PALEOocean Reactions

ReactionOceanNoTransport

N ocean boxes (default N=1 ie a single 0-D box), each with a surface and floor, no transport.

Parameters

• area[Vector{Float64}]=[1.0] (m^2), default_value=[1.0], description="surface / floor area (per box)"
• depth[Vector{Float64}]=[1.0] (m), default_value=[1.0], description="depth (per box)"

Methods and Variables

• do_setup_grid
  • volume (m^3), VT_ReactProperty, description="volume of ocean cells"
  • volume_total (m^3), VT_ReactProperty, description="total volume of ocean cells"
  • Abox (m^2), VT_ReactProperty, description="horizontal area of box"
  • zupper (m), VT_ReactProperty, description="depth of upper surface of box (m) 0 is surface, -100 is depth of 100 m"
  • zlower (m), VT_ReactProperty, description="depth of lower surface of box (m)"
  • zmid (m), VT_ReactProperty, description="mean depth of box"
  • rho_ref (kg m^-3), VT_ReactProperty, description="Ocean transport model density conversion factor (NB: this an artificial model quantity determined by the offline model for tracer transport, and may be distinct from physical ocean density, and from any density anomaly / potl density used by the offline physical model)"
  • pressure (dbar), VT_ReactProperty, description="Ocean pressure"
  • Afloor –> oceanfloor.Afloor (m^2), VT_ReactProperty, description="horizontal area of seafloor at base of box"
  • Afloor_total –> oceanfloor.Afloor_total (m^2), VT_ReactProperty, description="total area of seafloor"
  • zfloor –> oceanfloor.zfloor (m), VT_ReactProperty, description="depth of ocean floor (m, -ve)"
  • Asurf –> oceansurface.Asurf (m^2), VT_ReactProperty, description="horizontal area of oceansurface"

ReactionOceanTransport3box

3-box (Sarmiento and Toggweiler, 1984), (Toggweiler and Sarmiento, 1985) ocean model.

---------------------------------------
|  1 (s)                 | 2(h)        |
|                    -->--->-          |
|-------------------|----|  |          |   
|                   |    |  |     /|\  |
|                   |    |__|______|___|    
|                   |       |      |   |
|  3 (d)             -<--<--      \|/  |
|                  circT          fhd  |
|                                      |
----------------------------------------

Parameters

• circT[Float64]=2.0e7 (m^3 s^-1), default_value=2.0e7, description="overturning circulation"
• circfhd[Float64]=6.0e7 (m^3 s^-1), default_value=6.0e7, description="high latitude <-> deep exchange rate"
• temp[Vector{Float64}]=[21.5, 2.5, 2.5] (degrees C), default_value=[21.5, 2.5, 2.5], description="ocean temperature"
• temp_trackglobal[Bool]=false, default_value=false, description="track global temperature (apply offset of global temp -15C"

Methods and Variables for default Parameters

• do_setup_grid

  • volume (m^3), VT_ReactProperty, description="volume of ocean cells"
  • volume_total (m^3), VT_ReactProperty, description="total volume of ocean cells"
  • Abox (m^2), VT_ReactProperty, description="horizontal area of box"
  • zupper (m), VT_ReactProperty, description="depth of upper surface of box (m) 0 is surface, -100 is depth of 100 m"
  • zlower (m), VT_ReactProperty, description="depth of lower surface of box (m)"
  • zmid (m), VT_ReactProperty, description="mean depth of box"
  • rho_ref (kg m^-3), VT_ReactProperty, description="Ocean transport model density conversion factor (NB: this an artificial model quantity determined by the offline model for tracer transport, and may be distinct from physical ocean density, and from any density anomaly / potl density used by the offline physical model)"
  • pressure (dbar), VT_ReactProperty, description="Ocean pressure"
  • Afloor –> oceanfloor.Afloor (m^2), VT_ReactProperty, description="horizontal area of seafloor at base of box"
  • Afloor_total –> oceanfloor.Afloor_total (m^2), VT_ReactProperty, description="total area of seafloor"
  • zfloor –> oceanfloor.zfloor (m), VT_ReactProperty, description="depth of ocean floor (m, -ve)"
  • Asurf –> oceansurface.Asurf (m^2), VT_ReactProperty, description="horizontal area of oceansurface"
  • sal (psu), VT_ReactProperty, description="Ocean salinity"
  • rho (kg m^-3), VT_ReactProperty, description="physical ocean density"
  • open_area_fraction –> oceansurface.open_area_fraction (), VT_ReactProperty, description="fraction of area open to atmosphere"

• do_temperature

  • [TEMP] –> global.TEMP (K), VT_ReactDependency, description="global mean temperature"
  • temp (K), VT_ReactProperty, description="Ocean temperature"

ReactionOceanTransport6box

4+2-box ocean model from (Daines and Lenton, 2016) This is based on:

• the four-box model of (Hotinski et al., 2000)
• the five-box model of (Watson, 1995)
• the upwelling region representation of (Canfield, 2006)

There are two main ingredients here:

• An open-ocean 'intermediate/thermocline' box(i) from (Hotinski et al., 2000), coupled to the low-latitude surface box via an Ekman pumping term and to high latitude box (h) via an overturning circulation term. This is a more realistic representation of the open ocean than the 3-box (Sarmiento and Toggweiler, 1984), (Toggweiler and Sarmiento, 1985) model.

• A two-box shelf/slope (boxes r, rc), which can be configured as

  • an upwelling region (k_slopetype='OMZ'), cf Canfield (2006) with upwelling from the intermediate/thermocline box
  • a low-latitude shelf (k_slopetype='shelf') with exchange terms to low-latitude surface (s) and thermocline (i) boxes

  See Oxygen oases\Box Model 20150922\HotinskiCalc5Box.m, HotinskiConstants5Box.m, HotinskiCalcCirc6.m

       --------------------------------------------------
      | 5(r)      |  1 (s)                 | 2(h)        |
      |           |                        |             |
      |-----------|------------------------|             |   
      | 6(rc)     |                        |             |
      |           |  3 (i)                 |_____________|    
       -----------|                        |             |
         |        |------------------------              |
         |           4(d)                                |
         |                                               |
          -----------------------------------------------

