class LeewayObj(LagrangianArray):
"""Extending LagrangianArray with variables relevant for leeway objects.
"""
variables = LagrangianArray.add_variables([
('objectType', {'dtype': np.int16,
'unit': '1',
'default': 0}),
('orientation', {'dtype': np.int16,
'unit': '1',
'default': 1}),
('jibeProbability', {'dtype': np.float32,
'unit': '1/h',
'default': 0.04}),
('downwindSlope', {'dtype': np.float32,
'unit': '%',
'default': 1}),
('crosswindSlope', {'dtype': np.float32,
'unit': '1',
'default': 1}),
('downwindOffset', {'dtype': np.float32,
'unit': 'cm/s',
'default': 0}),
('crosswindOffset', {'dtype': np.float32,
'unit': 'cm/s',
'default': 0}),
('downwindEps', {'dtype': np.float32,
'unit': 'cm/s',
'default': 0}),
('crosswindEps', {'dtype': np.float32,
'unit': 'cm/s',
'default': 0})
])
class PelagicEgg(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic eggs
"""
variables = LagrangianArray.add_variables([
('diameter', {
'dtype': np.float32,
'units': 'm',
'default': 0.0014
}), # for NEA Cod
('neutral_buoyancy_salinity', {
'dtype': np.float32,
'units': '[]',
'default': 31.25
}), # for NEA Cod
('density', {
'dtype': np.float32,
'units': 'kg/m^3',
'default': 1028.
}),
('hatched', {
'dtype': np.float32,
'units': '',
'default': 0.
})
])
class Radionuclide(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for radionuclides
"""
variables = LagrangianArray.add_variables([
('diameter', {
'dtype': np.float32,
'units': 'm',
'default': 0.
}),
('neutral_buoyancy_salinity', {
'dtype': np.float32,
'units': '[]',
'default': 31.25
}), # for NEA Cod
('density', {
'dtype': np.float32,
'units': 'kg/m^3',
'default': 2650.
}), # Mineral particles
('specie', {
'dtype': np.int32,
'units': '',
'default': 0
}) #,
# ('transfer_rates1D', {'dtype':np.array(3, dtype=np.float32),
# 'units': '1/s',
# 'default': 0.})
])
class Lagrangian3DArray(LagrangianArray):
"""Extending LagrangianArray for elements moving in 3 dimensions
The Particle may be buoyant and/or subject to vertical mixing
buoyant bahaviour is described by terminal velocity
"""
variables = LagrangianArray.add_variables([
('wind_drift_factor', {
'dtype':
np.float32,
'units':
'1',
'description':
'Elements at surface are moved with this '
'fraction of the vind vector, in addition to currents '
'and Stokes drift',
'default':
0.02
}),
('terminal_velocity', {
'dtype': np.float32,
'units': 'm/s',
'description': 'Terminal rise/sinking velocity (buoyancy) '
'in the ocean column',
'default': 0.
})
])
class ShipObject(LagrangianArray):
"""Extending LagrangianArray with variables relevant for leeway objects.
