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\appendix |
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\chapter{\label{chapt:appendix}APPENDIX} |
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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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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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\section{\label{appendixSection:desginPattern}Design Pattern} |
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Design patterns are optimal solutions to commonly-occurring problems |
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in software design. Although originated as an architectural concept |
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for buildings and towns by Christopher Alexander \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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\subsection{\label{appendixSection:visitorPattern}Visitor Pattern} |
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Patterns are usually described using a format that includes the |
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following information: |
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\begin{enumerate} |
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\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
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discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
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in the literature. In this case it is common practice to document these nicknames or synonyms under |
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the heading of \emph{Aliases} or \emph{Also Known As}. |
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\item The \emph{motivation} or \emph{context} that this pattern applies |
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to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
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\item The \emph{solution} to the problem that the pattern |
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addresses. It describes how to construct the necessary work products. The description may include |
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pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
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collaborations, to show how the problem is solved. |
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\item The \emph{consequences} of using the given solution to solve a |
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problem, both positive and negative. |
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\end{enumerate} |
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\subsection{\label{appendixSection:templatePattern}Template Pattern} |
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As one of the latest advanced techniques emerged from |
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object-oriented community, design patterns were applied in some of |
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the modern scientific software applications, such as JMol, OOPSE |
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\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}. |
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\subsection{\label{appendixSection:factoryPattern}Factory Pattern} |
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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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|
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\section{\label{appendixSection:hierarchy}Hierarchy} |
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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 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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\section{\label{appendixSection:selectionSyntax}Selection Syntax} |
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\section{\label{appendixSection:hydrodynamics}Hydrodynamics} |
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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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\subsection{\label{appendixSection:templateMethod}Template Method} |
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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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\subsection{\label{appendixSection:staticProps}Factory Properties} |
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\section{\label{appendixSection:concepts}Concepts} |
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\subsection{\label{appendixSection:dynamicProps}Dynamics Properties} |
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OOPSE manipulates both traditional atoms as well as some objects |
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that {\it behave like atoms}. These objects can be rigid |
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collections of atoms or atoms which have orientational degrees of |
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freedom. Here is a diagram of the class heirarchy: |
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|
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%\begin{figure} |
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%\centering |
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%\includegraphics[width=3in]{heirarchy.eps} |
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%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
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%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
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%selection syntax allows the user to select any of the objects that |
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%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
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%\end{figure} |
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|
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\begin{itemize} |
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\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
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integrators and minimizers. |
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\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
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\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
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\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
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DirectionalAtom}s which behaves as a single unit. |
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\end{itemize} |
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|
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Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
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own names which are specified in the {\tt .md} file. In contrast, |
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RigidBodies are denoted by their membership and index inside a |
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particular molecule: [MoleculeName]\_RB\_[index] (the contents |
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inside the brackets depend on the specifics of the simulation). The |
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names of rigid bodies are generated automatically. For example, the |
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name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
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|
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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|
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The most general form of the select command is: {\tt select {\it |
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expression}} |
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|
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This expression represents an arbitrary set of StuntDoubles (Atoms |
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or RigidBodies) in {\sc oopse}. Expressions are composed of either |
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name expressions, index expressions, predefined sets, user-defined |
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expressions, comparison operators, within expressions, or logical |
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combinations of the above expression types. Expressions can be |
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combined using parentheses and the Boolean operators. |
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|
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\subsection{\label{appendixSection:logical}Logical expressions} |
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|
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The logical operators allow complex queries to be constructed out of |
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simpler ones using the standard boolean connectives {\bf and}, {\bf |
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or}, {\bf not}. Parentheses can be used to alter the precedence of |
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the operators. |
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|
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\begin{center} |
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\begin{tabular}{|ll|} |
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\hline |
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{\bf logical operator} & {\bf equivalent operator} \\ |
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\hline |
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and & ``\&'', ``\&\&'' \\ |
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or & ``$|$'', ``$||$'', ``,'' \\ |
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not & ``!'' \\ |
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\hline |
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\end{tabular} |
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\end{center} |
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|
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\subsection{\label{appendixSection:name}Name expressions} |
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|
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\begin{center} |
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\begin{tabular}{|llp{2in}|} |
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\hline {\bf type of expression} & {\bf examples} & {\bf translation |
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of |
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examples} \\ |
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\hline expression without ``.'' & select DMPC & select all |
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StuntDoubles |
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belonging to all DMPC molecules \\ |
