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fabm-niva-brom.yaml
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fabm-niva-brom.yaml
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require_initialization: true
instances:
#--------------------------------------------------------------------------
niva_brom_eqconst:
#--------------------------------------------------------------------------
niva_brom_carb:
initialization:
Alk: 2200.
DIC: 2100.
coupling:
Kc0: niva_brom_eqconst/Kc0
Kc1: niva_brom_eqconst/Kc1
Kc2: niva_brom_eqconst/Kc2
Kw: niva_brom_eqconst/Kw
Kb: niva_brom_eqconst/Kb
Kp1: niva_brom_eqconst/Kp1
Kp2: niva_brom_eqconst/Kp2
Kp3: niva_brom_eqconst/Kp3
Knh4: niva_brom_eqconst/Knh4
Kh2s: niva_brom_eqconst/Kh2s
# Kh2s2: niva_brom_eqconst/Kh2s2
KSi: niva_brom_eqconst/KSi
kso4: niva_brom_eqconst/kso4
kflu: niva_brom_eqconst/kflu
tot_free: niva_brom_eqconst/tot_free
# Constants calculated: Kc0 (Weiss, 1974), Kc1, Kc2 (Roy et al., 1993), Kw, Kp1,Kp2,Kp3 (DOE, 2004),
# Kb (Dickson,1990), KSi(Millero,1995), Knh4, Kh2s1(Luff et al, 2001), Kh2s2(Volkov 1984)
# dissociation for B, F according to (Dickson et al., 2007), more references in the code.
PO4: niva_brom_bio/PO4
NH4: niva_brom_bio/NH4
DON: niva_brom_bio/DON
Si: niva_brom_redox/Si
H2S: niva_brom_redox/H2S
Mn3: niva_brom_redox/Mn3
Mn4: niva_brom_redox/Mn4
Fe3: niva_brom_redox/Fe3
SO4: niva_brom_redox/SO4
#--------------------------------------------------------------------------
niva_brom_bio:
initialization:
O2: 200.
Phy: 0.01
Het: 0.01
PON: 0.01
DON: 0.0
NO3: 5.
PO4: 1.
NH4: 0.0
parameters:
# ---- Phy ----------
K_phy_gro: 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)
bm: 0.12 # Coefficient for growth dependence on t
cm: 1.4 # Coefficient for growth dependence on t
K_phy_mrt: 0.20 # 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)
# ----Het -----------
K_het_phy_gro: 1.1 #! Max.spec. rate of grazing of Zoo on Phy, (1/d), =0.9 (Gregoire, Lacroix, 2001), =1.5 (Burchard et al., 2006)
K_het_phy_lim: 0.5 #! Half-sat.const.for grazing of Zoo on Phy for Phy/Zoo ratio
K_het_pom_gro: 0.50 #! Max.spec.rate of grazing of Zoo on POP and bacteria, (1/d), =1.2 (Burchard et al., 2006)
K_het_pom_lim: 0.05 #! Half-sat.const.for grazing of Zoo on POP for POP/Zoo ratio
K_het_res: 0.02 #! Specific respiration rate =0.02 (Yakushev et al., 2007)
K_het_mrt: 0.05 #! %! Maximum specific rate of mortality of Zoo (1/d) =0.05 (Gregoire, Lacroix, 2001)
Uz: 0.5 #! Food absorbency for Zoo (nd) =0.5-0.7 (Savchuk, 2002)
Hz: 0.5 #! 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)
# ----N -------------
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)
# ----P ------------
K_po4_lim: 0.012 #! Half-sat. constant for uptake of PO4 by Phy
# ----Si------------
K_si_lim: 0.1 #! Half-sat. constant for uptake of Si_lim by Phy
# ----Sinking-------
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)
Whet: 1. #! Rate of sinking of Het (m/d), =1. (Yakushev et al., 2007)
# ---- Stoichiometric coefficients ----
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]
coupling:
NO2: niva_brom_redox/NO2
H2S: niva_brom_redox/H2S
Baan: niva_brom_redox/Baan
Baae: niva_brom_redox/Baae
Bhae: niva_brom_redox/Bhae
Bhan: niva_brom_redox/Bhan
Si: niva_brom_redox/Si
Sipart: niva_brom_redox/Sipart
DIC: niva_brom_carb/DIC
Alk: niva_brom_carb/Alk
Hplus: niva_brom_carb/Hplus
# Kp1: niva_brom_eqconst/Kp1
# Kp2: niva_brom_eqconst/Kp2
# Kp3: niva_brom_eqconst/Kp3
# Knh4: niva_brom_eqconst/Knh4
# KSi: niva_brom_eqconst/KSi
#--------------------------------------------------------------------------
niva_brom_redox:
initialization:
Mn2: 0.0
Mn3: 0.0
Mn4: 0.0
MnS: 0.0
MnCO3: 0.0
Fe2: 0.0
Fe3: 0.0
FeS: 0.0
FeCO3: 0.0
NO2: 0.0
Si: 0.0
Sipart: 0.0
H2S: 0.0
S0: 0.0
S2O3: 0.0
SO4: 25000.
