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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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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}] {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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|
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Design patterns are optimal solutions to commonly-occurring problems |
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in software design. Although originated as an architectural concept |
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for buildings and towns by Christopher Alexander |
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\cite{Alexander1987}, software patterns first became popular with |
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the wide acceptance of the book, Design Patterns: Elements of |
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Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
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the experience, knowledge and insights of developers who have |
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successfully used these patterns in their own work. Patterns are |
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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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|
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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{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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|
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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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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}. IntegratorFactory class is |
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declared as |
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|
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
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|
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class IntegratorFactory { |
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public: |
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static IntegratorFactory* |
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getInstance(); |
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protected: |
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IntegratorFactory(); |
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private: |
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static IntegratorFactory* instance_; |
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}; |
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|
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\end{lstlisting} |
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|
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The corresponding implementation is |
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|
143 |
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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() { |
148 |
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if (instance_ == NULL){ |
149 |
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instance_ = new IntegratorFactory; |
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} |
151 |
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return instance_; |
152 |
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} |
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|
154 |
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\end{lstlisting} |
155 |
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|
156 |
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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 |
159 |
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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 |
162 |
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termination. |
163 |
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|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
165 |
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|
166 |
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Categoried as a creational pattern, the Factory Method pattern deals |
167 |
|
|
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 |
169 |
|
|
implemented by delegating the creation operation to the subclasses. |
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Parameterized Factory pattern where factory method ( |
171 |
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|
createIntegrator member function) creates products based on the |
172 |
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|
identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If |
173 |
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the identifier has been already registered, the factory method will |
174 |
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|
