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Fixes doxygen configuration and missing module one-liners #820

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Hallberg-NOAA merged 3 commits into from
Jul 12, 2018
Merged

Fixes doxygen configuration and missing module one-liners #820

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f69cbf7
Doxygen config: only process ocean_model_MOM.F90 from coupled_driver
adcroft Jul 12, 2018
6478c01
Fixes for doxumentation using doxygen 1.8.4
adcroft Jul 12, 2018
f7be32d
Fixed documentation in MOM_debugging
adcroft Jul 12, 2018
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61 changes: 27 additions & 34 deletions config_src/coupled_driver/coupler_util.F90
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
!> Provides a couple of interfaces to allow more transparent and
!! robust extraction of the various fields in the coupler types.
module coupler_util

! This file is part of MOM6. See LICENSE.md for the license.

! This code provides a couple of interfaces to allow more transparent and
! robust extraction of the various fields in the coupler types.
use MOM_error_handler, only : MOM_error, FATAL, WARNING
use coupler_types_mod, only : coupler_2d_bc_type, ind_flux, ind_alpha
use coupler_types_mod, only : ind_csurf
Expand All @@ -15,24 +15,20 @@ module coupler_util

contains

!> Extract an array of values in a coupler bc type
subroutine extract_coupler_values(BC_struc, BC_index, BC_element, array_out, &
is, ie, js, je, conversion)
type(coupler_2d_bc_type), intent(in) :: BC_struc
integer, intent(in) :: BC_index, BC_element
real, dimension(:,:), intent(out) :: array_out
integer, optional, intent(in) :: is, ie, js, je
real, optional, intent(in) :: conversion
! Arguments: BC_struc - The type from which the data is being extracted.
! (in) BC_index - The boundary condition number being extracted.
! (in) BC_element - The element of the boundary condition being extracted.
! This could be ind_csurf, ind_alpha, ind_flux or ind_deposition.
! (out) array_out - The array being filled with the input values.
! (in, opt) is, ie, js, je - The i- and j- limits of array_out to be filled.
! These must match the size of the corresponding value array or an
! error message is issued.
! (in, opt) conversion - A number that every element is multiplied by, to
! permit sign convention or unit conversion.

type(coupler_2d_bc_type), intent(in) :: BC_struc !< The type from which the data is being extracted.
integer, intent(in) :: BC_index !< The boundary condition number being extracted.
integer, intent(in) :: BC_element !< The element of the boundary condition being extracted.
real, dimension(:,:), intent(out) :: array_out !< The array being filled with the input values.
integer, optional, intent(in) :: is !< Start i-index
integer, optional, intent(in) :: ie !< End i-index
integer, optional, intent(in) :: js !< Start j-index
integer, optional, intent(in) :: je !< End j-index
real, optional, intent(in) :: conversion !< A number that every element is multiplied by, to
!! permit sign convention or unit conversion.
! Local variables
real, pointer, dimension(:,:) :: Array_in
real :: conv
integer :: i, j, is0, ie0, js0, je0, i_offset, j_offset
Expand Down Expand Up @@ -78,24 +74,21 @@ subroutine extract_coupler_values(BC_struc, BC_index, BC_element, array_out, &

end subroutine extract_coupler_values

!> Set an array of values in a coupler bc type
subroutine set_coupler_values(array_in, BC_struc, BC_index, BC_element, &
is, ie, js, je, conversion)
real, dimension(:,:), intent(in) :: array_in
type(coupler_2d_bc_type), intent(inout) :: BC_struc
integer, intent(in) :: BC_index, BC_element
integer, optional, intent(in) :: is, ie, js, je
real, optional, intent(in) :: conversion
! Arguments: array_in - The array containing the values to load into the BC.
! (out) BC_struc - The type into which the data is being loaded.
! (in) BC_index - The boundary condition number being extracted.
! (in) BC_element - The element of the boundary condition being extracted.
! This could be ind_csurf, ind_alpha, ind_flux or ind_deposition.
! (in, opt) is, ie, js, je - The i- and j- limits of array_out to be filled.
! These must match the size of the corresponding value array or an
! error message is issued.
! (in, opt) conversion - A number that every element is multiplied by, to
! permit sign convention or unit conversion.

