!------------------------------------------------------------------------------- ! aed2_nml !------------------------------------------------------------------------------- ! ! List here the available aed2 modules to be included in the simulation. ! It is important they are listed in the correct order so dependecicies can be ! set during the model set-up phase. ! ! For further detail about available AED modules visit: ! aed.see.uwa.edu.au/research/models/AED ! !------------------------------------------------------------------------------- &aed2_models models = 'aed2_sedflux', 'aed2_oxygen', 'aed2_carbon', 'aed2_silica', 'aed2_nitrogen', 'aed2_phosphorus', 'aed2_organic_matter', 'aed2_phytoplankton', 'aed2_zooplankton', 'aed2_tracer', 'aed2_totals' / !############################################################################### ! aed2_sedflux ! sediment flux model types : ! "Constant" = sedimentation fluxes are constant values. ! "Constant2d" = Sedimentation fluxes may be different for ! different benthic cells - provided by driver ! "Dynamic" = Sedimentation fluxes may be different for ! different benthic cells at different times ! - computed by model ! "Dynamic2d" = Sedimentation fluxes may be different for ! different benthic cells at different times ! - computed by model !------------------------------------------------------------------------------- &aed2_sedflux sedflux_model = 'Constant' / !############################################################################### ! aed2_sed_constant ! Fsed_oxy = Sedimentation flux for oxygen ! Fsed_rsi = Sedimentation flux for silica ! Fsed_amm = Sedimentation flux for ammonia ! Fsed_nit = Sedimentation flux for nitrogen ! Fsed_frp = Sedimentation flux for phosphorus ! Fsed_pon = Sedimentation flux for particulate organic nitrogen ! Fsed_don = Sedimentation flux for dissolved organic nitrogen ! Fsed_pop = Sedimentation flux for particulate organic phosphorus ! Fsed_dop = Sedimentation flux for dissolved organic phosphorus ! Fsed_poc = Sedimentation flux for particulate organic carbon ! Fsed_doc = Sedimentation flux for dissolved organic carbon ! Fsed_dic = Sedimentation flux for dissolved inorganic carbon ! Fsed_ch4 = Sedimentation flux for methane ! Fsed_feii = Sedimentation flux for iron !------------------------------------------------------------------------------- &aed2_sed_constant !Fsed_oxy = -14.375 Fsed_oxy = -14.375 Fsed_rsi = 0.9745 Fsed_amm = 22.13 Fsed_nit = -8.57 Fsed_frp = 0.40 Fsed_pon = -0.01 Fsed_don = 0.0 Fsed_pop = -0.01 Fsed_dop = 0.0 Fsed_poc = 0.0 Fsed_doc = 0.0 Fsed_dic = 3.0 Fsed_ch4 = 0.5 Fsed_feii = 0.0 / !############################################################################### ! aed2_oxygen - AED oxygen model !------------------------------------------------------------------------------- ! oxy_initial [float, unit = mmol/m^3] ! initial O2 concentration (can be overwritten by GLM or TFV IC) ! Fsed_oxy [float, unit = mmol/m^2/day] ! sediment oxygen demand ! Ksed_oxy [float, unit = mmol/m^3] ! half-saturation concentration of oxygen sediment flux ! theta_sed_oxy [float, unit = - ] ! Arrhenius temperature multiplier for sediment oxygen flux ! Fsed_oxy_variable = Oxygen sedimentation variable link ! eg 'aed_sedflux_Fsed_oxy' will use the value supplied ! by the aed_sedflux model for Fsed_oxy ! ! NOTE: Processes such as photosynthesis and bacterial respiration from other ! AED modules should be configured to use the following names: ! aed_oxygen_oxy ! ! DIAGNOSTICS: ! !