invoke the corresponding creator (see List.~\ref{integratorCreator}) |
175 |
|
|
which utilizes the modern C++ template technique to avoid excess |
176 |
|
|
subclassing. |
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|
178 |
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
179 |
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|
180 |
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class IntegratorFactory { |
181 |
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public: |
182 |
|
|
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
183 |
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|
184 |
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bool registerIntegrator(IntegratorCreator* creator) { |
185 |
|
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return creatorMap_.insert(creator->getIdent(), creator).second; |
186 |
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|
} |
187 |
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|
188 |
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Integrator* createIntegrator(const string& id, SimInfo* info) { |
189 |
|
|
Integrator* result = NULL; |
190 |
|
|
CreatorMapType::iterator i = creatorMap_.find(id); |
191 |
|
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if (i != creatorMap_.end()) { |
192 |
|
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result = (i->second)->create(info); |
193 |
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} |
194 |
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return result; |
195 |
|
|
} |
196 |
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|
197 |
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private: |
198 |
|
|
CreatorMapType creatorMap_; |
199 |
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}; |
200 |
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\end{lstlisting} |
201 |
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|
202 |
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
203 |
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|
204 |
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class IntegratorCreator { |
205 |
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public: |
206 |
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IntegratorCreator(const string& ident) : ident_(ident) {} |
207 |
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|
208 |
tim |
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const string& getIdent() const { return ident_; } |
209 |
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|
210 |
|
|
virtual Integrator* create(SimInfo* info) const = 0; |
211 |
|
|
|
212 |
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private: |
213 |
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string ident_; |
214 |
tim |
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}; |
215 |
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2821 |
|
216 |
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template<class ConcreteIntegrator> |
217 |
|
|
class IntegratorBuilder : public IntegratorCreator { |
218 |
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public: |
219 |
|
|
IntegratorBuilder(const string& ident) |
220 |
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: IntegratorCreator(ident) {} |
221 |
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virtual Integrator* create(SimInfo* info) const { |
222 |
|
|
return new ConcreteIntegrator(info); |
223 |
|
|
} |
224 |
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}; |
225 |
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\end{lstlisting} |
226 |
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|
|
227 |
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
228 |
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|
229 |
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The visitor pattern is designed to decouple the data structure and |
230 |
|
|
algorithms used upon them by collecting related operation from |
231 |
|
|
element classes into other visitor classes, which is equivalent to |
232 |
|
|
adding virtual functions into a set of classes without modifying |
233 |
|
|
their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
234 |
|
|
structure of Visitor pattern which is used extensively in {\tt |
235 |
|
|
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
236 |
|
|
distinct operations are performed on different StuntDoubles (See the |
237 |
|
|
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
238 |
|
|
in List.~\ref{appendixScheme:element}). Since the hierarchies |
239 |
|
|
remains stable, it is easy to define a visit operation (see |
240 |
|
|
List.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
241 |
|
|
Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
242 |
|
|
manages a priority visitor list and handles the execution of every |
243 |
|
|
visitor in the priority list on different StuntDoubles. |
244 |
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|
245 |
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\begin{figure} |
246 |
|
|
\centering |
247 |
tim |
2826 |
