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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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reusable. They provide a ready-made solution that can be adapted to |
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different problems as necessary. Pattern are expressive. they |
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provide a common vocabulary of solutions that can express large |
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solutions succinctly. |
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solutions succinctly. As one of the latest advanced techniques |
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emerged from object-oriented community, design patterns were applied |
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in some of the modern scientific software applications, such as |
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JMol, {\sc OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004} |
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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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|
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Patterns are usually described using a format that includes the |
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following information: |
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\begin{enumerate} |
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\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
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discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
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in the literature. In this case it is common practice to document these nicknames or synonyms under |
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the heading of \emph{Aliases} or \emph{Also Known As}. |
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\item The \emph{motivation} or \emph{context} that this pattern applies |
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to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
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\item The \emph{solution} to the problem that the pattern |
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addresses. It describes how to construct the necessary work products. The description may include |
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pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
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collaborations, to show how the problem is solved. |
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\item The \emph{consequences} of using the given solution to solve a |
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problem, both positive and negative. |
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\end{enumerate} |
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|
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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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|
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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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variable, the logging utility which reports error and warning |
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messages to the console in {\sc OOPSE} is a good candidate for |
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applying the Singleton pattern to avoid the global namespace |
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pollution.Although the singleton pattern can be implemented in |
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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}. The declaration and |
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implementation of IntegratorFactory class are given by declared in |
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List.~\ref{appendixScheme:singletonDeclaration} and |
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Scheme.~\ref{appendixScheme:singletonImplementation} respectively. |
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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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\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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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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|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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|
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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 Scheme.~\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 |
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Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the |
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modern C++ template technique to avoid excess subclassing. |
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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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\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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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* 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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|
