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Fixes doxygen warnings mostly from config_src/external #1231

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Oct 28, 2020
Merged

Fixes doxygen warnings mostly from config_src/external #1231

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712eb82
Fixes doxygen warnings mostly from config_src/external
adcroft Oct 24, 2020
cedfea7
Merge branch 'dev/gfdl' into config-src-doxygen-fixes
Hallberg-NOAA Oct 27, 2020
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18 changes: 14 additions & 4 deletions config_src/external/GFDL_ocean_BGC/generic_tracer.F90
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Expand Up @@ -33,7 +33,17 @@ end subroutine generic_tracer_register

!> Initialize generic tracers
subroutine generic_tracer_init(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)
integer, intent(in) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes(3) !< Domain boundaries and axes
integer, intent(in) :: isc !< Computation start index in i direction
integer, intent(in) :: iec !< Computation end index in i direction
integer, intent(in) :: jsc !< Computation start index in j direction
integer, intent(in) :: jec !< Computation end index in j direction
integer, intent(in) :: isd !< Data start index in i direction
integer, intent(in) :: ied !< Data end index in i direction
integer, intent(in) :: jsd !< Data start index in j direction
integer, intent(in) :: jed !< Data end index in j direction
integer, intent(in) :: nk !< Number of levels in k direction
integer, intent(in) :: ntau !< Unknown
integer, intent(in) :: axes(3) !< Domain axes?
type(time_type), intent(in) :: init_time !< Time
real, dimension(:,:,:),target, intent(in) :: grid_tmask !< Mask
integer, dimension(:,:) , intent(in) :: grid_kmt !< Number of wet cells in column
Expand Down Expand Up @@ -61,7 +71,7 @@ subroutine generic_tracer_source(Temp,Salt,rho_dzt,dzt,hblt_depth,ilb,jlb,tau,dt
frunoff,grid_ht, current_wave_stress, sosga)
real, dimension(ilb:,jlb:,:), intent(in) :: Temp !< Potential temperature [deg C]
real, dimension(ilb:,jlb:,:), intent(in) :: Salt !< Salinity [psu]
real, dimension(ilb:,jlb:,:), intent(in) :: rho_dzt
real, dimension(ilb:,jlb:,:), intent(in) :: rho_dzt !< Unknown
real, dimension(ilb:,jlb:,:), intent(in) :: dzt !< Ocean layer thickness [m]
real, dimension(ilb:,jlb:), intent(in) :: hblt_depth !< Boundary layer depth
integer, intent(in) :: ilb !< Lower bounds of x extent of input arrays on data domain
Expand All @@ -71,14 +81,14 @@ subroutine generic_tracer_source(Temp,Salt,rho_dzt,dzt,hblt_depth,ilb,jlb,tau,dt
real, dimension(ilb:,jlb:), intent(in) :: grid_dat !< Unknown
type(time_type), intent(in) :: model_time !< Time
integer, intent(in) :: nbands !< Unknown
real, dimension(:), intent(in) :: max_wavelength_band
real, dimension(:), intent(in) :: max_wavelength_band !< Unknown
real, dimension(:,ilb:,jlb:), intent(in) :: sw_pen_band !< Shortwave penetration
real, dimension(:,ilb:,jlb:,:), intent(in) :: opacity_band !< Unknown
real, dimension(ilb:,jlb:),optional, intent(in) :: internal_heat !< Unknown
real, dimension(ilb:,jlb:),optional, intent(in) :: frunoff !< Unknown
real, dimension(ilb:,jlb:),optional, intent(in) :: grid_ht !< Unknown
real, dimension(ilb:,jlb:),optional , intent(in) :: current_wave_stress !< Unknown
real, optional , intent(in) :: sosga ! global avg. sea surface salinity
real, optional , intent(in) :: sosga !< Global average sea surface salinity
end subroutine generic_tracer_source

