Merge branch 'dev/gfdl' of https://github.com/Hallberg-NOAA/MOM6 into…

… Hallberg-NOAA-dev/gfdl

config_src/coupled_driver/ocean_model_MOM.F90

@@ -877,25 +877,28 @@ end subroutine ocean_model_init_sfc
 !WGA
 
 subroutine ocean_model_flux_init(OS)
-  type(ocean_state_type),  pointer :: OS
+  type(ocean_state_type), optional, pointer :: OS
+
   integer :: dummy
   character(len=128) :: default_ice_restart_file, default_ocean_restart_file
   character(len=40)  :: mod = "ocean_model_flux_init"  ! This module's name.
-
   type(param_file_type) :: param_file !< A structure to parse for run-time parameters
   type(directories) :: dirs_tmp  ! A structure containing several relevant directory paths.
   logical :: use_OCMIP_CFCs, use_MOM_generic_tracer
+  logical :: OS_is_set
+
+  OS_is_set = .false. ; if (present(OS)) OS_is_set = associated(OS)
 
   call get_MOM_Input(param_file, dirs_tmp, check_params=.false.)
 
   call get_param(param_file, mod, "USE_OCMIP2_CFC", use_OCMIP_CFCs, &
-                 default=.false.)
+                 default=.false., do_not_log=.true.)
   call get_param(param_file, mod, "USE_generic_tracer", use_MOM_generic_tracer,&
-                 default=.false.)
+                 default=.false., do_not_log=.true.)
 
   call close_param_file(param_file, quiet_close=.true.)
 
-  if(.not.associated(OS)) then
+  if(.not.OS_is_set) then
     if (use_OCMIP_CFCs)then
       default_ice_restart_file = 'ice_ocmip2_cfc.res.nc'
       default_ocean_restart_file = 'ocmip2_cfc.res.nc'
@@ -917,7 +920,7 @@ subroutine ocean_model_flux_init(OS)
 
   if (use_MOM_generic_tracer) then
 #ifdef _USE_GENERIC_TRACER
-    call MOM_generic_flux_init
+    call MOM_generic_flux_init()
 #else
     call MOM_error(FATAL, &
        "call_tracer_register: use_MOM_generic_tracer=.true. BUT not compiled with _USE_GENERIC_TRACER")

src/user/DOME2d_initialization.F90

@@ -27,7 +27,7 @@ module DOME2d_initialization
 public DOME2d_initialize_temperature_salinity
 public DOME2d_initialize_sponges
 
-character(len=40) :: mod = "DOEM2D_initialization" !< This module's name.
+character(len=40) :: mod = "DOME2D_initialization" !< This module's name.
 
 contains
 
@@ -43,7 +43,10 @@ subroutine DOME2d_initialize_topography ( D, G, param_file, max_depth )
   integer :: i, j
   real    :: x, bay_depth, l1, l2
   real    :: dome2d_width_bay, dome2d_width_bottom, dome2d_depth_bay
+! This include declares and sets the variable "version".
+#include "version_variable.h"
 
+  call log_version(param_file, mod, version, "")
   call get_param(param_file, mod, "DOME2D_SHELF_WIDTH", dome2d_width_bay, &
                  'Width of shelf, as fraction of domain, in 2d DOME configuration.', &
                  units='nondim',default=0.1)
@@ -82,26 +85,35 @@ subroutine DOME2d_initialize_topography ( D, G, param_file, max_depth )
 end subroutine DOME2d_initialize_topography
 
