Detailed Description

A tracer package that mimics salinity.

By Andrew Shao, 2016

This file contains the routines necessary to model a passive tracer that uses the same boundary fluxes as salinity. At the beginning of the run, salt is set to the same as tvS. Any deviations between this salt-like tracer and tvS signifies a difference between how active and passive tracers are treated.

Data Types
type	pseudo_salt_tracer_cs
	The control structure for the pseudo-salt tracer. More...

Functions/Subroutines
logical function, public	register_pseudo_salt_tracer (HI, GV, param_file, CS, tr_Reg, restart_CS)
	Register the pseudo-salt tracer with MOM6. More...

subroutine, public	initialize_pseudo_salt_tracer (restart, day, G, GV, h, diag, OBC, CS, sponge_CSp, tv)
	Initialize the pseudo-salt tracer. More...

subroutine, public	pseudo_salt_tracer_column_physics (h_old, h_new, ea, eb, fluxes, dt, G, GV, CS, tv, debug, evap_CFL_limit, minimum_forcing_depth)
	Apply sources, sinks and diapycnal diffusion to the tracers in this package. More...

integer function, public	pseudo_salt_stock (h, stocks, G, GV, CS, names, units, stock_index)
	Calculates the mass-weighted integral of all tracer stocks, returning the number of stocks it has calculated. If the stock_index is present, only the stock corresponding to that coded index is returned. More...

subroutine, public	pseudo_salt_tracer_surface_state (state, h, G, CS)
	This subroutine extracts the surface fields from this tracer package that are to be shared with the atmosphere in coupled configurations. This particular tracer package does not report anything back to the coupler. More...

subroutine, public	pseudo_salt_tracer_end (CS)
	Deallocate memory associated with this tracer package. More...

Function/Subroutine Documentation

◆ initialize_pseudo_salt_tracer()

subroutine, public pseudo_salt_tracer::initialize_pseudo_salt_tracer	(	logical, intent(in)	restart,
		type(time_type), intent(in), target	day,
		type(ocean_grid_type), intent(in)	G,
		type(verticalgrid_type), intent(in)	GV,
		real, dimension( g %isd: g %ied, g %jsd: g %jed, g %ke), intent(in)	h,
		type(diag_ctrl), intent(in), target	diag,
		type(ocean_obc_type), pointer	OBC,
		type(pseudo_salt_tracer_cs), pointer	CS,
		type(sponge_cs), pointer	sponge_CSp,
		type(thermo_var_ptrs), intent(in)	tv
	)

Initialize the pseudo-salt tracer.

Parameters

[in]	restart	.true. if the fields have already been read from a restart file.
[in]	day	Time of the start of the run.
[in]	g	The ocean's grid structure
[in]	gv	The ocean's vertical grid structure
[in]	h	Layer thicknesses [H ~> m or kg m-2]
[in]	diag	A structure that is used to regulate diagnostic output.
	obc	This open boundary condition type specifies whether, where, and what open boundary conditions are used.
	cs	The control structure returned by a previous call to register_pseudo_salt_tracer.
	sponge_csp	Pointer to the control structure for the sponges.
[in]	tv	A structure pointing to various thermodynamic variables

Definition at line 117 of file pseudo_salt_tracer.F90.

   logical,                            intent(in) :: restart !< .true. if the fields have already
                                                          !! been read from a restart file.
   type(time_type),            target, intent(in) :: day  !< Time of the start of the run.
   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_(G)), &
                                       intent(in) :: h    !< Layer thicknesses [H ~> m or kg m-2]
   type(diag_ctrl),            target, intent(in) :: diag !< A structure that is used to regulate
                                                          !! diagnostic output.
   type(ocean_OBC_type),               pointer    :: OBC  !< This open boundary condition type specifies
                                                          !! whether, where, and what open boundary
                                                          !! conditions are used.
   type(pseudo_salt_tracer_CS),        pointer    :: CS !< The control structure returned by a previous
                                                        !! call to register_pseudo_salt_tracer.
   type(sponge_CS),                    pointer    :: sponge_CSp !< Pointer to the control structure for the sponges.
   type(thermo_var_ptrs),              intent(in) :: tv   !< A structure pointing to various thermodynamic variables
 !   This subroutine initializes the tracer fields in CS%ps(:,:,:).
  
