mom_opacity mom_opacity::opacity_cs mom_opacity::optics_type integer, parameter integer, parameter mom_opacity::no_scheme no_scheme = 0 Coded integers to specify the opacity scheme. opacity_init integer, parameter integer, parameter mom_opacity::manizza_05 manizza_05 = 1 Coded integers to specify the opacity scheme. opacity_from_chl opacity_init set_opacity integer, parameter integer, parameter mom_opacity::morel_88 morel_88 = 2 Coded integers to specify the opacity scheme. opacity_from_chl opacity_init integer, parameter integer, parameter mom_opacity::single_exp single_exp = 3 Coded integers to specify the opacity scheme. opacity_init integer, parameter integer, parameter mom_opacity::double_exp double_exp = 4 Coded integers to specify the opacity scheme. opacity_init set_opacity character *(10), parameter character*(10), parameter mom_opacity::manizza_05_string manizza_05_string = "MANIZZA_05" String to specify the opacity scheme. opacity_init character *(10), parameter character*(10), parameter mom_opacity::morel_88_string morel_88_string = "MOREL_88" String to specify the opacity scheme. opacity_init character *(10), parameter character*(10), parameter mom_opacity::single_exp_string single_exp_string = "SINGLE_EXP" String to specify the opacity scheme. opacity_init character *(10), parameter character*(10), parameter mom_opacity::double_exp_string double_exp_string = "DOUBLE_EXP" String to specify the opacity scheme. opacity_init real, parameter real, parameter mom_opacity::op_diag_len op_diag_len = 1e-10 Lengthscale L used to remap opacity from op to 1/L * tanh(op * L) set_opacity subroutine, public subroutine, public mom_opacity::set_opacity (optics, sw_total, sw_vis_dir, sw_vis_dif, sw_nir_dir, sw_nir_dif, G, GV, US, CS, chl_2d, chl_3d) set_opacity optics optics sw_total sw_total sw_vis_dir sw_vis_dir sw_vis_dif sw_vis_dif sw_nir_dir sw_nir_dir sw_nir_dif sw_nir_dif G G GV GV US US CS CS chl_2d chl_2d chl_3d chl_3d This sets the opacity of sea water based based on one of several different schemes. optics An optics structure that has values set based on the opacities. sw_total Total shortwave flux into the ocean [Q R Z T-1 ~> W m-2] sw_vis_dir Visible, direct shortwave into the ocean [Q R Z T-1 ~> W m-2] sw_vis_dif Visible, diffuse shortwave into the ocean [Q R Z T-1 ~> W m-2] sw_nir_dir Near-IR, direct shortwave into the ocean [Q R Z T-1 ~> W m-2] sw_nir_dif Near-IR, diffuse shortwave into the ocean [Q R Z T-1 ~> W m-2] g The ocean's grid structure. gv The ocean's vertical grid structure. us A dimensional unit scaling type cs The control structure earlier set up by opacity_init. chl_2d Vertically uniform chlorophyll-A concentractions [mg m-3] chl_3d The chlorophyll-A concentractions of each layer [mg m-3] double_exp manizza_05 mom_error_handler::mom_error op_diag_len opacity_from_chl mom_diag_mediator::query_averaging_enabled subroutine subroutine mom_opacity::opacity_from_chl (optics, sw_total, sw_vis_dir, sw_vis_dif, sw_nir_dir, sw_nir_dif, G, GV, US, CS, chl_2d, chl_3d) opacity_from_chl optics optics sw_total sw_total sw_vis_dir sw_vis_dir sw_vis_dif sw_vis_dif sw_nir_dir sw_nir_dir sw_nir_dif sw_nir_dif G G GV GV US US CS CS chl_2d chl_2d chl_3d chl_3d This sets the "blue" band opacity based on chloophyll A concencentrations The red portion is lumped into the net heating at the surface. optics An optics structure that has values set based on the opacities. sw_total Total shortwave flux into the ocean [Q R Z T-1 ~> W m-2] sw_vis_dir Visible, direct shortwave into the ocean [Q R Z T-1 ~> W m-2] sw_vis_dif Visible, diffuse shortwave into the ocean [Q R Z T-1 ~> W m-2] sw_nir_dir Near-IR, direct shortwave into the ocean [Q R Z T-1 ~> W m-2] sw_nir_dif Near-IR, diffuse shortwave into the ocean [Q R Z T-1 ~> W m-2] g The ocean's grid structure. gv The ocean's vertical grid structure. us A dimensional unit scaling type cs The control structure. chl_2d Vertically uniform chlorophyll-A concentractions [mg m-3] chl_3d A 3-d field of chlorophyll-A concentractions [mg m-3] manizza_05 mom_error_handler::mom_error morel_88 opacity_morel sw_pen_frac_morel set_opacity real function, public real function, public mom_opacity::opacity_morel (chl_data) opacity_morel chl_data chl_data