This package contains python codes to perform simulations of multiple fibers at low Reynolds number. The fiber is discretized as a series of spherical beads connected by spring constraints. The motion of each bead in Stokes flow is given by the mobility relation, which relates the bead velocities to external forces applied on each bead.
This package is inspired from the RigidMultiblobsWall organization.
For the theory behind, see:
[1] U. Makanga, Simulating transport and clogging of elastic fibers in structured environments, M.Sc. Thesis (2020).
[2] E. Gauger and H. Stark, Numerical study of a microscopic artificial swimmer. Physical Review E 74, 021907 (2006).
[3] F. B. Usabiaga, B. Kallemov, B. Delmotte, A.P.S Bhalla, B. E. Griffith, and A. Donev, Hydrodynamics of suspensions of passive and active rigid particles : a rigid multiblob approach, Communications in applied mathematics and computional science 11, 217 (2016), arXiv: 1602.02170.
[4] U. Makanga, M. Sepahi, C. Duprat, and B. Delmotte, Obstacle-induced lateral dispersion and nontrivial trapping of flexible fibers settling in a viscous fluid (2023), Physical Review Fluids, 8(4):044303, arXiv: 2209.10692.
- configuration/: it contains generated .vertex and .clones files to run examples.
- fiber/: it contains a class to handle a single fiber.
- force/: it contains functions to compute external and internal elastic forces, see [1], [2] and [4].
- generate_vertex_and_clone_files/: it contains main files to generate .vertex and .clones files.
- integrator/: it contains the solver and the scheme to integrate the equation of motion.
- mobility/: it contains functions to compute the mobility matrix M and the product MF respectively via CPU (accelerated with numba) and GPU, see [3] and [4].
- multi_fibers/: it contains main files to run multi-fibers simulations, currently adapted in the case of sedimentation at low Reynolds number.
- quaternion/: it contains the class to handle quaternions.
- read_input/: it contains the class to read input data.
- visit/:
The package is implemented in python (version 3.x), so there is no need to compile it. However, we provide functions to compute the mobility matrix M and the matrix vector product MF with respectively numba and pycuda. All you need is to have the package numba installed in your python environment and a GPU compatible with CUDA to use the pycuda implementation.
We now explain how to run an example on a deformation of a flexible fiber settling in a viscous fluid. First, move to the directory 'multi-fibers/' and run the code as follows
mkdir output
python main_multi_fibers.py --input-file inputfile.dat
Please contact Ursy Makanga (ursy.makanga@polytechnique.edu) for any problems or suggestions regarding this package.