell_area_for_fast_physics
   long_name = area of the grid cell for fast physics
   units = m2
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1)
   type = real
   kind = kind_grid
 [ng]
@@ -3049,92 +3097,92 @@
   standard_name = log_pressure_at_Lagrangian_surface
   long_name = logarithm of pressure at Lagrangian surface
   units = Pa
-  dimensions = (starting_x_direction_index:ending_x_direction_index,1:vertical_dimension_for_fast_physics_plus_one,starting_y_direction_index:ending_y_direction_index)
+  dimensions = (starting_x_direction_index_alloc2:ending_x_direction_index_alloc2,1:vertical_dimension_for_fast_physics_plus_one,starting_y_direction_index_alloc2:ending_y_direction_index_alloc2)
   type = real
   kind = kind_dyn
 [phis]
   standard_name = surface_geopotential_at_Lagrangian_surface
   long_name = surface geopotential at Lagrangian surface
   units = m2 s-2
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1)
   type = real
   kind = kind_dyn
 [pkz]
   standard_name = finite_volume_mean_edge_pressure_raised_to_the_power_of_kappa
   long_name = finite-volume mean edge pressure raised to the power of kappa
   units = 1
-  dimensions = (starting_x_direction_index:ending_x_direction_index,starting_y_direction_index:ending_y_direction_index,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc2:ending_x_direction_index_alloc2,starting_y_direction_index_alloc2:ending_y_direction_index_alloc2,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [pt]
   standard_name = virtual_temperature_at_Lagrangian_surface
   long_name = virtual temperature at Lagrangian surface
   units = K
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [qvi]
   standard_name = gas_tracers_for_multi_gas_physics_at_Lagrangian_surface
   long_name = gas tracers for multi gas physics at Lagrangian surface
   units = kg kg-1
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics,0:number_of_gases_for_multi_gases_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics,1:number_of_gases_for_multi_gases_physics)
   type = real
   kind = kind_dyn
   active = (number_of_gases_for_multi_gases_physics > 0)
 [qv]
   standard_name = water_vapor_specific_humidity_at_Lagrangian_surface
   long_name = water vapor specific humidity updated by fast physics at Lagrangian surface
   units = kg kg-1
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [ql]
   standard_name = cloud_liquid_water_specific_humidity_at_Lagrangian_surface
   long_name = cloud liquid water specific humidity updated by fast physics at Lagrangian surface
   units = kg kg-1
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [qi]
   standard_name = cloud_ice_specific_humidity_at_Lagrangian_surface
   long_name = cloud ice specific humidity updated by fast physics at Lagrangian surface
   units = kg kg-1
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [qr]
   standard_name = cloud_rain_specific_humidity_at_Lagrangian_surface
   long_name = cloud rain specific humidity updated by fast physics at Lagrangian surface
   units = kg kg-1
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [qs]
   standard_name = cloud_snow_specific_humidity_at_Lagrangian_surface
   long_name = cloud snow specific humidity updated by fast physics at Lagrangian surface
   units = kg kg-1
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [qg]
   standard_name = cloud_graupel_specific_humidity_at_Lagrangian_surface
   long_name = cloud graupel specific humidity updated by fast physics at Lagrangian surface
   units = kg kg-1
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [qc]
   standard_name = cloud_fraction_at_Lagrangian_surface
   long_name = cloud fraction at Lagrangian surface
   units = none
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_fast_physics)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_fast_physics)
   type = real
   kind = kind_dyn
 [q_con]
   standard_name = cloud_condensed_water_specific_humidity_at_Lagrangian_surface
   long_name = cloud condensed water specific humidity updated by fast physics at Lagrangian surface
   units = kg kg-1
-  dimensions = (starting_x_direction_index_domain:ending_x_direction_index_domain,starting_y_direction_index_domain:ending_y_direction_index_domain,1:vertical_dimension_for_condensed_water_at_Lagrangian_surface)
+  dimensions = (starting_x_direction_index_alloc1:ending_x_direction_index_alloc1,starting_y_direction_index_alloc1:ending_y_direction_index_alloc1,1:vertical_dimension_for_condensed_water_at_Lagrangian_surface)
   type = real
   kind = kind_dyn
 [nthreads]

ccpp/data/GFS_typedefs.F90

@@ -2746,12 +2746,13 @@ subroutine sfcprop_create (Sfcprop, IM, Model)
        !
     end if
 
-       allocate (Sfcprop%rmol   (IM ))
-       allocate (Sfcprop%flhc   (IM ))
-       allocate (Sfcprop%flqc   (IM ))
-       Sfcprop%rmol        = clear_val
-       Sfcprop%flhc        = clear_val
-       Sfcprop%flqc        = clear_val
+    allocate (Sfcprop%rmol   (IM ))
+    allocate (Sfcprop%flhc   (IM ))
+    allocate (Sfcprop%flqc   (IM ))
+    Sfcprop%rmol        = clear_val
+    Sfcprop%flhc        = clear_val
+    Sfcprop%flqc        = clear_val
+
     if (Model%do_mynnsfclay) then
     ! For MYNN surface layer scheme
        !print*,"Allocating all MYNN-sfclay variables"