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infile.yaml
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# SOG code infile template
# SOG code infile for 356.5 day run starting at cruise 04-14 station
# S3 CTD cast (2004-10-19 12:22 LST).
grid:
model_depth:
value: 40
units: m
variable_name: grid%D
description: depth of modelled domain
grid_size:
value: 80
variable_name: grid%M
description: number of grid points
lambda_factor:
value: 0
variable_name: lambda
description: grid spacing parameter
location:
latitude:
value: 49.1253
units: deg
variable_name: latitude
description: latitude of modelled estuary
minor_axis:
value: 30e3
units: m
variable_name: Lx
description: length of minor axis (cross-estuary) of model domain
major_axis:
value: 120e3
units: m
variable_name: Ly
description: length of major axis (along-estuary) of model domain
open_ended_estuary:
value: False
variable_name: openEnd
description: open basin system (True) or closed system (False)
initial_conditions:
init_datetime:
value: 2004-10-19 12:22:00
variable_name: initDatetime
description: initial CTD profile date/time
CTD_file:
value: ../SOG-initial/ctd/SG-S3-2004-10-19.sog
variable_name: ctd_in
description: path/filename for initialization CTD file
# Give a path/filename for either STRATOGEM nutrients file
# or IOS bottle file; set the other to N/A
nutrients_file:
value: ../SOG-initial/stratogem_nuts/Nuts-S3-2004-10-19.sog
variable_name: nuts_in
description: path/filename for STRATOGEM nutrients data file
bottle_file:
value: N/A
variable_name: botl_in
description: path/filename for IOS nutrients bottle data file
chemistry_file:
value: ../SOG-initial/chem/Chem-SOG42-2010-73.sog
variable_name: chem_in
description: path/filename for IOS chemistry bottle data file
init_chl_ratios:
value: [0.33, 0.33, 0.33]
variable_name: Psplit
description: initial micro/nano/pico phytoplankton ratios from chlorophyl
nitrate_chl_conversion:
value: 1.600
units: mg/m^3 . uM N
variable_name: N2chl
description: phytoplankton nitrate to chlorophyl conversion factor
pCO2_atm:
value: 3.8e-4
units: atm
variable_name: pCO2_atm
description: partial pressure of atmospheric CO2
end_datetime:
value: 2005-10-11 00:22:00
variable_name: endDatetime
description: end of run date/time
numerics:
dt:
value: 900
units: s
variable_name: dt
description: time step
chem_dt:
value: 900
units: s
variable_name: chem_dt
description: internal chemistry time step
max_iter:
value: 30
variable_name: max_iter
description: max number of implicit solver iterations per time step
vary:
wind:
value: False
variable_name: vary%wind%enabled
description: use variation of wind initial conditions or forcing
# The following wind_* parameters are only used when wind == True
wind_fixed:
value: True
variable_name: vary%wind%fixed
description: use fixed value for wind initial conditions or forcing
# The wind_value parameter is only used when wind == True and
# wind_fixed == True
wind_value:
value: 0
units: m/s
variable_name: vary%wind%value
description: fixed value for wind initial conditions or forcing
# The wind_shift, wind_fraction and wind_addition parameters are
# only used when wind == True wind_fixed == False
wind_shift:
value: 0
units: yr
variable_name: vary%wind%value
description: fixed value for wind initial conditions or forcing
wind_fraction:
value: 1
variable_name: vary%wind%value
description: fixed value for wind initial conditions or forcing
wind_addition:
value: 0
units: m/s
variable_name: vary%wind%value
description: fixed value for wind initial conditions or forcing
cloud_fraction:
value: False
variable_name: vary%cf%enabled
description: use variation of cloud fraction initial conditions or forcing
# The following cloud_fraction_* parameters are only used when
# cloud_fraction == True
cloud_fraction_fixed:
value: True
variable_name: vary%cf%fixed
description: use fixed value for cloud fraction initial conditions or forcing
# The cloud_fraction_value parameter is only used when
# cloud_fraction == True and cloud_fraction_fixed == True
cloud_fraction_value:
value: 0
units: m/s
variable_name: vary%cf%value
description: fixed value for cloud fraction initial conditions or forcing
# The cloud_fraction_shift, cloud_fraction_fraction and
# cloud_fraction_addition parameters are only used when
# cloud_fraction == True cloud_fraction_fixed == False
cloud_fraction_shift:
value: 0
units: yr
variable_name: vary%cf%value
description: fixed value for cloud fraction initial conditions or forcing
cloud_fraction_fraction:
value: 1
variable_name: vary%cf%value
description: fixed value for cloud fraction initial conditions or forcing
cloud_fraction_addition:
value: 0
units: m/s
variable_name: vary%cf%value
description: fixed value for cloud fraction initial conditions or forcing
river_flows:
value: False
variable_name: vary%rivers%enabled
description: use variation of river flows initial conditions or forcing
# The following river_flows_* parameters are only used when river_flows == True
river_flows_fixed:
value: True
variable_name: vary%rivers%fixed
description: use fixed value for river flows initial conditions or forcing
# The river_flows_value parameter is only used when river_flows == True and
# river_flows_fixed == True
river_flows_value:
value: 0
units: m/s
variable_name: vary%rivers%value
description: fixed value for river flows initial conditions or forcing
# The river_flows_shift, river_flows_fraction and
# river_flows_addition parameters are only used when river_flows ==
# True river_flows_fixed == False
river_flows_shift:
value: 0
units: yr
variable_name: vary%rivers%value
description: fixed value for river flows initial conditions or forcing
river_flows_fraction:
value: 1
variable_name: vary%rivers%value
description: fixed value for river flows initial conditions or forcing
river_flows_addition:
value: 0
units: m/s
variable_name: vary%rivers%value
description: fixed value for river flows initial conditions or forcing
temperature:
value: False
variable_name: vary%temperature%enabled
description: use variation of air temperature initial conditions or forcing
# The following temperature_* parameters are only used when temperature == True
temperature_fixed:
value: True
variable_name: vary%temperature%fixed
description: use fixed value for temperature initial conditions or forcing
# The temperature_value parameter is only used when temperature == True and
# temperature_fixed == True
temperature_value:
value: 0
units: m/s
variable_name: vary%temperature%value
description: fixed value for temperature initial conditions or forcing
# The temperature_shift, temperature_fraction and
# temperature_addition parameters are only used when
# temperature == True temperature_fixed == False
temperature_shift:
value: 0
units: yr
variable_name: vary%temperature%value
description: fixed value for temperature initial conditions or forcing
temperature_fraction:
value: 1
variable_name: vary%temperature%value
description: fixed value for temperature initial conditions or forcing
temperature_addition:
value: 0
units: m/s
variable_name: vary%temperature%value
description: fixed value for temperature initial conditions or forcing
timeseries_results:
std_physics:
value: timeseries/std_phys_SOG.out
variable_name: std_phys_ts_out
description: path/filename for standard physics time series output
user_physics:
value: timeseries/user_phys_SOG.out
variable_name: user_phys_ts_out
description: path/filename for user physics time series output
std_biology:
value: timeseries/std_bio_SOG.out
variable_name: std_bio_ts_out
description: path/filename for standard biology time series output
user_biology:
value: timeseries/user_bio_SOG.out
variable_name: user_bio_ts_out
description: path/filename for user biology time series output
std_chemistry:
value: timeseries/std_chem_SOG.out
variable_name: std_chem_ts_out
description: path/filename for standard chemistry time series output
user_chemistry:
value: timeseries/user_chem_SOG.out
variable_name: user_chem_ts_out
description: path/filename for user chemistry time series output
profiles_results:
num_profiles:
value: 1
variable_name: noprof
description: number of profiles to output
# TODO: Replace year-day and day-second lists with a list of
# date/times for profile outputs
profile_days:
value: [303]
variable_name: profday
description: list of year-days to output profiles for
profile_times:
value: [43200]
variable_name: proftime
description: list of day-seconds to output profiles for
profile_file_base:
value: profiles/SOG
variable_name: profilesBase_fn
description: path/filename base for profiles (datetime will be appended)
user_profile_file_base:
value: profiles/SOG-user
