Science Modules / Inorganic Nutrients

NUT

Both the inorganic and organic, and dissolved and particulate forms of C, N and P are modelled explicitly along the degradation pathway of POM to DOM to dissolved inorganic matter (DIM). The decomposition and mineralisation process varies in response to temperature, and is additionally able to slow down under anaerobic conditions. The nitrogen cycle includes the additional processes of denitrification, nitrification and N2 fixation (discussed in the phytoplankton section) that are not in the carbon and phosphorus cycles, though note N2 levels are not tracked as a state variable. The phosphorus cycle also accounts for adsorption/desorption of PO4 onto suspended solids (SS), and adopts the Langmuir isotherm model as implemented by Chao et al. (2010).

The silica cycle is simpler and includes the processes of biological uptake of dissolved Si (RSi) by diatoms into the internal Si (ISi) pool, dissolved sediment fluxes of RSi, diatom mortality directly into the RSi sediment pool, settling of ISi. This relatively simple representation assumes that diatom frustules rapidly mineralize.

aed2_carbon : mass balance and functions related to carbon cycling

aed2_nitrogen : mass balance and functions related to nitrogen cycling

aed2_phosphorus : mass balance and functions related to phosphorus cycling

aed2_silica : mass balance and functions related to silica cycling



Variable Summary & Setup Options - aed_carbon

    Variable Name Description Units Variable Type Core/Optional
    CAR_dic dissolved inorganic carbon $$mmol\,m^{-3}$$ pelagic core
    CAR_ch4 methane $$mmol\,m^{-3}$$ pelagic core
    CAR_pH pH value - pelagic core
    Variable Name Description Units Variable Type Core/Optional
    CAR_pco2 partial pressure of CO2 in water atmatm pelagic diagnostic core
    CAR_ch4ox methane oxidation rate $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    CAR_sed_dic CO2 exchange across sediment/water interface $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    CAR_atm_co2_flux CO2 exchange across atm/water interface $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    CAR_atm_ch4_flux CH4 exchange across atm/water interface $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    Parameter Name Description Units Parameter Type Default Typical Range Comment
    dic_initial initial DIC cooncentrations $$mmol\,m^{-3}$$ float 0-2000 can be overwritten by GLM or TFV IC
    Fsed_dic sediment CO2 flux $$mmol\,m^{-2}\,day^{-1}$$ float 4e+00 - -
    Ksed_dic half-saturation oxygen concentration controlling CO2 flux $$mmol\,m^{-3}$$ float 30 - -
    theta_sed_dic Arrhenius temperature multiplier for sediment CO2 flux - float 1e+00 - -
    pH_initial initial pH values - float 8 7/09/2017 -
    atmco2 atmospheric CO2 concentration atm float 4e-04 - -
    ionic average ionic strength of the water column meq float - - -
    ch4_initial initial CH4 values $$mmol\,m^{-3}$$ float 5e+00 - -
    Rch4ox maximum reaction rate of CH4 oxidatin @ 20C - float 1e-02 - -
    Kch4ox half-saturation oxygen concentration for CH4 oxidation $$mmol\,m^{-3}$$ float 1e-02 - -
    vTch4ox Arrhenius temperature multiplier for CH4 oxidation - float 1e+00 - -
    Fsed_ch4 sediment CH4 flux $$mmol\,m^{-2}\,day^{-1}$$ float 4e+00 - -
    Ksed_ch4 half-saturation oxygen concentration controlling CH4 flux $$mmol\,m^{-3}$$ float 30 - -
    theta_sed_ch4 Arrhenius temperature multiplier for sediment CH4 flux - float 1e+00 - -
    methane_reactant_variable state variable to be consumed during CH4 oxidation - string - - -

    An example nml block for the carbon module is shown below:

    &aed2_carbon !-- DIC and pH dic_initial = 1600.5 Fsed_dic = 14.0 Ksed_dic = 20.0 theta_sed_dic = 1.08 !Fsed_dic_variable='Fsed_dic' pH_initial = 7.5 atmco2 = 390e-6 ionic = 0.1 !-- CH4 ch4_initial = 27.6 Rch4ox = 0.01 Kch4ox = 0.5 vTch4ox = 1.08 Fsed_ch4 = 0.5 Ksed_ch4 = 100.0 theta_sed_ch4 = 1.08 methane_reactant_variable='OXY_oxy' !Fsed_ch4_variable='Fsed_ch4' /

