IB2d!

Open Source Fluid-Structure Interaction software based on Peskin's Immersed Boundary Method

An easy to use immersed boundary method in 2D, with robust options for fiber-structure models with possible porosity and/or poroelasticity, advection-diffusion, and/or artificial forcing. 

The software has two full implementations - one in MATLAB and another in Python 3. The code can be found on my github site. It also contains over 60 examples that illustrate the breadth and functionality of the code.

If using the code for research purposes, please cite the following three papers:
 

  • N.A. Battista, A.J. Baird, L.A. Miller, A mathematical model and MATLAB code for muscle-fluid-structure simulations, Integ. Comp. Biol. 2015, LINK

  • N.A. Battista, W.C. Strickland, L.A. Miller,  IB2d:a Python and MATLAB implementation of the immersed
    boundary method,
    , Bioinspiration and Biomemetics 12(3): 036003, LINK

  • N.A. Battista, W.C. Strickland, A. Barrett, L.A. Miller, IB2d Reloaded: a more powerful Python and MATLAB implementation of the immersed boundary method, in press Math. Method. Appl. Sci. 41:8455-8480 (2018) PREPRINT, LINK

IB2d Papers!

Complementary Papers:
 

  • D.M. Senter, D.R. Douglas, W.C. Strickland, S. Thomas, A. Talkington, L.A. Miller, N.A. Battista, A Semi-Automated Finite Difference Mesh Creation Method for Use with Immersed Boundary Software IB2d and IBAMR, Bioinspiration and Biomimetics 16(1): 016008 (2021) [LINK]

IB2d Video Tutorials!

Video Tutorials (rough drafts):
 

  • Tutorial 1: https://youtu.be/PJyQA0vwbgU

    • An introduction to the immersed boundary method, fiber models, open source IB software, IB2d​, and some FSI examples!
       

  • Tutorial 2: https://youtu.be/jSwCKq0v84s

    • A tour of what comes with the IB2d software, how to download it, what Example subfolders contain and what input files are necessary to run a simulation
       

  • Tutorial 3https://youtu.be/I3TLpyEBXfE

    • An overview of how to construct immersed boundary geometries and create the input files (.vertex, .spring, etc.) for an IB2d simulation to run using the oscillating rubberband example from Tutorial 2 as a guide.
       

  • Tutorial 4https://youtu.be/4D4ruXbeCiQ

    • The basics of visualizing data using open source visualization software called VisIt (by Lawrence Livermore National Labs), visualizing the Lagrangian Points and Eulerian Data (colormaps for scalar data and vector fields for fluid velocity vectors)

IB2d Simulations of the Month!

(Colormap is vorticity)

A rigid cylinder is placed in the center of a channel, with an attached flexible tail. The tail is composed of springs, beams, and massive points, while the the rest of the geometry is held nearly rigid using target points.

Inflow begins on left side of the channel and moves right; it begins at 0 m/s and slowly ramps up to 5 m/s. It is clear that when the flow speed is high enough it induces vortex shedding off both the cylinder and tail, in addition to pushing around (and deforming) the tail.

(Image Credit: Gem Perkins, SoS TCNJ)

Jellyfish with Tentacles/Oral Arms!

Simulation by Jason Miles


Check out our paper: J.G. Miles, N.A. Battista, Naut Your Everyday Jellyfish Model: exploring how tentacles and oral arms affect locomotion, Fluids 4(3): 169 (2019)

(Colormap is the magnitude of velocity)

"Jellyfish Locomotion Model"

By Jason Miles (TCNJ Math Major)

Model based off of A. Hoover, L. Miller, A numerical study of the benefits of driving jellyfish bells at their natural frequency, J. Theor. Biol. 374: 13-25, 2015 

COSA_Jason.jpg

"Large Deformation Turek-Hron

FSI Benchmark"

"Asymmetric Damped Flexible Ball Oscillator"

A flexible ball is tethered to a channel by two springs, each of a different damping coefficient. The ball begins stretched from its equilibrium position and then oscillates back and forth. Vortices form and get shed off the ball as it changes direction

"Rayleigh Taylor Instability"

The Rayleigh-Taylor Instability arises when a heavier fluid sits atop a lighter fluid. Although initially stable, any slight perturbation to the interface will cause the instability to quickly grow!

This simulation uses the Boussinesq approximation to model slight density variations to allow the instability to occur.

"Seagrass in Oscillatory Flow"

"Undulating Swimmer"

   IB2d simulation of oscillating flow past a patch of starfish!

D.M. Senter, D.R. Douglas, W.C. Strickland, S. Thomas, A. Talkington, L.A. Miller, N.A. Battista, A Semi-Automated Finite Difference Mesh Creation Method for Use with Immersed Boundary Software IB2d and IBAMR, Bioinspiration and Biomimetics 16(1): 016008 (2021) [LINK]