!------------------------------------------------------------------------------- ! fabm_nml !------------------------------------------------------------------------------- ! ! List here the available FABM 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 FABM modules visit: ! fabm.sourceforge.net ! ! For further detail about available AED modules visit: ! aed.see.uwa.edu.au/research/models/AED ! &fabm_nml models = 'gotm_npzd', 'aed_oxygen', 'aed_carbon', 'aed_nitrogen', 'aed_phosphorus', 'aed_organic_matter', 'aed_phytoplankton', !'aed_zooplankton' / !------------------------------------------------------------------------------- ! gotm_npzd - GOTM nutrient-phytoplankton-zooplankton-detritus model !------------------------------------------------------------------------------- ! n_initial [float, unit = mmol/m^3] ! initial nutrient concentration ! p_initial [float, unit = mmol/m^3] ! initial phytoplankton concentration ! z_initial [float, unit = mmol/m^3] ! initial zooplankton concentration ! d_initial [float, unit = mmol/m^3] ! initial detritus concentration ! p0 [float, unit = mmol/m^3] ! minimum phytoplankton concentration ! z0 [float, unit = mmol/m^3] ! minimum zooplankton concentration ! w_p [float, unit = m/d] ! settling velocity of phytoplankton ! w_d [float, unit = m/d] ! settling velocity of detritus ! kc [float, unit = m^2/mmol N] ! attenuation constant for the self shading effect ! I_min [float, unit = W/m^2] ! minimum photosynthetically active radiation (PAR) ! rmax [float, unit = 1/d] ! maximum nutrient uptake rate ! gmax [float, unit = 1/d] ! maximum grazing rate ! Iv [float] ! Ivlev constant ! alpha [float, unit = mmol N/m^3] ! half saturation ! rpn [float, unit = 1/d] ! p --> n rate (p metabolism) ! rzn [float, unit = 1/d] ! z --> n rate (z metabolism) ! rdn [float, unit = 1/d] ! d --> n rate (remineralisation) ! rpdu [float, unit = 1/d] ! p --> d rate (p mortality), in euphotic zone ! rpdl [float, unit = 1/d] ! p --> d rate (p mortality), below euphotic zone ! rzd [float, unit = 1/d] ! z --> d rate (z mortality) !------------------------------------------------------------------------------- &gotm_npzd n_initial = 4.0, p_initial = 1e-15, z_initial = 1e-15, d_initial = 1.5, p0 = 0.0225, z0 = 0.0225, w_p = -0.05, w_d = -0.05, kc = 0.01, I_min = 2.0, rmax = 2.0, gmax = 0.50, Iv = 1.1, alpha = 1.25, rpn = 0.04, rzn = 0.03, rdn = 0.01, rpdu = 0.01, rpdl = 0.1, rzd = 0.02, dic_variable='aed_carbon_dic' / !------------------------------------------------------------------------------- !------------------------------------------------------------------------------- ! aed_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 ! ! NOTE: Processes such as photosynthesis and bacterial respiration from other ! AED modules should be configured to use the following names: ! aed_oxygen_oxy ! ! DIAGNOSTICS: ! - !------------------------------------------------------------------------------- &aed_oxygen oxy_initial = 225.0 Fsed_oxy = -50.0 Ksed_oxy = 50.0 theta_sed_oxy = 1.08 / !------------------------------------------------------------------------------- !------------------------------------------------------------------------------- ! 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: ! - !------------------------------------------------------------------------------- &aed_carbon !-- DIC and pH -- dic_initial = 1600.5 Fsed_dic = 3.0 Ksed_dic = 20.0 theta_sed_dic = 1.08 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='aed_oxygen_oxy' / !------------------------------------------------------------------------------- ! aed_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 ! !