mom_ale module reference

This module contains the main regridding routines.

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Data Types

ale_cs

ALE control structure.

Functions/Subroutines

ale_init()	This routine is typically called (from initialize_MOM in file MOM.F90 ) before the main time integration loop to initialize the regridding stuff.
ale_register_diags()	Initialize diagnostics for the ALE module.
adjustgridforintegrity()	Crudely adjust (initial) grid for integrity.
ale_end()	End of regridding (memory deallocation).
ale_main()	Takes care of (1) building a new grid and (2) remapping all variables between the old grid and the new grid.
ale_main_offline()	Takes care of (1) building a new grid and (2) remapping all variables between the old grid and the new grid.
ale_offline_inputs()	Regrid/remap stored fields used for offline tracer integrations.
ale_offline_tracer_final()	Remaps all tracers from h onto h_target.
check_grid()	Check grid for negative thicknesses.
ale_build_grid()	Generates new grid.
ale_regrid_accelerated()	For a state-based coordinate, accelerate the process of regridding by repeatedly applying the grid calculation algorithm.
remap_all_state_vars()	This routine takes care of remapping all variable between the old and the new grids.
ale_remap_scalar()	Remaps a single scalar between grids described by thicknesses h_src and h_dst.
ts_plm_edge_values()	Calculate edge values (top and bottom of layer) for T and S consistent with a PLM reconstruction in the vertical direction.
ale_plm_edge_values()	Calculate edge values (top and bottom of layer) 3d scalar array.
ts_ppm_edge_values()	Calculate edge values (top and bottom of layer) for T and S consistent with a PPM reconstruction in the vertical direction.
ale_initregridding()	Initializes regridding for the main ALE algorithm.
ale_getcoordinate()	Query the target coordinate interfaces positions.
ale_getcoordinateunits()	Query the target coordinate units.
ale_remap_init_conds()	Returns true if initial conditions should be regridded and remapped.
ale_update_regrid_weights()	Updates the weights for time filtering the new grid generated in regridding.
ale_updateverticalgridtype()	Update the vertical grid type with ALE information.
ale_writecoordinatefile()	Write the vertical coordinate information into a file.
ale_initthicknesstocoord()	Set h to coordinate values for fixed coordinate systems.

Detailed Description

Regridding comprises two steps:

1. Interpolation and creation of a new grid based on target interface densities (or any other criterion).

2. Remapping of quantities between old grid and new grid.

Original module written by Laurent White, 2008.06.09

Type Documentation

type mom_ale/ale_cs

ALE control structure.

Type fields

• % remap_uv_using_old_alg [logical] :: If true, uses the old “remapping via a delta z” method. If False, uses the new method that remaps between grids described by h.

• % regrid_time_scale [real] :: The time-scale used in blending between the current (old) grid and the target (new) grid [T ~> s].

• % regridcs [type(regridding_cs)] :: Regridding parameters and work arrays.

• % remapcs [type(remapping_cs)] :: Remapping parameters and work arrays.

• % nk [integer] :: Used only for queries, not directly by this module.

• % remap_after_initialization [logical] :: Indicates whether to regrid/remap after initializing the state.

• % answers_2018 [logical] :: If true, use the order of arithmetic and expressions for remapping that recover the answers from the end of 2018. Otherwise, use more robust and accurate forms of mathematically equivalent expressions.

• % show_call_tree [logical] :: For debugging.

• % diag [type(diag_ctrl),pointer] :: structure to regulate output

• % id_tracer_remap_tendency [integer(:),allocatable] :: diagnostic id

• % id_htracer_remap_tendency [integer(:),allocatable] :: diagnostic id

• % id_htracer_remap_tendency_2d [integer(:),allocatable] :: diagnostic id

• % do_tendency_diag [logical(:),allocatable] :: flag for doing diagnostics

• % id_dzregrid [integer] :: diagnostic id

• % id_u_preale [integer] :: diagnostic id for zonal velocity before ALE.

• % id_v_preale [integer] :: diagnostic id for meridional velocity before ALE.

• % id_h_preale [integer] :: diagnostic id for layer thicknesses before ALE.

• % id_t_preale [integer] :: diagnostic id for temperatures before ALE.

