Commit 3f2070f2 authored by Jorn Bruggeman's avatar Jorn Bruggeman
Browse files

partial test case clean-up

parent 207c653d
......@@ -6,6 +6,6 @@ instances:
k: 1.0 # decay rate (half-life = ln(2)/k) (d-1), default = 0.0
temperature_dependence: 1 # temperature dependence of decay (0: none, 1: Q10, 2: Arrhenius), default = 0
T_ref: 10.0 # temperature for which decay rate k is given (degree_C)
Q10: 2.0 # Q10 temperature coefficient (1: no temperature dependence) (-), default = 1.0
Q10: 2.0 # Q10 temperature coefficient (1: no temperature dependence) (-)
initialization:
c: 1.0 # concentration
c: 1.0 # concentration (quantity m-3)
This diff is collapsed.
......@@ -25,7 +25,7 @@ instances:
cyanotll: 13.5 # Cyanobacteria lower temperature limit (deg C), default = 13.5
cyanosll: 1.0 # Cyanobacteria lower salinity limit (PSU), default = 1.0
cyanosul: 10.0 # Cyanobacteria upper salinity limit (PSU), default = 10.0
flagtll: 100.0 # Flagellates half-saturation temp, squared (deg C), default = 100.0
flagtll: 100.0 # Flagellates half-saturation temp, squared ((deg C)2), default = 100.0
alphap: 0.25 # Half-saturation const, diatoms (mmol n/m3), default = 0.25
alphaf: 0.1 # Half-saturation const, flagellates (mmol n/m3), default = 0.1
alphab: 0.4 # Half-saturation const, cyanobacteria (mmol n/m3), default = 0.4
......@@ -37,7 +37,7 @@ instances:
toptz: 20.0 # Optimal temperature for grazing (deg C), default = 20.0
zcl1: 50.0 # Zooplankton closure parameter (-), default = 50.0
p0: 0.001 # Diatoms background value (mmol n/m3), default = 0.001
f0: 0.001 # Flagellates backgorund value (mmol n/m3), default = 0.001
f0: 0.001 # Flagellates background value (mmol n/m3), default = 0.001
b0: 0.001 # Cyanobacteria background value (mmol n/m3), default = 0.001
z0: 0.001 # Zooplankton background value (mmol n/m3), default = 0.001
imin_di: 35.0 # minimal optimal light radiation, diatoms (W/m2), default = 35.0
......
......@@ -2,53 +2,53 @@ instances:
npzd:
model: gotm/npzd
parameters:
p0: 0.0225
z0: 0.0225
w_p: -1.0
w_d: -5.0
kc: 0.03
I_min: 25.0
rmax: 1.0
gmax: 0.2
Iv: 1.1
alpha: 1.35
rpn: 0.01
rzn: 0.01
rdn: 0.003
rpdu: 0.02
rpdl: 0.1
rzd: 0.02
p0: 0.0225 # background phytoplankton concentration (mmol m-3), default = 0.0225
z0: 0.0225 # background zooplankton concentration (mmol m-3), default = 0.0225
kc: 0.03 # specific light extinction of phytoplankton and detritus (m2 mmol-1), default = 0.03
i_min: 25.0 # minimum light intensity in euphotic zone (W m-2), default = 25.0
rmax: 1.0 # maximum specific growth rate of phytoplankton (d-1), default = 1.0
gmax: 0.2 # maximum specific grazing rate of zooplankton (d-1), default = 0.5
iv: 1.1 # Ivlev grazing constant (m3 mmol-1), default = 1.1
alpha: 1.35 # half-saturation nutrient concentration for phytoplankton (mmol m-3), default = 0.3
rpn: 0.01 # loss rate of phytoplankton to nutrients (d-1), default = 0.01
rzn: 0.01 # loss rate of zooplankton to nutrients (d-1), default = 0.01
rdn: 0.003 # detritus remineralization rate (d-1), default = 0.003
rpdu: 0.02 # phytoplankton mortality in euphotic zone (d-1), default = 0.02
rpdl: 0.1 # phytoplankton mortality below euphotic zone (d-1), default = 0.1
rzd: 0.02 # zooplankton mortality (d-1), default = 0.02
w_p: -1.0 # vertical velocity of phytoplankton (<0 for sinking) (m d-1), default = -1.0
w_d: -5.0 # vertical velocity of detritus (<0 for sinking) (m d-1), default = -5.0
initialization:
nut: 4.5
phy: 1e-15
zoo: 1e-15
det: 4.5
nut: 4.5 # nutrients (mmol m-3)
phy: 1e-15 # phytoplankton (mmol m-3)
zoo: 1e-15 # zooplankton (mmol m-3)
det: 4.5 # detritus (mmol m-3)
predator:
model: examples/benthic_predator
parameters:
g_max: 0.7
K: 0.5
h: 0.05
interact_with_pelagic: false
interact_with_pelagic: false # food and waste are pelagic (not benthic), default = true
g_max: 0.7 # maximum population growth rate (d-1), default = 1.0
K: 0.5 # prey half-saturation (mmol m-2), default = 1.0
h: 0.05 # mortality (d-1), default = 0.05
initialization:
bm: 1.