   ! Local variables
   character(len=16) :: name     ! A variable's name in a NetCDF file.
   character(len=72) :: longname ! The long name of that variable.
   character(len=48) :: units    ! The dimensions of the variable.
   character(len=48) :: flux_units ! The units for age tracer fluxes, either
                                 ! years m3 s-1 or years kg s-1.
   logical :: OK
   integer :: i, j, k, is, ie, js, je, isd, ied, jsd, jed, nz
   integer :: IsdB, IedB, JsdB, JedB
  
   if (.not.associated(cs)) return
   if (.not.associated(cs%diff)) return
  
   is = g%isc ; ie = g%iec ; js = g%jsc ; je = g%jec ; nz = gv%ke
   isd = g%isd ; ied = g%ied ; jsd = g%jsd ; jed = g%jed
   isdb = g%IsdB ; iedb = g%IedB ; jsdb = g%JsdB ; jedb = g%JedB
  
   cs%Time => day
   cs%diag => diag
   name = "pseudo_salt"
  
   call query_vardesc(cs%tr_desc, name=name, caller="initialize_pseudo_salt_tracer")
   if ((.not.restart) .or. (.not.query_initialized(cs%ps, name, cs%restart_CSp))) then
     do k=1,nz ; do j=jsd,jed ; do i=isd,ied
       cs%ps(i,j,k) = tv%S(i,j,k)
     enddo ; enddo ; enddo
   endif
  
   if (associated(obc)) then
   ! Steal from updated DOME in the fullness of time.
   endif
  
   cs%id_psd = register_diag_field("ocean_model", "pseudo_salt_diff", cs%diag%axesTL, &
         day, "Difference between pseudo salt passive tracer and salt tracer", "psu")
  

◆ pseudo_salt_stock()

integer function, public pseudo_salt_tracer::pseudo_salt_stock	(	real, dimension(szi_(g),szj_(g),szk_(g)), intent(in)	h,
		real, dimension(:), intent(out)	stocks,
		type(ocean_grid_type), intent(in)	G,
		type(verticalgrid_type), intent(in)	GV,
		type(pseudo_salt_tracer_cs), pointer	CS,
		character(len=*), dimension(:), intent(out)	names,
		character(len=*), dimension(:), intent(out)	units,
		integer, intent(in), optional	stock_index
	)

Calculates the mass-weighted integral of all tracer stocks, returning the number of stocks it has calculated. If the stock_index is present, only the stock corresponding to that coded index is returned.

Parameters

[in]	g	The ocean's grid structure
[in]	gv	The ocean's vertical grid structure
[in]	h	Layer thicknesses [H ~> m or kg m-2]
[out]	stocks	the mass-weighted integrated amount of each tracer, in kg times concentration units [kg conc].
	cs	The control structure returned by a previous call to register_pseudo_salt_tracer.
[out]	names	The names of the stocks calculated.
[out]	units	The units of the stocks calculated.
[in]	stock_index	The coded index of a specific stock being sought.

Returns: Return value: the number of stocks calculated here.

Definition at line 252 of file pseudo_salt_tracer.F90.

   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_(G)), intent(in) :: h    !< Layer thicknesses [H ~> m or kg m-2]
   real, dimension(:),                 intent(out)   :: stocks !< the mass-weighted integrated amount of each
                                                               !! tracer, in kg times concentration units [kg conc].
   type(pseudo_salt_tracer_CS),        pointer       :: CS !< The control structure returned by a previous
                                                           !! call to register_pseudo_salt_tracer.
   character(len=*), dimension(:),     intent(out)   :: names  !< The names of the stocks calculated.
   character(len=*), dimension(:),     intent(out)   :: units  !< The units of the stocks calculated.
   integer, optional,                  intent(in)    :: stock_index !< The coded index of a specific stock
                                                               !! being sought.
   integer                                           :: pseudo_salt_stock !< Return value: the number of
                                                               !! stocks calculated here.
  
 ! This function calculates the mass-weighted integral of all tracer stocks,
 ! returning the number of stocks it has calculated.  If the stock_index
 ! is present, only the stock corresponding to that coded index is returned.
  
   integer :: i, j, k, is, ie, js, je, nz
   is = g%isc ; ie = g%iec ; js = g%jsc ; je = g%jec ; nz = gv%ke
  
   pseudo_salt_stock = 0
   if (.not.associated(cs)) return
   if (.not.associated(cs%diff)) return
  
   if (present(stock_index)) then ; if (stock_index > 0) then
     ! Check whether this stock is available from this routine.
  