\includegraphics[width=\linewidth]{visitor.eps} |
248 |
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\caption[The UML class diagram of Visitor patten] {The UML class |
249 |
|
|
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
250 |
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\end{figure} |
251 |
|
|
|
252 |
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\begin{figure} |
253 |
|
|
\centering |
254 |
|
|
\includegraphics[width=\linewidth]{hierarchy.eps} |
255 |
|
|
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
256 |
|
|
the class hierarchy. } \label{oopseFig:hierarchy} |
257 |
|
|
\end{figure} |
258 |
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|
259 |
|
|
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
260 |
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|
|
261 |
|
|
class StuntDouble { public: |
262 |
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|
virtual void accept(BaseVisitor* v) = 0; |
263 |
|
|
}; |
264 |
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|
265 |
|
|
class Atom: public StuntDouble { public: |
266 |
|
|
virtual void accept{BaseVisitor* v*} { |
267 |
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|
v->visit(this); |
268 |
|
|
} |
269 |
|
|
}; |
270 |
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|
|
271 |
|
|
class DirectionalAtom: public Atom { public: |
272 |
|
|
virtual void accept{BaseVisitor* v*} { |
273 |
|
|
v->visit(this); |
274 |
|
|
} |
275 |
|
|
}; |
276 |
|
|
|
277 |
|
|
class RigidBody: public StuntDouble { public: |
278 |
|
|
virtual void accept{BaseVisitor* v*} { |
279 |
|
|
v->visit(this); |
280 |
|
|
} |
281 |
|
|
}; |
282 |
|
|
|
283 |
|
|
\end{lstlisting} |
284 |
|
|
|
285 |
tim |
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
286 |
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|
287 |
|
|
class BaseVisitor{ |
288 |
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public: |
289 |
|
|
virtual void visit(Atom* atom); |
290 |
|
|
virtual void visit(DirectionalAtom* datom); |
291 |
|
|
virtual void visit(RigidBody* rb); |
292 |
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}; |
293 |
|
|
|
294 |
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class BaseAtomVisitor:public BaseVisitor{ public: |
295 |
|
|
virtual void visit(Atom* atom); |
296 |
|
|
virtual void visit(DirectionalAtom* datom); |
297 |
|
|
virtual void visit(RigidBody* rb); |
298 |
|
|
}; |
299 |
|
|
|
300 |
tim |
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class SSDAtomVisitor:public BaseAtomVisitor{ public: |
301 |
|
|
virtual void visit(Atom* atom); |
302 |
|
|
virtual void visit(DirectionalAtom* datom); |
303 |
|
|
virtual void visit(RigidBody* rb); |
304 |
|
|
}; |
305 |
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|
306 |
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class CompositeVisitor: public BaseVisitor { |
307 |
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public: |
308 |
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|
309 |
tim |
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typedef list<pair<BaseVisitor*, int> > VistorListType; |
310 |
|
|
typedef VistorListType::iterator VisitorListIterator; |
311 |
|
|
virtual void visit(Atom* atom) { |
312 |
|
|
VisitorListIterator i; |
313 |
|
|
BaseVisitor* curVisitor; |
314 |
|
|
for(i = visitorList.begin();i != visitorList.end();++i) { |
315 |
|
|
atom->accept(*i); |
316 |
|
|
} |
317 |
tim |
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} |
318 |
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|
319 |
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virtual void visit(DirectionalAtom* datom) { |
320 |
|
|
VisitorListIterator i; |
321 |
|
|
BaseVisitor* curVisitor; |
322 |
|
|
for(i = visitorList.begin();i != visitorList.end();++i) { |
323 |
|
|
atom->accept(*i); |
324 |
|
|
} |
325 |
tim |
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} |
326 |
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|
327 |
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virtual void visit(RigidBody* rb) { |
328 |
|
|
VisitorListIterator i; |
329 |
|
|
std::vector<Atom*> myAtoms; |
330 |
|
|
std::vector<Atom*>::iterator ai; |
331 |
|
|
myAtoms = rb->getAtoms(); |
332 |
|
|
for(i = visitorList.begin();i != visitorList.end();++i) {{ |
333 |
|
|
rb->accept(*i); |
334 |
|
|
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
335 |
|
|
(*ai)->accept(*i); |
336 |
|
|
} |
337 |
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} |
338 |
tim |
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|
339 |
|
|
void addVisitor(BaseVisitor* v, int priority); |
340 |
|
|
|
341 |
|
|
protected: |
342 |
|
|
VistorListType visitorList; |
343 |
tim |
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}; |
344 |
|
|
|
345 |
tim |
2821 |
\end{lstlisting} |
346 |
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|
347 |
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\section{\label{appendixSection:concepts}Concepts} |
348 |
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|
349 |