bm: 1.0 # predator density (mmol m-2)
coupling:
prey: predator_food/result
waste: predator_waste/result
prey: predator_food/result # prey (mmol m-2)
waste: predator_waste/result # waste (mmol m-2)
predator_habitat:
model: examples/vertical_distribution
parameters:
z_top: 10.
z_bot: 20.
w_top: 1
w_bot: 1
z_top: 10.0 # upper limit of vertical distribution (m)
z_bot: 20.0 # lower limit of vertical distribution (m)
w_top: 1.0 # weight at upper limit of vertical distribution (-)
w_bot: 1.0 # weight at lower limit of vertical distribution (-)
predator_food:
model: examples/depth_integral
coupling:
target: npzd/zoo
weights: predator_habitat/weights
target: npzd/zoo # variable to depth-integrate
weights: predator_habitat/weights # weights for vertical integration (-)
predator_waste:
model: examples/depth_integral
coupling:
target: npzd/nut
weights: predator_habitat/weights
target: npzd/nut # variable to depth-integrate
weights: predator_habitat/weights # weights for vertical integration (-)
This diff is collapsed.
......@@ -2,149 +2,149 @@ instances:
diatoms:
model: selma/phytoplankton
parameters:
c0: 0.001 # background concentration (mmol N/m3), default = 0.0
rfr: 0.0625 # phosphorus : nitrogen ratio (mol P/mol N), default = 0.0625
rfc: 6.625 # carbon : nitrogen ratio (mol C/mol N), default = 6.625
imin: 35.0 # minimal optimal light radiation (W/m2), default = 50.0
alpha: 0.25 # half-saturation for nutrient uptake (mmol N/m3), default = 0.25
r0: 1.3 # maximum growth rate (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: 0.5 # specific light attenuation (m2/mmol N)
sedrate: 2.25 # sedimentation rate (m/d), default = 0.0
tau_crit: 0.07 # critical shear stress (N/m2), default = 0.07
coupling:
aa: selma/aa # ammonium (mmol N/m3)
nn: selma/nn # nitrate (mmol N/m3)
o2: selma/o2 # oxygen (mmol O2/m3)
po: selma/po # phosphate (mmol P/m3)
dd: selma/dd # detritus (mmol N/m3)
fl: selma/fl # fluff (mmol N/m2)
c0: 0.001 # background concentration (mmol N/m3), default = 0.0
rfr: 0.0625 # phosphorus : nitrogen ratio (mol P/mol N), default = 0.0625
rfc: 6.625 # carbon : nitrogen ratio (mol C/mol N), default = 6.625
imin: 35.0 # minimal optimal light radiation (W/m2), default = 50.0
alpha: 0.25 # half-saturation for nutrient uptake (mmol N/m3), default = 0.25
r0: 1.3 # maximum growth rate (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: 0.5 # specific light attenuation (m2/mmol N)
sedrate: 2.25 # sedimentation rate (m/d), default = 0.0
tau_crit: 0.07 # critical shear stress (N/m2), default = 0.07
initialization:
c: 0.001 # concentration (mmol N/m3)
c: 0.001 # concentration (mmol N/m3)
coupling:
aa: selma/aa # ammonium (mmol N/m3)
nn: selma/nn # nitrate (mmol N/m3)
o2: selma/o2 # oxygen (mmol O2/m3)
po: selma/po # phosphate (mmol P/m3)
dd: selma/dd # detritus (mmol N/m3)
fl: selma/fl # fluff (mmol N/m2)
flagellates:
model: selma/phytoplankton
parameters:
c0: 0.001 # background concentration (mmol N/m3), default = 0.0
rfr: 0.0625 # phosphorus : nitrogen ratio (mol P/mol N), default = 0.0625
rfc: 6.625 # carbon : nitrogen ratio (mol C/mol N), default = 6.625
imin: 50.0 # minimal optimal light radiation (W/m2), default = 50.0