!> Update the tracers from bottom fluxes
Expand Down
92 changes: 60 additions & 32 deletions config_src/external/GFDL_ocean_BGC/generic_tracer_utils.F90
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Expand Up @@ -21,8 +21,10 @@ module g_tracer_utils
!> Tracer concentration in river runoff
real, allocatable, dimension(:,:) :: trunoff
logical :: requires_restart = .true. !< Unknown
!> Tracer source: filename, type, var name, units, record, gridfile
character(len=fm_string_len) :: src_file, src_var_name, src_var_unit, src_var_gridspec
character(len=fm_string_len) :: src_file !< Tracer source filename
character(len=fm_string_len) :: src_var_name !< Tracer source variable name
character(len=fm_string_len) :: src_var_unit !< Tracer source variable units
character(len=fm_string_len) :: src_var_gridspec !< Tracer source grid file name
integer :: src_var_record !< Unknown
logical :: requires_src_info = .false. !< Unknown
real :: src_var_unit_conversion = 1.0 !< This factor depends on the tracer. Ask Jasmin
Expand All @@ -38,7 +40,8 @@ module g_tracer_utils
type g_tracer_common
! type(g_diag_ctrl) :: diag_CS !< Unknown
!> Domain extents
integer :: isd,jsd
integer :: isd !< Start index of the data domain in the i-direction
integer :: jsd !< Start index of the data domain in the j-direction
end type g_tracer_common

!> Unknown dangerous module data!
Expand Down Expand Up @@ -102,18 +105,37 @@ subroutine g_tracer_set_csdiag(diag_CS)
end subroutine g_tracer_set_csdiag

subroutine g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)
integer, intent(in) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes(3) !< Unknown
integer, intent(in) :: isc !< Computation start index in i direction
integer, intent(in) :: iec !< Computation end index in i direction
integer, intent(in) :: jsc !< Computation start index in j direction
integer, intent(in) :: jec !< Computation end index in j direction
integer, intent(in) :: isd !< Data start index in i direction
integer, intent(in) :: ied !< Data end index in i direction
integer, intent(in) :: jsd !< Data start index in j direction
integer, intent(in) :: jed !< Data end index in j direction
integer, intent(in) :: nk !< Number of levels in k direction
integer, intent(in) :: ntau !< Unknown
integer, intent(in) :: axes(3) !< Domain axes?
real, dimension(isd:,jsd:,:),intent(in) :: grid_tmask !< Unknown
integer,dimension(isd:,jsd:),intent(in) :: grid_kmt !< Unknown
type(time_type), intent(in) :: init_time !< Unknown
end subroutine g_tracer_set_common

subroutine g_tracer_get_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,&
axes,grid_tmask,grid_mask_coast,grid_kmt,init_time,diag_CS)
integer, intent(out) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau !< Unknown
integer,optional, intent(out) :: axes(3) !< Unknown
integer, intent(out) :: isc !< Computation start index in i direction
integer, intent(out) :: iec !< Computation end index in i direction
integer, intent(out) :: jsc !< Computation start index in j direction
integer, intent(out) :: jec !< Computation end index in j direction
integer, intent(out) :: isd !< Data start index in i direction
integer, intent(out) :: ied !< Data end index in i direction
integer, intent(out) :: jsd !< Data start index in j direction
integer, intent(out) :: jed !< Data end index in j direction
integer, intent(out) :: nk !< Number of levels in k direction
integer, intent(out) :: ntau !< Unknown
integer, optional, intent(out) :: axes(3) !< Unknown
type(time_type), optional, intent(out) :: init_time !< Unknown
real, optional, dimension(:,:,:),pointer :: grid_tmask !< Unknown
real, optional, dimension(:,:,:), pointer :: grid_tmask !< Unknown
integer, optional, dimension(:,:), pointer :: grid_mask_coast !< Unknown
integer, optional, dimension(:,:), pointer :: grid_kmt !< Unknown
type(g_diag_ctrl), optional, pointer :: diag_CS !< Unknown
Expand All @@ -123,41 +145,43 @@ end subroutine g_tracer_get_common
subroutine g_tracer_get_4D(g_tracer_list,name,member,array_ptr)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
real, dimension(:,:,:,:), pointer :: array_ptr
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
real, dimension(:,:,:,:), pointer :: array_ptr !< Unknown
end subroutine g_tracer_get_4D

