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Added doxygen comments to MOM_diagnostics.F90
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Added doxygen comments to all of the subroutines in MOM_diagnostics.F90. All the
answers are bitwise identical.
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Caroline Cardinale authored and Caroline Cardinale committed Jun 21, 2017
1 parent e9b0a48 commit 3fdcb86
Showing 1 changed file with 123 additions and 63 deletions.
186 changes: 123 additions & 63 deletions src/diagnostics/MOM_diagnostics.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -168,39 +168,59 @@ module MOM_diagnostics
end type diagnostics_CS

contains

!> Diagnostics not more naturally calculated elsewhere are computed here.
subroutine calculate_diagnostic_fields(u, v, h, uh, vh, tv, ADp, CDp, fluxes, &
dt, G, GV, CS, eta_bt)
type(ocean_grid_type), intent(inout) :: G !< The ocean's grid structure
type(verticalGrid_type), intent(in) :: GV !< The ocean's vertical grid structure
real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in) :: u !< The zonal velocity, in m s-1
real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in) :: v !< The meridional velocity, in m s-1
real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h !< Layer thicknesses, in H (usually m or kg m-2)
real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in) :: uh
real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in) :: vh
type(thermo_var_ptrs), intent(in) :: tv !< A structure pointing to various thermodynamic variables
type(accel_diag_ptrs), intent(in) :: ADp
type(cont_diag_ptrs), intent(in) :: CDp
type(forcing), intent(in) :: fluxes
real, intent(in) :: dt !< The time difference in s since the last call to this subroutine
type(diagnostics_CS), intent(inout) :: CS
real, dimension(SZI_(G),SZJ_(G)), optional, intent(in) :: eta_bt
type(ocean_grid_type), intent(inout) :: G !< The ocean's grid structure.
type(verticalGrid_type), intent(in) :: GV !< The ocean's vertical grid
!! structure.
real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in) :: u !< The zonal velocity, in m s-1.
real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in) :: v !< The meridional velocity,
!! in m s-1.
real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h !< Layer thicknesses, in H
!! (usually m or kg m-2).
real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in) :: uh !< Transport through zonal faces
!! = u*h*dy, m3/s(Bouss)
!! kg/s(non-Bouss).
real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in) :: vh !< transport through meridional
!! faces = v*h*dx, m3/s(Bouss)
!! kg/s(non-Bouss).
type(thermo_var_ptrs), intent(in) :: tv !< A structure pointing to
!! various thermodynamic
!! variables.
type(accel_diag_ptrs), intent(in) :: ADp !< structure with pointers to
!! accelerations in momentum
!! equation.
type(cont_diag_ptrs), intent(in) :: CDp !< structure with pointers to
!! terms in continuity equation.
type(forcing), intent(in) :: fluxes !< A structure containing the
!! surface fluxes.
real, intent(in) :: dt !< The time difference in s since
!! the last call to this
!! subroutine.
type(diagnostics_CS), intent(inout) :: CS !< Control structure returned by
!! a previous call to
!! diagnostics_init.
real, dimension(SZI_(G),SZJ_(G)), optional, intent(in) :: eta_bt !< An optional barotropic
!! variable that gives the "correct" free surface height (Boussinesq) or total water column
!! mass per unit area (non-Boussinesq). This is used to dilate the layer thicknesses when
!! calculating interface heights, in m or kg m-2.

! Diagnostics not more naturally calculated elsewhere are computed here.

! Arguments:
! (in) u - zonal velocity component (m/s)
! (in) v - meridional velocity component (m/s)
! (in) h - layer thickness, meter(Bouss) kg/m^2(non-Bouss)
! (in) uh - transport through zonal faces = u*h*dy, m3/s(Bouss) kg/s(non-Bouss)
! (in) vh - transport through meridional faces = v*h*dx, m3/s(Bouss) kg/s(non-Bouss)
! (in) u - zonal velocity component (m/s).
! (in) v - meridional velocity component (m/s).
! (in) h - layer thickness, meter(Bouss) kg/m^2(non-Bouss).
! (in) uh - transport through zonal faces = u*h*dy, m3/s(Bouss) kg/s(non-Bouss).
! (in) vh - transport through meridional faces = v*h*dx, m3/s(Bouss) kg/s(non-Bouss).
! (in) tv - structure pointing to various thermodynamic variables.
! (in) ADp - structure with pointers to accelerations in momentum equation
! (in) CDp - structure with pointers to terms in continuity equation
! (in) dt - time difference in s since the last call to this subroutine
! (in) ADp - structure with pointers to accelerations in momentum equation.
! (in) CDp - structure with pointers to terms in continuity equation.
! (in) dt - time difference in s since the last call to this subroutine.
! (in) G - ocean grid structure.
! (in) GV - The ocean's vertical grid structure.
! (in) CS - control structure returned by a previous call to diagnostics_init
! (in) CS - control structure returned by a previous call to diagnostics_init.
! (in,opt) eta_bt - An optional barotropic variable that gives the "correct"
! free surface height (Boussinesq) or total water column
! mass per unit area (non-Boussinesq). This is used to
Expand Down Expand Up @@ -620,7 +640,10 @@ subroutine calculate_diagnostic_fields(u, v, h, uh, vh, tv, ADp, CDp, fluxes, &

