--- trunk/tengDissertation/Appendix.tex	2006/06/08 21:02:53	2831
+++ trunk/tengDissertation/Appendix.tex	2006/06/09 03:19:29	2841
@@ -1,24 +1,19 @@
 \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
-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
-poorly organized or extremely complex. Usually, these packages were
-contributed by scientists without official computer science
-training. The development of most MD applications are lack of strong
-coordination to enforce design and programming guidelines. Moreover,
-most MD programs also suffer from missing design and implement
-documents which is crucial to the maintenance and extensibility.
-Along the way of studying structural and dynamic processes in
-condensed phase systems like biological membranes and nanoparticles,
-we developed and maintained an Object-Oriented Parallel Simulation
-Engine ({\sc OOPSE}). This new molecular dynamics package has some
-unique features
+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\cite{Brooks1983, Vincent1995, Kale1999} that were developed
+to solve common MD problems and perform robust simulations .
+Unfortunately, most of them are commercial programs that are either
+poorly written or extremely complicate. Consequently, it prevents
+the researchers to reuse or extend those packages to do cutting-edge
+research effectively. Along the way of studying structural and
+dynamic processes in condensed phase systems like biological
+membranes and nanoparticles, we developed an open source
+Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new
+molecular dynamics package has some unique features
 \begin{enumerate}
   \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
 atom types (transition metals, point dipoles, sticky potentials,
@@ -64,11 +59,9 @@ 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}
@@ -113,11 +106,12 @@ 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 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
@@ -127,23 +121,27 @@ static data approach in {\sc OOPSE}. {\tt IntegratorFa
 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}. {\tt IntegratorFactory} class
-is declared as
-\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}]
+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_;
+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)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}]
 
+\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() {
@@ -154,128 +152,194 @@ Since constructor is declared as {\tt protected}, a cl
 }
 
 \end{lstlisting}
-Since constructor is declared as {\tt protected}, a client can not
-instantiate {\tt IntegratorFactory} directly. Moreover, since the
-member function {\tt getInstance} serves as the only entry of access
-to {\tt 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.
 
+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}
 
 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.
 
-Registers a creator with a type identifier. Looks up the type
-identifier in the internal map. If it is found, it invokes the
-corresponding creator for the type identifier and returns its
-result.
-\begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}]
+\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<string, IntegratorCreator*> CreatorMapType;
+public:
+  typedef std::map<string, IntegratorCreator*> CreatorMapType;
 
-    bool registerIntegrator(IntegratorCreator* creator) {
-      return creatorMap_.insert(creator->getIdent(), creator).second;
-    }
+  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;
+  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_;
+private:
+  CreatorMapType creatorMap_;
 };
 \end{lstlisting}
-\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)]Souce code of creator classes.},label={appendixScheme:integratorCreator}]
 
+\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
+
 class IntegratorCreator {
-  public:
+public:
     IntegratorCreator(const string& ident) : ident_(ident) {}
 
     const string& getIdent() const { return ident_; }
 
     virtual Integrator* create(SimInfo* info) const = 0;
 
-  private:
+private:
     string ident_;
 };
 
 template<class ConcreteIntegrator>
 class IntegratorBuilder : public IntegratorCreator {
-  public:
-    IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {}
-    virtual  Integrator* create(SimInfo* info) const {
-      return new ConcreteIntegrator(info);
-    }
+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. The operation being
-performed on a structure can be switched without changing the
-interfaces  of the elements. In other words, one can add virtual
-functions into a set of classes without modifying their interfaces.
-The UML class diagram of Visitor patten is shown in
-Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in
-Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern
-extensively.
+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 architecture of {\sc OOPSE}] {Overview of the structure
-of {\sc OOPSE}} \label{appendixFig:visitorUML}
+\caption[The UML class diagram of Visitor patten] {The UML class
+diagram of Visitor patten.} \label{appendixFig:visitorUML}
 \end{figure}
 
-\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
+\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}
 
-class BaseVisitor{
-  public:
-    virtual void visit(Atom* atom);
-    virtual void visit(DirectionalAtom* datom);
-    virtual void visit(RigidBody* rb);
+\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;
 };
 
-\end{lstlisting}
+class Atom: public StuntDouble { public:
+  virtual void accept{BaseVisitor* v*} {
+    v->visit(this);
+  }
+};
 
-\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
+class DirectionalAtom: public Atom { public:
+  virtual void accept{BaseVisitor* v*} {
+    v->visit(this);
+  }
+};
 
-class StuntDouble {
-  public:
-    virtual void accept(BaseVisitor* v) = 0;
+class RigidBody: public StuntDouble { public:
+  virtual void accept{BaseVisitor* v*} {
+    v->visit(this);
+  }
 };
 
-class Atom: 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 DirectionalAtom: public Atom {
-  public:
-    virtual void accept{BaseVisitor* v*} {
-      v->visit(this);
-    }
+class BaseAtomVisitor:public BaseVisitor{ public:
+  virtual void visit(Atom* atom);
+  virtual void visit(DirectionalAtom* datom);
+  virtual void visit(RigidBody* rb);
 };
 
-class RigidBody: public StuntDouble {
-  public:
-    virtual void accept{BaseVisitor* v*} {
-      v->visit(this);
+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<pair<BaseVisitor*, int> > 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<Atom*> myAtoms;
+    std::vector<Atom*>::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}
@@ -285,8 +349,8 @@ freedom.  A diagram of the class heirarchy is illustra
 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.  A diagram of the class heirarchy is illustrated in
-Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and
+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:
@@ -294,11 +358,6 @@ body in a DMPC molecule is DMPC\_RB\_0.
 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{figure}
-\centering
-\includegraphics[width=\linewidth]{heirarchy.eps}
-\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of
-the class heirarchy.
 \begin{itemize}
 \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
 integrators and minimizers.
@@ -307,20 +366,21 @@ DirectionalAtom}s which behaves as a single unit.
 \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
 DirectionalAtom}s which behaves as a single unit.
 \end{itemize}
-} \label{oopseFig:heirarchy}
-\end{figure}
 
 \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
