Upgrading to atmos_phys0_07_001 (#187)

Tag name (The PR title should also include the tag name):
`atmos_phys0_07_001`
Originator(s): @jimmielin

List all `development` PR URLs included in this PR and a short
description of each:
* Update extraterrestrial flux in TUV-x prior to calculating rate constants #152 by @boulderdaze
* Simplify deallocation of multiple objects associated with the TUV-x #156 by @boulderdaze
* Fill in errmsg, errflg in check_energy schemes #160 by @jimmielin
* Validates the MUSICA meta data against the CCPP standard names #162 by @boulderdaze
* Add constituent tendency updater #111 by @peverwhee
* Add cloud optical calculations for use in TUV-x #167 by @mattldawson
* Add initialize_constituents scheme #149 by @peverwhee
* Add diagnostics to TJ2016 test schemes #170 by @peverwhee
* update "radians" to "rad" #173 by @peverwhee
* Solar zenith angle and Earth-Sun distance #171 by @mattldawson
* Update standard names for tropopause_find #140 by @jimmielin
* Update surface albedo units #181 by @mattldawson
* don't set water species property for species that air_composition handles #185 by @peverwhee

List all test failures: N/A

doc/NamesNotInDictionary.txt

@@ -1,7 +1,7 @@
 
 #######################
 Date/time of when script was run:
-2024-11-18 15:44:54.993446
+2024-12-16 11:19:41.130567
 #######################
 
 Non-dictionary standard names found in the following metadata files:
@@ -108,12 +108,6 @@ atmospheric_physics/schemes/dry_adiabatic_adjust/dadadj.meta
 
 --------------------------
 
-atmospheric_physics/schemes/dry_adiabatic_adjust/dadadj_apply_qv_tendency.meta
-
-    - tendency_of_water_vapor_mixing_ratio_wrt_moist_air_and_condensed_water
-
---------------------------
-
 atmospheric_physics/schemes/zhang_mcfarlane/zm_conv_momtran.meta
 
     - atmosphere_detrainment_convective_mass_flux_for_deep_convection_for_convective_columns
@@ -252,6 +246,12 @@ atmospheric_physics/schemes/utilities/geopotential_temp.meta
 
 --------------------------
 
+atmospheric_physics/schemes/utilities/physics_tendency_updaters.meta
+
+    - ccpp_constituent_tendencies
+
+--------------------------
+
 atmospheric_physics/schemes/check_energy/check_energy_save_teout.meta
 
     - vertically_integrated_total_energy_at_end_of_physics_timestep
@@ -342,17 +342,17 @@ atmospheric_physics/schemes/tropopause_find/tropopause_find.meta
     - tropopause_air_pressure
     - tropopause_air_pressure_from_chemical_method
     - tropopause_air_pressure_from_climatological_method
-    - tropopause_air_pressure_from_climatology_dataset
     - tropopause_air_pressure_from_cold_point_method
     - tropopause_air_pressure_from_hybrid_stobie_linoz_with_climatological_backup_method
     - tropopause_air_pressure_from_lapse_rate_method
+    - tropopause_air_pressure_from_tropopause_climatology_dataset
     - tropopause_air_temperature
     - tropopause_air_temperature_from_chemical_method
     - tropopause_air_temperature_from_climatological_method
     - tropopause_air_temperature_from_cold_point_method
     - tropopause_air_temperature_from_hybrid_stobie_linoz_with_climatological_backup_method
     - tropopause_air_temperature_from_lapse_rate_method
-    - tropopause_calendar_days_from_climatology
+    - tropopause_calendar_days_from_tropopause_climatology
     - tropopause_geopotential_height_wrt_surface
     - tropopause_geopotential_height_wrt_surface_from_chemical_method
     - tropopause_geopotential_height_wrt_surface_from_climatological_method
@@ -374,10 +374,18 @@ atmospheric_physics/schemes/tropopause_find/tropopause_find.meta
 atmospheric_physics/schemes/musica/musica_ccpp.meta
 
     - blackbody_temperature_at_surface
+    - cloud_area_fraction
     - dynamic_constituents_for_musica_ccpp
-    - micm_solver_type
-    - number_of_grid_cells
+    - earth_sun_distance
+    - extraterrestrial_radiation_flux
     - photolysis_wavelength_grid_interfaces
+    - solar_zenith_angle
     - surface_albedo_due_to_UV_and_VIS_direct
 
+--------------------------
+
+atmospheric_physics/test/test_schemes/initialize_constituents.meta
+
+    - dynamic_constituents_for_initialize_constituents
+
 #######################

schemes/check_energy/check_energy_chng.F90

@@ -89,6 +89,9 @@ subroutine check_energy_chng_timestep_init( &
     character(len=512), intent(out)   :: errmsg         ! error message
     integer,            intent(out)   :: errflg         ! error flag
 
