fabm.yaml

# This is .YAML file for BROM biogoechemical model.
# Please don't write more than 72 symbols in one line, 
# never use "TAB" and simplify your life by adding references !
#----------------------------------------------------------------------
check_conservation: false
require_initialization: true
instances:
#----------------------------------------------------------------------
  B_NUT:
#----------------------------------------------------------------------
    long_name: main_nutrients
    model: niva/brom_main_nutrients
    initialization:
      NH4: 0.0
      NO2: 0.0
      NO3: 5.0
      PO4: 1.0
      Si:  5.0
#----------------------------------------------------------------------
  B_EQ:
#----------------------------------------------------------------------
    long_name: equilibrium_constÌants
    model: niva/brom_eq_constants
  B_C:
    long_name: carbon
    model: niva/brom_carbon
    initialization:
      DIC: 2130.0 # total dissolved inorganic carbon (mmol C/m^3)
      Alk: 2300.0 
    coupling:
      Kc0:   B_EQ/Kc0
      Kc1:   B_EQ/Kc1
      Kc2:   B_EQ/Kc2
      Hplus: B_pH/Hplus
#----------------------------------------------------------------------
  B_Ca:
#----------------------------------------------------------------------
    long_name: calcium
    model: niva/brom_calcium
    initialization:
      CaCO3: 0.0
    coupling:
      DIC: B_C/DIC
      CO3: B_C/CO3
    parameters:
      K_caco3_diss: 3.0  
        #! CaCO3 dissollution rate constant (1/d) (wide ranges 
        #  are given in (Luff et al., 2001))
      K_caco3_form: 0.0002  
        #! CaCO3 precipitation rate constant (1/d) (wide ranges 
        #  are given in (Luff et al., 2001))
      Wsed: 7.0 
        #! Rate of sinking of detritus (m/d), =0.4 (Savchuk, 2002), =5. (Gregoire, Lacroix, 2001), =1-370 (Alldredge, Gotschalk, 1988)
#----------------------------------------------------------------------
  B_pH:
#----------------------------------------------------------------------
    long_name: pH
    model: niva/brom_pH
    coupling:
      Kc1:      B_EQ/Kc1
      Kc2:      B_EQ/Kc2
      Kb:       B_EQ/Kb
      Kp1:      B_EQ/Kp1
      Kp2:      B_EQ/Kp2
      Kp3:      B_EQ/Kp3
      KSi:      B_EQ/KSi
      Knh4:     B_EQ/Knh4
      Kh2s:     B_EQ/Kh2s
      kso4:     B_EQ/kso4
      kflu:     B_EQ/kflu
      Kw:       B_EQ/Kw
      tot_free: B_EQ/tot_free
      DIC:      B_C/DIC
      PO4:      B_NUT/PO4
      Si:       B_NUT/Si
      NH4:      B_NUT/NH4
      H2S:      B_S/H2S
      SO4:      B_S/SO4
#----------------------------------------------------------------------
  B_BIO:
#----------------------------------------------------------------------
    long_name: bio
    model: niva/brom_bio
    initialization:
      Phy: 0.01
      Het: 0.01
      POML: 0.01
      POMR: 0.0001
      DOML: 0.0
      DOMR: 0.0
      O2:  300.0
    coupling:
      PO4:    B_NUT/PO4
      Si:     B_NUT/Si
      Sipart: B_Si/Sipart
      NH4:    B_NUT/NH4
      NO2:    B_NUT/NO2
      NO3:    B_NUT/NO3
      DIC:    B_C/DIC
      H2S:    B_S/H2S
      Baae:   B_BACT/Baae
      Bhae:   B_BACT/Bhae
      Baan:   B_BACT/Baan
      Bhan:   B_BACT/Bhan
      Hplus:  B_pH/Hplus
    parameters:
      K_phy_gro: 2.2 #1.75 #3.0 #2.7 #4.7 # 3. #4.7
        # Maximum specific growth rate (1/d) = 0.9-1.3 (Savchuk, 2002), 
        # = 3.(Gregoire, Lacroix, 2001) >!0.5 worked for Berre! 
      Iopt: 25.