real, dimension(:,:), intent(in) :: array_in !< The array containing the values to load into the BC.
type(coupler_2d_bc_type), intent(inout) :: BC_struc !< The type from which the data is being extracted.
integer, intent(in) :: BC_index !< The boundary condition number being extracted.
integer, intent(in) :: BC_element !< The element of the boundary condition being extracted.
!! This could be ind_csurf, ind_alpha, ind_flux or ind_deposition.
integer, optional, intent(in) :: is !< Start i-index
integer, optional, intent(in) :: ie !< End i-index
integer, optional, intent(in) :: js !< Start j-index
integer, optional, intent(in) :: je !< End j-index
real, optional, intent(in) :: conversion !< A number that every element is multiplied by, to
!! permit sign convention or unit conversion.
! Local variables
real, pointer, dimension(:,:) :: Array_out
real :: conv
integer :: i, j, is0, ie0, js0, je0, i_offset, j_offset
Expand Down
104 changes: 14 additions & 90 deletions config_src/coupled_driver/ocean_model_MOM.F90
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Original file line number Diff line number Diff line change
@@ -1,21 +1,15 @@
!> Top-level module for the MOM6 ocean model in coupled mode.
module ocean_model_mod

! This file is part of MOM6. See LICENSE.md for the license.

!-----------------------------------------------------------------------
!
! This is the top level module for the MOM6 ocean model. It contains routines
! for initialization, termination and update of ocean model state. This
! particular version wraps all of the calls for MOM6 in the calls that had
! been used for MOM4.
!
! <CONTACT EMAIL="Robert.Hallberg@noaa.gov"> Robert Hallberg
! </CONTACT>
!
!<OVERVIEW>
! This code is a stop-gap wrapper of the MOM6 code to enable it to be called
! in the same way as MOM4.
!</OVERVIEW>

use MOM, only : initialize_MOM, step_MOM, MOM_control_struct, MOM_end
use MOM, only : extract_surface_state, allocate_surface_state, finish_MOM_initialization
Expand Down Expand Up @@ -221,15 +215,12 @@ module ocean_model_mod

contains

!=======================================================================
! <SUBROUTINE NAME="ocean_model_init">
!
! <DESCRIPTION>
! Initialize the ocean model.
! </DESCRIPTION>

!> ocean_model_init initializes the ocean model, including registering fields
!! for restarts and reading restart files if appropriate.
!!
!! This subroutine initializes both the ocean state and the ocean surface type.
!! Because of the way that indicies and domains are handled, Ocean_sfc must have
!! been used in a previous call to initialize_ocean_type.
subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn)
type(ocean_public_type), target, &
intent(inout) :: Ocean_sfc !< A structure containing various publicly
Expand All @@ -246,11 +237,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn)
!! in the calculation of additional gas or other
!! tracer fluxes, and can be used to spawn related
!! internal variables in the ice model.

! This subroutine initializes both the ocean state and the ocean surface type.
! Because of the way that indicies and domains are handled, Ocean_sfc must have
! been used in a previous call to initialize_ocean_type.

! Local variables
real :: Rho0 ! The Boussinesq ocean density, in kg m-3.
real :: G_Earth ! The gravitational acceleration in m s-2.
! This include declares and sets the variable "version".
Expand Down Expand Up @@ -408,17 +395,6 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn)

call callTree_leave("ocean_model_init(")
end subroutine ocean_model_init
! </SUBROUTINE> NAME="ocean_model_init"


!=======================================================================
! <SUBROUTINE NAME="update_ocean_model">
!
! <DESCRIPTION>
! Update in time the ocean model fields. This code wraps the call to step_MOM
! with MOM4's call.
! </DESCRIPTION>
!

