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\appendix |
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\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} |
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Designing object-oriented software is hard, and designing reusable |
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object-oriented scientific software is even harder. Absence of |
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applying modern software development practices is the bottleneck of |
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Scientific Computing community\cite{Wilson2006}. For instance, in |
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the last 20 years , there are quite a few MD packages that were |
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developed to solve common MD problems and perform robust simulations |
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. However, many of the codes are legacy programs that are either |
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poorly organized or extremely complex. Usually, these packages were |
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contributed by scientists without official computer science |
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training. The development of most MD applications are lack of strong |
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coordination to enforce design and programming guidelines. Moreover, |
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most MD programs also suffer from missing design and implement |
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documents which is crucial to the maintenance and extensibility. |
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Along the way of studying structural and dynamic processes in |
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condensed phase systems like biological membranes and nanoparticles, |
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we developed and maintained an Object-Oriented Parallel Simulation |
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Engine ({\sc OOPSE}). This new molecular dynamics package has some |
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unique features |
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\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 |
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Sec.~\ref{appendixSection:appendixSection:DynamicProps}), |
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\texttt{Dump2XYZ} (see |
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Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro} |
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(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics}) |
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\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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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{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. |
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The following sections enumerates some of the patterns used in {\sc |
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OOPSE}. |
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|
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\subsection{\label{appendixSection:singleton}Singleton} |
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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}. {\tt IntegratorFactory} class |
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is declared as |
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}] |
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|
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class IntegratorFactory { |
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public: |
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static IntegratorFactory* getInstance(); |
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protected: |
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IntegratorFactory(); |
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private: |
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static IntegratorFactory* instance_; |
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}; |
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|
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\end{lstlisting} |
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The corresponding implementation is |
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\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}] |
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|
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IntegratorFactory::instance_ = NULL; |
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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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Since constructor is declared as {\tt protected}, a client can not |
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instantiate {\tt IntegratorFactory} directly. Moreover, since the |
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member function {\tt getInstance} serves as the only entry of access |
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to {\tt IntegratorFactory}, this approach fulfills the basic |
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requirement, a single instance. Another consequence of this approach |
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is the automatic destruction since static data are destroyed upon |
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program termination. |
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|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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|
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Categoried as a creational pattern, the Factory Method pattern deals |
