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\chapter{\label{chapt:appendix}APPENDIX} |
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\appendix |
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\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} |
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|
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Designing object-oriented software is hard, and designing reusable |
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object-oriented scientific software is even harder. Absence of |
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applying modern software development practices is the bottleneck of |
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Scientific Computing community\cite{Wilson2006}. For instance, in |
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the last 20 years , there are quite a few MD packages that were |
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developed to solve common MD problems and perform robust simulations |
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. However, many of the codes are legacy programs that are either |
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poorly organized or extremely complex. Usually, these packages were |
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contributed by scientists without official computer science |
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training. The development of most MD applications are lack of strong |
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coordination to enforce design and programming guidelines. Moreover, |
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most MD programs also suffer from missing design and implement |
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documents which is crucial to the maintenance and extensibility. |
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Along the way of studying structural and dynamic processes in |
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condensed phase systems like biological membranes and nanoparticles, |
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we developed and maintained an Object-Oriented Parallel Simulation |
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Engine ({\sc OOPSE}). This new molecular dynamics package has some |
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unique features |
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\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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|
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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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\subsection{\label{appendixSection:visitorPattern}Visitor Pattern} |
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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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\subsection{\label{appendixSection:templatePattern}Template Pattern} |
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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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\subsection{\label{appendixSection:factoryPattern}Factory Pattern} |
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\subsection{\label{appendixSection:singleton}Singleton} |
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|
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\section{\label{appendixSection:hierarchy}Hierarchy} |
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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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\section{\label{appendixSection:selectionSyntax}Selection Syntax} |
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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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\section{\label{appendixSection:hydrodynamics}Hydrodynamics} |
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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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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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\end{lstlisting} |
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|
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\subsection{\label{appendixSection:staticProps}Factory Properties} |
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The corresponding implementation is |
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|
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\subsection{\label{appendixSection:dynamicProps}Dynamics Properties} |
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\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] |
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|
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IntegratorFactory::instance_ = NULL; |
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|
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IntegratorFactory* getInstance() { |
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if (instance_ == NULL){ |
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instance_ = new IntegratorFactory; |
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} |
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return instance_; |
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} |
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|
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\end{lstlisting} |
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|
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Since constructor is declared as protected, a client can not |
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instantiate IntegratorFactory directly. Moreover, since the member |
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function getInstance serves as the only entry of access to |
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IntegratorFactory, this approach fulfills the basic requirement, a |
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single instance. Another consequence of this approach is the |
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automatic destruction since static data are destroyed upon program |
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termination. |
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|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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|
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Categoried as a creational pattern, the Factory Method pattern deals |
