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\appendix |
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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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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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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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for buildings and towns by Christopher Alexander |
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\cite{Alexander1987}, software patterns first became popular with |
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the wide acceptance of the book, Design Patterns: Elements of |
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Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
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the experience, knowledge and insights of developers who have |
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successfully used these patterns in their own work. Patterns are |
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reusable. They provide a ready-made solution that can be adapted to |
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different problems as necessary. Pattern are expressive. they |
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provide a common vocabulary of solutions that can express large |
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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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collections of atoms or atoms which have orientational degrees of |
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freedom. Here is a diagram of the class heirarchy: |
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|
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\begin{figure} |
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\centering |
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\includegraphics[width=3in]{heirarchy.eps} |
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\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
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The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
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selection syntax allows the user to select any of the objects that |
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are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
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\end{figure} |
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%\begin{figure} |
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%\centering |
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%\includegraphics[width=3in]{heirarchy.eps} |
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%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
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%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
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%selection syntax allows the user to select any of the objects that |
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%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
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%\end{figure} |
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\begin{itemize} |
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\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
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\subsection{\label{appendixSection:name}Name expressions} |
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\begin{center} |
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\begin{tabular}{|llp{3in}|} |
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\begin{tabular}{|llp{2in}|} |
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\hline {\bf type of expression} & {\bf examples} & {\bf translation |
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of |
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examples} \\ |
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\end{center} |
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For example, the phrase {\tt select mass > 16.0 and charge < -2} |
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wouldselect StuntDoubles which have mass greater than 16.0 and |
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would select StuntDoubles which have mass greater than 16.0 and |
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charges less than -2. |
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\subsection{\label{appendixSection:within}Within expressions} |
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\begin{figure} |
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\centering |
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\includegraphics[width=3in]{definition.pdf} |
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\includegraphics[width=3in]{definition.eps} |
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\caption[Definitions of the angles between directional objects]{ \\ |
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Any two directional objects (DirectionalAtoms and RigidBodies) have |
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a set of two angles ($\theta$, and $\omega$) between the z-axes of |