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\appendix |
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\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine (OOPSE)} |
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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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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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Gay-Berne ellipsoids, or other "lumpy"atoms with orientational |
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degrees of freedom), as well as rigid bodies. |
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\item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap |
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Beowulf clusters to obtain very efficient parallelism. |
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\item {\sc OOPSE} integrates the equations of motion using advanced methods for |
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orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T |
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ensembles. |
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\item {\sc OOPSE} can carry out simulations on metallic systems using the |
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Embedded Atom Method (EAM) as well as the Sutton-Chen potential. |
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\item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals. |
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\item {\sc OOPSE} can simulate systems containing the extremely efficient |
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extended-Soft Sticky Dipole (SSD/E) model for water. |
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\end{enumerate} |
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|
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\section{\label{appendixSection:architecture }Architecture} |
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|
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Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE} |
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uses C++ Standard Template Library (STL) and fortran modules as the |
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foundation. As an extensive set of the STL and Fortran90 modules, |
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{\sc Base Classes} provide generic implementations of mathematical |
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objects (e.g., matrices, vectors, polynomials, random number |
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generators) and advanced data structures and algorithms(e.g., tuple, |
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bitset, generic data, string manipulation). The molecular data |
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structures for the representation of atoms, bonds, bends, torsions, |
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rigid bodies and molecules \textit{etc} are contained in the {\sc |
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Kernel} which is implemented with {\sc Base Classes} and are |
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carefully designed to provide maximum extensibility and flexibility. |
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The functionality required for applications is provide by the third |
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layer which contains Input/Output, Molecular Mechanics and Structure |
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modules. Input/Output module not only implements general methods for |
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file handling, but also defines a generic force field interface. |
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Another important component of Input/Output module is the meta-data |
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file parser, which is rewritten using ANother Tool for Language |
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Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular |
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Mechanics module consists of energy minimization and a wide |
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varieties of integration methods(see Chap.~\ref{chapt:methodology}). |
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The structure module contains a flexible and powerful selection |
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library which syntax is elaborated in |
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Sec.~\ref{appendixSection:syntax}. The top layer is made of the main |
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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 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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\centering |
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\includegraphics[width=\linewidth]{architecture.eps} |
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\caption[The architecture of {\sc oopse}-3.0] {The architecture of |
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{\sc oopse}-3.0.} \label{appendixFig:architecture} |
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\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
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of {\sc OOPSE}} \label{appendixFig:architecture} |
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\end{figure} |
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|
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\section{\label{appendixSection:desginPattern}Design Pattern} |
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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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\subsection{\label{appendixSection:singleton}Singleton} |
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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, OOPSE |
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\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}. |
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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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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}. 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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List.~\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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\subsection{\label{appendixSection:singleton}Singleton} |
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The Singleton pattern ensures that only one instance of a class is |
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created. All objects that use an instance of that class use the same |
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instance. |
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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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\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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if (instance_ == NULL){ |