• % id_s_preale [integer] :: diagnostic id for salinities before ALE.

• % id_e_preale [integer] :: diagnostic id for interface heights before ALE.

• % id_vert_remap_h [integer] :: diagnostic id for layer thicknesses used for remapping

• % id_vert_remap_h_tendency [integer] :: diagnostic id for layer thickness tendency due to ALE

Function/Subroutine Documentation

subroutine mom_ale/ale_init(param_file, GV, US, max_depth, CS)

This routine is typically called (from initialize_MOM in file MOM.F90 ) before the main time integration loop to initialize the regridding stuff. We read the MOM_input file to register the values of different regridding/remapping parameters.

Parameters

• param_file :: [in] Parameter file

• gv :: [in] Ocean vertical grid structure

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

• max_depth :: [in] The maximum depth of the ocean [Z ~> m].

• cs :: Module control structure

Call to

ale_initregridding mom_error_handler::calltree_enter mom_error_handler::calltree_leave

Called from

mom_oda_driver_mod::init_oda

subroutine mom_ale/ale_register_diags(Time, G, GV, US, diag, CS)

Initialize diagnostics for the ALE module.

Parameters

• time :: [in] Time structure

• g :: [in] Grid structure

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

• gv :: [in] Ocean vertical grid structure

• diag :: [in] Diagnostics control structure

• cs :: Module control structure

Call to

mom_verticalgrid::get_thickness_units

subroutine mom_ale/adjustgridforintegrity(CS, G, GV, h)

Crudely adjust (initial) grid for integrity. This routine is typically called (from initialize_MOM in file MOM.F90 ) before the main time integration loop to initialize the regridding stuff. We read the MOM_input file to register the values of different regridding/remapping parameters.

Parameters

• cs :: Regridding parameters and options

• g :: [in] Ocean grid informations

• gv :: [in] Ocean vertical grid structure

• h :: [inout] Current 3D grid thickness that are to be adjusted [H ~> m or kg-2]

subroutine mom_ale/ale_end(CS)

End of regridding (memory deallocation). This routine is typically called (from MOM_end in file MOM.F90 ) after the main time integration loop to deallocate the regridding stuff.

Parameters

cs :: module control structure

subroutine mom_ale/ale_main(G, GV, US, h, u, v, tv, Reg, CS, OBC, dt, frac_shelf_h)

Takes care of (1) building a new grid and (2) remapping all variables between the old grid and the new grid. The creation of the new grid can be based on z coordinates, target interface densities, sigma coordinates or any arbitrary coordinate system.

Parameters

• g :: [in] Ocean grid informations

• gv :: [in] Ocean vertical grid structure

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

• h :: [inout] Current 3D grid obtained after the last time step [H ~> m or kg m-2]

• u :: [inout] Zonal velocity field [L T-1 ~> m s-1]

• v :: [inout] Meridional velocity field [L T-1 ~> m s-1]

• tv :: [inout] Thermodynamic variable structure

• reg :: Tracer registry structure

• cs :: Regridding parameters and options

• obc :: Open boundary structure

• dt :: [in] Time step between calls to ALE_main [T ~> s]

• frac_shelf_h :: Fractional ice shelf coverage

Call to

ale_update_regrid_weights mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint check_grid mom_diag_mediator::diag_update_remap_grids remap_all_state_vars

subroutine mom_ale/ale_main_offline(G, GV, h, tv, Reg, CS, OBC, dt)

Takes care of (1) building a new grid and (2) remapping all variables between the old grid and the new grid. The creation of the new grid can be based on z coordinates, target interface densities, sigma coordinates or any arbitrary coordinate system.

Parameters

• g :: [in] Ocean grid informations

• gv :: [in] Ocean vertical grid structure

• h :: [inout] Current 3D grid obtained after the last time step [H ~> m or kg-2]

• tv :: [inout] Thermodynamic variable structure

• reg :: Tracer registry structure

• cs :: Regridding parameters and options

• obc :: Open boundary structure

• dt :: [in] Time step between calls to ALE_main [T ~> s]

Call to

ale_update_regrid_weights mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint check_grid remap_all_state_vars

Called from

mom_offline_main::offline_advection_ale

subroutine mom_ale/ale_offline_inputs(CS, G, GV, h, tv, Reg, uhtr, vhtr, Kd, debug, OBC)

Regrid/remap stored fields used for offline tracer integrations. These input fields are assumed to have the same layer thicknesses at the end of the last offline interval (which should be a Zstar grid). This routine builds a grid on the runtime specified vertical coordinate.