alpha: 0.1 # half-saturation for nutrient uptake (mmol N/m3), default = 0.25
r0: 0.4 # maximum growth rate (1/d), default = 1.3
tlim: 1 # temperature limitation of growth (0: none, 1: flagellate-style, 2: cyanobacteria-style), default = 0
tll: 100.0 # half-saturation temperature, squared (degrees C^2), default = 100.0
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
kc: 0.5 # specific light attenuation (m2/mmol N)
coupling:
aa: selma/aa # ammonium (mmol N/m3)
nn: selma/nn # nitrate (mmol N/m3)
o2: selma/o2 # oxygen (mmol O2/m3)
po: selma/po # phosphate (mmol P/m3)
dd: selma/dd # detritus (mmol N/m3)
c0: 0.001 # background concentration (mmol N/m3), default = 0.0
rfr: 0.0625 # phosphorus : nitrogen ratio (mol P/mol N), default = 0.0625
rfc: 6.625 # carbon : nitrogen ratio (mol C/mol N), default = 6.625
imin: 50.0 # minimal optimal light radiation (W/m2), default = 50.0
alpha: 0.1 # half-saturation for nutrient uptake (mmol N/m3), default = 0.25
r0: 0.4 # maximum growth rate (1/d), default = 1.3
tlim: 1 # temperature limitation of growth (0: none, 1: flagellate-style, 2: cyanobacteria-style), default = 0
tll: 100.0 # half-saturation temperature, squared (degrees C^2), default = 100.0
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
kc: 0.5 # specific light attenuation (m2/mmol N)
initialization:
c: 0.001 # concentration (mmol N/m3)
c: 0.001 # concentration (mmol N/m3)
coupling:
aa: selma/aa # ammonium (mmol N/m3)
nn: selma/nn # nitrate (mmol N/m3)
o2: selma/o2 # oxygen (mmol O2/m3)
po: selma/po # phosphate (mmol P/m3)
dd: selma/dd # detritus (mmol N/m3)
cyanobacteria:
model: selma/phytoplankton
parameters:
c0: 0.001 # background concentration (mmol N/m3), default = 0.0
rfr: 0.0625 # phosphorus : nitrogen ratio (mol P/mol N), default = 0.0625
rfc: 6.625 # carbon : nitrogen ratio (mol C/mol N), default = 6.625
imin: 50.0 # minimal optimal light radiation (W/m2), default = 50.0
alpha: 0.4 # half-saturation for nutrient uptake (mmol N/m3), default = 0.25
r0: 0.75 # maximum growth rate (1/d), default = 1.3
nitrogen_fixation: true # whether nitrogen fixation is used to acquire nitrogen, default = false
tlim: 2 # temperature limitation of growth (0: none, 1: flagellate-style, 2: cyanobacteria-style), default = 0
tll: 13.5 # lower temperature limit (degrees C), default = 13.5
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
kc: 0.5 # specific light attenuation (m2/mmol N)
coupling:
aa: selma/aa # ammonium (mmol N/m3)
nn: selma/nn # nitrate (mmol N/m3)
o2: selma/o2 # oxygen (mmol O2/m3)
po: selma/po # phosphate (mmol P/m3)
dd: selma/dd # detritus (mmol N/m3)
c0: 0.001 # background concentration (mmol N/m3), default = 0.0
rfr: 0.0625 # phosphorus : nitrogen ratio (mol P/mol N), default = 0.0625
rfc: 6.625 # carbon : nitrogen ratio (mol C/mol N), default = 6.625
imin: 50.0 # minimal optimal light radiation (W/m2), default = 50.0
alpha: 0.4 # half-saturation for nutrient uptake (mmol N/m3), default = 0.25
r0: 0.75 # maximum growth rate (1/d), default = 1.3
nitrogen_fixation: true # whether nitrogen fixation is used to acquire nitrogen, default = false
tlim: 2 # temperature limitation of growth (0: none, 1: flagellate-style, 2: cyanobacteria-style), default = 0