------------------------------------------------------------------------------- &aed2_oxygen !oxy_initial = 388.4 Fsed_oxy = -14.375!-14.375, Manual: -38 - -6 Ksed_oxy = 15.875 !15.875, Manual: 15.6 theta_sed_oxy = 1.07 ! Fsed_oxy_variable = 'SDF_Fsed_oxy' / !############################################################################### ! aed_carbon - AED carbon model !------------------------------------------------------------------------------- ! dic_initial [float, unit = mmol/m^3] ! initial DIC concentration (can be overwritten by GLM or TFV IC) ! Fsed_dic [float, unit = mmol/m^2/day] ! sediment CO2 flux ! Ksed_dic [float, unit = mmol/m^3] ! half-saturation oxygen concentration controlling CO2 flux ! theta_sed_dic [float, unit = - ] ! Arrhenius temperature multiplier for sediment CO2 flux ! pH_initial [float, unit = - ] ! initial water column pH ! atmco2 [float, unit = ppm] ! atmospheric CO2 concentration ! ionic [float, unit = meq] ! average ionic strength of the water column ! ! ch4_initial [float, unit = mmol/m^3] ! initial CH4 concentration (can be overwritten by GLM or TFV IC) ! Rch4ox [float, unit = - ] ! maximum reaction rate of CH4 oxidation @ 20C ! Kch4ox [float, unit = ppm] ! half-saturation oxygen concentration for CH4 oxidation ! vTch4ox [float, unit = meq] ! Arrhenius temperature multiplier for CH4 oxidation ! Fsed_ch4 [float, unit = mmol/m^2/day] ! sediment CH4 flux ! Ksed_ch4 [float, unit = mmol/m^3] ! half-saturation oxygen concentration controlling CH4 flux ! theta_sed_ch4 [float, unit = - ] ! Arrhenius temperature multiplier for sediment CH4 flux ! methane_reactant_variable ! state variable to be consumed during CH4 oxidation ! ! NOTE: Processes such as photosynthesis and bacterial respiration from other ! AED modules should be configured to use the following names: ! aed_carbon_dic ! aed_carbon_ch4 ! aed_carbon_pH ! ! DIAGNOSTICS: ! - !------------------------------------------------------------------------------- &aed2_carbon !-- DIC and pH -- ! dic_initial = 3750 ! Mendota ~ 45 mg/L, Crystal ~ 1 mg/L Fsed_dic = 4.908 !3.0, IC not in manual Snortheim 4.908 Ksed_dic = 24.34 ! 20.0, Snortheim 24.338 theta_sed_dic = 1.02 ! 1.08, Snortheim 1.0212 Fsed_dic_variable='SDF_Fsed_dic' pH_initial = 8.4 ! 7.5, Snortheim 8.4 atmco2 = 400e-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='SDF_Fsed_ch4' / !############################################################################### ! aed2_silica ! rsi_initial = Initial silica value ! Fsed_rsi = Sediment flux for silica ! Ksed_rsi = Release rate for silica ! theta_sed_rsi = Temperature multiplier for silica flux ! silica_reactant_variable = link for silica reactant variable ! Fsed_rsi_variable = silica flux variable link !------------------------------------------------------------------------------- &aed2_silica !rsi_initial = 300 !Mendota 0.1-2 mg/L, or 3.6-214 mmol/m3; Crystal 0-0.3 mg/L Fsed_rsi = 0.6 !Manual: 0.6, Snortheim 0.975 Ksed_rsi = 153.5 !Manual: 150, Snortheim 153.51 theta_sed_rsi = 1.0302 ! 1.08, Snortheim 1.0302 silica_reactant_variable='OXY_oxy' Fsed_rsi_variable = 'SDF_Fsed_rsi' / !############################################################################### ! aed2_nitrogen - AED nitrogen model !