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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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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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|
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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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\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* 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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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 implementation of Singleton design pattern (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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|
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IntegratorFactory* getInstance() { |
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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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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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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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\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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class IntegratorFactory { |
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public: |
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typedef std::map<string, IntegratorCreator*> CreatorMapType; |
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public: |
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typedef std::map<string, IntegratorCreator*> CreatorMapType; |
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|
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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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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* 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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result = (i->second)->create(info); |
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} |
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return result; |
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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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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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private: |
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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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|
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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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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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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 string& ident) : 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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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. 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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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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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{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 |
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of {\sc OOPSE}} \label{appendixFig:visitorUML} |
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\caption[The UML class diagram of Visitor patten] {The UML class |
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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{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
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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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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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> |
\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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< |
\end{lstlisting} |
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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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< |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
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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 StuntDouble { |
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< |
public: |
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< |
virtual void accept(BaseVisitor* v) = 0; |
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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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< |
class Atom: public StuntDouble { |
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< |
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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> |
\end{lstlisting} |
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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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> |
|
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> |
class BaseVisitor{ |
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> |
public: |
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> |
virtual void visit(Atom* atom); |
| 290 |
> |
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 DirectionalAtom: public Atom { |
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< |
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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> |
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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|
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< |
class RigidBody: public StuntDouble { |
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public: |
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< |
virtual void accept{BaseVisitor* v*} { |
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< |
v->visit(this); |
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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; |
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> |
for(i = visitorList.begin();i != visitorList.end();++i) { |
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atom->accept(*i); |
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|
} |
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+ |
} |
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+ |
|
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virtual void visit(DirectionalAtom* datom) { |
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VisitorListIterator i; |
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BaseVisitor* curVisitor; |
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for(i = visitorList.begin();i != visitorList.end();++i) { |
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atom->accept(*i); |
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+ |
} |
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} |
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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; |
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myAtoms = rb->getAtoms(); |
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for(i = visitorList.begin();i != visitorList.end();++i) {{ |
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rb->accept(*i); |
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for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
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(*ai)->accept(*i); |
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} |
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} |
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|
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void addVisitor(BaseVisitor* v, int priority); |
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|
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protected: |
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+ |
VistorListType visitorList; |
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|
}; |
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|
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|
\end{lstlisting} |
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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. A diagram of the class heirarchy is illustrated in |
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< |
Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and |
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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 |
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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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|
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{figure} |
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\centering |
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\includegraphics[width=\linewidth]{heirarchy.eps} |
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\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of |
| 301 |
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the class heirarchy. |
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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 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} |
| 310 |
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} \label{oopseFig:heirarchy} |
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\end{figure} |
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|
| 370 |
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
| 371 |
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|
| 372 |
< |
The most general form of the select command is: {\tt select {\it |
| 373 |
< |
expression}}. This expression represents an arbitrary set of |
| 317 |
< |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
| 318 |
< |
composed of either name expressions, index expressions, predefined |
| 319 |
< |
sets, user-defined expressions, comparison operators, within |
| 320 |
< |
expressions, or logical combinations of the above expression types. |
| 321 |
< |
Expressions can be combined using parentheses and the Boolean |
| 322 |
< |
operators. |
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> |
{\sc OOPSE} provides a powerful selection utility to select |
| 373 |
> |
StuntDoubles. The most general form of the select command is: |
| 374 |
|
|
| 375 |
+ |
{\tt select {\it expression}}. |
| 376 |
+ |
|
| 377 |
+ |
This expression represents an arbitrary set of StuntDoubles (Atoms |
| 378 |
+ |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
| 379 |
+ |
name expressions, index expressions, predefined sets, user-defined |
| 380 |
+ |
expressions, comparison operators, within expressions, or logical |
| 381 |
+ |
combinations of the above expression types. Expressions can be |
| 382 |
+ |
combined using parentheses and the Boolean operators. |
| 383 |
+ |
|
| 384 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
| 385 |
|
|
| 386 |
|
The logical operators allow complex queries to be constructed out of |