Parameters

• slopetype[String]="OMZ", default_value="OMZ", allowed_values=["OMZ", "shelf"], description="type of shelf circulation (boxes r, rc)"
• circT[Float64]=1.93e7 (m^3 s^-1), default_value=1.93e7, description="overturning circulation (exchange high lat (h) to deep (d) and thermocline (i)"
• circfhd[Float64]=4.87e7 (m^3 s^-1), default_value=4.87e7, description="high latitude <-> deep exchange rate"
• circR[Float64]=2.0e7 (m^3 s^-1), default_value=2.0e7, description="upwelling thermocline (i) to slope (rc) to upwell (r) to low lat surface (s)"
• totalEkman[Float64]=6.0e7 (m^3 s^-1), default_value=6.0e7, description="total wind-driven Ekman pumping"
• circS[Float64]=1.0e6 (m^3 s^-1), default_value=1.0e6, description="upwell(r) <-> low lat surf box (s) exchange"
• temp[Vector{Float64}]=[21.5, 2.5, 2.5, 2.5, 21.5, 2.5] (degrees C), default_value=[21.5, 2.5, 2.5, 2.5, 21.5, 2.5], description="ocean temperature"
• temp_trackglobal[Bool]=false, default_value=false, description="track global temperature (apply offset of global temp -15C"

Methods and Variables for default Parameters

• do_setup_grid

  • volume (m^3), VT_ReactProperty, description="volume of ocean cells"
  • volume_total (m^3), VT_ReactProperty, description="total volume of ocean cells"
  • Abox (m^2), VT_ReactProperty, description="horizontal area of box"
  • zupper (m), VT_ReactProperty, description="depth of upper surface of box (m) 0 is surface, -100 is depth of 100 m"
  • zlower (m), VT_ReactProperty, description="depth of lower surface of box (m)"
  • zmid (m), VT_ReactProperty, description="mean depth of box"
  • rho_ref (kg m^-3), VT_ReactProperty, description="Ocean transport model density conversion factor (NB: this an artificial model quantity determined by the offline model for tracer transport, and may be distinct from physical ocean density, and from any density anomaly / potl density used by the offline physical model)"
  • pressure (dbar), VT_ReactProperty, description="Ocean pressure"
  • Afloor –> oceanfloor.Afloor (m^2), VT_ReactProperty, description="horizontal area of seafloor at base of box"
  • Afloor_total –> oceanfloor.Afloor_total (m^2), VT_ReactProperty, description="total area of seafloor"
  • zfloor –> oceanfloor.zfloor (m), VT_ReactProperty, description="depth of ocean floor (m, -ve)"
  • Asurf –> oceansurface.Asurf (m^2), VT_ReactProperty, description="horizontal area of oceansurface"
  • sal (psu), VT_ReactProperty, description="Ocean salinity"
  • rho (kg m^-3), VT_ReactProperty, description="physical ocean density"
  • open_area_fraction –> oceansurface.open_area_fraction (), VT_ReactProperty, description="fraction of area open to atmosphere"

• do_temperature

  • [TEMP] –> global.TEMP (K), VT_ReactDependency, description="global mean temperature"
  • temp (K), VT_ReactProperty, description="Ocean temperature"

ReactionOceanTransportColumn

Set up 1D ocean column grid, provide tracer transport using supplied eddy diffusivity Kz.

A netCDF file (name specified by grid_file parameter) should provide zupper, zmid, zlower (m) defining z coordinates of cell surfaces and centres for a 1D column.

Eddy diffusivity on cell upper surfaces should be provided by a variable Kz (m^2 s-1).

Parameters

• grid_file[String]="S2P3_depth80_m2amp04.nc", default_value="S2P3_depth80_m2amp04.nc", description="netcdf file with grid data (zmid, zupper, zlower)"
• column_area[Float64]=1.0 (m^2), default_value=1.0, description="column area"

Methods and Variables

METHODS PALEOboxes.DocStrings.Methods(:methods_setup) exception: ErrorException("PALEOocean.Ocean.OceanTransportColumn.ReactionOceanTransportColumn register_methods! not implemented")

METHODS PALEOboxes.DocStrings.Methods(:methods_do) exception: ErrorException("PALEOocean.Ocean.OceanTransportColumn.ReactionOceanTransportColumn register_methods! not implemented")

ReactionOceanTransportRomanielloICBM

Modern global and Black Sea ocean transport from (Romaniello and Derry, 2010) (Romaniello and Derry, 2010),

Global configurations (circname = Global_79_Box, circname = Global_13_Box):

The ocean Domain consists of three columns, :hlat, :gyre, :upw

Ocean box indices are:

  :hlat   :gyre   :upw
---------------------------
|  1    |  14   |  47     |
 |      |       |        |
  |     |       |       | 
   |    |       |      |
   | 13 |  46   | 79  |  
    -------------------

  :hlat   :gyre   :upw
---------------------------
|  1    |  4    |  9      |
 |      |       |        |
  |     |       |       | 
   |    |       |      |
   | 3  |  8    | 13  |  
   -------------------

The oceansurface Domain has three boxes, the oceanfloor Domain has 1 box per ocean box.

Black Sea configuration (circname = Black_Sea)

The ocean Domain consists of a single column. The oceansurface Domain has one box, the oceanfloor Domain has 1 box per ocean box.

Bosphorus outflow flux (Parameter bosph_outflow) is represented by Variables with default linking to a fluxBosphorusOutflow Domain:

bosph_outflow_<X> --> fluxBosphorusOutflow.flux_<X>

The .yaml configuration file can be used to configure a closed system by adding outflow flux back into the ocean surface:

variable_links:
    bosph_outflow_*: ocean.oceansurface.*_sms

Bosphorus inflow (plume) flux is represented by Variables with default linking to concentrations and source - sink fluxes in a BosphorusInflow Domain:

bosph_inflow_<X>_conc --> BosphorusInflow.<X>_conc
bosph_inflow_<X>_sms --> BosphorusInflow.<X>_sms    # will be -ve for flux into Black Sea

the .yaml configuration file can be used to configure a closed system by sourcing inflow flux from ocean surface:

variable_links:
    bosph_inflow_*_conc: ocean.oceansurface.*_conc
    bosph_inflow_*_sms: ocean.oceansurface.*_sms

Implementation

Reads Matlab .mat files created from the published SI with Matlab commands:

>> circ_global_79_box = Global_79_Box_ICBM_Params
>> circ_global_13_box = Global_13_Box_ICBM_Params
>> circ_black_sea = Black_Sea_ICBM_Params
>> save('romaniello_global79','-struct', 'circ_global_79_box',  '-v6')
>> save('romaniello_global13','-struct', 'circ_global_13_box',  '-v6')
>> save('romaniello_blacksea','-struct', 'circ_black_sea',  '-v6')

Parameters

• matdir[String]="romaniello2010_transport", default_value="romaniello2010_transport", description="folder with Romaniello (2010) transport and geometry data files"
• circname[String]="Global_79_Box", default_value="Global_79_Box", allowed_values=["Global79Box", "Global13Box", "Black_Sea"], description="transport matrix from Romaniello(2010) G3"
• set_temp[Bool]=true, default_value=true, description="true to provide and set ocean.temp variable to (very approximate) values"
• temp_trackglobal[Bool]=false, default_value=false, description="track global temperature (apply offset of global temp -15C"
• bosph_outflow[Float64]=6.04e11 (m^3 yr^-1), default_value=6.04e11, description="Bosphorus outflow (Black_Sea only)"
• bosph_inflow[Float64]=3.05e11 (m^3 yr^-1), default_value=3.05e11, description="Bosphorus inflow (plume, Black_Sea only)"