------------------------------------------------------------------------------- ! amm_initial [float, unit = mmol/m^3] ! initial NH4 concentration (can be overwritten by GLM or TFV IC) ! nit_initial [float, unit = mmol/m^3] ! initial NO3 concentration (can be overwritten by GLM or TFV IC) ! Rnitrif [float, unit = /day ] ! maximum reaction rate of nitrification @ 20C ! Rdenit [float, unit = /day ] ! maximum reaction rate of denitrification @ 20C ! Fsed_amm [float, unit = mmol/m^2/day] ! sediment NH4 flux ! Fsed_nit [float, unit = mmol/m^2/day] ! sediment NH4 flux ! Knitrif [float, unit = mmol/m^3 ] ! half-saturation oxygen concentration for CH4 oxidation ! Kdenit [float, unit = mmol/m^3 ] ! half-saturation oxygen concentration for CH4 oxidation ! Ksed_amm [float, unit = mmol/m^3] ! half-saturation oxygen concentration controlling NH4 flux ! Ksed_nit [float, unit = mmol/m^3] ! half-saturation oxygen concentration controlling NO3 flux ! theta_nitrif [float, unit = - ] ! Arrhenius temperature multiplier for nitrification ! theta_denit [float, unit = - ] ! Arrhenius temperature multiplier for denitrification ! theta_sed_amm [float, unit = - ] ! Arrhenius temperature multiplier for sediment NH4 flux ! theta_sed_nit [float, unit = - ] ! Arrhenius temperature multiplier for sediment NO3 flux ! nitrif_reactant_variable ! state variable to be consumed during nitrification ! denit_product_variable ! state variable to be incremented from denitrification ! ! NOTE: Processes such as phytoplankton uptake and zooplankton excretion from ! other AED modules should be configured to use the following names: ! aed_nitrogen_nit ! aed_nitrogen_amm ! ! DIAGNOSTICS: ! aed_nitrogen_denit ! !------------------------------------------------------------------------------- &aed2_nitrogen !amm_initial = 3 !Mendota ~ 0.1-0.3 mg/L or 1.28-3.84 mmol/m3; Crystal 0.003 - 0.02 mg/L !nit_initial = 9 !Mendota ~ 0.5-0.6 mg/L or 8-9.7 mmol/m3; Crystal 0.008-0.012 mg/L Rnitrif = 0.106 !Manual: 0.01 - 0.05 for lakes Rdenit = 0.065 !Snortheim 0.065, Manual: 0.01 - 0.04 for lakes Fsed_amm = 22.13 !Manual: 1.35 - 6.42 for lakes Fsed_nit = -9.466 !Manual: -21.4 - 7.14 Knitrif = 46.875 !Manual: 62.5 - 93.7 for lakes Kdenit = 15.24 !Manual: 12.5 - 15.6 for lakes Ksed_amm = 22.158 !Snortheim 22.158, Manual says 1.5-15.6 Ksed_nit = 1562 !Manual says 2-15.6 theta_nitrif = 1.08 theta_denit = 1.05 theta_sed_amm = 1.139 !Snortheim 1.139 theta_sed_nit = 1.055 !Snortheim 1.055 nitrif_reactant_variable='OXY_oxy' denit_product_variable='' !'NIT_N20' Fsed_amm_variable='SDF_Fsed_amm' Fsed_nit_variable='SDF_Fsed_nit' / !############################################################################### ! aed2_phosphorus - AED phosphorus model !------------------------------------------------------------------------------- ! frp_initial [float, unit = mmol/m^3] ! initial PO4 concentration (can be overwritten by GLM or TFV IC) ! Fsed_frp [float, unit = mmol/m^2/day] ! sediment PO4 flux ! Ksed_frp [float, unit = mmol/m^3] ! half-saturation oxygen concentration controlling PO4 flux ! theta_sed_frp [float, unit = - ] ! Arrhenius temperature multiplier for sediment PO4 flux ! phosphorus_reactant_variable [string] ! state variable linked to sediment release ! simPO4Adsorption [bool] ! switch to enable PO4 adsorption/desorption model ! ads_use_external_tss [bool] ! switch to set external environment variable as substrate ! po4sorption_target_variable [string] ! variable PO4 will adsorb onto (if not ads_use_external_tss) ! PO4AdsorptionModel [integer] ! sorption algorithm to use ! Kpo4p [float, unit = ] ! sorption constant ! ads_use_pH [bool] ! switch to enagge pH dependency in sorption algorithm ! Kadsratio [float, unit = ] ! sorption constant ! Qmax [float, unit = ] ! sorption constant ! w_po4ads [float, unit = m/d] ! settling rate of adsorbed PO4 ! ! NOTE: Processes such as PO4 uptake and bacterial mineralisation from other ! AED modules should be configured to use the following names: ! aed_phosphorus_frp ! aed_phosphorus_frp_ads ! ! DIAGNOSTICS: ! - ! !