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with the problem of creating objects without specifying the exact |
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class of object that will be created. Factory Method is typically |
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implemented by delegating the creation operation to the subclasses. |
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Parameterized Factory pattern where factory method ( |
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createIntegrator member function) creates products based on the |
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identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If |
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the identifier has been already registered, the factory method will |
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invoke the corresponding creator (see List.~\ref{integratorCreator}) |
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which utilizes the modern C++ template technique to avoid excess |
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subclassing. |
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|
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
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|
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class IntegratorFactory { |
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public: |
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typedef std::map<string, IntegratorCreator*> CreatorMapType; |
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|
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bool registerIntegrator(IntegratorCreator* creator) { |
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return creatorMap_.insert(creator->getIdent(), creator).second; |
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} |
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|
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Integrator* createIntegrator(const string& id, SimInfo* info) { |
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Integrator* result = NULL; |
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CreatorMapType::iterator i = creatorMap_.find(id); |
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if (i != creatorMap_.end()) { |
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result = (i->second)->create(info); |
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} |
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return result; |
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} |
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|
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private: |
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CreatorMapType creatorMap_; |
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}; |
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
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|
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class IntegratorCreator { |
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public: |
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IntegratorCreator(const string& ident) : ident_(ident) {} |
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|
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const string& getIdent() const { return ident_; } |
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|
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virtual Integrator* create(SimInfo* info) const = 0; |
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|
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private: |
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string ident_; |
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}; |
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|
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template<class ConcreteIntegrator> |
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class IntegratorBuilder : public IntegratorCreator { |
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public: |
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IntegratorBuilder(const string& ident) |
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: IntegratorCreator(ident) {} |
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virtual Integrator* create(SimInfo* info) const { |
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return new ConcreteIntegrator(info); |
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} |
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}; |
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\end{lstlisting} |
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|
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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|
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The visitor pattern is designed to decouple the data structure and |
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algorithms used upon them by collecting related operation from |
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element classes into other visitor classes, which is equivalent to |
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adding virtual functions into a set of classes without modifying |
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their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
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structure of Visitor pattern which is used extensively in {\tt |
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Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
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distinct operations are performed on different StuntDoubles (See the |
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class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
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in List.~\ref{appendixScheme:element}). Since the hierarchies |
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remains stable, it is easy to define a visit operation (see |
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List.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
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Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
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manages a priority visitor list and handles the execution of every |
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visitor in the priority list on different StuntDoubles. |
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|