Methods and Variables

• do_setup_grid

  • volume (m^3), VT_ReactProperty, description="volume of ocean cells"
  • volume_total (m^3), VT_ReactProperty, description="total volume of ocean cells"
  • Abox (m^2), VT_ReactProperty, description="horizontal area of box"
  • zupper (m), VT_ReactProperty, description="depth of upper surface of box (m) 0 is surface, -100 is depth of 100 m"
  • zlower (m), VT_ReactProperty, description="depth of lower surface of box (m)"
  • zmid (m), VT_ReactProperty, description="mean depth of box"
  • rho_ref (kg m^-3), VT_ReactProperty, description="Ocean transport model density conversion factor (NB: this an artificial model quantity determined by the offline model for tracer transport, and may be distinct from physical ocean density, and from any density anomaly / potl density used by the offline physical model)"
  • pressure (dbar), VT_ReactProperty, description="Ocean pressure"
  • Afloor –> oceanfloor.Afloor (m^2), VT_ReactProperty, description="horizontal area of seafloor at base of box"
  • Afloor_total –> oceanfloor.Afloor_total (m^2), VT_ReactProperty, description="total area of seafloor"
  • zfloor –> oceanfloor.zfloor (m), VT_ReactProperty, description="depth of ocean floor (m, -ve)"
  • Asurf –> oceansurface.Asurf (m^2), VT_ReactProperty, description="horizontal area of oceansurface"
  • sal (psu), VT_ReactProperty, description="Ocean salinity"
  • rho (kg m^-3), VT_ReactProperty, description="physical ocean density"
  • open_area_fraction –> oceansurface.open_area_fraction (), VT_ReactProperty, description="fraction of area open to atmosphere"

• do_temperature

  • [TEMP] –> global.TEMP (K), VT_ReactDependency, description="global mean temperature"
  • temp (K), VT_ReactProperty, description="Ocean temperature"

ReactionOceanTransportTMM

GCM ocean transport implementation using transport matrices in format defined by (Khatiwala, 2007) Requires download of Samar Khatiwala's TMM files (for MITgcm, UVic models) as described in https://github.com/samarkhatiwala/tmm where TM files are from http://kelvin.earth.ox.ac.uk/spk/Research/TMM/TransportMatrixConfigs/

NB: length(operatorID) must be 2, to define operatorID[1] for explicit and operatorID[2] for implicit matrices.

The base_path parameter sets the top level of the folder structure for the downloaded matrices.

Code based on TMM/tmm/models/petsc3.4/mitgchem/matlab/make_input_files_for_migchem_dic_biotic_model.m

Parameters

• base_path[String]="$TMMDir$/MITgcm_2.8deg", default_value="$TMMDir$/MITgcm_2.8deg", description="directory containing transport matrices"
• sal_norm[Bool]=false, default_value=false, description="apply salinity normalisation to transport matrix"
• use_annualmean[Bool]=false, default_value=false, description="true to read annual mean matrix"
• num_seasonal[Int64]=12, default_value=12, description="number of seasonal matrices"
• Aimp_deltat[Int64]=86400 (seconds), default_value=86400, description="timestep to derive upscaling factor for implicit transport matrix"
• kji_order[Bool]=true, default_value=true, description="true to sort indices into k,j,i order to optimise memory layout"
• pack_chunk_width[Int64]=4, default_value=4, allowed_values=[0, 2, 4, 8, 16], description="non-zero to enable SIMD packed transport matrix multiply"
• TMfpsize[Int64]=64 (bits), default_value=64, allowed_values=[32, 64], description="FP size for transport matrix"

Methods and Variables

• setup_grid_TMM
  • volume (m^3), VT_ReactProperty, description="volume of ocean cells"
  • volume_total (m^3), VT_ReactProperty, description="total volume of ocean cells"
  • Abox (m^2), VT_ReactProperty, description="horizontal area of box"
  • zupper (m), VT_ReactProperty, description="depth of upper surface of box (m) 0 is surface, -100 is depth of 100 m"
  • zlower (m), VT_ReactProperty, description="depth of lower surface of box (m)"
  • zmid (m), VT_ReactProperty, description="mean depth of box"
  • rho_ref (kg m^-3), VT_ReactProperty, description="Ocean transport model density conversion factor (NB: this an artificial model quantity determined by the offline model for tracer transport, and may be distinct from physical ocean density, and from any density anomaly / potl density used by the offline physical model)"
  • pressure (dbar), VT_ReactProperty, description="Ocean pressure"
  • Afloor –> oceanfloor.Afloor (m^2), VT_ReactProperty, description="horizontal area of seafloor at base of box"
  • Afloor_total –> oceanfloor.Afloor_total (m^2), VT_ReactProperty, description="total area of seafloor"
  • zfloor –> oceanfloor.zfloor (m), VT_ReactProperty, description="depth of ocean floor (m, -ve)"
  • Asurf –> oceansurface.Asurf (m^2), VT_ReactProperty, description="horizontal area of oceansurface"

ReactionLightColumn

Calculate light availability insol in ocean interior, given surface insolation surface_insol.

Includes: (i) a background_opacity; (ii) contributions from any Variables representing concentrations with non-zero specific_light_extinction attribute; (iii) any other opacity contributions added to the Target Variable opacity.

Parameters

• background_opacity[Float64]=0.04 (m-1), default_value=0.04, description="background opacity"

ReactionExportDirect

Vertical particle sinking represented as instantaneous transport, described by fixed matrices (suitable for small ocean models)

Transports a list of fluxes defined by parameter fluxlist, from input Target Variables with local name export_<flux in fluxlist> to output Contributor Variables remin_<flux in fluxlist>.

Matrices are defined by parameter transportocean for sinking within water column, and parameter transportfloor for flux to ocean floor.

For larger, column-based ocean models use ReactionExportDirectColumn.

Parameters

• fluxlist[Vector{String}]=["P", "N", "Corg"], default_value=["P", "N", "Corg"], description="names of fluxes to transport"
• transportocean[Vector{Vector{Float64}}]=Vector{Float64}[], default_value=Vector{Float64}[], description="matrix describing ocean export"
• transportfloor[Vector{Vector{Float64}}]=Vector{Float64}[], default_value=Vector{Float64}[], description="matrix describing oceanfloor export"
• conserv_errthresh[Float64]=1.0e-5, default_value=1.0e-5, description="error threshold for conservation check (fraction of input)"

ReactionExportDirectColumn

Vertical particle sinking represented as instantaneous transport. As ReactionExportDirect, but for regular column-based models with functional form of flux vs depth defined by exportfunction parameter.

