An Object Orïented Infrastructure for the Development of a Computer Modeling System for Electrochemical Analysis and Visualization by Eric Marcuzzi A Thesis Submitted to the Faculty of Graduate Studies and Research through the School of Computer Science in Partial Fulfillment of the Requirernents for the Degree of Master of Science at the Univers@ of Windsor Windsor, Ontario, Canada 1997 National Library Bibliothèque nationale du Canada Acquisitions and Acquisitions et Bibliographie Services senrices bibliographiques 395 WelliStreet 395. rue Wellmgton OttayiliaON K1A ON4 OttawON K1AW carlada canada The author has granted a non- L'auteur a accordé une licence non exclusive licence allowing the exclusive permettant à la National Library of Canada to Bibliothèque nationale du Canada de reproduce, loaq distriiute or sell reproduire, prêter, distncbuer ou copies of this thesis in microfonn, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/nlm, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor subsîantial extracts fiom it Ni la thèse ni des extraits substantiels may be printed or otherwise de celle-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. O Eric Marcuzzi 1997 ABSTRACT In this thesis a partial system design and implementation for a computer modelhg system, the VPMS (Vimial Proto-ping, Modelling and Simulation) system. which supports exteiisibility, reusability, distributivity and openness, is presented. This system identifies and cornpartmentahes modelling system functionaliry, such as numerical modelling and scientific visualization. giving rise to three ciass libraries which embody the functionality through layee of software abstraction. The system is presented in the context of an electrochemical application, although the design is extensible to other application domains. As a partial design and implementation it does not contain al1 functionality required of a modelling system, however. the design is such that new functionality may be added in a straighdonvard marner through the addition of layers of software abstraction or functional components (environrnents). Dedicated to Rosam Vitale: Cam, sempre nel mio cuore! 1 express my most sincere gratitude and most respect to Dr. Robert D. Kent whose guidance, support, dedication and supreme patience have enabled this work to corne to finiition. -1 extend my appreciation to Dr. Mordechay Schlesinger for his direction, support and insight throughout this work (I shdl always remember the preacher). I also convey my th& to Dr. Peter Tsin for his invaluable service on my comminee and instruction throughout my tenure at this univenity. 1 am fortunate to have been the beneficiary of the knowledge and wisdom of these three gentlemen. Thanks also go to the facuity, staff and graduate midents in the Schooi of Cornputer Science. Honorable mention and many ttianks go to Zina Janabi, Robert Yang and Doug Thistle. I wish to thank my family, most notably my parents, whose generosity and suppori have known no limit. They have dways been present when needed and close by when net Vour hely Megifb have been greatly appreciated). To the congregation of the CFDI, whose presence has been both inspirational and, at times, intoxicating, salute! My warmest appreciation goes to Paolo and Nocciolina who are a constant source of comfort and delight. Most irnportantly, thanks go to Rosanna Vitale. Cara Rosanna, non ho le parole per esprimere la mia gratitudine per la ma pazienza, l'appoggio, la forza, e i sacrifici che sono stati la fonte della mia perseveranza L'espressione di quesu, riguardo te la offTe il mio cuore mediante il mio amore per te. Table of Contents Abstract ........................................................................................................ iv Dedication .......................................... ..................................................... ...... v Acknowledgments: .......................................................................................... vi List of Figures ................................................................................................. xi Chapter 1 INTRODUCTION 1 -1 Thesis Goal ......................................................... .... 1 1-1 . 1 Context ........................................................................................ -1 1-2 Modelling .................. ....... .......................................................... 3 1.2.1 Numerical Modelling, Visualization and Electrochemistry ............ 4 1-3 Thesis Layout ....................................................................................... 8 Chapter 2 BACKGROUND RESEARCH 2.1 Introduction ........................................................................................... 9 2.2 Modelling ............................................................................................ 10 2.2.1 ~axwell" ................................................................................ -10 2.2.2 ~a~le"....................................................................................... 14 2.3 Visualkation ....................................................................................... -17 2.3.1 Reference Models ...................................................................... -17 2.3.2 Current Systems ......................................................................... 19 2.3.2.1 Dataflow ............................................................................. 19 2.3.2.2 Non-Dataflow Systems ...................................................... 24 2.4 Discussion ......................................................................................... -30 Chapter 3 SYSTEM DEVELOPMENT 3.1 Introduction ........................................................................................ -34 3.2 System Requirements and Design Goals ........................................ -35 3.2.1 Functional Requirernents and Goals ......................................... -35 3.2.2 Non-Functional Requirements and Goals .................................. 37 3.2.2.1 Modularity and Extensibility, Portability and Reusability ... -37 3.2.2.2 Complete Modelling System ...................................... .... ..... -38 3.2.2.3 Distnbutivity ..................... ..... ........................................ -39 3.3 System Design ...................... ........................................................... 40 3.3.1 Data ........................................................................................... 40 3.3.2 General Design .......................................................................... 41 3.3.2.1 Network Distribution ................................... ..... ................... 47 3.3.2.2 Security ............... .......................................................... 50 3.3.2.3 Use of Java ........................................................................ 51 3.3.3 System Component................... .. ............................................ -53 3.3.4 Design Specifics......................................................................... 54 3.3.4.1 Visualkation Class Library ................................................ -55 3.3.4.2 Model Class Library ........................................................... 57 3.3.4.3 Yoke Class Library .............. ... ........................................ 59 3.4 Discussion .......................................................................................... 61 Chapter 4 IMPLEMENTATION 5.2.1 Visualization Class Library ......................................................... 95 5.2.2 Model Class Library ................................................................... 95 5.2.3 Yoke Class Library ..................................................................... 96 5.3 Javam ................................................................................................. 97 5.3.1 Incorporation of JavaTM.............................................................. -97 5.3.2 Future lmplementation of Javam ................................................ 98 Chapter 6 CONCLUSIONS 6.1 Discussion ................................... .... ............................................... -101 6.2 Satisfaction of Goals ....................................................................... -102 APPENDIX A .............................................................................................. 106 APPENDIX B .............................................................................................. 112 APPEND tX C ..................... .. ................................................................. 120 BIBLIOGRAPHY .......................................................................................... 127 Via Auctoris ............................................................................................. 132 LIST OF FIGURES Figure 1.1: An example plate geometry overlaid with a mesh .................................... 7 Figure 1.2: Magnified view of Figure 1.1 ...................................................... ......... 7 Figure 1.3 : Illustration of modelling -stem organization ......................................... -8 Figure 2.1 : Sample plate geometry illustrating component elements ....................... 11 Fi-mire 2.2: Representation of