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\appendix |
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\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} |
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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{Wilson2006}. For instance, in |
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the 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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Along the way of studying structural and dynamic processes in |
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condensed phase systems like biological membranes and nanoparticles, |
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we developed and maintained an Object-Oriented Parallel Simulation |
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Engine ({\sc OOPSE}). This new molecular dynamics package has some |
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unique features |
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Absence of applying modern software development practices is the |
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bottleneck of Scientific Computing community\cite{Wilson2006}. In |
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the last 20 years , there are quite a few MD |
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packages\cite{Brooks1983, Vincent1995, Kale1999} that were developed |
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to solve common MD problems and perform robust simulations . |
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Unfortunately, most of them are commercial programs that are either |
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poorly written or extremely complicate. Consequently, it prevents |
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the researchers to reuse or extend those packages to do cutting-edge |
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research effectively. Along the way of studying structural and |
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dynamic processes in condensed phase systems like biological |
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membranes and nanoparticles, we developed an open source |
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Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new |
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molecular dynamics package has some unique features |
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\begin{enumerate} |
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\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
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atom types (transition metals, point dipoles, sticky potentials, |
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program of the package, \texttt{oopse} and it corresponding parallel |
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version \texttt{oopse\_MPI}, as well as other useful utilities, such |
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as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}), |
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\texttt{DynamicProps} (see |
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Sec.~\ref{appendixSection:appendixSection:DynamicProps}), |
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\texttt{Dump2XYZ} (see |
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Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro} |
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(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics}) |
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\texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}), |
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\texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}), |
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\texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics}) |
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\textit{etc}. |
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\begin{figure} |
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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, {\sc |
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OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. |
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The following sections enumerates some of the patterns used in {\sc |
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OOPSE}. |
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OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2005} |
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\textit{etc}. The following sections enumerates some of the patterns |
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used in {\sc OOPSE}. |
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\subsection{\label{appendixSection:singleton}Singleton} |
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diagram of Visitor patten.} \label{appendixFig:visitorUML} |
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\end{figure} |
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%\begin{figure} |
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%\centering |
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%\includegraphics[width=\linewidth]{hierarchy.eps} |
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%\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
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%the class hierarchy. |
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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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%integrators and minimizers. |
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%\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
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%\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
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%\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
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%DirectionalAtom}s which behaves as a single unit. |
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%\end{itemize} |
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%} \label{oopseFig:hierarchy} |
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%\end{figure} |
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{hierarchy.eps} |
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\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
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the class hierarchy. } \label{oopseFig:hierarchy} |
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\end{figure} |
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
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on the specifics of the simulation). The names of rigid bodies are |
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generated automatically. For example, the name of the first rigid |
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body in a DMPC molecule is DMPC\_RB\_0. |
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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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integrators and minimizers. |
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\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
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\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
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\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
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DirectionalAtom}s which behaves as a single unit. |
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\end{itemize} |
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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