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fabm-jrc-bsem.yaml
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fabm-jrc-bsem.yaml
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require_initialization: true
instances:
bsem:
model: jrc/bsem
parameters:
fluff: false # include fluff layer (-), default = false
sfl_ni: 0.0 # constant surface nitrate flux (mmol N/m2/d), default = 0.0
sfl_am: 0.0 # mmolminimum phyto small concentration?? (mmol N/m3), default = 0.0
pl0: 0.0225 # minimum phyto large concentration (mmol N/m3), default = 0.0225
ps0: 0.0225 # minimum phyto small concentration (mmol N/m3), default = 0.0225
alpha_l: 0.8 # initial slope of P-I curve for large phyto (-), default = 0.8
alpha_s: 0.35 # initial slope of P-I curve for small phyto (-), default = 0.35
sigma_l: 1.2 # maximum growth rate large phyto (1/d), default = 1.2
sigma_s: 1.0 # maximum growth rate small phyto (1/d), default = 1.0
beta_l: 0.0015 # initial slope of P-I curve for large phyto (-), default = 0.0015
beta_s: 0.35 # initial slope of P-I curve for small phyto (-), default = 0.35
kb: 0.01 # shelf shading attenuation (-), default = 0.01
ka_l: 0.3 # half-saturation for amm uptake large phyto (-), default = 0.3
ka_s: 0.2 # half-saturation for amm uptake small phyto (-), default = 0.2
kn_l: 0.5 # half-saturation for ni uptake large phyto (-), default = 0.5
kn_s: 0.3 # half-saturation for ni uptake small phyto (-), default = 0.3
mpl: 0.05 # mortality rate for large phyto (1/d), default = 0.005
mps: 0.06 # mortality rate for small phyto (1/d), default = 0.006
Q10: 2.0 # temperature control of large phytoplankton growth (-), default = 2.0
phyZ: 0.7 # Phytoplankton assimilation efficiency (-), default = 0.7
g_zs: 0.8 # maximum grazing rate of zoo small (1/d), default = 0.8
g_zl: 0.5 # maximum grazing rate of zoo large (1/d), default = 0.5
g_zn: 0.5 # maximum grazing rate of noctiluca (1/d), default = 0.5
g_zg: 0.15 # maximum grazing rate of gelatinous zoo (1/d), default = 0.15
k_zs: 0.4 # half-sat cte for zoo small grazing (-), default = 0.4
k_zl: 0.5 # half-sat cte for zoo large grazing (-), default = 0.5
k_zn: 0.4 # half-sat cte for zoo noctiuca grazing (-), default = 0.4
kn_zg: 0.25 # half-sat cte for zoo gelatinous grazing (-), default = 0.25
mzs: 0.1 # mortality rate of zoo small (1/d), default = 0.1
mzl0: 0.25 # default mortality rate of zoo large (1/d), default = 0.25
mzn: 0.15 # mortality rate of noctiluca (1/d), default = 0.15
mnzg: 0.02 # mortality rate of gelatinous (1/d), default = 0.02
mpzg0: 0.1 # default predation mortality rate of zoo gelatinous (1/d), default = 0.1
mu_zs: 0.06 # excretion rate of zoo small (1/d), default = 0.06
mu_zl: 0.05 # excretion rate of zoo large (1/d), default = 0.05
mu_zn: 0.06 # excretion rate of zoo noctiluca (1/d), default = 0.06
mu_zg: 0.08 # excretion rate of zoo gelatinous (1/d), default = 0.08
epsilon_n0: 0.05 # default remineralisation rate of dn (1/d), default = 0.05
R0: 150.0 # half-sat value for dn remineralisation (-), default = 150.0
w_dn: 5.0 # Detritus sedimentation rate (m/d), default = 5.0
r_n0: 0.1 # default nitrification rate (1/d), default = 0.1
r_a0: 0.01 # Amm oxid rate by nit (1/d), default = 0.1
r_s: 0.001 # HS oxid rate by nit (1/d), default = 0.1
r_o: 0.1 # HS oxid rate by oxyg (1/d), default = 0.1
r_u: 0.0 # HS oxid rate by other procc (1/d), default = 0.1
s1: 5.3 # reduced nitrate/oxidized detritus (-), default = 5.3
s2: 6.625 # oxygen production/recycled nitrogen (-), default = 6.625
s4: 2.0 # nitrification (-), default = 6.625
lds: 3.5 # rate of detritus sinking into sediment (m/d), default = 3.5
lsd: 25.0 # rate of sediment resuspension (1/d), default = 25.0
tau_crit: 0.07 # critical bottom stress (N /m2), default = 0.07
lsa: 0.001 # rate of sediment mineralisation (1/d), default = 0.001
bsa: 0.15 # temperature control of sediment mineralisation (1/deg C), default = 0.15
pvel_c: 4.5 # A constant for adjusting oxygen flux (-), default = 3.5
temp_bio_high: 25.0 # Upper temperature control of biological reactions (deg C), default = 20.0
temp_bio_low: 5.0 # Lower temperature control of biological reactions (deg C), default = 5.0
par_lim: 75.0 # PAR limitation for photo inhibition (W/m**2), default = 75.0
temp_zg_lim: 16.0 # Gelationous zooplankton critical temperature (deg C), default = 16.0
ox_zoop_grazing: 200.0 # Oxygen control for zooplankton grazing (mmol O2/m3), default = 200.0
ox_min: 0.05 # Oxygen minimum allowed value (mmol O2/m3), default = 0.05
ox_lim_exc: 300.0 # Oxygen control for zooplankton excretion (mmol O2/m3), default = 300.0
ox_suboxic: 10.0 # Oxygen control for suboxic conditions (mmol O2/m3), default = 10.0
zl_pred_lost: 1.0 # Fraction of Zl lost by predation (-), default = 0.5
initialization:
pl: 0.0045 # PhytoLarge (mmol N/m**3)
ps: 0.0045 # PhytoSmall (mmol N/m**3)
zs: 0.0025 # MicroZoo (mmol N/m**3)
zl: 0.0025 # MesoZoo (mmol N/m**3)
zn: 0.0025 # Noctiluca (mmol N/m**3)
zg: 0.0025 # Mnemiopsis (mmol N/m**3)
dn: 0.07 # detritus (mmol N/m**3)
am: 0.07 # ammonium (mmol N/m**3)
ni: 4.5 # nitrate (mmol N/m**3)
o2: 350.0 # oxygen (mmol O2/m**3)
hs: 4.5 # hydrogen sulfide (mmol HS/m**3)