variable_name: userprofilesBase_fn
description: path/filename base for user profiles (datetime appended)
halocline_file:
value: profiles/halo-SOG.out
variable_name: haloclines_fn
description: path/filename for halocline results
hoffmueller_file:
value: profiles/hoff-SOG.dat
variable_name: Hoffmueller_fn
description: path/filename for Hoffmueller results
user_hoffmueller_file:
value: profiles/hoff-SOG-user.dat
variable_name: userHoffmueller_fn
description: path/filename for user Hoffmueller results
# TODO: Replace Hoffmueller results start and end year, day & second
# with date/times
hoffmueller_start_year:
value: 2004
variable_name: Hoff_startyr
description: year to start Hoffmueller results output
hoffmueller_start_day:
value: 294
variable_name: Hoff_startday
description: day to start Hoffmueller results output
hoffmueller_start_sec:
value: 43200
variable_name: Hoff_startsec
description: second to start Hoffmueller results output
hoffmueller_end_year:
value: 2005
variable_name: Hoff_endyr
description: year to end Hoffmueller results output
hoffmueller_end_day:
value: 305
variable_name: Hoff_endday
description: day to end Hoffmueller results output
hoffmueller_end_sec:
value: 43200
variable_name: Hoff_endsec
description: second to end Hoffmueller results output
hoffmueller_interval:
value: 1
variable_name: Hoff_interval
description: days between Hoffmueller results outputs
physics:
bottom_boundary_conditions:
constant_temperature:
value: False
variable_name: temp_constant
description: is bottom temperature constant over time?
temperature_fit_coefficients:
value: [9.07, -0.088, -0.906, 0.0, -0.030, -0.088, 0.0]
variable_name: c(:,2)
description: temperature (constant, seasonal and biseasonal components)
salinity_fit_coefficients:
value: [29.62605865, 0.10374454, -0.03562458, 0, -0.14156091,
-0.06348989, 0]
variable_name: c(:,1)
description: salinity (constant, seasonal and biseasonal components)
phyto_fluor_fit_coefficients:
value: [0.58316137, -0.11206845, 0.26241523, 0, 0, 0, 0]
variable_name: c(:,3)
description: phytoplankton from fluorescence (constant & seasonal)
nitrate_fit_coefficients:
value: [30.5, 0, 0, 0, 0, 0, 0]
variable_name: c(:,4)
description: nitrate bottom boundary condition (constant)
silicon_fit_coefficients:
value: [54, 0, 0, 0, 0, 0, 0]
variable_name: c(:,5)
description: silicon bottom boundary condition (constant)
DIC_fit_coefficients:
value: [2065.98993, 9.18035435, -3.15241908, 0, -12.52672493,
-5.618220366, 0]
variable_name: c(:,6)
description: DIC (constant, seasonal & biseasonal from salinity fit)
dissolved_oxygen_fit_coefficients:
value: [198.9274, 28.6893, -46.9640, -3.7259, 6.4774, -2.7972, 0]
variable_name: c(:,7)
description: dissolved oxygen bottom boundary condition (constant)
alkalinity_fit_coefficients:
value: [2097.300118, 6.25890810, -2.14923091, 0, -8.540367,
-3.83034506, 0]
variable_name: c(:,8)
description: alkalinity (constant, seasonal & biseasonal from salinity)
ammonium_fit_coefficients:
value: [1, 0, 0, 0, 0, 0, 0]
variable_name: c(:,9)
description: ammonium bottom boundary condition (constant)
phyto_ratio_fit_coefficients:
value: [1.25948868, 0, 0, 0, 0.97697686, 0.46289294, 0]
variable_name: c(:,10)
description: ratio of pico/micro phytoplankton (constant & biseasonal)
turbulence:
momentum_wave_break_diffusivity:
value: 1.0e-4
units: m^2/s
variable_name: nu%m%int_wave
description: internal wave breaking diffusivity for momentum qtys
scalar_wave_break_diffusivity:
value: 1.0e-5
units: m^2/s
variable_name: nu%T%int_wave, nu%S%int_wave
description: internal wave breaking diffusivity for scalar qtys
shear_diffusivity_smoothing:
value: [0.375, 0.5]
variable_name: shear_diff_smooth
description: shear diffusivity smoothing parameters
fresh_water:
flux:
mean_total_flow:
value: 3624
units: m^3/s
variable_name: Qbar
description: mean total fresh water flow
common_exponent:
value: 0.2
variable_name: F_SOG
description: exponential for SoG/RI common component of flux
SoG_exponent:
value: 1
variable_name: F_RI
description: exponent for extra SoG term component of flux
scale_factor:
value: 11.87e-10
variable_name: Fw_scale
description: fresh water scale factor for rivers flows
add_freshwater_on_surface:
value: False
variable_name: Fw_surface
description: add all of the fresh water on the surface?