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with the problem of creating objects without specifying the exact |
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class of object that will be created. Factory Method is typically |
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implemented by delegating the creation operation to the subclasses. |
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|
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Registers a creator with a type identifier. Looks up the type |
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identifier in the internal map. If it is found, it invokes the |
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corresponding creator for the type identifier and returns its |
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result. |
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}] |
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|
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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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|
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Integrator* createIntegrator(const string& id, SimInfo* info); |
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|
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private: |
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CreatorMapType creatorMap_; |
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}; |
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|
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}] |
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|
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bool IntegratorFactory::unregisterIntegrator(const string& id) { |
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return creatorMap_.erase(id) == 1; |
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} |
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|
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Integrator* IntegratorFactory::createIntegrator(const string& id, |
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SimInfo* info) { |
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CreatorMapType::iterator i = creatorMap_.find(id); |
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if (i != creatorMap_.end()) { |
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return (i->second)->create(info); |
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} else { |
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return NULL; |
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} |
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} |
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|
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}] |
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|
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class IntegratorCreator { |
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public: |
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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) : IntegratorCreator(ident) {} |
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virtual Integrator* create(SimInfo* info) const { |
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return new ConcreteIntegrator(info); |
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} |
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}; |
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\end{lstlisting} |
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|
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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|
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The purpose of the Visitor Pattern is to encapsulate an operation |
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that you want to perform on the elements. The operation being |
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performed on a structure can be switched without changing the |
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interfaces of the elements. In other words, one can add virtual |
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functions into a set of classes without modifying their interfaces. |
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The UML class diagram of Visitor patten is shown in |
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Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
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Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
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extensively. |
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|
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\begin{figure} |
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|
\centering |
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\includegraphics[width=\linewidth]{visitor.eps} |
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\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
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|
of {\sc OOPSE}} \label{appendixFig:visitorUML} |
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\end{figure} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
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|
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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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\end{lstlisting} |
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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 { |
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public: |
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virtual void accept(BaseVisitor* v) = 0; |
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}; |
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|