Transports a list of fluxes defined by parameter fluxlist, from input Target Variables with local name export_<flux in fluxlist> to output Contributor Variables remin_<flux in fluxlist>.

Parameters

• fluxlist[Vector{String}]=String[], default_value=String[], description="names of fluxes to transport"
• transportfloor[Bool]=true, default_value=true, description="true to provide oceanfloor flux, false to recycle flux into lowest ocean cell"
• exportfunction[String]="SumExp", default_value="SumExp", allowed_values=["Martin", "SumExp"], description="functional form for particle flux vs depth"
• input_frac[Vector{Float64}]=[1.0], default_value=[1.0], description="fractions of input for each component ([1.0] for Martin, length=number of components for SumExp"
• sumexp_scale[Vector{Float64}]=[500.0] (m), default_value=[500.0], description="length scales for each component of exponential decay of flux with depth"
• martin_rovera[Float64]=0.858, default_value=0.858, description="Martin power law exponent: flux \propto depth^rovera"
• martin_depthmin[Float64]=100.0 (m), default_value=100.0, description="Martin power law minimum depth for start of decay with depth"

ReactionSinkFloat

Vertical particle advection.

Applied to all concentration Variables with non-zero attribute :vertical_movement (m d-1, +ve upwards), using naming convention <name>_conc to identify <name>_sms Deriv Variable to apply to. An optional variable <name>_w may be defined that overrides :vertical_movement to define spatially-variable vertical motion.

Parameters

• transportfloor[Bool]=true, default_value=true, description="true to provide oceanfloor flux, false to recycle flux into lowest ocean cell"

ReactionBioProdPrest

P-limited biological production, configurable to restore P to specified level or to consume fraction of nutrients

Parameters

• bioprod[Vector{Int64}]=Int64[], default_value=Int64[], allowed_values=[0, 1, 2, 3], description="production type (per cell): 0 - none, 1 - restore to absolute conc, 2 - consume fraction of nutrients supplied, 3 - restore to fraction of ocean mean"
• bioprodval[Vector{Float64}]=Float64[] (m-3 or none), default_value=Float64[], description="conc or frac corresponding to 'bioprod'"
• rCorgPO4[Float64]=106.0, default_value=106.0, description="Corg:P Redfield ratio of organic matter produced"
• rNPO4[Float64]=16.0, default_value=16.0, description="N:P Redfield ratio of organic matter produced"
• rCcarbCorg[Float64]=0.0, default_value=0.0, description="ratio of Ccarb to Corg produced"
• trest[Float64]=0.1 (yr), default_value=0.1, description="restoring timescale"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_bio_prod_Prest
  • volume (m^3), VT_ReactDependency, description="ocean cell volume"
  • volume_total (m^3), VT_ReactDependency, description="ocean total volume"
  • P_conc (mol m^-3), VT_ReactDependency, description="total P concentration"
  • Prod_Corg –> %reaction%Prod_Corg (mol yr-1), VT_ReactProperty, description="organic carbon production rate"
  • Prod_Ccarb –> %reaction%Prod_Ccarb (mol yr-1), VT_ReactProperty, description="carbonate production rate"
  • P_sms (mol yr-1), VT_ReactContributor, description="total dissolved P source minus sink"
  • [O2_sms] (mol yr-1), VT_ReactContributor, description="O2 source minus sink"
  • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="TAlk source minus sink"
  • [DIC_sms] (mol yr-1), VT_ReactContributor, description="DIC source minus sink"
  • [enable_bioprod] –> global.enable_bioprod (), VT_ReactDependency, description="optional forcing, =0.0 to disable, !=0.0 to enable"
  • [PELCALC] –> global.PELCALC (), VT_ReactDependency, description="optional forcing for pelagic calcification"
  • [prod_P] (mol yr-1), VT_ReactContributor, description="flux P"
  • [prod_N] (mol yr-1), VT_ReactContributor, description="flux N"
  • [prod_Corg] (mol yr-1), VT_ReactContributor, description="flux Corg"
  • [prod_Ccarb] (mol yr-1), VT_ReactContributor, description="flux Ccarb"
• totals
  • Prod_Corg –> %reaction%Prod_Corg (mol yr-1), VT_ReactDependency, description="organic carbon production rate"
  • Prod_Ccarb –> %reaction%Prod_Ccarb (mol yr-1), VT_ReactDependency, description="carbonate production rate"
  • Prod_Corg_total (mol yr-1), VT_ReactProperty, description="total organic carbon production rate"
  • Prod_Ccarb_total (mol yr-1), VT_ReactProperty, description="total carbonate production rate"

ReactionBioProdMMPop

Ocean phytoplankton biological production.

Configurable to represent oxygenic photosynthesizers with P, N limitation, nitrogen fixers, anoxygenic photosynthesis limited by electron donor availability.

Export production or production is represented as a combination of limiting factors:

population_size x nutrient_limitation x light_limitation x temperature_limitation x electron_donor_limitation

population_size may be either implicit (either a constant or ∝ nutrient concentration, generating GENIE-like parameterisations of export production), or represented explicitly as a state variable (in which case production is accumulated into a state variable phytP_conc, and k_grazeresprate defines a background loss rate that is exported).

Export production is than partitioned into DOM flux (components domprod_P, domprod_N, domprod_Corg) and particulate flux (components partprod_P, partprod_N, partprod_Corg, partprod_Ccarb) fractions according to parameter k_nuDOM.

See (Kriest et al., 2010) for a comparison of models of this type.

Production functional forms

population_size

Set by k_poptype parameter:

• Constant: k_uPO4 (mol P / m-3 / yr) (represents export production)
• Nutrient: k_mu*P_conc (mol P / m-3 / yr) (represents export production)
• Pop : k_mu*phytP_conc (mol P / m-3 / yr) (represents growth of explicit population phtyP_conc)

nutrient_limitation

Set by k_nuttype parameter:

• PO4MM: P_conc / (P_conc + k_KPO4)
• PO4NMM: P, N limited phytoplankton export production: cf GENIE 2N2T_PO4MM_NO3, (Fennel, 2005)
• PO4NMMNfix: P limited nitrogen-fixer export production: cf GENIE 2N2T_PO4MM_NO3, (Fennel, 2005)

light_limitation

Set by k_lightlim parameter:

• fixed: constant k_Irel
• linear: GENIE-like form k_Irel*insol/PB.Constants.k_solar_presentday where insol (W m-2) is provided insolation in each cell
• MM: MITgcm-like saturating form zInsol/(k_Ic + zInsol) where zInsol = k_Irel*insol and insol is provided PAR in each cell
• QE: Saturating light limitation of rate vs (local) PAR k_Irel*insol, derived from photosynthetic QE k_alphaQE and chl absorption cross section k_thetaChlC. See eg (Geider, 1987) for summary of notation and unit conversions.