tll: 13.5 # lower temperature limit (degrees C), default = 13.5
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
kc: 0.5 # specific light attenuation (m2/mmol N)
initialization:
c: 0.001 # concentration (mmol N/m3)
c: 0.001 # concentration (mmol N/m3)
coupling:
aa: selma/aa # ammonium (mmol N/m3)
nn: selma/nn # nitrate (mmol N/m3)
o2: selma/o2 # oxygen (mmol O2/m3)
po: selma/po # phosphate (mmol P/m3)
dd: selma/dd # detritus (mmol N/m3)
zooplankton:
model: selma/zooplankton
parameters:
c0: 0.001 # background concentration (mmol N/m3), default = 0.0
rfr: 0.0625 # phosphorus : nitrogen ratio (mol P/mol N), default = 0.0625
rfc: 6.625 # carbon : nitrogen ratio (mol C/mol N), default = 6.625
nprey: 3 # number of prey, default = 1
pref3: 0.5 # preference for prey 3 (-), default = 1.0
nue: 0.01 # respiration rate (m3/d/mmol N), default = 0.01
sigma_b: 0.03 # mortality rate (m3/d/mmol N), default = 0.03
iv: 1.2 # Ivlev constant, quadratic (1/(mmol N/m3)3), default = 1.2
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 N/m3)
prey2: flagellates/c # prey 2 (mmol N/m3)
prey3: cyanobacteria/c # prey 3 (mmol N/m3)
aa: selma/aa # ammonium (mmol N/m3)
po: selma/po # phosphate (mmol P/m3)
dd: selma/dd # detritus (mmol N/m3)
o2: selma/o2 # oxygen (mmol O2/m3)
c0: 0.001 # background concentration (mmol N/m3), default = 0.0
rfr: 0.0625 # phosphorus : nitrogen ratio (mol P/mol N), default = 0.0625
rfc: 6.625 # carbon : nitrogen ratio (mol C/mol N), default = 6.625
nprey: 3 # number of prey, default = 1
pref3: 0.5 # preference for prey 3 (-), default = 1.0
nue: 0.01 # respiration rate (m3/d/mmol N), default = 0.01
sigma_b: 0.03 # mortality rate (m3/d/mmol N), default = 0.03
iv: 1.2 # Ivlev constant, quadratic (1/(mmol N/m3)3), default = 1.2
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
initialization:
c: 0.001 # concentration (mmol N/m3)
c: 0.001 # concentration (mmol N/m3)
coupling:
prey1: diatoms/c # prey 1 (mmol N/m3)
prey2: flagellates/c # prey 2 (mmol N/m3)
prey3: cyanobacteria/c # prey 3 (mmol N/m3)
aa: selma/aa # ammonium (mmol N/m3)
po: selma/po # phosphate (mmol P/m3)
dd: selma/dd # detritus (mmol N/m3)
o2: selma/o2 # oxygen (mmol O2/m3)
selma:
model: selma/selma
parameters:
env_type: marine # (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: 0.5 # specific light attenuation of detritus (m2/mmol N)
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
maxsed: 1000.0 # maximum active sediment density (mmol N/m2), default = 1000.0
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
env_type: marine # (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: 0.5 # specific light attenuation of detritus (m2/mmol N)
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
maxsed: 1000.0 # maximum active sediment density (mmol N/m2), default = 1000.0
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: 20.0 # nitrate (mmol N/m3)
aa: 1.0 # ammonium (mmol N/m3)
dd: 0.0 # detritus (mmol N/m3)
o2: 280.0 # oxygen (mmol O2/m3)
po: 4.0 # phosphate (mmol P/m3)
nn: 20.0 # nitrate (mmol N/m3)
aa: 1.0 # ammonium (mmol N/m3)
dd: 0.0 # detritus (mmol N/m3)
o2: 280.0 # oxygen (mmol O2/m3)
