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

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long-range hydrodynamic forces directly in its equations of motion allowing more realistic modeling of the dynamics of phase separation and other processes depending on large length-scale interactions. In the DPD methodology, the fundamental particles are "beads" that represent small regions of fluid material rather than the atoms and molecules familiar from MD simulations. All degrees of freedom smaller than a bead radius are assumed to have been integrated out leaving only coarse-grained interactions between beads [11]. As can be seen from Figure 1-1(b), each sphere in this picture represents a bead. MesoDyn is a new tool for the prediction of mesoscale structures of soft-condensed matter. These are the patterns of size 10 to 100 nm which can be found for example in polymer blends, block-copolymer systems, surfactant aggregates in detergent materials (e.g. shampoo), latex particles, or drug delivery systems [11]. As can be seen from Figure 1-1(c), the big sphere in this picture represents an oil droplet. A hybrid simulation is a combination of the DPD simulation and MesoDyn simulation [4]. In Figure 1-1(d), each small sphere is a bead, and the big sphere is an oil droplet. There are two ways for users to build a simulation program using the Culgi Library. First, users can develop a program in C++ which includes the Culgi Library. This way is straightforward for experienced C++ programmers. But because most users of Culgi are chemists without background in programming, building a C++ program for them is too difficult or almost impossible. So this way is only welcomed by a few users who know C++. Second, the Culgi Library can be packed into a dynamic library file which can be accessed by other more accessible programming languages like Tcl. Then, users can compose a script in which Culgi commands are used (See Figure 1-2). This way is used much more often than the first way, because some of the Culgi users are familiar with Tcl script. Appendix C shows the Tcl source code of the DPD simulation example shown in Figure 1-1(b). As can be seen from this example, one hundred lines of source code are needed to make a simple DPD simulation program. It is still not very easy for the majority of the users. Culgi Library by C++ Culgi.dll + Tcl Interpreter Scripts Figure 1-2. Current way to use Culgi Library Thus, a software environment is needed in order to help the users build simulation applications efficiently and easily. The assignment for this project is to design and develop a prototype for such an environment. In the research report of this project [12], we analyzed the users of Culgi and gave out a user-user - 2 -
elationship model (see Figure 1-3). In this model, “Culgi Developers” refers to the people who develop the Culgi software package; “Application Authors” here mainly refers to industry computational chemists (ICCs), who know some in programming and are able to develop small programs; and “End Users” here mainly refers to bench chemists (BCs), who don’t know programming but need to use simulation applications to do simulation in order to predict possible solutions to a special problem. In general, the simulation application to bench chemists should contain a Graphical User Interface, in which uses can set the values to some parameters about a simulation. Then the application should perform calculations to predict the result. Culgi Developers Components or functions Application Authors (ICCs) Applications End Users (BCs) Figure 1-3. The user-user relationship model This user-user relationship model means that the Culgi developers develop the Culgi software package for the application authors. Then the application authors build simulation applications with Culgi for the end users. Thus ICCs are the Culgi target group, and BCs are Culgi end users. The end users can communicate with the application authors and put forward their requirements and suggestions directly. Then the application authors should make simulation programs to solve some special problems for end users. If the application authors can not solve the problem themselves or they need new functions in Culgi Library, they can contact the Culgi developers. The Culgi developers will develop new functions according to the suggestions from the application authors. Because the Application Authors are not professional programmers, we concluded that we need a programming environment to help the application authors to develop simulation applications. This system should provide a programming editor which makes programming easy; as well as be able to export an end user application with a Graphics User Interface (GUI) for the end users. By studying the various concepts in current programming environments, a conclusion is made that the system to be designed should be a graphical programming environment in which a program can be built by clicking, - 3 -
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: Chapter 1 Introduction Culgi stands
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 and 62: Chapter 6 Conclusion The goal of th
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Chapter 7 Bibliography [1] Craig La
Page 65 and 66:
Appendix A. Class Diagrams Figure A
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Figure A-4 Class Diagram of “Sequ
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Appendix B. Tables Table B-1 Functi
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Table B-3 Functionalities of Class
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Table B-5 Functionalities of class
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Table B-7 Properties of input param
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Appendix C. DPD Simulation # DPD Si
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$plot SetSize 400 400 $plot Load My
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Master's Thesis - Computer Graphics and Visualization - TU Delft

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