temperature_limitation

Set by k_templim parameter:

• Constant: constant value 1.0
• Eppley: Eppley curve, normalized to 1.0 at 0 deg C, exp(0.0633*(temp - PB.Constants.k_CtoK))

electron_donor_limitation

Set by k_edonor parameter:

• H2O: constant 1.0, no electron-donor limitation on production
• H2S: H2S_conc / (H2S_conc + k_KH2S) production limited by H2S concentration

Examples

Parameters

• rCorgPO4[Float64]=106.0, default_value=106.0, description="Corg:P Redfield ratio of organic matter produced"
• rNPO4[Float64]=16.0, default_value=16.0, description="N:P Redfield ratio of organic matter produced"
• rCcarbCorg[Float64]=0.0, default_value=0.0, description="ratio of Ccarb to Corg produced"
• rCcarbCorg_fixed[Bool]=true, default_value=true, description="Ccarb:Corg rain ratio true for fixed, false for sat. state dependent"
• k_r0[Float64]=0.044372, default_value=0.044372, description="initial rain-ratio for sat. state dependent rain ratio"
• k_eta[Float64]=0.8053406, default_value=0.8053406, description="exponent for sat. state dependent rain ratio"
• nuDOM[Float64]=0.66, default_value=0.66, description="fraction of production to DOM reservoir"
• depthlimit[Float64]=-200.0 (m), default_value=-200.0, description="depth limit for production"
• k_poptype[String]="Constant", default_value="Constant", allowed_values=["Constant", "Nutrient", "Pop"], description="population / growth rate model"
• k_uPO4[Float64]=0.002 (mol P / m-3 / yr), default_value=0.002, description="for k_poptype = 'Constant': max rate, constant ie of form k_O_uPO4 * (light, nut etc)"
• k_mu[Float64]=NaN (1/yr), default_value=NaN, description="for k_poptype = 'Nutrient', 'Pop': max prod/growth rate (at 0C if templim=='Eppley')"
• k_grazeresprate[Float64]=NaN (1/yr), default_value=NaN, description="for k_poptype = 'Pop' imposed const loss (mortality) rate"
• k_templim[String]="Constant", default_value="Constant", allowed_values=["Constant", "Eppley"], description="temperature limitation factor"
• k_lightlim[String]="linear", default_value="linear", allowed_values=["linear", "MM", "fixed", "QE"], description="Light limitation function"
• k_Irel[Float64]=1.0, default_value=1.0, description="multiplier for forcing-supplied insolation"
• k_Ic[Float64]=30.0 (W/m^2), default_value=30.0, description="saturating irradiance for 'MM' case"
• k_alphaQE[Float64]=7.0 (mgC/mgChl/Wpar m^-2/d-1), default_value=7.0, description="chla-specific initial slope of the photosynthesis-light curve for lightlim='QE'"
• k_thetaChlC[Float64]=0.03 (mg Chl / mgC), default_value=0.03, description="Chl:Corg ratio for explicit population k_poptype=Pop"
• k_epsilonChl[Float64]=0.012 (m^2/mg Chl), default_value=0.012, description="chl absorption coeff (for self shielding) for k_poptype='Pop'"
• k_nuttype[String]="PO4MM", default_value="PO4MM", allowed_values=["PO4MM", "PO4NMM", "PO4NMMNfix"], description="Nutrient limitation / nitrogen fixation function"
• k_KPO4[Float64]=NaN (mol P m-3 ), default_value=NaN, description="limitation at low [P] MM half-max constant"
• k_KN[Float64]=0.0 (mol NO3+NH4 m-3), default_value=0.0, description="limitation at low nitrogen"
• k_prefNH3[Float64]=10.0, default_value=10.0, description="preference for ammonia over nitrate"
• k_edonor[String]="H2O", default_value="H2O", allowed_values=["H2O", "H2S"], description="electron donor (H2O for oxygenic phototroph"
• k_KH2S[Float64]=0.001 (mol H2S m-3), default_value=0.001, description="limitation at low [H2S] MM half-max constant"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

• RateStoich_edonorO2eq
  • edonorO2eq (mol O2eq yr-1), VT_ReactDependency, description="O2eq e- donor consumption (H2O) by oxygenic photosynthesis"
  • [O2_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=edonorO2eq"
• do_bio_prod_MM_pop
  • volume (m^3), VT_ReactDependency, description="ocean cell volume"
  • zupper (m), VT_ReactDependency, description="cell depth (-ve)"
  • open_area_fraction –> oceansurface.open_area_fraction (), VT_ReactDependency, description="fraction of area open to atmosphere"
  • P_conc (mol m^-3), VT_ReactDependency, description="total P concentration"
  • [OmegaCA] (), VT_ReactDependency, description="calcite saturation state"
  • [rate_bioprod] –> global.rate_bioprod (), VT_ReactDependency, description="optional forcing, multiplier for productivity"
  • [PELCALC] –> global.PELCALC (), VT_ReactDependency, description="optional forcing for pelagic calcification"
  • Prod_Corg –> %reaction%Prod_Corg (mol yr-1), VT_ReactProperty, description="organic carbon production rate"
  • Prod_Ccarb –> %reaction%Prod_Ccarb (mol yr-1), VT_ReactProperty, description="carbonate production rate"
  • P_sms (mol yr-1), VT_ReactContributor, description="total dissolved P source minus sink"
  • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="TAlk source minus sink"
  • [DIC_sms] (mol yr-1), VT_ReactContributor, description="DIC source minus sink"
  • [partprod_P] (mol yr-1), VT_ReactContributor, description="flux P"
  • [partprod_N] (mol yr-1), VT_ReactContributor, description="flux N"
  • [partprod_Corg] (mol yr-1), VT_ReactContributor, description="flux Corg"
  • [partprod_Ccarb] (mol yr-1), VT_ReactContributor, description="flux Ccarb"
  • [domprod_P] (mol yr-1), VT_ReactContributor, description="flux P"
  • [domprod_N] (mol yr-1), VT_ReactContributor, description="flux N"
  • [domprod_Corg] (mol yr-1), VT_ReactContributor, description="flux Corg"
  • [domprod_Ccarb] (mol yr-1), VT_ReactContributor, description="flux Ccarb"
  • edonorO2eq (mol O2eq yr-1), VT_ReactProperty, description="O2eq e- donor consumption (H2O) by oxygenic photosynthesis"
  • insol (W m-2), VT_ReactDependency, description="photosynthetic radiative flux"
• totals
  • Prod_Corg –> %reaction%Prod_Corg (mol yr-1), VT_ReactDependency, description="organic carbon production rate"
  • edonorO2eq (mol O2eq yr-1), VT_ReactDependency, description="O2eq e- donor consumption (H2O) by oxygenic photosynthesis"
  • Prod_Ccarb –> %reaction%Prod_Ccarb (mol yr-1), VT_ReactDependency, description="carbonate production rate"
  • Prod_Corg_total (mol yr-1), VT_ReactProperty, description="total organic carbon production rate"
  • edonorO2eq_total (mol O2eq yr-1), VT_ReactProperty, description="total O2eq e- donor consumption (H2O) by oxygenic photosynthesis"
  • Prod_Ccarb_total (mol yr-1), VT_ReactProperty, description="total carbonate production rate"

ReactionAirSea(Sc_function, sol_function, frac_function, gas_name)
ReactionAirSeaO2
ReactionAirSeaCO2
ReactionAirSeaCO2
ReactionAirSeaFixedSolubility

Calculate atmosphere to ocean gas flux, mol/yr.