Parameters

• cs :: Regridding parameters and options

• g :: [in] Ocean grid informations

• gv :: [in] Ocean vertical grid structure

• h :: [inout] Layer thicknesses

• tv :: [inout] Thermodynamic variable structure

• reg :: Tracer registry structure

• uhtr :: [inout] Zonal mass fluxes

• vhtr :: [inout] Meridional mass fluxes

• kd :: [inout] Input diffusivites

• debug :: [in] If true, then turn checksums

• obc :: Open boundary structure

Call to

ale_remap_scalar mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint mom_debugging::check_column_integrals check_grid mom_diag_vkernels::interpolate_column mom_tracer_registry::mom_tracer_chkinv mom_diag_vkernels::reintegrate_column remap_all_state_vars

Called from

mom_offline_main::update_offline_fields

subroutine mom_ale/ale_offline_tracer_final(G, GV, h, tv, h_target, Reg, CS, OBC)

Remaps all tracers from h onto h_target. This is intended to be called when tracers are done offline. In the case where transports don’t quite conserve, we still want to make sure that layer thicknesses offline do not drift too far away from the online model.

Parameters

• g :: [in] Ocean grid informations

• gv :: [in] Ocean vertical grid structure

• h :: [inout] Current 3D grid obtained after the last time step [H ~> m or kg-2]

• tv :: [inout] Thermodynamic variable structure

• h_target :: [inout] Current 3D grid obtained after last time step [H ~> m or kg-2]

• reg :: Tracer registry structure

• cs :: Regridding parameters and options

• obc :: Open boundary structure

Call to

mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint check_grid remap_all_state_vars

subroutine mom_ale/check_grid(G, GV, h, threshold)

Check grid for negative thicknesses.

Parameters

• g :: [in] Ocean grid structure

• gv :: [in] Ocean vertical grid structure

• h :: [in] Current 3D grid obtained after the last time step [H ~> m or kg m-2]

• threshold :: [in] Value below which to flag issues, [H ~> m or kg m-2]

Called from

ale_main ale_main_offline ale_offline_inputs ale_offline_tracer_final

subroutine mom_ale/ale_build_grid(G, GV, regridCS, remapCS, h, tv, debug, frac_shelf_h)

Generates new grid.

Parameters

• g :: [in] Ocean grid structure

• gv :: [in] Ocean vertical grid structure

• regridcs :: [in] Regridding parameters and options

• remapcs :: [in] Remapping parameters and options

• tv :: [inout] Thermodynamical variable structure

• h :: [inout] Current 3D grid obtained after the last time step [H ~> m or kg-2]

• debug :: [in] If true, show the call tree

• frac_shelf_h :: Fractional ice shelf coverage

Call to

mom_error_handler::calltree_enter mom_error_handler::calltree_leave

subroutine mom_ale/ale_regrid_accelerated(CS, G, GV, h, tv, n, u, v, OBC, Reg, dt, dzRegrid, initial)

For a state-based coordinate, accelerate the process of regridding by repeatedly applying the grid calculation algorithm.

Parameters

• cs :: ALE control structure

• g :: [inout] Ocean grid

• gv :: [in] Vertical grid

• h :: [inout] Original thicknesses [H ~> m or kg-2]

• tv :: [inout] Thermo vars (T/S/EOS)

• n :: [in] Number of times to regrid

• u :: [inout] Zonal velocity [L T-1 ~> m s-1]

• v :: [inout] Meridional velocity [L T-1 ~> m s-1]

• obc :: Open boundary structure

• reg :: Tracer registry to remap onto new grid

• dt :: [in] Model timestep to provide a timescale for regridding [T ~> s]

• dzregrid :: [inout] Final change in interface positions

• initial :: [in] Whether we’re being called from an initialization routine (and expect diagnostics to work)

Call to

ale_update_regrid_weights mom_domains::do_group_pass remap_all_state_vars

subroutine mom_ale/remap_all_state_vars(CS_remapping, CS_ALE, G, GV, h_old, h_new, Reg, OBC, dxInterface, u, v, debug, dt)

This routine takes care of remapping all variable between the old and the new grids. When velocity components need to be remapped, thicknesses at velocity points are taken to be arithmetic averages of tracer thicknesses. This routine is called during initialization of the model at time=0, to remap initiali conditions to the model grid. It is also called during a time step to update the state.

