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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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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 |
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bottleneck limiting progress in the Scientific Computing |
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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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\section{\label{appendixSection:desginPattern}Design Pattern} |
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\section{\label{appendixSection:architecture }Architecture} |
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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 |
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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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\section{\label{appendixSection:desginPattern}Design Patterns} |
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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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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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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{} \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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\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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\subsection{\label{appendixSection:factoryMethod}Factory Methods} |
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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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One of the most popular Factory pattern is Parameterized Factory |
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pattern which creates products based on their identifiers (see |
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Scheme.~\ref{appendixScheme:factoryDeclaration}). If the identifier |
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has been already registered, the factory method will invoke the |
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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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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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The purpose of the Visitor Pattern is to encapsulate an operation |
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that you want to perform on the elements of a data structure. In |
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this way, you can change the operation being performed on a |
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structure without the need of changing the classes of the elements |
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that you are operating on. |
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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 a 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 Scheme.~\ref{appendixScheme:element}). Since the hierarchies |
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remain stable, it is easy to define a visit operation (see |
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Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
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Note that using Composite pattern\cite{Gamma1994}, CompositeVisitor |
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manages a priority visitor list and handles the execution of every |
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visitor in the priority list on different StuntDoubles. |
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|
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\subsection{\label{appendixSection:templateMethod}Template Method} |
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
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|
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class IntegratorFactory { public: |
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static IntegratorFactory* getInstance(); 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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\section{\label{appendixSection:hierarchy}Hierarchy} |
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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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\subsection{\label{appendixSection:selectionSyntax}Selection Syntax} |
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IntegratorFactory::instance_ = NULL; |
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|
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\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
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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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\subsection{\label{appendixSection:staticProps}Static Properties} |
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\end{lstlisting} |
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|
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\subsection{\label{appendixSection:dynamicProps}Dynamics Properties} |
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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 { 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> class IntegratorBuilder : public |
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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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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
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|
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class StuntDouble { |
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public: |
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virtual void accept(BaseVisitor* v) = 0; |
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}; |
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|
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class Atom: public StuntDouble { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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class DirectionalAtom: public Atom { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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class RigidBody: public StuntDouble { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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\end{lstlisting} |
