mom_set_diffusivity mom_set_diffusivity::diffusivity_diags mom_set_diffusivity::set_diffusivity_cs integer integer mom_set_diffusivity::id_clock_kappashear id_clock_kappashear CPU time clocks. set_diffusivity set_diffusivity_init integer integer mom_set_diffusivity::id_clock_cvmix_ddiff id_clock_cvmix_ddiff CPU time clocks. set_diffusivity set_diffusivity_init subroutine, public subroutine, public mom_set_diffusivity::set_diffusivity (u, v, h, u_h, v_h, tv, fluxes, optics, visc, dt, G, GV, US, CS, Kd_lay, Kd_int, Kd_extra_T, Kd_extra_S) set_diffusivity u u v v h h u_h u_h v_h v_h tv tv fluxes fluxes optics optics visc visc dt dt G G GV GV US US CS CS Kd_lay Kd_lay Kd_int Kd_int Kd_extra_T Kd_extra_T Kd_extra_S Kd_extra_S Sets the interior vertical diffusion of scalars due to the following processes: Shear-driven mixing: two options, Jackson et at. and KPP interior;Background mixing via CVMix (Bryan-Lewis profile) or the scheme described by Harrison & Hallberg, JPO 2008;Double-diffusion, old method and new method via CVMix;Tidal mixing: many options available, see MOM_tidal_mixing.F90; In addition, this subroutine has the option to set the interior vertical viscosity associated with processes 1,2 and 4 listed above, which is stored in viscKv_slow. Vertical viscosity due to shear-driven mixing is passed via viscKv_shear g The ocean's grid structure. gv The ocean's vertical grid structure. us A dimensional unit scaling type u The zonal velocity [L T-1 ~> m s-1]. v The meridional velocity [L T-1 ~> m s-1]. h Layer thicknesses [H ~> m or kg m-2]. u_h Zonal velocity interpolated to h points [L T-1 ~> m s-1]. v_h Meridional velocity interpolated to h points [L T-1 ~> m s-1]. tv Structure with pointers to thermodynamic fields. Out is for tvTempxPmE. fluxes A structure of thermodynamic surface fluxes optics A structure describing the optical properties of the ocean. visc Structure containing vertical viscosities, bottom boundary layer properies, and related fields. dt Time increment [T ~> s]. cs Module control structure. kd_lay Diapycnal diffusivity of each layer [Z2 T-1 ~> m2 s-1]. kd_int Diapycnal diffusivity at each interface [Z2 T-1 ~> m2 s-1]. kd_extra_t The extra diffusivity at interfaces of kd_extra_s The extra diffusivity at interfaces of add_drag_diffusivity add_lotw_bbl_diffusivity add_mlrad_diffusivity mom_kappa_shear::calc_kappa_shear_vertex mom_error_handler::calltree_enter mom_error_handler::calltree_leave mom_error_handler::calltree_waypoint mom_cvmix_ddiff::compute_ddiff_coeffs double_diffusion find_n2 find_tke_to_kd mom_full_convection::full_convection id_clock_cvmix_ddiff id_clock_kappashear mom_isopycnal_slopes::vert_fill_ts subroutine subroutine mom_set_diffusivity::find_tke_to_kd (h, tv, dRho_int, N2_lay, j, dt, G, GV, US, CS, TKE_to_Kd, maxTKE, kb) find_tke_to_kd h h tv tv dRho_int dRho_int N2_lay N2_lay j j dt dt G G GV GV US US CS CS TKE_to_Kd TKE_to_Kd maxTKE maxTKE kb kb Convert turbulent kinetic energy to diffusivity. g The ocean's grid structure gv The ocean's vertical grid structure us A dimensional unit scaling type h Layer thicknesses [H ~> m or kg m-2] tv Structure containing pointers to any available thermodynamic fields. drho_int Change in locally referenced potential density across each interface [R ~> kg m-3]. n2_lay The squared buoyancy frequency of the layers [T-2 ~> s-2]. j j-index of row to work on dt Time increment [T ~> s]. cs Diffusivity control structure tke_to_kd The conversion rate between the TKE dissipated within a layer and the diapycnal diffusivity witin that layer, usually (~Rho_0 / (G_Earth * dRho_lay)) [Z2 T-1 / Z3 T-3 = T2 Z-1 ~> s2 m-1] maxtke The energy required to for a layer to entrain to its maximum realizable thickness [Z3 T-3 ~> m3 s-3] kb Index of lightest layer denser than the buffer layer, or -1 without a bulk mixed layer. mom_eos::eos_domain set_density_ratios set_diffusivity subroutine subroutine mom_set_diffusivity::find_n2 (h, tv, T_f, S_f, fluxes, j, G, GV, US, CS, dRho_int, N2_lay, N2_int, N2_bot) find_n2 h h tv tv T_f T_f S_f S_f fluxes fluxes j j G G GV GV US US CS CS dRho_int dRho_int N2_lay N2_lay N2_int N2_int N2_bot N2_bot Calculate Brunt-Vaisala frequency, N^2. g The ocean's grid structure gv