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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{wilson}. For instance, in the |
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last 20 years , there are quite a few MD packages that were |
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The absence of modern software development practices has been a |
5 |
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bottleneck limiting progress in the Scientific Computing |
6 |
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community\cite{Wilson2006}. In the last 20 years , a large number of |
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few MD packages\cite{Brooks1983, Vincent1995, Kale1999} 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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. Most of these are commercial programs that are either poorly |
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written or extremely complicated to use correctly. This situation |
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prevents researchers from reusing or extending those packages to do |
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cutting-edge research effectively. In the process of studying |
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structural and dynamic processes in condensed phase systems like |
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biological membranes and nanoparticles, we developed an open source |
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Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new |
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molecular dynamics package has some unique features |
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\begin{enumerate} |
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\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
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atom types (transition metals, point dipoles, sticky potentials, |
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Gay-Berne ellipsoids, or other "lumpy"atoms with orientational |
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degrees of freedom), as well as rigid bodies. |
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\item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap |
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Beowulf clusters to obtain very efficient parallelism. |
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\item {\sc OOPSE} integrates the equations of motion using advanced methods for |
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orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T |
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ensembles. |
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\item {\sc OOPSE} can carry out simulations on metallic systems using the |
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Embedded Atom Method (EAM) as well as the Sutton-Chen potential. |
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\item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals. |
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\item {\sc OOPSE} can simulate systems containing the extremely efficient |
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extended-Soft Sticky Dipole (SSD/E) model for water. |
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\end{enumerate} |
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|
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\section{\label{appendixSection:desginPattern}Design Pattern} |
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\section{\label{appendixSection:architecture }Architecture} |
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|
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Mainly written by C++ and Fortran90, {\sc OOPSE} uses C++ Standard |
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Template Library (STL) and fortran modules as a foundation. As an |
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extensive set of the STL and Fortran90 modules, {\sc Base Classes} |
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provide generic implementations of mathematical objects (e.g., |
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matrices, vectors, polynomials, random number generators) and |
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advanced data structures and algorithms(e.g., tuple, bitset, generic |
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data and string manipulation). The molecular data structures for the |
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representation of atoms, bonds, bends, torsions, rigid bodies and |
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molecules \textit{etc} are contained in the {\sc Kernel} which is |
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implemented with {\sc Base Classes} and are carefully designed to |
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provide maximum extensibility and flexibility. The functionality |
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required for applications is provided by the third layer which |
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contains Input/Output, Molecular Mechanics and Structure modules. |
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The Input/Output module not only implements general methods for file |
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handling, but also defines a generic force field interface. Another |
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important component of Input/Output module is the parser for |
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meta-data files, which has been implemented using the ANother Tool |
53 |
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for Language Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. |
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The Molecular Mechanics module consists of energy minimization and a |
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wide varieties of integration methods(see |
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Chap.~\ref{chapt:methodology}). The structure module contains a |