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|
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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{ |
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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 CompositeVisitor: public BaseVisitor { |
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public: |
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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 = visitorScheme.begin();i != visitorScheme.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 = visitorScheme.begin();i != visitorScheme.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 = visitorScheme.begin();i != visitorScheme.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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protected: |
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VistorListType visitorList; |
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}; |
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\end{lstlisting} |
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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. Objects below others on the diagram inherit |
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data structures and functions from their parent classes above them.} |
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\label{oopseFig:hierarchy} |
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\end{figure} |
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> |
|
| 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. |
| 332 |
> |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
| 333 |
> |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
| 334 |
> |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
| 335 |
> |
DirectionalAtom}s which behaves as a single unit. |
| 336 |
> |
\end{itemize} |
| 337 |
> |
|
| 338 |
> |
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
| 339 |
> |
|
| 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 |
| 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 |
| 350 |
> |
combined using parentheses and the Boolean operators. |
| 351 |
> |
|
| 352 |
> |
\subsection{\label{appendixSection:logical}Logical expressions} |
| 353 |
> |
|
| 354 |
> |
The logical operators allow complex queries to be constructed out of |
| 355 |
> |
simpler ones using the standard boolean connectives {\bf and}, {\bf |
| 356 |
> |
or}, {\bf not}. Parentheses can be used to alter the precedence of |
| 357 |
> |
the operators. |
| 358 |
> |
|
| 359 |
> |
\begin{center} |
| 360 |
> |
\begin{tabular}{|ll|} |
| 361 |
> |
\hline |
| 362 |
> |
{\bf logical operator} & {\bf equivalent operator} \\ |
| 363 |
> |
\hline |
| 364 |
> |
and & ``\&'', ``\&\&'' \\ |
| 365 |
> |
or & ``$|$'', ``$||$'', ``,'' \\ |
| 366 |
> |
not & ``!'' \\ |
| 367 |
> |
\hline |
| 368 |
> |
\end{tabular} |
| 369 |
> |
\end{center} |
| 370 |
> |
|
| 371 |
> |
\subsection{\label{appendixSection:name}Name expressions} |
| 372 |
> |
|
| 373 |
> |
\begin{center} |
| 374 |
> |
\begin{tabular}{|llp{2in}|} |
| 375 |
> |
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
| 376 |
> |
of |
| 377 |
> |
examples} \\ |
| 378 |
> |
\hline expression without ``.'' & select DMPC & select all |
| 379 |
> |
StuntDoubles |
| 380 |
> |
belonging to all DMPC molecules \\ |
| 381 |
> |
& select C* & select all atoms which have atom types beginning with C |
| 382 |
> |
\\ |
| 383 |
> |
& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
| 384 |
> |
only select the rigid bodies, and not the atoms belonging to them). \\ |
| 385 |
> |
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
| 386 |
> |
O\_TIP3P |
| 387 |
> |
atoms belonging to TIP3P molecules \\ |
| 388 |
> |
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
| 389 |
> |
the first |
| 390 |
> |
RigidBody in each DMPC molecule \\ |
| 391 |
> |
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
| 392 |
> |
molecule \\ |
| 393 |
> |
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
| 394 |
> |
select all atoms |
| 395 |
> |
belonging to all rigid bodies within all DMPC molecules \\ |
| 396 |
> |
\hline |
| 397 |
> |
\end{tabular} |
| 398 |
> |
\end{center} |
| 399 |
> |
|
| 400 |
> |
\subsection{\label{appendixSection:index}Index expressions} |
| 401 |
> |
|
| 402 |
> |
\begin{center} |
| 403 |
> |
\begin{tabular}{|lp{4in}|} |
| 404 |
> |
\hline |
| 405 |
> |
{\bf examples} & {\bf translation of examples} \\ |
| 406 |
> |
\hline |
| 407 |
> |
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
| 408 |
> |
select 20 to 30 & select all of the StuntDoubles belonging to |
| 409 |
> |
molecules which have global indices between 20 (inclusive) and 30 |
| 410 |
> |
(exclusive) \\ |
| 411 |
> |
\hline |
| 412 |
> |
\end{tabular} |
| 413 |
> |
\end{center} |
| 414 |
> |
|
| 415 |
> |
\subsection{\label{appendixSection:predefined}Predefined sets} |
| 416 |
> |
|
| 417 |
> |
\begin{center} |
| 418 |
> |
\begin{tabular}{|ll|} |
| 419 |
> |
\hline |
| 420 |
> |
{\bf keyword} & {\bf description} \\ |
| 421 |
> |
\hline |
| 422 |
> |
all & select all StuntDoubles \\ |
| 423 |
> |
none & select none of the StuntDoubles \\ |
| 424 |
> |
\hline |
| 425 |
> |
\end{tabular} |
| 426 |
> |
\end{center} |
| 427 |
> |
|
| 428 |
> |
\subsection{\label{appendixSection:userdefined}User-defined expressions} |
| 429 |
> |
|
| 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}}. Once defined, the user can specify such terms in |
| 434 |
> |
boolean expressions |
| 435 |
> |
|
| 436 |
> |
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
| 437 |
> |
|
| 438 |
> |
{\tt select SSDWATER} |
| 439 |
> |
|
| 440 |
> |
\subsection{\label{appendixSection:comparison}Comparison expressions} |
| 441 |
> |
|
| 442 |
> |
StuntDoubles can be selected by using comparision operators on their |
| 443 |
> |
properties. The general form for the comparison command is: a |
| 444 |
> |
property name, followed by a comparision operator and then a number. |
| 445 |
> |
|
| 446 |
> |
\begin{center} |
| 447 |
> |
\begin{tabular}{|l|l|} |
| 448 |
> |
\hline |
| 449 |
> |
{\bf property} & mass, charge \\ |
| 450 |
> |