The ocean's vertical grid structure us A dimensional unit scaling type h Layer thicknesses [H ~> m or kg m-2] tv Structure containing pointers to any available thermodynamic fields. t_f layer temperature with the values in massless layers s_f Layer salinities with values in massless fluxes A structure of thermodynamic surface fluxes j j-index of row to work on cs Diffusivity control structure drho_int Change in locally referenced potential density n2_int The squared buoyancy frequency at the interfaces [T-2 ~> s-2]. n2_lay The squared buoyancy frequency of the layers [T-2 ~> s-2]. n2_bot The near-bottom squared buoyancy frequency [T-2 ~> s-2]. mom_eos::eos_domain set_diffusivity subroutine subroutine mom_set_diffusivity::double_diffusion (tv, h, T_f, S_f, j, G, GV, US, CS, Kd_T_dd, Kd_S_dd) double_diffusion tv tv h h T_f T_f S_f S_f j j G G GV GV US US CS CS Kd_T_dd Kd_T_dd Kd_S_dd Kd_S_dd This subroutine sets the additional diffusivities of temperature and salinity due to double diffusion, using the same functional form as is used in MOM4.1, and taken from an NCAR technical note (REF?) that updates what was in Large et al. (1994). All the coefficients here should probably be made run-time variables rather than hard-coded constants. TodoFind reference for NCAR tech note above. g The ocean's grid structure. gv The ocean's vertical grid structure. us A dimensional unit scaling type tv Structure containing pointers to any available thermodynamic fields; absent fields have NULL ptrs. h Layer thicknesses [H ~> m or kg m-2]. t_f layer temperatures with the values in massless layers s_f Layer salinities with values in massless j Meridional index upon which to work. cs Module control structure. kd_t_dd Interface double diffusion diapycnal kd_s_dd Interface double diffusion diapycnal mom_eos::eos_domain set_diffusivity subroutine subroutine mom_set_diffusivity::add_drag_diffusivity (h, u, v, tv, fluxes, visc, j, TKE_to_Kd, maxTKE, kb, G, GV, US, CS, Kd_lay, Kd_int, Kd_BBL) add_drag_diffusivity h h u u v v tv tv fluxes fluxes visc visc j j TKE_to_Kd TKE_to_Kd maxTKE maxTKE kb kb G G GV GV US US CS CS Kd_lay Kd_lay Kd_int Kd_int Kd_BBL Kd_BBL This routine adds diffusion sustained by flow energy extracted by bottom drag. g The ocean's grid structure gv The ocean's vertical grid structure us A dimensional unit scaling type u The zonal velocity [L T-1 ~> m s-1] v The meridional velocity [L T-1 ~> m s-1] h Layer thicknesses [H ~> m or kg m-2] tv Structure containing pointers to any available thermodynamic fields. fluxes A structure of thermodynamic surface fluxes visc Structure containing vertical viscosities, bottom boundary layer properies, and related fields j j-index of row to work on tke_to_kd The conversion rate between the TKE TKE dissipated within a layer and the diapycnal diffusivity witin that layer, usually (~Rho_0 / (G_Earth * dRho_lay)) [Z2 T-1 / Z3 T-3 = T2 Z-1 ~> s2 m-1] maxtke The energy required to for a layer to entrain to its maximum-realizable thickness [Z3 T-3 ~> m3 s-3] kb Index of lightest layer denser than the buffer layer, or -1 without a bulk mixed layer cs Diffusivity control structure kd_lay The diapycnal diffusivity in layers, [Z2 T-1 ~> m2 s-1]. kd_int The diapycnal diffusivity at interfaces, kd_bbl Interface BBL diffusivity [Z2 T-1 ~> m2 s-1]. set_diffusivity subroutine subroutine mom_set_diffusivity::add_lotw_bbl_diffusivity (h, u, v, tv, fluxes, visc, j, N2_int, G, GV, US, CS, Kd_BBL, Kd_lay, Kd_int) add_lotw_bbl_diffusivity h h u u v v tv tv fluxes fluxes visc visc j j N2_int N2_int G G GV GV US US CS CS Kd_BBL Kd_BBL Kd_lay Kd_lay Kd_int Kd_int Calculates a BBL diffusivity use a Prandtl number 1 diffusivity with a law of the wall turbulent viscosity, up to a BBL height where the energy used for mixing has consumed the mechanical TKE input. g Grid structure gv Vertical grid structure us A dimensional unit scaling type u u component of flow [L T-1 ~> m s-1] v v component of flow [L T-1 ~> m s-1] h Layer thickness [H ~> m or kg m-2] tv Structure containing pointers to any available thermodynamic fields. fluxes Surface fluxes structure visc Structure containing vertical viscosities, bottom boundary layer properies, and related fields. j j-index