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flexible and powerful selection library which syntax is elaborated |
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in Sec.~\ref{appendixSection:syntax}. The top layer is made of the |
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main program of the package, \texttt{oopse} and it corresponding |
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parallel version \texttt{oopse\_MPI}, as well as other useful |
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utilities, such as \texttt{StatProps} (see |
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Sec.~\ref{appendixSection:StaticProps}), \texttt{DynamicProps} (see |
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Sec.~\ref{appendixSection:DynamicProps}), \texttt{Dump2XYZ} (see |
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Sec.~\ref{appendixSection:Dump2XYZ}), \texttt{Hydro} (see |
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Sec.~\ref{appendixSection:hydrodynamics}) \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 Patterns} |
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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 \cite{alexander}, |
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software patterns first became popular with the wide acceptance of |
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the book, Design Patterns: Elements of Reusable Object-Oriented |
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Software \cite{gamma94}. Patterns reflect the experience, knowledge |
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and insights of developers who have successfully used these patterns |
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in their own work. Patterns are reusable. They provide a ready-made |
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solution that can be adapted to different problems as necessary. |
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Pattern are expressive. they provide a common vocabulary of |
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solutions that can express large solutions succinctly. |
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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. As one of the latest advanced |
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techniques to emerge from object-oriented community, design patterns |
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were applied in some of the modern scientific software applications, |
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such as JMol, {\sc OOPSE}\cite{Meineke2005} and |
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PROTOMOL\cite{Matthey2004} \textit{etc}. The following sections |
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enumerates some of the patterns used in {\sc OOPSE}. |
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|
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Patterns are usually described using a format that includes the |
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following information: |
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\begin{enumerate} |
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\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
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discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
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in the literature. In this case it is common practice to document these nicknames or synonyms under |
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the heading of \emph{Aliases} or \emph{Also Known As}. |
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\item The \emph{motivation} or \emph{context} that this pattern applies |
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to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
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\item The \emph{solution} to the problem that the pattern |
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addresses. It describes how to construct the necessary work products. The description may include |
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pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
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collaborations, to show how the problem is solved. |
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\item The \emph{consequences} of using the given solution to solve a |
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problem, both positive and negative. |
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\end{enumerate} |
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\subsection{\label{appendixSection:singleton}Singletons} |
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|
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As one of the latest advanced techniques emerged from |
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object-oriented community, design patterns were applied in some of |
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the modern scientific software applications, such as JMol, OOPSE |
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\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}. |
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The Singleton pattern not only provides a mechanism to restrict |
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instantiation of a class to one object, but also provides a global |
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point of access to the object. Although the singleton pattern can be |
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implemented in various ways to account for different aspects of the |
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software designs, such as lifespan control \textit{etc}, we only use |
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the static data approach in {\sc OOPSE}. The declaration and |
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implementation of IntegratorFactory class are given by declared in |
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List.~\ref{appendixScheme:singletonDeclaration} and |
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Scheme.~\ref{appendixScheme:singletonImplementation} respectively. |