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}] |
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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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bool IntegratorFactory::unregisterIntegrator(const string& id) { |
195 |
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return creatorMap_.erase(id) == 1; |
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} |
197 |
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|
198 |
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Integrator* IntegratorFactory::createIntegrator(const string& id, |
199 |
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SimInfo* info) { |
200 |
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CreatorMapType::iterator i = creatorMap_.find(id); |
201 |
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if (i != creatorMap_.end()) { |
202 |
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return (i->second)->create(info); |
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} else { |
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return NULL; |
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} |
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} |
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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 Factory pattern (III)].},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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|
188 |
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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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|
192 |
< |
private: |
192 |
> |
private: |
193 |
|
string ident_; |
194 |
|
}; |
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|
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|
template<class ConcreteIntegrator> |
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class IntegratorBuilder : public IntegratorCreator { |
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public: |
199 |
< |
IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {} |
200 |
< |
virtual Integrator* create(SimInfo* info) const { |
201 |
< |
return new ConcreteIntegrator(info); |
202 |
< |
} |
198 |
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public: |
199 |
> |
IntegratorBuilder(const string& ident) |
200 |
> |
: IntegratorCreator(ident) {} |
201 |
> |
virtual Integrator* create(SimInfo* info) const { |
202 |
> |
return new ConcreteIntegrator(info); |
203 |
> |
} |
204 |
|
}; |
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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 |
212 |
< |
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. |
214 |
< |
The UML class diagram of Visitor patten is shown in |
215 |
< |
Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
216 |
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Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
217 |
< |
extensively. |
209 |
> |
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 |
212 |
> |
adding virtual functions into a set of classes without modifying |
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> |
their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
214 |
> |
structure of Visitor pattern which is used extensively in {\tt |
215 |
> |
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
216 |
> |
distinct operations are performed on different StuntDoubles (See the |
217 |
> |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
218 |
> |
in Scheme.~\ref{appendixScheme:element}). Since the hierarchies |
219 |
> |
remains stable, it is easy to define a visit operation (see |
220 |
> |
Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
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> |
Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
222 |
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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} |
226 |
|
\centering |
227 |
|
\includegraphics[width=\linewidth]{visitor.eps} |
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\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
229 |
< |
of {\sc OOPSE}} \label{appendixFig:visitorUML} |
228 |
> |
\caption[The UML class diagram of Visitor patten] {The UML class |
229 |
> |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
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\end{figure} |
231 |
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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} |
233 |
> |
\centering |
234 |
> |
\includegraphics[width=\linewidth]{hierarchy.eps} |
235 |
> |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
236 |
> |
the class hierarchy. } \label{oopseFig:hierarchy} |
237 |
> |
\end{figure} |
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|
|
239 |
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class BaseVisitor{ |
240 |
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public: |
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< |
virtual void visit(Atom* atom); |
242 |
< |
virtual void visit(DirectionalAtom* datom); |
259 |
< |
virtual void visit(RigidBody* rb); |
239 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
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> |
|
241 |
> |
class StuntDouble { public: |
242 |
> |
virtual void accept(BaseVisitor* v) = 0; |
243 |
|
}; |
244 |
|
|
245 |
+ |
class Atom: public StuntDouble { public: |
246 |
+ |
virtual void accept{BaseVisitor* v*} { |