end subroutine calculate_diagnostic_fields


!> This subroutine finds location of R_in in an increasing ordered
!! list, Rlist, returning as k the element such that
!! Rlist(k) <= R_in < Rlist(k+1), and where wt and wt_p are the linear
!! weights that should be assigned to elements k and k+1.
subroutine find_weights(Rlist, R_in, k, nz, wt, wt_p)
real, intent(in) :: Rlist(:), R_in
integer, intent(inout) :: k
Expand Down Expand Up @@ -681,13 +704,22 @@ subroutine find_weights(Rlist, R_in, k, nz, wt, wt_p)

end subroutine find_weights

!> Subroutine calculates vertical integrals of several tracers, along
!! with the mass-weight of these tracers, the total column mass, and the
!! carefully calculated column height.
subroutine calculate_vertical_integrals(h, tv, fluxes, G, GV, CS)
type(ocean_grid_type), intent(inout) :: 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_(G)), intent(in) :: h !< Layer thicknesses, in H (usually m or kg m-2)
type(thermo_var_ptrs), intent(in) :: tv !< A structure pointing to various thermodynamic variables
type(forcing), intent(in) :: fluxes
type(diagnostics_CS), intent(inout) :: CS
type(ocean_grid_type), intent(inout) :: 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_(G)), intent(in) :: h !< Layer thicknesses, in H
!! (usually m or kg m-2).
type(thermo_var_ptrs), intent(in) :: tv !< A structure pointing to various
!! thermodynamic variables.
type(forcing), intent(in) :: fluxes !< A structure containing the
!! surface fluxes.
type(diagnostics_CS), intent(inout) :: CS !< A control structure returned
!! by a previous call to
!! diagnostics_init.

! Subroutine calculates vertical integrals of several tracers, along
! with the mass-weight of these tracers, the total column mass, and the
Expand Down Expand Up @@ -802,17 +834,28 @@ subroutine calculate_vertical_integrals(h, tv, fluxes, G, GV, CS)

end subroutine calculate_vertical_integrals


!> This subroutine calculates terms in the mechanical energy budget.
subroutine calculate_energy_diagnostics(u, v, h, uh, vh, ADp, CDp, G, CS)
type(ocean_grid_type), intent(inout) :: G !< The ocean's grid structure
real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in) :: u !< The zonal velocity, in m s-1
real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in) :: v !< The meridional velocity, in m s-1
real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h !< Layer thicknesses, in H (usually m or kg m-2)
real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in) :: uh
real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in) :: vh
type(accel_diag_ptrs), intent(in) :: ADp
type(cont_diag_ptrs), intent(in) :: CDp
type(diagnostics_CS), intent(inout) :: CS
type(ocean_grid_type), intent(inout) :: G !< The ocean's grid structure.
real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in) :: u !< The zonal velocity, in m s-1.
real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in) :: v !< The meridional velocity,
!! in m s-1.
real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h !< Layer thicknesses, in H
!! (usually m or kg m-2).
real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in) :: uh !< Transport through zonal
!! faces=u*h*dy: m3/s (Bouss)
!! kg/s(non-Bouss).
real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in) :: vh !< Transport through merid
!! faces=v*h*dx: m3/s (Bouss)
!! kg/s(non-Bouss).
type(accel_diag_ptrs), intent(in) :: ADp !< Structure pointing to
!! accelerations in momentum
!! equation.
type(cont_diag_ptrs), intent(in) :: CDp !< Structure pointing to terms
!! in continuity equations.
type(diagnostics_CS), intent(inout) :: CS !< Control structure returned by
!! a previous call to
!! diagnostics_init.

! This subroutine calculates terms in the mechanical energy budget.

