JCFD: A Software to model an Application in Bio Fluid Dynamics

JCFD
A Software to model an Application in Bio Fluid Dynamics.

Christian Wüst
Computational Mathematics
University of Zurich
christian.wuest@math.uzh.ch

Founded by the University of Zurich and the ETH Zurich 2004-2005. Programmed by Philipp Thomann and Christian Wüst. Further developped for my Master Thesis (2005) and my PhD Thesis (soon).

Motivation
We created a program that is adapted for the biological application of dung fly sperm flow simulation. Nevertheless it is used for solving other types of differential equations. It is written in Java and provides several interfaces to Matlab. The tests are run on a parallel Computer using shared memory parallelisation (SunFire 6800 with 32 CPUs and 144 GB RAM).

Why develop another code
Currently there exists big variety of finite-element software, free and commercial code. Our intention to write the whole code on our own was to be able to have an easy extendable and customizable software. Changing bits even in most detailed parts is often hardly possible in adopted code. As soon as it comes to a method that affects certain parts of the existing algorithm it is very comfortable to have self-written code.
However, there are highly optimized components in existing software impossible to implement in a moderate time frame. Therefore we adopted black-boxes for handling grid refinement and for solving the equation system.

How to get it
We stongly recommend that you run the software on our parallel machine. To do that you have to

Ask our system group (support@math.uzh.ch) for an account.
Once you have a user name, get a license key for the solver and store it in a text file in your home directory as "pardiso.lic".
Open a console and type "eclipse" to run Eclipse. Choose the default workspace. In the menubar choose "Window/Open Perspective/CVS Repository Exploring". Right-click in the left panel and choose "New/Repository Location. Fill in these configurations.
To download the project to your account, expand the new location to "HEAD/mathcomp". Right-click "mathcomp" and choose "check out".
To run the console version open a console and type the commands a shown in my thesis.
To run the GUI version you may either start it from the console launching the class "mathcomp.gui.cfd.MainCFD". You may launch it in Eclipse by changing the perspective to "Java" and right-click "mathcomp.gui.cfd.MainCFD" and choose "Run as.../Java Application".

Documentation
We provde a brief Javadoc code documentation of a Java project. For further documentation check section 1.4 of my thesis or contact me directly.

Christian Wüst
christian.wuest@math.uzh.ch