247 |
+ |
v->visit(this); |
248 |
+ |
} |
249 |
+ |
}; |
250 |
+ |
|
251 |
+ |
class DirectionalAtom: public Atom { public: |
252 |
+ |
virtual void accept{BaseVisitor* v*} { |
253 |
+ |
v->visit(this); |
254 |
+ |
} |
255 |
+ |
}; |
256 |
+ |
|
257 |
+ |
class RigidBody: public StuntDouble { public: |
258 |
+ |
virtual void accept{BaseVisitor* v*} { |
259 |
+ |
v->visit(this); |
260 |
+ |
} |
261 |
+ |
}; |
262 |
+ |
|
263 |
|
\end{lstlisting} |
264 |
|
|
265 |
< |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
265 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
266 |
|
|
267 |
< |
class StuntDouble { |
268 |
< |
public: |
269 |
< |
virtual void accept(BaseVisitor* v) = 0; |
267 |
> |
class BaseVisitor{ |
268 |
> |
public: |
269 |
> |
virtual void visit(Atom* atom); |
270 |
> |
virtual void visit(DirectionalAtom* datom); |
271 |
> |
virtual void visit(RigidBody* rb); |
272 |
|
}; |
273 |
|
|
274 |
< |
class Atom: public StuntDouble { |
275 |
< |
public: |
276 |
< |
virtual void accept{BaseVisitor* v*} { |
277 |
< |
v->visit(this); |
275 |
< |
} |
274 |
> |
class BaseAtomVisitor:public BaseVisitor{ public: |
275 |
> |
virtual void visit(Atom* atom); |
276 |
> |
virtual void visit(DirectionalAtom* datom); |
277 |
> |
virtual void visit(RigidBody* rb); |
278 |
|
}; |
279 |
|
|
280 |
< |
class DirectionalAtom: public Atom { |
281 |
< |
public: |
282 |
< |
virtual void accept{BaseVisitor* v*} { |
283 |
< |
v->visit(this); |
280 |
> |
class CompositeVisitor: public BaseVisitor { |
281 |
> |
public: |
282 |
> |
|
283 |
> |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
284 |
> |
typedef VistorListType::iterator VisitorListIterator; |
285 |
> |
virtual void visit(Atom* atom) { |
286 |
> |
VisitorListIterator i; |
287 |
> |
BaseVisitor* curVisitor; |
288 |
> |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
289 |
> |
atom->accept(*i); |
290 |
|
} |
291 |
< |
}; |
291 |
> |
} |
292 |
|
|
293 |
< |
class RigidBody: public StuntDouble { |
294 |
< |
public: |
295 |
< |
virtual void accept{BaseVisitor* v*} { |
296 |
< |
v->visit(this); |
293 |
> |
virtual void visit(DirectionalAtom* datom) { |
294 |
> |
VisitorListIterator i; |
295 |
> |
BaseVisitor* curVisitor; |
296 |
> |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
297 |
> |
atom->accept(*i); |
298 |
|
} |
299 |
< |
}; |
299 |
> |
} |
300 |
|
|
301 |
+ |
virtual void visit(RigidBody* rb) { |
302 |
+ |
VisitorListIterator i; |
303 |
+ |
std::vector<Atom*> myAtoms; |
304 |
+ |
std::vector<Atom*>::iterator ai; |
305 |
+ |
myAtoms = rb->getAtoms(); |
306 |
+ |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) {{ |
307 |
+ |
rb->accept(*i); |
308 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
309 |
+ |
(*ai)->accept(*i); |
310 |
+ |
} |
311 |
+ |
} |
312 |
+ |
|
313 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
314 |
+ |
|
315 |
+ |
protected: |
316 |
+ |
VistorListType visitorList; |
317 |
+ |
}; |
318 |
|
\end{lstlisting} |
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+ |
|
320 |
|
\section{\label{appendixSection:concepts}Concepts} |
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|
|
322 |
|
OOPSE manipulates both traditional atoms as well as some objects |
323 |
|
that {\it behave like atoms}. These objects can be rigid |
324 |
|
collections of atoms or atoms which have orientational degrees of |
325 |
< |
freedom. Here is a diagram of the class heirarchy: |
326 |
< |
|
327 |
< |
\begin{figure} |
328 |
< |
\centering |
329 |
< |
\includegraphics[width=3in]{heirarchy.eps} |
330 |
< |
\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ The |
331 |
< |
class heirarchy of StuntDoubles in {\sc oopse}-3.0. |
325 |
> |
freedom. A diagram of the class hierarchy is illustrated in |
326 |
> |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
327 |
> |
DirectionalAtom in {\sc OOPSE} have their own names which are |
328 |
> |
specified in the {\tt .md} file. In contrast, RigidBodies are |
329 |
> |
denoted by their membership and index inside a particular molecule: |
330 |
> |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
331 |
> |
on the specifics of the simulation). The names of rigid bodies are |
332 |
> |
generated automatically. For example, the name of the first rigid |
333 |
> |
body in a DMPC molecule is DMPC\_RB\_0. |
334 |
|
\begin{itemize} |
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|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
336 |
|
integrators and minimizers. |
338 |
|
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
339 |
|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
340 |
|
DirectionalAtom}s which behaves as a single unit. |
341 |
< |
\end{itemize}} \label{oopseFig:heirarchy} |
313 |
< |
\end{figure} |
341 |
> |
\end{itemize} |
342 |
|
|
315 |
– |
Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
316 |
– |
own names which are specified in the {\tt .md} file. In contrast, |
317 |
– |
RigidBodies are denoted by their membership and index inside a |
318 |
– |
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
319 |
– |
inside the brackets depend on the specifics of the simulation). The |
320 |
– |
names of rigid bodies are generated automatically. For example, the |
321 |
– |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
322 |
– |
|
343 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
344 |
|
|
345 |
< |
The most general form of the select command is: {\tt select {\it |
346 |
< |
expression}}. This expression represents an arbitrary set of |
