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\appendix |
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\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} |
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|
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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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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 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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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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|
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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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|
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The Singleton pattern not only provides a mechanism to restrict |
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instantiation of a class to one object, but also provides a global |
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point of access to the object. Currently implemented as a global |
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pollution.Although the singleton pattern can be implemented in |
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various ways to account for different aspects of the software |
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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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static data approach in {\sc OOPSE}. IntegratorFactory class is |
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declared as |
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|
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class IntegratorFactory { |
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public: |
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static IntegratorFactory* getInstance(); |
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protected: |
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IntegratorFactory(); |
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private: |
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static IntegratorFactory* instance_; |
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}; |
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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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|
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class IntegratorFactory { |
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public: |
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static IntegratorFactory* |
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getInstance(); |
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protected: |
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IntegratorFactory(); |
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private: |
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static IntegratorFactory* instance_; |
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}; |
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|
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\end{lstlisting} |
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|
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The corresponding implementation is |
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}] |
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|
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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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IntegratorFactory* getInstance() { |
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} |
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return instance_; |
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} |
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|
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\end{lstlisting} |
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Since constructor is declared as {\tt protected}, a client can not |
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instantiate {\tt IntegratorFactory} directly. Moreover, since the |
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member function {\tt getInstance} serves as the only entry of access |
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to {\tt IntegratorFactory}, this approach fulfills the basic |
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requirement, a single instance. Another consequence of this approach |
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is the automatic destruction since static data are destroyed upon |
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program termination. |
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|
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Since constructor is declared as protected, a client can not |
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instantiate IntegratorFactory directly. Moreover, since the member |
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function getInstance serves as the only entry of access to |
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IntegratorFactory, this approach fulfills the basic requirement, a |
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single instance. Another consequence of this approach is the |
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automatic destruction since static data are destroyed upon program |
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termination. |
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|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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Categoried as a creational pattern, the Factory Method pattern deals |
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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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\begin{lstlisting}[float,caption={[].},label={appendixScheme:factoryDeclaration}] |
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class IntegratorCreator; |
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class IntegratorFactory { |
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public: |
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typedef std::map<std::string, IntegratorCreator*> CreatorMapType; |
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Parameterized Factory pattern where factory method ( |
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createIntegrator member function) creates products based on the |
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identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If |
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the identifier has been already registered, the factory method will |
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invoke the corresponding creator (see List.~\ref{integratorCreator}) |
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which utilizes the modern C++ template technique to avoid excess |
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subclassing. |
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|
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/** |
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* Registers a creator with a type identifier |
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* @return true if registration is successful, otherwise return false |
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* @id the identification of the concrete object |
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* @creator the object responsible to create the concrete object |
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*/ |
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bool registerIntegrator(IntegratorCreator* creator); |
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
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|
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/** |
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* Looks up the type 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 result. |
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* @return a pointer of the concrete object, return NULL if no creator is registed for |
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* creating this concrete object |
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* @param id the identification of the concrete object |
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*/ |
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Integrator* createIntegrator(const std::string& id, SimInfo* info); |
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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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|
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private: |
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CreatorMapType creatorMap_; |
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}; |
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[].},label={appendixScheme:factoryDeclarationImplementation}] |