"""
variables = LagrangianArray.add_variables([
('orientation', {'dtype': np.int16,
'unit': '1',
'default': 1}),
('length', {'dtype': np.float32,
'unit': 'm',
'default': 80}),
('height', {'dtype': np.float32,
'unit': 'm',
'default': 9}),
('draft', {'dtype': np.float32, # wet part of ship [m]
'unit': 'm',
'default': 4.0}),
('beam', {'dtype': np.float32, # width of ship
'unit': 'm',
'default': 10}),
('wind_drag_coeff', {'dtype': np.float32, # Cf
'unit': '1',
'default': 1}),
('water_drag_coeff', {'dtype': np.float32, # Cd
'unit': '1',
'default': 1}),
('jibeProbability', {'dtype': np.float32,
'unit': '1/h',
'default': 0.04}),
])
class Lagrangian3DArray(LagrangianArray):
"""Extending LagrangianArray for elements moving in 3 dimensions
The Particle may be buoyant and/or subject to vertical mixing
buoyant bahaviour is described by terminal velocity
"""
variables = LagrangianArray.add_variables([
('terminal_velocity', {'dtype': np.float32,
'units': 'm/s',
'default': 0.})])
class PelagicPlankton(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic eggs
"""
variables = LagrangianArray.add_variables([
('diameter', {'dtype': np.float32,
'units': 'm',
'default': 0.0014}), # for NEA Cod
('neutral_buoyancy_salinity', {'dtype': np.float32,
'units': '[]',
'default': 31.25}), # for NEA Cod
('density', {'dtype': np.float32,
'units': 'kg/m^3',
'default': 1028.}),
('age_seconds', {'dtype': np.float32,
'units': 's',
'default': 0.}),
('hatched', {'dtype': np.int64,
'units': '',
'default': 0}),
('stage_fraction', {'dtype': np.float32, #KK: Added to track percentage of development time completed
'units': '',
'default': 0.}),
('length', {'dtype': np.float32,
'units': 'mm',
'default': 4.0}),
('weight', {'dtype': np.float32,
'units': 'mg',
'default': 0.08}),
('Eb', {'dtype': np.float32,
'units': 'ugEm2',
'default': 0.}),
('light', {'dtype': np.float32,
'units': 'ugEm2',
'default': 0.}),
('growth_rate', {'dtype': np.float32,
'units': '%',
'default': 0.}),
('ingestion_rate', {'dtype': np.float32,
'units': '%',
'default': 0.}),
('stomach_fullness', {'dtype': np.float32,
'units': '%',
'default': 0.}),
('stomach', {'dtype': np.float32,
'units': '',
'default': 0.}),
('survival', {'dtype': np.float32,
'units': '',
'default': 1.})])
class Oil(LagrangianArray):
"""Extending LagrangianArray with variables relevant for oil particles."""
variables = LagrangianArray.add_variables([
('mass_oil', {'dtype': np.float32,
'units': 'kg',
'default': 1}),
('viscosity', {'dtype': np.float32,
#'unit': 'mm2/s (centiStokes)',
'units': 'N s/m2 (Pa s)',
'default': 0.005}),
('density', {'dtype': np.float32,
'units': 'kg/m^3',
'default': 880}),
('wind_drift_factor', {'dtype': np.float32,
'units': '%',
'default': 0.03}),
('age_exposure_seconds', {'dtype': np.float32,
'units': 's',
'default': 0}),
('age_emulsion_seconds', {'dtype': np.float32,
'units': 's',
'default': 0}),
('bulltime', {'dtype': np.float32,
'units': 's',
'default': 0}),
('interfacial_area', {'dtype': np.float32,
'units': 'm2',
'default': 0}),
('mass_dispersed', {'dtype': np.float32,
'units': 'kg',
'default': 0}),
('mass_evaporated', {'dtype': np.float32,
'units': 'kg',
'default': 0}),
('mass_biodegraded', {'dtype': np.float32,
'units': 'kg',
'default': 0}),
('fraction_evaporated', {'dtype': np.float32,
'units': '%',
'default': 0}),
('water_fraction', {'dtype': np.float32,
'units': '%',
'default': 0}),
('oil_film_thickness', {'dtype': np.float32,
'units': 'm',
'default': 0.001})])
class ShipObject(LagrangianArray):
"""Extending LagrangianArray with variables relevant for leeway objects.
