opendrift.models.larvalfish_extended

Attributes

logger

Classes

LarvalFishExtendedElement	Extending Lagrangian3DArray with specific properties for larval fish
LarvalFishExtended	Extended biological particle trajectory model based on OpenDrift.

Module Contents

opendrift.models.larvalfish_extended.logger

class opendrift.models.larvalfish_extended.LarvalFishExtendedElement(**kwargs)

Bases: opendrift.models.oceandrift.Lagrangian3DArray

Extending Lagrangian3DArray with specific properties for larval fish and generic biological particles (e.g. phytoplankton).

Initialises a LagrangianArray with given properties.

Args:

Keyword arguments (kwargs) with names corresponding to the OrderedDict ‘variables’ of the class, and corresponding values. The values must be ndarrays of equal length, or scalars. All (or none) variables must be given, unless a default value is specified in the OrderedDict ‘variables’ An empty object may be created by giving no input.

variables

class opendrift.models.larvalfish_extended.LarvalFishExtended(*args, **kwargs)

Bases: opendrift.models.oceandrift.OceanDrift

Extended biological particle trajectory model based on OpenDrift.

Extends the base LarvalFish model with:

• Configurable vertical behavior: depth-keeping and diel vertical migration (DVM) using solar elevation for day/night detection.

• Support for both larval fish and phytoplankton particle types.

• Multiple egg hatching methods (temperature-dependent or fixed-time).

• Adaptive depth-band targeting with configurable band widths.

Vertical behavior modes

• none: No active vertical movement (passive drift).

• depth: Maintain a preferred depth band around z_pref.

• dvm: Diel vertical migration between z_day (daytime) and z_night (nighttime) depths, using solar_elevation() to determine day/night state.

Particle types

• larva: Full egg/hatching/growth lifecycle. Only hatched larvae exhibit active vertical behavior; eggs remain passive.

• phytoplankton: All particles have active vertical behavior from the start. No egg/growth stages.

Initialise OpenDriftSimulation

Args:

seed: integer or None. A given integer will yield identical

random numbers drawn each simulation. Random numbers are e.g. used to distribute particles spatially when seeding, and may be used by modules (subclasses) for e.g. diffusion. Specifying a fixed value (default: 0) is useful for sensitivity tests. With seed = None, different random numbers will be drawn for subsequent runs, even with identical configuration/input.

iomodule: name of module used to export data

default: netcdf, see opendrift.io for more alternatives. iomodule is module/filename without preceeding io_

loglevel: set to 0 (default) to retrieve all debug information.

Provide a higher value (e.g. 20) to receive less output.

logtime: if True, a time stamp is given for each logging line.

logtime can also be given as a python time specifier (e.g. ‘%H:%M:%S’)

logfile:

None (default) to send output to console. A string to send output to logfile. Or to get output to both terminal and file:

[<filename.log>, logging.StreamHandler(sys.stdout)]

ElementType

Any trajectory model implementation must define an ElementType.

required_variables

Any trajectory model implementation must list needed variables.

_compute_band_half_width(z)

Compute depth band half-width: clamp(dz_min, dz_rel*|z|, dz_max).

_target_into_band(z, center, half_w)

Return target depth that moves z into [center-half_w, center+half_w].

If z is already inside the band, returns z (no movement).

_apply_vertical_behavior()

Apply active vertical behavior based on configured mode.

Modes

• none: No active vertical movement.

• depth: Maintain depth band around z_pref.

• dvm: Diel vertical migration between z_day and z_night, using solar_elevation() for day/night detection.

For larvae (particle_type=’larva’), only hatched larvae (not eggs) exhibit active vertical behavior. Eggs remain passive. For phytoplankton, all particles are active.

update_fish_larvae()

update()

Update particle state: biology, advection, mixing, vertical behavior.