        # Optimal irradiance (W/m2) =50 (Savchuk, 2002)
      phy_t_dependence: 3   # select dependence of Phy growth rate on temperature:
                            # (1) Old (ERGOM); (2) for Arctic; (3) ERSEM
      K_phy_mrt: 0.15 
        # Specific rate of mortality, (1/d) = 0.3-0.6 (Savchuk, 2002), = 0.05 (Gregoire, Lacroix, 2001)   
      K_phy_exc: 0.10       # Specific rate of excretion, (1/d) = 0.01 (Burchard et al., 2006)
      K_het_phy_gro: 1.2    #! Max.spec. rate of grazing of Zoo on Phy, (1/d), =0.9 (Gregoire, Lacroix, 2001), =1.5 (Burchard et al., 2006)   was 1.1 
      K_het_phy_lim: 0.5    #! Half-sat.const.for grazing of Zoo on Phy for Phy/Zoo ratio
      K_het_pom_gro: 0.5    #! Max.spec.rate of grazing of Zoo on POP, (1/d), =1.2 (Burchard et al., 2006)
      K_het_bac_gro: 0.8    #! Max.spec.rate of grazing of Zoo on bacteria, (1/d)
      K_het_pom_lim: 0.05   #! Half-sat.const.for grazing of Zoo on POP for POP/Zoo  ratio
      K_het_res: 0.10       #! Specific respiration rate =0.02 (Yakushev et al., 2007)
      K_het_mrt: 0.15       #! %! Maximum specific rate of mortality of Zoo (1/d) =0.05 (Gregoire, Lacroix, 2001)  
      Uz: 0.5               #! Food absorbency for Zoo(Het) (nd) =0.5-0.7 (Savchuk, 2002)
      Hz: 0.4               #! Ratio betw. diss. and part. excretes of Zoo (nd), =0.5 (Gregoire, Lacroix, 2001)  
      limGrazBac:  2.       #! Limiting parameter for bacteria grazing by Zoo, =2. (Yakushev et al., 2007)
      K_nox_lim: 0.1        #! Half-sat.const.for uptake of NO3+NO2 (uM) =0.5 (Gregoire, Lacroix, 2001)
      K_nh4_lim: 0.02       #! Half-sat.const.for uptake of NH4 (uM) =0.2 (Gregoire, Lacroix, 2001)
      K_psi: 1.46           #! Strength of NH4 inhibition of NO3 uptake constant (uM-1) =1.46_rk (Gregoire, Lacroix, 2001)
      K_nfix: 0.4           #! Maximum specific rate of N-fixation (1/d) =0.5 (Savchuk, 2002)
      K_po4_lim: 0.012      #! Half-sat. constant for uptake of PO4 by Phy
      K_si_lim: 0.5         #! Half-sat. constant for uptake of Si_lim by Phy
      K_POML_DOML: 0.15       #! Specific rate of Autolysis of POML to DOML
      K_POMR_DOMR: 0.00001       #! Specific rate of Autolysis of POMR to DOMR
      K_POML_ox: 0.02       #! Specific rate of oxidation of POML with O2
      K_POMR_ox: 0.002       #! Specific rate of oxidation of POMR with O2
      K_DOML_ox: 0.10        #! Specific rate of oxidation of DOML with O2
      K_DOMR_ox: 0.10        #! Specific rate of oxidation of DOMR with O2
      K_omox_o2: 1.         #! half sat. of o2 for OM mineralization
      Wsed: 7.0        #! Rate of sinking of detritus (m/d), =0.4 (Savchuk, 2002), =5. (Gregoire, Lacroix, 2001), =1-370 (Alldredge, Gotschalk, 1988)
      Wphy: 0.2        #! Rate of sinking of Phy (m/d), =0.1-0.5 (Savchuk, 2002)
      Whet: 0.3         #! Rate of sinking of Het (m/d), =1. (Yakushev et al., 2007)
      r_n_p: 16.0      #! N[uM]/P[uM]
      r_o_n: 6.625     #! O2[uM]/N[uM]
      r_c_n: 6.625     #! C[uM]/N[uM]  
      r_si_n: 1.0      #! Si[uM]/N[uM]
#----------------------------------------------------------------------
  B_BACT:
#----------------------------------------------------------------------
    long_name: bacteria
    model: niva/brom_bact
    initialization:
      Baae: 0.01
      Bhae: 0.01
      Baan: 0.01
      Bhan: 0.01
    coupling:
      NH4:      B_NUT/NH4
      DOML:     B_BIO/DOML
      DOMR:     B_BIO/DOMR
      POML:     B_BIO/POML
      POMR:     B_BIO/POMR
      O2:       B_BIO/O2
      PO4:      B_NUT/PO4
      DIC:      B_C/DIC
      H2S:      B_S/H2S
      Nitrif1:  B_N/Nitrif1
      Nitrif2:  B_N/Nitrif2
      anammox:  B_N/Anammox
      fe_ox1:   B_Fe/fe_ox1
      fe_rd:    B_Fe/fe_rd
      mn_ox1:   B_Mn/mn_ox1
      mn_rd1:   B_Mn/mn_rd1
      mn_rd2:   B_Mn/mn_rd2
      hs_ox:    B_S/hs_ox
      hs_no3:   B_S/hs_no3
      s2o3_ox:  B_S/s2o3_ox
      s0_ox:    B_S/s0_ox
      DcTOM_O2:  B_BIO/DcTOM_O2
      DcTOM_NOX:   B_N/DcTOM_NOX
      DcTOM_MnX:  B_Mn/DcTOM_MnX
      DcTOM_Fe:   B_Fe/DcTOM_Fe