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Since the 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:singleton}Singleton} |
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The Singleton pattern ensures that only one instance of a class is |
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created. All objects that use an instance of that class use the same |
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instance. |
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\subsection{\label{appendixSection:factoryMethod}Factory Methods} |
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|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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The Factory Method pattern is a creational pattern which deals with |
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The Factory Method pattern is a creational pattern and deals with |
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|
the problem of creating objects without specifying the exact class |
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of object that will be created. Factory Method solves this problem |
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by defining a separate method for creating the objects, which |
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subclasses can then override to specify the derived type of product |
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that will be created. |
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of object that will be created. Factory method is typically |
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implemented by delegating the creation operation to the subclasses. |
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Parameterized Factory pattern where factory method ( |
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createIntegrator member function) creates products based on the |
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identifier (see Scheme.~\ref{appendixScheme:factoryDeclaration}). If |
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the identifier has been already registered, the factory method will |
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invoke the corresponding creator (see |
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Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the |
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modern C++ template technique to avoid excess subclassing. |
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|
|
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– |
|
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|
\subsection{\label{appendixSection:visitorPattern}Visitor} |
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The purpose of the Visitor Pattern is to encapsulate an operation |
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that you want to perform on the elements of a data structure. In |
70 |
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this way, you can change the operation being performed on a |
71 |
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structure without the need of changing the classes of the elements |
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that you are operating on. |
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|
|
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The visitor pattern is designed to decouple the data structure and |
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algorithms used upon them by collecting related operation from |
129 |
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element classes into other visitor classes, which is equivalent to |
130 |
+ |
adding virtual functions into a set of classes without modifying |
131 |
+ |
their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
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structure of a Visitor pattern which is used extensively in {\tt |
133 |
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Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
134 |
+ |
distinct operations are performed on different StuntDoubles (See the |
135 |
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class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
136 |
+ |
in Scheme.~\ref{appendixScheme:element}). Since the hierarchies |
137 |
+ |
remain stable, it is easy to define a visit operation (see |
138 |
+ |
Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
139 |
+ |
Note that using Composite pattern\cite{Gamma1994}, CompositeVisitor |
140 |
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manages a priority visitor list and handles the execution of every |
141 |
+ |
visitor in the priority list on different StuntDoubles. |
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|
|
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\subsection{\label{appendixSection:templateMethod}Template Method} |
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
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|
|
145 |
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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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class IntegratorFactory { public: |
146 |
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static IntegratorFactory* getInstance(); protected: |
147 |
> |
IntegratorFactory(); |
148 |
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private: |
149 |
> |
static IntegratorFactory* instance_; |
150 |
> |
}; |
151 |
|
|
152 |
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\section{\label{appendixSection:concepts}Concepts} |
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> |
\end{lstlisting} |
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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 |
84 |
< |
freedom. Here is a diagram of the class heirarchy: |
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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}] |
155 |
|
|
156 |
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IntegratorFactory::instance_ = NULL; |
157 |
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|
158 |
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IntegratorFactory* getInstance() { |
159 |