Baae: 0.01
Bhae: 0.01
Baan: 0.01
Bhan: 0.01
CaCO3: 5.0
CH4: 0.001
FeS2: 0.0
parameters:
# ---- Model parameters ------
Wbact: 0.4 #! Rate of sinking of bacteria (Bhae,Baae,Bhan,Baan) (1/d), (Yakushev et al.,2007)
Wm: 7.0 #! Rate of accelerated sinking of particles with settled metal hydroxides (1/d), (Yakushev et al.,2007)
# specific rates of biogeochemical processes
#---- Mn---------
K_mn_ox1: 0.1 #! Specific rate of oxidation of Mn2 to Mn3 with O2 (1/d).
K_mn_ox2: 0.2 #! Specific rate of oxidation of Mn3 to Mn4 with O2 (1/d)
K_mn_rd1: 0.5 #! Specific rate of reduction of Mn4 to Mn3 with H2S (1/d)
K_mn_rd2: 1.0 #! Specific rate of reduction of Mn3 to Mn2 with H2S (1/d)
K_mns: 1500. #! Conditional equilibrium constant for MnS from Mn2 with H2S (M)
K_mns_diss: 0.0005 #! Specific rate of dissolution of MnS to Mn2 and H2S (1/d)
K_mns_form: 0.00001 #! Specific rate of formation of MnS from Mn2 with H2S (1/d)
K_mnco3: 1. #! Conditional equilibrium constant % 1.8e-11 (M) (Internet) 1 uM2 for Mn2+CO3->MnCO3 (Meysman,2003)
K_mnco3_diss: 7.e-7 #! Specific rate of dissolution of MnCO3 (1/d) =6.8e-7 (2.5 X 10-1 yr-1 (Van Cappellen, Wang, 1996) !1x10-4 yr-1) (Hunter et al, 98)
K_mnco3_form: 0.1e-4 #! Specific rate of formation of MnCO3 (1/d) =2.7e-7 (1. X 10-4 yr-1 (Van Cappellen, Wang, 1996)!1x10-4 yr-1) (Hunter et al, 98))
K_mnco3_ox: 0.0027 #! Specific rate of oxidation of MnCO3 with O2 (1/d)=0.0027 ( 1x10^(-6) M/yr (Van Cappellen, Wang, 1996).
K_DON_mn: 0.001 #! Specific rate of oxidation of DON with Mn4 (1/d)
K_PON_mn: 0.001 #! Specific rate of oxidation of PON with Mn4 (1/d)
s_mnox_mn2: 0.01 #! threshold of Mn2 oxidation (uM Mn) (Yakushev et al.,2007)
s_mnox_mn3: 0.01 #! threshold of Mn3 oxidation (uM Mn) (Yakushev et al.,2007)
s_mnrd_mn4: 0.01 #! threshold of Mn4 reduciton (uM Mn) (Yakushev et al.,2007)
s_mnrd_mn3: 0.01 #! threshold of Mn3 reduciton (uM Mn) (Yakushev et al.,2007)
#---- Fe---------
K_fe_ox1: 0.5 #!Specific rate of oxidation of Fe2 to Fe3 with O2 (1/d), =4. (Konovalov et al., 2006)
K_fe_ox2: 0.001 #!0.1! Specific rate of oxidation of Fe2 to Fe3 with MnO2 (1/d) =0.74 (Konovalov et al., 2006); 3x10^6 1/(M yr) is estimated in Van Cappellen-Wang-96
K_fe_rd: 1.2 #!0.5! Specific rate of reduction of Fe3 to Fe2 with H2S (1/day) *=0.05 (Konovalov et al., 2006)
K_fes: 2510.0 #!FeS equilibrium constant (Solubility Product Constant) (uM)=2510 ( 2.51x10-6 mol cm-3, Bektursuniva,11)
K_fes_form: 5.e-4 #!Specific rate of precipitation of FeS from Fe2 with H2S (1/day)=1.e-5 (4x10-3 1/yr, Bektursunova,11)
K_fes_diss: 1.e-6 #!Specific rate of dissollution of FeS to Fe2 and H2S (1/day)=3.e-6 (1x10-3 1/yr, Bektursunova,11)
K_fes_ox: 0.001 #!Specific rate of oxidation of FeS with O2 (1/day)=0.001(3x10^5 1/(M yr),(Van Cappellen, Wang, 1996)
K_DON_fe: 0.00005 #!-0.0003 ! % Specific rate of oxidation of DON with Fe3 (1/day)
K_PON_fe: 0.00001 #!-0.0001 ! % Specific rate of oxidation of PON with Fe3 (1/day)
K_fes2_form: 1.e-6 #!specific rate of FeS2 formation by FeS oxidation by H2S (1/day)=0.000009 (10^(-4) L/mol/s (Rickard-97)
K_fes2_ox: 4.38e-4 #!specific rate of pyrite oxidation by O2 (1/uM/d)=4.38x10^(-4) 1/micromolar/day (Wijsman et al -2002).