 !> Initialize thicknesses according to coordinate mode
-subroutine DOME2d_initialize_thickness ( h, G, GV, param_file )
-  type(ocean_grid_type),                     intent(in)  :: G !< Ocean grid structure
-  type(verticalGrid_type),                   intent(in)  :: GV !< Vertical grid structure
-  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), intent(out) :: h !< Layer thicknesses
-  type(param_file_type),                     intent(in)  :: param_file !< Parameter file structure
+subroutine DOME2d_initialize_thickness ( h, G, GV, param_file, just_read_params )
+  type(ocean_grid_type),   intent(in)  :: G  !< Ocean grid structure
+  type(verticalGrid_type), intent(in)  :: GV !< Vertical grid structure
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), &
+                           intent(out) :: h           !< The thickness that is being initialized, in m.
+  type(param_file_type),   intent(in)  :: param_file  !< A structure indicating the open file
+                                                      !! to parse for model parameter values.
+  logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
+                                                      !! only read parameters without changing h.
+
   ! Local variables
-  real :: e0(SZK_(G))     ! The resting interface heights, in m, usually !
-                          ! negative because it is positive upward.      !
-  real :: eta1D(SZK_(G)+1)! Interface height relative to the sea surface !
-                          ! positive upward, in m.                       !
+  real :: e0(SZK_(GV))     ! The resting interface heights, in m, usually !
+                           ! negative because it is positive upward.      !
+  real :: eta1D(SZK_(GV)+1)! Interface height relative to the sea surface !
+                           ! positive upward, in m.                       !
   integer :: i, j, k, is, ie, js, je, nz
   real    :: x
   real    :: delta_h
   real    :: min_thickness
-  character(len=40) :: verticalCoordinate
   real    :: dome2d_width_bay, dome2d_width_bottom, dome2d_depth_bay
+  logical :: just_read    ! If true, just read parameters but set nothing.
+  character(len=40) :: verticalCoordinate
 
   is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = G%ke
 
-  call MOM_mesg("MOM_initialization.F90, DOME2d_initialize_thickness: setting thickness")
+  just_read = .false. ; if (present(just_read_params)) just_read = just_read_params
+
+  if (.not.just_read) &
+    call MOM_mesg("MOM_initialization.F90, DOME2d_initialize_thickness: setting thickness")
 
   call get_param(param_file,mod,"MIN_THICKNESS",min_thickness, &
                  default=1.e-3, do_not_log=.true.)
@@ -114,6 +126,8 @@ subroutine DOME2d_initialize_thickness ( h, G, GV, param_file )
   call get_param(param_file, mod, "DOME2D_SHELF_DEPTH", dome2d_depth_bay, &
                  default=0.2, do_not_log=.true.)
 
+  if (just_read) return ! All run-time parameters have been read, so return.
+
   ! WARNING: this routine specifies the interface heights so that the last layer
   !          is vanished, even at maximum depth. In order to have a uniform
   !          layer distribution, use this line of code within the loop:
@@ -202,13 +216,17 @@ end subroutine DOME2d_initialize_thickness
 
 
 !> Initialize temperature and salinity in the 2d DOME configuration
-subroutine DOME2d_initialize_temperature_salinity ( T, S, h, G, param_file, eqn_of_state)
+subroutine DOME2d_initialize_temperature_salinity ( T, S, h, G, param_file, &
+                     eqn_of_state, just_read_params)
   type(ocean_grid_type),                     intent(in)  :: G !< Ocean grid structure
   real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(out) :: T !< Potential temperature (degC)
   real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(out) :: S !< Salinity (ppt)
   real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(in)  :: h !< Layer thickness (m or Pa)
   type(param_file_type),                     intent(in)  :: param_file !< Parameter file structure
   type(EOS_type),                            pointer     :: eqn_of_state !< Equation of state structure
+  logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
+                                                      !! only read parameters without changing h.
+
   ! Local variables
   integer   :: i, j, k, is, ie, js, je, nz
   real      :: x;
@@ -217,11 +235,14 @@ subroutine DOME2d_initialize_temperature_salinity ( T, S, h, G, param_file, eqn_
   real      :: S_ref, T_ref;        ! Reference salinity and temperature within surface layer
   real      :: S_range, T_range;    ! Range of salinities and temperatures over the vertical
   real      :: xi0, xi1;
+  logical :: just_read    ! If true, just read parameters but set nothing.
   character(len=40) :: verticalCoordinate
   real    :: dome2d_width_bay, dome2d_width_bottom, dome2d_depth_bay
 
