class LarvalFishElement(Lagrangian3DArray):
"""
Extending Lagrangian3DArray with specific properties for larval and juvenile stages of fish
"""
variables = Lagrangian3DArray.add_variables([
('diameter', {'dtype': np.float32,
'units': 'm',
'default': 0.0014}), # for NEA Cod
('neutral_buoyancy_salinity', {'dtype': np.float32,
'units': 'PSU',
'default': 31.25}), # for NEA Cod
('stage_fraction', {'dtype': np.float32, # to track percentage of development time completed
'units': '',
'default': 0.}),
('hatched', {'dtype': np.int64, # 0 for eggs, 1 for larvae
'units': '',
'default': 0}),
('length', {'dtype': np.float32,
'units': 'mm',
'default': 0}),
('weight', {'dtype': np.float32,
'units': 'mg',
'default': 0.08}),
('survival', {'dtype': np.float32, # Not yet used
'units': '',
'default': 1.})])
class SedimentElement(Lagrangian3DArray):
# Lagrangian3DArray has already the variables terminal_velocity, and wind_drift_factor
variables = Lagrangian3DArray.add_variables([
(
'settled',
{
'dtype': np.int16, # 0 is active, 1 is settled
'units': '1',
'default': 0
}),
('age_seconds', {
'dtype': np.float32,
'units': 's',
'default': 0
}),
('terminal_velocity', {
'dtype': np.float32,
'units': 'm/s',
'default': -0.001
}), # 1 mm/s negative buoyancy
('critical_shear_stress', {
'dtype': np.float32,
'units': 'N/m2',
'default': 0.0
})
])
class BivalveLarvaeObj(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic eggs/larvae
"""
variables = Lagrangian3DArray.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.
}),
('terminal_velocity', {
'dtype': np.float32,
'units': 'm/s',
'default': 0.
})
])
class FishLarvaeOrientObj(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic larvae and orientation
"""
variables = Lagrangian3DArray.add_variables([('neutral_buoyancy_salinity',
{
'dtype': np.float32,
'units': '[]',
'default': 31.25
}),
('age_seconds', {
'dtype': np.float32,
'units': 's',
'default': 0.
}),
('density', {
'dtype': np.float32,
'units': 'kg/m^3',
'default': 1028.
}),
('terminal_velocity', {
'dtype': np.float32,
'units': 'm/s',
'default': 0.
}),
('light', {
'dtype': np.float32,
'units': 'ugEm2',
'default': 0.
})])
class TemplateElementType(Lagrangian3DArray):
"""Extending LagrangianArray with relevant properties."""
# Define and name the properties which the elements shall have.
# These are added to the inherited properties (e.g. from OceanDrift)
# Property names may be freely chosen, but the "update" function (below)
# will refer to the names in the specifications of the processes.
#
# The "default" value is used for alle elements, unless a custom
# value is provided at time of seeding:
# o.seed_elements(......., <property>=<value>)
#
# The default value can also be updated by the user
# before seeding with the config mechanism:
# o.set_config('seed:<property>', <new default value>)
#
# The "units" attribute is used for labeling.
variables = Lagrangian3DArray.add_variables([('new_property_1', {
'dtype': np.float32,
'units': '1',
'default': 0
}), ('new_property_2', {
'dtype': np.float32,
'units': '1',
'default': 0
})])
class SedimentElement(Lagrangian3DArray):
variables = Lagrangian3DArray.add_variables([
('settled', {'dtype': np.uint8, # 0 is active, 1 is settled
'units': '1',
'default': 0}),
('terminal_velocity', {'dtype': np.float32,
'units': 'm/s',
'default': -0.001}) # 1 mm/s negative buoyancy
])
class PlastElement(Lagrangian3DArray):
variables = Lagrangian3DArray.add_variables([('terminal_velocity', {
'dtype': np.float32,
'units': 'm/s',
'level': OceanDrift.CONFIG_LEVEL_ESSENTIAL,
'description':
'Positive value means rising particles (positive buoyancy)',
'default': 0.01
})])
class FishLarvaeObj(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic eggs/larvae
"""
variables = Lagrangian3DArray.add_variables([
('flexion_stage', {'dtype': np.int64,
'units': '',
'default': 0}),
('u_swim', {'dtype': np.float32,
'units': 'm/s',
'default': 0.}),
('v_swim', {'dtype': np.float32,
'units': 'm/s',
'default': 0.})]) # pre_flexion,flexion,post_flexion 0,1,2 - to implement
class LobsterLarvaeObj(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic eggs/larvae
"""
variables = Lagrangian3DArray.add_variables([('light', {
'dtype': np.float32,
'units': 'ugEm2',
'default': 0.
