--- trunk/tengDissertation/Appendix.tex 2006/06/07 18:34:05 2815 +++ trunk/tengDissertation/Appendix.tex 2006/06/09 02:54:01 2840 @@ -1,10 +1,8 @@ \appendix \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} -Designing object-oriented software is hard, and designing reusable -object-oriented scientific software is even harder. Absence of -applying modern software development practices is the bottleneck of -Scientific Computing community\cite{Wilson2006}. For instance, in +Absence of applying modern software development practices is the +bottleneck of Scientific Computing community\cite{Wilson2006}. In the last 20 years , there are quite a few MD packages that were developed to solve common MD problems and perform robust simulations . However, many of the codes are legacy programs that are either @@ -64,11 +62,9 @@ as \texttt{StatProps} (see Sec.~\ref{appendixSection:S program of the package, \texttt{oopse} and it corresponding parallel version \texttt{oopse\_MPI}, as well as other useful utilities, such as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}), -\texttt{DynamicProps} (see -Sec.~\ref{appendixSection:appendixSection:DynamicProps}), -\texttt{Dump2XYZ} (see -Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro} -(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics}) +\texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}), +\texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}), +\texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics}) \textit{etc}. \begin{figure} @@ -113,46 +109,258 @@ OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \t As one of the latest advanced techniques emerged from object-oriented community, design patterns were applied in some of the modern scientific software applications, such as JMol, {\sc -OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. -The following sections enumerates some of the patterns used in {\sc -OOPSE}. +OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2005} +\textit{etc}. The following sections enumerates some of the patterns +used in {\sc OOPSE}. \subsection{\label{appendixSection:singleton}Singleton} -The Singleton pattern ensures that only one instance of a class is -created. All objects that use an instance of that class use the same -instance. +The Singleton pattern not only provides a mechanism to restrict +instantiation of a class to one object, but also provides a global +point of access to the object. Currently implemented as a global +variable, the logging utility which reports error and warning +messages to the console in {\sc OOPSE} is a good candidate for +applying the Singleton pattern to avoid the global namespace +pollution.Although the singleton pattern can be implemented in +various ways to account for different aspects of the software +designs, such as lifespan control \textit{etc}, we only use the +static data approach in {\sc OOPSE}. IntegratorFactory class is +declared as + +\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] + +class IntegratorFactory { +public: + static IntegratorFactory* + getInstance(); +protected: + IntegratorFactory(); +private: + static IntegratorFactory* instance_; +}; + +\end{lstlisting} + +The corresponding implementation is + +\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] + +IntegratorFactory::instance_ = NULL; + +IntegratorFactory* getInstance() { + if (instance_ == NULL){ + instance_ = new IntegratorFactory; + } + return instance_; +} + +\end{lstlisting} + +Since constructor is declared as protected, a client can not +instantiate IntegratorFactory directly. Moreover, since the member +function getInstance serves as the only entry of access to +IntegratorFactory, this approach fulfills the basic requirement, a +single instance. Another consequence of this approach is the +automatic destruction since static data are destroyed upon program +termination. + \subsection{\label{appendixSection:factoryMethod}Factory Method} -The Factory Method pattern is a creational pattern which deals with -the problem of creating objects without specifying the exact class -of object that will be created. Factory Method solves this problem -by defining a separate method for creating the objects, which -subclasses can then override to specify the derived type of product -that will be created. +Categoried as a creational pattern, the Factory Method pattern deals +with the problem of creating objects without specifying the exact +class of object that will be created. Factory Method is typically +implemented by delegating the creation operation to the subclasses. +Parameterized Factory pattern where factory method ( +createIntegrator member function) creates products based on the +identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If +the identifier has been already registered, the factory method will +invoke the corresponding creator (see List.