     ! No stocks from this routine are being checked yet.  Return 0.
     return
   endif ; endif
  
   call query_vardesc(cs%tr_desc, name=names(1), units=units(1), caller="pseudo_salt_stock")
   units(1) = trim(units(1))//" kg"
   stocks(1) = 0.0
   do k=1,nz ; do j=js,je ; do i=is,ie
     stocks(1) = stocks(1) + cs%diff(i,j,k) * &
                          (g%mask2dT(i,j) * g%areaT(i,j) * h(i,j,k))
   enddo ; enddo ; enddo
   stocks(1) = gv%H_to_kg_m2 * stocks(1)
  
   pseudo_salt_stock = 1
  

◆ pseudo_salt_tracer_column_physics()

subroutine, public pseudo_salt_tracer::pseudo_salt_tracer_column_physics	(	real, dimension(szi_(g),szj_(g),szk_(g)), intent(in)	h_old,
		real, dimension(szi_(g),szj_(g),szk_(g)), intent(in)	h_new,
		real, dimension(szi_(g),szj_(g),szk_(g)), intent(in)	ea,
		real, dimension(szi_(g),szj_(g),szk_(g)), intent(in)	eb,
		type(forcing), intent(in)	fluxes,
		real, intent(in)	dt,
		type(ocean_grid_type), intent(in)	G,
		type(verticalgrid_type), intent(in)	GV,
		type(pseudo_salt_tracer_cs), pointer	CS,
		type(thermo_var_ptrs), intent(in)	tv,
		logical, intent(in)	debug,
		real, intent(in), optional	evap_CFL_limit,
		real, intent(in), optional	minimum_forcing_depth
	)

Apply sources, sinks and diapycnal diffusion to the tracers in this package.

Parameters

[in]	g	The ocean's grid structure
[in]	gv	The ocean's vertical grid structure
[in]	h_old	Layer thickness before entrainment [H ~> m or kg m-2].
[in]	h_new	Layer thickness after entrainment [H ~> m or kg m-2].
[in]	ea	an array to which the amount of fluid entrained
[in]	eb	an array to which the amount of fluid entrained
[in]	fluxes	A structure containing pointers to thermodynamic and tracer forcing fields. Unused fields have NULL ptrs.
[in]	dt	The amount of time covered by this call [s]
	cs	The control structure returned by a previous call to register_pseudo_salt_tracer.
[in]	tv	A structure pointing to various thermodynamic variables
[in]	debug	If true calculate checksums
[in]	evap_cfl_limit	Limit on the fraction of the water that can be fluxed out of the top layer in a timestep [nondim]
[in]	minimum_forcing_depth	The smallest depth over which fluxes can be applied [m]

Definition at line 175 of file pseudo_salt_tracer.F90.

   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_(G)), &
                            intent(in) :: h_old !< Layer thickness before entrainment [H ~> m or kg m-2].
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
                            intent(in) :: h_new !< Layer thickness after entrainment [H ~> m or kg m-2].
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
                            intent(in) :: ea   !< an array to which the amount of fluid entrained
                                               !! from the layer above during this call will be
                                               !! added [H ~> m or kg m-2].
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
                            intent(in) :: eb   !< an array to which the amount of fluid entrained
                                               !! from the layer below during this call will be
                                               !! added [H ~> m or kg m-2].
   type(forcing),           intent(in) :: fluxes !< A structure containing pointers to thermodynamic
                                               !! and tracer forcing fields.  Unused fields have NULL ptrs.
   real,                    intent(in) :: dt   !< The amount of time covered by this call [s]
   type(pseudo_salt_tracer_CS), pointer :: CS  !< The control structure returned by a previous
                                               !! call to register_pseudo_salt_tracer.
   type(thermo_var_ptrs),   intent(in) :: tv   !< A structure pointing to various thermodynamic variables
   logical,                 intent(in) :: debug !< If true calculate checksums
   real,          optional, intent(in) :: evap_CFL_limit !< Limit on the fraction of the water that can
                                               !! be fluxed out of the top layer in a timestep [nondim]
   real,          optional, intent(in) :: minimum_forcing_depth !< The smallest depth over which
                                               !! fluxes can be applied [m]
  
 !   This subroutine applies diapycnal diffusion and any other column
 ! tracer physics or chemistry to the tracers from this file.
  