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OOPSE manipulates both traditional atoms as well as some objects |
350 |
|
|
that {\it behave like atoms}. These objects can be rigid |
351 |
|
|
collections of atoms or atoms which have orientational degrees of |
352 |
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2836 |
freedom. A diagram of the class hierarchy is illustrated in |
353 |
|
|
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
354 |
tim |
2829 |
DirectionalAtom in {\sc OOPSE} have their own names which are |
355 |
|
|
specified in the {\tt .md} file. In contrast, RigidBodies are |
356 |
|
|
denoted by their membership and index inside a particular molecule: |
357 |
|
|
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
358 |
|
|
on the specifics of the simulation). The names of rigid bodies are |
359 |
|
|
generated automatically. For example, the name of the first rigid |
360 |
|
|
body in a DMPC molecule is DMPC\_RB\_0. |
361 |
tim |
2838 |
\begin{itemize} |
362 |
|
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
363 |
|
|
integrators and minimizers. |
364 |
|
|
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
365 |
|
|
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
366 |
|
|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
367 |
|
|
DirectionalAtom}s which behaves as a single unit. |
368 |
|
|
\end{itemize} |
369 |
tim |
2688 |
|
370 |
tim |
2730 |
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
371 |
|
|
|
372 |
tim |
2837 |
{\sc OOPSE} provides a powerful selection utility to select |
373 |
|
|
StuntDoubles. The most general form of the select command is: |
374 |
tim |
2730 |
|
375 |
tim |
2837 |
{\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 |
tim |
2730 |
\subsection{\label{appendixSection:logical}Logical expressions} |
385 |
|
|
|
386 |
|
|
The logical operators allow complex queries to be constructed out of |
387 |
|
|
simpler ones using the standard boolean connectives {\bf and}, {\bf |
388 |
|
|
or}, {\bf not}. Parentheses can be used to alter the precedence of |
389 |
|
|
the operators. |
390 |
|
|
|
391 |
|
|
\begin{center} |
392 |
|
|
\begin{tabular}{|ll|} |
393 |
|
|
\hline |
394 |
|
|
{\bf logical operator} & {\bf equivalent operator} \\ |
395 |
|
|
\hline |
396 |
|
|
and & ``\&'', ``\&\&'' \\ |
397 |
|
|
or & ``$|$'', ``$||$'', ``,'' \\ |
398 |
|
|
not & ``!'' \\ |
399 |
|
|
\hline |
400 |
|
|
\end{tabular} |
401 |
|
|
\end{center} |
402 |
|
|
|
403 |
|
|
\subsection{\label{appendixSection:name}Name expressions} |
404 |
|
|
|
405 |
|
|
\begin{center} |
406 |
tim |
2805 |
\begin{tabular}{|llp{2in}|} |
407 |
tim |
2730 |
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
408 |
|
|
of |
409 |
|
|
examples} \\ |
410 |
|
|
\hline expression without ``.'' & select DMPC & select all |
411 |
|
|
StuntDoubles |
412 |
|
|
belonging to all DMPC molecules \\ |
413 |
|
|
& select C* & select all atoms which have atom types beginning with C |
414 |
|
|
\\ |
415 |
|
|
& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
416 |
|
|
only select the rigid bodies, and not the atoms belonging to them). \\ |
417 |
|
|
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
418 |
|
|
O\_TIP3P |
419 |
|
|
atoms belonging to TIP3P molecules \\ |
420 |
|
|
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
421 |
|
|
the first |
422 |
|
|
RigidBody in each DMPC molecule \\ |
423 |
|
|
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
424 |
|
|
molecule \\ |
425 |
|
|
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
426 |
|
|
select all atoms |
427 |
|
|
belonging to all rigid bodies within all DMPC molecules \\ |
428 |
|
|
\hline |
429 |
|
|
\end{tabular} |
430 |
|
|
\end{center} |
431 |
|
|
|
432 |
|
|
\subsection{\label{appendixSection:index}Index expressions} |
433 |
|
|
|
434 |
|
|
\begin{center} |
435 |
|
|
\begin{tabular}{|lp{4in}|} |
436 |
|
|
\hline |
437 |
|
|
{\bf examples} & {\bf translation of examples} \\ |
438 |
|
|
\hline |
439 |
|
|
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
440 |
|
|
select 20 to 30 & select all of the StuntDoubles belonging to |
441 |
|
|
molecules which have global indices between 20 (inclusive) and 30 |
442 |
|
|
(exclusive) \\ |
443 |
|
|
\hline |
444 |
|
|
\end{tabular} |
445 |
|
|
\end{center} |
446 |
|
|
|
447 |
|
|
\subsection{\label{appendixSection:predefined}Predefined sets} |
448 |
|
|
|
449 |
|
|
\begin{center} |
450 |
|
|
\begin{tabular}{|ll|} |
451 |
|
|
\hline |
452 |
|
|
{\bf keyword} & {\bf description} \\ |
453 |
|
|
\hline |
454 |
|
|
all & select all StuntDoubles \\ |
455 |
|
|
none & select none of the StuntDoubles \\ |
456 |
|
|
\hline |
457 |
|
|
\end{tabular} |
458 |
|
|
\end{center} |
459 |
|
|
|
460 |
|
|
\subsection{\label{appendixSection:userdefined}User-defined expressions} |
461 |
|
|
|
462 |
|
|
Users can define arbitrary terms to represent groups of |
463 |
|
|
StuntDoubles, and then use the define terms in select commands. The |
464 |
|
|
general form for the define command is: {\bf define {\it term |
465 |
tim |
2815 |
expression}}. Once defined, the user can specify such terms in |
466 |
|
|