327 |
< |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
328 |
< |
composed of either name expressions, index expressions, predefined |
329 |
< |
sets, user-defined expressions, comparison operators, within |
330 |
< |
expressions, or logical combinations of the above expression types. |
331 |
< |
Expressions can be combined using parentheses and the Boolean |
332 |
< |
operators. |
345 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
346 |
> |
StuntDoubles. The most general form of the select command is: |
347 |
|
|
348 |
+ |
{\tt select {\it expression}}. |
349 |
+ |
|
350 |
+ |
This expression represents an arbitrary set of StuntDoubles (Atoms |
351 |
+ |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
352 |
+ |
name expressions, index expressions, predefined sets, user-defined |
353 |
+ |
expressions, comparison operators, within expressions, or logical |
354 |
+ |
combinations of the above expression types. Expressions can be |
355 |
+ |
combined using parentheses and the Boolean operators. |
356 |
+ |
|
357 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
358 |
|
|
359 |
|
The logical operators allow complex queries to be constructed out of |
485 |
|
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
486 |
|
also be used to compute the density distributions of other molecules |
487 |
|
in a reference frame {\it fixed to the body-fixed reference frame} |
488 |
< |
of a selected atom or rigid body. |
488 |
> |
of a selected atom or rigid body. Due to the fact that the selected |
489 |
> |
StuntDoubles from two selections may be overlapped, {\tt |
490 |
> |
StaticProps} performs the calculation in three stages which are |
491 |
> |
illustrated in Fig.~\ref{oopseFig:staticPropsProcess}. |
492 |
|
|
493 |
+ |
\begin{figure} |
494 |
+ |
\centering |
495 |
+ |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
496 |
+ |
\caption[A representation of the three-stage correlations in |
497 |
+ |
\texttt{StaticProps}]{This diagram illustrates three-stage |
498 |
+ |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
499 |
+ |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
500 |
+ |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
501 |
+ |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
502 |
+ |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
503 |
+ |
the contrary, the third stage($C$ and $C$) are completely |
504 |
+ |
overlapping} \label{oopseFig:staticPropsProcess} |
505 |
+ |
\end{figure} |
506 |
+ |
|
507 |
|
There are five seperate radial distribution functions availiable in |
508 |
|
OOPSE. Since every radial distrbution function invlove the |
509 |
|
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
547 |
|
\end{description} |
548 |
|
|
549 |
|
The vectors (and angles) associated with these angular pair |
550 |
< |
distribution functions are most easily seen in the figure below: |
550 |
> |
distribution functions are most easily seen in |
551 |
> |
Fig.~\ref{oopseFig:gofr} |
552 |
|
|
553 |
|
\begin{figure} |
554 |
|
\centering |
559 |
|
their body-fixed frames.} \label{oopseFig:gofr} |
560 |
|
\end{figure} |
561 |
|
|
521 |
– |
Due to the fact that the selected StuntDoubles from two selections |
522 |
– |
may be overlapped, {\tt StaticProps} performs the calculation in |
523 |
– |
three stages which are illustrated in |
524 |
– |
Fig.~\ref{oopseFig:staticPropsProcess}. |
525 |
– |
|
526 |
– |
\begin{figure} |
527 |
– |
\centering |
528 |
– |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
529 |
– |
\caption[A representation of the three-stage correlations in |
530 |
– |
\texttt{StaticProps}]{This diagram illustrates three-stage |
531 |
– |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
532 |
– |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
533 |
– |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
534 |
– |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
535 |
– |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
536 |
– |
the contrary, the third stage($C$ and $C$) are completely |
537 |
– |
overlapping} \label{oopseFig:staticPropsProcess} |
538 |
– |
\end{figure} |
539 |
– |
|
562 |
|
The options available for {\tt StaticProps} are as follows: |
563 |
|
\begin{longtable}[c]{|EFG|} |
564 |
|
\caption{StaticProps Command-line Options} |
621 |
|
select different types of atoms is already present in the code. |
622 |
|
|
623 |
|
For large simulations, the trajectory files can sometimes reach |
624 |
< |
sizes in excess of several gigabytes. In order to effectively |
625 |
< |
analyze that amount of data. In order to prevent a situation where |
626 |
< |
the program runs out of memory due to large trajectories, |
627 |
< |
\texttt{dynamicProps} will estimate the size of free memory at |
628 |
< |
first, and determine the number of frames in each block, which |
607 |
< |
allows the operating system to load two blocks of data |
624 |
> |
sizes in excess of several gigabytes. In order to prevent a |
625 |
> |
situation where the program runs out of memory due to large |
626 |
> |
trajectories, \texttt{dynamicProps} will estimate the size of free |
627 |
> |
memory at first, and determine the number of frames in each block, |
628 |
> |
which allows the operating system to load two blocks of data |
629 |
|
simultaneously without swapping. Upon reading two blocks of the |
630 |
|
trajectory, \texttt{dynamicProps} will calculate the time |
631 |
|
correlation within the first block and the cross correlations |