po: 4.0 # phosphate (mmol P/m3)
ammonium_input:
model: constant_surface_flux
parameters:
flux: 6.94e-07 # flux (positive for into water) (UNITS m-2 s-1)
flux: 6.94e-07 # flux (positive for into water) (UNITS m-2 s-1)
coupling:
target: selma/aa # target variable (UNITS m-3)
target: selma/aa # target variable (UNITS m-3)
nitrate_input:
model: constant_surface_flux
parameters:
flux: 9.61e-07 # flux (positive for into water) (UNITS m-2 s-1)
flux: 9.61e-07 # flux (positive for into water) (UNITS m-2 s-1)
coupling:
target: selma/nn # target variable (UNITS m-3)
target: selma/nn # target variable (UNITS m-3)
phosphate_input:
model: constant_surface_flux
parameters:
flux: 1.74e-08 # flux (positive for into water) (UNITS m-2 s-1)
flux: 1.74e-08 # flux (positive for into water) (UNITS m-2 s-1)
coupling:
target: selma/po # target variable (UNITS m-3)
target: selma/po # target variable (UNITS m-3)
......@@ -2,127 +2,127 @@ instances:
ammonium:
model: su/pools
parameters:
has_nitrogen: true
has_nitrogen: true # whether this pool contains nitrogen, default = false
initialization:
N: 14
N: 14.0 # nitrogen (ugN L-1)
nitrate:
model: su/pools
parameters:
has_nitrogen: true
has_nitrogen: true # whether this pool contains nitrogen, default = false
initialization:
N: 140
N: 140.0 # nitrogen (ugN L-1)
phosphate:
model: su/pools
parameters:
has_phosphorus: true
has_phosphorus: true # whether this pool contains phosphorus, default = false
initialization:
P: 3.1
P: 3.1 # phosphorus (ugP L-1)
DIC:
model: su/pools
parameters:
has_carbon: true
has_carbon: true # whether this pool contains carbon, default = false
initialization:
C: 240
C: 240.0 # carbon (ugC L-1)
DOC:
model: su/pools
parameters:
has_carbon: true
has_carbon: true # whether this pool contains carbon, default = false
initialization:
C: 240
C: 240.0 # carbon (ugC L-1)
sDOM:
model: su/pools
parameters:
has_carbon: true
has_nitrogen: true
has_phosphorus: true
has_nitrogen: true # whether this pool contains nitrogen, default = false
has_phosphorus: true # whether this pool contains phosphorus, default = false
has_carbon: true # whether this pool contains carbon, default = false
initialization:
C: 12
N: 1.4
P: 0.31
C: 12.0 # carbon (ugC L-1)
N: 1.4 # nitrogen (ugN L-1)
P: 0.31 # phosphorus (ugP L-1)
cDOM:
model: su/pools
parameters:
has_carbon: true
has_nitrogen: true
has_phosphorus: true
has_nitrogen: true # whether this pool contains nitrogen, default = false
has_phosphorus: true # whether this pool contains phosphorus, default = false
has_carbon: true # whether this pool contains carbon, default = false
initialization:
C: 0
N: 0
P: 0
C: 0.0 # carbon (ugC L-1)
N: 0.0 # nitrogen (ugN L-1)
P: 0.0 # phosphorus (ugP L-1)
POM:
model: su/pools
parameters:
has_silicate: true
has_silicate: true # whether this pool contains silicate, default = false
initialization:
S: 10
S: 10.0 # silicate (ugSi L-1)
algae:
model: su/algae
initialization:
aC: 1
aN: 0.25
aP: 0.02
aChl: 0.06
initialization:
aC: 1.0 # core algae C-biomass (ugC L-1)
aN: 0.25 # core algae N-biomass (ugN L-1)
aP: 0.02 # core algae P-biomass (ugP L-1)
aChl: 0.06 # core algae Chl-biomass (ugChl L-1)
coupling:
NH4: ammonium/N
NO3: nitrate/N
DIP: phosphate/P