    Variable Summary & Setup Options - aed_nitrogen

    Variable Name Description Units Variable Type Core/Optional
    NIT_amm ammonium, NH4 - pelagic core
    NIT_nit nitrate, NO3 $$mmol\,m^{-3}$$ pelagic core
    NIT_n2o nitrous oxide, N2O $$mmol\,m^{-3}$$ pelagic optional
    Variable Name Description Units Variable Type Core/Optional
    NIT_nitrif nitrification rate $$mmol\,m^{-3}\,day^{-1}$$ pelagic diagnostic core
    NIT_denit denitrification rate $$mmol\,m^{-3}\,day^{-1}$$ pelagic diagnostic core
    NIT_annamox anammox rate $$mmol\,m^{-3}\,day^{-1}$$ pelagic diagnostic core
    NIT_dnra dnra rate $$mmol\,m^{-3}\,day^{-1}$$ pelagic diagnostic core
    NIT_atm_N2O_flux N2O exchange across atm/water interface $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    NIT_sed_amm NH4 exchange across sediment/water interface $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    NIT_sed_nit NO3 exchange across sediment/water interface $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    NIT_sed_n2o N2O exchange across sediment/water interface $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    NIT_sed_n2oprod - $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    Parameter Name Description Units Parameter Type Default Typical Range Comment
    amm_initial initial CH4 cooncentrations $$mmol\,m^{-3}$$ float 0-2000 can be overwritten by GLM or TFV IC
    nit_initial initial NO3 cooncentrations $$mmol\,m^{-3}$$ float 0-2000 can be overwritten by GLM or TFV IC
    Fsed_amm sediment NH4 flux $$mmol\,m^{-2}\,day^{-1}$$ float 4e+00 - -
    Ksed_amm half-saturation oxygen concentration controlling NH4 flux $$mmol\,m^{-3}$$ float 25 - -
    Fsed_nit sediment NO3 flux $$mmol\,m^{-2}\,day^{-1}$$ float -5e+00 - -
    Ksed_nit half-saturation oxygen concentration controlling NO3 flux $$mmol\,m^{-3}$$ float 100 - -
    theta_sed_amm Arrhenius temperature multiplier for sediment NH4 flux - float 1e+00 - -
    theta_sed_nit Arrhenius temperature multiplier for sediment NO3 flux - float 1e+00 - -
    Rnitrif maximum reaction rate of nitrification @ 20C $$day^{-1}$$ float 1e-01 - -
    Rdenit maximum reaction rate of denitrification @ 20C $$day^{-1}$$ float 3e-01 - -
    Knitrif half-saturation oxygen concentration for nitrification $$mmol\,m^{-3}$$ float 8e+01 - -
    Kdenit half-saturation oxygen concentration for denitrification $$mmol\,m^{-3}$$ float 2 - -
    nitrif_reactant_variable state variable to be consumed during nitrifition - string - - -
    denit_reactant_variable state variable to be consumed during denitrifition - string - - -

    An example nml block for the nitrogen module is shown below:

    &aed2_nitrogen ! Initial values amm_initial = 12.7 nit_initial = 23.5 n2o_initial = 23.5 ! Reaction rates of core pathways Rnitrif = 0.12 Knitrif = 78.1 theta_nitrif = 1.08, nitrif_reactant_variable='OXY_oxy', Rdenit = 0.26, Kdenit = 2.0, theta_denit = 1.08, Ranammox = 0.001, Kanmx_nit = 2.0, Kanmx_amm = 2.0, Rdnra = 0.01, Kdnra_oxy = 2.0, ! N2O option reaction rates simN2O = .false. Rn2o = 0.05, Cn2o_atm = 0.32 ! ppm !-- Sediment fluxes Fsed_amm = 3.5, Ksed_amm = 25.0, Fsed_nit = -4.5, Ksed_nit = 100.0, Fsed_n2o = -4.5, Ksed_n2o = 100.0, theta_sed_amm = 1.08, theta_sed_nit = 1.08, Fsed_amm_variable='SDF_Fsed_amm' Fsed_nit_variable='SDF_Fsed_nit' /

