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fabm.yaml
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instances:
diatoms:
model: selmaprotbas/phytoplankton
parameters:
c0: 0.006625 # background concentration (mmol C/m3), default = 0.0
rfr: 0.009434 # phosphorus : carbon ratio (mol P/mol C), default = 1/106 = 0.009434
rfn: 0.150943 # nitrogen : carbon ratio (mol N/mol C), default = 16/106 = 0.150943
rfs: 0.141509 # silica : carbon ratio (mol Si/mol C), default = 0.000
alpha_light: 0.1 # the slope of light-dependent growth (d-1 [W/m2]-1), default = 0.1)
alpha: 1.65625 # half-saturation for nutrient uptake (mmol C/m3), default = 1.65625 (#J: 0.25 mmol N/m3)
beta: 3.7 # temperature growth correction factor (-), default = 3.7
r0: 1.3 # maximum growth rate at 20 degrees C (1/d), default = 1.3
nb: 0.01 # excretion rate (1/d), default = 0.01
deltao: 0.02 # mortality rate (1/d), default = 0.02
Yc: 6.25 # carbon : chlorophyll a ratio (mmol C/mg Chl a), default = 6.25
wz: -0.5 # vertical velocity (positive: upwards/floating, negative: downwards/sinking) (m/d), default = 0.0
kc: 0.0754716981 # specific light attenuation (m2/mmol C)
coupling:
aa: selmaprotbas/aa # ammonium (mmol N/m3)
nn: selmaprotbas/nn # nitrate (mmol N/m3)
o2: selmaprotbas/o2 # oxygen (mmol O2/m3)
po: selmaprotbas/po # phosphate (mmol P/m3)
si: selmaprotbas/si # silicate (mmol Si/m3)
dd_c: selmaprotbas/dd_c # carbon detritus (mmol C/m3)
dd_p: selmaprotbas/dd_p # phosphorus detritus (mmol P/m3)
dd_n: selmaprotbas/dd_n # nitrogen detritus (mmol N/m3)
dd_si: selmaprotbas/dd_si # silica detritus (mmol Si/m3)
initialization:
c: 0.006625 # concentration (mmol C/m3)
flagellates:
model: selmaprotbas/phytoplankton
parameters:
c0: 0.006625 # background concentration (mmol C/m3), default = 0.0
rfr: 0.009434 # phosphorus : carbon ratio (mol P/mol C), default = 1/106 = 0.009434
rfn: 0.150943 # nitrogen : carbon ratio (mol N/mol C), default = 16/106 = 0.150943
rfs: 0 # silica : carbon ratio (mol Si/mol C), default = 0.000
alpha_light: 0.1 # the slope of light-dependent growth (d-1 [W/m2]-1), default = 0.1)
alpha: 1.65625 # half-saturation for nutrient uptake (mmol C/m3), default = 1.65625 (#J: 0.25 mmol N/m3)
beta: 3.7 # temperature growth correction factor (-), default = 3.7
r0: 1.3 # maximum growth rate at 20 degrees C (1/d), default = 1.3
nb: 0.01 # excretion rate (1/d), default = 0.01
deltao: 0.02 # mortality rate (1/d), default = 0.02
wz: 0.0
Yc: 6.25 # carbon : chlorophyll a ratio (mmol C/mg Chl a), default = 6.25
kc: 0.0754716981 # specific light attenuation (m2/mmol C)
coupling:
aa: selmaprotbas/aa # ammonium (mmol N/m3)
nn: selmaprotbas/nn # nitrate (mmol N/m3)
o2: selmaprotbas/o2 # oxygen (mmol O2/m3)
po: selmaprotbas/po # phosphate (mmol P/m3)
si: selmaprotbas/si # silicate (mmol Si/m3)
dd_c: selmaprotbas/dd_c # carbon detritus (mmol C/m3)
dd_p: selmaprotbas/dd_p # phosphorus detritus (mmol P/m3)
dd_n: selmaprotbas/dd_n # nitrogen detritus (mmol N/m3)
dd_si: selmaprotbas/dd_si # silica detritus (mmol Si/m3)
initialization:
c: 0.006625 # concentration (mmol C/m3)
cyanobacteria:
model: selmaprotbas/phytoplankton
parameters:
c0: 0.006625 # background concentration (mmol C/m3), default = 0.0
rfr: 0.009434 # phosphorus : carbon ratio (mol P/mol C), default = 1/106 = 0.009434
rfn: 0.150943 # nitrogen : carbon ratio (mol N/mol C), default = 16/106 = 0.150943
rfs: 0 # silica : carbon ratio (mol Si/mol C), default = 0.000
alpha_light: 0.1 # the slope of light-dependent growth (d-1 [W/m2]-1), default = 0.1)
alpha: 1.65625 # half-saturation for nutrient uptake (mmol C/m3), default = 1.65625 (#J: 0.25 mmol N/m3)
beta: 3.7 # temperature growth correction factor (-), default = 3.7
r0: 1.3 # maximum growth rate at 20 degrees C (1/d), default = 1.3
nitrogen_fixation: true # whether nitrogen fixation is used to acquire nitrogen, default = false
nb: 0.01 # excretion rate (1/d), default = 0.01
deltao: 0.02 # mortality rate (1/d), default = 0.02
Yc: 6.25 # carbon : chlorophyll a ratio (mmol C/mg Chl a), default = 6.25
wz: 0.1 # vertical velocity (positive: upwards/floating, negative: downwards/sinking) (m/d), default = 0.0
buoyancy_regulation: true
par_limit1: 21.9
par_limit2: 6.6
par_limit3: 2.2
vert_vel1: -0.3
vert_vel2: -0.1
vert_vel3: 0
vert_vel4: 0.1
kc: 0.0754716981 # specific light attenuation (m2/mmol C)
coupling:
aa: selmaprotbas/aa # ammonium (mmol N/m3)
nn: selmaprotbas/nn # nitrate (mmol N/m3)
o2: selmaprotbas/o2 # oxygen (mmol O2/m3)
po: selmaprotbas/po # phosphate (mmol P/m3)
si: selmaprotbas/si # silicate (mmol Si/m3)
dd_c: selmaprotbas/dd_c # carbon detritus (mmol C/m3)
dd_p: selmaprotbas/dd_p # phosphorus detritus (mmol P/m3)
dd_n: selmaprotbas/dd_n # nitrogen detritus (mmol N/m3)
dd_si: selmaprotbas/dd_si # silica detritus (mmol Si/m3)
initialization:
c: 0.006625 # concentration (mmol C/m3)
zooplankton:
model: selmaprotbas/zooplankton
parameters:
c0: 0.006625 # background concentration (mmol C/m3), default = 0.0
rfr: 0.009434 # phosphorus : carbon ratio (mol P/mol C), default = 1/106 = 0.009434
rfn: 0.150943 # nitrogen : carbon ratio (mol N/mol C), default = 16/106 = 0.150943
rfs: 0 # silica : carbon ratio (mol Si/mol C), default = 0
nprey: 3 # number of prey, default = 1
pref3: 0.5 # preference for prey 3 (-), default = 1.0
prey_rfs1: 0.141509 # Si:C ratio for prey 1 (-). Important to mention nutrient ratios of prey here if they deviate from the defaults, default = 0.000
nue: 0.001509 # respiration rate (m3/d/mmol C), default = 0.001509
sigma_b: 0.004528 # mortality rate (m3/d/mmol C), default = 0.004528
iv: 0.27341 # Ivlev constant, quadratic (1/(mmol C/m3)2), default = 0.27341
graz: 0.5 # grazing rate (1/d), default = 0.5
toptz: 20.0 # optimal temperature for grazing (deg C), default = 20.0
zcl1: 50.0 # closure parameter (-), default = 50.0
coupling:
prey1: diatoms/c # prey 1 (mmol C/m3)
prey2: flagellates/c # prey 2 (mmol C/m3)
prey3: cyanobacteria/c # prey 3 (mmol C/m3)
aa: selmaprotbas/aa # ammonium (mmol N/m3)
po: selmaprotbas/po # phosphate (mmol P/m3)
si: selmaprotbas/si # silicate (mmol Si/m3)
dd_c: selmaprotbas/dd_c # carbon detritus (mmol C/m3)
dd_p: selmaprotbas/dd_p # phosphorus detritus (mmol P/m3)
dd_n: selmaprotbas/dd_n # nitrogen detritus (mmol N/m3)
dd_si: selmaprotbas/dd_si # silica detritus (mmol Si/m3)
o2: selmaprotbas/o2 # oxygen (mmol O2/m3)