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& select C* & select all atoms which have atom types beginning with C |
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\\ |
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& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
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only select the rigid bodies, and not the atoms belonging to them). \\ |
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\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
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O\_TIP3P |
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atoms belonging to TIP3P molecules \\ |
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& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
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the first |
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RigidBody in each DMPC molecule \\ |
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& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
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molecule \\ |
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\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
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select all atoms |
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belonging to all rigid bodies within all DMPC molecules \\ |
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\hline |
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\end{tabular} |
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\end{center} |
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|
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\subsection{\label{appendixSection:index}Index expressions} |
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|
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\begin{center} |
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\begin{tabular}{|lp{4in}|} |
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\hline |
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{\bf examples} & {\bf translation of examples} \\ |
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\hline |
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select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
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select 20 to 30 & select all of the StuntDoubles belonging to |
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molecules which have global indices between 20 (inclusive) and 30 |
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(exclusive) \\ |
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\hline |
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\end{tabular} |
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\end{center} |
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|
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\subsection{\label{appendixSection:predefined}Predefined sets} |
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|
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\begin{center} |
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\begin{tabular}{|ll|} |
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\hline |
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{\bf keyword} & {\bf description} \\ |
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\hline |
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all & select all StuntDoubles \\ |
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none & select none of the StuntDoubles \\ |
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\hline |
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\end{tabular} |
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\end{center} |
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|
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\subsection{\label{appendixSection:userdefined}User-defined expressions} |
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|
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Users can define arbitrary terms to represent groups of |
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StuntDoubles, and then use the define terms in select commands. The |
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general form for the define command is: {\bf define {\it term |
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expression}} |
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|
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Once defined, the user can specify such terms in boolean expressions |
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|
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{\tt define SSDWATER SSD or SSD1 or SSDRF} |
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|
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{\tt select SSDWATER} |
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|
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\subsection{\label{appendixSection:comparison}Comparison expressions} |
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|
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StuntDoubles can be selected by using comparision operators on their |
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properties. The general form for the comparison command is: a |
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property name, followed by a comparision operator and then a number. |
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|
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\begin{center} |
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\begin{tabular}{|l|l|} |
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\hline |
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{\bf property} & mass, charge \\ |
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{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
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``$<=$'', ``$!=$'' \\ |
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\hline |
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\end{tabular} |
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\end{center} |
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|
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For example, the phrase {\tt select mass > 16.0 and charge < -2} |
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would select StuntDoubles which have mass greater than 16.0 and |
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charges less than -2. |
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|
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\subsection{\label{appendixSection:within}Within expressions} |
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|
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The ``within'' keyword allows the user to select all StuntDoubles |
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within the specified distance (in Angstroms) from a selection, |
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including the selected atom itself. The general form for within |
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selection is: {\tt select within(distance, expression)} |
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|
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For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
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select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
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atoms. |
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|
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\section{\label{appendixSection:tools}Tools which use the selection command} |
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|
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\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
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|
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Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
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be opened by other molecular dynamics viewers such as Jmol and VMD. |
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The options available for Dump2XYZ are as follows: |
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|
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|
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\begin{longtable}[c]{|EFG|} |
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\caption{Dump2XYZ Command-line Options} |
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\\ \hline |
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{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
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\endhead |
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\hline |
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\endfoot |
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-h & {\tt -{}-help} & Print help and exit \\ |
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-V & {\tt -{}-version} & Print version and exit \\ |
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-i & {\tt -{}-input=filename} & input dump file \\ |
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-o & {\tt -{}-output=filename} & output file name \\ |
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-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
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-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
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-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
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-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
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-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
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-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
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-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
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& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
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& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
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& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
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-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
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converted. \\ |
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& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
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& {\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}. |
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\end{longtable} |
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|
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|
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\subsection{\label{appendixSection:StaticProps}StaticProps} |
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|
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{\tt StaticProps} can compute properties which are averaged over |