      DcTOM_SOX:   B_S/DcTOM_SOX
      DcTOM_CH4: B_CH4/DcTOM_CH4
    parameters:
      K_Baae_gro: 0.25
         #!  Baae maximum specific growth rate (1/d) (Yakushev, 2013)
      K_Baae_mrt: 0.005
         #!  Baae specific rate of mortality (1/d) (Yakushev et al., 2013)
      K_Baae_mrt_h2s: 0.899
         #!  Baae increased specific rate of mortality due to H2S (1/d) (Yakushev et al., 2013)
      limBaae: 5.0
         #! Limiting parameter for nutrient consumprion by Baae (nd) (Yakushev, 2013)
      K_Bhae_gro:  0.25
         #!  Bhae maximum specific growth rate (1/d) (Yakushev, 2013)
      K_Bhae_mrt:  0.05
         #!  Bhae specific rate of mortality (1/d) (Yakushev, 2013)
      K_Bhae_mrt_h2s: 0.799
         #!  Bhae increased specific rate of mortality due to H2S (1/d)  (Yakushev, 2013)      
      limBhae: 5.0
         #! Limiting parameter for OM consumprion by Bhae (nd) (Yakushev, 2013)
      K_Baan_gro: 2.5
         #!  Baan maximum specific growth rate (1/d) (Yakushev, 2013)
      K_Baan_mrt: 0.01
         #!  Baan specific rate of mortality (1/d) (Yakushev, 2013)
      limBaan: 5.0
         #! Limiting parameter for nutrient consumprion by Baan (nd) (Yakushev, 2013)
      K_Bhan_gro: 1.50
         #!  Bhan maximum specific growth rate (1/d) (Yakushev, 2013)
      K_Bhan_mrt: 0.01
         #changed for co2marine, test #0.01(worked before) #!  Bhan specific rate of mortality (1/d) (Yakushev, 2013)
      K_Bhan_mrt_o2: 0.899
         #!  Bhan increased specific rate of mortality due to O2 (1/d) (Yakushev, 2013)
      limBhan: 2.0
         #! Limiting parameter for OM consumprion by Bhan (nd) (Yakushev, 2013) 
      Wbact: 0.4
         #! Rate of sinking of bacteria (Bhae,Baae,Bhan,Baan) (1/d), (Yakushev et al.,2007)

#----------------------------------------------------------------------
  B_N:
#----------------------------------------------------------------------
    long_name: nitrogen_cycle
    model: niva/brom_nitrogen
    coupling:
      NH4: B_NUT/NH4
      NO2: B_NUT/NO2
      NO3: B_NUT/NO3
      DIC: B_C/DIC
      O2:  B_BIO/O2
      DOML: B_BIO/DOML
      DOMR: B_BIO/DOMR
      POML: B_BIO/POML
      POMR: B_BIO/POMR
      PO4: B_NUT/PO4
    parameters:
      K_nitrif1: 0.001
         # Spec.rate of 1st st. of nitrification
      K_nitrif2: 0.1
         # Spec.rate of 2d st. of nitrification
      K_POML_NO3: 0.0025
         # Spec.rate of 1 stage of denitrif of POML
      K_POML_NO2: 0.0025
         # Spec.rate of 2 stage of denitrif of POML
      K_POMR_NO3: 0.0000125
         # Spec.rate of 1 stage of denitrif of POMR
      K_POMR_NO2: 0.000125
         # Spec.rate of 2 stage of denitrif of POMR
      K_DOML_NO3: 0.0025
         # Spec.rate of 1 stage of denitrif of DOML
      K_DOML_NO2: 0.0025
         # Spec.rate of 2 stage of denitrif of DOML
      K_DOMR_NO3: 0.000025
         # Spec.rate of 1 stage of denitrif of DOMR
      K_DOMR_NO2: 0.000125
         # Spec.rate of 2 stage of denitrif of DOMR
      K_omno_no3: 0.005
         # Half sat. of no3 for OM denitr. (uM N)
      K_omno_no2: 0.005
         # Half sat. of no2 for OM denitr. (uM N)
      K_annamox: 0.8
         # Spec.rate of Anammox (1/d) (Gregoire, Lacroix, 2001)
      O2s_nf: 5.
         # Threshold of O2 saturation for nitrification (uM)
      O2s_dn: 10.0
         # Threshold of O2 for denitrification, anammox, Mn reduction (uM O2)
      s_OM_refr: 50.0   # threshold of refractory OM for decay
      r_n_p:   16.0  # N[uM]/P[uM] =  16./1.
      r_c_n:   6.625 # C[uM]/N[uM] = 106./16.
      r_n_no3: 0.075 # N[uM]/NO3[uM]= 16./212.
      r_n_no2: 0.113 # N[uM]/NO2[uM]= 16./141.3
#----------------------------------------------------------------------
  B_CH4:
#----------------------------------------------------------------------
    long_name: methane
    model: niva/brom_methane
    parameters:
      s_omso_o2: 25.0
         # threshold of o2 for OM sulfate reduction
      s_omso_no3: 5.0
         # threshold of noX for OM sulfate reduction
      s_omch_so4: 30.