This sets the blue-wavelength opacity according to the scheme proposed by Morel and Antoine (1994). chl_data The chlorophyll-A concentration in mg m-3. The returned opacity [m-1] opacity_from_chl real function real function mom_opacity::sw_pen_frac_morel (chl_data) sw_pen_frac_morel chl_data chl_data This sets the penetrating shortwave fraction according to the scheme proposed by Morel and Antoine (1994). chl_data The chlorophyll-A concentration in mg m-3. The returned penetrating shortwave fraction [nondim] opacity_from_chl real function, public real function, public mom_opacity::opacity_manizza (chl_data) opacity_manizza chl_data chl_data This sets the blue-wavelength opacity according to the scheme proposed by Manizza, M. et al, 2005. chl_data The chlorophyll-A concentration in mg m-3. The returned opacity [m-1] subroutine, public subroutine, public mom_opacity::extract_optics_slice (optics, j, G, GV, opacity, opacity_scale, penSW_top, penSW_scale) extract_optics_slice optics optics j j G G GV GV opacity opacity opacity_scale opacity_scale penSW_top penSW_top penSW_scale penSW_scale This subroutine returns a 2-d slice at constant j of fields from an optics_type, with the potential for rescaling these fields. optics An optics structure that has values of opacities and shortwave fluxes. j j-index to extract g The ocean's grid structure. gv The ocean's vertical grid structure. opacity The opacity in each band, i-point, and layer opacity_scale A factor by which to rescale the opacity. pensw_top The shortwave radiation [Q R Z T-1 ~> W m-2] pensw_scale A factor by which to rescale the shortwave flux. mom_bulk_mixed_layer::bulkmixedlayer mom_forcing_type::extractfluxes1d subroutine, public subroutine, public mom_opacity::extract_optics_fields (optics, nbands) extract_optics_fields optics optics nbands nbands Set arguments to fields from the optics type. optics An optics structure that has values of opacities and shortwave fluxes. nbands The number of penetrating bands of SW radiation integer function, public integer function, public mom_opacity::optics_nbands (optics) optics_nbands optics optics Return the number of bands of penetrating shortwave radiation. optics An optics structure that has values of opacities and shortwave fluxes. The number of penetrating bands of SW radiation mom_forcing_type::calculatebuoyancyflux1d mom_forcing_type::calculatebuoyancyflux2d mom_diabatic_driver::diabatic_ale mom_diabatic_driver::diabatic_ale_legacy mom_forcing_type::extractfluxes1d subroutine, public subroutine, public mom_opacity::absorbremainingsw (G, GV, US, h, opacity_band, nsw, optics, j, dt, H_limit_fluxes, adjustAbsorptionProfile, absorbAllSW, T, Pen_SW_bnd, eps, ksort, htot, Ttot, TKE, dSV_dT) absorbremainingsw G G GV GV US US h h opacity_band opacity_band nsw nsw optics optics j j dt dt H_limit_fluxes H_limit_fluxes adjustAbsorptionProfile adjustAbsorptionProfile absorbAllSW absorbAllSW T T Pen_SW_bnd Pen_SW_bnd eps eps ksort ksort htot htot Ttot Ttot TKE TKE dSV_dT dSV_dT Apply shortwave heating below the boundary layer (when running with the bulk mixed layer inhereted from GOLD) or throughout the water column. In addition, it causes all of the remaining SW radiation to be absorbed, provided that the total water column thickness is greater than H_limit_fluxes. For thinner water columns, the heating is scaled down proportionately, the assumption being that the remaining heating (which is left in Pen_SW) should go into an (absent for now) ocean bottom sediment layer. g The ocean's grid structure. gv The ocean's vertical grid structure. us A dimensional unit scaling type nsw Number of bands of penetrating shortwave radiation. h Layer thicknesses [H ~> m or kg m-2]. opacity_band Opacity in each band of penetrating shortwave radiation [H-1 ~> m-1 or m2 kg-1]. The indicies are band, i, k. optics An optics structure that has values of opacities and shortwave fluxes. j j-index to work on. dt Time step [T ~> s]. h_limit_fluxes If the total ocean depth is less than this, they are scaled away to avoid numerical instabilities [H ~> m or kg m-2]. This would not be necessary if a finite heat capacity mud-layer were added. adjustabsorptionprofile If true, apply heating above the layers in which it