boolean expressions |
467 |
tim |
2730 |
|
468 |
|
|
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
469 |
|
|
|
470 |
|
|
{\tt select SSDWATER} |
471 |
|
|
|
472 |
|
|
\subsection{\label{appendixSection:comparison}Comparison expressions} |
473 |
|
|
|
474 |
|
|
StuntDoubles can be selected by using comparision operators on their |
475 |
|
|
properties. The general form for the comparison command is: a |
476 |
|
|
property name, followed by a comparision operator and then a number. |
477 |
|
|
|
478 |
|
|
\begin{center} |
479 |
|
|
\begin{tabular}{|l|l|} |
480 |
|
|
\hline |
481 |
|
|
{\bf property} & mass, charge \\ |
482 |
|
|
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
483 |
|
|
``$<=$'', ``$!=$'' \\ |
484 |
|
|
\hline |
485 |
|
|
\end{tabular} |
486 |
|
|
\end{center} |
487 |
|
|
|
488 |
|
|
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
489 |
tim |
2805 |
would select StuntDoubles which have mass greater than 16.0 and |
490 |
tim |
2730 |
charges less than -2. |
491 |
|
|
|
492 |
|
|
\subsection{\label{appendixSection:within}Within expressions} |
493 |
|
|
|
494 |
|
|
The ``within'' keyword allows the user to select all StuntDoubles |
495 |
|
|
within the specified distance (in Angstroms) from a selection, |
496 |
|
|
including the selected atom itself. The general form for within |
497 |
|
|
selection is: {\tt select within(distance, expression)} |
498 |
|
|
|
499 |
|
|
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
500 |
|
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
501 |
|
|
atoms. |
502 |
|
|
|
503 |
|
|
|
504 |
tim |
2811 |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
505 |
tim |
2730 |
|
506 |
|
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
507 |
|
|
|
508 |
|
|
{\tt StaticProps} can compute properties which are averaged over |
509 |
|
|
some or all of the configurations that are contained within a dump |
510 |
|
|
file. The most common example of a static property that can be |
511 |
|
|
computed is the pair distribution function between atoms of type $A$ |
512 |
tim |
2815 |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
513 |
|
|
also be used to compute the density distributions of other molecules |
514 |
|
|
in a reference frame {\it fixed to the body-fixed reference frame} |
515 |
|
|
of a selected atom or rigid body. |
516 |
tim |
2730 |
|
517 |
|
|
There are five seperate radial distribution functions availiable in |
518 |
|
|
OOPSE. Since every radial distrbution function invlove the |
519 |
|
|
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
520 |
|
|
-{}-sele2} must be specified to tell StaticProps which bodies to |
521 |
|
|
include in the calculation. |
522 |
|
|
|
523 |
|
|
\begin{description} |
524 |
|
|
\item[{\tt -{}-gofr}] Computes the pair distribution function, |
525 |
|
|
\begin{equation*} |
526 |
|
|
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
527 |
|
|
\sum_{j \in B} \delta(r - r_{ij}) \rangle |
528 |
|
|
\end{equation*} |
529 |
|
|
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
530 |
|
|
function. The angle is defined by the intermolecular vector |
531 |
|
|
$\vec{r}$ and $z$-axis of DirectionalAtom A, |
532 |
|
|
\begin{equation*} |
533 |
|
|
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
534 |
|
|
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
535 |
|
|
\theta_{ij} - \cos \theta)\rangle |
536 |
|
|
\end{equation*} |
537 |
|
|
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
538 |
|
|
function. The angle is defined by the $z$-axes of the two |
539 |
|
|
DirectionalAtoms A and B. |
540 |
|
|
\begin{equation*} |
541 |
|
|
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
542 |
|
|
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
543 |
|
|
\omega_{ij} - \cos \omega)\rangle |
544 |
|
|
\end{equation*} |
545 |
|
|
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
546 |
|
|
space $\theta, \omega$ defined by the two angles mentioned above. |
547 |
|
|
\begin{equation*} |
548 |
|
|
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
549 |
|
|
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
550 |
|
|
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
551 |
|
|
\omega)\rangle |
552 |
|
|
\end{equation*} |
553 |
|
|
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
554 |
|
|
B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
555 |
|
|
and {\tt -{}-refsele} must be given to define A's internal |
556 |
|
|
coordinate set as the reference frame for the calculation. |
557 |
|
|
\end{description} |
558 |
|
|
|
559 |
|
|
The vectors (and angles) associated with these angular pair |
560 |
|
|
distribution functions are most easily seen in the figure below: |
561 |
|
|
|
562 |
|
|
\begin{figure} |
563 |
|
|
\centering |
564 |
tim |
2805 |
\includegraphics[width=3in]{definition.eps} |
565 |
tim |
2730 |
\caption[Definitions of the angles between directional objects]{ \\ |
566 |
|
|
Any two directional objects (DirectionalAtoms and RigidBodies) have |
567 |
|
|
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
568 |
|
|
their body-fixed frames.} \label{oopseFig:gofr} |
