stoked 1.0.0

Simulation and visualization of Stokesian dynamics for N interacting particles

StokeD

StokeD solves the Stokesian dynamics (SD) equations for N interacting particles. SD is a generalization of Brownian dynamics (BD) that includes hydrodynamic coupling interactions.

Electrically charged particles repulsed from each other confined in a harmonic potential

Seven particles spinning due to an applied torque; the rotation of the fluid results in translational motion of the outer particles

Features

• Hydrodynamic coupling interactions can be turned on or off
• Flexible interface for user-defined particle interactions
• Several interactions already available: point electrostatics and electrodynamics, screened Coulomb, van der Walls, hard-sphere collisions, gravity
• Animation module for visualizing trajectories

Installation

StokeD can be installed with pip

pip install stoked

Usage

See the examples folder for how to use StokeD.

Run any of the available examples without explicit installation using uv:

Command	Description
uvx stoked free_particle	Free Brownian diffusion in 3D
uvx stoked estatics	Electrostatic interactions with harmonic confinement
uvx stoked ellipsoid	Ellipsoidal particle with external force and torque
uvx stoked tt_coupling	Hydrodynamic translation-translation coupling
uvx stoked rt_coupling	Hydrodynamic rotation-translation coupling
uvx stoked bigaussian_potential	Particle in double-well potential

For full documentation, see docs folder.

License

StokeD is licensed under the terms of the MIT license.