distribution_depth:
value: 3
units: m
variable_name: Fw_depth
description: depth to distribute fresh water flux over
include_fresh_water_nutrients:
value: True
variable_name: use_Fw_nutrients
description: include influence of fresh water nutrients in biology
northern_return_flow:
value: True
variable_name: Northern_return
description: include fresh water return flow from the north?
# The next 7 "northern" parameters are only used when
# northern_return_flow == True
northern_influence_strength:
value: 0.8863 # 1 / 43
units: m
variable_name: strength
description: strength of northern influence
northern_influence_integration_time_scale:
value: 2
units: d
variable_name: tauN
description: integration time scale for northern influence
northern_water_depth_peak:
value: 23
units: m
variable_name: central_depth
description: depth peak of incoming northerrn water
northern_water_upper_extension:
value: 12
units: m
variable_name: upper_width
description: upward extension of incoming northern water
northern_water_lower_extension:
value: 10
units: m
variable_name: lower_width
description: downward extension of incoming northern water
northern_water_power_riverflow_influence:
value: 0.
variable_name: power
description: power on the river flow influence on northern water
northern_water_normalization_riverflow_influence:
value: 2500
units: m^3/s
variable_name: Fo
description: normalization on the river flow influence on north water
salinity_fit:
bottom_salinity:
value: 30
variable_name: cbottom
description: salinity at bottom of modelled domain
alpha:
value: 2440
variable_name: calpha
description: alpha coefficient of fresh water salinity fit
alpha2:
value: 1
variable_name: calpha2
description: alpha2 coefficient of fresh water salinity fit
# For the Strait of Georgia the fresh water salinity fit
# doesn't actually have an alpha2 coefficient but we set it to
# 1 to avoid dividing by zero. The beta=0 value below causes
# the terms containing alpha2 to be eliminated from the
# calculation.
gamma:
value: 0.0633
variable_name: cgamma
description: gamma coefficient of fresh water salinity fit
beta:
value: 0
variable_name: cbeta
description: beta coefficient of fresh water salinity fit
river_alkalinity_fit:
river_alkalinity_zero:
value: 873.7440
variable_name: river_Alk_0
description: river alkalinity at zero discharge
river_alkalinity_decay:
value: -1.5e-4
variable_name: river_Alk_decay
description: river alkalinity decay with discharge
river_pH:
value: 7.7
variable_name: pH_riv
description: pH of river water
upwelling:
max_upwelling_velocity:
value: 2.5e-5
units: m/s
variable_name: upwell_const
description: maximum upwelling velocity
variation_depth_param:
value: 11.7
units: m
variable_name: d
description: upwelling variation depth parameter
K_PAR_fit:
# Coefficients for Photosynthetic Available Radiation (PAR)
# elimination (K) from Collins, et al (2008)
ialpha:
value: 0.091
variable_name: ialpha
description: alpha coefficient of K-PAR fit
ibeta:
value: 0.0433
variable_name: ibeta
description: beta coefficient of K-PAR fit
igamma:
value: 2.62e-22
variable_name: igamma
description: gamma coefficient of K-PAR fit
isigma:
value: 5.5
variable_name: isigma
description: sigma coefficient of K-PAR fit
itheta:
value: 0.445
variable_name: itheta
description: theta coefficient of K-PAR fit
idl:
value: 2.56
variable_name: idl
description: dl coefficient of K-PAR fit
biology:
include_phytoplankton:
value: True
variable_name: biology
description: include phytoplankton in model? (init to zero if False)
include_flagellates:
value: True
variable_name: flagellates
description: include flagellates in model?