Parameters

• cs_remapping :: [in] Remapping control structure

• cs_ale :: [in] ALE control structure

• g :: [in] Ocean grid structure

• gv :: [in] Ocean vertical grid structure

• h_old :: [in] Thickness of source grid [H ~> m or kg-2]

• h_new :: [in] Thickness of destination grid [H ~> m or kg-2]

• reg :: Tracer registry structure

• obc :: Open boundary structure

• dxinterface :: [in] Change in interface position

• u :: [inout] Zonal velocity [L T-1 ~> m s-1]

• v :: [inout] Meridional velocity [L T-1 ~> m s-1]

• debug :: [in] If true, show the call tree

• dt :: [in] time step for diagnostics [T ~> s]

Call to

mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint mom_open_boundary::obc_direction_n

Called from

ale_main ale_main_offline ale_offline_inputs ale_offline_tracer_final ale_regrid_accelerated

subroutine mom_ale/ale_remap_scalar(CS, G, GV, nk_src, h_src, s_src, h_dst, s_dst, all_cells, old_remap, answers_2018)

Remaps a single scalar between grids described by thicknesses h_src and h_dst. h_dst must be dimensioned as a model array with GVke layers while h_src can have an arbitrary number of layers specified by nk_src.

Parameters

• cs :: [in] Remapping control structure

• g :: [in] Ocean grid structure

• gv :: [in] Ocean vertical grid structure

• nk_src :: [in] Number of levels on source grid

• h_src :: [in] Level thickness of source grid [H ~> m or kg-2]

• s_src :: [in] Scalar on source grid

• h_dst :: [in] Level thickness of destination grid [H ~> m or kg-2]

• s_dst :: [inout] Scalar on destination grid

• all_cells :: [in] If false, only reconstruct for non-vanished cells. Use all vanished layers otherwise (default).

• old_remap :: [in] If true, use the old “remapping_core_w” method, otherwise use “remapping_core_h”.

• answers_2018 :: [in] If true, use the order of arithmetic and expressions that recover the answers for remapping from the end of 2018. Otherwise, use more robust forms of the same expressions.

Call to

mom_remapping::dzfromh1h2

Called from

ale_offline_inputs mom_tracer_initialization_from_z::mom_initialize_tracer_from_z

subroutine mom_ale/ts_plm_edge_values(CS, S_t, S_b, T_t, T_b, G, GV, tv, h, bdry_extrap)

Calculate edge values (top and bottom of layer) for T and S consistent with a PLM reconstruction in the vertical direction. Boundary reconstructions are PCM unless bdry_extrap is true.

Parameters

• g :: [in] ocean grid structure

• gv :: [in] Ocean vertical grid structure

• cs :: [inout] module control structure

• s_t :: [inout] Salinity at the top edge of each layer

• s_b :: [inout] Salinity at the bottom edge of each layer

• t_t :: [inout] Temperature at the top edge of each layer

• t_b :: [inout] Temperature at the bottom edge of each layer

• tv :: [in] thermodynamics structure

• h :: [in] layer thickness [H ~> m or kg m-2]

• bdry_extrap :: [in] If true, use high-order boundary extrapolation within boundary cells

Call to

ale_plm_edge_values

Called from

mom_pressureforce_fv::pressureforce_fv_bouss mom_pressureforce_fv::pressureforce_fv_nonbouss mom_state_initialization::trim_for_ice

subroutine mom_ale/ale_plm_edge_values(CS, G, GV, h, Q, bdry_extrap, Q_t, Q_b)

Calculate edge values (top and bottom of layer) 3d scalar array. Boundary reconstructions are PCM unless bdry_extrap is true.