------------------------------------------------------------------------------- &aed2_phosphorus !frp_initial = 1 !Mendota ~ 0.040-0.050 mg/L or 1.3-1.6 mmolP/m3; Crystal 0.005-0.020 mg/L Fsed_frp = 0.29140 !Manual: 0.08 - 0.125 Ksed_frp = 15.543 !69.543, Manual: 15.6 theta_sed_frp = 1.0824 !1.0324, Snortheim 1.0324, Manual: phosphorus_reactant_variable = '' !'OXY_oxy' ! Fsed_frp_variable ='SDF_Fsed_frp' simPO4Adsorption = .true. ads_use_external_tss = .true. po4sorption_target_variable ='' PO4AdsorptionModel = 1 !Manual: Kpo4p = 0.1 !Manual: ads_use_pH = .false. Kadsratio= 0.7 !Manual: 0.7 !Qmax = 1.0 !Manual: Qmax = 0.00016 !Manual: 0.00016 w_po4ads = -1.2 !Manual: None / !############################################################################### ! aed2_organic_matter - AED organic matter model !------------------------------------------------------------------------------- ! pom_initial [float, unit = mmol/m^3] ! initial PON conc (can be overwritten by GLM or TFV IC) ! dom_initial [float, unit = mmol/m^3] ! initial DON conc (can be overwritten by GLM or TFV IC) ! w_pom [float, unit = m/day] ! settling rate of detrital N pool ! Rpom_miner [float, unit = /day ] ! hydrolysis/breakdown rate of detrital N pool @ 20C ! Rdom_miner [float, unit = /day ] ! mineralisation rate of DON pool @ 20C ! Fsed_pom [float, unit = mmol/m^2/day] ! sediment PON flux (note this is extra to sedimentation) ! Fsed_dom [float, unit = mmol/m^2/day] ! sediment DON flux ! Kpom_miner [float, unit = mmol/m^3 ] ! half-saturation oxygen concentration for PON breakdown ! Kdom_miner [float, unit = mmol/m^3 ] ! half-saturation oxygen concentration for DON mineralisation ! Ksed_dom [float, unit = mmol/m^3] ! half-saturation oxygen concentration controlling DON flux ! theta_pom_miner [float, unit = - ] ! Arrhenius temperature multiplier for PON breakdown ! theta_dom_miner [float, unit = - ] ! Arrhenius temperature multiplier for DON mineralisation ! theta_sed_dom [float, unit = - ] ! Arrhenius temperature multiplier for sediment DON flux ! dom_miner_product_variable [string] ! state variable to be product of DON mineralisation ! KeDOM [float, unit = /m /(mmol C/m^3)] ! specific light attenuation coefificent for DOM ! KePOM [float, unit = /m /(mmol C/m^3)] ! specific light attenuation coefificent for POM ! doc_miner_reactant_variable [string] ! state variable to be linked to rate of DOC mineralisation ! ! NOTE: Generic use of POM/DOM in the above descriptions, use C/N/P below ! ! NOTE: Processes such as phyto or zoop excretion within any other ! AED modules should be configured to use the following names: ! aed_organic_matter_doc aed_organic_matter_poc ! aed_organic_matter_don aed_organic_matter_pon ! aed_organic_matter_dop aed_organic_matter_pop ! ! DIAGNOSTICS: ! - ! !------------------------------------------------------------------------------- &aed2_organic_matter !-- ORGANIC NITROGEN pon_initial = 50.0 don_initial = 50.0 w_pon = -0.1238 !Snortheim -0.1238, Manual: -1 Rpon_miner = 0.035 !Manual: 0.005 - 0.03, Emily: 0.035 Rdon_miner = 0.01 !Manual: 0.003 - 0.05 Fsed_pon = -0.01 !Manual: None Fsed_don = 0.1 !Manual: 0.07 - 0.57 Kpon_miner = 62.5 !Manual: 47 - 78 (lakes) Kdon_miner = 62.5 !Manual: 47 - 78 (lakes) Ksed_don = 4.5 !Snortheim 4.5, Manual: 100 theta_pon_miner = 1.08 theta_don_miner = 1.08 theta_sed_don = 1.08 don_miner_product_variable='NIT_amm' !