s_feox_fe2: 0.001 #!threshold of Fe2 reduciton
s_ferd_fe3: 0.01 #!threshold of Fe3 reduciton (uM Fe)
K_feco3: 15. #!10. !2.e-2 ! Conditional equilibrium constant % 1.8e-11 (M) (Internet) 1 uM2 for Mn2+CO3->FeCO3 (Meysman,2003)
K_feco3_diss: 7.e-4 #!Specific rate of dissolution of FeCO3 (1/day)=6.8e-7 !2.5 X 10-1 yr-1 (Van Cappellen, Wang, 1996) !1x10-4 yr-1 (Hunter et al, 98)
K_feco3_form: 3.e-4 #!Specific rate of formation of FeCO3 (1/day)=2.7e-7 !! 1. X 10-4 yr-1(Van Cappellen, Wang, 1996)!1x10-4 yr-1 (Hunter et al, 98)
K_feco3_ox: 0.0027 #!Specific rate of oxidation of FeCO3 with O2 (1/day)=0.0027 ( 1x10^(-6) M/yr (Van Cappellen, Wang, 1996).
#---- S---------
K_hs_ox: 0.5 #! Specific rate of oxidation of H2S to S0 with O2 (1/d), =0.1 (Gregoire, Lacroix, 2001)
K_s0_ox: 0.02 #! 0.02 Specific rate of oxidation of S0 with O2 (1/d), (Yakushev, Neretin,1997)
K_s2o3_ox: 0.01 #! Specific rate of oxidation of S2O3 with O2 (1/d), (Yakushev, Neretin,1997)
K_so4_rd: 5.e-6 #! Specific rate of OM sulfate reduction with sulfate (1/d), (Yakushev, Neretin,1997)
K_s2o3_rd: 0.001 #! Specific rate of OM sulfate reduction with thiosulfate (1/d) (Yakushev, Neretin,1997)
K_s0_disp: 0.001 #! Specific rate of S0 dispropotionation (1/d) (Yakushev,2013)
K_s0_no3: 0.9 #! Specific rate of oxidation of S0 with NO3 (1/d) (Yakushev,2013)
K_s2o3_no3: 0.01 #! Specific rate of oxidation of S2O3 with NO3 (1/d) (Yakushev,2013)
K_mnrd_hs: 1.0 #! half sat. of Mn reduction (uM S) (Yakushev,2013)
K_ferd_hs: 1.0 #! half sat. of Fe reduction (uM S) (Yakushev,2013)
#---- N---------!
K_DON_ox: 0.05 #! Specific rate of oxidation of DON with O2 (1/d) = 0.1(Savchuk, 2002)
K_PON_ox: 0.002 #! Specific rate of oxidation of PON with O2 (1/d) =0.002 (Savchuk, 2002), =0.07 (Gregoire, Lacroix, 2001)
Tda: 13.0 #! Temperature control coefficient for OM decay (Burchard et al., 2006)
beta_da: 20.0 #! Temperature control coefficient for OM decay (Burchard et al., 2006)
K_omox_o2: 1.0 #! Half sat. of o2 for OM mineralization (uM) (Yakushev,2013)
K_PON_DON: 0.1 #! Specific rate of Autolysis of PON to DON (1/d), =0.02 (Burchard et al., 2006)
K_nitrif1: 0.01 #! Spec.rate of 1st st. of nitrification, (1/d), =0.01 (Yakushev,2013) =0.1(Savchuk, 2002) =0.1 (Gregoire, Lacroix, 2001)
K_nitrif2: 0.1 #! Spec.rate of 2d st. of nitrification, (1/d), =0.1 (Yakushev,2013)
K_denitr1: 0.16 #! Spec.rate of 1 stage of denitrif =0.16 (Yakushev, Neretin,1997),= 0.5(Savchuk, 2002),= 0.015(Gregoire, Lacroix, 2001)
K_denitr2: 0.25 #! Spec.rate of 2 stage of denitrif =0.22 (Yakushev, Neretin,1997)
K_omno_no3: 0.001 #! Half sat. of no3 for OM denitr. (uM N) (Yakushev,2013)
K_omno_no2: 0.001 #! Half sat. of no2 for OM denitr. (uM N) (Yakushev,2013)
K_hs_no3: 0.8 #! Spec.rate of thiodenitrification (1/d), =.015 (Gregoire, Lacroix, 2001)
K_annamox: 0.8 #! Spec.rate of Anammox (1/d), (Gregoire, Lacroix, 2001)
#---- O2--------!
