Master's Thesis - Computer Graphics and Visualization - TU Delft

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validity of each module uploaded as well. Add a debug tool to the Culgi GPE. At this moment, if errors exist in a user’s program, it can only be found when the program is running. The errors will be complained about by the Tcl interpreter. The debug tool will check the validation of a user’s program before it is running. It will check not only the validation of the input parameters, but also the logic of a user’s program. Make the Sequence Editor intelligent. It means to develop a mechanism to predict the users’ intention and give out several suggestions to users about the next step. For example, if a module “A” is created by a user, the system will guess the types of simulation programs the user wants to build. If the system predicts that this user will do simulation programs in “TypeA” and “TypeB”, it will show the user the modules needed in “TypeA” and “TypeB” separately. And if the system finds that there is contradiction in the user’s previous work, it will give out warnings and point out the contradicting part. We can also make this system into a general purpose programming environment that can be applied to other libraries very easily. This general purpose programming environment can pack the commands of a library into modules automatically. And it also supports if-else, switch, and loop structures. If there is a new library, like a library for mathematics, or for physics, this programming environment can be applied to it automatically. The Culgi GPE will be designed and developed continually after this prototype. We hope that several years later, all computational chemists can build simulation programs with this system. - 52 -
Chapter 7 Bibliography [1] Craig Larman, “Applying UML and Patterns: An Introduction to Object-Oriented Analysis and Design and Iterative Development, Third Edition”. Prentice Hall PTR, 2004 [2] Alexandru C.Telea. Visualisation and Simulation with Object-Oriented Networks. PhD thesis, Technische Universiteit Eindhoven, 2000. [3] “pipeline pilot, an introduction”, SciTegic, 2003 http://www.scitegic.com/products_services/pipeline_pilot.htm [4] A.V.Kyrylyuk, F.H.Case and J.G.E.M.Fraaije, Property Prediction and Hybrid Modeling for Combinatorial Materials, QSAR & Combinatorial Science, Volume 24, Issue 1 , Pages 131 – 137, March 2005 [5] C. P. Botha, “Techniques and Software Architectures for Medical Visualisation and Image Processing”, PhD thesis, Delft University of Technology, 2005. [6] Michel F. Sanner, Daniel. Stoffler and Arthur J. Olson, ViPEr, a Visual Programming Environment for Python. In Proceedings of the 10 th International Python Conference, February 2002. [7] Mark Lutz, David Ascher, “Learning Python, Second Edition”, O’REILLY, December 2003 [8] IEEE Std 830-1998: “IEEE Recommended Practice for Software Requirements Specifications”. IEEE. 1998 [10] J. M. Haile, “Molecular Dynamics Simulation: Elementry Methods”, Wiley-Interscience, March, 1997 [11] Molecular Simulations, Inc , “Cerius 2 Property Prediction”, June 2000. http://www.scripps.edu/rc/softwaredocs/msi/cerius45/proppred/C2PropPred3.9TOC.doc.html [12] Ruixin Wang, “Programming Environments For A Molecular Simulation System”, literature research report of the master’s thesis, December, 2004. - 53 -
Page 1:
A Graphical Programming Environment
Page 5 and 6:
Preface This project started in Sep
Page 7 and 8:
Abstract Culgi stands for Chemistry
Page 9 and 10:
Contents Abstract..................
Page 11 and 12: Chapter 1 Introduction Culgi stands
Page 13 and 14: elationship model (see Figure 1-3).
Page 15 and 16: Chapter 2 Requirement Analysis This
Page 17 and 18: loop in which users only need to sp
Page 19 and 20: Primary actor: -Simulation Program
Page 21 and 22: Req04 Select a module in the librar
Page 23 and 24: Chapter 3 Design Models In chapter
Page 25 and 26: also generates the same result as (
Page 27 and 28: 3.3 The Concept Editor 3.3.1 Descri
Page 29 and 30: (a) Step1 Build Box Step2 Create Vi
Page 31 and 32: 3.5.1 Multi view of modules In the
Page 33 and 34: 3.5.2 Various widgets to display a
Page 35 and 36: a correct order. These source codes
Page 37 and 38: Chapter 4 Implementation of the Cul
Page 39 and 40: library. Meanwhile, the interface p
Page 41 and 42: For example, in Figure 3-5(b), the
Page 43 and 44: The Module Editor is a tool for cre
Page 45 and 46: corresponding operations. Figure 4-
Page 47 and 48: The second problem is about how to
Page 49 and 50: sequence. From these approaches, we
Page 51 and 52: Chapter 5 Results and Test The prev
Page 53 and 54: (a) Before click. (b) After an item
Page 55 and 56: instance of the module setDPDEnviro
Page 57 and 58: (a) Make only “Oil” visible (b)
Page 59 and 60: Feedbacks from the novices of Culgi
Page 61: Chapter 6 Conclusion The goal of th
Page 65 and 66: Appendix A. Class Diagrams Figure A
Page 67 and 68: Figure A-4 Class Diagram of “Sequ
Page 69 and 70: Appendix B. Tables Table B-1 Functi
Page 71 and 72: Table B-3 Functionalities of Class
Page 73 and 74: Table B-5 Functionalities of class
Page 75 and 76: Table B-7 Properties of input param
Page 77 and 78: Appendix C. DPD Simulation # DPD Si
Page 79: $plot SetSize 400 400 $plot Load My
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Master's Thesis - Computer Graphics and Visualization - TU Delft

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