+    errmsg = ''
+    errflg = 0
+
     !------------------------------------------------
     ! Physics total energy.
     !------------------------------------------------
@@ -276,6 +279,9 @@ subroutine check_energy_chng_run( &
 
     integer :: i
 
+    errmsg = ''
+    errflg = 0
+
     !------------------------------------------------
     ! Physics total energy.
     !------------------------------------------------

schemes/check_energy/check_energy_fix.F90

@@ -11,7 +11,7 @@ module check_energy_fix
   ! Add heating rate required for global mean total energy conservation
 !> \section arg_table_check_energy_fix_run Argument Table
 !! \htmlinclude arg_table_check_energy_fix_run.html
-  subroutine check_energy_fix_run(ncol, pver, pint, gravit, heat_glob, ptend_s, eshflx, scheme_name)
+  subroutine check_energy_fix_run(ncol, pver, pint, gravit, heat_glob, ptend_s, eshflx, scheme_name, errmsg, errflg)
     ! Input arguments
     integer,            intent(in)    :: ncol           ! number of atmospheric columns
     integer,            intent(in)    :: pver           ! number of vertical layers
@@ -22,11 +22,17 @@ subroutine check_energy_fix_run(ncol, pver, pint, gravit, heat_glob, ptend_s, es
     real(kind_phys),    intent(out)   :: eshflx(:)      ! effective sensible heat flux [W m-2]
                                                         ! for check_energy_chng
 
+    ! Output arguments
     character(len=64),  intent(out)   :: scheme_name    ! scheme name
+    character(len=512), intent(out)   :: errmsg         ! error message
+    integer,            intent(out)   :: errflg         ! error flag
 
     ! Local variables
     integer :: i
 
+    errmsg = ''
+    errflg = 0
+
     ! Set scheme name for check_energy_chng
     scheme_name = "check_energy_fix"
 

schemes/check_energy/check_energy_fix.meta

@@ -53,3 +53,15 @@
   type = character | kind = len=64
   dimensions = ()
   intent = out
+[ errmsg ]
+  standard_name = ccpp_error_message
+  units = none
+  type = character | kind = len=512
+  dimensions = ()
+  intent = out
+[ errflg ]
+  standard_name = ccpp_error_code
+  units = 1
+  type = integer
+  dimensions = ()
+  intent = out

schemes/check_energy/check_energy_gmean/check_energy_gmean.F90

@@ -19,7 +19,8 @@ subroutine check_energy_gmean_run( &
        pint, &
        te_ini_dyn, teout, &
        tedif_glob, heat_glob, &
-       teinp_glob, teout_glob, psurf_glob, ptopb_glob)
+       teinp_glob, teout_glob, psurf_glob, ptopb_glob, &
+       errmsg, errflg)
 
     ! This scheme is non-portable due to dependency: Global mean module gmean from src/utils
     use gmean_mod, only: gmean
@@ -43,10 +44,16 @@ subroutine check_energy_gmean_run( &
     real(kind_phys),    intent(out)   :: psurf_glob     ! global mean surface pressure [Pa]
     real(kind_phys),    intent(out)   :: ptopb_glob     ! global mean top boundary pressure [Pa]
 
+    character(len=512), intent(out)   :: errmsg         ! error message
+    integer,            intent(out)   :: errflg         ! error flag
+
     ! Local variables
     real(kind_phys) :: te(ncol, 4)                      ! total energy of input/output states (copy)
     real(kind_phys) :: te_glob(4)                       ! global means of total energy
 
+    errmsg = ''
+    errflg = 0
+
     ! Copy total energy out of input and output states.
     ! These four fields will have their global means calculated respectively
     te(:ncol, 1) = te_ini_dyn(:ncol)        ! Input energy using dycore energy formula [J m-2]

schemes/check_energy/check_energy_gmean/check_energy_gmean.meta

@@ -84,3 +84,15 @@
   type = real | kind = kind_phys
   dimensions = ()
   intent = out
+[ errmsg ]
+  standard_name = ccpp_error_message
+  units = none
+  type = character | kind = len=512
+  dimensions = ()
+  intent = out
+[ errflg ]
+  standard_name = ccpp_error_code
+  units = 1
+  type = integer
+  dimensions = ()
+  intent = out

schemes/check_energy/check_energy_save_teout.F90

@@ -13,14 +13,19 @@ module check_energy_save_teout
 
 !> \section arg_table_check_energy_save_teout_run Argument Table
 !! \htmlinclude arg_table_check_energy_save_teout_run.html
-  subroutine check_energy_save_teout_run(ncol, te_cur_dyn, teout)
+  subroutine check_energy_save_teout_run(ncol, te_cur_dyn, teout, errmsg, errflg)
 
     ! Input arguments
     integer,            intent(in)    :: ncol           ! number of atmospheric columns
     real(kind_phys),    intent(in)    :: te_cur_dyn (:) ! dycore  formula: current total energy [J m-2]
 
     ! Output arguments
     real(kind_phys),    intent(out)   :: teout(:)       ! total energy for global fixer in next timestep [J m-2]
+    character(len=512), intent(out)   :: errmsg         ! error message
+    integer,            intent(out)   :: errflg         ! error flag
+
+    errmsg = ''
+    errflg = 0
 