 ! The arguments to this subroutine are redundant in that
 !     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
  
   ! Local variables
   real :: year, h_total, scale, htot, Ih_limit
   integer :: secs, days
   integer :: i, j, k, is, ie, js, je, nz, k_max
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)) :: h_work ! Used so that h can be modified
  
   is = g%isc ; ie = g%iec ; js = g%jsc ; je = g%jec ; nz = gv%ke
  
   if (.not.associated(cs)) return
   if (.not.associated(cs%diff)) return
  
   if (debug) then
     call hchksum(tv%S,"salt pre pseudo-salt vertdiff", g%HI)
     call hchksum(cs%ps,"pseudo_salt pre pseudo-salt vertdiff", g%HI)
   endif
  
   ! This uses applyTracerBoundaryFluxesInOut, usually in ALE mode
   if (present(evap_cfl_limit) .and. present(minimum_forcing_depth)) then
     do k=1,nz ; do j=js,je ; do i=is,ie
       h_work(i,j,k) = h_old(i,j,k)
     enddo ; enddo ; enddo
     call applytracerboundaryfluxesinout(g, gv, cs%ps, dt, fluxes, h_work, &
       evap_cfl_limit, minimum_forcing_depth, out_flux_optional=fluxes%netSalt)
     call tracer_vertdiff(h_work, ea, eb, dt, cs%ps, g, gv)
   else
     call tracer_vertdiff(h_old, ea, eb, dt, cs%ps, g, gv)
   endif
  
   do k=1,nz ; do j=js,je ; do i=is,ie
     cs%diff(i,j,k) = cs%ps(i,j,k)-tv%S(i,j,k)
   enddo ; enddo ; enddo
  
   if (debug) then
     call hchksum(tv%S,"salt post pseudo-salt vertdiff", g%HI)
     call hchksum(cs%ps,"pseudo_salt post pseudo-salt vertdiff", g%HI)
   endif
  
   if (cs%id_psd>0) call post_data(cs%id_psd, cs%diff, cs%diag)
  

◆ pseudo_salt_tracer_end()

subroutine, public pseudo_salt_tracer::pseudo_salt_tracer_end ( type(pseudo_salt_tracer_cs), pointer CS )

Deallocate memory associated with this tracer package.

Parameters

cs	The control structure returned by a previous call to register_pseudo_salt_tracer.

Definition at line 324 of file pseudo_salt_tracer.F90.

   type(pseudo_salt_tracer_CS), pointer :: CS !< The control structure returned by a previous
                                               !! call to register_pseudo_salt_tracer.
   integer :: m
  
   if (associated(cs)) then
     if (associated(cs%ps)) deallocate(cs%ps)
     if (associated(cs%diff)) deallocate(cs%diff)
     deallocate(cs)
   endif

◆ pseudo_salt_tracer_surface_state()

subroutine, public pseudo_salt_tracer::pseudo_salt_tracer_surface_state	(	type(surface), intent(inout)	state,
		real, dimension( g %isd: g %ied, g %jsd: g %jed, g %ke), intent(in)	h,
		type(ocean_grid_type), intent(in)	G,
		type(pseudo_salt_tracer_cs), pointer	CS
	)

This subroutine extracts the surface fields from this tracer package that are to be shared with the atmosphere in coupled configurations. This particular tracer package does not report anything back to the coupler.

Parameters

[in]	g	The ocean's grid structure.
[in,out]	state	A structure containing fields that describe the surface state of the ocean.
[in]	h	Layer thickness [H ~> m or kg m-2].
	cs	The control structure returned by a previous call to register_pseudo_salt_tracer.

Definition at line 301 of file pseudo_salt_tracer.F90.

   type(ocean_grid_type),  intent(in)    :: G  !< The ocean's grid structure.
   type(surface),          intent(inout) :: state !< A structure containing fields that
                                               !! describe the surface state of the ocean.
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
                           intent(in)    :: h  !< Layer thickness [H ~> m or kg m-2].
   type(pseudo_salt_tracer_CS), pointer  :: CS !< The control structure returned by a previous
                                               !! call to register_pseudo_salt_tracer.
  