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if (instance_ == NULL){ |
160 |
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instance_ = new IntegratorFactory; |
161 |
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} |
162 |
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return instance_; |
163 |
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} |
164 |
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|
165 |
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\end{lstlisting} |
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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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|
169 |
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class IntegratorFactory { public: |
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typedef std::map<string, IntegratorCreator*> CreatorMapType; |
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|
172 |
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bool registerIntegrator(IntegratorCreator* creator) { |
173 |
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return creatorMap_.insert(creator->getIdent(), creator).second; |
174 |
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} |
175 |
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|
176 |
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Integrator* createIntegrator(const string& id, SimInfo* info) { |
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Integrator* result = NULL; |
178 |
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CreatorMapType::iterator i = creatorMap_.find(id); |
179 |
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if (i != creatorMap_.end()) { |
180 |
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result = (i->second)->create(info); |
181 |
+ |
} |
182 |
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return result; |
183 |
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} |
184 |
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|
185 |
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private: |
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CreatorMapType creatorMap_; |
187 |
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}; |
188 |
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\end{lstlisting} |
189 |
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|
190 |
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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 { |
193 |
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public: |
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IntegratorCreator(const string& ident) : ident_(ident) {} |
195 |
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|
196 |
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const string& getIdent() const { return ident_; } |
197 |
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|
198 |
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virtual Integrator* create(SimInfo* info) const = 0; |
199 |
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|
200 |
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private: |
201 |
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string ident_; |
202 |
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}; |
203 |
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|
204 |
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template<class ConcreteIntegrator> class IntegratorBuilder : public |
205 |
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IntegratorCreator { |
206 |
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public: |
207 |
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IntegratorBuilder(const string& ident) |
208 |
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: IntegratorCreator(ident) {} |
209 |
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virtual Integrator* create(SimInfo* info) const { |
210 |
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return new ConcreteIntegrator(info); |
211 |
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} |
212 |
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}; |
213 |
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\end{lstlisting} |
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|
215 |
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
216 |
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|
217 |
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class StuntDouble { |
218 |
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public: |
219 |
+ |
virtual void accept(BaseVisitor* v) = 0; |
220 |
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}; |
221 |
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|
222 |
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class Atom: public StuntDouble { |
223 |
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public: |
224 |
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virtual void accept{BaseVisitor* v*} { |
225 |
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v->visit(this); |
226 |
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} |
227 |
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}; |
228 |
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|
229 |
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class DirectionalAtom: public Atom { |
230 |
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public: |
231 |
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virtual void accept{BaseVisitor* v*} { |
232 |
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v->visit(this); |
233 |
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} |
234 |
+ |
}; |
235 |
+ |
|
236 |
+ |
class RigidBody: public StuntDouble { |
237 |
+ |
public: |
238 |
+ |
virtual void accept{BaseVisitor* v*} { |
239 |
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v->visit(this); |
240 |
+ |
} |
241 |
+ |
}; |
242 |
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|
243 |
+ |
\end{lstlisting} |
244 |
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|
245 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
246 |
+ |
|
247 |
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class BaseVisitor{ |
248 |
+ |
public: |
249 |
+ |
virtual void visit(Atom* atom); |
250 |
+ |
virtual void visit(DirectionalAtom* datom); |
251 |
