Commit 4b26f3be authored by Jorn Bruggeman's avatar Jorn Bruggeman
Browse files

converted examples-npzd-benthos to yaml

parent d78d7bfd
!-------------------------------------------------------------------------------
! fabm_nml
!-------------------------------------------------------------------------------
! models [string array]
! a comma-separated list of one or model model names
!-------------------------------------------------------------------------------
&fabm_nml
models = 'gotm_npzd','examples_benthic_predator'
/
!-------------------------------------------------------------------------------
! gotm_npzd - GOTM nutrient-phytoplankton-zooplankton-detritus model
!-------------------------------------------------------------------------------
! n_initial [float, unit = mmol/m^3]
! initial nutrient concentration
! p_initial [float, unit = mmol/m^3]
! initial phytoplankton concentration
! z_initial [float, unit = mmol/m^3]
! initial zooplankton concentration
! d_initial [float, unit = mmol/m^3]
! initial detritus concentration
! p0 [float, unit = mmol/m^3]
! minimum phytoplankton concentration
! z0 [float, unit = mmol/m^3]
! minimum zooplankton concentration
! w_p [float, unit = m/d]
! settling velocity of phytoplankton
! w_d [float, unit = m/d]
! settling velocity of detritus
! kc [float, unit = m^2/mmol N]
! attenuation constant for the self shading effect
! I_min [float, unit = W/m^2]
! minimum photosynthetically active radiation (PAR)
! rmax [float, unit = 1/d]
! maximum nutrient uptake rate
! gmax [float, unit = 1/d]
! maximum grazing rate
! Iv [float]
! Ivlev constant
! alpha [float, unit = mmol N/m^3]
! half saturation
! rpn [float, unit = 1/d]
! p --> n rate (p metabolism)
! rzn [float, unit = 1/d]
! z --> n rate (z metabolism)
! rdn [float, unit = 1/d]
! d --> n rate (remineralisation)
! rpdu [float, unit = 1/d]
! p --> d rate (p mortality), in euphotic zone
! rpdl [float, unit = 1/d]
! p --> d rate (p mortality), below euphotic zone
! rzd [float, unit = 1/d]
! z --> d rate (z mortality)
!-------------------------------------------------------------------------------
&gotm_npzd
n_initial = 4.5,
p_initial = 1e-15,
z_initial = 1e-15,
d_initial = 4.5,
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,
/
!-------------------------------------------------------------------------------
! examples_benthic_predator - Idealized benthic predator model
!-------------------------------------------------------------------------------
&examples_benthic_predator
waste_target_variable = 'gotm_npzd_nut'
prey_source_variable = 'gotm_npzd_phy'
pred_initial = 1.
g_max = 1.
K = .2
h = 0.1
/
\ No newline at end of file
instances:
npzd:
model: gotm/npzd
parameters:
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 # 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: 1.0 # maximum population growth rate (d-1), default = 1.0
K: 0.2 # prey half-saturation (mmol m-3), default = 1.0
h: 0.1 # mortality (d-1), default = 0.05
initialization:
bm: 1.0 # predator density (mmol m-2)
coupling:
prey: npzd/phy # prey (mmol m-3)
waste: npzd/nut # waste (mmol m-3)
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