-- ORGANIC PHOSPHORUS pop_initial = 1.0 dop_initial = 1.0 !w_pop = -0.1238 !Manual: -1 w_pop = -1 !Manual: -1 Rpop_miner = 0.03 !Manual: 0.01 - 0.03 (maybe up to 0.099?) Rdop_miner = 0.01 !Manual: 0.01 - 0.05 Fsed_pop = -0.01 !Manual: ?? Fsed_dop = 0.03 !Manual: 0.03 Kpop_miner = 62.5 !Manual: 47 - 78 (lakes) Kdop_miner = 62.5 !Manual: 47 - 78 (lakes) Ksed_dop = 40.5 !Manual: 150 for estuaries? theta_pop_miner = 1.08 theta_dop_miner = 1.08 theta_sed_dop = 1.08 dop_miner_product_variable='PHS_frp' !-- ORGANIC CARBON poc_initial = 80.0 doc_initial = 400.0 w_poc = -0.1238 !Snortheim -0.1238, Manual: -1 Rpoc_miner = 0.04 !Manual: 0.01 - 0.07 (0.008) Rdoc_miner = 0.003 !Manual: 0.035 - 0.05 Fsed_poc = -0.01 !Manual: ? Fsed_doc = 0.044 !??, originally set to 0 Kpoc_miner = 62.5 !Manual: 47 - 78 (lakes) Kdoc_miner = 62.5 !Manual: 47 - 78 (lakes) Ksed_doc = 16.81 !Manual: ?? theta_poc_miner = 1.08 theta_doc_miner = 1.08 theta_sed_doc = 1.08 KeDOM=0.001 ! for DOC, should be about 0.003 KePOM=0.001 doc_miner_reactant_variable='OXY_oxy' doc_miner_product_variable= 'CAR_dic' ! Fsed_pon_variable='SDF_Fsed_pon' ! Fsed_don_variable='SDF_Fsed_don' ! Fsed_pop_variable='SDF_Fsed_pop' ! Fsed_dop_variable='SDF_Fsed_dop' ! Fsed_poc_variable='SDF_Fsed_poc' ! Fsed_doc_variable='SDF_Fsed_doc' / !############################################################################### ! aed2_phytoplankton - AED phytoplankton model !------------------------------------------------------------------------------- ! num_phytos [integer] ! number of phytoplankton groups within this module to include ! num_phytos [integer] ! list of ID's of groups in aed_phyto_pars.nml (len=num_phyto) ! X_excretion_target_variable [string] ! state variable to receive C, N or P from excretion ! X_mortality_target_variable [string] ! state variable to receive C, N or P from mortality ! X_uptake_target_variable [string] ! state variable to be linked for C,N,P,Si or O2 uptake ! ! NOTE: Users must supply a valid "aed_phyto_pars.nml" file ! ! ! NOTE: Processes such as zoop grazing or turbidity calc within any other ! AED modules should be configured to use the following names: ! aed_phytoplankton_name (where name is as defined in the nml) ! aed_phytoplankton_name_IN (internal nitrogen) ! aed_phytoplankton_name_IP (internal phosphorus) ! ! DIAGNOSTICS: ! aed_phytoplankton_name_fI (light limitation) ! aed_phytoplankton_name_fT (temp limitation) ! aed_phytoplankton_name_fS (salinity limitation) ! aed_phytoplankton_name_fN (nitrogen limitation) ! aed_phytoplankton_name_fP (phosphorus limitation) ! aed_phytoplankton_name_fSi (silica limitation) ! aed_phytoplankton_tchla (total module chlorophyll-a) ! aed_phytoplankton_gpp (total module gross primary productivity) ! !------------------------------------------------------------------------------- &aed2_phytoplankton num_phytos = 4 the_phytos = 1,2,3,4 p_excretion_target_variable='OGM_dop' n_excretion_target_variable='OGM_don' c_excretion_target_variable='OGM_doc' si_excretion_target_variable='' p_mortality_target_variable='OGM_pop' n_mortality_target_variable='OGM_pon' c_mortality_target_variable='OGM_poc' si_mortality_target_variable='' p1_uptake_target_variable='PHS_frp' n1_uptake_target_variable='NIT_nit' n2_uptake_target_variable='NIT_amm' si_uptake_target_variable='SIL_rsi' do_uptake_target_variable='OXY_oxy' c_uptake_target_variable='CAR_dic' / !