!> update_ocean_model uses the forcing in Ice_ocean_boundary to advance the
!! ocean model's state from the input value of Ocean_state (which must be for
Expand Down Expand Up @@ -449,7 +425,7 @@ subroutine update_ocean_model(Ice_ocean_boundary, OS, Ocean_sfc, &
logical, optional, intent(in) :: Ocn_fluxes_used !< If present, this indicates whether the
!! cumulative thermodynamic fluxes from the ocean,
!! like frazil, have been used and should be reset.

! Local variables
type(time_type) :: Master_time ! This allows step_MOM to temporarily change
! the time that is seen by internal modules.
type(time_type) :: Time1 ! The value of the ocean model's time at the
Expand Down Expand Up @@ -676,20 +652,6 @@ subroutine update_ocean_model(Ice_ocean_boundary, OS, Ocean_sfc, &

call callTree_leave("update_ocean_model()")
end subroutine update_ocean_model
! </SUBROUTINE> NAME="update_ocean_model"


!=======================================================================
! <SUBROUTINE NAME="ocean_model_restart">
!
! <DESCRIPTION>
! write out restart file.
! Arguments:
! timestamp (optional, intent in) : A character string that represents the model time,
! used for writing restart. timestamp will prepend to
! the any restart file name as a prefix.
! </DESCRIPTION>
!

!> This subroutine writes out the ocean model restart file.
subroutine ocean_model_restart(OS, timestamp)
Expand Down Expand Up @@ -728,13 +690,6 @@ subroutine ocean_model_restart(OS, timestamp)
end subroutine ocean_model_restart
! </SUBROUTINE> NAME="ocean_model_restart"

!=======================================================================
! <SUBROUTINE NAME="ocean_model_end">
!
! <DESCRIPTION>
! Close down the ocean model
! </DESCRIPTION>

!> ocean_model_end terminates the model run, saving the ocean state in a restart
!! and deallocating any data associated with the ocean.
subroutine ocean_model_end(Ocean_sfc, Ocean_state, Time)
Expand All @@ -745,22 +700,11 @@ subroutine ocean_model_end(Ocean_sfc, Ocean_state, Time)
!! upon termination.
type(time_type), intent(in) :: Time !< The model time, used for writing restarts.

! This subroutine terminates the model run, saving the ocean state in a
! restart file and deallocating any data associated with the ocean.

! Arguments: Ocean_sfc - An ocean_public_type structure that is to be
! deallocated upon termination.
! (inout) Ocean_state - A pointer to the structure containing the internal
! ocean state to be deallocated upon termination.
! (in) Time - The model time, used for writing restarts.

call ocean_model_save_restart(Ocean_state, Time)
call diag_mediator_end(Time, Ocean_state%diag)
call MOM_end(Ocean_state%MOM_CSp)
if (Ocean_state%use_ice_shelf) call ice_shelf_end(Ocean_state%Ice_shelf_CSp)
end subroutine ocean_model_end
! </SUBROUTINE> NAME="ocean_model_end"


!> ocean_model_save_restart causes restart files associated with the ocean to be
!! written out.
Expand All @@ -772,12 +716,6 @@ subroutine ocean_model_save_restart(OS, Time, directory, filename_suffix)
!! write these restart files.
character(len=*), optional, intent(in) :: filename_suffix !< An optional suffix (e.g., a time-stamp)
!! to append to the restart file names.
! Arguments: Ocean_state - A structure containing the internal ocean state (in).
! (in) Time - The model time at this call. This is needed for mpp_write calls.
! (in, opt) directory - An optional directory into which to write these restart files.
! (in, opt) filename_suffix - An optional suffix (e.g., a time-stamp) to append
! to the restart file names.

