Awesome

Author: Nicholas A. Battista, Ph.D. <br> Email: <a href="mailto:battistn[at]tcnj[.]edu"> battistn[at]tcnj.edu </a> <br> Website: <a href="http://battistn.pages.tcnj.edu"> http://battistn.pages.tcnj.edu </a> <br> Department: Mathematics & Statistics (<a href="https://mathstat.tcnj.edu/">TCNJ MATH</a>) <br> Institution: The College of New Jersey (<a href="https://tcnj.edu/">TCNJ</a>) <br>

<H4>An easy to use immersed boundary method in 2D, with full implementations in MATLAB and Python that contains over 75 built-in examples, including multiple options for fiber-structure models and advection-diffusion, Boussinesq approximations, and/or artificial forcing. </H4> <h3 style="color:red;"> If you use this software for research, educational, or recreational purposes, please let Nick Battista (<a href="mailto:battistn[at]tcnj.edu">battistn[at]tcnj[.]edu</a>) know! </h3> <hr> </hr> <H3>If you use the code for research, please cite the following papers:</H3>

N.A. Battista, A.J. Baird, L.A. Miller, A mathematical model and MATLAB code for muscle-fluid-structure simulations, Integ. Comp. Biol. 55(5):901-911 (2015), <a href="http://www.ncbi.nlm.nih.gov/pubmed/26337187"> LINK </a>
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 (2017), <a href="http://iopscience.iop.org/article/10.1088/1748-3190/aa5e08/meta"> LINK </a>
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) <a href="http://onlinelibrary.wiley.com/doi/10.1002/mma.4708/epdf?author_access_token=HKAwHFmV1yKY6_lY4_I0dU4keas67K9QMdWULTWMo8P3KIzKeMHgO9D_yBVf1ZxhuLjZr3RgM74HKTOZj3MqwU9I9Skl8KVs-2ruPFMgjIXF0QlZful2HU6NM7TQ0wkl"> LINK </a>

<hr> </hr> <H3>IB2d Video Tutorials:</H3>

Tutorial 1: <a href="https://youtu.be/PJyQA0vwbgU"> https://youtu.be/PJyQA0vwbgU </a>
An introduction to the immersed boundary method, fiber models, open source IB software, IB2d, and some FSI examples!
Tutorial 2: <a href="https://youtu.be/jSwCKq0v84s"> https://youtu.be/jSwCKq0v84s </a>
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 3: <a href="https://youtu.be/I3TLpyEBXfE"> https://youtu.be/I3TLpyEBXfE </a>
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 4: <a href="https://youtu.be/4D4ruXbeCiQ"> https://youtu.be/4D4ruXbeCiQ </a>
The basics of visualizing data using open source visualization software called <a href="https://wci.llnl.gov/simulation/computer-codes/visit/"> VisIt </a> (by Lawrence Livermore National Labs), visualizing the Lagrangian Points and Eulerian Data (colormaps for scalar data and vector fields for fluid velocity vectors)

Substantial speed-ups in performance for fluid solver and force spreading operations in MATLAB implementation. Speeds-ups in Python implementation forthcoming (February 2024): <br/><br/>

<p align="center"> <img width="464" height="273" src="https://static.wixstatic.com/media/50968c_1c29f0b383544da79b47167d551a199c~mv2.webp"> </p> <H5 align="center"> <ins> Figure</ins>: Showing the percent runtimes when compared to IB2d's previous implementations, i.e., the</br> ratio of runtimes x 100. The simulation involved a square grid with an equal number of grid </br> cells (Nx) in the x- and y- directions. The corresponding # of Lagrangian points for each case was 2*Nx. </br></br> </H5>

Our software release paper on the recenty added concentration dynamics infrastructure was published in Bioinspiration & Biomimetics. More information can be found at the following link:

M. Santiago, N.A. Battista, L.A. Miller, S. Khatri, <a href="https://doi.org/10.1088/1748-3190/ac4afa"> Passive concentration dynamics incorporated into the library IB2d, a two-dimensional implementation of the immersed boundary method </a>, Bioinspiration & Biomimetics 17: 036003 (2022)
<a href="https://www.mateasantiago.com"> Matea Santiago </a> has updated the advection-diffusion solver to a third-order WENO scheme.
We have released a semi-automatic meshing tool, <a href="https://github.com/dmsenter89/MeshmerizeMe"> MeshmerizeMe </a>, to help discretize Lagrangian geometries. More information can be found in our software release paper:

D.M. Senter, D.R. Douglas, W.C. Strickland, S. Thomas, A. Talkington, L.A. Miller, N.A. Battista, <a href="https://doi.org/10.1088/1748-3190/ababb0"> A Semi-Automated Finite Difference Mesh Creation Method for Use with Immersed Boundary Software IB2d and IBAMR </a>, Bioinspiration and Biomimetics 16(1): 016008 (2021) </br>
The MATLAB plotting routine is incompatible with MATLAB R2020a and R2020b. If you run into this issue, please consider visualizing the .vtk data with <a href="https://wci.llnl.gov/simulation/computer-codes/visit/"> VisIt </a> or <a href="https://www.paraview.org/"> ParaView </a> instead.

<hr> </hr> <H4> VisIt Workaround for macOS 11 (Big Sur) </H4>

--> Many VisIt users have gotten the following error when trying to open visualization files:

<p align="center"> "The MetaData server running on localhost could not get the file list for the current directory" </p>

--> To circumvent this error, try opening VisIt from the command line. Try the following:

<ol type="1"> <li> In your terminal, change directory until you're in the directory you want to open (eg - the viz_IB2d folder) </li> <li> In your terminal, type: /Applications/VisIt.app/Contents/Resources/bin/visit -gui (or the correct path based to where you installed VisIt) </li> </ol> <hr> </hr>