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class Atom: public StuntDouble { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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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 { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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class RigidBody: public StuntDouble { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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\end{lstlisting} |
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\section{\label{appendixSection:concepts}Concepts} |
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|
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\begin{figure} |
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|
\centering |
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|
\includegraphics[width=\linewidth]{heirarchy.eps} |
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\caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class |
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|
heirarchy of StuntDoubles in {\sc OOPSE}.} |
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|
\label{oopseFig:heirarchy} |
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\end{figure} |
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|
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OOPSE manipulates both traditional atoms as well as some objects |
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|
that {\it behave like atoms}. These objects can be rigid |
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|
collections of atoms or atoms which have orientational degrees of |
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freedom. A diagram of the class heirarchy is illustrated in |
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|
Fig.~\ref{oopseFig:heirarchy}. |
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|
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|
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\begin{itemize} |
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|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
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integrators and minimizers. |
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\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
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\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
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|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
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|
DirectionalAtom}s which behaves as a single unit. |
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\end{itemize} |
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|
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Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
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own names which are specified in the {\tt .md} file. In contrast, |
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RigidBodies are denoted by their membership and index inside a |
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|
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
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|
|
inside the brackets depend on the specifics of the simulation). The |
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|
names of rigid bodies are generated automatically. For example, the |
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name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
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|
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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|
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|
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The most general form of the select command is: {\tt select {\it |
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expression}}. This expression represents an arbitrary set of |
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|
|
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
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|
|
composed of either name expressions, index expressions, predefined |
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|
|
sets, user-defined expressions, comparison operators, within |
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|
|
expressions, or logical combinations of the above expression types. |
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|
Expressions can be combined using parentheses and the Boolean |
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|
|
operators. |
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|
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\subsection{\label{appendixSection:logical}Logical expressions} |
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|
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|
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The logical operators allow complex queries to be constructed out of |
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|
simpler ones using the standard boolean connectives {\bf and}, {\bf |
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|
|
or}, {\bf not}. Parentheses can be used to alter the precedence of |
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|
|
the operators. |
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|
|
|
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|
|
\begin{center} |
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|
|
\begin{tabular}{|ll|} |
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|
|
\hline |
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|
|
{\bf logical operator} & {\bf equivalent operator} \\ |
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|
|
\hline |
350 |
|
|
and & ``\&'', ``\&\&'' \\ |
351 |
|
|
or & ``$|$'', ``$||$'', ``,'' \\ |
352 |
|
|
not & ``!'' \\ |
353 |
|
|
\hline |
