softmobility 1.1.0

Python package to compute the mobility of a soft body in Stokes flows.

SoftMobility is a Python library for modelling deformable assemblies of spheres in Stokes flows. It is intended for scientific users who want to define soft bodies, compute mobility tensors, run differentiable simulations, and optimize design parameters with JAX.

The package is imported as in Python as softmobility.

Try the notebooks online

The fastest way to get a feel for SoftMobility is to run a notebook directly in your browser via Google Colab — no clone, fork, or local install required. The first cell of every notebook installs SoftMobility from this repository when it detects a Colab runtime (locally the cell is a no-op).

Click a badge below to launch the corresponding notebook in Colab.

Tutorials (library introduction):

• 01_assembly_creation

• 02_rigid_mobility

• 03_soft_mobility_simulation

• 04_optimization

• 05_figure_styling

Examples (validation cases & case studies):

• 01_sinking_rigid_body

• 02_sinking_fiber

• 03_rotating_fiber

• 04_fiber_in_shear

• 05_jeffery_rigid

• 06_jeffery_soft

• 07_three_sphere_swimmer

• 08_soft_surfer

For any notebook not listed above, you can build a Colab URL by hand by replacing the GitHub URL prefix https://github.com/C0PEP0D/SoftMobility/blob/ with https://colab.research.google.com/github/C0PEP0D/SoftMobility/blob/.

Installation

SoftMobility requires Python 3.10 or newer. For a new user, the safest path is to work in an isolated environment. Two equivalent recipes follow — pick the one that matches the tooling you already use. The Sphinx installation page in the documentation contains the same recipes plus troubleshooting notes (Apple Silicon, GPU JAX builds, etc.).

With venv

git clone https://github.com/C0PEP0D/SoftMobility.git
cd SoftMobility
python -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -e .

With conda

If you prefer conda (or the faster, drop-in mamba) for environment management, the recommended pattern is to let conda manage the Python sandbox and let pip install the package itself — JAX and a few other dependencies install more reliably from PyPI than from conda-forge:

git clone https://github.com/C0PEP0D/SoftMobility.git
cd SoftMobility
conda create -n softmobility python=3.11
conda activate softmobility
python -m pip install --upgrade pip
python -m pip install -e .

Or, equivalently, use the bundled environment.yml (which performs the same steps in a single command and must be run from the repository root because of the -e . editable install):

git clone https://github.com/C0PEP0D/SoftMobility.git
cd SoftMobility
conda env create -f environment.yml
conda activate softmobility

Verify the installation:

python -c "import softmobility as sm; print(sm.__version__)"

Quick Start

Start with the built-in input and flow objects:

import jax.numpy as jnp
import softmobility as sm

gravity = sm.gravity_field(g=9.81)
flow = sm.shear_flow(shear_rate=1.0)

pos = jnp.array([0.0, 2.0, 0.0])
print(gravity.vector(pos))      # [0, 0, -9.81]
print(flow.velocity(pos))       # [2, 0, 0]
print(flow.gradient(pos))       # velocity-gradient matrix

A complete simulation uses three pieces:

1. sm.SoftBody for the deformable sphere assembly.

2. sm.Flow and optional sm.Field or sm.Scalar inputs.

3. sm.FlowBodyRollout to integrate the body trajectory.

import jax.numpy as jnp
import softmobility as sm

yaml_text = """
dof_names: [x]
design_names: [radius, length, k]
defaults:
  x0: 0.1
  radius: 0.25
  length: 1.0
  k: 1.0
spheres:
  - radius: radius
    position: [-length / 2, 0, 0]
    orientation: [0, x0, 0]
    torque: [0, -k * x0, 0]
  - radius: radius
    position: [length / 2, 0, 0]
    orientation: [0, -x0, 0]
    torque: [0, k * x0, 0]
"""

body = sm.SoftBody(yaml_text, verbose=False)
rollout = sm.FlowBodyRollout(body, sm.no_flow())

positions, orientations, dofs = rollout.rollout(
    dt=0.01,
    n_steps=100,
    init_position=jnp.zeros(3),
    init_orientation=jnp.zeros(3),
)

Tutorials and examples

The notebooks ship in two folders. softmobility/tutorials contains pedagogical walk-throughs of the API, while softmobility/examples collects validation cases against published results and original case studies. New users should start with tutorials/01_assembly_creation and work through the tutorials before moving on to the examples.

Tutorials (softmobility/tutorials/)

• 01_assembly_creation.ipynb — methods to create a sphere assembly

• 02_rigid_mobility.ipynb — mobility properties of a rigid sphere assembly

• 03_soft_mobility_simulation.ipynb — soft mobility tensors and simulation of a trajectory

• 04_optimization.ipynb — optimization principles

• 05_figure_styling.ipynb — paper-figure aesthetics with figstyle

Examples (softmobility/examples/)

• 01_sinking_rigid_body.ipynb — sinking trajectory of a rigid body

• 02_sinking_fiber.ipynb — settling flexible fiber

• 03_rotating_fiber.ipynb — rotating elastic fiber

• 04_fiber_in_shear.ipynb — flexible fiber with intrinsic curvature in shear flow

• 05_jeffery_rigid.ipynb — Jeffery orbits of a rigid dumbbell

• 06_jeffery_soft.ipynb — Jeffery orbit of an elastic dumbbell

• 07_three_sphere_swimmer.ipynb — three-sphere swimmer with a passive elastic arm

• 08_soft_surfer.ipynb — soft surfer in Taylor-Green vortices

Build the documentation locally

The Sphinx sources live in docs/source. To build the HTML pages, first install the development tools (which include Sphinx and its extensions):

pip install -r requirements-dev.txt

Then build from the repository root:

make -C docs html
open docs/build/html/index.html        # macOS
xdg-open docs/build/html/index.html    # Linux

The strict, warnings-as-errors build that mirrors CI is documented in the Developers page (docs/source/developers.rst).

Contributing

Contributions are welcome. The Developers page in the documentation (docs/source/developers.rst) covers the development install, running the tests, building the docs strictly, the versioning and release process, and the policy for opening issues and pull requests. Please read it before sending a PR.

License

SoftMobility is distributed under the 3-clause BSD license. See LICENSE for details.