should have occurred to get the correct mean depth (and potential energy change) of the shortwave that should be absorbed by each layer. absorballsw If true, apply heating above the layers in which it should have occurred to get the correct mean depth (and potential energy change) of the shortwave that should be absorbed by each layer. t Layer potential/conservative temperatures [degC] pen_sw_bnd Penetrating shortwave heating in each band that hits the bottom and will will be redistributed through the water column [degC H ~> degC m or degC kg m-2], size nsw x G isd: G ied. eps Small thickness that must remain in each layer, and which will not be subject to heating [H ~> m or kg m-2] ksort Density-sorted k-indicies. htot Total mixed layer thickness [H ~> m or kg m-2]. ttot Depth integrated mixed layer temperature [degC H ~> degC m or degC kg m-2] dsv_dt The partial derivative of specific volume with temperature [R-1 degC-1]. tke The TKE sink from mixing the heating throughout a layer [R Z3 T-2 ~> J m-2]. mom_diabatic_aux::applyboundaryfluxesinout mom_bulk_mixed_layer::bulkmixedlayer subroutine, public subroutine, public mom_opacity::sumswoverbands (G, GV, US, h, nsw, optics, j, dt, H_limit_fluxes, absorbAllSW, iPen_SW_bnd, netPen) sumswoverbands G G GV GV US US h h nsw nsw optics optics j j dt dt H_limit_fluxes H_limit_fluxes absorbAllSW absorbAllSW iPen_SW_bnd iPen_SW_bnd netPen netPen This subroutine calculates the total shortwave heat flux integrated over bands as a function of depth. This routine is only called for computing buoyancy fluxes for use in KPP. This routine does not updat e the state. 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]. nsw The number of bands of penetrating shortwave radiation, perhaps from optics_nbands(optics), optics An optics structure that has values set based on the opacities. j j-index to work on. dt Time step [T ~> s]. h_limit_fluxes the total depth at which the surface fluxes start to be limited to avoid excessive heating of a thin ocean [H ~> m or kg m-2] absorballsw If true, ensure that all shortwave radiation is absorbed in the ocean water column. ipen_sw_bnd The incident penetrating shortwave heating in each band that hits the bottom and will be redistributed through the water column [degC H ~> degC m or degC kg m-2]; size nsw x G isd: G ied. netpen Net penetrating shortwave heat flux at each mom_forcing_type::calculatebuoyancyflux1d subroutine, public subroutine, public mom_opacity::opacity_init (Time, G, GV, US, param_file, diag, CS, optics) opacity_init Time Time G G GV GV US US param_file param_file diag diag CS CS optics optics This routine initalizes the opacity module, including an optics_type. time The current model time. g The ocean's grid structure. gv model vertical grid structure us A dimensional unit scaling type param_file A structure to parse for run-time parameters. diag A structure that is used to regulate diagnostic output. cs A pointer that is set to point to the control structure for this module. optics An optics structure that has parameters set and arrays allocated here. double_exp double_exp_string manizza_05 manizza_05_string mom_error_handler::mom_error mom_error_handler::mom_mesg morel_88 morel_88_string no_scheme mom_diag_mediator::register_diag_field single_exp single_exp_string mom_string_functions::uppercase subroutine, public subroutine, public mom_opacity::opacity_end (CS, optics) opacity_end CS CS optics optics cs An opacity control structure that should be deallocated. optics An optics type structure that should be deallocated. Routines used to calculate the opacity of the ocean. opacity_from_chl: In this routine, the Morel (modified) or Manizza (modified) schemes use the "blue" band in the paramterizations to determine the e-folding depth of the incoming shortwave attenuation. The red portion is lumped into the net heating at the surface. Morel, A., 1988: Optical modeling of the upper ocean in relation to its biogenous matter content (case-i waters)., J. Geo. Res., 93, 10,749-10,768. Manizza, M., C. LeQuere, A. J. Watson, and E. T. Buitenhuis, 2005: Bio-optical feedbacks among phytoplankton, upper ocean physics and sea-ice in a global model, Geophys. Res. Let., 32, L05603, doi:10.1029/2004GL020778.