aed2_carbon
aed2_nitrogen
aed2_phosphorus
aed2_silica
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.
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 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 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 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'
/