     ! nb hplin: note that in physpkg.F90, the pbuf is updated to the previous dyn timestep
     ! through itim_old. Need to check if we need to replicate such pbuf functionality

schemes/check_energy/check_energy_save_teout.meta

@@ -23,3 +23,15 @@
   type = real | kind = kind_phys
   dimensions = (horizontal_loop_extent)
   intent = out
+[ errmsg ]
+  standard_name = ccpp_error_message
+  units = none
+  type = character | kind = len=512
+  dimensions = ()
+  intent = out
+[ errflg ]
+  standard_name = ccpp_error_code
+  units = 1
+  type = integer
+  dimensions = ()
+  intent = out

schemes/check_energy/check_energy_zero_fluxes.F90

@@ -12,7 +12,7 @@ module check_energy_zero_fluxes
 
 !> \section arg_table_check_energy_zero_fluxes_run Argument Table
 !! \htmlinclude arg_table_check_energy_zero_fluxes_run.html
-  subroutine check_energy_zero_fluxes_run(ncol, name, flx_vap, flx_cnd, flx_ice, flx_sen)
+  subroutine check_energy_zero_fluxes_run(ncol, name, flx_vap, flx_cnd, flx_ice, flx_sen, errmsg, errflg)
     ! Input arguments
     integer,            intent(in)     :: ncol           ! number of atmospheric columns
 
@@ -22,6 +22,11 @@ subroutine check_energy_zero_fluxes_run(ncol, name, flx_vap, flx_cnd, flx_ice, f
     real(kind_phys),    intent(out)    :: flx_cnd(:)     ! boundary flux of liquid+ice (precip?) [m s-1]
     real(kind_phys),    intent(out)    :: flx_ice(:)     ! boundary flux of ice (snow?) [m s-1]
     real(kind_phys),    intent(out)    :: flx_sen(:)     ! boundary flux of sensible heat [W m-2]
+    character(len=512), intent(out)    :: errmsg         ! error message
+    integer,            intent(out)    :: errflg         ! error flag
+
+    errmsg = ''
+    errflg = 0
 
     ! reset values to zero
     name = ''

schemes/check_energy/check_energy_zero_fluxes.meta

@@ -41,3 +41,15 @@
   type = real | kind = kind_phys
   dimensions = (horizontal_loop_extent)
   intent = out
+[ errmsg ]
+  standard_name = ccpp_error_message
+  units = none
+  type = character | kind = len=512
+  dimensions = ()
+  intent = out
+[ errflg ]
+  standard_name = ccpp_error_code
+  units = 1
+  type = integer
+  dimensions = ()
+  intent = out

schemes/check_energy/dycore_energy_consistency_adjust.F90

@@ -16,7 +16,8 @@ subroutine dycore_energy_consistency_adjust_run( &
       do_consistency_adjust, &
       scaling_dycore, &
       tend_dTdt, &
-      tend_dTdt_local)
+      tend_dTdt_local, &
+      errmsg, errflg)
 
     ! Input arguments
     integer,            intent(in)    :: ncol                  ! number of atmospheric columns
@@ -26,7 +27,12 @@ subroutine dycore_energy_consistency_adjust_run( &
     real(kind_phys),    intent(in)    :: tend_dTdt(:,:)        ! model physics temperature tendency [K s-1]
 
     ! Output arguments
-    real(kind_phys),    intent(out) :: tend_dTdt_local(:,:)  ! (scheme) temperature tendency [K s-1]
+    real(kind_phys),    intent(out)   :: tend_dTdt_local(:,:)  ! (scheme) temperature tendency [K s-1]
+    character(len=512), intent(out)   :: errmsg                ! error message
+    integer,            intent(out)   :: errflg                ! error flag
+
+    errmsg = ''
+    errflg = 0
 
     if (do_consistency_adjust) then
       ! original formula for scaling of temperature:

schemes/check_energy/dycore_energy_consistency_adjust.meta

@@ -41,3 +41,15 @@
   type = real | kind = kind_phys
   dimensions = (horizontal_loop_extent, vertical_layer_dimension)
   intent = out
+[ errmsg ]
+  standard_name = ccpp_error_message
+  units = none
+  type = character | kind = len=512
+  dimensions = ()
+  intent = out
+[ errflg ]
+  standard_name = ccpp_error_code
+  units = 1
+  type = integer
+  dimensions = ()
+  intent = out

schemes/dry_adiabatic_adjust/dadadj.meta

@@ -119,6 +119,7 @@
   type = real | kind = kind_phys
   dimensions = (horizontal_loop_extent, vertical_layer_dimension)
   intent = out
+  constituent = True
 [ dadpdf ]
   standard_name = binary_indicator_for_dry_adiabatic_adjusted_grid_cell
   units = fraction

schemes/held_suarez/held_suarez_1994.meta

@@ -50,7 +50,7 @@
   intent = in
 [ clat ]
   standard_name = latitude
-  units = radians
+  units = rad
   type = real | kind = kind_phys
   dimensions = (horizontal_loop_extent)
   intent = in