         # Threshold of of SO4 for methane production from OM
      K_DOML_ch4: 0.00014
         # Specific rate of methane production from DON (Lopes et al., 2011)
      K_POML_ch4: 0.00014
         # Specific rate of methane production from POML
      K_POMR_ch4: 0.0000014
         # Specific rate of methane production from POMR
      K_DOMR_ch4: 0.0000014
         # Specific rate of methane production from DOMR
      K_ch4_o2: 0.14
         # Specific rate of oxidation of CH4 with O2 (calculated from XXX, 0.4 1/d for O2= 100)
      K_ch4_so4: 0.0000274
         # Specific rate of oxidation of CH4 with SO4
      s_OM_refr: 100.0   # threshold of refractory OM for decay
      r_n_p: 16.0   # N[uM]/P[uM]
      r_c_n: 6.625  # C[uM]/N[uM]
    initialization:
      CH4: 0.0 
    coupling:
      DIC: B_C/DIC
      O2:  B_BIO/O2
      DOML: B_BIO/DOML
      DOMR: B_BIO/DOMR
      POML: B_BIO/POML
      POMR: B_BIO/POMR
      NO3: B_NUT/NO3
      PO4: B_NUT/PO4
      NH4: B_NUT/NH4
      SO4: B_S/SO4
#----------------------------------------------------------------------
  B_S:
#----------------------------------------------------------------------
    long_name: sulfur_cycle
    model: niva/brom_sulfur
    initialization:
      H2S:    0.0
      S0:     0.0
      S2O3:   0.0
      SO4:    25000.
    coupling:
      NH4: B_NUT/NH4
      NO3: B_NUT/NO3
      DIC: B_C/DIC
      O2:  B_BIO/O2
      DOML: B_BIO/DOML
      DOMR: B_BIO/DOMR
      POML: B_BIO/POML
      POMR: B_BIO/POMR
      PO4: B_NUT/PO4
      NH4: B_NUT/NH4
    parameters:
      K_hs_ox: 0.5
         # Specific rate of oxidation of H2S to S0 with O2 (1/d)
      K_s0_ox: 0.02
         # Specific rate of oxidation of S0 with O2
      K_s2o3_ox: 0.005
        # Specific rate of oxidation of S2O3 with O2
      K_POML_so4: 0.000001
        # Specific rate of POML sulfate reduction with sulfate
      K_POML_s2o3: 0.0001
        # Specific rate of OM sulfate reduction with thiosulfate
      K_POMR_so4: 0.0000000001
        # Specific rate of POML sulfate reduction with thiosulfate
      K_POMR_s2o3: 0.000005
        # Specific rate of POMR sulfate reduction with sulfate
      K_DOML_so4: 0.0000001
        # Specific rate of DOML sulfate reduction with thiosulfate
      K_DOML_s2o3: 0.005
        # Specific rate of DOML sulfate reduction with sulfate
      K_DOMR_so4: 0.000000001
        # Specific rate of DOMR sulfate reduction with thiosulfate
      K_DOMR_s2o3: 0.000005
        # Specific rate of DOMR sulfate reduction with sulfate
      K_s0_disp:  0.001
         # Specific rate of S0 dispropotionation
      K_hs_no3: 0.8
         # Spec.rate of thiodenitrification (1/d)
      K_s0_no3:   0.9   # Specific rate of oxidation of S0 with NO3
      K_s2o3_no3: 0.01  # Specific rate of oxidation of S2O3 with NO3
      s_omso_o2: 25.0   # threshold of o2 for OM sulfate reduction
      s_omso_no3: 5.0   # threshold of noX for OM sulfate reduction
      s_OM_refr: 100.0   # threshold of refractory OM for decay
      r_n_p: 16.0   # N[uM]/P[uM]
      r_c_n: 6.625  # C[uM]/N[uM]
      r_n_s: 0.302  # N[uM]/S[uM]
#----------------------------------------------------------------------
  B_Fe:
#----------------------------------------------------------------------
    long_name: iron
    model: niva/brom_fe
    initialization:
      Fe2:    0.5
      Fe3:    0.0
      FeS:    0.0
      FeCO3:  0.0
      FeS2:   0.0
      Fe3PO42: 0.0
      PO4_Fe3: 0.0
    coupling:
      Mn2:   B_Mn/Mn2
      Mn3:   B_Mn/Mn3
      Mn4:   B_Mn/Mn4
      H2S:   B_S/H2S
      S0:    B_S/S0
      SO4:   B_S/SO4
      Si:    B_NUT/Si
      DIC:   B_C/DIC
