Panayiotis Steele
July 15, 2005

Project Proposal

Organization:  NRL Computational Multiphysics Systems Laboratory
Mentor Name:  Dr. John G. Michopoulos

I.Title
Symbolic Algebra and Visualization Enhancements of a 2D-Visual Programming 
Environment for Multiphysics Mechatronic Systems Simulation.  

II.Problem Statement
There is a well established need for the development of a symbolic algebra module 
(or "actor") for Ptolemy-II, a two dimensional visual environment for heterogeneous 
and concurrent modeling of physical systems. The current capabilities of the 
system are limited to simple algebraic manipulations and multi-dimensional 
entity representations and visualizations. Capturing the forward and inverse 
kinematic behavior of complex hybrid physical systems (such as mechatronic 
systems used for various applications) is of primary importance for various 
application areas including, material testing, component manufacturing  and 
robotics. An additional problem associated with Ptolemy-II is that it does not 
contain a 3D graphics visualization actor. 

III.Purpose
The main goal of this project is to develop an actor for Ptolemy-II that uses 
the Mathematica kernel as its calculation engine.  The actor will be able to 
accept Mathematica expressions presented to its input port or/and its expression
definition field,  then link to the Mathematica kernel-the computational engine
behind the Mathematica user interface-evaluate them and finally return the resulting 
expressions to the actors output ports.  A secondary goal (depending on the 
timely development of the actor) is the utilization of this actor is to model 
and simulate the mechatronic system of the Computational Multiphysics Systems 
Laboratory (CMSL) called the "6D-Loader" system.  This system has six degrees 
of kinematic freedom for applying displacements and rotation and measuring 
reaction forces and moments resulting from the response of appropriately 
selected  composite material specimens.  Integration with Mathematica and its 
symbolic algebra capabilities is necessary to model this machine because its 
kinematic behavior is described by a set of  very complex system of nonlinear 
equations, while the behavior of the specimen is governed by a coupled system of
partial differential equations.  These equations are not solvable by hand, and
Mathematica's assistance is highly warranted to solve them easily.  Ptolemy-II 
and specifically the 2D visual programming editor called "Vergil" will be used 
to model both the visual and the functional behavior of the machine.
The project will help immensely in the CMSL, even if the second goal is not 
realized.  My mentor has already started modeling the machine and my actor will
greatly facilitate completion of this task. Furthermore, a Mathematica actor 
for Ptolemy-II could be used to capture and  model the behavior of other physical 
systems as well. 
This project is a good and very appropriate topic for the Computer Systems 
Laboratory because it requires the integration of  various applications:  
Ptolemy-II, the Mathematica kernel and the J/Link interface of Mathematica to 
other applications. This will be done by utilizing existing libraries, as well 
as the development of custom developed methods to parse the input to and output
from the Mathematica actor, within the context of this project.

IV.Scope of Study
I will have to integrate various programs together seamlessly, so that input 
from Ptolemy can be translated into input for Mathematica, and output from 
Mathematica can be translated into output and input for Ptolemy.  I will 
collect software performance data and meta-data, and use them to optimize my 
final design of the integrated software. I will also research as needed so that
I can understand what I am doing and make my project work.  For example, I need
to look up functions in the J/Link library to connect directly to the Mathematica
kernel and JavaView for displaying multi-dimensional graphics from withing Prolemy.

V.Background
As far as research done in this general area, my mentor has started simulating 
the machine that I will finish simulating.  With the Mathematica actor, no one 
has tried what I will be doing, but other computer scientists have created their
own actors for other applications.  Yet others have created programs that interface
with Mathematica using J/Link.  I am going to combine the two.
The two most important documents for another student to get up to speed would 
be the Ptolemy II documentation, which can be found at http://ptolemy.eecs.berkeley.edu/ptolemyII 
and http://embedded.eecs.berkeley.edu/concurrency/ptolemy/index.html, and the 
J/Link documentation provided with the Mathematica software.  The J/Link documentation
can also be found at
http://documents.wolfram.com/v5/Add-onsLinks/JLink/index.html.

VI.Procedure and Methodology
There are several new things I will need to learn, including all about J/Link, 
a fair amount about Mathematica syntax, how to program a Ptolemy actor so that 
it interfaces correctly with the core Ptolemy program, and how to add it to the 
Ptolemy source.  I may also need to learn some of the Mathematica programming 
language.  The only graphics I will need are a simple JPanel in a pop-up JFrame 
to display Mathematica graphs.  The only data I will need to collect are those 
that I need to program, i.e. not experimental data; rather, research and system
performance data.  I will test the program as I go along by writing only small 
sections of code at a time and testing the code in a small environment outside 
Ptolemy (a standalone application).  Then, after the code executes correctly 
outside of Ptolemy, I will run it in Ptolemy to see what, if any, errors arise,
and fix them. 

VII.Expected Results; Value to Others
I expect two results to be accomplished by the end of this mentorship.  One is 
having a finished, working, polished actor that other people can use and not be
confused.  The other is to complete a simulation of the multiphysics and 
multi-dimensional mechatronic system present in the lab. Another possible result
will be the application of what I learn from the previous tasks towards the 
development of a visualization actor that will accept Ptolemy expressions and 
will produce JavaView representations of these expressions.
The final results and analyses of the project will be presented in a paper, with
all the code and relevant screenshots attached.  I will also prepare a poster 
with a brief overview of the project.
Possible contributions of this project to future researchers include having a 
powerful mathematical computational engine available for Ptolemy developers, 
increased ease of modeling of systems with Ptolemy, and an increased variety of
the problems that can be solved with Ptolemy.