354 |
|
|
\end{tabular} |
355 |
|
|
\end{center} |
356 |
|
|
|
357 |
|
|
\subsection{\label{appendixSection:name}Name expressions} |
358 |
|
|
|
359 |
|
|
\begin{center} |
360 |
tim |
2805 |
\begin{tabular}{|llp{2in}|} |
361 |
tim |
2730 |
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
362 |
|
|
of |
363 |
|
|
examples} \\ |
364 |
|
|
\hline expression without ``.'' & select DMPC & select all |
365 |
|
|
StuntDoubles |
366 |
|
|
belonging to all DMPC molecules \\ |
367 |
|
|
& select C* & select all atoms which have atom types beginning with C |
368 |
|
|
\\ |
369 |
|
|
& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
370 |
|
|
only select the rigid bodies, and not the atoms belonging to them). \\ |
371 |
|
|
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
372 |
|
|
O\_TIP3P |
373 |
|
|
atoms belonging to TIP3P molecules \\ |
374 |
|
|
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
375 |
|
|
the first |
376 |
|
|
RigidBody in each DMPC molecule \\ |
377 |
|
|
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
378 |
|
|
molecule \\ |
379 |
|
|
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
380 |
|
|
select all atoms |
381 |
|
|
belonging to all rigid bodies within all DMPC molecules \\ |
382 |
|
|
\hline |
383 |
|
|
\end{tabular} |
384 |
|
|
\end{center} |
385 |
|
|
|
386 |
|
|
\subsection{\label{appendixSection:index}Index expressions} |
387 |
|
|
|
388 |
|
|
\begin{center} |
389 |
|
|
\begin{tabular}{|lp{4in}|} |
390 |
|
|
\hline |
391 |
|
|
{\bf examples} & {\bf translation of examples} \\ |
392 |
|
|
\hline |
393 |
|
|
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
394 |
|
|
select 20 to 30 & select all of the StuntDoubles belonging to |
395 |
|
|
molecules which have global indices between 20 (inclusive) and 30 |
396 |
|
|
(exclusive) \\ |
397 |
|
|
\hline |
398 |
|
|
\end{tabular} |
399 |
|
|
\end{center} |
400 |
|
|
|
401 |
|
|
\subsection{\label{appendixSection:predefined}Predefined sets} |
402 |
|
|
|
403 |
|
|
\begin{center} |
404 |
|
|
\begin{tabular}{|ll|} |
405 |
|
|
\hline |
406 |
|
|
{\bf keyword} & {\bf description} \\ |
407 |
|
|
\hline |
408 |
|
|
all & select all StuntDoubles \\ |
409 |
|
|
none & select none of the StuntDoubles \\ |
410 |
|
|
\hline |
411 |
|
|
\end{tabular} |
412 |
|
|
\end{center} |
413 |
|
|
|
414 |
|
|
\subsection{\label{appendixSection:userdefined}User-defined expressions} |
415 |
|
|
|
416 |
|
|
Users can define arbitrary terms to represent groups of |
417 |
|
|
StuntDoubles, and then use the define terms in select commands. The |
418 |
|
|
general form for the define command is: {\bf define {\it term |
419 |
tim |
2815 |
expression}}. Once defined, the user can specify such terms in |
420 |
|
|
boolean expressions |
421 |
tim |
2730 |
|
422 |
|
|
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
423 |
|
|
|
424 |
|
|
{\tt select SSDWATER} |
425 |
|
|
|
426 |
|
|
\subsection{\label{appendixSection:comparison}Comparison expressions} |
427 |
|
|
|
428 |
|
|
StuntDoubles can be selected by using comparision operators on their |
429 |
|
|
properties. The general form for the comparison command is: a |
430 |
|
|
property name, followed by a comparision operator and then a number. |
431 |
|
|
|
432 |
|
|
\begin{center} |
433 |
|
|
\begin{tabular}{|l|l|} |
434 |
|
|
\hline |
435 |
|
|
{\bf property} & mass, charge \\ |
436 |
|
|
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
437 |
|
|
``$<=$'', ``$!=$'' \\ |
438 |
|
|
\hline |
439 |
|
|
\end{tabular} |
440 |
|
|
\end{center} |
441 |
|
|
|
442 |
|
|
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
443 |
tim |
2805 |
would select StuntDoubles which have mass greater than 16.0 and |
444 |
tim |
2730 |
charges less than -2. |
445 |
|
|
|
446 |
|
|
\subsection{\label{appendixSection:within}Within expressions} |
447 |
|
|
|
448 |
|
|
The ``within'' keyword allows the user to select all StuntDoubles |
449 |
|
|
within the specified distance (in Angstroms) from a selection, |
450 |
|
|
including the selected atom itself. The general form for within |
451 |
|
|
selection is: {\tt select within(distance, expression)} |
452 |
|
|
|
453 |
|
|
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
454 |
|
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
455 |
|
|
atoms. |
456 |
|
|
|
457 |
|
|
|
458 |
tim |
2811 |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
459 |
tim |
2730 |
|
460 |
|
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
461 |
|
|
|
462 |
|
|
{\tt StaticProps} can compute properties which are averaged over |
463 |
|
|
some or all of the configurations that are contained within a dump |
464 |
|
|
file. The most common example of a static property that can be |
465 |
|
|
computed is the pair distribution function between atoms of type $A$ |
466 |
tim |
2815 |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
467 |
|
|
also be used to compute the density distributions of other molecules |
468 |
|
|
in a reference frame {\it fixed to the body-fixed reference frame} |
469 |
|
|
of a selected atom or rigid body. |
470 |
tim |
2730 |
|
471 |
|
|
There are five seperate radial distribution functions availiable in |
472 |
|
|
OOPSE. Since every radial distrbution function invlove the |
473 |
|
|
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
474 |
|
|
-{}-sele2} must be specified to tell StaticProps which bodies to |
475 |
|
|
include in the calculation. |
476 |
|
|
|
477 |
|
|
\begin{description} |
478 |
|
|
\item[{\tt -{}-gofr}] Computes the pair distribution function, |
479 |
|
|
\begin{equation*} |
480 |
|
|
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
481 |
|
|
\sum_{j \in B} \delta(r - r_{ij}) \rangle |
482 |
|
|
\end{equation*} |
483 |
|
|
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
484 |
|
|
function. The angle is defined by the intermolecular vector |
485 |
|
|
$\vec{r}$ and $z$-axis of DirectionalAtom A, |
486 |
|
|
\begin{equation*} |
487 |
|
|
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
488 |
|
|