+ |
virtual void visit(RigidBody* rb); |
252 |
+ |
}; |
253 |
+ |
|
254 |
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class BaseAtomVisitor:public BaseVisitor{ |
255 |
+ |
public: |
256 |
+ |
virtual void visit(Atom* atom); |
257 |
+ |
virtual void visit(DirectionalAtom* datom); |
258 |
+ |
virtual void visit(RigidBody* rb); |
259 |
+ |
}; |
260 |
+ |
|
261 |
+ |
class CompositeVisitor: public BaseVisitor { |
262 |
+ |
public: |
263 |
+ |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
264 |
+ |
typedef VistorListType::iterator VisitorListIterator; |
265 |
+ |
virtual void visit(Atom* atom) { |
266 |
+ |
VisitorListIterator i; |
267 |
+ |
BaseVisitor* curVisitor; |
268 |
+ |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
269 |
+ |
atom->accept(*i); |
270 |
+ |
} |
271 |
+ |
} |
272 |
+ |
|
273 |
+ |
virtual void visit(DirectionalAtom* datom) { |
274 |
+ |
VisitorListIterator i; |
275 |
+ |
BaseVisitor* curVisitor; |
276 |
+ |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
277 |
+ |
atom->accept(*i); |
278 |
+ |
} |
279 |
+ |
} |
280 |
+ |
|
281 |
+ |
virtual void visit(RigidBody* rb) { |
282 |
+ |
VisitorListIterator i; |
283 |
+ |
std::vector<Atom*> myAtoms; |
284 |
+ |
std::vector<Atom*>::iterator ai; |
285 |
+ |
myAtoms = rb->getAtoms(); |
286 |
+ |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
287 |
+ |
rb->accept(*i); |
288 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
289 |
+ |
(*ai)->accept(*i); |
290 |
+ |
} |
291 |
+ |
} |
292 |
+ |
|
293 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
294 |
+ |
protected: |
295 |
+ |
VistorListType visitorList; |
296 |
+ |
}; |
297 |
+ |
\end{lstlisting} |
298 |
+ |
|
299 |
|
\begin{figure} |
300 |
|
\centering |
301 |
< |
\includegraphics[width=3in]{heirarchy.pdf} |
302 |
< |
\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
303 |
< |
The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
91 |
< |
selection syntax allows the user to select any of the objects that |
92 |
< |
are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
301 |
> |
\includegraphics[width=\linewidth]{visitor.eps} |
302 |
> |
\caption[The UML class diagram of Visitor patten] {The UML class |
303 |
> |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
304 |
|
\end{figure} |
305 |
|
|
306 |
+ |
\begin{figure} |
307 |
+ |
\centering |
308 |
+ |
\includegraphics[width=\linewidth]{hierarchy.eps} |
309 |
+ |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
310 |
+ |
the class hierarchy. Objects below others on the diagram inherit |
311 |
+ |
data structures and functions from their parent classes above them.} |
312 |
+ |
\label{oopseFig:hierarchy} |
313 |
+ |
\end{figure} |
314 |
+ |
|
315 |
+ |
\section{\label{appendixSection:concepts}Concepts} |
316 |
+ |
|
317 |
+ |
OOPSE manipulates both traditional atoms as well as some objects |
318 |
+ |
that {\it behave like atoms}. These objects can be rigid |
319 |
+ |
collections of atoms or atoms which have orientational degrees of |
320 |
+ |
freedom. A diagram of the class hierarchy is illustrated in |
321 |
+ |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
322 |
+ |
DirectionalAtom in {\sc OOPSE} have their own names which are |
323 |
+ |
specified in the meta data file. In contrast, RigidBodies are |
324 |
+ |
denoted by their membership and index inside a particular molecule: |
325 |
+ |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
326 |
+ |
on the specifics of the simulation). The names of rigid bodies are |
327 |
+ |
generated automatically. For example, the name of the first rigid |
328 |
+ |
body in a DMPC molecule is DMPC\_RB\_0. |
329 |
|
\begin{itemize} |
330 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
331 |
|
integrators and minimizers. |
335 |
|
DirectionalAtom}s which behaves as a single unit. |
336 |
|
\end{itemize} |
337 |
|
|
104 |
– |
Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
105 |
– |
own names which are specified in the {\tt .md} file. In contrast, |
106 |
– |
RigidBodies are denoted by their membership and index inside a |
107 |
– |
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
108 |
– |
inside the brackets depend on the specifics of the simulation). The |
109 |
– |
names of rigid bodies are generated automatically. For example, the |
110 |
– |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
111 |
– |
|
338 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
339 |
|
|
340 |
< |
The most general form of the select command is: {\tt select {\it |
341 |
< |
expression}} |
340 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
341 |
> |
StuntDoubles. The most general form of the select command is: |
342 |
|
|
343 |
+ |
{\tt select {\it expression}}. |
344 |
+ |
|
345 |
|
This expression represents an arbitrary set of StuntDoubles (Atoms |
346 |
< |
or RigidBodies) in {\sc oopse}. Expressions are composed of either |
346 |
> |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
347 |
|
name expressions, index expressions, predefined sets, user-defined |
348 |
|
expressions, comparison operators, within expressions, or logical |
349 |
|
combinations of the above expression types. Expressions can be |
371 |
|
\subsection{\label{appendixSection:name}Name expressions} |
372 |
|
|
373 |
|
\begin{center} |
374 |
< |
\begin{tabular}{|llp{3in}|} |
374 |
> |
\begin{tabular}{|llp{2in}|} |
375 |
|
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
376 |
|
of |
377 |
|
examples} \\ |
430 |
|
Users can define arbitrary terms to represent groups of |
431 |
|
StuntDoubles, and then use the define terms in select commands. The |
432 |
|
general form for the define command is: {\bf define {\it term |
433 |
< |
expression}} |
433 |
> |
expression}}. Once defined, the user can specify such terms in |
434 |
> |
boolean expressions |
435 |
|
|
207 |
– |
Once defined, the user can specify such terms in boolean expressions |
208 |
– |
|
436 |
|
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
437 |
|
|
438 |
|
{\tt select SSDWATER} |
454 |
|
\end{center} |
455 |
|
|
456 |
|
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
457 |
< |
wouldselect StuntDoubles which have mass greater than 16.0 and |
457 |
> |
would select StuntDoubles which have mass greater than 16.0 and |
458 |
|
charges less than -2. |
459 |
|
|
460 |
|
\subsection{\label{appendixSection:within}Within expressions} |