}), ('u_swim', {
'dtype': np.float32,
'units': 'm/s',
'default': 0.
}), ('v_swim', {
'dtype': np.float32,
'units': 'm/s',
'default': 0.
})])
class LobsterLarvaeObj(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic eggs/larvae
"""
variables = Lagrangian3DArray.add_variables([('neutral_buoyancy_salinity',
{
'dtype': np.float32,
'units': '[]',
'default': 31.25
}),
('age_seconds', {
'dtype': np.float32,
'units': 's',
'default': 0.
}),
('density', {
'dtype': np.float32,
'units': 'kg/m^3',
'default': 1028.
}),
('terminal_velocity', {
'dtype': np.float32,
'units': 'm/s',
'default': 0.
}),
('light', {
'dtype': np.float32,
'units': 'ugEm2',
'default': 0.
}),
('metamorphosis', {
'dtype': np.float32,
'units': '[]',
'default': 0.
}),
('u_swim', {
'dtype': np.float32,
'units': 'm/s',
'default': 0.
}),
('v_swim', {
'dtype': np.float32,
'units': 'm/s',
'default': 0.
})])
class TemplateElementType(Lagrangian3DArray):
"""
Extending LagrangianArray with relevant properties.
Define and name the properties which the elements shall have.
These are added to the inherited properties (e.g. from OceanDrift)
Property names may be freely chosen, but the "update" function (below)
will refer to the names in the specifications of the processes.
"""
variables = Lagrangian3DArray.add_variables([('new_property_1', {
'dtype': np.float32,
'units': '1',
'default': 0
}), ('new_property_2', {
'dtype': np.float32,
'units': '1',
'default': 0
})])
class PelagicPlankton(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic plankton
"""
variables = Lagrangian3DArray.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
('age_seconds', {'dtype': np.float32,
'units': 's',
'default': 0.}),
('light', {'dtype': np.float32,
'units': 'ugEm2',
'default': 0.}),
('survival', {'dtype': np.float32, # generic load to track mortality
'units': '',
'default': 1.})])
class SedimentElement(Lagrangian3DArray):
# Lagrangian3DArray has already the variables terminal_velocity, and wind_drift_factor
variables = Lagrangian3DArray.add_variables([
(
'settled',
{
'dtype': np.int16, # 0 is active, 1 is settled
'units': '1',
'default': 0
}),
('age_seconds', {
'dtype': np.float32,
'units': 's',
'default': 0
}),
('terminal_velocity', {
'dtype': np.float32,
'units': 'm/s',
'default': -0.001
}), # 1 mm/s negative buoyancy
('critical_shear_stress', {
'dtype': np.float32,
'units': 'N/m2',
'default': 0.0
}),
(
'd50',
{
'dtype': np.float32, # median grain size
'units': 'm',
'default': 125.0 * 1e-6
}),
(
'density',
{
'dtype': np.float32, # grain density = mass_solid/volume_solid
'units': 'kg/m^3',
'default': 2650.
}),
])
class SeaLiceElement(Lagrangian3DArray):
"""
Extending Lagrangian3DArray with specific properties for larval and
juvenile stages of sea lice into super individuals
"""
variables = Lagrangian3DArray.add_variables([
('LicePerFish', {
'dtype': np.float32,
'units': '',
'default': 0.5
}),
('AvFishW8', {
'dtype': np.float32,
'units': 'kg',
'default': 4.5
}),
('particle_biomass', {
'dtype': np.float32,
'units': 'kg',
'default': 1000.
}),
('hatched', {
'dtype': np.float32,
'units': '',
'default': 0.
}),
('nauplii', {
'dtype': np.float32,
'units': '',
'default': 0.
}),
('copepodid', {
'dtype': np.float32,
'units': '',
'default': 0.
}),
('dead', {
'dtype': np.float32,
'units': '',
'default': 0.
}),
('eliminated', {
'dtype': np.int8,
'units': '',
'default': 0
}),
('degree_days', {
'dtype': np.float32,
'units': '',
'default': 0
}), #range 40-170
('safe_salinity_above', {
'dtype': np.int8,
'units': '',
'default': 0
}),
('temperature_above', {
'dtype': np.float32,
'units': '',
'default': 10
}),
('temperature_below', {
'dtype': np.float32,
'units': '',
'default': 10
}),
('light', {
'dtype': np.float32,
'units': 'µmol photon s−1 m−2',
'default': 0.
}),
])
class PelagicPlankton(Lagrangian3DArray):
"""Extending Lagrangian3DArray with specific properties for pelagic plankton
"""
variables = Lagrangian3DArray.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, # generic load to track mortality
'units': '',
'default': 1.
})
])