############################################################################### ! aed2_zooplankton - AED zooplankton model !------------------------------------------------------------------------------- ! num_zoops [integer] ! number of zooplankton groups within this module to include ! the_zoops [integer] ! list of ID's of groups in aed_zoop_pars.nml (len=num_zoops) ! dX_target_variable [string] ! state variable linked to provide/receive dissoved OM ! pX_target_variable [string] ! state variable linked to provide/receive particulate OM ! ! NOTE: Users must supply a valid "aed_zoops_pars.nml" file ! ! ! NOTE: Processes such as zoop grazing or turbidity calc within any other ! AED modules should be configured to use the following names: ! aed_zooplankton_name (where name is as defined in the nml) ! ! DIAGNOSTICS: ! - ! !------------------------------------------------------------------------------- &aed2_zooplankton num_zoops = 3 the_zoops = 1,2,3 dn_target_variable='OGM_don' ! dissolved nitrogen target variable pn_target_variable='OGM_pon' ! particulate nitrogen target variable dp_target_variable='OGM_dop' ! dissolved phosphorus target variable pp_target_variable='OGM_pop' ! particulate phosphorus target variable dc_target_variable='OGM_doc' ! dissolved carbon target variable pc_target_variable='OGM_poc' ! particulate carbon target variable / !############################################################################### ! aed2_pathogens ! num_pathogens = number of pathogens to model ! the_pathogens = list of pathogens classes (referencing the pathogens database) !------------------------------------------------------------------------------- &aed2_pathogens num_pathogens = 1 the_pathogens = 1 !,3,5 / !############################################################################### ! aed2_tracer ! num_tracers = number of tracers to model ! decay = list of decay rates for the tracers ! settling = list of settling rates for the tracers ! fsed = list of sedimentation fluxes for the tracers !------------------------------------------------------------------------------- &aed2_tracer num_tracers = 1 decay = 0 !, 0, 0, ... settling = -0.1 !, 0, 0, .... fsed = 0 !, 0, 0, ... epsilon = 0.02 !, 0.02, 0.02 tau_0 = 0.01 !, 0.01, 0.01 tau_r = 1.0 !, 1.0, 1.0 Ke_ss = 0.02 !, 0.02, 0.02 retention_time = .true. / !############################################################################### ! aed2_totals ! TN_vars = list of variable contributing to total nitrogen ! TN_varscale = scaling of TN variables contribution ! TP_vars = list of variable contributing to total phosphorus ! TP_varscale = scaling of TP variables contribution ! TOC_vars = list of variable contributing to total organic carbon ! TOC_varscale = scaling of TOC variables contribution ! TSS_vars = list of variable contributing to total suspended solids ! TSS_varscale = scaling of TSS variables contribution !------------------------------------------------------------------------------- &aed2_totals TN_vars = 'NIT_nit', 'NIT_amm', 'OGM_don', 'OGM_pon', 'PHY_CYANONPCH2', ! 'PHY_green_IN' TN_varscale = 1.0, 1.0, 1.0, 1.0, 0.15 TP_vars = 'PHS_frp', 'PHS_frp_ads', 'OGM_dop', 'OGM_pop' TP_varscale = 1.0, 1.0, 1.0, 1.0 TOC_vars = 'OGM_doc', 'OGM_poc', 'PHY_CYANOPCH1', 'PHY_CYANONPCH2', 'PHY_CHLOROPCH3', 'PHY_DIATOMPCH4' TOC_varscale = 1.0, 1.0, 1.0, 1.0, 1.0, 1.0 TSS_vars = 'TRC_ss1', ! 'PHY_green' !, .... ! TSS_varscale = 0.1,0.1 !, /