------------------------------------------------------------------------------- &aed_nitrogen amm_initial = 12.5 nit_initial = 27.6 Rnitrif = 0.1 Rdenit = 0.5 Fsed_amm = 10.0 Fsed_nit = -0.5 Knitrif = 78.1 Kdenit = 2.0 Ksed_amm = 20.0 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 = 'aed_oxygen_oxy' denit_product_variable = '' !#'aed_nitrogen_N20' / !------------------------------------------------------------------------------- ! aed_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: ! - ! !------------------------------------------------------------------------------- &aed_phosphorus frp_initial = 0.29 Fsed_frp = 0.010 Ksed_frp = 50.0 theta_sed_frp = 1.08 phosphorus_reactant_variable = '' !#'aed_oxygen_oxy' simPO4Adsorption = .false. ads_use_external_tss = .false. po4sorption_target_variable ='' PO4AdsorptionModel = 1 Kpo4p = 0.1 ads_use_pH = .false. Kadsratio= 1.0 Qmax = 1.0 w_po4ads = -0.2 / !------------------------------------------------------------------------------- ! aed_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: ! - ! !------------------------------------------------------------------------------- &aed_organic_matter !-- ORGANIC NITROGEN pon_initial = 50.0 don_initial = 50.0 w_pon = 0.1 Rpon_miner = 0.01 Rdon_miner = 0.01 Fsed_pon = -0.01 Fsed_don = 5.0 Kpon_miner = 31.25 Kdon_miner = 31.25 Ksed_don = 4.5 theta_pon_miner = 1.08 theta_don_miner = 1.08 theta_sed_don = 1.08 don_miner_product_variable='aed_nitrogen_amm' !-- ORGANIC PHOSPHORUS pop_initial = 1.0 dop_initial = 1.0 w_pop = 0.1 Rpop_miner = 0.001 Rdop_miner = 0.0001 Fsed_pop = -0.01 Fsed_dop = -900.0 Kpop_miner = 31.25 Kdop_miner = 31.25 Ksed_dop = 40.5 theta_pop_miner = 1.08 theta_dop_miner = 1.08 theta_sed_dop = 1.08 dop_miner_product_variable='aed_phosphorus_frp' !-- ORGANIC CARBON poc_initial = 40.0 doc_initial = 60.0 w_poc = 0.1 Rpoc_miner = 0.01 Rdoc_miner = 0.01 Fsed_poc = 0.00 Fsed_doc = 15.0 Kpoc_miner = 31.25 Kdoc_miner = 31.25 Ksed_doc = 4.5 theta_poc_miner = 1.08 theta_doc_miner = 1.08 theta_sed_doc = 1.08 KeDOM=0.001 KePOM=0.001 doc_miner_reactant_variable='aed_oxygen_oxy' doc_miner_product_variable= 'aed_carbon_dic' / !------------------------------------------------------------------------------- ! aed_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) ! !------------------------------------------------------------------------------- &aed_phytoplankton num_phytos = 2 the_phytos = 1,2 p_excretion_target_variable ='aed_organic_matter_dop' n_excretion_target_variable ='aed_organic_matter_don' c_excretion_target_variable ='aed_organic_matter_doc' si_excretion_target_variable ='' p_mortality_target_variable ='aed_organic_matter_pop' n_mortality_target_variable ='aed_organic_matter_pon' c_mortality_target_variable ='aed_organic_matter_poc' si_mortality_target_variable ='' p1_uptake_target_variable ='aed_phosphorus_frp' n1_uptake_target_variable ='aed_nitrogen_nit' n2_uptake_target_variable ='aed_nitrogen_amm' si_uptake_target_variable ='' !#'aed_silica_rsi' do_uptake_target_variable ='aed_oxygen_oxy' c_uptake_target_variable ='aed_carbon_dic' / !------------------------------------------------------------------------------- ! aed_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: ! - ! !------------------------------------------------------------------------------- &aed_zooplankton num_zoops = 1 the_zoops = 1 dn_target_variable='aed_organic_matter_don' ! dissolved nitrogen target pn_target_variable='aed_organic_matter_pon' ! particulate nitrogen target dp_target_variable='aed_organic_matter_dop' ! dissolved phosphorus target pp_target_variable='aed_organic_matter_pop' ! particulate phosphorus target dc_target_variable='aed_organic_matter_doc' ! dissolved carbon target pc_target_variable='aed_organic_matter_poc' ! particulate carbon target /