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bool IntegratorFactory::unregisterIntegrator(const std::string& id) { |
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return creatorMap_.erase(id) == 1; |
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bool registerIntegrator(IntegratorCreator* creator) { |
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return creatorMap_.insert(creator->getIdent(), creator).second; |
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} |
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|
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Integrator* IntegratorFactory::createIntegrator(const std::string& id, SimInfo* info) { |
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Integrator* createIntegrator(const string& id, SimInfo* info) { |
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Integrator* result = NULL; |
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CreatorMapType::iterator i = creatorMap_.find(id); |
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if (i != creatorMap_.end()) { |
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//invoke functor to create object |
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return (i->second)->create(info); |
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} else { |
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return NULL; |
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result = (i->second)->create(info); |
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} |
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return result; |
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} |
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|
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private: |
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CreatorMapType creatorMap_; |
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}; |
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[].},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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IntegratorCreator(const std::string& ident) : ident_(ident) {} |
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virtual ~IntegratorCreator() {} |
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const std::string& getIdent() const { return ident_; } |
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class IntegratorCreator { |
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public: |
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IntegratorCreator(const string& ident) : ident_(ident) {} |
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|
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const string& getIdent() const { return ident_; } |
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|
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virtual Integrator* create(SimInfo* info) const = 0; |
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|
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private: |
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std::string ident_; |
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}; |
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private: |
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string ident_; |
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}; |
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|
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template<class ConcreteIntegrator> |
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class IntegratorBuilder : public IntegratorCreator { |
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public: |
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IntegratorBuilder(const std::string& ident) : IntegratorCreator(ident) {} |
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virtual Integrator* create(SimInfo* info) const {return new ConcreteIntegrator(info);} |
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}; |
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template<class ConcreteIntegrator> |
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class IntegratorBuilder : public IntegratorCreator { |
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public: |
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IntegratorBuilder(const string& ident) |
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: IntegratorCreator(ident) {} |
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virtual Integrator* create(SimInfo* info) const { |
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return new ConcreteIntegrator(info); |
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} |
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}; |
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\end{lstlisting} |
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|
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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|
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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 class heirarchy of the |
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elements that you are operating on. |
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The visitor pattern is designed to decouple the data structure and |
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algorithms used upon them by collecting related operation from |
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element classes into other visitor classes, which is equivalent to |
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adding virtual functions into a set of classes without modifying |
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their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
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structure of Visitor pattern which is used extensively in {\tt |
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Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
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distinct operations are performed on different StuntDoubles (See the |
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class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
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in List.~\ref{appendixScheme:element}). Since the hierarchies |
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remains stable, it is easy to define a visit operation (see |
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List.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
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Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
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manages a priority visitor list and handles the execution of every |
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visitor in the priority list on different StuntDoubles. |
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|
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\begin{lstlisting}[float,caption={[].},label={appendixScheme:visitor}] |
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class BaseVisitor{ |
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public: |
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virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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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 UML class diagram of Visitor patten] {The UML class |
| 252 |
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diagram of Visitor patten.} \label{appendixFig:visitorUML} |
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> |
\end{figure} |
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|
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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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|
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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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|
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class StuntDouble { public: |
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virtual void accept(BaseVisitor* v) = 0; |
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}; |
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|
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class Atom: public StuntDouble { public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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class DirectionalAtom: public Atom { public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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> |
}; |
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> |
|
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> |
class RigidBody: public StuntDouble { public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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> |
|
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|
\end{lstlisting} |
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\begin{lstlisting}[float,caption={[].},label={appendixScheme:element}] |
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class StuntDouble { |