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
| 451 |
> |
``$<=$'', ``$!=$'' \\ |
| 452 |
> |
\hline |
| 453 |
> |
\end{tabular} |
| 454 |
> |
\end{center} |
| 455 |
> |
|
| 456 |
> |
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
| 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} |
| 461 |
> |
|
| 462 |
> |
The ``within'' keyword allows the user to select all StuntDoubles |
| 463 |
> |
within the specified distance (in Angstroms) from a selection, |
| 464 |
> |
including the selected atom itself. The general form for within |
| 465 |
> |
selection is: {\tt select within(distance, expression)} |
| 466 |
> |
|
| 467 |
> |
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
| 468 |
> |
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
| 469 |
> |
atoms. |
| 470 |
> |
|
| 471 |
> |
|
| 472 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
| 473 |
> |
|
| 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 $B$, $g_{AB}(r)$. {\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 |
| 514 |
> |
-{}-sele2} must be specified to tell StaticProps which bodies to |
| 515 |
> |
include in the calculation. |
| 516 |
> |
|
| 517 |
> |
\begin{description} |
| 518 |
> |
\item[{\tt -{}-gofr}] Computes the pair distribution function, |
| 519 |
> |
\begin{equation*} |
| 520 |
> |
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
| 521 |
> |
\sum_{j \in B} \delta(r - r_{ij}) \rangle |
| 522 |
> |
\end{equation*} |
| 523 |
> |
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
| 524 |
> |
function. The angle is defined by the intermolecular vector |
| 525 |
> |
$\vec{r}$ and $z$-axis of DirectionalAtom A, |
| 526 |
> |
\begin{equation*} |
| 527 |
> |
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
| 528 |
> |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
| 529 |
> |
\theta_{ij} - \cos \theta)\rangle |
| 530 |
> |
\end{equation*} |
| 531 |
> |
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
| 532 |
> |
function. The angle is defined by the $z$-axes of the two |
| 533 |
> |
DirectionalAtoms A and B. |
| 534 |
> |
\begin{equation*} |
| 535 |
> |
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
| 536 |
> |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
| 537 |
> |
\omega_{ij} - \cos \omega)\rangle |
| 538 |
> |
\end{equation*} |
| 539 |
> |
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
| 540 |
> |
space $\theta, \omega$ defined by the two angles mentioned above. |
| 541 |
> |
\begin{equation*} |
| 542 |
> |
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
| 543 |
> |
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
| 544 |
> |
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
| 545 |
> |
\omega)\rangle |
| 546 |
> |
\end{equation*} |
| 547 |
> |
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
| 548 |
> |
B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
| 549 |
> |
and {\tt -{}-refsele} must be given to define A's internal |
| 550 |
> |
coordinate set as the reference frame for the calculation. |
| 551 |
> |
\end{description} |
| 552 |
> |
|
| 553 |
> |
The vectors (and angles) associated with these angular pair |
| 554 |
> |
distribution functions are most easily seen in |
| 555 |
> |
Fig.~\ref{oopseFig:gofr}. |
| 556 |
> |
|
| 557 |
> |
The options available for {\tt StaticProps} are as follows: |
| 558 |
> |
\begin{longtable}[c]{|EFG|} |
| 559 |
> |
\caption{StaticProps Command-line Options} |
| 560 |
> |
\\ \hline |
| 561 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 562 |
> |
\endhead |
| 563 |
> |
\hline |
| 564 |
> |
\endfoot |
| 565 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
| 566 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
| 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 |
| 583 |
> |
& {\tt -{}-gofr} & $g(r)$ \\ |
| 584 |
> |
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
| 585 |
> |
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
| 586 |
> |
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
| 587 |
> |
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
| 588 |
> |
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
| 589 |
> |
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
| 590 |
> |
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
| 591 |
> |
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
| 592 |
> |
\end{longtable} |
| 593 |
> |
|
| 594 |
> |
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
| 595 |
> |
|
| 596 |
> |
{\tt DynamicProps} computes time correlation functions from the |
| 597 |
> |
configurations stored in a dump file. Typical examples of time |
| 598 |
> |
correlation functions are the mean square displacement and the |
| 599 |
> |
velocity autocorrelation functions. Once again, the selection |
| 600 |
> |
syntax can be used to specify the StuntDoubles that will be used for |
| 601 |
> |
the calculation. A general time correlation function can be thought |
| 602 |
> |
of as: |
| 603 |
> |
\begin{equation} |
| 604 |
> |
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
| 605 |
> |
\end{equation} |
| 606 |
> |
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
| 607 |
> |
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
| 608 |
> |
vector property associated with an atom of type $B$ at a different |
| 609 |
> |
time $t^{\prime}$. In most autocorrelation functions, the vector |
| 610 |
> |
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
| 611 |
> |
$B$) are identical, and the three calculations built in to {\tt |
| 612 |
> |
DynamicProps} make these assumptions. It is possible, however, to |
| 613 |
> |
make simple modifications to the {\tt DynamicProps} code to allow |
| 614 |
> |
the use of {\it cross} time correlation functions (i.e. with |
| 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} |
| 648 |
> |
\\ \hline |
| 649 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 650 |
> |
\endhead |
| 651 |
> |
\hline |
| 652 |
> |
\endfoot |
| 653 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
| 654 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
| 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 |
| 662 |
> |
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
| 663 |
> |
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
| 664 |
> |
-d& {\tt -{}-dcorr} & compute dipole correlation function |
| 665 |
> |
\end{longtable} |
| 666 |
> |
|
| 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} |