include_remineralization:
value: True
variable_name: remineralization
description: include remineralization in model?
include_microzooplankton:
value: True
variable_name: microzooplankton
description: include microzooplankton in model?
single_species_light:
value: False
variable_name: strong_limitation
description: high light limitation for single species case
mesozooplankton:
mesozoo_winter_conc:
value: 0.369
units: uM N
variable_name: rate_mesozoo%winterconc
description: mesozooplankton background concentration
mesozoo_summer_conc:
value: 1.0
units: uM N
variable_name: rate_mesozoo%summerconc
description: mesozooplankton relative summer concentration
mesozoo_summer_peak_magnitudes:
value: [0.339, 0.0, 0.0]
units: uM N
variable_name: rate_mesozoo%sumpeakval
description: magnitude of mesozooplankton summer concentration peaks
mesozoo_summer_peak_days:
value: [217.000, 229.000, 300.000]
units: year-day
variable_name: rate_mesozoo%sumpeakpos
description: times of mesozooplankton summer concentration peaks
mesozoo_summer_peak_widths:
value: [114.0, 51.600, 40.000]
units: year-days
variable_name: rate_mesozoo%sumpeakwid
description: widths of mesozooplankton summer concentration peaks
mesozoo_max_ingestion:
value: 1.39e-5
units: uM N / s
variable_name: rate_mesozoo%R
description: mesozooplankton maximum ingestion rate @ 20 deg C
mesozoo_assimilation_efficiency:
value: 0.5
variable_name: rate_mesozoo%eff
description: mesozooplankton grazed mass assimilation efficiency
mesozoo_natural_mortality:
value: 2.3e-6
units: uM N / s
variable_name: rate_mesozoo%Rm
description: mesozooplankton natural mortality rate @ 20 deg C
mesozoo_excretion:
value: 1.39e-6
units: uM N / s
variable_name: rate_mesozoo%excr
description: mesozooplankton excretion rate @ 20 deg C
mesozoo_grazing_limit:
value: 0.500
units: uM N
variable_name: rate_mesozoo%PredSlope
description: mesozooplankton total grazing limit
mesozoo_grazing_half_saturation:
value: 1.000
units: uM N
variable_name: rate_mesozoo%HalfSat
description: mesozooplankton total grazing half saturation constant
mesozoo_diatom_preference:
value: 0.250
variable_name: rate_mesozoo%MicroPref
description: mesozooplankton preference for diatoms
mesozoo_diatom_grazing_limit:
value: 0.000
units: uM N
variable_name: rate_mesozoo%MicroPredSlope
description: mesozooplankton diatom grazing limit
mesozoo_diatom_grazing_half_saturation:
value: 0.200
units: uM N
variable_name: rate_mesozoo%MicroHalfSat
description: mesozooplankton diatom grazing half saturation constant
mesozoo_nano_preference:
value: 0.200
variable_name: rate_mesozoo%NanoPref
description: mesozooplankton preference for nano-phytoplankton
mesozoo_nano_grazing_limit:
value: 0.2
units: uM N
variable_name: rate_mesozoo%NanoPredSlope
description: mesozooplankton nano-phyto grazing limit
mesozoo_nano_grazing_half_saturation:
value: 1.000
units: uM N
variable_name: rate_mesozoo%NanoHalfSat
description: mesozooplankton nano-phyto grazing half saturation const
mesozoo_pico_preference:
value: 0.200
variable_name: rate_mesozoo%PicoPref
description: mesozooplankton preference for pico-phytoplankton
mesozoo_pico_grazing_limit:
value: 0.0
units: uM N
variable_name: rate_mesozoo%PicoPredSlope
description: mesozooplankton pico-phyto grazing limit
mesozoo_pico_grazing_half_saturation:
value: 0.4
units: uM N
variable_name: rate_mesozoo%PicoHalfSat