569 |
|
|
\end{figure} |
570 |
|
|
|
571 |
tim |
2815 |
Due to the fact that the selected StuntDoubles from two selections |
572 |
|
|
may be overlapped, {\tt StaticProps} performs the calculation in |
573 |
|
|
three stages which are illustrated in |
574 |
|
|
Fig.~\ref{oopseFig:staticPropsProcess}. |
575 |
|
|
|
576 |
|
|
\begin{figure} |
577 |
|
|
\centering |
578 |
|
|
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
579 |
|
|
\caption[A representation of the three-stage correlations in |
580 |
tim |
2816 |
\texttt{StaticProps}]{This diagram illustrates three-stage |
581 |
|
|
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
582 |
|
|
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
583 |
|
|
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
584 |
|
|
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
585 |
|
|
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
586 |
|
|
the contrary, the third stage($C$ and $C$) are completely |
587 |
|
|
overlapping} \label{oopseFig:staticPropsProcess} |
588 |
tim |
2815 |
\end{figure} |
589 |
|
|
|
590 |
tim |
2730 |
The options available for {\tt StaticProps} are as follows: |
591 |
|
|
\begin{longtable}[c]{|EFG|} |
592 |
|
|
\caption{StaticProps Command-line Options} |
593 |
|
|
\\ \hline |
594 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
595 |
|
|
\endhead |
596 |
|
|
\hline |
597 |
|
|
\endfoot |
598 |
|
|
-h& {\tt -{}-help} & Print help and exit \\ |
599 |
|
|
-V& {\tt -{}-version} & Print version and exit \\ |
600 |
tim |
2809 |
-i& {\tt -{}-input} & input dump file \\ |
601 |
|
|
-o& {\tt -{}-output} & output file name \\ |
602 |
|
|
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
603 |
|
|
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
604 |
|
|
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
605 |
|
|
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
606 |
|
|
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
607 |
|
|
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
608 |
|
|
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
609 |
|
|
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
610 |
|
|
& {\tt -{}-molname} & molecule name \\ |
611 |
|
|
& {\tt -{}-begin} & begin internal index \\ |
612 |
|
|
& {\tt -{}-end} & end internal index \\ |
613 |
tim |
2730 |
\hline |
614 |
|
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
615 |
|
|
\hline |
616 |
|
|
& {\tt -{}-gofr} & $g(r)$ \\ |
617 |
|
|
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
618 |
|
|
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
619 |
|
|
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
620 |
|
|
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
621 |
|
|
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
622 |
|
|
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
623 |
|
|
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
624 |
|
|
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
625 |
|
|
\end{longtable} |
626 |
|
|
|
627 |
|
|
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
628 |
|
|
|
629 |
|
|
{\tt DynamicProps} computes time correlation functions from the |
630 |
|
|
configurations stored in a dump file. Typical examples of time |
631 |
|
|
correlation functions are the mean square displacement and the |
632 |
|
|
velocity autocorrelation functions. Once again, the selection |
633 |
|
|
syntax can be used to specify the StuntDoubles that will be used for |
634 |
|
|
the calculation. A general time correlation function can be thought |
635 |
|
|
of as: |
636 |
|
|
\begin{equation} |
637 |
|
|
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
638 |
|
|
\end{equation} |
639 |
|
|
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
640 |
|
|
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
641 |
|
|
vector property associated with an atom of type $B$ at a different |
642 |
|
|
time $t^{\prime}$. In most autocorrelation functions, the vector |
643 |
|
|
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
644 |
|
|
$B$) are identical, and the three calculations built in to {\tt |
645 |
|
|
DynamicProps} make these assumptions. It is possible, however, to |
646 |
|
|
make simple modifications to the {\tt DynamicProps} code to allow |
647 |
|
|
the use of {\it cross} time correlation functions (i.e. with |
648 |
|
|
different vectors). The ability to use two selection scripts to |
649 |
|
|
select different types of atoms is already present in the code. |
650 |
|
|
|
651 |
tim |
2815 |
For large simulations, the trajectory files can sometimes reach |
652 |
|
|
sizes in excess of several gigabytes. In order to effectively |
653 |
|
|
analyze that amount of data. In order to prevent a situation where |
654 |
|
|
the program runs out of memory due to large trajectories, |
655 |
|
|
\texttt{dynamicProps} will estimate the size of free memory at |
656 |
|
|
first, and determine the number of frames in each block, which |
657 |
|
|
allows the operating system to load two blocks of data |
658 |
|
|
simultaneously without swapping. Upon reading two blocks of the |
659 |
|
|
