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\chapter{\label{chapt:appendix}APPENDIX} |
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Designing object-oriented software is hard, and designing reusable |
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object-oriented scientific software is even harder. Absence of |
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applying modern software development practices is the bottleneck of |
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Scientific Computing community\cite{wilson}. For instance, in the |
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last 20 years , there are quite a few MD packages that were |
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developed to solve common MD problems and perform robust simulations |
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. However, many of the codes are legacy programs that are either |
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poorly organized or extremely complex. Usually, these packages were |
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contributed by scientists without official computer science |
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training. The development of most MD applications are lack of strong |
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coordination to enforce design and programming guidelines. Moreover, |
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most MD programs also suffer from missing design and implement |
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documents which is crucial to the maintenance and extensibility. |
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\section{\label{appendixSection:desginPattern}Design Pattern} |
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Design patterns are optimal solutions to commonly-occurring problems |
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in software design. Although originated as an architectural concept |
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for buildings and towns by Christopher Alexander \cite{alexander}, |
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software patterns first became popular with the wide acceptance of |
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the book, Design Patterns: Elements of Reusable Object-Oriented |
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Software \cite{gamma94}. Patterns reflect the experience, knowledge |
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and insights of developers who have successfully used these patterns |
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in their own work. Patterns are reusable. They provide a ready-made |
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solution that can be adapted to different problems as necessary. |
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Pattern are expressive. they provide a common vocabulary of |
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solutions that can express large solutions succinctly. |
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Patterns are usually described using a format that includes the |
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following information: |
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\begin{enumerate} |
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\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
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discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
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in the literature. In this case it is common practice to document these nicknames or synonyms under |
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the heading of \emph{Aliases} or \emph{Also Known As}. |
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\item The \emph{motivation} or \emph{context} that this pattern applies |
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to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
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\item The \emph{solution} to the problem that the pattern |
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addresses. It describes how to construct the necessary work products. The description may include |
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pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
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collaborations, to show how the problem is solved. |
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\item The \emph{consequences} of using the given solution to solve a |
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problem, both positive and negative. |
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\end{enumerate} |
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As one of the latest advanced techniques emerged from |
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object-oriented community, design patterns were applied in some of |
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the modern scientific software applications, such as JMol, OOPSE |
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\cite{Meineke05} and PROTOMOL \cite{} \textit{etc}. |
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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The Factory Method pattern is a creational pattern which deals with |
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the problem of creating objects without specifying the exact class |
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of object that will be created. Factory Method solves this problem |
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by defining a separate method for creating the objects, which |
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subclasses can then override to specify the derived type of product |
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that will be created. |
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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The purpose of the Visitor Pattern is to encapsulate an operation |
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that you want to perform on the elements of a data structure. In |
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this way, you can change the operation being performed on a |
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structure without the need of changing the classes of the elements |
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that you are operating on. |
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\subsection{\label{appendixSection:templateMethod}Template Method} |
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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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\section{\label{appendixSection:hierarchy}Hierarchy} |
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\subsection{\label{appendixSection:selectionSyntax}Selection Syntax} |
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\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
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\subsection{\label{appendixSection:staticProps}Static Properties} |
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\subsection{\label{appendixSection:dynamicProps}Dynamics Properties} |