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some or all of the configurations that are contained within a dump |
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file. The most common example of a static property that can be |
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computed is the pair distribution function between atoms of type $A$ |
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and other atoms of type $B$, $g_{AB}(r)$. StaticProps can also be |
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used to compute the density distributions of other molecules in a |
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reference frame {\it fixed to the body-fixed reference frame} of a |
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selected atom or rigid body. |
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|
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There are five seperate radial distribution functions availiable in |
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OOPSE. Since every radial distrbution function invlove the |
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calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
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-{}-sele2} must be specified to tell StaticProps which bodies to |
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include in the calculation. |
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|
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\begin{description} |
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\item[{\tt -{}-gofr}] Computes the pair distribution function, |
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\begin{equation*} |
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g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
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\sum_{j \in B} \delta(r - r_{ij}) \rangle |
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\end{equation*} |
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\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
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function. The angle is defined by the intermolecular vector |
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$\vec{r}$ and $z$-axis of DirectionalAtom A, |
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\begin{equation*} |
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g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
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\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
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\theta_{ij} - \cos \theta)\rangle |
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\end{equation*} |
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\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
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function. The angle is defined by the $z$-axes of the two |
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DirectionalAtoms A and B. |
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\begin{equation*} |
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g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
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\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
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\omega_{ij} - \cos \omega)\rangle |
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\end{equation*} |
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\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
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space $\theta, \omega$ defined by the two angles mentioned above. |
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\begin{equation*} |
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g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
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\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
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\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
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\omega)\rangle |
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\end{equation*} |
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\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
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B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
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and {\tt -{}-refsele} must be given to define A's internal |
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coordinate set as the reference frame for the calculation. |
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\end{description} |
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|
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The vectors (and angles) associated with these angular pair |
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distribution functions are most easily seen in the figure below: |
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|
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\begin{figure} |
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\centering |
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\includegraphics[width=3in]{definition.eps} |
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\caption[Definitions of the angles between directional objects]{ \\ |
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Any two directional objects (DirectionalAtoms and RigidBodies) have |
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a set of two angles ($\theta$, and $\omega$) between the z-axes of |
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their body-fixed frames.} \label{oopseFig:gofr} |
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> |
\end{figure} |
| 346 |
> |
|
| 347 |
> |
The options available for {\tt StaticProps} are as follows: |
| 348 |
> |
\begin{longtable}[c]{|EFG|} |
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> |
\caption{StaticProps Command-line Options} |
| 350 |
> |
\\ \hline |
| 351 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 352 |
> |
\endhead |
| 353 |
> |
\hline |
| 354 |
> |
\endfoot |
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> |
-h& {\tt -{}-help} & Print help and exit \\ |
| 356 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
| 357 |
> |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 358 |
> |
-o& {\tt -{}-output=filename} & output file name \\ |
| 359 |
> |
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
| 360 |
> |
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
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> |
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
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> |
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
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& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
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& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
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& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
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> |
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
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& {\tt -{}-molname=STRING} & molecule name \\ |
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> |
& {\tt -{}-begin=INT} & begin internal index \\ |
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> |
& {\tt -{}-end=INT} & end internal index \\ |
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> |
\hline |
| 371 |
> |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 372 |
> |
\hline |
| 373 |
> |
& {\tt -{}-gofr} & $g(r)$ \\ |
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> |
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
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> |
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
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> |
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
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> |
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
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> |
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
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> |
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
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& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
| 381 |
> |
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
| 382 |
> |
\end{longtable} |
| 383 |
> |
|
| 384 |
> |
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
| 385 |
> |
|
| 386 |
> |
{\tt DynamicProps} computes time correlation functions from the |
| 387 |
> |
configurations stored in a dump file. Typical examples of time |
| 388 |
> |
correlation functions are the mean square displacement and the |
| 389 |
> |
velocity autocorrelation functions. Once again, the selection |
| 390 |
> |
syntax can be used to specify the StuntDoubles that will be used for |
| 391 |
> |
the calculation. A general time correlation function can be thought |
| 392 |
> |
of as: |
| 393 |
> |
\begin{equation} |
| 394 |
> |
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
| 395 |
> |
\end{equation} |
| 396 |
> |
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
| 397 |
> |
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
| 398 |
> |
vector property associated with an atom of type $B$ at a different |
| 399 |
> |
time $t^{\prime}$. In most autocorrelation functions, the vector |
| 400 |
> |
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
| 401 |
> |
$B$) are identical, and the three calculations built in to {\tt |
| 402 |
> |
DynamicProps} make these assumptions. It is possible, however, to |
| 403 |
> |
make simple modifications to the {\tt DynamicProps} code to allow |
| 404 |
> |
the use of {\it cross} time correlation functions (i.e. with |
| 405 |
> |
different vectors). The ability to use two selection scripts to |
| 406 |
> |
select different types of atoms is already present in the code. |
| 407 |
> |
|
| 408 |
> |
The options available for DynamicProps are as follows: |
| 409 |
> |
\begin{longtable}[c]{|EFG|} |
| 410 |
> |
\caption{DynamicProps Command-line Options} |
| 411 |
> |
\\ \hline |
| 412 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 413 |
> |
\endhead |
| 414 |
> |
\hline |
| 415 |
> |
\endfoot |
| 416 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
| 417 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
| 418 |
> |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 419 |
> |
-o& {\tt -{}-output=filename} & output file name \\ |
| 420 |
> |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
| 421 |
> |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 422 |
> |
\hline |
| 423 |
> |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 424 |
> |
\hline |
| 425 |
> |
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
| 426 |
> |
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
| 427 |
> |
-d& {\tt -{}-dcorr} & compute dipole correlation function |
| 428 |
> |
\end{longtable} |
| 429 |
> |
|
| 430 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