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instance_ = new IntegratorFactory; |
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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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|
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|
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|
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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The Factory Method pattern is a creational pattern which deals with |
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the problem of creating objects without specifying the exact class |
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of object that will be created. Factory Method solves this problem |
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by defining a separate method for creating the objects, which |
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subclasses can then override to specify the derived type of product |
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that will be created. |
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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 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 |
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List.~\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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\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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|
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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()) { |
172 |
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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={[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 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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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) |
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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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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 classes of the elements |
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that you are operating on. |
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|
|
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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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\subsection{\label{appendixSection:templateMethod}Template Method} |
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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 |
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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*} { |
259 |
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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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|
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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); |
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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 BaseAtomVisitor:public BaseVisitor{ public: |
275 |
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virtual void visit(Atom* atom); |
276 |
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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 SSDAtomVisitor:public BaseAtomVisitor{ public: |
281 |
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virtual void visit(Atom* atom); |
282 |
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virtual void visit(DirectionalAtom* datom); |
283 |
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virtual void visit(RigidBody* rb); |
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}; |
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|
286 |
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class CompositeVisitor: public BaseVisitor { |
287 |
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public: |
288 |
+ |
|
289 |
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typedef list<pair<BaseVisitor*, int> > VistorListType; |
290 |
+ |
typedef VistorListType::iterator VisitorListIterator; |
291 |
+ |
virtual void visit(Atom* atom) { |
292 |
+ |
VisitorListIterator i; |
293 |
+ |
BaseVisitor* curVisitor; |
294 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
295 |
+ |
atom->accept(*i); |
296 |
+ |
} |
297 |
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} |
298 |
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|
299 |
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virtual void visit(DirectionalAtom* datom) { |
300 |
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VisitorListIterator i; |
301 |
+ |
BaseVisitor* curVisitor; |
302 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
303 |
+ |
atom->accept(*i); |
304 |
+ |
} |
305 |
+ |
} |
306 |
+ |
|
307 |
+ |
virtual void visit(RigidBody* rb) { |
308 |
+ |
VisitorListIterator i; |
309 |
+ |
std::vector<Atom*> myAtoms; |
310 |
+ |
std::vector<Atom*>::iterator ai; |
311 |
+ |
myAtoms = rb->getAtoms(); |
312 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) {{ |
313 |
+ |
rb->accept(*i); |
314 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
315 |
+ |
(*ai)->accept(*i); |
316 |
+ |
} |
317 |
+ |
} |
318 |
+ |
|
319 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
320 |
+ |
|
321 |
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protected: |
322 |
+ |
VistorListType visitorList; |
323 |
+ |
}; |
324 |
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|
325 |
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\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 |
331 |
|
collections of atoms or atoms which have orientational degrees of |
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< |
freedom. Here is a diagram of the class heirarchy: |
333 |
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|
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%\begin{figure} |
335 |
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%\centering |
336 |
< |
%\includegraphics[width=3in]{heirarchy.eps} |
337 |
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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 |
339 |
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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 |
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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: |
337 |
> |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
338 |
> |
on the specifics of the simulation). The names of rigid bodies are |
339 |
> |
generated automatically. For example, the name of the first rigid |
340 |
> |
body in a DMPC molecule is DMPC\_RB\_0. |
341 |
|
\begin{itemize} |
342 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
343 |
|
integrators and minimizers. |
347 |
|
DirectionalAtom}s which behaves as a single unit. |
348 |
|
\end{itemize} |
349 |
|
|
113 |
– |
Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
114 |
– |
own names which are specified in the {\tt .md} file. In contrast, |
115 |
– |
RigidBodies are denoted by their membership and index inside a |
116 |
– |
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
117 |
– |
