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fabm-niva-oxydep-bioplast.yaml
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fabm-niva-oxydep-bioplast.yaml
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# 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:
#--------------------------------------------------------------------------
# niva_oxydep:
#----------------------------------------------------------------------
B_OXYDEP:
#----------------------------------------------------------------------
long_name: oxydep
model: niva/oxydep
initialization:
Phy: 0.01
Het: 0.01
POM: 0.01
DOM: 0.0
NUT: 5.
Oxy: 200.
parameters:
# Oxy
O2_suboxic: 30. # O2 threshold for oxic/suboxic switch (mmol/m3)
# PHY
Max_uptake: 2.7 # Maximum nutrient uptake rate (1/d)
Knut: 0.8 # 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)
t_upt_min: 10. # Low t limit for uptake rate dependence on t
t_upt_max: 32. # High t limit for uptake rate dependence on t
# 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: 0.17 # Specific rate of Phy excretion, (1/d)
r_phy_pom_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: 0.4 # Max.spec. rate of grazing of ZOO on PHY, (1/d)
Kphy: 0.3 # 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: 0.02 # Specific ZOO mortality rate (1/d)
uz: 0.6 # Food absorbency for Zoo (nd)
hz: 0.5 # Ratio between diss. and part. excretes of Zoo (nd)
# POM
r_pom_dom: 0.005 # Specific rate of POM decomposition, (1/d)
r_pom_nut_oxy: 0.005 # Specific rate of POM oxic decay, (1/d)
r_pom_nut_nut: 0.003 # Specific rate of POM denitrification, (1/d)
# DOM
r_dom_nut_oxy: 0.015 # Specific rate of DOM oxic decay, (1/d)
r_dom_nut_nut: 0.010 # 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: 0.4 # 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: 20. # 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: -0.25 # PHY sinking rate, (m/d), negative for downward movement
Whet: -0.4 # HET sinking rate, (m/d)
Wpom: -15. # POM sinking rate, (m/d)
##----------------------------------------------------------------------
B_BIOPLAST:
##----------------------------------------------------------------------
long_name: bioplast
model: niva/brom_bioplast
initialization:
MP_free: 0.0
MP_biof: 0.0
MP_het: 0.0
MP_det: 0.0
coupling:
HET: B_OXYDEP/Het
PHY: B_OXYDEP/Phy
POM: B_OXYDEP/POM
DOM: B_OXYDEP/DOM
MortHet: B_OXYDEP/MortHet
POM_decay_ox: B_OXYDEP/POM_decay_ox
POM_decay_denitr: B_OXYDEP/POM_decay_denitr
GrowthPhy: B_OXYDEP/GrowthPhy
RespPhy: B_OXYDEP/RespPhy
ExcrPhy: B_OXYDEP/ExcrPhy
MortPhy: B_OXYDEP/MortPhy
GrazPhy: B_OXYDEP/GrazPhy
GrazPOM: B_OXYDEP/GrazPOM
RespHet: B_OXYDEP/RespHet
Autolys: B_OXYDEP/Autolys
parameters:
# Degradation
MP_free_decay: 0.0000 # maximum rate of photodegradation in seawater 0.00017 (1/d) reported (Andrady, 2011, Brandon et al., 2016)
MP_biof_decay: 0.0000 # mean rate of degradation (weight loss) due to biofouling 0.00012 (1/d) (Muthukumar et al., 2011. Table 2)
MP_det_decay: 0.0000 # maximum rate of degradation of plastic in detrit (1/d) CHANGE
# Biofouling and ingestion parameters
MP_free_biof: 0.00 #0.5 # maximum rate of biofouling of MP_free (1/d) CHANGE NO
# rate_het_filtr: 7 #00001 # NOT THIS: rate of filtration by het ((m3/mmolN/m3)/d) FIND IN SAVCHUK BOOK
max_free_het: 1. #1.9 #0.50 #17 # maximum rate of ingestion of MP_free by het
thr_free: 0.01 # threshold constant for ingestion of MP_free by het
max_biof_het: 0. #0.50 #17 # maximum rate of ingestion of MP_biof by het
thr_biof: 0.01 # threshold constant for ingestion of MP_biof by het
Kmp_phy: 10. # "partitioning" coefficient for MP at Phy
# Sinking
Wfree: -0.0 #-0.0 # MP free sinking rate, (m /d) "-" is needed for using with FVCOM
Wbiof: -0.25 # -0.1 # MP biofouled sinking rate, (m/d) "-" is needed for using with FVCOM
Whet: -0.4 # HET sinking rate, (m/d)
Wpom: -15. # POM sinking rate, (m/d)
# from OxyDep
uz: 0.6 # Food absorbance for Zoo (nd)
hz: 0.5 # Ratio between diss. and part. excretes of Zoo (nd)