   ! This particular tracer package does not report anything back to the coupler.
   ! The code that is here is just a rough guide for packages that would.
  
   integer :: m, is, ie, js, je, isd, ied, jsd, jed
   is = g%isc ; ie = g%iec ; js = g%jsc ; je = g%jec
   isd = g%isd ; ied = g%ied ; jsd = g%jsd ; jed = g%jed
  
   if (.not.associated(cs)) return
  
   ! By design, this tracer package does not return any surface states.
  

◆ register_pseudo_salt_tracer()

logical function, public pseudo_salt_tracer::register_pseudo_salt_tracer	(	type(hor_index_type), intent(in)	HI,
		type(verticalgrid_type), intent(in)	GV,
		type(param_file_type), intent(in)	param_file,
		type(pseudo_salt_tracer_cs), pointer	CS,
		type(tracer_registry_type), pointer	tr_Reg,
		type(mom_restart_cs), pointer	restart_CS
	)

Register the pseudo-salt tracer with MOM6.

Parameters

[in]	hi	A horizontal index type structure
[in]	gv	The ocean's vertical grid structure
[in]	param_file	A structure to parse for run-time parameters
	cs	The control structure returned by a previous call to register_pseudo_salt_tracer.
	tr_reg	A pointer that is set to point to the control structure for the tracer advection and diffusion module
	restart_cs	A pointer to the restart control structure

Definition at line 60 of file pseudo_salt_tracer.F90.

   type(hor_index_type),       intent(in) :: HI   !< A horizontal index type 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(pseudo_salt_tracer_CS),  pointer  :: CS !< The control structure returned by a previous
                                                !! call to register_pseudo_salt_tracer.
   type(tracer_registry_type), pointer    :: tr_Reg !< A pointer that is set to point to the control
                                                   !! structure for the tracer advection and
                                                   !! diffusion module
   type(MOM_restart_CS),       pointer    :: restart_CS !< A pointer to the restart control structure
 ! This subroutine is used to register tracer fields and subroutines
 ! to be used with MOM.
  
   ! Local variables
   character(len=40)  :: mdl = "pseudo_salt_tracer" ! This module's name.
   character(len=200) :: inputdir ! The directory where the input files are.
   character(len=48)  :: var_name ! The variable's name.
   character(len=3)   :: name_tag ! String for creating identifying pseudo_salt
 ! This include declares and sets the variable "version".
 #include "version_variable.h"
   real, pointer :: tr_ptr(:,:,:) => null()
   logical :: register_pseudo_salt_tracer
   integer :: isd, ied, jsd, jed, nz, i, j
   isd = hi%isd ; ied = hi%ied ; jsd = hi%jsd ; jed = hi%jed ; nz = gv%ke
  
   if (associated(cs)) then
     call mom_error(warning, "register_pseudo_salt_tracer called with an "// &
                              "associated control structure.")
     return
   endif
   allocate(cs)
  
   ! Read all relevant parameters and write them to the model log.
   call log_version(param_file, mdl, version, "")
  
   allocate(cs%ps(isd:ied,jsd:jed,nz)) ; cs%ps(:,:,:) = 0.0
   allocate(cs%diff(isd:ied,jsd:jed,nz)) ; cs%diff(:,:,:) = 0.0
  
   cs%tr_desc = var_desc(trim("pseudo_salt"), "psu", &
                      "Pseudo salt passive tracer", caller=mdl)
  
   tr_ptr => cs%ps(:,:,:)
   call query_vardesc(cs%tr_desc, name=var_name, caller="register_pseudo_salt_tracer")
   ! Register the tracer for horizontal advection, diffusion, and restarts.
   call register_tracer(tr_ptr, tr_reg, param_file, hi, gv, name="pseudo_salt", &
                        longname="Pseudo salt passive tracer", units="psu", &
                        registry_diags=.true., restart_cs=restart_cs, &
                        mandatory=.not.cs%pseudo_salt_may_reinit)
  
   cs%tr_Reg => tr_reg
   cs%restart_CSp => restart_cs
   register_pseudo_salt_tracer = .true.
  

Detailed Description

Data Types

Functions/Subroutines

Function/Subroutine Documentation

◆ initialize_pseudo_salt_tracer()

◆ pseudo_salt_stock()

◆ pseudo_salt_tracer_column_physics()

◆ pseudo_salt_tracer_end()

◆ pseudo_salt_tracer_surface_state()

◆ register_pseudo_salt_tracer()