inside the brackets depend on the specifics of the simulation). The |
118 |
– |
names of rigid bodies are generated automatically. For example, the |
119 |
– |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
120 |
– |
|
350 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
351 |
|
|
352 |
< |
The most general form of the select command is: {\tt select {\it |
353 |
< |
expression}} |
352 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
353 |
> |
StuntDoubles. The most general form of the select command is: |
354 |
|
|
355 |
+ |
{\tt select {\it expression}}. |
356 |
+ |
|
357 |
|
This expression represents an arbitrary set of StuntDoubles (Atoms |
358 |
< |
or RigidBodies) in {\sc oopse}. Expressions are composed of either |
358 |
> |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
359 |
|
name expressions, index expressions, predefined sets, user-defined |
360 |
|
expressions, comparison operators, within expressions, or logical |
361 |
|
combinations of the above expression types. Expressions can be |
442 |
|
Users can define arbitrary terms to represent groups of |
443 |
|
StuntDoubles, and then use the define terms in select commands. The |
444 |
|
general form for the define command is: {\bf define {\it term |
445 |
< |
expression}} |
445 |
> |
expression}}. Once defined, the user can specify such terms in |
446 |
> |
boolean expressions |
447 |
|
|
216 |
– |
Once defined, the user can specify such terms in boolean expressions |
217 |
– |
|
448 |
|
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
449 |
|
|
450 |
|
{\tt select SSDWATER} |
489 |
|
some or all of the configurations that are contained within a dump |
490 |
|
file. The most common example of a static property that can be |
491 |
|
computed is the pair distribution function between atoms of type $A$ |
492 |
< |
and other atoms of type $B$, $g_{AB}(r)$. StaticProps can also be |
493 |
< |
used to compute the density distributions of other molecules in a |
494 |
< |
reference frame {\it fixed to the body-fixed reference frame} of a |
495 |
< |
selected atom or rigid body. |
492 |
> |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
493 |
> |
also be used to compute the density distributions of other molecules |
494 |
> |
in a reference frame {\it fixed to the body-fixed reference frame} |
495 |
> |
of a selected atom or rigid body. Due to the fact that the selected |
496 |
> |
StuntDoubles from two selections may be overlapped, {\tt |
497 |
> |
StaticProps} performs the calculation in three stages which are |
498 |
> |
illustrated in Fig.~\ref{oopseFig:staticPropsProcess}. |
499 |
> |
|
500 |
> |
\begin{figure} |
501 |
> |
\centering |
502 |
> |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
503 |
> |
\caption[A representation of the three-stage correlations in |
504 |
> |
\texttt{StaticProps}]{This diagram illustrates three-stage |
505 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
506 |
> |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
507 |
> |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
508 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
509 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
510 |
> |
the contrary, the third stage($C$ and $C$) are completely |
511 |
> |
overlapping} \label{oopseFig:staticPropsProcess} |
512 |
> |
\end{figure} |
513 |
|
|
514 |
|
There are five seperate radial distribution functions availiable in |
515 |
|
OOPSE. Since every radial distrbution function invlove the |
554 |
|
\end{description} |
555 |
|
|
556 |
|
The vectors (and angles) associated with these angular pair |
557 |
< |
distribution functions are most easily seen in the figure below: |
557 |
> |
distribution functions are most easily seen in |
558 |
> |
Fig.~\ref{oopseFig:gofr} |
559 |
|
|
560 |
|
\begin{figure} |
561 |
|
\centering |
627 |
|
different vectors). The ability to use two selection scripts to |
628 |
|
select different types of atoms is already present in the code. |
629 |
|
|
630 |
+ |
For large simulations, the trajectory files can sometimes reach |
631 |
+ |
sizes in excess of several gigabytes. In order to prevent a |
632 |
+ |
situation where the program runs out of memory due to large |
633 |
+ |
trajectories, \texttt{dynamicProps} will estimate the size of free |
634 |
+ |
memory at first, and determine the number of frames in each block, |
635 |
+ |
which allows the operating system to load two blocks of data |
636 |
+ |
simultaneously without swapping. Upon reading two blocks of the |
637 |
+ |
trajectory, \texttt{dynamicProps} will calculate the time |
638 |
+ |
correlation within the first block and the cross correlations |
639 |
+ |
between the two blocks. This second block is then freed and then |
640 |
+ |
incremented and the process repeated until the end of the |
641 |
+ |
trajectory. Once the end is reached, the first block is freed then |
642 |
+ |
incremented, until all frame pairs have been correlated in time. |
643 |
+ |
This process is illustrated in |
644 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
645 |
+ |
|
646 |
+ |
\begin{figure} |
647 |
+ |
\centering |
648 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
649 |
+ |
\caption[A representation of the block correlations in |
650 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
651 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
652 |
+ |
the self correlation of the block, and the open blocks are read one |
653 |
+ |
at a time and the cross correlations between blocks are calculated.} |
654 |
+ |
\label{oopseFig:dynamicPropsProcess} |
655 |
+ |
\end{figure} |
656 |
+ |
|
657 |
|
The options available for DynamicProps are as follows: |
658 |
|
\begin{longtable}[c]{|EFG|} |
659 |
|
\caption{DynamicProps Command-line Options} |
680 |
|
|
681 |
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
682 |
|
|
683 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
684 |
< |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
685 |
< |
The options available for Dump2XYZ are as follows: |
683 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
684 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
685 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
686 |
> |
as follows: |
687 |
|
|
688 |
|
|
689 |
|
\begin{longtable}[c]{|EFG|} |
713 |
|
& {\tt -{}-refsele} & In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}. |
714 |
|
\end{longtable} |
715 |
|
|
716 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
716 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
717 |
|
|
718 |
+ |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
719 |
+ |
center of resistance. Both tensors at the center of diffusion can |
720 |
+ |
also be reported from the program, as well as the coordinates for |
721 |
+ |
the beads which are used to approximate the arbitrary shapes. The |
722 |
+ |
options available for Hydro are as follows: |
723 |
|
\begin{longtable}[c]{|EFG|} |
724 |
|
\caption{Hydrodynamics Command-line Options} |
725 |
|
\\ \hline |
732 |
|
-i & {\tt -{}-input} & input dump file \\ |
733 |
|
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
734 |
|
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
735 |
< |
& {\tt -{}-model} & hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
735 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
736 |
|
\end{longtable} |