PALEOocean Reactions
Ocean geometry and circulation transport
PALEOocean.Ocean.OceanNoTransport.ReactionOceanNoTransport — TypeReactionOceanNoTransportN 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_gridvolume(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"
PALEOocean.Ocean.OceanTransport3box.ReactionOceanTransport3box — TypeReactionOceanTransport3box3-box (Sarmiento and Toggweiler, 1984), (Toggweiler and Sarmiento, 1985) ocean model.
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+PALEOocean Reactions · PALEOocean Documentation PALEOocean Reactions
Ocean geometry and circulation transport
PALEOocean.Ocean.OceanNoTransport.ReactionOceanNoTransport — TypeReactionOceanNoTransport
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_gridvolume (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"
sourcePALEOocean.Ocean.OceanTransport3box.ReactionOceanTransport3box — TypeReactionOceanTransport3box
3-box (Sarmiento and Toggweiler, 1984), (Toggweiler and Sarmiento, 1985) ocean model.
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| 1 (s) | 2(h) |
| -->--->- |
|-------------------|----| | |
@@ -9,7 +9,7 @@
| 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 (Kelvin), VT_ReactProperty, description="Ocean temperature"
sourcePALEOocean.Ocean.OceanTransport6box.ReactionOceanTransport6box — TypeReactionOceanTransport6box
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
--------------------------------------------------
+----------------------------------------
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 (Kelvin), VT_ReactProperty, description="Ocean temperature"
sourcePALEOocean.Ocean.OceanTransport6box.ReactionOceanTransport6box — TypeReactionOceanTransport6box
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
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| 5(r) | 1 (s) | 2(h) |
| | | |
|-----------|------------------------| |
@@ -19,10 +19,10 @@
| |------------------------ |
| 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 (Kelvin), VT_ReactProperty, description="Ocean temperature"
sourcePALEOocean.Ocean.OceanTransportTMM.ReactionOceanTransportTMM — TypeReactionOceanTransportTMM
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_TMMvolume (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"
sourcePALEOocean.Ocean.OceanTransportColumn.ReactionOceanTransportColumn — TypeReactionOceanTransportColumn
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")
sourceVertical Transport
PALEOocean.Ocean.VerticalTransport.ReactionLightColumn — TypeReactionLightColumn
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"
sourcePALEOocean.Ocean.VerticalTransport.ReactionExportDirect — TypeReactionExportDirect
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)"
sourcePALEOocean.Ocean.VerticalTransport.ReactionExportDirectColumn — TypeReactionExportDirectColumn
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"
sourcePALEOocean.Ocean.VerticalTransport.ReactionSinkFloat — TypeReactionSinkFloat
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"
sourceBiological Production
PALEOocean.Ocean.BioProd.ReactionBioProdPrest — TypeReactionBioProdPrest
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_Prestvolume (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"
totalsProd_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"
sourcePALEOocean.Ocean.BioProd.ReactionBioProdMMPop — TypeReactionBioProdMMPop
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_Irellinear: GENIE-like form k_Irel*insol/PB.Constants.k_solar_presentday where insol (W m-2) is provided insolation in each cellMM: MITgcm-like saturating form zInsol/(k_Ic + zInsol) where zInsol = k_Irel*insol and insol is provided PAR in each cellQE: 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 1.0Eppley: 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 productionH2S: H2S_conc / (H2S_conc + k_KH2S) production limited by H2S concentration
Examples
k_poptypek_nuttypek_lightlimk_templimk_edonorReference Constant PO4MM linear Constant H2O P and light limited export production, as used by GENIE (Ridgwell et al., 2007) Pop PO4MM QE Eppley H2O P and light limited phytoplankton population
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_edonorO2eqedonorO2eq (mol O2eq yr-1), VT_ReactDependency, description="O2eq e- donor consumption (H2O) by oxygenic photosynthesis"- [
O2_sms] (), VT_ReactContributor, description="generated by RateStoich rate=edonorO2eq"
do_bio_prod_MM_popvolume (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"
totalsProd_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"
sourceOcean surface air-sea flux
PALEOocean.Oceansurface.AirSeaExchange.ReactionAirSea — TypeReactionAirSea(Sc_function, sol_function, frac_function, gas_name)
+ -----------------------------------------------
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 (Kelvin), VT_ReactProperty, description="Ocean temperature"
sourcePALEOocean.Ocean.OceanTransportTMM.ReactionOceanTransportTMM — TypeReactionOceanTransportTMM
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_TMMvolume (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"
sourcePALEOocean.Ocean.OceanTransportColumn.ReactionOceanTransportColumn — TypeReactionOceanTransportColumn
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")
sourceVertical Transport
PALEOocean.Ocean.VerticalTransport.ReactionLightColumn — TypeReactionLightColumn
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"
sourcePALEOocean.Ocean.VerticalTransport.ReactionExportDirect — TypeReactionExportDirect
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)"
sourcePALEOocean.Ocean.VerticalTransport.ReactionExportDirectColumn — TypeReactionExportDirectColumn
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"
sourcePALEOocean.Ocean.VerticalTransport.ReactionSinkFloat — TypeReactionSinkFloat
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"
sourceBiological Production
PALEOocean.Ocean.BioProd.ReactionBioProdPrest — TypeReactionBioProdPrest
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_Prestvolume (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"
totalsProd_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"
sourcePALEOocean.Ocean.BioProd.ReactionBioProdMMPop — TypeReactionBioProdMMPop
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_Irellinear: GENIE-like form k_Irel*insol/PB.Constants.k_solar_presentday where insol (W m-2) is provided insolation in each cellMM: MITgcm-like saturating form zInsol/(k_Ic + zInsol) where zInsol = k_Irel*insol and insol is provided PAR in each cellQE: 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 1.0Eppley: 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 productionH2S: H2S_conc / (H2S_conc + k_KH2S) production limited by H2S concentration
Examples
k_poptypek_nuttypek_lightlimk_templimk_edonorReference Constant PO4MM linear Constant H2O P and light limited export production, as used by GENIE (Ridgwell et al., 2007) Pop PO4MM QE Eppley H2O P and light limited phytoplankton population
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_edonorO2eqedonorO2eq (mol O2eq yr-1), VT_ReactDependency, description="O2eq e- donor consumption (H2O) by oxygenic photosynthesis"- [
O2_sms] (), VT_ReactContributor, description="generated by RateStoich rate=edonorO2eq"
do_bio_prod_MM_popvolume (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"
totalsProd_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"
sourceOcean surface air-sea flux
PALEOocean.Oceansurface.AirSeaExchange.ReactionAirSea — TypeReactionAirSea(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.