      PO4:   B_NUT/PO4
      NH4:   B_NUT/NH4
      O2:    B_BIO/O2
      DOML:   B_BIO/DOML
      DOMR:   B_BIO/DOMR
      POML:   B_BIO/POML
      POMR:   B_BIO/POMR
      Hplus: B_pH/Hplus
    parameters: 
      Wm: 10.0 # (m/d)
        # Rate of accel. sink. of part. with settled metal hydroxides
      K_fe_ox1: 0.5 # (1/d)
        # Specific rate of oxidation of Fe2 to Fe3  with O2:  1.e9 (M/yr) (Boudrau, 1996)
      K_fe_ox2: 0.001 # (1/d)
        # Specific rate of oxidation of Fe2 to Fe3  with MnO2 and Mn(III):
      K_fe_rd: 0.5 # (1/d)
        # Specific rate of reduction of Fe3 to Fe2  with H2S:
      K_fes: 2510. # (uM)
        # FeS equilibrium constant: 2.51e-6 mol/cm3  (Katsev, 2006)
      K_fes_form: 5.e-4 # (1/d)
        # Specific rate of precipitation of FeS from Fe2 with H2S: 4.e-5 (mol/g/yr)  (Katsev, 2006)
      K_fes_diss: 1.0e-5  # (1/d)
        # Specific rate of dissollution of FeS to Fe2 and H2S: 1.e-3 (1/yr) (Katsev, 2006)
      K_fes_ox: 1.0e-5 #0.001 # (1/d)
        # Specific rate of oxidation of FeS with O2: 2.e7 - 3.e5 (M/yr) (VanCapellan, 1996)
      K_DOML_fe: 0.000025 # (1/d)
        # Specific rate of oxidation of DOML with Fe3 (1/day) 5.e-5 (1/d) (Boudrau, 1996)
      K_POML_fe: 0.000005 # (1/d)
        # Specific rate of oxidation of POML with Fe3 (1/day) 1.e-5 (1/d) (Boudrau, 1996)
      K_POMR_fe: 0.0000001 # (1/d)
        # Specific rate of oxidation of POMR with Fe3 (1/day) 1.e-5 (1/d) (Boudrau, 1996)
      K_DOMR_fe: 0.0000001 # (1/d)
        # Specific rate of oxidation of DOMR with Fe3 (1/day) 1.e-5 (1/d) (Boudrau, 1996)
      K_fes2_form: 0.000001 # (1/d)
        # Specific rate of FeS2 formation by FeS oxidation by H2S: 9.e-6 (M/d) (Rickard, Luther, 1997)
      K_fes2_ox: 0.00044 # (1/d)
        # Specific rate of pyrite oxidation by O2: .00044 (1/d) (Bektursunova, 2011)
      s_feox_fe2: 0.001 # (uM Fe)
        # Threshold of Fe2 oxidation
      s_ferd_fe3: 0.01 # (uM Fe)
        # Threshold of Fe3 reduciton (uM Fe)
      K_feco3: 4000. (uM2)
        # Conditional equilibrium constant for FeCO3: 4.e-15 ((mol/cm3)2) (Katsev, 2006)
      K_feco3_diss: 7.e-4 # (1/d)
        # Specific rate of dissolution of FeCO3: 2.5e-1 - 1.e-2 (1/yr) (Wersin, 1990)
      K_feco3_form: 3.e-4 # (1/d)
        # Specific rate of formation of FeCO3: 1.e-6 - 1.e-2 (mol/g/yr) (Wersin, 1990)
      K_feco3_ox: 0.0027 # (1/d)
        # Specific rate of oxidation of FeCO3 with O2: (assumed)
      K_fe3po42: 1800. #0.018 #0.18 # (uM**5)
        #! Conditional equilibrium constant for Fe3PO4: 3.e-50 (mol/cm3)^5  (Katsev, 2006)
      K_fe3po42_diss: 2.7e-3 # (1/d)
        #!Specific rate of dissolution for Fe3PO4: 1. (1/yr)  (Katsev, 2006)
      K_fe3po42_form: 1e-11 #1e-9 # (1/d)
        #!Specific rate of formation for Fe3PO4: 1.7e-9 (mol/g/yr)  (Katsev, 2006)
      K_fe3po42_ox: 0.0027 # (1/d)
        #!Specific rate of oxidation of FeCO3 with O2: (assumed)
      K_ferd_hs:  1.0 # (uM S)
        # half sat. of Fe reduction: (assumed)
      K_omno_no3: 0.001 # (uM N)
        # Half sat. of no3 for OM denitr.: (assumed)
      O2s_dn: 10.0 # (uM O2)
        # Threshold of O2 for denitrification, anammox, Mn reduction: (assumed)
      K_PO4_Fe3: 10000
         #!partitioning coef PO4 on Fe3 
      Sad_Fe3: 0.001
         #!sorption sites on Fe3 0.01 Katsev, 2006
      s_OM_refr: 100.0   # threshold of refractory OM for decay
      r_n_p: 16.0  # N[uM]/P[uM]
      r_c_n: 6.625 # C[uM]/N[uM]
      r_fe_n: 26.5 # Fe[uM]/N[uM] (Boudrau, 1996)
      r_fe3_p: 2.7
        # Fe[uM]/P[uM] partitioning coeff. for Fe oxide (Yakushev, 2007)
      r_fe3_si: 300000.
