PyAFV

PyAFV is a Python implementation of the active finite Voronoi (AFV) model in 2D.

The AFV framework was introduced and developed in, for example, Refs. [1, 2, 3].

Check out the Getting started, Examples, Multiprocessing, Performance, Calibration, Citing PyAFV, Contributing to PyAFV, and API reference sections for further information, including how to install the package, usage examples, multiprocess domain decomposition, benchmarks, local development, and the complete API reference.

• Explore a collection of usage examples in Jupyter notebooks on Google Colab.

• See also an interactive simulation demo using PyAFV on Prof. Dapeng (Max) Bi’s homepage!

Note

For the latest updates, see the GitHub repository.

Contents

• Home
• 1. Getting started
  • 1.1. Installation
  • 1.2. A simple example
• 2. Examples
  • 2.1. Relaxation to mechanical equilibrium
  • 2.2. Active finite Voronoi (AFV) dynamics
  • 2.3. Connectivity between cells
  • 2.4. Custom plotting
  • 2.5. Periodic boundary conditions
  • 2.6. Varying cell target areas from cell to cell
• 3. Multiprocessing
  • 3.1. Basic usage
  • 3.2. Repeated build steps
  • 3.3. Halo width
  • 3.4. Decomposition method
  • 3.5. Visualization
  • 3.6. A complete example
  • 3.7. Running on clusters
• 4. Performance
  • 4.1. Measuring performance
  • 4.2. Benchmarking backends
  • 4.3. Benchmarking parallel build
  • 4.4. Benchmarking hybrid parallel build: MPI + Python multiprocessing
• 5. Calibration
  • 5.1. How to calibrate against the DP model
  • 5.2. Usage of the DP simulator
• 6. Citing PyAFV
• 7. Contributing to PyAFV
  • 7.1. Code of Conduct
  • 7.2. How to contribute
  • 7.3. Coding standards
  • 7.4. Documentation requirements
  • 7.5. Writing tests
  • 7.6. Featured examples
  • 7.7. Submitting a pull request
  • 7.8. Reporting issues
  • 7.9. Code review process
  • 7.10. Questions?
• 8. API reference
  • 8.1. pyafv
  • 8.2. pyafv.PhysicalParams
  • 8.3. pyafv.FiniteVoronoiSimulator
  • 8.4. pyafv.ParallelFiniteVoronoiSimulator
  • 8.5. pyafv.visualize_2d
  • 8.6. pyafv.visualize_2d_parallel
  • 8.7. pyafv.target_delta
  • 8.8. pyafv.calibrate
  • 8.9. Experimental APIs

Caution

Future versions may introduce changes to features and APIs.

References

[1]

J. Huang, H. Levine, and D. Bi. Bridging the gap between collective motility and epithelial–mesenchymal transitions through the active finite voronoi model. Soft Matter, 19(48):9389–9398, 2023. doi:10.1039/D3SM00327B.

[2]

E. Teomy, D. A. Kessler, and H. Levine. Confluent and nonconfluent phases in a model of cell tissue. Phys. Rev. E, 98:042418, Oct 2018. doi:10.1103/PhysRevE.98.042418.

[3]

W. Wang and B. A. Camley. Divergence of detachment forces in the finite Voronoi model. arXiv preprint arXiv:2604.15481, 2026. doi:10.48550/arXiv.2604.15481.

[4]

J.-Q. Lv, P.-C. Chen, Y.-P. Chen, H.-Y. Liu, S.-D. Wang, J. Bai, C.-L. Lv, Y. Li, Y. Shao, X.-Q. Feng, and B. Li. Active hole formation in epithelioid tissues. Nature Physics, 20(8):1313–1323, 2024. doi:10.1038/s41567-024-02504-1.

Indices

• Index

• Module Index