"""
variables = LagrangianArray.add_variables([
('orientation', {'dtype': np.int16,
'units': '1',
'default': 1}),
('length', {'dtype': np.float32,
'units': 'm',
'min': 1,
'max': 500,
'description': 'Length of ship',
'level': OpenDriftSimulation.CONFIG_LEVEL_ESSENTIAL,
'default': 80}),
('height', {'dtype': np.float32,
'units': 'm',
'min': 1,
'max': 100,
'description': 'Total height of ship',
'level': OpenDriftSimulation.CONFIG_LEVEL_ESSENTIAL,
'default': 8}),
('draft', {'dtype': np.float32, # wet part of ship [m]
'units': 'm',
'min': 1,
'max': 20,
'description': 'Draft of ship (depth below water)',
'level': OpenDriftSimulation.CONFIG_LEVEL_ESSENTIAL,
'default': 4.0}),
('beam', {'dtype': np.float32, # width of ship
'min': 1,
'max': 50,
'units': 'm',
'description': 'Beam (width) of ship',
'level': OpenDriftSimulation.CONFIG_LEVEL_ESSENTIAL,
'default': 10}),
('wind_drag_coeff', {'dtype': np.float32, # Cf
'units': '1',
'default': 1}),
('water_drag_coeff', {'dtype': np.float32, # Cd
'units': '1',
'default': 1}),
('jibeProbability', {'dtype': np.float32,
'units': '1/h',
'default': 0.04}),
])
class LeewayObj(LagrangianArray):
"""Extending LagrangianArray with variables relevant for leeway objects.
"""
variables = LagrangianArray.add_variables([
('object_type', {'dtype': np.uint16,
'units': '1',
'seed': False,
'default': 0}),
('orientation', {'dtype': np.uint8,
'units': '1',
'description': '0/1 is left/right of downwind. Randomly chosen at seed time',
'seed': False,
'default': 1}),
('jibe_probability', {'dtype': np.float32,
'units': '1/h',
'description': 'Probability per hour that an object may change orientation (jibing)',
'default': 0.04}),
('downwind_slope', {'dtype': np.float32,
'units': '%',
'seed': False,
'default': 1}),
('crosswind_slope', {'dtype': np.float32,
'units': '1',
'seed': False,
'default': 1}),
('downwind_offset', {'dtype': np.float32,
'units': 'cm/s',
'seed': False,
'default': 0}),
('crosswind_offset', {'dtype': np.float32,
'units': 'cm/s',
'seed': False,
'default': 0}),
('downwind_eps', {'dtype': np.float32,
'units': 'cm/s',
'seed': False,
'default': 0}),
('crosswind_eps', {'dtype': np.float32,
'units': 'cm/s',
'seed': False,
'default': 0})
])
class TemplateElementType(LagrangianArray):
"""Extending LagrangianArray with relevant properties."""
# Define and name the properties which the elements shall have.
# These are added to the four core properties (ID, lon, lat, z)
# inherited from the basic/generic LagrangianArray class.
# Property names may be freely chosen, but the "update" function (below)
# will refer to the names in the specifications of the processes.
variables = LagrangianArray.add_variables([('mass_oil', {
'dtype': np.float32,
'unit': 'kg'
}), ('mass_evaporated', {
'dtype': np.float32,
'unit': 'kg',
'default': 0
}), ('mass_emulsion', {
'dtype': np.float32,
'unit': 'kg',
'default': 0
})])
class PelagicPlankton(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic eggs
"""
variables = LagrangianArray.add_variables([('area', {
'dtype': np.float32,
'units': 'm2',
'default': 0.
}), ('length', {
'dtype': np.float32,
'units': 'm',
'default': 0.
}), ('diameter', {
'dtype': np.float32,
'units': 'm',
'default': 0.
}), ('age_seconds', {
'dtype': np.float32,
'units': 's',
'default': 0.
}), ('plantpart', {
'dtype': np.int32,
'units': '',
'default': 0
}), ('weight', {
'dtype': np.float32,
'units': 'kg',
'default': 0.
}), ('volume', {
'dtype': np.float32,
'units': 'm3',
'default': 0.
}), ('density', {
'dtype': np.float32,
'units': 'kg/m3',
'default': 0.