trajectory, \texttt{dynamicProps} will calculate the time |
660 |
|
|
correlation within the first block and the cross correlations |
661 |
|
|
between the two blocks. This second block is then freed and then |
662 |
|
|
incremented and the process repeated until the end of the |
663 |
|
|
trajectory. Once the end is reached, the first block is freed then |
664 |
|
|
incremented, until all frame pairs have been correlated in time. |
665 |
tim |
2816 |
This process is illustrated in |
666 |
|
|
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
667 |
tim |
2815 |
|
668 |
tim |
2816 |
\begin{figure} |
669 |
|
|
\centering |
670 |
|
|
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
671 |
|
|
\caption[A representation of the block correlations in |
672 |
|
|
\texttt{dynamicProps}]{This diagram illustrates block correlations |
673 |
|
|
processing in \texttt{dynamicProps}. The shaded region represents |
674 |
|
|
the self correlation of the block, and the open blocks are read one |
675 |
|
|
at a time and the cross correlations between blocks are calculated.} |
676 |
|
|
\label{oopseFig:dynamicPropsProcess} |
677 |
|
|
\end{figure} |
678 |
|
|
|
679 |
tim |
2730 |
The options available for DynamicProps are as follows: |
680 |
|
|
\begin{longtable}[c]{|EFG|} |
681 |
|
|
\caption{DynamicProps Command-line Options} |
682 |
|
|
\\ \hline |
683 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
684 |
|
|
\endhead |
685 |
|
|
\hline |
686 |
|
|
\endfoot |
687 |
|
|
-h& {\tt -{}-help} & Print help and exit \\ |
688 |
|
|
-V& {\tt -{}-version} & Print version and exit \\ |
689 |
tim |
2809 |
-i& {\tt -{}-input} & input dump file \\ |
690 |
|
|
-o& {\tt -{}-output} & output file name \\ |
691 |
|
|
& {\tt -{}-sele1} & select first StuntDouble set \\ |
692 |
|
|
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
693 |
tim |
2730 |
\hline |
694 |
|
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
695 |
|
|
\hline |
696 |
|
|
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
697 |
|
|
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
698 |
|
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
699 |
|
|
\end{longtable} |
700 |
|
|
|
701 |
tim |
2811 |
\section{\label{appendixSection:tools}Other Useful Utilities} |
702 |
|
|
|
703 |
|
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
704 |
|
|
|
705 |
tim |
2821 |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
706 |
|
|
which can be opened by other molecular dynamics viewers such as Jmol |
707 |
|
|
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
708 |
|
|
as follows: |
709 |
tim |
2811 |
|
710 |
|
|
|
711 |
|
|
\begin{longtable}[c]{|EFG|} |
712 |
|
|
\caption{Dump2XYZ Command-line Options} |
713 |
|
|
\\ \hline |
714 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
715 |
|
|
\endhead |
716 |
|
|
\hline |
717 |
|
|
\endfoot |
718 |
|
|
-h & {\tt -{}-help} & Print help and exit \\ |
719 |
|
|
-V & {\tt -{}-version} & Print version and exit \\ |
720 |
|
|
-i & {\tt -{}-input} & input dump file \\ |
721 |
|
|
-o & {\tt -{}-output} & output file name \\ |
722 |
|
|
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
723 |
|
|
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
724 |
|
|
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
725 |
|
|
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
726 |
|
|
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
727 |
|
|
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
728 |
|
|
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
729 |
|
|
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
730 |
|
|
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
731 |
|
|
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
732 |
|
|
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
733 |
|
|
converted. \\ |
734 |
|
|
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
735 |
|
|
& {\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}. |
736 |
|
|
\end{longtable} |
737 |
|
|
|
738 |
tim |
2815 |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
739 |
tim |
2821 |
|
740 |
|
|
{\tt Hydro} can calculate resistance and diffusion tensors at the |
741 |
|
|
center of resistance. Both tensors at the center of diffusion can |
742 |
|
|
also be reported from the program, as well as the coordinates for |
743 |
|
|
the beads which are used to approximate the arbitrary shapes. The |
744 |
|
|
options available for Hydro are as follows: |
745 |
tim |
2811 |
\begin{longtable}[c]{|EFG|} |
746 |
|
|
\caption{Hydrodynamics Command-line Options} |
747 |
|
|
\\ \hline |
748 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
749 |
|
|
\endhead |
750 |
|
|
\hline |
751 |
|
|
\endfoot |
752 |
|
|
-h & {\tt -{}-help} & Print help and exit \\ |
753 |
|
|
-V & {\tt -{}-version} & Print version and exit \\ |
754 |
|
|
-i & {\tt -{}-input} & input dump file \\ |
755 |
|
|
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
756 |
|
|
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
757 |
tim |
2815 |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
758 |
tim |
2811 |
\end{longtable} |