initialization:
c: 0.006625 # concentration (mmol C/m3)
selmaprotbas:
model: selmaprotbas/selmaprotbas
parameters:
env_type: fresh # (Define environment type, either fresh or marine), default = marine
wdz: -4.5 # vertical velocity of detritus (positive: upwards/floating, negative: downwards/sinking) (m/d), default = -4.5
wpo4: -1.0 # vertical velocity of suspended P-Fe (positive: upwards/floating, negative: downwards/sinking) (m/d), default = -1.0
dn: 0.003 # detritus mineralization rate (1/d), default = 0.003
dn_sed: 0.002 # sediment mineralization rate (1/d), default = 0.002
kc: 0.0754716981 # specific light attenuation of detritus (m2/mmol C)
q10_rec: 0.15 # temperature dependence of detritus remineralization (1/K), default = 0.15
ade_r0: 0.1 # maximum chemoautolithotrophic denitrification rate (1/d), default = 0.1
alphaade: 1.0 # half-saturation constant for chemoautolithotrophic denitrification (mmol N/m3), default = 1.0
q10_recs: 0.175 # temperature dependence of sediment remineralization (1/K), default = 0.175
tau_crit: 0.07 # critical shear stress (N/m2), default = 0.07
sedrate: 2.25 # detritus sedimentation rate (m/d), default = 2.25
erorate: 6.0 # sediment erosion rate (1/d), default = 6.0
sedratepo4: 0.5 # P-Fe sedimentation rate (m/d), default = 0.5
eroratepo4: 6.0 # P-Fe erosion rate (1/d), default = 6.0
po4ret: 0.18 # phosphate retention rate, oxic sediments (-), default = 0.18
pburialrate: 0.007 # phosphate burial rate (1/d), default = 0.007
fl_burialrate: 0.001 # sediment burial rate (1/d), default = 0.001
pliberationrate: 0.1 # phosphate liberation rate, anoxic sediments (1/d), default = 0.1
ipo4th: 100.0 # maximum phosphorus density available for burial (mmol P/m2), default = 100.0
br0: 0.03 # bioresuspension rate (1/d), default = 0.03
fds: 0.7 # fraction of sediment remineralization fueled by denitrification (-), default = 0.7
pvel: 5.0 # piston velocity (m/d), default = 5.0
newflux: 2 # oxygen flux type (-), default = 2
initialization:
nn: 3.5 # nitrate (mmol N/m3)
aa: 0.85 # ammonium (mmol N/m3)
dd_c: 0.0 # carbon detritus (mmol C/m3)
dd_p: 0.0 # phosphorus detritus (mmol P/m3)
dd_n: 0.0 # nitrogen detritus (mmol N/m3)
dd_si: 20.0 # silica detritus (mmol Si/m3)
o2: 280.0 # oxygen (mmol O2/m3)
po: 0.216 # phosphate (mmol P/m3)
si: 1.000 # silicate (mmol Si/m3)
fl_c: 99.375 # carbon fluff (mmol C/m2)
fl_p: 0.9375 # phosphorus fluff (mmol P/m2)
fl_n: 15 # nitrogen fluff (mmol N/m2)
fl_si: 14.0625 # silica fluff (mmol Si/m2)
pb: 0.03 # phosphate bound to iron in sediment (mmol C/m2)
pw: 0.001 # phosphate bound to iron in water (mmol C/m3)
# Atmospheric input
ammonium_input:
model: constant_surface_flux
parameters:
flux: 0.0 # flux (positive for into water) (UNITS m-2 s-1)
coupling:
target: selmaprotbas/aa # target variable (UNITS m-3)
nitrate_input:
model: constant_surface_flux
parameters:
flux: 0.0 # flux (positive for into water) (UNITS m-2 s-1)
coupling:
target: selmaprotbas/nn # target variable (UNITS m-3)
phosphate_input:
model: constant_surface_flux
parameters:
flux: 0.0 # flux (positive for into water) (UNITS m-2 s-1)
coupling:
target: selmaprotbas/po # target variable (UNITS m-3)