        #! Fe[uM]/Si[uM] partitioning coeff. for Fe oxide
#----------------------------------------------------------------------
  B_Mn:
#----------------------------------------------------------------------
    long_name: manganese
    model: niva/brom_manganese
    initialization:
      Mn2:    0.5
      Mn3:    0.0
      Mn4:    0.0
      MnS:    0.0
      MnCO3:  0.0
    coupling:
      S0:    B_S/S0
      H2S:   B_S/H2S
      DIC:   B_C/DIC
      PO4:   B_NUT/PO4
      NH4:   B_NUT/NH4
      O2:    B_BIO/O2
      DOML:   B_BIO/DOML
      DOMR:   B_BIO/DOMR
      POML:   B_BIO/POML
      POMR:   B_BIO/POMR
      Hplus:  B_pH/Hplus
    parameters:
      Wm: 10.0 # (m/d)
        # Rate of accel. sink. of part. with settled metal hydroxides
      K_mn_ox1: 0.02 #0.1 # (1/d)
        # Specific rate of oxidation of Mn2 to Mn3 with O2 (Tebo,1991,Yakushev,2007)
      K_mn_ox2: 0.02 #0.2 # (1/d)
        # Specific rate of oxidation of Mn3 to Mn4 with O2 (Tebo,1991,Yakushev,2007)
      K_mn_rd1: 0.2 #0.5 # (1/d)
        # Specific rate of reduction of Mn4 to Mn3 with H2S (Tebo,1991,Yakushev,2007)
      K_mn_rd2: 0.2 #0.5 #1.0 # (1/d)
        # Specific rate of reduction of Mn3 to Mn2 with H2S (Tebo,1991,Yakushev,2007)
      K_mns:  3000. #1500. #7.4e-12 # (uM)
        # Conditional equilibrium constant for MnS from Mn2 with H2S (M) 7.4e-18 M (Brezonik, 2011)
      K_mns_diss: 0.0005 # (1/d)
        # Specific rate of dissolution of MnS to Mn2 and H2S (assumed)
      K_mns_form: 0.0001 # (1/d)
        # Spec. rate of form. of MnS from Mn2 with H2S (assumed)
      K_mns_ox: 0.0027 # (1/d)
        # Specific rate of oxidation of MnS with O2 (assumed)
      K_mnco3: 4000. #1800 #18. # (uM2)
        # Conditional equilibrium constant for MnCO3 1.e-10 - 1.e-13 (M2) (Jensen, 2002)
      K_mnco3_diss: 7.e-4 # (1/d)
        # Specific rate of dissolution of MnCO3 1.e-2 - 1.e3 (1/yr) (Wersin, 1990)
      K_mnco3_form: 3.e-4 # (1/d)
        # Specific rate of formation of MnCO3 1.e-4 - 1.e-2 (mol/g/yr) (Wersin, 1990)
      K_mnco3_ox: 0.0027 # (1/d)
        # Specific rate of oxidation of MnCO3 with O2 (assumed)
      K_DOML_mn4: 0.00005 # (1/d)
        # Specific rate of oxidation of DOML with Mn4 (assumed)
      K_POML_mn4: 0.00005 # (1/d)
        # Specific rate of oxidation of POML with Mn4 (assumed)
      K_POMR_mn4: 0.000001 # (1/d)
        # Specific rate of oxidation of POMR with Mn4 (assumed)
      K_DOMR_mn4: 0.000001 # (1/d)
        # Specific rate of oxidation of DOMR with Mn4 (assumed)
      K_DOML_mn3: 0.0001 # (1/d)
        # Specific rate of oxidation of DOML with Mn3 (assumed)
      K_POML_mn3: 0.0001 # (1/d)
        # Specific rate of oxidation of POML with Mn3 (assumed)
      K_POMR_mn3: 0.000001 # (1/d)
        # Specific rate of oxidation of POMR with Mn3 (assumed)
      K_DOMR_mn3: 0.000001 # (1/d)
        # Specific rate of oxidation of DOMR with Mn3 (assumed)
      s_mnox_mn2: 0.01 # (uM Mn)
        # threshold of Mn2 oxidation (Yakushev, 2007)
      s_mnox_mn3: 0.01 # (uM Mn)
        # threshold of Mn3 oxidation (Yakushev, 2007)
      s_mnrd_mn4: 0.01 # (uM Mn)
        # threshold of Mn4 reduciton  (Yakushev, 2007)
      s_mnrd_mn3: 0.01 # (uM Mn)
        # threshold of Mn3 reduciton  (Yakushev, 2007)
      O2s_dn: 10.0 # (uM O2)
        # Threshold of O2 for denitrification, anammox, Mn reduction (Yakushev, 2007)
      K_mnrd_hs: 1.0 # (uM S)
        # half sat. of Mn reduction (uM S) (Yakushev, 2007)
      K_mnox_o2: 2.0 # (uM O2)
        # Half sat. of Mn oxidation (uM O2) (Yakushev, 2007)
      s_OM_refr: 100.0   # threshold of refractory OM for decay
      r_mn_n: 13.25
        # Mn[uM]/N[uM] (Boudrau, 1996)
      r_mn3_p: 0.67
        # Mn[uM]/P[uM] complex stoichiometric coeff. for Mn(III) (Yakushev, 2007)
      r_n_p: 16.0  # N[uM]/P[uM]
      r_c_n: 6.625 # C[uM]/N[uM]
#----------------------------------------------------------------------
  B_Si:
#----------------------------------------------------------------------
    long_name: silicon
    model: niva/brom_silicon
    initialization:
      Sipart: 0.0
    coupling:
      Si: B_NUT/Si
    parameters:
      Wsed: 7.0 # Rate of sinking of detritus (m/d)
        # Sinking (Gregoire, Lacroix, 2001)
      K_sipart_diss: 0.06
        # Si particulate biogenic dissollution rate constant (1/d) 0.08 (Popova,2004)
      K_sipart_diss_limit: 30.