   is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = G%ke
 
+  just_read = .false. ; if (present(just_read_params)) just_read = just_read_params
+
   call get_param(param_file,mod,"REGRIDDING_COORDINATE_MODE", verticalCoordinate, &
                  default=DEFAULT_COORDINATE_MODE, do_not_log=.true.)
   call get_param(param_file, mod, "DOME2D_SHELF_WIDTH", dome2d_width_bay, &
@@ -230,10 +251,16 @@ subroutine DOME2d_initialize_temperature_salinity ( T, S, h, G, param_file, eqn_
                  default=0.3, do_not_log=.true.)
   call get_param(param_file, mod, "DOME2D_SHELF_DEPTH", dome2d_depth_bay, &
                  default=0.2, do_not_log=.true.)
-  call get_param(param_file,mod,"S_REF",S_ref,'Reference salinity',units='1e-3',fail_if_missing=.true.)
-  call get_param(param_file,mod,"T_REF",T_ref,'Refernce temperature',units='C',fail_if_missing=.true.)
-  call get_param(param_file,mod,"S_RANGE",S_range,'Initial salinity range',units='1e-3',default=2.0)
-  call get_param(param_file,mod,"T_RANGE",T_range,'Initial temperature range',units='1e-3',default=0.0)
+  call get_param(param_file,mod,"S_REF",S_ref,'Reference salinity',units='1e-3', &
+                fail_if_missing=.not.just_read, do_not_log=just_read)
+  call get_param(param_file,mod,"T_REF",T_ref,'Refernce temperature',units='C', &
+                fail_if_missing=.not.just_read, do_not_log=just_read)
+  call get_param(param_file,mod,"S_RANGE",S_range,'Initial salinity range', &
+                units='1e-3', default=2.0, do_not_log=just_read)
+  call get_param(param_file,mod,"T_RANGE",T_range,'Initial temperature range', &
+                units='1e-3', default=0.0, do_not_log=just_read)
+
+  if (just_read) return ! All run-time parameters have been read, so return.
 
   T(:,:,:) = 0.0
   S(:,:,:) = 0.0

src/user/DOME_initialization.F90

@@ -90,22 +90,30 @@ end subroutine DOME_initialize_topography
 
 ! -----------------------------------------------------------------------------
 !> This subroutine initializes layer thicknesses for the DOME experiment
-subroutine DOME_initialize_thickness(h, G, GV, param_file)
-  type(ocean_grid_type),   intent(in) :: G  !< The ocean's grid structure.
-  type(verticalGrid_type), intent(in) :: GV !< The ocean's vertical grid structure.
-  real, intent(out), dimension(SZI_(G),SZJ_(G),SZK_(GV)) :: h !< The thickness that is being initialized.
-  type(param_file_type),   intent(in) :: param_file !< A structure indicating the open file
-                                                    !! to parse for model parameter values.
-
-  real :: e0(SZK_(G)+1)     ! The resting interface heights, in m, usually !
+subroutine DOME_initialize_thickness(h, G, GV, param_file, just_read_params)
+  type(ocean_grid_type),   intent(in)  :: G           !< The ocean's grid structure.
+  type(verticalGrid_type), intent(in)  :: GV          !< The ocean's vertical grid structure.
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), &
+                           intent(out) :: h           !< The thickness that is being initialized, in m.
+  type(param_file_type),   intent(in)  :: param_file  !< A structure indicating the open file
+                                                      !! to parse for model parameter values.
+  logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
+                                                      !! only read parameters without changing h.
+
+  real :: e0(SZK_(GV)+1)    ! The resting interface heights, in m, usually !
                             ! negative because it is positive upward.      !
-  real :: eta1D(SZK_(G)+1)  ! Interface height relative to the sea surface !
+  real :: eta1D(SZK_(GV)+1) ! Interface height relative to the sea surface !
                             ! positive upward, in m.                       !
+  logical :: just_read    ! If true, just read parameters but set nothing.
   character(len=40)  :: mod = "DOME_initialize_thickness" ! This subroutine's name.
   integer :: i, j, k, is, ie, js, je, nz
 
   is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = G%ke
 
+  just_read = .false. ; if (present(just_read_params)) just_read = just_read_params
+
+  if (just_read) return ! This subroutine has no run-time parameters.
+
   call MOM_mesg("  DOME_initialization.F90, DOME_initialize_thickness: setting thickness", 5)
 
   e0(1)=0.0