!> Unknown
subroutine g_tracer_get_3D(g_tracer_list,name,member,array_ptr)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
real, dimension(:,:,:), pointer :: array_ptr !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
real, dimension(:,:,:), pointer :: array_ptr !< Unknown
end subroutine g_tracer_get_3D

!> Unknown
subroutine g_tracer_get_2D(g_tracer_list,name,member,array_ptr)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
real, dimension(:,:), pointer :: array_ptr !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
real, dimension(:,:), pointer :: array_ptr !< Unknown
end subroutine g_tracer_get_2D

!> Unknown
subroutine g_tracer_get_4D_val(g_tracer_list,name,member,array,isd,jsd)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
integer, intent(in) :: isd,jsd !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
integer, intent(in) :: isd !< Unknown
integer, intent(in) :: jsd !< Unknown
real, dimension(isd:,jsd:,:,:), intent(out):: array !< Unknown
end subroutine g_tracer_get_4D_val

!> Unknown
subroutine g_tracer_get_3D_val(g_tracer_list,name,member,array,isd,jsd,ntau,positive)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
integer, intent(in) :: isd,jsd !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
integer, intent(in) :: isd !< Unknown
integer, intent(in) :: jsd !< Unknown
integer, optional, intent(in) :: ntau !< Unknown
logical, optional, intent(in) :: positive !< Unknown
real, dimension(isd:,jsd:,:), intent(out):: array !< Unknown
Expand All @@ -169,33 +193,35 @@ end subroutine g_tracer_get_3D_val
subroutine g_tracer_get_2D_val(g_tracer_list,name,member,array,isd,jsd)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
integer, intent(in) :: isd,jsd !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
integer, intent(in) :: isd !< Unknown
integer, intent(in) :: jsd !< Unknown
real, dimension(isd:,jsd:), intent(out):: array !< Unknown
end subroutine g_tracer_get_2D_val

!> Unknown
subroutine g_tracer_get_real(g_tracer_list,name,member,value)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
real, intent(out):: value
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
real, intent(out):: value !< Unknown
end subroutine g_tracer_get_real

!> Unknown
subroutine g_tracer_get_string(g_tracer_list,name,member,string)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
character(len=fm_string_len), intent(out) :: string !< Unknown
end subroutine g_tracer_get_string

!> Unknown
subroutine g_tracer_set_2D(g_tracer_list,name,member,array,isd,jsd,weight)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
integer, intent(in) :: isd,jsd !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
integer, intent(in) :: isd !< Unknown
integer, intent(in) :: jsd !< Unknown
real, dimension(isd:,jsd:),intent(in) :: array !< Unknown
real, optional ,intent(in) :: weight !< Unknown
end subroutine g_tracer_set_2D
Expand All @@ -204,8 +230,9 @@ end subroutine g_tracer_set_2D
subroutine g_tracer_set_3D(g_tracer_list,name,member,array,isd,jsd,ntau)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
integer, intent(in) :: isd,jsd !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
integer, intent(in) :: isd !< Unknown
integer, intent(in) :: jsd !< Unknown
integer, optional, intent(in) :: ntau !< Unknown
real, dimension(isd:,jsd:,:), intent(in) :: array !< Unknown
end subroutine g_tracer_set_3D
Expand All @@ -214,16 +241,17 @@ end subroutine g_tracer_set_3D
subroutine g_tracer_set_4D(g_tracer_list,name,member,array,isd,jsd)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
integer, intent(in) :: isd,jsd !< Unknown
real, dimension(isd:,jsd:,:,:), intent(in) :: array !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
integer, intent(in) :: isd !< Unknown
integer, intent(in) :: jsd !< Unknown
real, dimension(isd:,jsd:,:,:), intent(in) :: array !< Unknown
end subroutine g_tracer_set_4D

