Biohydrodynamics MATLAB Toolbox

A. Munnier and B. Pinçon

Institut Elie Cartan (Nancy)	INRIA Lorraine Projet CORIDA

Contents

• More animations are available in the Demos Gallery page and here.
• BhT is free (distributed under licence GNU GPL).

Introduction

Biohydrodynamics Toolbox (BhT) is a collection of M-Files for the design, the simulation and the analysis of animal motions in fluids. Animals are modeled as systems of articulated rigid solids. More widely, BhT allows one to perform easily any kind of numerical simulation involving 2d motions of solids in an ideal fluid (simulations of so-called fluid-structure interaction systems).

An articulated fish	An articulated bird

Demos

BhT includes tools to realize short videos. Click on the images below to play the related QuickTime movies.

Swimming fish (7.5 Mo) Fish starting from rest. Unbounded fluid domain. Trajectory of the center of mass displayed. Velocity vector of the center of mass displayed.
Flapping bird (3.1 Mo) Bird starting from rest. Unbounded fluid domain. Flapping optimized to minimize the torques of the joints. Velocity vector of the center of mass displayed.
Ellipse-shaped solid in a box filled by a fluid (664 Ko) Bounded fluid domain. Buoyant force taken into account. Collisions with the boundary managed.
Fall of two ellipse-shaped solids in a fluid (932 Ko) Buoyant force taken into account. Collisions between solids managed.
Six ellipse-shaped solids in a fluid (1.8 Mo) The blue solids have a larger density than the fluid's and the red ones, a smaller. Buoyant force taken into account. Collisions between solids managed.

More videos are available in the Demos Gallery page and here.

Some of BhT's features

• BhT deals with ideal fluid only (i. e. inviscid and incompressible) and whose flow is assumed to be irrotational (i. e. vortex free).
• The strong coupling between Solid and Fluid Mechanics is taken into account (no bodies hydrodynamically decoupled hypothesis).
• Animals' articulations are prescribed by the user as functions of time.
• Buoyant force and collisions are managed.
• Fast computations (a few seconds for the Fall of two ellipse-shaped solids example above on a common laptop and a couple of minutes for the Swimming fish).
• High accuracy (based on fully explicit equations of motion and the implementation of the Nyström's method to compute the fluid potential).  

BhT documentation

BhT contains a complete documentation involving examples and tutorials.

Easy experiment design

Simulations are fast and easy to make. Once you have decided what your simulation will be, all of its features are described in a unique text-file by means of intuitive fields.

Example of what a text-file describing an experiment looks like

max time = 90 time step = 0.1 mesh size = 0.2 fluid density = 1 fish = {        initial position = [0;0;0]        initial velocity = [0;0;0]        colormap = autumn     link = {           label = head           mfilename = bht_ellipse           settings = [2,0.5,0,0,1]           density = 1.2   }     link = {           label = second           father = head           mfilename = bht_ellipse           settings = [2,0.5,0,0,1]           hinge coord = [3;0]           hinge local coord = [-3;0]           density = 1.2   }     link = {           label = third           father = second           mfilename = bht_ellipse           settings = [2,0.5,0,0,1]           hinge coord = [3;0]           hinge local coord = [-3;0]                           }         }

Efficiency of locomotions strategies

BhT provides tools to study and optimize swimming or flapping strategies in terms of energy, power and torques.

• Computation of the energy balance (energy of the fluid, energy of the deformations...).
• Computation of the power expended by the animal.
• Computation of the torques of the joints.

Example of what can be done using BhT as regards energy, power and torques.

About BhT

• BhT has been developed and tested with MATLAB 7.4.  
• BhT is distributed under licence GNU GPL.
• BhT project is hosted by Inria Gforge.
• Please report bugs, ask your questions or merely share your BhT's simulations on the forum.

Downloads

• Biohydrodynamics Toolbox + Documentation (download page).
• Biohydrodynamics Toolbox on Matlab Central (download page).