About this manual

This document describes a package of computer software called IBIS that implements the immersed boundary method in a new user-friendly way. For all of the applications of the IB method listed above, the method was applied by people with expertise in each of fluid dynamics, numerical analysis, and scientific programming; people who had spent a good deal of time learning IB ideas and the intricacies of implementing them. Even when adapting someone else's numerical routines for the IB method to a new problem, it is much easier to break the routines than it is to successfully modify them. The important feature of the new IBIS software is that it has been developed so that people without expertise in any of fluid dynamics, numerical analysis, or scientific programming can use it with relative ease and with very little need for interaction with the core numerical routines. Because of the numerous technical difficulties involved in implementing the IB method, we saw the need for more user-friendly software that is capable of performing IB simulations without significant modifications to the basic numerical routines that solve the model equations. IBIS was produced to meet this need. IBIS involves a simple new language for setting up IB problems, a preprocessor that translates commands in that language into input data for the core numerical software, and graphical tools for visualizing and animating simulation results.

The organization of this document is as follows:

• First, a detailed example of the use of IBIS is given. This example will show the simplicity of IBIS's preprocessor and postprocessors and show the power of the IB method.
• Second, an introduction to theory behind the immersed boundary method is given. This introduction includes a description of the model fluid equations and a model of the elastic objects within the domain. It is not necessary that the user know all the details of the method, but a basic understanding is helpful in picking important parameters for the numerical simulations.
• Third, a brief description of the IBIS user software package is given. This introduction describes the the different software components of the IBIS package and their function.
• The next section contains the IBIS preprocessor programming guide. which gives programming details for a language designed explicitly for initialization of two-dimensional IB simulations.
• Then the user specified programs for controlling the immersed boundaries and sources/sinks are described. These programs allow one to actively change the immersed boundary to create force which alter the fluid flow, or to add or remove fluid from a specified region of space.
• The next section containds several detailed examples, including examples with active immersed boundaries, and with fluid sources and sinks.
• Lastly, the file formats for input to and output from the IBIS software are described.