of row to work on n2_int Square of Brunt-Vaisala at interfaces [T-2 ~> s-2] cs Diffusivity control structure kd_bbl Interface BBL diffusivity [Z2 T-1 ~> m2 s-1] kd_lay Layer net diffusivity [Z2 T-1 ~> m2 s-1] kd_int Interface net diffusivity [Z2 T-1 ~> m2 s-1] set_diffusivity subroutine subroutine mom_set_diffusivity::add_mlrad_diffusivity (h, fluxes, j, G, GV, US, CS, TKE_to_Kd, Kd_lay, Kd_int) add_mlrad_diffusivity h h fluxes fluxes j j G G GV GV US US CS CS TKE_to_Kd TKE_to_Kd Kd_lay Kd_lay Kd_int Kd_int This routine adds effects of mixed layer radiation to the layer diffusivities. g The ocean's grid structure gv The ocean's vertical grid structure us A dimensional unit scaling type h Layer thicknesses [H ~> m or kg m-2] fluxes Surface fluxes structure j The j-index to work on cs Diffusivity control structure tke_to_kd The conversion rate between the TKE TKE dissipated within a layer and the diapycnal diffusivity witin that layer, usually (~Rho_0 / (G_Earth * dRho_lay)) [Z2 T-1 / Z3 T-3 = T2 Z-1 ~> s2 m-1] kd_lay The diapycnal diffusivity in layers [Z2 T-1 ~> m2 s-1]. kd_int The diapycnal diffusivity at interfaces set_diffusivity subroutine, public subroutine, public mom_set_diffusivity::set_bbl_tke (u, v, h, fluxes, visc, G, GV, US, CS, OBC) set_bbl_tke u u v v h h fluxes fluxes visc visc G G GV GV US US CS CS OBC OBC This subroutine calculates several properties related to bottom boundary layer turbulence. g The ocean's grid structure gv The ocean's vertical grid structure us A dimensional unit scaling type u The zonal velocity [L T-1 ~> m s-1] v The meridional velocity [L T-1 ~> m s-1] h Layer thicknesses [H ~> m or kg m-2] fluxes A structure of thermodynamic surface fluxes visc Structure containing vertical viscosities, bottom boundary layer properies, and related fields. cs Diffusivity control structure obc Open boundaries control structure. mom_open_boundary::obc_direction_e mom_open_boundary::obc_direction_n subroutine subroutine mom_set_diffusivity::set_density_ratios (h, tv, kb, G, GV, US, CS, j, ds_dsp1, rho_0) set_density_ratios h h tv tv kb kb G G GV GV US US CS CS j j ds_dsp1 ds_dsp1 rho_0 rho_0 g The ocean's grid structure. gv The ocean's vertical grid structure. h Layer thicknesses [H ~> m or kg m-2]. tv Structure containing pointers to any available thermodynamic fields; absent fields have NULL ptrs. kb Index of lightest layer denser than the buffer layer, or -1 without a bulk mixed layer. us A dimensional unit scaling type cs Control structure returned by previous call to diabatic_entrain_init. j Meridional index upon which to work. ds_dsp1 Coordinate variable (sigma-2) difference across an interface divided by the difference across the interface below it [nondim] rho_0 Layer potential densities relative to mom_eos::eos_domain find_tke_to_kd subroutine, public subroutine, public mom_set_diffusivity::set_diffusivity_init (Time, G, GV, US, param_file, diag, CS, int_tide_CSp, halo_TS, double_diffuse) set_diffusivity_init Time Time G G GV GV US US param_file param_file diag diag CS CS int_tide_CSp int_tide_CSp halo_TS halo_TS double_diffuse double_diffuse time The current model time g The ocean's grid structure. gv The ocean's vertical grid structure. us A dimensional unit scaling type param_file A structure to parse for run-time parameters. diag A structure used to regulate diagnostic output. cs pointer set to point to the module control structure. int_tide_csp A pointer to the internal tides control structure halo_ts The halo size of tracer points that must be valid for the calculations in set_diffusivity. double_diffuse If present, this indicates whether some version of double diffusion is being used. id_clock_cvmix_ddiff id_clock_kappashear mom_kappa_shear::kappa_shear_at_vertex mom_diag_mediator::register_diag_field mom_tidal_mixing::tidal_mixing_init subroutine, public subroutine, public mom_set_diffusivity::set_diffusivity_end (CS) set_diffusivity_end CS CS Clear pointers and dealocate memory. cs Control structure for this module mom_bkgnd_mixing::bkgnd_mixing_end mom_cvmix_shear::cvmix_shear_end mom_tidal_mixing::tidal_mixing_end user_change_diffusivity::user_change_diff_end Calculate vertical diffusivity from all mixing processes.