mom_generic_tracer module reference

Drives the generic version of tracers TOPAZ and CFC and other GFDL BGC components.

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Data Types

mom_generic_tracer_cs

Control structure for generic tracers.

Functions/Subroutines

register_mom_generic_tracer()

Initializes the generic tracer packages and adds their tracers to the list Adds the tracers in the list of generic tracers to the set of MOM tracers (i.e., MOM-register them) Register these tracers for restart.

initialize_mom_generic_tracer()

Initialize phase II: Initialize required variables for generic tracers There are some steps of initialization that cannot be done in register_MOM_generic_tracer This is the place and time to do them: Set the grid mask and initial time for all generic tracers.

mom_generic_tracer_column_physics()

Column physics for generic tracers.

mom_generic_tracer_stock()

This subroutine calculates mass-weighted integral on the PE either of all available tracer concentrations, or of a tracer that is being requested specifically, returning the number of stocks it has calculated.

mom_generic_tracer_min_max()

This subroutine find the global min and max of either of all available tracer concentrations, or of a tracer that is being requested specifically, returning the number of tracers it has gone through.

array_global_min_max()

Find the global maximum and minimum of a tracer array and return the locations of the extrema.

mom_generic_tracer_surface_state()

This subroutine calculates the surface state and sets coupler values for those generic tracers that have flux exchange with atmosphere.

mom_generic_flux_init()

mom_generic_tracer_fluxes_accumulate()

mom_generic_tracer_get()

Copy the requested tracer into an array.

end_mom_generic_tracer()

This subroutine deallocates the memory owned by this module.

Detailed Description

Drives the generic version of tracers TOPAZ and CFC and other GFDL BGC components.

Type Documentation

type mom_generic_tracer/mom_generic_tracer_cs

Control structure for generic tracers.

Type fields
  • % ic_file [character (len=200)] :: The file in which the generic tracer initial values can be found, or an empty string for internal initialization.

  • % z_ic_file [logical] :: If true, the

  • % tracer_ic_val [real] :: The initial value assigned to tracers.

  • % tracer_land_val [real] :: The values of tracers used where land is masked out.

  • % tracers_may_reinit [logical] :: If true, tracers may go through the initialization code if they are not found in the restart files.

  • % diag [type(diag_ctrl),pointer] :: A structure that is used to regulate the timing of diagnostic output.

  • % restart_csp [type(mom_restart_cs),pointer] :: Restart control structure.

  • % g_tracer_list [type( g_tracer_type ),pointer] :: Pointer to the first element of the linked list of generic tracers.

  • % h_to_m [integer] :: Auxiliary to access GVH_to_m in routines that do not have access to GV.

Function/Subroutine Documentation

function mom_generic_tracer/register_mom_generic_tracer(HI, GV, param_file, CS, tr_Reg, restart_CS) [logical]

Initializes the generic tracer packages and adds their tracers to the list Adds the tracers in the list of generic tracers to the set of MOM tracers (i.e., MOM-register them) Register these tracers for restart.

Parameters
  • hi :: [in] Horizontal index ranges

  • gv :: [in] The ocean’s vertical grid structure

  • param_file :: [in] A structure to parse for run-time parameters

  • cs :: Pointer to the control structure for this module

  • tr_reg :: Pointer to the control structure for the tracer advection and diffusion module.

  • restart_cs :: Pointer to the restart control structure.

Call to

g_registered g_tracer_utils::g_tracer_get_alias mom_error_handler::mom_error mom_tracer_registry::register_tracer

subroutine mom_generic_tracer/initialize_mom_generic_tracer(restart, day, G, GV, US, h, param_file, diag, OBC, CS, sponge_CSp, ALE_sponge_CSp)

Initialize phase II: Initialize required variables for generic tracers There are some steps of initialization that cannot be done in register_MOM_generic_tracer This is the place and time to do them: Set the grid mask and initial time for all generic tracers. Diag_register them. Z_diag_register them.

This subroutine initializes the NTR tracer fields in tr(:,:,:,:) and it sets up the tracer output.

Parameters
  • restart :: [in] .true. if the fields have already been read from a restart file.

  • day :: [in] Time of the start of the run.

