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designs, such as lifespan control \textit{etc}, we only use the |
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static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class |
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is declared as |
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}] |
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> |
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
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class IntegratorFactory { |
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public: |
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\end{lstlisting} |
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The corresponding implementation is |
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\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}] |
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> |
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] |
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|
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IntegratorFactory::instance_ = NULL; |
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|
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with the problem of creating objects without specifying the exact |
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class of object that will be created. Factory Method is typically |
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implemented by delegating the creation operation to the subclasses. |
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{\tt Integrator} class Parameterized Factory pattern where factory |
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method ({\tt createIntegrator} member function) creates products |
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based on the identifier (see |
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List.~\ref{appendixScheme:factoryDeclaration}). If the identifier |
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has been already registered, the factory method will invoke the |
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corresponding creator (see List.~\ref{integratorCreator}) which |
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utilizes the modern C++ template technique to avoid subclassing. |
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of {\tt IntegratorFactory} class.},label={appendixScheme:factoryDeclaration}] |
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|
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Registers a creator with a type identifier. Looks up the type |
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identifier in the internal map. If it is found, it invokes the |
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corresponding creator for the type identifier and returns its |
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result. |
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}] |
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– |
|
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class IntegratorFactory { |
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public: |
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typedef std::map<string, IntegratorCreator*> CreatorMapType; |
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CreatorMapType creatorMap_; |
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}; |
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\end{lstlisting} |
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)]Souce code of creator classes.},label={appendixScheme:integratorCreator}] |
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> |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
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|
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class IntegratorCreator { |
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public: |
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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. The operation being |
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performed on a structure can be switched without changing the |
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interfaces of the elements. In other words, one can add virtual |
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interfaces of the elements. In other words, one can add virtual |
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functions into a set of classes without modifying their interfaces. |
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The UML class diagram of Visitor patten is shown in |
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Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
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Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
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extensively. |
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Fig.~\ref{appendixFig:visitorUML} demonstrates the structure of |
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Visitor pattern which is used extensively in {\tt Dump2XYZ}. In |
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order to convert an OOPSE dump file, a series of distinct and |
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unrelated operations are performed on different StuntDoubles. |
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Visitor allows one to keep related operations together by packing |
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them into one class. {\tt BaseAtomVisitor} is a typical example of |
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visitor in {\tt Dump2XYZ} program{see |
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List.~\ref{appendixScheme:visitor}}. In contrast to the operations, |
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the object structure or element classes rarely change(See |
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Fig.~\ref{oopseFig:heirarchy} and |
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List.~\ref{appendixScheme:element}). |
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|
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+ |
|
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{visitor.eps} |
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\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
251 |
< |
of {\sc OOPSE}} \label{appendixFig:visitorUML} |
250 |
> |
\caption[The UML class diagram of Visitor patten] {The UML class |
251 |
> |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
252 |
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\end{figure} |
253 |
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|
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
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virtual void visit(RigidBody* rb); |
261 |
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}; |
262 |
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|
263 |
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class BaseAtomVisitor:public BaseVisitor{ public: |
264 |
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virtual void visit(Atom* atom); |
265 |
+ |
virtual void visit(DirectionalAtom* datom); |
266 |
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virtual void visit(RigidBody* rb); |
267 |
+ |
}; |
268 |
+ |
|
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\end{lstlisting} |
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|
271 |
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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. |
315 |
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\begin{figure} |
316 |
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\centering |
317 |
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\includegraphics[width=\linewidth]{heirarchy.eps} |
318 |
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\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of |
319 |
< |
the class heirarchy. |
320 |
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\begin{itemize} |
321 |
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\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
322 |
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integrators and minimizers. |
323 |
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\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
324 |
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\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
325 |
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\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
326 |
< |
DirectionalAtom}s which behaves as a single unit. |
327 |
< |
\end{itemize} |
328 |
< |
} \label{oopseFig:heirarchy} |
329 |
< |
\end{figure} |
315 |
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%\begin{figure} |
316 |
> |
%\centering |
317 |
> |
%\includegraphics[width=\linewidth]{heirarchy.eps} |
318 |
> |
%\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of |
319 |
> |
%the class heirarchy. |
320 |
> |
%\begin{itemize} |
321 |
> |
%\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
322 |
> |
%integrators and minimizers. |
323 |
> |
%\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
324 |
> |
%\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
325 |
> |
%\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
326 |
> |
%DirectionalAtom}s which behaves as a single unit. |
327 |
> |
%\end{itemize} |
328 |
> |
%} \label{oopseFig:heirarchy} |
329 |
> |
%\end{figure} |
330 |
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|
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
332 |
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|