        # Si particulate maximum concentration (uM), that is biogenic and can be dissolved 
      K_sipart_to_minerals: 0.9
        # Si_part transformation into minerals not modeled here (1/d) (DeMaster, 2003)
      Si_diss_max: 800.
        # Max conc. of diss Si for precipitation (mmol/m**3) (Strakhov, 1978)
#----------------------------------------------------------------------
  B_Bubble:
#----------------------------------------------------------------------
    long_name: bubble
    model: niva/brom_bubble
    initialization:
      CO2g: 0.0
    coupling:
      DIC:  B_C/DIC
      pCO2:  B_C/pCO2
    parameters:
      N_bub: 5000
        # number of bubbles (-)
      R: 8.314 
        # gas constant (n m)/(TK Mol)
      pi: 3.14159
        # Pi number (-)
      TK: 273.15
        # Kelvin to Celsius conversion (deg Kelvin)
      P_A: 101325.0
        # Atmospheric pressure (pa)
      g: 9.8 
        # gravitational acceleration (m/s2)
      sigma: 72.86E-3
        # surface tension for water (N/m)
      Henry: 3.3E-1
        # Henry constant for CO2 (mmol/m3/Pa) 3.3 10-4 mol/m3/Pa (Sanders,2015)
      Df: 1.65e-9
        # CO2 diffusivity (m2/s) 1.65e-9 m2/s(Perry,Green,2008) 1.6e-5 m2/s (Engineering ToolBox,2018)
      K_CO2g_diss: 100
        # rate of dissolutsion of gaseous CO2 (1/day) (100s of seconds for 100% (Liang,2011))
      W_float: -34560.