Expand Down Expand Up @@ -1001,10 +1044,13 @@ subroutine calculate_energy_diagnostics(u, v, h, uh, vh, ADp, CDp, G, CS)

end subroutine calculate_energy_diagnostics


!> This subroutine registers fields to calculate a diagnostic time derivative.
subroutine register_time_deriv(f_ptr, deriv_ptr, CS)
real, dimension(:,:,:), target :: f_ptr, deriv_ptr
type(diagnostics_CS), pointer :: CS
real, dimension(:,:,:), target :: f_ptr !< Field whose derivative is taken.
real, dimension(:,:,:), target :: deriv_ptr !< Field in which the calculated time derivatives
!! placed.
type(diagnostics_CS), pointer :: CS !< Control structure returned by previous call to
!! diagnostics_init.

! This subroutine registers fields to calculate a diagnostic time derivative.
! Arguments:
Expand Down Expand Up @@ -1035,11 +1081,13 @@ subroutine register_time_deriv(f_ptr, deriv_ptr, CS)

end subroutine register_time_deriv


!> This subroutine calculates all registered time derivatives.
subroutine calculate_derivs(dt, G, CS)
real, intent(in) :: dt !< The time interval over which differences occur, in s
type(ocean_grid_type), intent(inout) :: G !< The ocean's grid structure
type(diagnostics_CS), intent(inout) :: CS
real, intent(in) :: dt !< The time interval over which differences occur,
!! in s.
type(ocean_grid_type), intent(inout) :: G !< The ocean's grid structure.
type(diagnostics_CS), intent(inout) :: CS !< Control structure returned by previous call to
!! diagnostics_init.

! This subroutine calculates all registered time derivatives.
! Arguments:
Expand All @@ -1062,16 +1110,23 @@ subroutine calculate_derivs(dt, G, CS)

end subroutine calculate_derivs

! #@# This subroutine needs a doxygen description
subroutine MOM_diagnostics_init(MIS, ADp, CDp, Time, G, GV, param_file, diag, CS)
type(ocean_internal_state), intent(in) :: MIS
type(accel_diag_ptrs), intent(inout) :: ADp
type(cont_diag_ptrs), intent(inout) :: CDp
type(time_type), intent(in) :: Time
type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure
type(verticalGrid_type), intent(in) :: GV !< The ocean's vertical grid structure
type(param_file_type), intent(in) :: param_file !< A structure to parse for run-time parameters
type(diag_ctrl), target, intent(inout) :: diag
type(diagnostics_CS), pointer :: CS
type(ocean_internal_state), intent(in) :: MIS !< For "MOM Internal State" a set of pointers to
!! the fields and accelerations that make up the
!! ocean's internal physical state.
type(accel_diag_ptrs), intent(inout) :: ADp !< Structure with pointers to momentum equation
!! terms.
type(cont_diag_ptrs), intent(inout) :: CDp !< Structure with pointers to continuity
!! equation terms.
type(time_type), intent(in) :: Time !< Current model time.
type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure.
type(verticalGrid_type), intent(in) :: GV !< The ocean's vertical grid structure.
type(param_file_type), intent(in) :: param_file !< A structure to parse for run-time
!! parameters.
type(diag_ctrl), target, intent(inout) :: diag !< Structure to regulate diagnostic output.
type(diagnostics_CS), pointer :: CS !< Pointer set to point to control structure
!! for this module.

! Arguments
! (in) MIS - For "MOM Internal State" a set of pointers to the fields and
Expand Down Expand Up @@ -1329,13 +1384,18 @@ subroutine MOM_diagnostics_init(MIS, ADp, CDp, Time, G, GV, param_file, diag, CS

end subroutine MOM_diagnostics_init


!> This subroutine sets up diagnostics upon which other diagnostics depend.
subroutine set_dependent_diagnostics(MIS, ADp, CDp, G, CS)
type(ocean_internal_state), intent(in) :: MIS
type(accel_diag_ptrs), intent(inout) :: ADp
type(cont_diag_ptrs), intent(inout) :: CDp
type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure
type(diagnostics_CS), pointer :: CS
type(ocean_internal_state), intent(in) :: MIS !< For "MOM Internal State" a set of pointers to
!! the fields and accelerations making up ocean
!! internal physical state.
type(accel_diag_ptrs), intent(inout) :: ADp !< Structure pointing to accelerations in
!! momentum equation.
type(cont_diag_ptrs), intent(inout) :: CDp !< Structure pointing to terms in continuity
!! equation.
type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure.
type(diagnostics_CS), pointer :: CS !< Pointer to the control structure for this
!! module.

! This subroutine sets up diagnostics upon which other diagnostics depend.
! Arguments:
Expand Down

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