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

The following state variables are core or optional STATE variables within aed2_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

The following state variables are core or optional DIAGNOSTIC variables within aed2_oxygen

Variable Name Description Units Variable Type Core/Optional
CAR_PCO2 partial pressure of CO2 in water $$atm$$ pelagic diagnostic core
CAR_CH4OX methane oxidation rate $$mmol\,m^{-3}\,day^{-1}$$ pelagic diagnostic core
CAR_SED_DIC CO2 exchange across sed/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

The following parameters and configuration variables are available to be set via the nml module block:


Parameter Name Description Units Parameter Type Default Typical Range Comment
dic_initial initial DIC cooncentrations mmol/m**3 float 0 0-2000 can be overwritten by GLM or TFV IC
Fsed_dic sediment CO2 flux mmol/m**2/day float 0.0 -
Ksed_dic half-saturation oxygen concentration controlling CO2 flux mmol/m**3 float - -
theta_sed_dic Arrhenius temperature multiplier for sediment CO2 flux - float 1.08 -
pH_initial initial pH values - float 8 7 - 9
atmco2 atmospheric CO2 concentration atm float 367e-6 -
ionic average ionic strength of the water column meq float - -
ch4_initial initial CH4 values mmol/m**3 float - -
Rch4ox maximum reaction rate of CH4 oxidatin @ 20C - float - -
Kch4ox half-saturation oxygen concentration for CH4 oxidation mmol/m**3 float - -
vTch4ox Arrhenius temperature multiplier for CH4 oxidation - float 1.08 -
Fsed_ch4 sediment CH4 flux mmol/m**2/day float 0.0 -
Ksed_ch4 half-saturation oxygen concentration controlling CH4 flux mmol/m**3 float - -
theta_sed_ch4 Arrhenius temperature multiplier for sediment CH4 flux - float 1.08 -
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_initial = 1600.5 Fsed_dic = 3.0 Ksed_dic = 20.0 theta_sed_dic = 1.08 Fsed_dic_variable='Fsed_dic' pH_initial = 7.5 atmco2 = 370e-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

The following state variables are core or optional STATE variables within aed2_nitrogen

Variable Name Description Units Variable Type Core/Optional
WQ_NIT_AMM ammonium, NH4 mmol m^{-3} pelagic core
WQ_NIT_NIT nitrate, NO3 mmol m^{-3} pelagic core
WQ_CAR_PH PH values - pelagic core
WQ_NIT_DON dissolved organic nitrogen mmol m^{-3} pelagic core
WQ_NIT_PON partical organic nitrogen mmol m^{-3} pelagic core

The following state variables are core or optional DIAGNOSTIC variables within aed2_oxygen

Variable Name Description Units Variable Type Core/Optional
TN total nitrogen mmol/m**3 pelagic diagnostic core
TKN totall kjeldahl nitrogen mmol/m**3 pelagic diagnostic core
NIT_NITRIF nitrification rate mmol/m**3/d pelagic diagnostic core
NIT_DENIT denitrification rate mmol/m**3/d pelagic diagnostic core
NIT_ANAMMOX anammox rate mmol/m**3/d pelagic diagnostic core
NIT_DNRA dnra rate mmol/m**3/d pelagic diagnostic core
NIT_ATM_N2O_FLUX N2O exchange across atm/water interface mmol/m**2/d pelagic diagnostic core
NIT_SED_AMM CH4 exchange across sediment/water interface mmol/m**2/d pelagic diagnostic core
NIT_SED_NIT NO3 exchange across sediment/water interface mmol/m**2/d pelagic diagnostic core
NIT_SED_N2O N2O exchange across sediment/water interface mmol/m**2/d pelagic diagnostic core

The following parameters and configuration variables are available to be set via the nml module block:


Parameter Name Description Units Parameter Type Default Typical Range Comment
amm_initial initial CH4 cooncentrations mmol/m**3 float 0 0-2000 can be overwritten by GLM or TFV IC
nit_initial initial NO3 cooncentrations mmol/m**3 float 0 0-2000 can be overwritten by GLM or TFV IC
Fsed_amm sediment NH4 flux mmol/m**2/day float 0.0 -
Ksed_amm half-saturation oxygen concentration controlling NH4 flux mmol/m**3 float - -
Fsed_nit sediment NO3 flux mmol/m**2/day float 0.0 -
Ksed_nit half-saturation oxygen concentration controlling NO3 flux mmol/m**3 float - -
theta_sed_amm Arrhenius temperature multiplier for sediment NH4 flux - float 1.08 -
theta_sed_nit Arrhenius temperature multiplier for sediment NO3 flux - float 1.08 -
Rnitrif maximum reaction rate of nitrification @ 20C /day float - -
Rdenit maximum reaction rate of denitrification @ 20C /day float - -
Knitrif half-saturation oxygen concentration for nitrification mmol/m**3 float - -
Kdenit half-saturation oxygen concentration for denitrification mmol/m**3 float - -
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 amm_initial = 12.7, !average for 08-Sep-2009 nit_initial = 23.5, !average for 08-Sep-2009 Rnitrif = 0.1, Rdenit = 0.26, !from WC denit rates Fsed_amm = 3.5, !maximum measured by Keryn #BB Fsed_nit = -4.5, !maximum measured by Keryn Knitrif = 78.1, Kdenit = 2.0, Ksed_amm = 25.0, Ksed_nit = 100.0, theta_nitrif = 1.08, theta_denit = 1.08, theta_sed_amm = 1.08, theta_sed_nit = 1.08, nitrif_reactant_variable='OXY_oxy', denit_product_variable='', !'N20', !Fsed_amm_variable='Fsed_amm' !Fsed_nit_variable='Fsed_nit' /

Variable Summary & Setup Options - aed_phosphorus

The following state variables are core or optional STATE variables within aed2_phosphorus

Variable Name Description Units Variable Type Core/Optional
WQ_PHS_FRP phosphate, PO4 mmol m^{-3} pelagic core
WQ_PHS_FRP_ADS adsorbed phosphorus mmol m^{-3} pelagic core
WQ_OGM_DOP dissolved organic phosphorus mmol m^{-3} pelagic core
WQ_OGM_POP partical organic phosphorus mmol m^{-3} pelagic core

The following state variables are core or optional DIAGNOSTIC variables within aed2_oxygen

Variable Name Description Units Variable Type Core/Optional
TP total phosphorus mmol/m**3 pelagic diagnostic core
TPO4 totall inorganic phosphorus mmol/m**3 pelagic diagnostic core
SED_FRP PO4 exchange across sed/water interface mmol/m**2/d pelagic diagnostic core

The following parameters and configuration variables are available to be set via the nml module block:


Parameter Name Description Units Parameter Type Default Typical Range Comment
frp_initial initial PO4 cooncentrations mmol/m**3 float 0 0-2000 can be overwritten by GLM or TFV IC
Fsed_frp sediment PO4 flux mmol/m**2/day float 0.0 -
Ksed_frp half-saturation oxygen concentration controlling PO4 flux mmol/m**3 float - -
theta_sed_frp Arrhenius temperature multiplier for sediment PO4 flux - float 1.08 -
simPO4Adsorption switch to enable PO4 adsorption/desorption model - T?F .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 - -
ads_use_pH switch to enagge pH dependency in sorption algorithm - T?F .false. .true./.false.
kadsration sorption constant - float - -
Qmax sorption constant - float - -
w_po4ads settling rate of adsorbed PO4 - float - -

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

&aed2_phosphorus frp_initial = 0.29 Fsed_frp = 0.2 ! #BB Ksed_frp = 50.0 theta_sed_frp = 1.10 phosphorus_reactant_variable ='OXY_oxy' !Fsed_frp_variable ='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 = -0.01 /

Variable Summary & Setup Options - aed_silica

The following state variables are core or optional STATE variables within aed2_silica

Variable Name Description Units Variable Type Core/Optional
WQ_SIL_RSI silica mmol m^{-3} pelagic core

The following state variables are core or optional DIAGNOSTIC variables within aed2_oxygen

Variable Name Description Units Variable Type Core/Optional
SIL_SED_RS sediment reactive Si flux mmol/m**2/day pelagic diagnostic core

The following parameters and configuration variables are available to be set via the nml module block:


Parameter Name Description Units Parameter Type Default Typical Range Comment
rsi_initial initial Si cooncentrations mmol/m**3 float 0 0-2000 can be overwritten by GLM or TFV IC
Fsed_rsi sediment Si flux mmol/m**2/day float 0.0 -
Ksed_rsi half-saturation oxygen concentration controlling Si flux mmol/m**3 float - -
theta_sed_rsi Arrhenius temperature multiplier for sediment Si flux - float 1.08 -
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 = 1.8 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.


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