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
489 |
|
|
\theta_{ij} - \cos \theta)\rangle |
490 |
|
|
\end{equation*} |
491 |
|
|
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
492 |
|
|
function. The angle is defined by the $z$-axes of the two |
493 |
|
|
DirectionalAtoms A and B. |
494 |
|
|
\begin{equation*} |
495 |
|
|
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
496 |
|
|
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
497 |
|
|
\omega_{ij} - \cos \omega)\rangle |
498 |
|
|
\end{equation*} |
499 |
|
|
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
500 |
|
|
space $\theta, \omega$ defined by the two angles mentioned above. |
501 |
|
|
\begin{equation*} |
502 |
|
|
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
503 |
|
|
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
504 |
|
|
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
505 |
|
|
\omega)\rangle |
506 |
|
|
\end{equation*} |
507 |
|
|
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
508 |
|
|
B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
509 |
|
|
and {\tt -{}-refsele} must be given to define A's internal |
510 |
|
|
coordinate set as the reference frame for the calculation. |
511 |
|
|
\end{description} |
512 |
|
|
|
513 |
|
|
The vectors (and angles) associated with these angular pair |
514 |
|
|
distribution functions are most easily seen in the figure below: |
515 |
|
|
|
516 |
|
|
\begin{figure} |
517 |
|
|
\centering |
518 |
tim |
2805 |
\includegraphics[width=3in]{definition.eps} |
519 |
tim |
2730 |
\caption[Definitions of the angles between directional objects]{ \\ |
520 |
|
|
Any two directional objects (DirectionalAtoms and RigidBodies) have |
521 |
|
|
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
522 |
|
|
their body-fixed frames.} \label{oopseFig:gofr} |
523 |
|
|
\end{figure} |
524 |
|
|
|
525 |
tim |
2815 |
Due to the fact that the selected StuntDoubles from two selections |
526 |
|
|
may be overlapped, {\tt StaticProps} performs the calculation in |
527 |
|
|
three stages which are illustrated in |
528 |
|
|
Fig.~\ref{oopseFig:staticPropsProcess}. |
529 |
|
|
|
530 |
|
|
\begin{figure} |
531 |
|
|
\centering |
532 |
|
|
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
533 |
|
|
\caption[A representation of the three-stage correlations in |
534 |
tim |
2816 |
\texttt{StaticProps}]{This diagram illustrates three-stage |
535 |
|
|
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
536 |
|
|
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
537 |
|
|
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
538 |
|
|
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
539 |
|
|
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
540 |
|
|
the contrary, the third stage($C$ and $C$) are completely |
541 |
|
|
overlapping} \label{oopseFig:staticPropsProcess} |
542 |
tim |
2815 |
\end{figure} |
543 |
|
|
|
544 |
tim |
2730 |
The options available for {\tt StaticProps} are as follows: |
545 |
|
|
\begin{longtable}[c]{|EFG|} |
546 |
|
|
\caption{StaticProps Command-line Options} |
547 |
|
|
\\ \hline |
548 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
549 |
|
|
\endhead |
550 |
|
|
\hline |
551 |
|
|
\endfoot |
552 |
|
|
-h& {\tt -{}-help} & Print help and exit \\ |
553 |
|
|
-V& {\tt -{}-version} & Print version and exit \\ |
554 |
tim |
2809 |
-i& {\tt -{}-input} & input dump file \\ |
555 |
|
|
-o& {\tt -{}-output} & output file name \\ |
556 |
|
|
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
557 |
|
|
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
558 |
|
|
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
559 |
|
|
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
560 |
|
|
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
561 |
|
|
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
562 |
|
|
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
563 |
|
|
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
564 |
|
|
& {\tt -{}-molname} & molecule name \\ |
565 |
|
|
& {\tt -{}-begin} & begin internal index \\ |
566 |
|
|
& {\tt -{}-end} & end internal index \\ |
567 |
tim |
2730 |
\hline |
568 |
|
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
569 |
|
|
\hline |
570 |
|
|
& {\tt -{}-gofr} & $g(r)$ \\ |
571 |
|
|
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
572 |
|
|
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
573 |
|
|
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
574 |
|
|
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
575 |
|
|
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
576 |
|
|
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
577 |
|
|
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
578 |
|
|
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
579 |
|
|
\end{longtable} |
580 |
|
|
|
581 |
|
|
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
582 |
|
|
|
583 |
|
|
{\tt DynamicProps} computes time correlation functions from the |
584 |
|
|
configurations stored in a dump file. Typical examples of time |
585 |
|
|
correlation functions are the mean square displacement and the |
586 |
|
|
velocity autocorrelation functions. Once again, the selection |
587 |
|
|
syntax can be used to specify the StuntDoubles that will be used for |
588 |
|
|
the calculation. A general time correlation function can be thought |
589 |
|
|
of as: |
590 |
|
|
\begin{equation} |
591 |
|
|
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
592 |
|
|
\end{equation} |
593 |
|
|
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
594 |
|
|
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
595 |
|
|
vector property associated with an atom of type $B$ at a different |
596 |
|
|
time $t^{\prime}$. In most autocorrelation functions, the vector |
597 |
|
|
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
598 |
|
|
$B$) are identical, and the three calculations built in to {\tt |
599 |
|
|
DynamicProps} make these assumptions. It is possible, however, to |
600 |
|
|