DIC: DIC/C
sDOMC: sDOM/C
sDOMN: sDOM/N
sDOMP: sDOM/P
DOC: DOC/C
NH4: ammonium/N # ammonium (ugN L-1)
NO3: nitrate/N # nitrate (ugN L-1)
DIP: phosphate/P # dissolved inorganic phosphorus (ugP L-1)
DIC: DIC/C # dissolved inorganic carbon (ugC L-1)
sDOMC: sDOM/C # semi-labile dissolved organic material-carbon (ugC L-1)
sDOMN: sDOM/N # semi-labile dissolved organic material-nitrogen (ugN L-1)
sDOMP: sDOM/P # semi-labile dissolved organic material-phosphorus (ugP L-1)
DOC: DOC/C # dissolved organic carbon (ugC L-1)
bacteria:
model: su/bacteria
initialization:
bC: 1
initialization:
bC: 1.0 # core bacterial C-biomass (ugC L-1)
coupling:
NH4: ammonium/N
NO3: nitrate/N
DIP: phosphate/P
DIC: DIC/C
DOC: DOC/C
sDOMC: sDOM/C
sDOMN: sDOM/N
sDOMP: sDOM/P
cDOMC: cDOM/C
cDOMN: cDOM/N
cDOMP: cDOM/P
NH4: ammonium/N # ammonium (ugN L-1)
NO3: nitrate/N # nitrate (ugN L-1)
DIP: phosphate/P # dissolved inorganic phosphorus (ugP L-1)
DIC: DIC/C # dissolved inorganic carbon (ugC L-1)
DOC: DOC/C # dissolved organic carbon (ugC L-1)
sDOMC: sDOM/C # semi-labile dissolved organic material-carbon (ugC L-1)
sDOMN: sDOM/N # semi-labile dissolved organic material-nitrogen (ugN L-1)
sDOMP: sDOM/P # semi-labile dissolved organic material-phosphorus (ugP L-1)
cDOMC: cDOM/C # combined dissolved organic material-carbon (ugC L-1)
cDOMN: cDOM/N # combined dissolved organic material-nitrogen (ugN L-1)
cDOMP: cDOM/P # combined dissolved organic material-phosphorus (ugP L-1)
PB:
long_name: Perfect Beast
long_name: Perfect Beast
model: su/mixo
parameters:
mUm: 0.7
mUphot: 0.35
Smix: 0
Svol: 1
mChlCabs: 0.03
nprey: 2
preyESD1: 10.50
preyESD2: 1
pref1: 1
pref2: 1
steal1: 1
steal2: 0
kpmax: 1.852
SSi: false
mChlCabs: 0.03 # absolute maximum Chl:C (gChl (gC)-1), default = 0.03
Smix: 0 # switch to mix C input; 0 if substitutional; 1 if additive mixotrophic interaction (dl), default = 0
Svol: 1 # switch to share cell volume; 0 if feeding vacuole does not compromise ChlCmax (dl), default = 0
mUm: 0.7 # maximum possible growth rate (day-1), default = 0.7
mUphot: 0.35 # maximum phototrophic growth rate (day-1), default = 0.35
kpmax: 1.852 # kleptochloroplast photosynthetic rate (gC/gC/day), default = 0.0
SSi: false # switch to activate silicate limitation, default = false
nprey: 2 # number of prey types, default = 0
preyESD1: 10.5 # size in ESD1 (um)
pref1: 1.0 # prey preference1 (dl)
steal1: 1 # steal or not chloroplasts from prey1
preyESD2: 1.0 # size in ESD2 (um)
pref2: 1.0 # prey preference2 (dl)
steal2: 0 # steal or not chloroplasts from prey2
initialization:
mC: 1
mN: 0.2
mP: 0.02
mChl: 0.01
mF: 1e-12
mFN: 0
mFP: 0
mFChl: 1e-18
mC: 1.0 # core C-biomass (ugC L-1)
mN: 0.2 # core N-biomass (ugN L-1)
mP: 0.02 # core P-biomass (ugP L-1)
mChl: 0.01 # core Chl-biomass (ugChl L-1)
mF: 1e-12 # food vacuole C-biomass (ugC L-1)
mFN: 0.0 # food vacuole N-biomass (ugN L-1)
mFP: 0.0 # food vacuole P-biomass (ugP L-1)
mFChl: 1e-18 # food vacuole Chl-biomass (ugChl L-1)
coupling:
prey1: algae
prey2: bacteria
NH4: ammonium
NO3: nitrate
DIP: phosphate
DIC: DIC
NH4: ammonium
NO3: nitrate
DIP: phosphate
DIC: DIC
sDOMC: sDOM
sDOMN: sDOM
sDOMP: sDOM
DOC: DOC
RPs: POM
DOC: DOC
RPs: POM