data_lidnesnes/fabm.yaml at main · BottomRedoxModel/data_lidnesnes · GitHub

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require_initialization: true
instances:
#--------------------------------------------------------------------------
  niva_oxydep:
    initialization:
      Phy: 0.01
      Het: 0.01
      POM: 0.01
      DOM: 0.0
      NUT: 5.
      Oxy: 200.
    parameters:
# Oxy
      O2_suboxic: 40.    # O2 threshold for oxic/suboxic switch (mmol/m3)
# PHY
      Max_uptake: 0.8 #1.0    # Maximum nutrient uptake rate (1/d)
      Knut: 0.5          # Half-sat.const. for uptake of NUT by phy for NUT/PHY ratio, (1/d)
      q10: 2.0           # Coefficient for uptake rate dependence on t (as in ERSEM)
#      bm: 0.12           # Coefficient for uptake rate dependence on t
#      cm: 1.4            # Coefficient for uptake rate dependence on t
      ir_min: 25.        # bioshading parameter, (nd)
      Iopt: 25.          # Optimal irradiance (W/m2) =50 (Savchuk, 2002)
      r_phy_nut: 0.05    # Specific respiration rate, (1/d)
      r_phy_pom: 0.15    # Specific rate of Phy mortality, (1/d)
      r_phy_dom: 0.15    # Specific rate of Phy excretion, (1/d)
      r_phy_om_anox: 0.4 # Specific rate of Phy mortality in suboxid/anoxic conditions(1/d)
      O2_add_mor_phy: 20. # Threshold O2 value for additional Phy mortality, (mmol/m3)
# HET
      r_phy_het: 0.5     # Max.spec. rate of grazing of ZOO on PHY, (1/d)
      Kphy: 0.5          # Half-sat.const.for grazing of Zoo on Phy for Phy/Zoo ratio, (nd)
      r_pop_het: 0.7     # Max.spec. rate of grazing of ZOO on POM , (1/d)
      Kpop: 2.0          # Half-sat.const.for grazing of ZOO on POM for POM/ZOO ratio, (nd)
      r_het_nut: 0.05    # Specific ZOO respiration rate (1/d)
      r_het_pom: 0.05    # Specific ZOO mortality rate (1/d)
      uz: 0.5            # Food absorbency for Zoo (nd)
      hz: 0.5            # Ratio between diss. and part. excretes of Zoo (nd)
      Trel: 1e2          # Relaxation time
# POM
      r_pom_dom: 0.10      # Specific rate of POM decomposition, (1/d)
      r_pom_nut_oxy: 0.002  # Specific rate of POM oxic decay, (1/d)
      r_pom_nut_nut: 0.001 # Specific rate of POM denitrification, (1/d)
# DOM
      r_dom_nut_oxy: 0.004  # Specific rate of DOM oxic decay, (1/d)
      r_dom_nut_nut: 0.001 # Specific rate of DOM denitrification, (1/d)
      Tda: 13.             # Coefficient for dependence of mineralization on t
      beta_da: 20.         # Coefficient for dependence of mineralization on t
# Lower boundary
      Bu: 0.5            # Burial coeficient for lower boundary (0<Bu<1), 1 - for no burying, (nd)
      Trel: 1.e6         # Relaxation time for exchange with the sediments (s/m)
      b_ox: 0.            # OXY in the sediment, (mmol/m3)
      b_dom_ox: 2.       # OM in the sediment (oxic conditions), (mmol/m3)
      b_dom_anox: 10.     # OM in the sediment (anoxic conditions), (mmol/m3)
      b_nut: 0.           # NUT in the sediment, (mmol/m3)
# Upper boundary
      pvel: 5.           # wind speed, (m/s)
      a0: 31.25,         # oxygen saturation parameter, (mmol/m3)
      a1: 14.603         # oxygen saturation parameter, (nd)
      a2: 0.4025         # oxygen saturation parameter, (1/degC)
# Stochiometric coefficients
      NtoB: 0.016        # N[uM]/BIOMASS [mg/m3], (uM(N) / mgWW/m3)
      OtoN: 8.625        # Redfield (138/16) to NO3, (uM(O)/uM(N))
      NtoN: 5.3          # Richards denitrification (84.8/16.), (uM(N)/uM(N))
# Sinking
      Wphy: -0.8        # PHY sinking rate, (m/d)
      Whet: -0.4        # HET sinking rate, (m/d)
      Wpom: -1.2 #-1.8        # POM sinking rate, (m/d)
#------------------------------------------------------------
  niva_brom_acetate:
    initialization:
      acetate: 0.0
    parameters:
# acetate
      r_acetate_miner: 0.113  # Specific rate of acetate oxic mineralization, (1/d)
      Tda: 13.              # Coefficient for dependence of mineralization on t
      beta_da: 20.          # Coefficient for dependence of mineralization on t
      Wacetate: -0.            # acetate sinking rate, (m/d)
      Bu: 0.9              # Burial coeficient for lower boundary (0<Bu<1), 1 - for no burying, (nd)
      mg_s_ratio: 1.51     # 1.297 g Mg/kg (l) in 35.1 PSU, i.e. 0.053 mM or 53 uM in 35 PSU (uM/PSU)
    coupling:
      Oxy: niva_oxydep/Oxy
#  niva_oxydep_cod:
#    initialization:
#      CHON: 0.0
#    parameters:
# CHON
#      r_CHON_nut_oxy: 0.113  # Specific rate of CHON oxic mineralization, (1/d)
#      Tda: 13.              # Coefficient for dependence of mineralization on t
#      beta_da: 20.          # Coefficient for dependence of mineralization on t
#      Wchon: -0.            # CHON sinking rate, (m/d)
#      Bu: 0.9              # Burial coeficient for lower boundary (0<Bu<1), 1 - for no burying, (nd)
#    coupling:
#      Oxy: niva_oxydep/Oxy
# REFERENCES:
#  Yakushev E. et al 2013. Modelling of the Meromictic Fjord Hunnbunn (Norway) with an Oxygen Depletion Model (OxyDep). In: E.V.Yakushev (ed.) Chemical Structure of Pelagic Redox Interfaces: Observation and Modeling, Hdb Env Chem (2013) 22: 203-234, DOI 10.1007/698_2012_145, Springer-Verlag Berlin Heidelberg
# IMPORTANT !!!! _ <TAB> is NOT allowed here, used <Space> only !!!!