    Variable Summary & Setup Options - aed_phosphorus

    Variable Name Description Units Variable Type Core/Optional
    PHS_frp phosphate, PO4 $$mmol\,m^{-3}$$ pelagic core
    PHS_frp_ads adsorbed phosphorus $$mmol\,m^{-3}$$ pelagic core
    Variable Name Description Units Variable Type Core/Optional
    SED_frp PO4 exchange across sed/water interface $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    Parameter Name Description Units Parameter Type Default Typical Range Comment
    frp_initial initial PO4 cooncentrations $$mmol\,m^{-3}$$ float 0-2000 can be overwritten by GLM or TFV IC
    Fsed_frp sediment PO4 flux $$mmol\,m^{-2}\,day^{-1}$$ float - -
    Ksed_frp half-saturation oxygen concentration controlling PO4 flux $$mmol\,m^{-3}$$ float - - -
    theta_sed_frp Arrhenius temperature multiplier for sediment PO4 flux - float 1e+00 - -
    simPO4Adsorption switch to enable PO4 adsorption/desorption model - bolean .false. .true./.false. -
    po4sorption_target_variable variable PO4 will adsorb onto (if not ads_use_external_tss) - string - - -
    PO4AdsorptionModel sorption algorithm to use - Integer - - -
    kpo4p sorption constant - float 1e-01 - -
    ads_use_pH switch to enagge pH dependency in sorption algorithm - bolean .false. .true./.false. -
    kadsration sorption constant - float 1 - -
    Qmax sorption constant - float 1 - -
    w_po4ads settling rate of adsorbed PO4 - float -9999 - -

    An example nml block for the phosphorus module is shown below:

    &aed2_phosphorus frp_initial = 0.29 Fsed_frp = 0.08 Ksed_frp = 80.0 theta_sed_frp = 1.08 phosphorus_reactant_variable ='OXY_oxy' Fsed_frp_variable ='SDF_Fsed_frp' simPO4Adsorption = .true. ads_use_external_tss = .false. po4sorption_target_variable ='TRC_ss1' PO4AdsorptionModel = 1 Kpo4p = 0.1 ads_use_pH = .false. Kadsratio= 1.0 Qmax = 1.0 w_po4ads = -9999 /

    Variable Summary & Setup Options - aed_silica

    Variable Name Description Units Variable Type Core/Optional
    SIL_rsi silica $$mmol\,m^{-3}$$ pelagic core
    Variable Name Description Units Variable Type Core/Optional
    SIL_sed_rs sediment reactive Si flux $$mmol\,m^{-2}\,day^{-1}$$ pelagic diagnostic core
    Parameter Name Description Units Parameter Type Default Typical Range Comment
    rsi_initial initial Si cooncentrations $$mmol\,m^{-3}$$ float 0-2000 can be overwritten by GLM or TFV IC
    Fsed_rsi sediment Si flux $$mmol\,m^{-2}\,day^{-1}$$ float - -
    Ksed_rsi half-saturation oxygen concentration controlling Si flux $$mmol\,m^{-3}$$ float 50 - -
    theta_sed_rsi Arrhenius temperature multiplier for sediment Si flux - float 1e+00 - -
    silica_reactant_variable link for silica reactant variable - string - - -
    Fsed_rsi_variable silica flux variable link - string - - -

    An example nml block for the silica module is shown below:

    &aed2_silica rsi_initial = 12.5 Fsed_rsi = 0. Ksed_rsi = 50.0 theta_sed_rsi = 1.08 silica_reactant_variable='OXY_oxy' !Fsed_rsi_variable = 'SDF_Fsed_rsi' /



    Examples

    Example 1: Simulated vs. measured nitrate concentration at site of SUC of Swan River.
    Example 2: Simulated vs. measured FRP concentration at site of SUC of Swan River.


    Publications & References

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