!> Unknown
subroutine g_tracer_set_real(g_tracer_list,name,member,value)
character(len=*), intent(in) :: name !< Unknown
character(len=*), intent(in) :: member !< Unknown
type(g_tracer_type), pointer :: g_tracer_list, g_tracer !< Unknown
type(g_tracer_type), pointer :: g_tracer_list !< Unknown
real, intent(in) :: value !< Unknown
end subroutine g_tracer_set_real

Expand Down Expand Up @@ -265,7 +293,7 @@ end subroutine g_tracer_get_next
!! Since the surface flux from the atmosphere (%stf) has the units of mol/m^2/sec the resulting
!! tracer concentration has units of mol/Kg
subroutine g_tracer_vertdiff_G(g_tracer, h_old, ea, eb, dt, kg_m2_to_H, m_to_H, tau, mom)
type(g_tracer_type), pointer :: g_tracer
type(g_tracer_type), pointer :: g_tracer !< Unknown
!> Layer thickness before entrainment, in m or kg m-2.
real, dimension(g_tracer_com%isd:,g_tracer_com%jsd:,:), intent(in) :: h_old
!> The amount of fluid entrained from the layer above, in H.
Expand All @@ -278,7 +306,7 @@ subroutine g_tracer_vertdiff_G(g_tracer, h_old, ea, eb, dt, kg_m2_to_H, m_to_H,
real, intent(in) :: m_to_H !< A conversion factor that translates m into the units
!! of h_old (H).
integer, intent(in) :: tau !< Unknown
logical, intent(in), optional :: mom
logical, intent(in), optional :: mom !< Unknown
end subroutine g_tracer_vertdiff_G

end module g_tracer_utils
4 changes: 2 additions & 2 deletions config_src/external/ODA_hooks/ocean_da_types.F90
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Expand Up @@ -7,7 +7,6 @@ module ocean_da_types_mod

private


!> Example type for ocean ensemble DA state
type, public :: OCEAN_CONTROL_STRUCT
integer :: ensemble_size
Expand Down Expand Up @@ -54,7 +53,8 @@ module ocean_da_types_mod
real, dimension(:,:,:), pointer :: analysis => NULL() !< ensemble member analysis
type(forward_operator_type), pointer :: obs_def => NULL() !< observation forward operator
type(time_type) :: time !< profile time type
real :: i_index, j_index !< model longitude and latitude indices respectively
real :: i_index !< model longitude indices respectively
real :: j_index !< model latitude indices respectively
real, dimension(:,:), pointer :: k_index !< model depth indices
type(time_type) :: tdiff !< difference between model time and observation time
character(len=128) :: filename
Expand Down
6 changes: 3 additions & 3 deletions config_src/external/ODA_hooks/write_ocean_obs.F90
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Expand Up @@ -20,16 +20,16 @@ integer function open_profile_file(name, nvar, grid_lon, grid_lat,thread,fset)
integer, intent(in), optional :: nvar !< Number of variables
real, dimension(:), optional, intent(in) :: grid_lon !< Longitude [degreeE]
real, dimension(:), optional, intent(in) :: grid_lat !< Latitude [degreeN]
integer, intent(in), optional :: thread !< Thread
integer, intent(in), optional :: fset !< File set
integer, optional, intent(in) :: thread !< Thread number
integer, optional, intent(in) :: fset !< File set

open_profile_file=-1
end function open_profile_file

!> Write a profile
subroutine write_profile(unit,profile)
integer, intent(in) :: unit !< File unit
type(ocean_profile_type), intent(in) :: profile !< Profile
type(ocean_profile_type), intent(in) :: profile !< Profile to write

return
end subroutine write_profile
Expand Down
2 changes: 1 addition & 1 deletion src/parameterizations/vertical/MOM_CVMix_KPP.F90
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Expand Up @@ -173,7 +173,7 @@ module MOM_CVMix_KPP

!>@{ CPU time clocks
integer :: id_clock_KPP_calc, id_clock_KPP_compute_BLD, id_clock_KPP_smoothing
!!@}
!>@}

#define __DO_SAFETY_CHECKS__

Expand Down