Ichthyop: A Lagrangian tool for modelling ichthyoplankton dynamics

Full Changelog: https://github.com/ichthyop/ichthyop/compare/v3.4.2...v3.5.0-beta.1

Release Notes — Java Changes (3.4.2 → 3.5.0)

New Features

New biological/behavioral processes

Exponential growth model (ExponentialGrowthAction.java): new growth process where length grows exponentially as a function of temperature (L(t) = L₀ · exp(bTᶜt)), configurable with b, c, max_length, initial_length parameters, and kills the particle with a new LARGE mortality cause if it exceeds max_length.

Rafting process (RaftingAction.java): moves a particle to the surface once a given age/size threshold is reached, so it can "raft" at the surface.

Generic process activation/deactivation framework (AbstractAction.java): every action now supports activation_variable (age or length), activation_minimum_class_value, and activation_maximum_class_value, letting any action be turned on/off based on particle age or length via a new isActive(particle) helper. This replaces several bespoke age.min/age.max implementations previously scattered across orientation actions (CardinalOrientationAction, RheotaxisOrientationAction, ReefOrientationAction) and is now applied consistently across AdvectionAction, BitAction, BuoyancyAction, DebGrowthAction, DebGrowthAction_LP, GradientMoveAction, HDispAction, LethalSaltAction, LethalTempAction, LinearGrowthAction, MigrationAction, OntogeneticMigrationAction, RecruitmentStainAction, RecruitmentZoneAction, SnoozeAction, SoleGrowthAction, SwimmingAction, VDispAction, WaveDriftFileAction, WindAction, WindDriftAction, and WindDriftFileAction.

Swimming/orientation velocity now supports age, length, or CSV-based calculation

SwimmingAction.java and OrientationVelocity.java (used by CardinalOrientationAction, RheotaxisOrientationAction, ReefOrientationAction) now share a common mechanism to compute swimming speed either from a CSV file (age- or length-indexed) or from a formula based on body length (swimming.body.length.speed), controlled by new swimming.speed.mode and swimming.speed.csv.enabled parameters.

RheotaxisOrientationAction.java: new can.swim.against.current parameter to let particles swim against the current instead of being capped at current speed.

ReefOrientationAction.java: new attraction.mode parameter (edges or barycenter) to choose whether particles are attracted to the closest edge/vertex of a target polygon or its barycenter; internal distance/closest-point computations refactored into pluggable strategies.

New/expanded output trackers

AgeTracker.java: new tracker recording particle age (days) in the NetCDF output.

AbstractInitialStateTracker.java, InitialFloatTracker.java, InitialLatTracker.java, InitialLonTracker.java: new infrastructure to record "initial state" variables (lon_init, lat_init) once per particle at release time rather than at every time step.

ReleaseZoneTracker.java now extends AbstractInitialStateTracker instead of AbstractTracker, and ZoneRelease.java registers it via the new addPredefinedInitialStateTracker.

OutputManager.java: adds support for initial-state trackers (writeInitialStateToNetCDF), invoked by ReleaseManager.java on every release event.

IParticle / Particle.java: new getLength() accessor exposed at the particle level.

Dataset improvements

New getBottomDepth(double[] pGrid) method added to IDataset and implemented across dataset classes (NemoDataset, Mars3dCommon, Roms3dCommon, Mercator_3D, NoveltisDataset); used by MigrationAction to replace the old getBathy bounding logic.

2D datasets (GlobCurrent, Mars2dCommon, Mercator2dDataset, NemoDataset_2D, OscarDataset, Regular2D, Regular2DProjected, Roms2dDataset) now return 1 from get_nz() instead of throwing UnsupportedOperationException, improving compatibility of generic code paths with 2D runs.

MigrationAction.java: new optional method=linear mode (getDepthLinear) that linearly interpolates particle depth between day/night targets around sunrise/sunset instead of a step function.

WaveDriftFileAction.java: refactored variable naming (Stokes components separated from wave velocity/period), new wave_constant_over_depth and depth_max parameters, and NaN-safe handling of Stokes drift components.

WindDriftFileAction.java: added a latitude-flip patch (shiftLat) to correctly handle wind files whose latitude dimension is decreasing.

Bug Fixes

DebGrowthAction_LP.java: fixed an incorrect unit conversion for energy conductance (V_dot) and corrected the structural growth flux computation (flow_p_G), which was previously divided by E_G twice.

GradientMoveAction.java: fixed a sign/direction bug in Cell.direction() and corrected the velocity unit conversion (cm/s → m/s).

LethalTempAction.java / LethalSaltAction.java: consolidated and corrected the logic for constant vs. CSV-file-based lethal temperature/salinity thresholds; previously the growth-stage-based branching could apply mismatched thresholds.

LengthStage.java: fixed the stage-lookup logic (getStage), which could return incorrect indices near stage boundaries.

AbstractStage.java: corrected the validation check comparing the number of stage tags vs. thresholds (now expects tags.length == thresholds.length + 1).

RequiredVariable.java: interpolation now skips NaN values instead of propagating them into the interpolated result.

Mercator_3D.java: particle grid index lookups changed from floor to round for depth/coordinate calculations.

DatasetUtil.java: fixed date-parsing patterns (yyyy-MM-dd → yyyy-M-d) to correctly parse single-digit month/day values in NetCDF time units.

RecruitmentStainAction.java: particle is now explicitly lock()ed upon recruitment in a stain.

VonMisesRandom.java: added support for a fixed random seed (via ParameterManager / app.seed block) to make simulations reproducible.

Refactors / Internal Changes

BuoyancyAction.java: density computation refactored into pluggable functional interfaces (getDensity), with a new density.method (constant/file) and density.class (age/length) parameter pair replacing the old implicit CSV-file detection.

LinearGrowthAction.java: growth computation split into growWithFood/growWithoutFood strategies, gated by a new growth.food.enabled flag, and now takes an explicit initial_length parameter instead of using the first stage threshold.

SoleGrowthAction.java: also switched to an explicit initial_length parameter and made length/stage trackers independently toggleable.

CheckGrowthParam.java: now also recognizes action.growth.exponential as a valid growth module (alongside action.growth and action.growthDeb), enforcing that only one growth module is active at a time.

ParticleMortality.java: added new LARGE mortality cause (for the exponential growth cap).

Minor UI reorganizations in IchthyopView.java (WMS server list) and NewConfigView.java (generic template promoted to top of the config tree).

Bug fix

Release zone output was computed at record frequency, which led sometimes to -1 values. Now it is computed just after release event (Eliot bug)

In the MigrationAction.java, positive depth values were not converted to negative ones, contrary to what is stated on the console

Bug in bouncing when 2D datasets are used (bug introduced in 3.4)

New features

Particle age is provided as a standard output

Particle initial longitudes and latitudes are provided as a standard output

In MigrationAction, the depth of the particle can be linearly interpolated between sunrise and sunset. And the daytime depth is reached at the maximum of the day, and conversely for the night time depth

For RheotaxisOrientationAction, possibility to control whether particles can swim against the current or not with the can.swim.against.current parameter. Default if false.

Adding possibility to use speed in bodylength/seconds for orientation velocity calculation (#123).

In ReefOrientationAction, possibility to use either polygon edges or barycenters to computed distances to reefs (Celine's request)

Rafting process has been implemented (#114): the particle moves at the surface when reaching a certain age.

Exponential growth has been implemented (#115)

For each processes, user now can control whether it is active or not, depending on either age or length (if growth is activated).