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{visitor.eps} |
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\caption[The UML class diagram of Visitor patten] {The UML class |
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diagram of Visitor patten.} \label{appendixFig:visitorUML} |
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\end{figure} |
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|
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{hierarchy.eps} |
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\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
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the class hierarchy. } \label{oopseFig:hierarchy} |
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\end{figure} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
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|
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class StuntDouble { public: |
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virtual void accept(BaseVisitor* v) = 0; |
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}; |
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|
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class Atom: public StuntDouble { public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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class DirectionalAtom: public Atom { public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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class RigidBody: public StuntDouble { public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
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|
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class BaseVisitor{ |
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public: |
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virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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}; |
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|
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class BaseAtomVisitor:public BaseVisitor{ public: |
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virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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}; |
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|
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class SSDAtomVisitor:public BaseAtomVisitor{ public: |
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virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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}; |
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|
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class CompositeVisitor: public BaseVisitor { |
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public: |
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|
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typedef list<pair<BaseVisitor*, int> > VistorListType; |
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typedef VistorListType::iterator VisitorListIterator; |
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virtual void visit(Atom* atom) { |
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VisitorListIterator i; |
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BaseVisitor* curVisitor; |
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for(i = visitorList.begin();i != visitorList.end();++i) { |
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atom->accept(*i); |
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} |
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} |
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|
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virtual void visit(DirectionalAtom* datom) { |
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VisitorListIterator i; |
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BaseVisitor* curVisitor; |
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for(i = visitorList.begin();i != visitorList.end();++i) { |
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atom->accept(*i); |
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} |
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} |
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|
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virtual void visit(RigidBody* rb) { |
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VisitorListIterator i; |
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std::vector<Atom*> myAtoms; |
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std::vector<Atom*>::iterator ai; |
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myAtoms = rb->getAtoms(); |
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for(i = visitorList.begin();i != visitorList.end();++i) {{ |
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rb->accept(*i); |
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for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
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(*ai)->accept(*i); |
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} |
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} |
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|
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void addVisitor(BaseVisitor* v, int priority); |
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|
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protected: |
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VistorListType visitorList; |
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}; |
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|
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\end{lstlisting} |
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|
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\section{\label{appendixSection:concepts}Concepts} |
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|
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OOPSE manipulates both traditional atoms as well as some objects |
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that {\it behave like atoms}. These objects can be rigid |
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collections of atoms or atoms which have orientational degrees of |
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freedom. A diagram of the class hierarchy is illustrated in |
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Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
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DirectionalAtom in {\sc OOPSE} have their own names which are |
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specified in the {\tt .md} file. In contrast, RigidBodies are |
