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Stokes: Python package to create triangulated surface mesh and solve hydrodynamic Stokes equation

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Stokes: create triangulated surface meshes and solve hydrodynamic Stokes equation

two_cilia.png

This is a collection of Python packages previously used to solve biological hydrodynamics problems, see references [3,4] below

  • FBEM: routines to solve Stokes equation using a third-party hydrodynamic solver
    (Liu's fast multipole boundary element method FMM-BEM, see references [1,2])
  • mesh: routines to be create triangulated meshes to be used as input files for FBEM
    • mesh.plot: routines for 3D mesh visualizations
  • simulation_helpers: helpful routines to run large-scale simulations with multi-threading.

Installation:

  • Please use setup.py; run as python setup.py develop to install code in development mode.
  • Copy FBEM executables to FBEM/exe folder (see FBEM README).
  • Additional packages can be installed for 3D mesh visualizaiton (see mesh README).

Usage

  • Please see examples in /example/
  • The folders of the individual subprojects contain additional README files.

Authors

If you want to use this code in a scientific publication, please cite [3].

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Stokes: Python package to create triangulated surface mesh and solve hydrodynamic Stokes equation

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