  • g :: [inout] The ocean’s grid structure

  • gv :: [in] The ocean’s vertical grid structure

  • us :: [in] A dimensional unit scaling type

  • h :: [in] Layer thicknesses [H ~> m or kg m-2]

  • param_file :: [in] A structure to parse for run-time parameters

  • diag :: [in] Regulates diagnostic output.

  • obc :: This open boundary condition type specifies whether, where, and what open boundary conditions are used.

  • cs :: Pointer to the control structure for this module.

  • sponge_csp :: Pointer to the control structure for the sponges.

  • ale_sponge_csp :: Pointer to the control structure for the ALE sponges.

Call to

g_tracer_utils::g_tracer_get_alias g_tracer_utils::g_tracer_set_csdiag mom_error_handler::mom_error mom_tracer_initialization_from_z::mom_initialize_tracer_from_z mom_tracer_z_init::tracer_z_init

subroutine mom_generic_tracer/mom_generic_tracer_column_physics(h_old, h_new, ea, eb, fluxes, Hml, dt, G, GV, CS, tv, optics, evap_CFL_limit, minimum_forcing_depth)

Column physics for generic tracers. Get the coupler values for generic tracers that exchange with atmosphere Update generic tracer concentration fields from sources and sinks. Vertically diffuse generic tracer concentration fields. Update generic tracers from bottom and their bottom reservoir.

This subroutine applies diapycnal diffusion and any other column tracer physics or chemistry to the tracers from this file. CFCs are relatively simple, as they are passive tracers. with only a surface flux as a source.

Parameters
  • g :: [in] The ocean’s grid structure

  • gv :: [in] The ocean’s vertical grid structure

  • h_old :: [in] Layer thickness before entrainment [H ~> m or kg m-2].

  • h_new :: [in] Layer thickness after entrainment [H ~> m or kg m-2].

  • ea :: [in] The amount of fluid entrained from the layer

  • eb :: [in] The amount of fluid entrained from the layer

  • fluxes :: [in] A structure containing pointers to thermodynamic and tracer forcing fields.

  • hml :: [in] Mixed layer depth [Z ~> m]

  • dt :: [in] The amount of time covered by this call [s]

  • cs :: Pointer to the control structure for this module.

  • tv :: [in] A structure pointing to various thermodynamic variables

  • optics :: [in] The structure containing optical properties.

  • evap_cfl_limit :: [in] Limits how much water can be fluxed out of the top layer Stored previously in diabatic CS.

  • minimum_forcing_depth :: [in] The smallest depth over which fluxes can be applied [H ~> m or kg m-2]

Call to

mom_tracer_diabatic::applytracerboundaryfluxesinout g_tracer_utils::g_tracer_get_alias g_tracer_utils::g_tracer_set_csdiag mom_diag_mediator::get_diag_time_end mom_spatial_means::global_area_mean mom_error_handler::mom_error

function mom_generic_tracer/mom_generic_tracer_stock(h, stocks, G, GV, CS, names, units, stock_index) [integer]

This subroutine calculates mass-weighted integral on the PE either of all available tracer concentrations, or of a tracer that is being requested specifically, 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
  • g :: [in] The ocean’s grid structure

  • gv :: [in] The ocean’s vertical grid structure

  • h :: [in] Layer thicknesses [H ~> m or kg m-2]

  • stocks :: [out] The mass-weighted integrated amount of each tracer, in kg times concentration units [kg conc].

  • cs :: Pointer to the control structure for this module.

  • names :: [out] The names of the stocks calculated.

  • units :: [out] The units of the stocks calculated.

  • stock_index :: [in] The coded index of a specific stock being sought.

Return

undefined :: Return value, the number of stocks calculated here.

Call to

g_tracer_utils::g_tracer_get_alias

Called from

mom_tracer_flow_control::call_tracer_stocks

function mom_generic_tracer/mom_generic_tracer_min_max(ind_start, got_minmax, gmin, gmax, xgmin, ygmin, zgmin, xgmax, ygmax, zgmax, G, CS, names, units) [integer]

This subroutine find the global min and max of either of all available tracer concentrations, or of a tracer that is being requested specifically, returning the number of tracers it has gone through.

Parameters
  • ind_start :: [in] The index of the tracer to start with

  • got_minmax :: [out] Indicates whether the global min and max are found for each tracer

  • gmin :: [out] Global minimum of each tracer, in kg times concentration units.