468 |
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
469 |
|
atoms. |
470 |
|
|
244 |
– |
\section{\label{appendixSection:tools}Tools which use the selection command} |
471 |
|
|
472 |
< |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
472 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
473 |
|
|
248 |
– |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
249 |
– |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
250 |
– |
The options available for Dump2XYZ are as follows: |
251 |
– |
|
252 |
– |
|
253 |
– |
\begin{longtable}[c]{|EFG|} |
254 |
– |
\caption{Dump2XYZ Command-line Options} |
255 |
– |
\\ \hline |
256 |
– |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
257 |
– |
\endhead |
258 |
– |
\hline |
259 |
– |
\endfoot |
260 |
– |
-h & {\tt -{}-help} & Print help and exit \\ |
261 |
– |
-V & {\tt -{}-version} & Print version and exit \\ |
262 |
– |
-i & {\tt -{}-input=filename} & input dump file \\ |
263 |
– |
-o & {\tt -{}-output=filename} & output file name \\ |
264 |
– |
-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
265 |
– |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
266 |
– |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
267 |
– |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
268 |
– |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
269 |
– |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
270 |
– |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
271 |
– |
& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
272 |
– |
& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
273 |
– |
& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
274 |
– |
-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
275 |
– |
converted. \\ |
276 |
– |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
277 |
– |
& {\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}. |
278 |
– |
\end{longtable} |
279 |
– |
|
280 |
– |
|
474 |
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
475 |
|
|
476 |
|
{\tt StaticProps} can compute properties which are averaged over |
477 |
|
some or all of the configurations that are contained within a dump |
478 |
|
file. The most common example of a static property that can be |
479 |
|
computed is the pair distribution function between atoms of type $A$ |
480 |
< |
and other atoms of type $B$, $g_{AB}(r)$. StaticProps can also be |
481 |
< |
used to compute the density distributions of other molecules in a |
482 |
< |
reference frame {\it fixed to the body-fixed reference frame} of a |
483 |
< |
selected atom or rigid body. |
480 |
> |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
481 |
> |
also be used to compute the density distributions of other molecules |
482 |
> |
in a reference frame {\it fixed to the body-fixed reference frame} |
483 |
> |
of a selected atom or rigid body. Due to the fact that the selected |
484 |
> |
StuntDoubles from two selections may be overlapped, {\tt |
485 |
> |
StaticProps} performs the calculation in three stages which are |
486 |
> |
illustrated in Fig.~\ref{oopseFig:staticPropsProcess}. |
487 |
|
|
488 |
+ |
\begin{figure} |
489 |
+ |
\centering |
490 |
+ |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
491 |
+ |
\caption[A representation of the three-stage correlations in |
492 |
+ |
\texttt{StaticProps}]{This diagram illustrates three-stage |
493 |
+ |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
494 |
+ |
numbers of selected StuntDobules from {\tt -{}-sele1} and {\tt |
495 |
+ |
-{}-sele2} respectively, while $C$ is the number of StuntDobules |
496 |
+ |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
497 |
+ |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
498 |
+ |
the contrary, the third stage($C$ and $C$) are completely |
499 |
+ |
overlapping} \label{oopseFig:staticPropsProcess} |
500 |
+ |
\end{figure} |
501 |
+ |
|
502 |
+ |
\begin{figure} |
503 |
+ |
\centering |
504 |
+ |
\includegraphics[width=3in]{definition.eps} |
505 |
+ |
\caption[Definitions of the angles between directional objects]{Any |
506 |
+ |
two directional objects (DirectionalAtoms and RigidBodies) have a |
507 |
+ |
set of two angles ($\theta$, and $\omega$) between the z-axes of |
508 |
+ |
their body-fixed frames.} \label{oopseFig:gofr} |
509 |
+ |
\end{figure} |
510 |
+ |
|
511 |
|
There are five seperate radial distribution functions availiable in |
512 |
|
OOPSE. Since every radial distrbution function invlove the |
513 |
|
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
551 |
|
\end{description} |
552 |
|
|
553 |
|
The vectors (and angles) associated with these angular pair |
554 |
< |
distribution functions are most easily seen in the figure below: |
554 |
> |
distribution functions are most easily seen in |
555 |
> |
Fig.~\ref{oopseFig:gofr}. |
556 |
|
|
337 |
– |
\begin{figure} |
338 |
– |
\centering |
339 |
– |
\includegraphics[width=3in]{definition.pdf} |
340 |
– |
\caption[Definitions of the angles between directional objects]{ \\ |
341 |
– |
Any two directional objects (DirectionalAtoms and RigidBodies) have |
342 |
– |
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
343 |
– |
their body-fixed frames.} \label{oopseFig:gofr} |
344 |
– |
\end{figure} |
345 |
– |
|
557 |
|
The options available for {\tt StaticProps} are as follows: |
558 |
|
\begin{longtable}[c]{|EFG|} |
559 |
|
\caption{StaticProps Command-line Options} |
564 |
|
\endfoot |
565 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
566 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
567 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
568 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
569 |
< |
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
570 |
< |
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
571 |
< |
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
572 |
< |
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
573 |
< |
& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
574 |
< |
& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
575 |
< |
& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
576 |
< |
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
577 |
< |
& {\tt -{}-molname=STRING} & molecule name \\ |
578 |
< |
& {\tt -{}-begin=INT} & begin internal index \\ |
579 |
< |
& {\tt -{}-end=INT} & end internal index \\ |
