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# Line 129 | Line 129 | is declared as
129   designs, such as lifespan control \textit{etc}, we only use the
130   static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class
131   is declared as
132 < \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}]
132 > \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
133  
134 <  class IntegratorFactory {
135 <    public:
136 <      static IntegratorFactory* getInstance();
137 <    protected:
138 <      IntegratorFactory();
139 <    private:
140 <      static IntegratorFactory* instance_;
141 <  };
134 > class IntegratorFactory {
135 > public:
136 >  static IntegratorFactory*
137 >  getInstance();
138 > protected:
139 >  IntegratorFactory();
140 > private:
141 >  static IntegratorFactory* instance_;
142 > };
143 >
144   \end{lstlisting}
145   The corresponding implementation is
146 < \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}]
146 > \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
147  
148   IntegratorFactory::instance_ = NULL;
149  
# Line 151 | Line 153 | IntegratorFactory* getInstance() {
153    }
154    return instance_;
155   }
156 +
157   \end{lstlisting}
158   Since constructor is declared as {\tt protected}, a client can not
159   instantiate {\tt IntegratorFactory} directly. Moreover, since the
# Line 166 | Line 169 | implemented by delegating the creation operation to th
169   with the problem of creating objects without specifying the exact
170   class of object that will be created. Factory Method is typically
171   implemented by delegating the creation operation to the subclasses.
172 + {\tt Integrator} class Parameterized Factory pattern where factory
173 + method ({\tt createIntegrator} member function) creates products
174 + based on the identifier (see
175 + List.~\ref{appendixScheme:factoryDeclaration}). If the identifier
176 + has been already registered, the factory method will invoke the
177 + corresponding creator (see List.~\ref{integratorCreator}) which
178 + utilizes the modern C++ template technique to avoid subclassing.
179 + \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of {\tt IntegratorFactory} class.},label={appendixScheme:factoryDeclaration}]
180  
181 < Registers a creator with a type identifier. Looks up the type
182 < identifier in the internal map. If it is found, it invokes the
183 < corresponding creator for the type identifier and returns its
173 < result.
174 < \begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}]
175 <  class IntegratorCreator;
176 <  class IntegratorFactory {
177 <    public:
178 <      typedef std::map<string, IntegratorCreator*> CreatorMapType;
181 > class IntegratorFactory {
182 > public:
183 >  typedef std::map<string, IntegratorCreator*> CreatorMapType;
184  
185 <      bool registerIntegrator(IntegratorCreator* creator);
186 <
182 <      Integrator* createIntegrator(const string& id, SimInfo* info);
183 <
184 <    private:
185 <      CreatorMapType creatorMap_;
186 <  };
187 < \end{lstlisting}
188 <
189 < \begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}]
190 <  bool IntegratorFactory::unregisterIntegrator(const string& id) {
191 <    return creatorMap_.erase(id) == 1;
185 >  bool registerIntegrator(IntegratorCreator* creator) {
186 >    return creatorMap_.insert(creator->getIdent(), creator).second;
187    }
188  
189 <  Integrator*
190 <  IntegratorFactory::createIntegrator(const string& id, SimInfo* info) {
189 >  Integrator* createIntegrator(const string& id, SimInfo* info) {
190 >    Integrator* result = NULL;
191      CreatorMapType::iterator i = creatorMap_.find(id);
192      if (i != creatorMap_.end()) {
193 <      //invoke functor to create object
199 <      return (i->second)->create(info);
200 <    } else {
201 <      return NULL;
193 >      result = (i->second)->create(info);
194      }
195 +    return result;
196    }
197 +
198 + private:
199 +  CreatorMapType creatorMap_;
200 + };
201   \end{lstlisting}
202 + \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
203  
204 < \begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}]
205 <
208 <  class IntegratorCreator {
209 <  public:
204 > class IntegratorCreator {
205 > public:
206      IntegratorCreator(const string& ident) : ident_(ident) {}
207  
208      const string& getIdent() const { return ident_; }
209  
210      virtual Integrator* create(SimInfo* info) const = 0;
211  
212 <  private:
212 > private:
213      string ident_;
214 <  };
214 > };
215  
216 <  template<class ConcreteIntegrator>
217 <  class IntegratorBuilder : public IntegratorCreator {
218 <  public:
219 <    IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {}
220 <    virtual  Integrator* create(SimInfo* info) const {
221 <      return new ConcreteIntegrator(info);
222 <    }
223 <  };
216 > template<class ConcreteIntegrator>
217 > class IntegratorBuilder : public IntegratorCreator {
218 > public:
219 >  IntegratorBuilder(const string& ident)
220 >                   : IntegratorCreator(ident) {}
221 >  virtual  Integrator* create(SimInfo* info) const {
222 >    return new ConcreteIntegrator(info);
223 >  }
224 > };
225   \end{lstlisting}
226  
227   \subsection{\label{appendixSection:visitorPattern}Visitor}
# Line 232 | Line 229 | interfaces  of the elements. In other words, one can a
229   The purpose of the Visitor Pattern is to encapsulate an operation
230   that you want to perform on the elements. The operation being
231   performed on a structure can be switched without changing the
232 < interfaces  of the elements. In other words, one can add virtual
232 > interfaces of the elements. In other words, one can add virtual
233   functions into a set of classes without modifying their interfaces.