! Note: This is a new routine - it will need to exist for the new incremental
! checkpointing. It will also be called by ocean_model_end, giving the same
! restart behavior as now in FMS.
Expand All @@ -804,8 +742,7 @@ subroutine ocean_model_save_restart(OS, Time, directory, filename_suffix)

end subroutine ocean_model_save_restart

!=======================================================================

!> Initialize the public ocean type
subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, maskmap, &
gas_fields_ocn)
type(domain2D), intent(in) :: input_domain !< The ocean model domain description
Expand Down Expand Up @@ -860,6 +797,11 @@ subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, maskmap,

end subroutine initialize_ocean_public_type

!> This subroutine translates the coupler's ocean_data_type into MOM's
!! surface state variable. This may eventually be folded into the MOM
!! code that calculates the surface state in the first place.
!! Note the offset in the arrays because the ocean_data_type has no
!! halo points in its arrays and always uses absolute indicies.
subroutine convert_state_to_ocean_type(sfc_state, Ocean_sfc, G, patm, press_to_z)
type(surface), intent(inout) :: sfc_state !< A structure containing fields that
!! describe the surface state of the ocean.
Expand All @@ -871,11 +813,7 @@ subroutine convert_state_to_ocean_type(sfc_state, Ocean_sfc, G, patm, press_to_z
real, optional, intent(in) :: patm(:,:) !< The pressure at the ocean surface, in Pa.
real, optional, intent(in) :: press_to_z !< A conversion factor between pressure and
!! ocean depth in m, usually 1/(rho_0*g), in m Pa-1.
! This subroutine translates the coupler's ocean_data_type into MOM's
! surface state variable. This may eventually be folded into the MOM
! code that calculates the surface state in the first place.
! Note the offset in the arrays because the ocean_data_type has no
! halo points in its arrays and always uses absolute indicies.
! Local variables
real :: IgR0
character(len=48) :: val_str
integer :: isc_bnd, iec_bnd, jsc_bnd, jec_bnd
Expand Down Expand Up @@ -968,15 +906,6 @@ subroutine convert_state_to_ocean_type(sfc_state, Ocean_sfc, G, patm, press_to_z

end subroutine convert_state_to_ocean_type


!=======================================================================
! <SUBROUTINE NAME="ocean_model_init_sfc">
!
! <DESCRIPTION>
! This subroutine extracts the surface properties from the ocean's internal
! state and stores them in the ocean type returned to the calling ice model.
! </DESCRIPTION>

!> This subroutine extracts the surface properties from the ocean's internal
!! state and stores them in the ocean type returned to the calling ice model.
!! It has to be separate from the ocean_initialization call because the coupler
Expand All @@ -986,7 +915,6 @@ subroutine ocean_model_init_sfc(OS, Ocean_sfc)
type(ocean_public_type), intent(inout) :: Ocean_sfc !< A structure containing various publicly
!! visible ocean surface properties after initialization, whose
!! elements have their data set here.

integer :: is, ie, js, je

is = OS%grid%isc ; ie = OS%grid%iec ; js = OS%grid%jsc ; je = OS%grid%jec
Expand All @@ -998,7 +926,6 @@ subroutine ocean_model_init_sfc(OS, Ocean_sfc)
call convert_state_to_ocean_type(OS%sfc_state, Ocean_sfc, OS%grid)

end subroutine ocean_model_init_sfc
! </SUBROUTINE NAME="ocean_model_init_sfc">

!> ocean_model_flux_init is used to initialize properties of the air-sea fluxes
!! as determined by various run-time parameters. It can be called from
Expand All @@ -1023,9 +950,6 @@ subroutine ocean_model_flux_init(OS, verbosity)

end subroutine ocean_model_flux_init

!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
! Ocean_stock_pe - returns stocks of heat, water, etc. for conservation checks.!
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
!> Ocean_stock_pe - returns the integrated stocks of heat, water, etc. for conservation checks.
!! Because of the way FMS is coded, only the root PE has the integrated amount,
!! while all other PEs get 0.
Expand Down
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