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denoted by their membership and index inside a particular molecule: |
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[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
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on the specifics of the simulation). The names of rigid bodies are |
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generated automatically. For example, the name of the first rigid |
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body in a DMPC molecule is DMPC\_RB\_0. |
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\begin{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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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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|
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{\sc OOPSE} provides a powerful selection utility to select |
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StuntDoubles. The most general form of the select command is: |
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|
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{\tt select {\it expression}}. |
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|
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This expression represents an arbitrary set of StuntDoubles (Atoms |
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or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
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name expressions, index expressions, predefined sets, user-defined |
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expressions, comparison operators, within expressions, or logical |
388 |
> |
combinations of the above expression types. Expressions can be |
389 |
> |
combined using parentheses and the Boolean operators. |
390 |
> |
|
391 |
> |
\subsection{\label{appendixSection:logical}Logical expressions} |
392 |
> |
|
393 |
> |
The logical operators allow complex queries to be constructed out of |
394 |
> |
simpler ones using the standard boolean connectives {\bf and}, {\bf |
395 |
> |
or}, {\bf not}. Parentheses can be used to alter the precedence of |
396 |
> |
the operators. |
397 |
> |
|
398 |
> |
\begin{center} |
399 |
> |
\begin{tabular}{|ll|} |
400 |
> |
\hline |
401 |
> |
{\bf logical operator} & {\bf equivalent operator} \\ |
402 |
> |
\hline |
403 |
> |
and & ``\&'', ``\&\&'' \\ |
404 |
> |
or & ``$|$'', ``$||$'', ``,'' \\ |
405 |
> |
not & ``!'' \\ |
406 |
> |
\hline |
407 |
> |
\end{tabular} |
408 |
> |
\end{center} |
409 |
> |
|
410 |
> |
\subsection{\label{appendixSection:name}Name expressions} |
411 |
> |
|
412 |
> |
\begin{center} |
413 |
> |
\begin{tabular}{|llp{2in}|} |
414 |
> |
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
415 |
> |
of |
416 |
> |
examples} \\ |
417 |
> |
\hline expression without ``.'' & select DMPC & select all |
418 |
> |
StuntDoubles |
419 |
> |
belonging to all DMPC molecules \\ |
420 |
> |
& select C* & select all atoms which have atom types beginning with C |
421 |
> |
\\ |
422 |
> |
& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
423 |
> |
only select the rigid bodies, and not the atoms belonging to them). \\ |
424 |
> |
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
425 |
> |
O\_TIP3P |
426 |
> |
atoms belonging to TIP3P molecules \\ |
427 |
> |
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
428 |
> |
the first |
429 |
> |
RigidBody in each DMPC molecule \\ |
430 |
> |
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
431 |
> |
molecule \\ |
432 |
> |
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
433 |
> |
select all atoms |
434 |
> |
belonging to all rigid bodies within all DMPC molecules \\ |
435 |
> |
\hline |
436 |
> |
\end{tabular} |
437 |
> |
\end{center} |
438 |
> |
|
439 |
> |
\subsection{\label{appendixSection:index}Index expressions} |
440 |
> |
|
441 |
> |
\begin{center} |
442 |
> |
\begin{tabular}{|lp{4in}|} |
443 |
> |
\hline |
444 |
> |
{\bf examples} & {\bf translation of examples} \\ |
445 |
> |
\hline |
446 |
> |
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
447 |
> |
select 20 to 30 & select all of the StuntDoubles belonging to |
448 |
> |
molecules which have global indices between 20 (inclusive) and 30 |
449 |
> |
(exclusive) \\ |
450 |
> |
\hline |
451 |
> |
\end{tabular} |
452 |
> |
\end{center} |
453 |
> |
|
454 |
> |
\subsection{\label{appendixSection:predefined}Predefined sets} |
455 |
> |
|
456 |
> |
\begin{center} |
457 |
> |
\begin{tabular}{|ll|} |
458 |
> |
\hline |
459 |
> |
{\bf keyword} & {\bf description} \\ |
460 |
> |
\hline |
461 |
> |
all & select all StuntDoubles \\ |
462 |
> |
none & select none of the StuntDoubles \\ |
463 |
> |
\hline |
464 |
> |
\end{tabular} |
465 |
> |
\end{center} |
466 |
> |
|
467 |
> |
\subsection{\label{appendixSection:userdefined}User-defined expressions} |
468 |
> |
|
469 |
> |
Users can define arbitrary terms to represent groups of |
470 |
> |
StuntDoubles, and then use the define terms in select commands. The |
471 |
> |
general form for the define command is: {\bf define {\it term |
472 |
> |
expression}}. Once defined, the user can specify such terms in |
473 |
> |
boolean expressions |
474 |
> |
|
475 |
> |
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
476 |
> |
|
477 |
> |
{\tt select SSDWATER} |
478 |
> |
|
479 |
> |
\subsection{\label{appendixSection:comparison}Comparison expressions} |
480 |
> |
|
481 |
> |
StuntDoubles can be selected by using comparision operators on their |
482 |
> |
properties. The general form for the comparison command is: a |
483 |
> |
property name, followed by a comparision operator and then a number. |
484 |
> |
|
485 |
> |
\begin{center} |
486 |
> |
\begin{tabular}{|l|l|} |
487 |
> |
\hline |
488 |
> |
{\bf property} & mass, charge \\ |
489 |
> |
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
490 |
> |
``$<=$'', ``$!=$'' \\ |
491 |
> |
\hline |
492 |
> |
\end{tabular} |
493 |
> |
\end{center} |
494 |
> |
|
495 |
> |
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
496 |
> |
would select StuntDoubles which have mass greater than 16.0 and |
497 |
> |
charges less than -2. |
498 |
> |
|
499 |
> |
\subsection{\label{appendixSection:within}Within expressions} |
500 |
> |
|
501 |
> |
The ``within'' keyword allows the user to select all StuntDoubles |
502 |
> |
within the specified distance (in Angstroms) from a selection, |
503 |
> |
including the selected atom itself. The general form for within |
504 |
> |
selection is: {\tt select within(distance, expression)} |
505 |
> |
|
506 |
> |