description: mesozooplankton pico-phyto grazing half saturation const
mesozoo_PON_preference:
value: 0.150
variable_name: rate_mesozoo%PON_Pref
description: mesozooplankton preference for PON
mesozoo_PON_grazing_limit:
value: 0.000
units: uM N
variable_name: rate_mesozoo%PON_PredSlope
description: mesozooplankton PON feeding limit
mesozoo_PON_grazing_half_saturation:
value: 0.400
units: uM N
variable_name: rate_mesozoo%PON_HalfSat
description: mesozooplankton PON feeding half saturation const
mesozoo_microzoo_preference:
value: 0.150
variable_name: rate_mesozoo%Z_Pref
description: mesozooplankton preference for microzooplankton
mesozoo_microzoo_grazing_limit:
value: 1.000
units: uM N
variable_name: rate_mesozoo%Z_PredSlope
description: mesozooplankton microzooplankton grazing limit
mesozoo_microzoo_grazing_half_saturation:
value: 1.200
units: uM N
variable_name: rate_mesozoo%Z_HalfSat
description: mesozooplankton microzoo grazing half saturation const
mesodinium_rubrum:
mesorub_max_ingestion:
value: 0.8e-5
units: uM N / s
variable_name: rate_mesorub%R
description: mesodinium rubrum maximum ingestion rate @ 20 deg C
mesorub_assimilation_efficiency:
value: 0.6
variable_name: rate_mesorub%eff
description: mesodinium rubrum grazed mass assimilation efficiency
mesorub_grazing_limit:
value: 0.4
units: uM N
variable_name: rate_mesozoo%PicoPredSlope
description: mesodinium rubrum grazing limit
mesorub_grazing_half_saturation:
value: 1.0
units: uM N
variable_name: rate_mesozoo%PicoHalfSat
description: mesodinium rubrum grazing half saturation constant
microzooplankton:
microzoo_max_ingestion:
value: 1.5e-5
units: uM N / s
variable_name: rate_uzoo%R
description: microzooplankton maximum ingestion rate @ 20 deg C
microzoo_assimilation_efficiency:
value: 0.6
variable_name: rate_uzoo%eff
description: microzooplankton grazed mass assimilation efficiency
microzoo_natural_mortality:
value: 0.700E-06
units: uM N / s
variable_name: rate_uzoo%Rm
description: microzooplankton natural mortality rate @ 20 deg C
microzoo_excretion:
value: 0.500E-07
units: uM N / s
variable_name: rate_uzoo%excr
description: microzooplankton excretion rate @ 20 deg C
microzoo_grazing_limit:
value: 0.500
units: uM N
variable_name: rate_uzoo%PredSlope
description: microzooplankton total grazing limit
microzoo_grazing_half_saturation:
value: 1.250
units: uM N
variable_name: rate_uzoo%HalfSat
description: microzooplankton total grazing half saturation constant
microzoo_pico_preference:
value: 0.280
variable_name: rate_uzoo%PicoPref
description: microzooplankton preference for pico-phytoplankton
microzoo_pico_grazing_limit:
value: 0.400
units: uM N
variable_name: rate_uzoo%PicoPredSlope
description: microzooplankton pico-phyto grazing limit
microzoo_pico_grazing_half_saturation:
value: 1.000
units: uM N
variable_name: rate_uzoo%PicoHalfSat
description: microzooplankton pico-phyto grazing half saturation const
microzoo_micro_preference:
value: 0.280
variable_name: rate_uzoo%MicroPref
description: microzooplankton preference for micro-phytoplankton
microzoo_micro_grazing_limit:
value: 0.300
units: uM N
variable_name: rate_uzoo%MicroPredSlope
description: microzooplankton micro-phyto grazing limit
microzoo_micro_grazing_half_saturation:
value: 1.000
units: uM N
variable_name: rate_uzoo%MicroHalfSat
description: microzooplankton micro-phyto grazing half saturation const
microzoo_nano_preference:
value: 0.170