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public: |
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virtual void accept(BaseVisitor* v) = 0; |
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}; |
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|
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< |
class Atom: public StuntDouble { |
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< |
public: |
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< |
virtual void accept{BaseVisitor* v*} {v->visit(this);} |
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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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|
| 290 |
< |
class DirectionalAtom: public Atom { |
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< |
public: |
| 292 |
< |
virtual void accept{BaseVisitor* v*} {v->visit(this);} |
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< |
}; |
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> |
class BaseVisitor{ |
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> |
public: |
| 292 |
> |
virtual void visit(Atom* atom); |
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> |
virtual void visit(DirectionalAtom* datom); |
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> |
virtual void visit(RigidBody* rb); |
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> |
}; |
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|
| 297 |
< |
class RigidBody: public StuntDouble { |
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< |
public: |
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< |
virtual void accept{BaseVisitor* v*} {v->visit(this);} |
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< |
}; |
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> |
class BaseAtomVisitor:public BaseVisitor{ public: |
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> |
virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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> |
}; |
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|
|
| 303 |
+ |
class SSDAtomVisitor:public BaseAtomVisitor{ public: |
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+ |
virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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+ |
virtual void visit(RigidBody* rb); |
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+ |
}; |
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+ |
|
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+ |
class CompositeVisitor: public BaseVisitor { |
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public: |
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+ |
|
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+ |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
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+ |
typedef VistorListType::iterator VisitorListIterator; |
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+ |
virtual void visit(Atom* atom) { |
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+ |
VisitorListIterator i; |
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+ |
BaseVisitor* curVisitor; |
| 317 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
| 318 |
+ |
atom->accept(*i); |
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+ |
} |
| 320 |
+ |
} |
| 321 |
+ |
|
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+ |
virtual void visit(DirectionalAtom* datom) { |
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+ |
VisitorListIterator i; |
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+ |
BaseVisitor* curVisitor; |
| 325 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
| 326 |
+ |
atom->accept(*i); |
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+ |
} |
| 328 |
+ |
} |
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+ |
|
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+ |
virtual void visit(RigidBody* rb) { |
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+ |
VisitorListIterator i; |
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+ |
std::vector<Atom*> myAtoms; |
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+ |
std::vector<Atom*>::iterator ai; |
| 334 |
+ |
myAtoms = rb->getAtoms(); |
| 335 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) {{ |
| 336 |
+ |
rb->accept(*i); |
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+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
| 338 |
+ |
(*ai)->accept(*i); |
| 339 |
+ |
} |
| 340 |
+ |
} |
| 341 |
+ |
|
| 342 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
| 343 |
+ |
|
| 344 |
+ |
protected: |
| 345 |
+ |
VistorListType visitorList; |
| 346 |
+ |
}; |
| 347 |
+ |
|
| 348 |
|
\end{lstlisting} |
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|
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|
\section{\label{appendixSection:concepts}Concepts} |
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|
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|
OOPSE manipulates both traditional atoms as well as some objects |
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that {\it behave like atoms}. These objects can be rigid |
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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} |
| 358 |
< |
%\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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|
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freedom. A diagram of the class hierarchy is illustrated in |
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Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
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DirectionalAtom in {\sc OOPSE} have their own names which are |
| 358 |
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specified in the {\tt .md} file. In contrast, RigidBodies are |
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denoted by their membership and index inside a particular molecule: |
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[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
| 361 |
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on the specifics of the simulation). The names of rigid bodies are |
| 362 |
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generated automatically. For example, the name of the first rigid |
| 363 |
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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 |
| 366 |
|
integrators and minimizers. |
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|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
| 370 |
|
DirectionalAtom}s which behaves as a single unit. |
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|
\end{itemize} |
| 297 |
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|
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Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
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own names which are specified in the {\tt .md} file. In contrast, |
| 300 |
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RigidBodies are denoted by their membership and index inside a |
| 301 |
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particular molecule: [MoleculeName]\_RB\_[index] (the contents |
| 302 |
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inside the brackets depend on the specifics of the simulation). The |
| 303 |
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names of rigid bodies are generated automatically. For example, the |
| 304 |
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name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
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|
| 373 |
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
| 374 |
|
|
| 375 |
< |
The most general form of the select command is: {\tt select {\it |
| 376 |
< |
expression}}. This expression represents an arbitrary set of |
| 310 |
< |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
| 311 |
< |
composed of either name expressions, index expressions, predefined |
| 312 |
< |
sets, user-defined expressions, comparison operators, within |
| 313 |
< |
expressions, or logical combinations of the above expression types. |
| 314 |
< |
Expressions can be combined using parentheses and the Boolean |
| 315 |
< |
operators. |
| 375 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
| 376 |
> |
StuntDoubles. The most general form of the select command is: |
| 377 |
|
|
| 378 |
+ |
{\tt select {\it expression}}. |
| 379 |
+ |
|
| 380 |
+ |
This expression represents an arbitrary set of StuntDoubles (Atoms |
| 381 |
+ |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
| 382 |
+ |
name expressions, index expressions, predefined sets, user-defined |
| 383 |
+ |
expressions, comparison operators, within expressions, or logical |
| 384 |
+ |
combinations of the above expression types. Expressions can be |
| 385 |
+ |
combined using parentheses and the Boolean operators. |
| 386 |
+ |
|
| 387 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
| 388 |
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|
| 389 |
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The logical operators allow complex queries to be constructed out of |