O2s_nf: 5. #! threshold of O2 saturation for nitrification, (uM), =10. (Gregoire, Lacroix, 2001)
O2s_dn: 10.0 #! threshold of O2 for denitrification, anammox, Mn reduction (uM O2), =40 (0.72 mgO2/l) (Savchuk, 2002)
s_omox_o2: 0.01 #! threshold of o2 for OM mineralization (uM O2) (Yakushev,2013)
s_omno_o2: 25.0 #! threshold of o2 for OM denitrification (uM O2) (Yakushev,2013)
s_omso_o2: 25.0 #! threshold of o2 for OM sulfate reduction (uM O2) (Yakushev,2013)
s_omso_no3: 5.0 #! threshold of noX for OM sulfate reduction (uM O2) (Yakushev,2013)
K_mnox_o2: 2.0 #! half sat. of Mn oxidation (uM O2) (Yakushev,2013)
#---- C--------!
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))
K_DON_ch4: 0.00014 #! Specific rate of methane production from DON (1/d) (Lopes et al., 2011)
K_PON_ch4: 0.00014 #! Specific rate of methane production from PON (1/d) (Lopes et al., 2011)
K_ch4_o2: 0.14 #! Specific rate of oxidation of CH4 with O2 (1/d) =0.14 (Lopes et al., 2011)
K_ch4_so4: 0.0000274 #! Specific rate of oxidation of CH4 with SO4 (1/uM/day) (0.0274 m3 /mol-1 day-1 Lopes et al., 2011)
s_omch_so4: 30. #! threshold of of SO4 for methane production from OM (uM) (Lopes et al., 2011)
#---- Si-------!
K_sipart_diss: 0.080 #! Si dissollution rate constant (1/d), =0.008 (Popova, Srokosz, 2009)
#---- Bacteria-!
K_Baae_gro: 0.1 #! 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: 2.0 #! Limiting parameter for nutrient consumprion by Baae (nd) (Yakushev, 2013)
K_Bhae_gro: 0.5 #! Bhae maximum specific growth rate (1/d) (Yakushev, 2013)
K_Bhae_mrt: 0.01 #! 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: 0.2 #! Baan maximum specific growth rate (1/d) (Yakushev, 2013)
K_Baan_mrt: 0.005 #! Baan specific rate of mortality (1/d) (Yakushev, 2013)
limBaan: 2.0 #! Limiting parameter for nutrient consumprion by Baan (nd) (Yakushev, 2013)
K_Bhan_gro: 0.15 #! Bhan maximum specific growth rate (1/d) (Yakushev, 2013)
K_Bhan_mrt: 0.01 #! 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)
#---- Stoichiometric coefficients ----!
r_fe_n: 26.5 #! Fe[uM]/N[uM] (Boudreau, 1996)
r_mn_n: 13.25 #! Mn[uM]/N[uM] (Boudreau, 1996)
f: 0.66 #! conversion factor relating solid and dissolved species concentrations
r_fe3_p: 2.7 #! Fe[uM]/P[uM] partitioning coeff. for Fe oxide (Yakushev et al., 2007)
r_mn3_p: 0.67 #! Mn[uM]/P[uM] complex stoichiometric coeff. for Mn(III) (Yakusheve al., 2007)
r_fe3_si: 3. #! Fe[uM]/Si[uM] partitioning coeff. for Fe oxide
coupling:
O2: niva_brom_bio/O2 # O2: niva_oxydep/oxy
NH4: niva_brom_bio/NH4
NO3: niva_brom_bio/NO3
PO4: niva_brom_bio/PO4
PON: niva_brom_bio/PON
DON: niva_brom_bio/DON
# Wsed: niva_brom_bio/Wsed
Kp1: niva_brom_eqconst/Kp1
Kp2: niva_brom_eqconst/Kp2
Kp3: niva_brom_eqconst/Kp3
Knh4: niva_brom_eqconst/Knh4
Kh2s: niva_brom_eqconst/Kh2s
KSi: niva_brom_eqconst/KSi
Kc0: niva_brom_eqconst/Kc0
Alk: niva_brom_carb/Alk
DIC: niva_brom_carb/DIC
Hplus: niva_brom_carb/Hplus
Om_Ca: niva_brom_carb/Om_Ca
Om_Ar: niva_brom_carb/Om_Ar
CO3: niva_brom_carb/CO3
pCO2: niva_brom_carb/pCO2
Ca: niva_brom_carb/Ca
# 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), 479496, doi:10.1016/0098-3004(95)00115-8, 1996.
# Burchard H., Bolding K., Kühn 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.
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