NB: ReactionAirSea not used directly - use as ReactionAirSeaO2 etc.

Runs in oceansurface Domain, calculates per-oceansurface-cell atmosphere to ocean gas flux (mol yr-1) for a gas X using stagnant film model:

flux_X = Asurf * open_area_fraction * vpiston * (solX(pXatm) - X_conc)

Asurf and open_area_fraction should be defined by oceansurface variables.

Piston velocity vpiston and gas solutibility solX are defined by gas specific functions (eg an empirical wind-velocity dependent Schmidt factor, and temperature and salinity dependent solubility).

If Parameter moistair = true, atmospheric partial pressure pXatm should be supplied as the equivalent for dry air (~ volume mixing ratio in dry air * pressure ), and is then corrected assuming saturated H2O at the ocean surface temperature.

ReactionAirSeaO2

See ReactionAirSea

• Piston velocity: Schmidt factor from (Sarmiento and Gruber, 2006)
• Solubility: from (Wanninkhof, 1992)

Parameters

• solubility_fixed[Bool]=false, default_value=false, description="use fixed solubility"
• sol_fix_henry_coeff[Float64]=NaN (mol l-1 atm-1), default_value=NaN, description="Henry's law coefficient for solubility_fixed=true"
• moistair[Bool]=true, default_value=true, description="apply correction for moist air"
• piston_fixed[Bool]=true, default_value=true, description="use fixed piston velocity"
• piston[Float64]=NaN (m d-1), default_value=NaN, description="fixed piston velocity"
• TempKmin[Float64]=-Inf (K), default_value=-Inf, description="GENIE bug compatibility - lower limit on temperature for solubility"
• atm_partial_pressure_min_zero[Bool]=false, default_value=false, description="true to clamp -ve values of atmospheric partial pressure to zero when calculating flux"
• ocean_conc_min_zero[Bool]=false, default_value=false, description="true to clamp -ve values of ocean concentration to zero when calculating flux"

Methods and Variables for default Parameters

• do_air_sea_flux
  • Asurf (m^2), VT_ReactDependency, description="horizontal area of oceansurface"
  • open_area_fraction (), VT_ReactDependency, description="fracton of surface open to atmosphere (0-1.0)"
  • pXatm –> atm.pO2atm (atm), VT_ReactDependency, description="gas X atmospheric partial pressure"
  • X_conc –> ocean.oceansurface.O2_conc (mol m-3), VT_ReactDependency, description="ocean concentration [gas X]"
  • flux_X –> fluxAtmtoOceansurface.flux_O2 (mol yr-1), VT_ReactContributor, description="air -> sea gas X flux"
  • temp –> ocean.oceansurface.temp (K), VT_ReactDependency, description="ocean surface temperature"
  • sal –> ocean.oceansurface.sal (psu), VT_ReactDependency, description="ocean salinity"

ReactionAirSeaCO2

See ReactionAirSea

• Piston velocity: Schmidt factor from (Wanninkhof, 1992)
• Solubility: calculated from ocean.CO2_conc, ocean.pCO2atm defined by ocean carbonate chemistry.
• Isotope fractionation: equilibrium and kinetic fractionation from (Zhang et al., 1995)

Parameters

• solubility_fixed[Bool]=false, default_value=false, description="use fixed solubility"
• sol_fix_henry_coeff[Float64]=NaN (mol l-1 atm-1), default_value=NaN, description="Henry's law coefficient for solubility_fixed=true"
• moistair[Bool]=true, default_value=true, description="apply correction for moist air"
• piston_fixed[Bool]=true, default_value=true, description="use fixed piston velocity"
• piston[Float64]=NaN (m d-1), default_value=NaN, description="fixed piston velocity"
• TempKmin[Float64]=-Inf (K), default_value=-Inf, description="GENIE bug compatibility - lower limit on temperature for solubility"
• atm_partial_pressure_min_zero[Bool]=false, default_value=false, description="true to clamp -ve values of atmospheric partial pressure to zero when calculating flux"
• ocean_conc_min_zero[Bool]=false, default_value=false, description="true to clamp -ve values of ocean concentration to zero when calculating flux"

ReactionAirSeaCH4

See ReactionAirSea

• Piston velocity: Schmidt factor from (Wanninkhof, 1992)
• Solubility: from (Wanninkhof, 1992)
• Isotope fractionation: NB: TODO no isotope fractionation

Parameters

• solubility_fixed[Bool]=false, default_value=false, description="use fixed solubility"
• sol_fix_henry_coeff[Float64]=NaN (mol l-1 atm-1), default_value=NaN, description="Henry's law coefficient for solubility_fixed=true"
• moistair[Bool]=true, default_value=true, description="apply correction for moist air"
• piston_fixed[Bool]=true, default_value=true, description="use fixed piston velocity"
• piston[Float64]=NaN (m d-1), default_value=NaN, description="fixed piston velocity"
• TempKmin[Float64]=-Inf (K), default_value=-Inf, description="GENIE bug compatibility - lower limit on temperature for solubility"
• atm_partial_pressure_min_zero[Bool]=false, default_value=false, description="true to clamp -ve values of atmospheric partial pressure to zero when calculating flux"
• ocean_conc_min_zero[Bool]=false, default_value=false, description="true to clamp -ve values of ocean concentration to zero when calculating flux"

ReactionAirSeaFixedSolubility

See ReactionAirSea

• Piston velocity: fixed value from piston Parameter
• Solubility: fixed value from sol_fix_henry_coeff