make simple modifications to the {\tt DynamicProps} code to allow |
601 |
|
|
the use of {\it cross} time correlation functions (i.e. with |
602 |
|
|
different vectors). The ability to use two selection scripts to |
603 |
|
|
select different types of atoms is already present in the code. |
604 |
|
|
|
605 |
tim |
2815 |
For large simulations, the trajectory files can sometimes reach |
606 |
|
|
sizes in excess of several gigabytes. In order to effectively |
607 |
|
|
analyze that amount of data. In order to prevent a situation where |
608 |
|
|
the program runs out of memory due to large trajectories, |
609 |
|
|
\texttt{dynamicProps} will estimate the size of free memory at |
610 |
|
|
first, and determine the number of frames in each block, which |
611 |
|
|
allows the operating system to load two blocks of data |
612 |
|
|
simultaneously without swapping. Upon reading two blocks of the |
613 |
|
|
trajectory, \texttt{dynamicProps} will calculate the time |
614 |
|
|
correlation within the first block and the cross correlations |
615 |
|
|
between the two blocks. This second block is then freed and then |
616 |
|
|
incremented and the process repeated until the end of the |
617 |
|
|
trajectory. Once the end is reached, the first block is freed then |
618 |
|
|
incremented, until all frame pairs have been correlated in time. |
619 |
tim |
2816 |
This process is illustrated in |
620 |
|
|
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
621 |
tim |
2815 |
|
622 |
tim |
2816 |
\begin{figure} |
623 |
|
|
\centering |
624 |
|
|
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
625 |
|
|
\caption[A representation of the block correlations in |
626 |
|
|
\texttt{dynamicProps}]{This diagram illustrates block correlations |
627 |
|
|
processing in \texttt{dynamicProps}. The shaded region represents |
628 |
|
|
the self correlation of the block, and the open blocks are read one |
629 |
|
|
at a time and the cross correlations between blocks are calculated.} |
630 |
|
|
\label{oopseFig:dynamicPropsProcess} |
631 |
|
|
\end{figure} |
632 |
|
|
|
633 |
tim |
2730 |
The options available for DynamicProps are as follows: |
634 |
|
|
\begin{longtable}[c]{|EFG|} |
635 |
|
|
\caption{DynamicProps Command-line Options} |
636 |
|
|
\\ \hline |
637 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
638 |
|
|
\endhead |
639 |
|
|
\hline |
640 |
|
|
\endfoot |
641 |
|
|
-h& {\tt -{}-help} & Print help and exit \\ |
642 |
|
|
-V& {\tt -{}-version} & Print version and exit \\ |
643 |
tim |
2809 |
-i& {\tt -{}-input} & input dump file \\ |
644 |
|
|
-o& {\tt -{}-output} & output file name \\ |
645 |
|
|
& {\tt -{}-sele1} & select first StuntDouble set \\ |
646 |
|
|
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
647 |
tim |
2730 |
\hline |
648 |
|
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
649 |
|
|
\hline |
650 |
|
|
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
651 |
|
|
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
652 |
|
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
653 |
|
|
\end{longtable} |
654 |
|
|
|
655 |
tim |
2811 |
\section{\label{appendixSection:tools}Other Useful Utilities} |
656 |
|
|
|
657 |
|
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
658 |
|
|
|
659 |
tim |
2821 |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
660 |
|
|
which can be opened by other molecular dynamics viewers such as Jmol |
661 |
|
|
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
662 |
|
|
as follows: |
663 |
tim |
2811 |
|
664 |
|
|
|
665 |
|
|
\begin{longtable}[c]{|EFG|} |
666 |
|
|
\caption{Dump2XYZ Command-line Options} |
667 |
|
|
\\ \hline |
668 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
669 |
|
|
\endhead |
670 |
|
|
\hline |
671 |
|
|
\endfoot |
672 |
|
|
-h & {\tt -{}-help} & Print help and exit \\ |
673 |
|
|
-V & {\tt -{}-version} & Print version and exit \\ |
674 |
|
|
-i & {\tt -{}-input} & input dump file \\ |
675 |
|
|
-o & {\tt -{}-output} & output file name \\ |
676 |
|
|
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
677 |
|
|
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
678 |
|
|
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
679 |
|
|
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
680 |
|
|
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
681 |
|
|
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
682 |
|
|
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
683 |
|
|
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
684 |
|
|
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
685 |
|
|
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
686 |
|
|
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
687 |
|
|
converted. \\ |
688 |
|
|
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
689 |
|
|
& {\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}. |
690 |
|
|
\end{longtable} |
691 |
|
|
|
692 |
tim |
2815 |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
693 |
tim |
2821 |
|
694 |
|
|
{\tt Hydro} can calculate resistance and diffusion tensors at the |
695 |
|
|
center of resistance. Both tensors at the center of diffusion can |
696 |
|
|
also be reported from the program, as well as the coordinates for |
697 |
|
|
the beads which are used to approximate the arbitrary shapes. The |
698 |
|
|
options available for Hydro are as follows: |
699 |
tim |
2811 |
\begin{longtable}[c]{|EFG|} |
700 |
|
|
\caption{Hydrodynamics Command-line Options} |
701 |
|
|
\\ \hline |
702 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
703 |
|
|
\endhead |
704 |
|
|
\hline |
705 |
|
|
\endfoot |
706 |
|
|
-h & {\tt -{}-help} & Print help and exit \\ |
707 |
|
|
-V & {\tt -{}-version} & Print version and exit \\ |
708 |
|
|
-i & {\tt -{}-input} & input dump file \\ |
709 |
|
|
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
710 |
|
|
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
711 |
tim |
2815 |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
712 |
tim |
2811 |
\end{longtable} |