~\ref{integratorCreator}) +which utilizes the modern C++ template technique to avoid excess +subclassing. + +\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] + +class IntegratorFactory { +public: + typedef std::map CreatorMapType; + + bool registerIntegrator(IntegratorCreator* creator) { + return creatorMap_.insert(creator->getIdent(), creator).second; + } + + Integrator* createIntegrator(const string& id, SimInfo* info) { + Integrator* result = NULL; + CreatorMapType::iterator i = creatorMap_.find(id); + if (i != creatorMap_.end()) { + result = (i->second)->create(info); + } + return result; + } + +private: + CreatorMapType creatorMap_; +}; +\end{lstlisting} + +\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] + +class IntegratorCreator { +public: + IntegratorCreator(const string& ident) : ident_(ident) {} + + const string& getIdent() const { return ident_; } + + virtual Integrator* create(SimInfo* info) const = 0; + +private: + string ident_; +}; + +template +class IntegratorBuilder : public IntegratorCreator { +public: + IntegratorBuilder(const string& ident) + : IntegratorCreator(ident) {} + virtual Integrator* create(SimInfo* info) const { + return new ConcreteIntegrator(info); + } +}; +\end{lstlisting} + \subsection{\label{appendixSection:visitorPattern}Visitor} -The purpose of the Visitor Pattern is to encapsulate an operation -that you want to perform on the elements of a data structure. In -this way, you can change the operation being performed on a -structure without the need of changing the classes of the elements -that you are operating on. +The visitor pattern is designed to decouple the data structure and +algorithms used upon them by collecting related operation from +element classes into other visitor classes, which is equivalent to +adding virtual functions into a set of classes without modifying +their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the +structure of Visitor pattern which is used extensively in {\tt +Dump2XYZ}. In order to convert an OOPSE dump file, a series of +distinct operations are performed on different StuntDoubles (See the +class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration +in List.~\ref{appendixScheme:element}). Since the hierarchies +remains stable, it is easy to define a visit operation (see +List.~\ref{appendixScheme:visitor}) for each class of StuntDouble. +Note that using Composite pattern\cite{Gamma1994}, CompositVisitor +manages a priority visitor list and handles the execution of every +visitor in the priority list on different StuntDoubles. + +\begin{figure} +\centering +\includegraphics[width=\linewidth]{visitor.eps} +\caption[The UML class diagram of Visitor patten] {The UML class +diagram of Visitor patten.} \label{appendixFig:visitorUML} +\end{figure} + +\begin{figure} +\centering +\includegraphics[width=\linewidth]{hierarchy.eps} +\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of +the class hierarchy. } \label{oopseFig:hierarchy} +\end{figure} + +\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] + +class StuntDouble { public: + virtual void accept(BaseVisitor* v) = 0; +}; + +class Atom: public StuntDouble { public: + virtual void accept{BaseVisitor* v*} { + v->visit(this); + } +}; + +class DirectionalAtom: public Atom { public: + virtual void accept{BaseVisitor* v*} { + v->visit(this); + } +}; + +class RigidBody: public StuntDouble { public: + virtual void accept{BaseVisitor* v*} { + v->visit(this); + } +}; + +\end{lstlisting} + +\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] + +class BaseVisitor{ +public: + virtual void visit(Atom* atom); + virtual void visit(DirectionalAtom* datom); + virtual void visit(RigidBody* rb); +}; + +class BaseAtomVisitor:public BaseVisitor{ public: + virtual void visit(Atom* atom); + virtual void visit(DirectionalAtom* datom); + virtual void visit(RigidBody* rb); +}; + +class SSDAtomVisitor:public BaseAtomVisitor{ public: + virtual void visit(Atom* atom); + virtual void visit(DirectionalAtom* datom); + virtual void visit(RigidBody* rb); +}; + +class CompositeVisitor: public BaseVisitor { +public: + + typedef list > VistorListType; + typedef VistorListType::iterator VisitorListIterator; + virtual void visit(Atom* atom) { + VisitorListIterator i; + BaseVisitor* curVisitor; + for(i = visitorList.begin();i != visitorList.end();++i) { + atom->accept(*i); + } + } + + virtual void visit(DirectionalAtom* datom) { + VisitorListIterator i; + BaseVisitor* curVisitor; + for(i = visitorList.begin();i != visitorList.end();++i) { + atom->accept(*i); + } + } + + virtual void visit(RigidBody* rb) { + VisitorListIterator i; + std::vector myAtoms; + std::vector::iterator ai; + myAtoms = rb->getAtoms(); + for(i = visitorList.begin();i != visitorList.end();++i) {{ + rb->accept(*i); + for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ + (*ai)->accept(*i); + } + } + + void addVisitor(BaseVisitor* v, int priority); + + protected: + VistorListType visitorList; +}; + +\end{lstlisting} + \section{\label{appendixSection:concepts}Concepts} OOPSE manipulates both traditional atoms as well as some objects that {\it behave like atoms}. These objects can be rigid collections of atoms or atoms which have orientational degrees of -freedom. Here is a diagram of the class heirarchy: - -%\begin{figure} -%\centering -%\includegraphics[width=3in]{heirarchy.eps} -%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ -%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The -%selection syntax allows the user to select any of the objects that -%are descended from a StuntDouble.