NB: moistair correction is not applied

Parameters

• solubility_fixed[Bool]=true, default_value=true, description="use fixed solubility"
• sol_fix_henry_coeff[Float64]=NaN (mol l-1 atm-1), default_value=NaN, description="Henry's law coefficient for solubility_fixed=true"
• moistair[Bool]=false, default_value=false, description="apply correction for moist air"
• piston_fixed[Bool]=true, default_value=true, description="use fixed piston velocity"
• piston[Float64]=NaN (m d-1), default_value=NaN, description="fixed piston velocity"
• TempKmin[Float64]=-Inf (K), default_value=-Inf, description="GENIE bug compatibility - lower limit on temperature for solubility"
• atm_partial_pressure_min_zero[Bool]=false, default_value=false, description="true to clamp -ve values of atmospheric partial pressure to zero when calculating flux"
• ocean_conc_min_zero[Bool]=false, default_value=false, description="true to clamp -ve values of ocean concentration to zero when calculating flux"

Methods and Variables for default Parameters

• do_air_sea_flux
  • Asurf (m^2), VT_ReactDependency, description="horizontal area of oceansurface"
  • open_area_fraction (), VT_ReactDependency, description="fracton of surface open to atmosphere (0-1.0)"
  • pXatm –> atm.pXatm (atm), VT_ReactDependency, description="gas X atmospheric partial pressure"
  • X_conc –> ocean.oceansurface.X_conc (mol m-3), VT_ReactDependency, description="ocean concentration [gas X]"
  • flux_X –> fluxAtmtoOceansurface.flux_X (mol yr-1), VT_ReactContributor, description="air -> sea gas X flux"

ReactionShelfCarb

Shallow-water carbonate burial controlled by carbonate saturation state (after (Caldeira and Rampino, 1993))

Carbonate burial rate in cell i is shelf_Ccarb[i] = carbsedshallow * shelfareanorm[i] * '(OmegaAR[i]-1.0)^1.7wherecarbsedshallow(mol C yr-1) controls the global rate, andshelfareanorm[i]` controls the spatial distribution among ocean shelf cells.

Parameters

• carbsedshallow[Float64]=1.4355e12 (mol C yr-1), default_value=1.4355e12, description="total carbonate deposition rate"
• shelfareanorm[Vector{Float64}]=Float64[], default_value=Float64[], description="per box distribution of carbonate burial (length=Domain size, must sum to 1.0)"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_shelf_carb
  • fluxOceanfloor_soluteflux_DIC –> fluxOceanfloor.soluteflux_DIC (mol yr-1), VT_ReactContributor, description="flux DIC"
  • fluxOceanfloor_soluteflux_TAlk –> fluxOceanfloor.soluteflux_TAlk (mol yr-1), VT_ReactContributor, description="flux TAlk"
  • [fluxOceanfloor_soluteflux_Ca] –> fluxOceanfloor.soluteflux_Ca (mol yr-1), VT_ReactContributor, description="flux Ca"
  • [fluxOceanBurial_flux_Ccarb] –> fluxOceanBurial.flux_Ccarb (mol yr-1), VT_ReactContributor, description="flux Ccarb"
  • [shelfarea_force] –> global.shelfarea_force (), VT_ReactDependency, description="optional forcing multiplier for carbsedshallow (defaults to 1.0)"
  • OmegaAR –> ocean.oceanfloor.OmegaAR (), VT_ReactDependency, description="aragonite saturation"
  • shelf_Ccarb (mol yr-1), VT_ReactProperty, description="shelf Ccarb burial"
• totals
  • shelf_Ccarb (mol yr-1), VT_ReactDependency, description="shelf Ccarb burial"
  • shelf_Ccarb_total (mol yr-1), VT_ReactProperty, description="total shelf Ccarb burial"

ReactionBurialEffCarb

Deep ocean carbonate burial as a carbonate-saturation-state-dependent fraction of carbonate flux.

Parameterisation from (Caldeira and Rampino, 1993), intended for use in ocean box models with a single deep ocean box.

Fraction of input carbonate flux buried flys is a function of oceanfloor carbonate saturation state.

Carbonate burial flux flux_Ccarb = particulateflux_Ccarb * flys, where Fraction of input carbonate flux buried flys is a function of carbonate saturation state.

Can be used with a spatially resolved model to provide a saturation-state dependent switch that allows burial of oceanfloor carbonate flux only above the lysocline.

Parameter burial_eff_function sets the functional form used for burial fraction flys:

• "Caldeira1993": flys = 0.5*(1.0+tanh(k0([CO3] -k1)))

(after (Caldeira and Rampino, 1993), intended for use with the single deep ocean box in a 3-box ocean model)

• "OmegaCA": flys = 1 - 0.5 * erfc(m0*(Ω_CA - m1)) (burial efficiency a function of oceanfloor saturation state)

Parameters

• burial_eff_function[String]="Caldeira1993", default_value="Caldeira1993", allowed_values=["Caldeira1993", "OmegaCA"], description="functional form for burial efficiency"
• k0[Float64]=26.0 (m3/mol), default_value=26.0, description="Caldeira1993: burial frac 'steepness' with CO3 concentration"
• k1[Float64]=0.11 (mol/m3), default_value=0.11, description="Caldeira1993: CO3 concentration at burial frac 0.5"
• m0[Float64]=10.0, default_value=10.0, description="OmegaCA: burial frac 'steepness' with OmegaCA"
• m1[Float64]=1.0, default_value=1.0, description="OmegaCA: OmegaCA at burial frac 0.5"
• hascarbseddeep[Vector{Bool}]=Bool[], default_value=Bool[], description="per box flag to enable (length=Domain size)"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_burial_eff_carb
  • fluxOceanfloor_soluteflux_DIC –> fluxOceanfloor.soluteflux_DIC (mol yr-1), VT_ReactContributor, description="flux DIC"
  • fluxOceanfloor_soluteflux_TAlk –> fluxOceanfloor.soluteflux_TAlk (mol yr-1), VT_ReactContributor, description="flux TAlk"
  • [fluxOceanfloor_soluteflux_Ca] –> fluxOceanfloor.soluteflux_Ca (mol yr-1), VT_ReactContributor, description="flux Ca"
  • [fluxOceanBurial_flux_Ccarb] –> fluxOceanBurial.flux_Ccarb (mol yr-1), VT_ReactContributor, description="flux Ccarb"
  • particulateflux_Ccarb (mol yr-1), VT_ReactTarget, description="input carbonate particulate flux"
  • deep_Ccarb (mol yr-1), VT_ReactProperty, description="deep unresolved Ccarb burial"
  • flys (), VT_ReactProperty, description="fraction of Ccarb export buried"
  • CO3_conc –> ocean.oceanfloor.CO3_conc (mol m-3), VT_ReactDependency, description="CO3 concentration"
• totals
  • deep_Ccarb (mol yr-1), VT_ReactDependency, description="deep unresolved Ccarb burial"
  • deep_Ccarb_total (mol yr-1), VT_ReactProperty, description="total deep unresolved Ccarb burial"

ReactionBurialEffCorgP

Burial efficiency (fraction of particulateflux input) for Corg and P.