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
507 |
> |
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
508 |
> |
atoms. |
509 |
> |
|
510 |
> |
|
511 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
512 |
> |
|
513 |
> |
\subsection{\label{appendixSection:StaticProps}StaticProps} |
514 |
> |
|
515 |
> |
{\tt StaticProps} can compute properties which are averaged over |
516 |
> |
some or all of the configurations that are contained within a dump |
517 |
> |
file. The most common example of a static property that can be |
518 |
> |
computed is the pair distribution function between atoms of type $A$ |
519 |
> |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
520 |
> |
also be used to compute the density distributions of other molecules |
521 |
> |
in a reference frame {\it fixed to the body-fixed reference frame} |
522 |
> |
of a selected atom or rigid body. |
523 |
> |
|
524 |
> |
There are five seperate radial distribution functions availiable in |
525 |
> |
OOPSE. Since every radial distrbution function invlove the |
526 |
> |
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
527 |
> |
-{}-sele2} must be specified to tell StaticProps which bodies to |
528 |
> |
include in the calculation. |
529 |
> |
|
530 |
> |
\begin{description} |
531 |
> |
\item[{\tt -{}-gofr}] Computes the pair distribution function, |
532 |
> |
\begin{equation*} |
533 |
> |
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
534 |
> |
\sum_{j \in B} \delta(r - r_{ij}) \rangle |
535 |
> |
\end{equation*} |
536 |
> |
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
537 |
> |
function. The angle is defined by the intermolecular vector |
538 |
> |
$\vec{r}$ and $z$-axis of DirectionalAtom A, |
539 |
> |
\begin{equation*} |
540 |
> |
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
541 |
> |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
542 |
> |
\theta_{ij} - \cos \theta)\rangle |
543 |
> |
\end{equation*} |
544 |
> |
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
545 |
> |
function. The angle is defined by the $z$-axes of the two |
546 |
> |
DirectionalAtoms A and B. |
547 |
> |
\begin{equation*} |
548 |
> |
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
549 |
> |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
550 |
> |
\omega_{ij} - \cos \omega)\rangle |
551 |
> |
\end{equation*} |
552 |
> |
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
553 |
> |
space $\theta, \omega$ defined by the two angles mentioned above. |
554 |
> |
\begin{equation*} |
555 |
> |
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
556 |
> |
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
557 |
> |
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
558 |
> |
\omega)\rangle |
559 |
> |
\end{equation*} |
560 |
> |
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
561 |
> |
B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
562 |
> |
and {\tt -{}-refsele} must be given to define A's internal |
563 |
> |
coordinate set as the reference frame for the calculation. |
564 |
> |
\end{description} |
565 |
> |
|
566 |
> |
The vectors (and angles) associated with these angular pair |
567 |
> |
distribution functions are most easily seen in the figure below: |
568 |
> |
|
569 |
> |
\begin{figure} |
570 |
> |
\centering |
571 |
> |
\includegraphics[width=3in]{definition.eps} |
572 |
> |
\caption[Definitions of the angles between directional objects]{ \\ |
573 |
> |
Any two directional objects (DirectionalAtoms and RigidBodies) have |
574 |
> |
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
575 |
> |
their body-fixed frames.} \label{oopseFig:gofr} |
576 |
> |
\end{figure} |
577 |
> |
|
578 |
> |
Due to the fact that the selected StuntDoubles from two selections |
579 |
> |
may be overlapped, {\tt StaticProps} performs the calculation in |
580 |
> |
three stages which are illustrated in |
581 |
> |
Fig.~\ref{oopseFig:staticPropsProcess}. |
582 |
> |
|
583 |
> |
\begin{figure} |
584 |
> |
\centering |
585 |
> |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
586 |
> |
\caption[A representation of the three-stage correlations in |
587 |
> |
\texttt{StaticProps}]{This diagram illustrates three-stage |
588 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
589 |
> |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
590 |
> |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
591 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
592 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
593 |
> |
the contrary, the third stage($C$ and $C$) are completely |
594 |
> |
overlapping} \label{oopseFig:staticPropsProcess} |
595 |
> |
\end{figure} |
596 |
> |
|
597 |
> |
The options available for {\tt StaticProps} are as follows: |
598 |
> |
\begin{longtable}[c]{|EFG|} |
599 |
> |
\caption{StaticProps Command-line Options} |
600 |
> |
\\ \hline |
601 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
602 |
> |
\endhead |
603 |
> |
\hline |
604 |
> |
\endfoot |
605 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
606 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
607 |
> |
-i& {\tt -{}-input} & input dump file \\ |
608 |
> |
-o& {\tt -{}-output} & output file name \\ |
609 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
610 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
611 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
612 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
613 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
614 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
615 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
616 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
617 |
> |
& {\tt -{}-molname} & molecule name \\ |
618 |
> |
& {\tt -{}-begin} & begin internal index \\ |
619 |
> |
& {\tt -{}-end} & end internal index \\ |
620 |
> |
\hline |
621 |
> |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
622 |
> |
\hline |
623 |
> |
& {\tt -{}-gofr} & $g(r)$ \\ |
624 |
> |
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
625 |
> |
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
626 |
> |
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
627 |
> |
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
628 |
> |
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
629 |
> |
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
630 |
> |
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
631 |
> |
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
632 |
> |
\end{longtable} |
633 |
> |
|
634 |
> |
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
635 |
> |
|
636 |
> |
{\tt DynamicProps} computes time correlation functions from the |
637 |
> |
configurations stored in a dump file. Typical examples of time |
