API reference¶

All public APIs are documented here with full signatures, parameters, and governing equations.

Module layout¶

jbubble/
├── __init__.py           # run_simulation, fit_parameters, SaveSpec, SolverConfig, solve_eom, FitResult
├── simulation.py         # SimulationResult
├── solver.py             # SaveSpec, SolverConfig, solve_eom
├── metrics.py            # mse_radius, mse_emission, …
├── fitting.py            # fit_parameters, FitResult, Parameter, unwrap
├── bubble/
│   ├── state.py          # BubbleState
│   ├── property.py       # Property, ConstantProperty, NeuralProperty, as_property
│   ├── gas.py            # GasModel, PolytropicGas, VanDerWaalsGas
│   ├── shell.py          # ShellModel, NoShell, LipidShell, ThickShell, surface tension Properties
│   ├── medium.py         # MediumModel, NewtonianMedium, KelvinVoigtMedium, NeoHookeanMedium, PowerLawMedium
│   └── eom.py            # EquationOfMotion, RayleighPlesset, ModifiedRayleighPlesset, KellerMiksis
├── acoustics/
│   └── emission.py       # EmissionModel, IncompressibleMonopole, QuasiAcoustic
├── pulse/
│   ├── __init__.py       # ToneBurst, SampledPulse, ChirpPulse, NeuralPulse, Scaled, Summed, Offset, envelopes
│   └── shapes.py         # PulseShape, Sine, Square, Sawtooth, Rectangular, …
├── style/                # light.mplstyle, dark.mplstyle (Matplotlib styles)
└── utils/
    ├── presets.py        # BubblePreset, free_bubble, lipid_bubble, thick_shell_bubble
    └── gridsweep.py      # GridSweep

Import conventions¶

Only top-level orchestration functions are re-exported from the package root:

# Top-level imports
from jbubble import (
    run_simulation,
    fit_parameters,
    SaveSpec,
    SolverConfig,
    solve_eom,
    FitResult,
)

# Subpackage imports (required for all model classes)
from jbubble.bubble.eom import KellerMiksis, RayleighPlesset
from jbubble.bubble.gas import PolytropicGas, VanDerWaalsGas
from jbubble.bubble.shell import NoShell, LipidShell, ThickShell
from jbubble.bubble.shell import (
    GompertzSurfaceTension,
    MarmottantSurfaceTension,
    SmoothMarmottantSurfaceTension,
)
from jbubble.bubble.medium import (
    NewtonianMedium,
    KelvinVoigtMedium,
    NeoHookeanMedium,
    PowerLawMedium,
)
from jbubble.bubble.property import ConstantProperty, NeuralProperty
from jbubble.bubble.state import BubbleState
from jbubble.acoustics import IncompressibleMonopole, QuasiAcoustic
from jbubble.pulse import ToneBurst, ChirpPulse, SampledPulse, NeuralPulse
from jbubble.pulse import SoftRectangularEnvelope, HannEnvelope, TukeyEnvelope
from jbubble.pulse.shapes import Sine, Square, Sawtooth
from jbubble.utils.presets import free_bubble, lipid_bubble, thick_shell_bubble
from jbubble.utils.gridsweep import GridSweep
from jbubble.fitting import Parameter, unwrap

Pages¶

Page	Contents
bubble	State, Property, gas, shell, medium, EoM classes
pulse	ToneBurst, ChirpPulse, SampledPulse, NeuralPulse, envelopes, composition
shapes	PulseShape subclasses (Sine, Square, Rectangular, …)
acoustics	EmissionModel, IncompressibleMonopole, QuasiAcoustic
solver	SaveSpec, SolverConfig, solve_eom
simulation	SimulationResult, run_simulation
metrics	Differentiable loss functions
fitting	fit_parameters, FitResult, Parameter, unwrap
utils	Presets, GridSweep, figure styles