567 |
> |
-i& {\tt -{}-input} & input dump file \\ |
568 |
> |
-o& {\tt -{}-output} & output file name \\ |
569 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
570 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
571 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
572 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
573 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
574 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
575 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
576 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
577 |
> |
& {\tt -{}-molname} & molecule name \\ |
578 |
> |
& {\tt -{}-begin} & begin internal index \\ |
579 |
> |
& {\tt -{}-end} & end internal index \\ |
580 |
|
\hline |
581 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
582 |
|
\hline |
615 |
|
different vectors). The ability to use two selection scripts to |
616 |
|
select different types of atoms is already present in the code. |
617 |
|
|
618 |
+ |
For large simulations, the trajectory files can sometimes reach |
619 |
+ |
sizes in excess of several gigabytes. In order to prevent a |
620 |
+ |
situation where the program runs out of memory due to large |
621 |
+ |
trajectories, \texttt{dynamicProps} will first estimate the size of |
622 |
+ |
free memory, and determine the number of frames in each block, which |
623 |
+ |
will allow the operating system to load two blocks of data |
624 |
+ |
simultaneously without swapping. Upon reading two blocks of the |
625 |
+ |
trajectory, \texttt{dynamicProps} will calculate the time |
626 |
+ |
correlation within the first block and the cross correlations |
627 |
+ |
between the two blocks. This second block is then freed and then |
628 |
+ |
incremented and the process repeated until the end of the |
629 |
+ |
trajectory. Once the end is reached, the first block is freed then |
630 |
+ |
incremented, until all frame pairs have been correlated in time. |
631 |
+ |
This process is illustrated in |
632 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
633 |
+ |
|
634 |
+ |
\begin{figure} |
635 |
+ |
\centering |
636 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
637 |
+ |
\caption[A representation of the block correlations in |
638 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
639 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
640 |
+ |
the self correlation of the block, and the open blocks are read one |
641 |
+ |
at a time and the cross correlations between blocks are calculated.} |
642 |
+ |
\label{oopseFig:dynamicPropsProcess} |
643 |
+ |
\end{figure} |
644 |
+ |
|
645 |
|
The options available for DynamicProps are as follows: |
646 |
|
\begin{longtable}[c]{|EFG|} |
647 |
|
\caption{DynamicProps Command-line Options} |
652 |
|
\endfoot |
653 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
654 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
655 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
656 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
657 |
< |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
658 |
< |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
655 |
> |
-i& {\tt -{}-input} & input dump file \\ |
656 |
> |
-o& {\tt -{}-output} & output file name \\ |
657 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
658 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
659 |
|
\hline |
660 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
661 |
|
\hline |
664 |
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
665 |
|
\end{longtable} |
666 |
|
|
667 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
667 |
> |
\section{\label{appendixSection:tools}Other Useful Utilities} |
668 |
> |
|
669 |
> |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
670 |
> |
|
671 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
672 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
673 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
674 |
> |
as follows: |
675 |
> |
|
676 |
> |
|
677 |
> |
\begin{longtable}[c]{|EFG|} |
678 |
> |
\caption{Dump2XYZ Command-line Options} |
679 |
> |
\\ \hline |
680 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
681 |
> |
\endhead |
682 |
> |
\hline |
683 |
> |
\endfoot |
684 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
685 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
686 |
> |
-i & {\tt -{}-input} & input dump file \\ |
687 |
> |
-o & {\tt -{}-output} & output file name \\ |
688 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
689 |
> |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
690 |
> |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
691 |
> |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
692 |
> |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
693 |
> |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
694 |
> |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
695 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
696 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
697 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
698 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
699 |
> |
converted. \\ |
700 |
> |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
701 |
> |
& {\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}. |
702 |
> |
\end{longtable} |
703 |
> |
|
704 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
705 |
> |
|
706 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
707 |
> |
center of resistance. Both tensors at the center of diffusion can |
708 |
> |
also be reported from the program, as well as the coordinates for |
709 |
> |
the beads which are used to approximate the arbitrary shapes. The |
710 |
> |
options available for Hydro are as follows: |
711 |
> |
\begin{longtable}[c]{|EFG|} |
712 |
> |
\caption{Hydrodynamics Command-line Options} |
713 |
> |
\\ \hline |
714 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
715 |
> |
\endhead |
716 |
> |
\hline |
717 |
> |
\endfoot |
718 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
719 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
720 |
> |
-i & {\tt -{}-input} & input dump file \\ |
721 |
> |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
722 |
> |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
723 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
724 |
> |
\end{longtable} |