Parameters

• cs :: [in] module control structure

• g :: [in] ocean grid structure

• gv :: [in] Ocean vertical grid structure

• h :: [in] layer thickness [H ~> m or kg m-2]

• q :: [in] 3d scalar array

• bdry_extrap :: [in] If true, use high-order boundary extrapolation within boundary cells

• q_t :: [inout] Scalar at the top edge of each layer

• q_b :: [inout] Scalar at the bottom edge of each layer

Call to

plm_functions::plm_extrapolate_slope plm_functions::plm_monotonized_slope plm_functions::plm_slope_wa

Called from

ts_plm_edge_values

subroutine mom_ale/ts_ppm_edge_values(CS, S_t, S_b, T_t, T_b, G, GV, tv, h, bdry_extrap)

Calculate edge values (top and bottom of layer) for T and S consistent with a PPM reconstruction in the vertical direction. Boundary reconstructions are PCM unless bdry_extrap is true.

Parameters

• g :: [in] ocean grid structure

• gv :: [in] Ocean vertical grid structure

• cs :: [inout] module control structure

• s_t :: [inout] Salinity at the top edge of each layer

• s_b :: [inout] Salinity at the bottom edge of each layer

• t_t :: [inout] Temperature at the top edge of each layer

• t_b :: [inout] Temperature at the bottom edge of each layer

• tv :: [in] thermodynamics structure

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

• bdry_extrap :: [in] If true, use high-order boundary extrapolation within boundary cells

Call to

regrid_edge_values::edge_values_implicit_h4 ppm_functions::ppm_boundary_extrapolation ppm_functions::ppm_reconstruction

Called from

mom_pressureforce_fv::pressureforce_fv_bouss mom_pressureforce_fv::pressureforce_fv_nonbouss

subroutine mom_ale/ale_initregridding(GV, US, max_depth, param_file, mdl, regridCS)

Initializes regridding for the main ALE algorithm.

Parameters

• gv :: [in] Ocean vertical grid structure

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

• max_depth :: [in] The maximum depth of the ocean [Z ~> m].

• param_file :: [in] parameter file

• mdl :: [in] Name of calling module

• regridcs :: [out] Regridding parameters and work arrays

Called from

ale_init

function mom_ale/ale_getcoordinate(CS) [real]

Query the target coordinate interfaces positions.

Parameters

cs :: module control structure

function mom_ale/ale_getcoordinateunits(CS) [character(len=20)]

Query the target coordinate units.

Parameters

cs :: module control structure

function mom_ale/ale_remap_init_conds(CS) [logical]

Returns true if initial conditions should be regridded and remapped.

Parameters

cs :: module control structure

subroutine mom_ale/ale_update_regrid_weights(dt, CS)

Updates the weights for time filtering the new grid generated in regridding.

Parameters

• dt :: [in] Time-step used between ALE calls [T ~> s]

• cs :: ALE control structure

Called from

ale_main ale_main_offline ale_regrid_accelerated

subroutine mom_ale/ale_updateverticalgridtype(CS, GV)

Update the vertical grid type with ALE information. This subroutine sets information in the verticalGrid_type to be consistent with the use of ALE mode.

Parameters

• cs :: ALE control structure

• gv :: vertical grid information

Called from

mom_oda_driver_mod::init_oda

subroutine mom_ale/ale_writecoordinatefile(CS, GV, directory)

Write the vertical coordinate information into a file. This subroutine writes out a file containing any available data related to the vertical grid used by the MOM ocean model when in ALE mode.

Parameters

• cs :: module control structure

• gv :: [in] ocean vertical grid structure

• directory :: [in] directory for writing grid info

Call to

mom_io::create_file

subroutine mom_ale/ale_initthicknesstocoord(CS, G, GV, h)

Set h to coordinate values for fixed coordinate systems.

Parameters

• cs :: [inout] module control structure

• g :: [in] module grid structure

• gv :: [in] Ocean vertical grid structure

• h :: [out] layer thickness [H ~> m or kg m-2]

Call to

mom_regridding::getstaticthickness

Called from

mom_oda_driver_mod::init_oda