638 |
> |
correlation functions are the mean square displacement and the |
639 |
> |
velocity autocorrelation functions. Once again, the selection |
640 |
> |
syntax can be used to specify the StuntDoubles that will be used for |
641 |
> |
the calculation. A general time correlation function can be thought |
642 |
> |
of as: |
643 |
> |
\begin{equation} |
644 |
> |
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
645 |
> |
\end{equation} |
646 |
> |
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
647 |
> |
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
648 |
> |
vector property associated with an atom of type $B$ at a different |
649 |
> |
time $t^{\prime}$. In most autocorrelation functions, the vector |
650 |
> |
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
651 |
> |
$B$) are identical, and the three calculations built in to {\tt |
652 |
> |
DynamicProps} make these assumptions. It is possible, however, to |
653 |
> |
make simple modifications to the {\tt DynamicProps} code to allow |
654 |
> |
the use of {\it cross} time correlation functions (i.e. with |
655 |
> |
different vectors). The ability to use two selection scripts to |
656 |
> |
select different types of atoms is already present in the code. |
657 |
> |
|
658 |
> |
For large simulations, the trajectory files can sometimes reach |
659 |
> |
sizes in excess of several gigabytes. In order to effectively |
660 |
> |
analyze that amount of data. In order to prevent a situation where |
661 |
> |
the program runs out of memory due to large trajectories, |
662 |
> |
\texttt{dynamicProps} will estimate the size of free memory at |
663 |
> |
first, and determine the number of frames in each block, which |
664 |
> |
allows the operating system to load two blocks of data |
665 |
> |
simultaneously without swapping. Upon reading two blocks of the |
666 |
> |
trajectory, \texttt{dynamicProps} will calculate the time |
667 |
> |
correlation within the first block and the cross correlations |
668 |
> |
between the two blocks. This second block is then freed and then |
669 |
> |
incremented and the process repeated until the end of the |
670 |
> |
trajectory. Once the end is reached, the first block is freed then |
671 |
> |
incremented, until all frame pairs have been correlated in time. |
672 |
> |
This process is illustrated in |
673 |
> |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
674 |
> |
|
675 |
> |
\begin{figure} |
676 |
> |
\centering |
677 |
> |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
678 |
> |
\caption[A representation of the block correlations in |
679 |
> |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
680 |
> |
processing in \texttt{dynamicProps}. The shaded region represents |
681 |
> |
the self correlation of the block, and the open blocks are read one |
682 |
> |
at a time and the cross correlations between blocks are calculated.} |
683 |
> |
\label{oopseFig:dynamicPropsProcess} |
684 |
> |
\end{figure} |
685 |
> |
|
686 |
> |
The options available for DynamicProps are as follows: |
687 |
> |
\begin{longtable}[c]{|EFG|} |
688 |
> |
\caption{DynamicProps Command-line Options} |
689 |
> |
\\ \hline |
690 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
691 |
> |
\endhead |
692 |
> |
\hline |
693 |
> |
\endfoot |
694 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
695 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
696 |
> |
-i& {\tt -{}-input} & input dump file \\ |
697 |
> |
-o& {\tt -{}-output} & output file name \\ |
698 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
699 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
700 |
> |
\hline |
701 |
> |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
702 |
> |
\hline |
703 |
> |
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
704 |
> |
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
705 |
> |
-d& {\tt -{}-dcorr} & compute dipole correlation function |
706 |
> |
\end{longtable} |
707 |
> |
|
708 |
> |
\section{\label{appendixSection:tools}Other Useful Utilities} |
709 |
> |
|
710 |
> |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
711 |
> |
|
712 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
713 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
714 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
715 |
> |
as follows: |
716 |
> |
|
717 |
> |
|
718 |
> |
\begin{longtable}[c]{|EFG|} |
719 |
> |
\caption{Dump2XYZ Command-line Options} |
720 |
> |
\\ \hline |
721 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
722 |
> |
\endhead |
723 |
> |
\hline |
724 |
> |
\endfoot |
725 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
726 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
727 |
> |
-i & {\tt -{}-input} & input dump file \\ |
728 |
> |
-o & {\tt -{}-output} & output file name \\ |
729 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
730 |
> |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
731 |
> |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
732 |
> |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
733 |
> |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
734 |
> |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
735 |
> |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
736 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
737 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
738 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
739 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
740 |
> |
converted. \\ |
741 |
> |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
742 |
> |
& {\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}. |
743 |
> |
\end{longtable} |
744 |
> |
|
745 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
746 |
> |
|
747 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
748 |
> |
center of resistance. Both tensors at the center of diffusion can |
749 |
> |
also be reported from the program, as well as the coordinates for |
750 |
> |
the beads which are used to approximate the arbitrary shapes. The |
751 |
> |
options available for Hydro are as follows: |
752 |
> |
\begin{longtable}[c]{|EFG|} |
753 |
> |
\caption{Hydrodynamics Command-line Options} |
754 |
> |
\\ \hline |
755 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
756 |
> |
\endhead |
757 |
> |
\hline |
758 |
> |
\endfoot |
759 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
760 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
761 |
> |
-i & {\tt -{}-input} & input dump file \\ |
762 |
> |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
763 |
> |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
764 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
765 |
> |
\end{longtable} |