Input organic matter flux is given by particulateflux_Corg, N, P. A fraction of Corg and P is buried to output flux fluxOceanBurial.flux_, Corg, P, Porg, PFe, Pauth, where P is the total P burial flux and Porg, PFe, Pauth are the three P burial mineral phases. The remainder of the input flux is transferred to reminflux_Corg, N, P, where it would usually be linked to a ReactionRemin to be remineralized.

The fraction of Corg buried is given by a burial efficiency function, with options set by Parameter burial_eff_function:

• Prescribed: Corg burial in cell i = Corg particulateflux * BECorgNorm*Parameter BECorg[i]
• Ozaki2011: Corg burial in cell i = Corg particulateflux * BECorgNorm*burialEffCorg_Ozaki2011(sedimentation_rate)
• Dunne2007: corg burial in cell i = Corg particulateflux * BECorgNorm*burialEffCorg_Dunne2007(Corg particulateflux, Afloor)
• ConstantBurialRate: Corg burial in cell i = BECorgNorm*Parameter BECorg[i] (independent of Corg flux)

It is also possible to set Parameter FixedCorgBurialTotal, in which case the ocean total Corg burial rate is fixed, and the per-cell Corg burial fluxes calculated as above are then normalized to reach this global total rate.

P burial efficiency is defined as P:Corg ratios for components Porg, PFe, Pauth by parameters BPorgCorg, BPFeCorg, BPauthCorg. If these are Vectors of length > 1, they define interpolated functions of oceanfloor [O2] on a grid defined by parameter BPO2. If they are all Vectors of length 1, they define fixed Corg:P ratios.

Parameters

• BECorgNorm[Float64]=1.0, default_value=1.0, description="overall normalization factor for Corg burial (or total Corg burial for ConstantBurialRate)"
• burial_eff_function[String]="Prescribed", default_value="Prescribed", allowed_values=["Prescribed", "Ozaki2011", "Dunne2007", "ConstantBurialRate"], description="Corg burial efficiency parameterisation (or ConstantBurialRate)"
• BECorg[Vector{Float64}]=Float64[], default_value=Float64[], description="prescribed fraction seafloor Corg flux buried (or per-cell fraction of total Corg for ConstantBurialRate)"
• FixedCorgBurialTotal[Float64]=NaN (mol C yr-1), default_value=NaN, description="if != NaN, fix total ocean Corg burial rate by renormalizing per-cell fluxes"
• BPO2[Vector{Float64}]=[NaN] (mol O2 m-3), default_value=[NaN], description="[O2] points for interpolated oxygen-dependent P:Corg (length 1 for O2-independent P:Corg)"
• BPorgCorg[Vector{Float64}]=[0.0] (mol P (mol Corg)-1), default_value=[0.0], description="P:Corg for organic P burial fraction at each BPO2 (Vector length 1 for O2-independent P:Corg)"
• BPFeCorg[Vector{Float64}]=[0.0] (mol P (mol Corg)-1), default_value=[0.0], description="P:Corg for Fe-associated P burial fraction at each BPO2 (Vector length 1 for O2-independent P:Corg)"
• BPauthCorg[Vector{Float64}]=[0.0] (mol P (mol Corg)-1), default_value=[0.0], description="P:Corg for CFA-associated P burial fraction at each BPO2 (Vector length 1 for O2-independent P:Corg)"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables

• do_burial_eff_CorgP
  • particulateflux_Corg (mol yr-1), VT_ReactTarget, description="input particulate flux Corg"
  • particulateflux_P (mol yr-1), VT_ReactTarget, description="input particulate flux P"
  • particulateflux_N (mol yr-1), VT_ReactTarget, description="input particulate flux N"
  • reminflux_Corg (mol yr-1), VT_ReactContributor, description="output unburied particulate flux Corg"
  • reminflux_P (mol yr-1), VT_ReactContributor, description="output unburied particulate flux P"
  • reminflux_N (mol yr-1), VT_ReactContributor, description="output unburied particulate flux N"
  • [fluxOceanBurial_flux_Corg] –> fluxOceanBurial.flux_Corg (mol yr-1), VT_ReactContributor, description="flux Corg"
  • [fluxOceanBurial_flux_Porg] –> fluxOceanBurial.flux_Porg (mol yr-1), VT_ReactContributor, description="flux Porg"
  • [fluxOceanBurial_flux_PFe] –> fluxOceanBurial.flux_PFe (mol yr-1), VT_ReactContributor, description="flux PFe"
  • [fluxOceanBurial_flux_Pauth] –> fluxOceanBurial.flux_Pauth (mol yr-1), VT_ReactContributor, description="flux Pauth"
  • [fluxOceanBurial_flux_P] –> fluxOceanBurial.flux_P (mol yr-1), VT_ReactContributor, description="flux P"
  • burial_eff_Corg (), VT_ReactProperty, description="Corg burial efficiency"
  • [sedimentation_rate] (m yr-1), VT_ReactDependency, description="sedimentation rate"
  • [O2_conc] –> ocean.oceanfloor.O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
  • [Afloor] –> oceanfloor.Afloor (m^2), VT_ReactDependency, description="horizontal area of seafloor at base of box"

ReactionForceInsolationModernEarth

Calculate time and latitude dependent daily mean modern Earth surface solar insolation.

Daily mean photosynthetically-active surface insolation

`insolation` = TOA flux * (1 - `albedo`) * `parfrac`

See insolMITgcmDIC for details.

Parameters

• albedo[Float64]=0.6, default_value=0.6, description="mean planetary albedo"
• parfrac[Float64]=1.0, default_value=1.0, description="fraction of radiation that is photosynthetically active"
• latitude[Vector{Float64}]=Float64[] (degrees N), default_value=Float64[], description="if non-empty, override grid latitude and set explicitly for each surface cell"

Methods and Variables for default Parameters

• do_force_insolation
  • tforce –> global.tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • insolation (W m-2), VT_ReactProperty, description="daily mean surface insolation"

insolMITgcmDIC(Timeyr,latdeg; albedo=0.6, solar=1360.0, parfrac=1.0) -> sfac

MITgcm DIC package insol function directly translated from fortran. Similar to (Brock, 1981).

NB: there are three normalization constants here: solar, albedo, parfrac to define top-of-atmosphere flux (from astronomical formulae) -> a crude approx to ground level flux (taking into account clouds etc) -> photosynthetic PAR flux

C !DESCRIPTION:
C find light as function of date and latitude
C based on paltridge and parson

Arguments:

• Timeyr: yr, model time, NB: year assumed to start in winter
• latdeg: deg, latitudes
• albedo: planetary albedo (ie correct for top-of-atmosphere to ground-level, clouds etc)
• solar: W m-2 solar constant
• parfrac: photosynthetically active fraction

Returns:

• sfac: daily average photosynthetically active solar radiation just below surface