  • gmax :: [out] Global maximum of each tracer, in kg times concentration units.

  • xgmin :: [out] The x-position of the global minimum

  • ygmin :: [out] The y-position of the global minimum

  • zgmin :: [out] The z-position of the global minimum

  • xgmax :: [out] The x-position of the global maximum

  • ygmax :: [out] The y-position of the global maximum

  • zgmax :: [out] The z-position of the global maximum

  • g :: [in] The ocean’s grid structure

  • cs :: Pointer to the control structure for this module.

  • names :: [out] The names of the stocks calculated.

  • units :: [out] The units of the stocks calculated.

Return

undefined :: Return value, the number of tracers done here.

Call to

array_global_min_max g_tracer_utils::g_tracer_get_alias

Called from

mom_tracer_flow_control::call_tracer_stocks

subroutine mom_generic_tracer/array_global_min_max(tr_array, tmask, isd, jsd, isc, iec, jsc, jec, nk, g_min, g_max, geo_x, geo_y, geo_z, xgmin, ygmin, zgmin, xgmax, ygmax, zgmax)

Find the global maximum and minimum of a tracer array and return the locations of the extrema.

Parameters
  • isd :: [in] The starting data domain i-index

  • jsd :: [in] The starting data domain j-index

  • tr_array :: [in] The tracer array to search for extrema

  • tmask :: [in] A mask that is 0 for points to exclude

  • isc :: [in] The starting compute domain i-index

  • iec :: [in] The ending compute domain i-index

  • jsc :: [in] The starting compute domain j-index

  • jec :: [in] The ending compute domain j-index

  • nk :: [in] The number of vertical levels

  • g_min :: [out] The global minimum of tr_array

  • g_max :: [out] The global maximum of tr_array

  • geo_x :: [in] The geographic x-positions of points

  • geo_y :: [in] The geographic y-positions of points

  • geo_z :: [in] The vertical pseudo-positions of points

  • xgmin :: [out] The x-position of the global minimum

  • ygmin :: [out] The y-position of the global minimum

  • zgmin :: [out] The z-position of the global minimum

  • xgmax :: [out] The x-position of the global maximum

  • ygmax :: [out] The y-position of the global maximum

  • zgmax :: [out] The z-position of the global maximum

Called from

mom_generic_tracer_min_max

subroutine mom_generic_tracer/mom_generic_tracer_surface_state(sfc_state, h, G, GV, CS)

This subroutine calculates the surface state and sets coupler values for those generic tracers that have flux exchange with atmosphere.

This subroutine sets up the fields that the coupler needs to calculate the CFC fluxes between the ocean and atmosphere.

Parameters
  • g :: [in] The ocean’s grid structure

  • gv :: [in] The ocean’s vertical grid structure

  • sfc_state :: [inout] A structure containing fields that describe the surface state of the ocean.

  • h :: [in] Layer thicknesses [H ~> m or kg m-2]

  • cs :: Pointer to the control structure for this module.

Call to

mom_diag_mediator::get_diag_time_end mom_spatial_means::global_area_mean

subroutine mom_generic_tracer/mom_generic_flux_init(verbosity)
Parameters

verbosity :: [in] A 0-9 integer indicating a level of verbosity.

Call to

g_registered mom_error_handler::mom_error

subroutine mom_generic_tracer/mom_generic_tracer_fluxes_accumulate(flux_tmp, weight)
Parameters
  • flux_tmp :: [in] A structure containing pointers to thermodynamic and tracer forcing fields.

  • weight :: [in] A weight for accumulating this flux

Call to

generic_tracer::generic_tracer_coupler_accumulate

Called from

ocean_model_mod::update_ocean_model

subroutine mom_generic_tracer/mom_generic_tracer_get(name, member, array, CS)

Copy the requested tracer into an array.

Parameters
  • name :: [in] Name of requested tracer.

  • member :: [in] The tracer element to return.

  • array :: [out] Array filled by this routine.

  • cs :: Pointer to the control structure for this module.

subroutine mom_generic_tracer/end_mom_generic_tracer(CS)

This subroutine deallocates the memory owned by this module.

Parameters

cs :: Pointer to the control structure for this module.