} \label{oopseFig:heirarchy} -%\end{figure} - +freedom. A diagram of the class hierarchy is illustrated in +Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and +DirectionalAtom in {\sc OOPSE} have their own names which are +specified in the {\tt .md} file. In contrast, RigidBodies are +denoted by their membership and index inside a particular molecule: +[MoleculeName]\_RB\_[index] (the contents inside the brackets depend +on the specifics of the simulation). The names of rigid bodies are +generated automatically. For example, the name of the first rigid +body in a DMPC molecule is DMPC\_RB\_0. \begin{itemize} \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the integrators and minimizers. @@ -162,25 +370,20 @@ Every Molecule, Atom and DirectionalAtom in {\sc OOPSE DirectionalAtom}s which behaves as a single unit. \end{itemize} -Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their -own names which are specified in the {\tt .md} file. In contrast, -RigidBodies are denoted by their membership and index inside a -particular molecule: [MoleculeName]\_RB\_[index] (the contents -inside the brackets depend on the specifics of the simulation). The -names of rigid bodies are generated automatically. For example, the -name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. - \section{\label{appendixSection:syntax}Syntax of the Select Command} -The most general form of the select command is: {\tt select {\it -expression}}. This expression represents an arbitrary set of -StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are -composed of either name expressions, index expressions, predefined -sets, user-defined expressions, comparison operators, within -expressions, or logical combinations of the above expression types. -Expressions can be combined using parentheses and the Boolean -operators. +{\sc OOPSE} provides a powerful selection utility to select +StuntDoubles. The most general form of the select command is: +{\tt select {\it expression}}. + +This expression represents an arbitrary set of StuntDoubles (Atoms +or RigidBodies) in {\sc OOPSE}. Expressions are composed of either +name expressions, index expressions, predefined sets, user-defined +expressions, comparison operators, within expressions, or logical +combinations of the above expression types. Expressions can be +combined using parentheses and the Boolean operators. + \subsection{\label{appendixSection:logical}Logical expressions} The logical operators allow complex queries to be constructed out of @@ -377,14 +580,14 @@ Fig.~\ref{oopseFig:staticPropsProcess}. \centering \includegraphics[width=\linewidth]{staticPropsProcess.eps} \caption[A representation of the three-stage correlations in -\texttt{StaticProps}]{Three-stage processing in -\texttt{StaticProps}. $S_1$ and $S_2$ are the numbers of selected -stuntdobules from {\tt -{}-sele1} and {\tt -{}-sele2} respectively, -while $C$ is the number of stuntdobules appearing at both sets. The -first stage($S_1-C$ and $S_2$) and second stages ($S_1$ and $S_2-C$) -are completely non-overlapping. On the contrary, the third stage($C$ -and $C$) are completely overlapping} -\label{oopseFig:staticPropsProcess} +\texttt{StaticProps}]{This diagram illustrates three-stage +processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the +numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt +-{}-sele2} respectively, while $C$ is the number of stuntdobules +appearing at both sets. The first stage($S_1-C$ and $S_2$) and +second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On +the contrary, the third stage($C$ and $C$) are completely +overlapping} \label{oopseFig:staticPropsProcess} \end{figure} The options available for {\tt StaticProps} are as follows: @@ -462,7 +665,20 @@ incremented, until all frame pairs have been correlate incremented and the process repeated until the end of the trajectory. Once the end is reached, the first block is freed then incremented, until all frame pairs have been correlated in time. +This process is illustrated in +Fig.~\ref{oopseFig:dynamicPropsProcess}. +\begin{figure} +\centering +\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} +\caption[A representation of the block correlations in +\texttt{dynamicProps}]{This diagram illustrates block correlations +processing in \texttt{dynamicProps}. The shaded region represents +the self correlation of the block, and the open blocks are read one +at a time and the cross correlations between blocks are calculated.} +\label{oopseFig:dynamicPropsProcess} +\end{figure} + The options available for DynamicProps are as follows: \begin{longtable}[c]{|EFG|} \caption{DynamicProps Command-line Options} @@ -489,10 +705,10 @@ Dump2XYZ can transform an OOPSE dump file into a xyz f \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} -Dump2XYZ can transform an OOPSE dump file into a xyz file which can -be opened by other molecular dynamics viewers such as Jmol and -VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as -follows: +{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file +which can be opened by other molecular dynamics viewers such as Jmol +and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are +as follows: \begin{longtable}[c]{|EFG|} @@ -523,7 +739,12 @@ The options available for Hydro are as follows: \end{longtable} \subsection{\label{appendixSection:hydrodynamics}Hydro} -The options available for Hydro are as follows: + +{\tt Hydro} can calculate resistance and diffusion tensors at the +center of resistance. Both tensors at the center of diffusion can +also be reported from the program, as well as the coordinates for +the beads which are used to approximate the arbitrary shapes. The +options available for Hydro are as follows: \begin{longtable}[c]{|EFG|} \caption{Hydrodynamics Command-line Options} \\ \hline