sourcePALEOocean.Oceansurface.AirSeaExchange.ReactionAirSeaO2 — TypeReactionAirSeaO2
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_fluxAsurf (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"
sourcePALEOocean.Oceansurface.AirSeaExchange.ReactionAirSeaCO2 — TypeReactionAirSeaCO2
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"
sourcePALEOocean.Oceansurface.AirSeaExchange.ReactionAirSeaCH4 — TypeReactionAirSeaCH4
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"
sourcePALEOocean.Oceansurface.AirSeaExchange.ReactionAirSeaFixedSolubility — TypeReactionAirSeaFixedSolubility
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_fluxAsurf (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"
sourceOcean floor burial
Carbonate burial
PALEOocean.Oceanfloor.Burial.ReactionShelfCarb — TypeReactionShelfCarb
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_carbfluxOceanfloor_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"
totalsshelf_Ccarb (mol yr-1), VT_ReactDependency, description="shelf Ccarb burial"shelf_Ccarb_total (mol yr-1), VT_ReactProperty, description="total shelf Ccarb burial"
sourcePALEOocean.Oceanfloor.Burial.ReactionBurialEffCarb — TypeReactionBurialEffCarb
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_carbfluxOceanfloor_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"
totalsdeep_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"
sourceOrganic carbon and phosphorus burial
PALEOocean.Oceanfloor.Burial.ReactionBurialEffCorgP — TypeReactionBurialEffCorgP
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_CorgPparticulateflux_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"
sourceGlobal
PALEOocean.Global.Insolation.ReactionForceInsolationModernEarth — TypeReactionForceInsolationModernEarth
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_insolationtforce –> 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"
sourcePALEOocean.Global.Insolation.insolMITgcmDIC — FunctioninsolMITgcmDIC(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:
+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.
sourcePALEOocean.Oceansurface.AirSeaExchange.ReactionAirSeaO2 — TypeReactionAirSeaO2
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_fluxAsurf (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"
sourcePALEOocean.Oceansurface.AirSeaExchange.ReactionAirSeaCO2 — TypeReactionAirSeaCO2
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"
sourcePALEOocean.Oceansurface.AirSeaExchange.ReactionAirSeaCH4 — TypeReactionAirSeaCH4
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"
sourcePALEOocean.Oceansurface.AirSeaExchange.ReactionAirSeaFixedSolubility — TypeReactionAirSeaFixedSolubility
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_fluxAsurf (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"
sourceOcean floor burial
Carbonate burial
PALEOocean.Oceanfloor.Burial.ReactionShelfCarb — TypeReactionShelfCarb
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_carbfluxOceanfloor_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"
totalsshelf_Ccarb (mol yr-1), VT_ReactDependency, description="shelf Ccarb burial"shelf_Ccarb_total (mol yr-1), VT_ReactProperty, description="total shelf Ccarb burial"
sourcePALEOocean.Oceanfloor.Burial.ReactionBurialEffCarb — TypeReactionBurialEffCarb
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_carbfluxOceanfloor_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"
totalsdeep_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"
sourceOrganic carbon and phosphorus burial
PALEOocean.Oceanfloor.Burial.ReactionBurialEffCorgP — TypeReactionBurialEffCorgP
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_CorgPparticulateflux_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"
sourceGlobal
PALEOocean.Global.Insolation.ReactionForceInsolationModernEarth — TypeReactionForceInsolationModernEarth
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_insolationtforce –> 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"
sourcePALEOocean.Global.Insolation.insolMITgcmDIC — FunctioninsolMITgcmDIC(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 winterlatdeg: deg, latitudesalbedo: planetary albedo (ie correct for top-of-atmosphere to ground-level, clouds etc)solar: W m-2 solar constantparfrac: photosynthetically active fraction
Returns:
sfac: daily average photosynthetically active solar radiation just below surface
sourceSettings
This document was generated with Documenter.jl version 1.4.1 on Friday 14 June 2024. Using Julia version 1.6.7.
Arguments:
Timeyr: yr, model time, NB: year assumed to start in winterlatdeg: deg, latitudesalbedo: planetary albedo (ie correct for top-of-atmosphere to ground-level, clouds etc)solar: W m-2 solar constantparfrac: photosynthetically active fraction
Returns:
sfac: daily average photosynthetically active solar radiation just below surface