})])
class PelagicShrimp(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic eggs
"""
variables = LagrangianArray.add_variables([
('diameter', {
'dtype': np.float32,
'units': 'm',
'default': 0.0003
}), # size eggs shrimps
('density', {
'dtype': np.float32,
'units': 'kg/m^3',
'default': 1028.
}), # density eggs/larvae of shrimp
('age_seconds', {
'dtype': np.float32,
'units': 's',
'default': 0.
}),
(
'duration',
{
'dtype': np.float32, # Duration of the crustacean stages
'units': 's',
'default': 1.74 * 86400
}),
(
'stages_end_buoyancy',
{
'dtype': np.
int16, # Precise the stage when the buoyancy is no more efficient
'units': '[]',
'default': 2
}),
(
'TotalLength',
{
'dtype': np.
float32, # Size of the Post Larvae to use for the swimming /!\ could be explored for younger stages
'units': 'mm',
'default': 4.26
}),
(
'particles_velocity',
{
'dtype': np.
float32, # Swimming velocity used or not according to the configuration (see later)
'units': 'm/s',
'default': 0.
}),
(
'stages',
{
'dtype': np.
int16, # Stages of the larvae (0 = eggs, e.g.:0=eggs, 1= Nauplius, 2=Protozoea, 3=Mysis, 4= Postlarvae)
'units': '[]',
'default': 0
})
])
# Function to change the stages of the larvae if the 'duration' is lower than the time of drift
def updateEggStages(self):
self.elements.stages[
self.elements.age_seconds >= self.elements.duration] += 1
self.elements.stages[self.elements.stages >= 4] = 4
# Function to compute the duration of the stages according to Temperature of Water. The new duration will be added to the previous,
# in order to have UpdateEggStages working well.
def updateEggDuration(self):
Temperature = self.environment.sea_water_temperature[np.all([
self.elements.age_seconds >= self.elements.duration,
self.elements.stages < 4
], 0)]
B = np.array([1.59, 2.76, 3.77, 3.76])
stages = np.int16(self.elements.stages[np.all([
self.elements.age_seconds >= self.elements.duration,
self.elements.stages < 4
], 0)])
self.elements.duration[np.all([
self.elements.age_seconds >= self.elements.duration,
self.elements.stages < 4
], 0)] += (
np.exp(-0.076 * Temperature + B[stages])
) * 86400 # Equation can be modified to fit other coefficients in case of PLD = a+b*Temperature. Could be modified to include Salinity
class LarvalFish(Lagrangian3DArray):
"""
Extending Lagrangian3DArray with specific properties for larval and juvenile stages of fish
"""
variables = LagrangianArray.add_variables([
('diameter', {
'dtype': np.float32,
'units': 'm',
'default': 0.0014
}), # for NEA Cod
('neutral_buoyancy_salinity', {
'dtype': np.float32,
'units': '[]',
'default': 31.25
}), # for NEA Cod
('density', {
'dtype': np.float32,
'units': 'kg/m^3',
'default': 1028.
}),
('survival', {
'dtype': np.float32,
'units': 'rate',
'default': 1.0
}),
('development', {
'dtype': np.float32,
'units': 'rate',
'default': 0.0
}),
('age_seconds', {
'dtype': np.float32,
'units': 's',
'default': 0.
}),
('hatched', {
'dtype': np.int64,
'units': '',
'default': 0
}),
(
'age',
{
'dtype': np.
float32, # Added to track percentage of competency time completed
'units': '',
'default': 0.
}),
('length', {
'dtype': np.float32,
'units': 'mm',
'default': 10.0
}),
('weight', {
'dtype': np.float32,
'units': 'mg',
'default': 0.08
}),
('light', {
'dtype': np.float32,
'units': 'ugEm2',
'default': 0.
}),
('light_surface', {
'dtype': np.float32,
'units': 'ugEm2',
'default': 0.
}),
('growth_rate', {
'dtype': np.float32,
'units': '%/dt',
'default': 0.
}),
('survival', {
'dtype': np.float32,
'units': '',
'default': 1.
})
])