variable_name: rate_uzoo%NanoPref
description: microzooplankton preference for nano-phytoplankton
microzoo_nano_grazing_limit:
value: 0.500
units: uM N
variable_name: rate_uzoo%NanoPredSlope
description: microzooplankton nano-phyto grazing limit
microzoo_nano_grazing_half_saturation:
value: 1.000
units: uM N
variable_name: rate_uzoo%NanoHalfSat
description: microzooplankton nano-phyto grazing half saturation const
microzoo_PON_preference:
value: 0.090
variable_name: rate_uzoo%PON_Pref
description: microzooplankton preference for PON
microzoo_PON_grazing_limit:
value: 0.600
units: uM N
variable_name: rate_uzoo%PON_PredSlope
description: microzooplankton PON grazing limit
microzoo_PON_grazing_half_saturation:
value: 2.000
units: uM N
variable_name: rate_uzoo%PON_HalfSat
description: microzooplankton PON grazing half saturation const
microzoo_microzoo_preference:
value: 0.180
variable_name: rate_uzoo%PON_Pref
description: microzooplankton preference for microzoo cannibalism
microzoo_microzoo_grazing_limit:
value: 0.300
units: uM N
variable_name: rate_uzoo%PON_PredSlope
description: microzooplankton microzoo grazing limit
microzoo_microzoo_grazing_half_saturation:
value: 0.500
units: uM N
variable_name: rate_uzoo%PON_HalfSat
description: microzooplankton microzoo grazing half saturation const
phytoplankton_growth:
micro_max_growth:
value: 0.600E-04
units: 1/s
variable_name: rate_micro%R
description: micro-phyto maximum growth rate
# Hitchcock 1980, 1.4 d-1 for T. nordenskelii at 10degrees
nano_max_growth:
value: 0.250E-04
units: 1/s
variable_name: rate_nano%R
description: nano-phyto maximum growth rate
# Yih 2004, 0.5 d-1 for Mesodinium rubrum (at 15 degrees) and
# Q10**2 tuned up and at Q10**1
pico_max_growth:
value: 0.250E-04
units: 1/s
variable_name: rate_pico%R
description: pico-phyto maximum growth rate
micro_optimal_light:
value: 42.000
units: W/m^2
variable_name: rate_micro%Iopt
description: micro-phyto growth optimal light level
# Durbin, 1974 3.3 lg/s for T. nordenskelii at 10 degrees
nano_optimal_light:
value: 37.000
units: W/m^2
variable_name: rate_nano%Iopt
description: nano-phyto growth optimal light level
# Yih plus Cloern 1977 Half-sat very similar
pico_optimal_light:
value: 10.000
units: W/m^2
variable_name: rate_pico%Iopt
description: pico-phyto growth optimal light level
micro_max_temperature:
value: 35
units: deg C
variable_name: rate_micro%maxtemp
description: micro-phyto growth high temperature limit
# Durbin, 1974 T. nordenskelli cannot grow at 18 degrees
# general diatoms increase this
nano_max_temperature:
value: 35
units: deg C
variable_name: rate_nano%maxtemp
description: nano-phyto growth high temperature limit
# Mesodinium, Cloern 1977
pico_max_temperature:
value: 35
units: deg C
variable_name: rate_pico%maxtemp
description: pico-phyto growth high temperature limit
micro_temperature_range:
value: 5
units: deg C
variable_name: rate_micro%temprange
description: micro-phyto growth limit range below max temperature
# equal growth at 10 and 15 so range down 8
# (which Q10 should be about const)
nano_temperature_range:
value: 5
units: deg C
variable_name: rate_nano%temprange
description: nano-phyto growth limit range below max temperature
# starts turning over earlier
pico_temperature_range:
value: 5
units: deg C
variable_name: rate_pico%temprange
description: pico-phyto growth limit range below max temperature
micro_Q10_exponent:
value: 1
variable_name: rate_micro%Q10exp
description: micro-phyto growth Q10 temperature effect exponent
# 1 for T. n. but 2 is better for S.c.
nano_Q10_exponent:
value: 1
variable_name: rate_nano%Q10exp
description: nano-phyto growth Q10 temperature effect exponent
# Cloern 1977 data 2.0 not working try 1.0
pico_Q10_exponent:
value: 1
variable_name: rate_pico%Q10exp
description: pico-phyto growth Q10 temperature effect exponent
micro_gamma_loss:
value: 0
variable_name: rate_micro%gamma
description: micro-phyto growth light limitation loss parameter
nano_gamma_loss:
value: 0
variable_name: rate_nano%gamma
description: nano-phyto growth light limitation loss parameter
pico_gamma_loss:
value: 0
variable_name: rate_pico%gamma
description: pico-phyto growth light limitation loss parameter
micro_NO3_half_saturation:
value: 2.0
variable_name: rate_micro%k
description: micro-phyto growth NO3 half-saturation constant
nano_NO3_half_saturation:
value: 0.5
variable_name: rate_nano%k
description: nano-phyto growth NO3 half-saturation constant
pico_NO3_half_saturation:
value: 0.1
variable_name: rate_pico%k
description: pico-phyto growth NO3 half-saturation constant
micro_NO3_vs_NH_preference:
value: 1.0
variable_name: rate_micro%kapa
description: micro-phyto growth preference for NO3 over NH factor
nano_NO3_vs_NH_preference:
value: 0.5
variable_name: rate_nano%kapa
description: nano-phyto growth preference for NO3 over NH factor
pico_NO3_vs_NH_preference:
value: 0.300
variable_name: rate_pico%kapa
description: pico-phyto growth preference for NO3 over NH factor
micro_NH_inhibition_exponent:
value: 0
variable_name: rate_micro%gamma_o
description: micro-phyto growth exponential NH inhibition of NO3 uptake
nano_NH_inhibition_exponent:
value: 0
variable_name: rate_nano%gamma_o
description: nano-phyto growth exponential NH inhibition of NO3 uptake
pico_NH_inhibition_exponent:
value: 0
variable_name: rate_pico%gamma_o
description: pico-phyto growth exponential NH inhibition of NO3 uptake
micro_half_saturation:
value: 0
variable_name: rate_micro%N_o
description: micro-phyto growth overal half-saturation constant
nano_half_saturation:
value: 0
variable_name: rate_nano%N_o
description: nano-phyto growth overal half-saturation constant
pico_half_saturation:
value: 0
variable_name: rate_pico%N_o
description: pico-phyto growth overal half-saturation constant
micro_N_inhibition_exponent:
value: 0
variable_name: rate_micro%N_x
description: micro-phyto growth N inhibition exponent
nano_N_inhibition_exponent:
value: 0
variable_name: rate_nano%N_x
description: nano-phyto growth N inhibition exponent
pico_N_inhibition_exponent:
value: 0
variable_name: rate_pico%N_x
description: pico-phyto growth N inhibition exponent
micro_Si_N_ratio:
value: 2.
variable_name: rate_micro%Si_ratio
description: micro-phyto silicon/nitrogen ratio
nano_Si_N_ratio:
value: 0
variable_name: rate_nano%Si_ratio
description: nano-phyto silicon/nitrogen ratio
pico_Si_N_ratio:
value: 0
variable_name: rate_pico%Si_ratio
description: pico-phyto silicon/nitrogen ratio
micro_Si_half_saturation:
value: 0.600
variable_name: rate_micro%K_Si
description: micro-phyto growth Si half saturation constant
nano_Si_half_saturation:
value: 0
variable_name: rate_nano%K_Si
description: nano-phyto growth Si half saturation constant
pico_Si_half_saturation:
value: 0
variable_name: rate_pico%K_Si
description: pico-phyto growth Si half saturation constant
micro_natural_mortality:
value: 0.265E-05