        # Rate of floating (m/d) 20 cm/sec = *86400(to_day)/100(to_m)= 17280 m/d, here we put upper limit 
##----------------------------------------------------------------------
#  B_Ba:
##----------------------------------------------------------------------
#    long_name: barium
#    model: niva/brom_ba
#    initialization:
#      Ba: 0.0
#      BaSO4: 0.001
#    coupling:
#      SO4: B_S/SO4
#    parameters:
#      Wsed: 5.0 # Rate of sinking of detritus (m/d)
#        # Sinking (Gregoire, Lacroix, 2001)
##----------------------------------------------------------------------
#  B_Ba:
##----------------------------------------------------------------------
#    long_name: barium
#    model: niva/brom_ba
#    initialization:
#      Ba: 0.0
#      BaSO4: 0.001
#    coupling:
#      SO4: B_S/SO4
#    parameters:
#      Wsed: 5.0 # Rate of sinking of detritus (m/d)
#        # Sinking (Gregoire, Lacroix, 2001)
##----------------------------------------------------------------------
#  B_Ni:
##----------------------------------------------------------------------
#    long_name: nickel
#    model: niva/brom_ni
#    initialization:
#      Ni: 0.0
#      NiS: 0.0
#      Ni_POM: 0.0
#      Ni_DOM: 0.0
#      Ni_biota: 0.0
#      Ni_Mn4: 0.0
#      Ni_FeS: 0.0
#      Ni_FeS2: 0.0
#    coupling:
#      H2S: B_S/H2S
#      Mn4: B_Mn/Mn4
#      FeS: B_Fe/FeS
#      FeS2: B_Fe/FeS2
#      O2:  B_BIO/O2
##      Hplus: B_pH/Hplus
#    parameters:
#      K_NiS: 2510.
#        # Solubility Product Constant,   default=2510.0_rk
#      K_NiS_form: 5.e-5 
#        # Specific rate of precipitation of NiS from Ni with H2S',   default=5.e-5_rk
#      K_NiS_diss: 1.e-6 
#        # Specific rate of dissollution of NiS to Ni and H2S',   default=1.e-6_rk
#      K_NiS_ox: 1.e-6 
#        # Specific rate of oxidation of NiS with O2',   default=1.e-6_rk
#      r_mn4_ni: 80.
#        # Mn4[uM]/Ni[uM] partitioning coeff. for Mn4 (REF)
#      r_fes_ni: 833.    
#        # FeS[uM]/Ni[uM] partitioning coeff. for FeS (REF)
#      r_fes2_ni: 600.
#        # FeS2[uM]/Ni[uM] partitioning coeff. for FeS2 (REF)
#      Wsed: 5.0 
#        #! Rate of sinking of detritus (m/d), =0.4 (Savchuk, 2002), 
#        # =5. (Gregoire, Lacroix, 2001), =1-370 (Alldredge, Gotschalk, 1988)
#      Wphy: 0.2
#        #! Rate of sinking of Phy (m/d), =0.1-0.5 (Savchuk, 2002)
#      Wm: 10.0
#        #  Rate of accel. sink. of metal  (m/d)
##      KNi_Mn4: 100000
#        #!partitioning coef Ni on Mn4 
##      Sad_Mn4: 0.001
#        #!sorption sites on Fe3 0.01 Katsev, 2006??????
##      KNi_FeS: 100000
#        #!partitioning coef Ni on FeS 
##      Sad_FeS: 0.001
#        #!sorption sites on Fe3 0.01 Katsev, 2006??????
##      KNi_FeS2: 100000
#        #!partitioning coef Ni on FeS 
##      Sad_FeS2: 0.001
#        #!sorption sites on Fe3 0.01 Katsev, 2006??????
#      Rel: 1.0
#        #  Coeff. of relaxation  (-)
##----------------------------------------------------------------------
#  B_PART:
##----------------------------------------------------------------------
#    long_name: partitioning
#    model: niva/brom_partitioning
#    coupling:
#      Subst_biota: B_Ni/Ni_biota 
#      Subst_POM: B_Ni/Ni_POM
#      Subst_DOM: B_Ni/Ni_DOM
#      Subst_dis: B_Ni/Ni
#      Subst_miner: B_Ni/NiS
#      Baae:   B_BACT/Baae
#      Bhae:   B_BACT/Bhae
#      Baan:   B_BACT/Baan
#      Bhan:   B_BACT/Bhan
#      DOMR:   B_BIO/DOMR
#      POMR:   B_BIO/POMR
#      DOML:   B_BIO/DOML
#      POML:   B_BIO/POML
#      Phy:    B_BIO/Phy
#      Het:    B_BIO/Het
#----------------------------------------------------------------------
# REFERENCES:
#  Alldredge, A.L. and Gotschalk, C., 1988. In situ settling behavior of marine snow. Limnology and Oceanography, 33(3), pp.339-351.
#  Boudreau, B. P.: A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments, Comput. Geosci., 22(5), 479-496, doi:10.1016/0098-3004(95)00115-8, 1996.
#  Burchard H., Bolding K., Khn W., Meister A., Neumann T. and Umlauf L., 2006. Description of a flexible and extendable physicalbiogeochemical model system for the water column. Journal of Marine Systems, 61(3), 180-211.
#  Dickson AG. 1990. Thermodynamics of the dissociation of boric acid in synthetic seawater from 273.15 to 318.15 K. Deep-Sea Research Part a-Oceanographic Research Papers. 37:755-766
#  Dickson, A.G., Sabine, C.L. and Christian, J.R., 2007. Guide to Best Practices for Ocean CO2 Measurements.
#  DOE (1994) Handbook of methods for the analysis of the various parameters of the carbon dioxide system in sea water; version 2, A. G. Dickson & C. Goyet, eds., ORNL/CDIAC-74.
#  Gregoire M. and Lacroix G., 2001. Study of the oxygen budget of the Black Sea waters using a 3D coupled hydrodynamicalbiogeochemical model. Journal of marine systems, 31(1), pp.175-202.
#  Konovalov, S.K., Murray, J.W., Luther, G.W.,  Tebo, B.M., 2006. Processes controlling the Redox budget for oxic/anoxic water column of the Black Sea. Deep Sea Research (II) 53: 1817-1841. 
#  Link JS, Griswold CA, Methratta ET, Gunnard J, Editors. 2006. Documentation for the Energy Modeling and Analysis eXercise (EMAX). US Dep. Commer., Northeast Fish. Sci. Cent. Ref. Doc. 06-15; 166 p.
#  Millero FJ , 1995 Thermodynamics of the carbon dioxide system in the oceans. Geochimica et Cosmochimica Acta 59 (4), 661-677
#  Luff R., Haeckel M., and Wallmann K. 2001. Robust and fast FORTRAN and MATLAB libraries to calculate pH distributions in marine systems, Comput. Geosci., 27, 157169
#  Popova EE, Srokosz MA. 2009. Modelling the ecosystem dynamics at the Iceland-Faeroes Front: Biophysical interactions, J. Mar. Syst., 77(1-2), 182196, doi:10.1016/j.jmarsys.2008.12.005, 2009.
#  Savchuk O. 2002. Nutrient biogeochemical cycles in the Gulf of Riga: scaling up field studies with a mathematical model. J. Mar. Syst. 32: 253-280.
#  Volkov II. 1984. Geokhimiya Sery v Osadkakh Okeana (Geochemistry of Sulfur in Ocean Sedi-ments), Nauka, Moscow, USSR.
#  Van Cappellen P., Wang, Y. F. 1996: Cycling of iron and manganese in surface sediments: A general theory for the coupled transport and reaction of carbon, oxygen, nitrogen, sulfur, iron, and manganese, Am. J. Sci., 296(3), 197243, doi:10.2475/ajs.296.3.197, 1996.
#  Weiss RF. 1974 Carbon dioxide in water and seawater: the solubility of a non-ideal gas.Marine Chemistry 2:203-215.
#  Yakushev E., Neretin L., 1997. One-dimensional modelling of nitrogen and sulphur cycles in the aphotic zones of the Black Sea and Arabian Sea. Global Biogeochem. Cycles 11 3.,401414.
#  Yakushev EV, Pollehne F., Jost G., Kuznetsov I., Schneider B., Umlauf L. 2007. Analysis of the water column oxic/anoxic interface in the Black and Baltic seas with a numerical model, Mar. Chem., 107(3), 388410.
#  Yakushev E. 2013. RedOx Layer Model: A Tool for Analysis of the Water Column Oxic/Anoxic Interface Processes. 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 !!!!