234 < The UML class diagram of Visitor patten is shown in
235 < Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in
236 < Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern
237 < extensively.
234 > Fig.~\ref{appendixFig:visitorUML} demonstrates the structure of
235 > Visitor pattern which is used extensively in {\tt Dump2XYZ}. In
236 > order to convert an OOPSE dump file, a series of distinct and
237 > unrelated operations are performed on different StuntDoubles.
238 > Visitor allows one to keep related operations together by packing
239 > them into one class. {\tt BaseAtomVisitor} is a typical example of
240 > visitor in {\tt Dump2XYZ} program{see
241 > List.~\ref{appendixScheme:visitor}}. In contrast to the operations,
242 > the object structure or element classes rarely change(See
243 > Fig.~\ref{oopseFig:heirarchy} and
244 > List.~\ref{appendixScheme:element}).
245  
246 +
247   \begin{figure}
248   \centering
249 < \includegraphics[width=\linewidth]{architecture.eps}
250 < \caption[The architecture of {\sc OOPSE}] {Overview of the structure
251 < of {\sc OOPSE}} \label{appendixFig:visitorUML}
249 > \includegraphics[width=\linewidth]{visitor.eps}
250 > \caption[The UML class diagram of Visitor patten] {The UML class
251 > diagram of Visitor patten.} \label{appendixFig:visitorUML}
252   \end{figure}
253  
254   \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
255 <  class BaseVisitor{
256 <    public:
257 <      virtual void visit(Atom* atom);
258 <      virtual void visit(DirectionalAtom* datom);
259 <      virtual void visit(RigidBody* rb);
260 <  };
255 >
256 > class BaseVisitor{
257 > public:
258 >  virtual void visit(Atom* atom);
259 >  virtual void visit(DirectionalAtom* datom);
260 >  virtual void visit(RigidBody* rb);
261 > };
262 >
263 > class BaseAtomVisitor:public BaseVisitor{ public:
264 >  virtual void visit(Atom* atom);
265 >  virtual void visit(DirectionalAtom* datom);
266 >  virtual void visit(RigidBody* rb);
267 > };
268 >
269   \end{lstlisting}
270  
271   \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
259 –  class StuntDouble {
260 –    public:
261 –      virtual void accept(BaseVisitor* v) = 0;
262 –  };
272  
273 <  class Atom: public StuntDouble {
274 <    public:
275 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
276 <  };
273 > class StuntDouble {
274 > public:
275 >  virtual void accept(BaseVisitor* v) = 0;
276 > };
277  
278 <  class DirectionalAtom: public Atom {
279 <    public:
280 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
281 <  };
278 > class Atom: public StuntDouble {
279 > public:
280 >  virtual void accept{BaseVisitor* v*} {
281 >    v->visit(this);
282 >  }
283 > };
284  
285 <  class RigidBody: public StuntDouble {
286 <    public:
287 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
288 <  };
285 > class DirectionalAtom: public Atom {
286 > public:
287 >  virtual void accept{BaseVisitor* v*} {
288 >    v->visit(this);
289 >  }
290 > };
291  
292 + class RigidBody: public StuntDouble {
293 + public:
294 +  virtual void accept{BaseVisitor* v*} {
295 +    v->visit(this);
296 +  }
297 + };
298 +
299   \end{lstlisting}
300 +
301   \section{\label{appendixSection:concepts}Concepts}
302  
303   OOPSE manipulates both traditional atoms as well as some objects
304   that {\it behave like atoms}.  These objects can be rigid
305   collections of atoms or atoms which have orientational degrees of
306 < freedom.  Here is a diagram of the class heirarchy:
307 <
306 > freedom.  A diagram of the class heirarchy is illustrated in
307 > Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and
308 > DirectionalAtom in {\sc OOPSE} have their own names which are
309 > specified in the {\tt .md} file. In contrast, RigidBodies are
310 > denoted by their membership and index inside a particular molecule:
311 > [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
312 > on the specifics of the simulation). The names of rigid bodies are
313 > generated automatically. For example, the name of the first rigid
314 > body in a DMPC molecule is DMPC\_RB\_0.
315   %\begin{figure}
316   %\centering
317 < %\includegraphics[width=3in]{heirarchy.eps}
318 < %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
319 < %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
320 < %selection syntax allows the user to select any of the objects that
321 < %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
317 > %\includegraphics[width=\linewidth]{heirarchy.eps}
318 > %\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of
319 > %the class heirarchy.
320 > %\begin{itemize}
321 > %\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
322 > %integrators and minimizers.
323 > %\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
324 > %\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
325 > %\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
326 > %DirectionalAtom}s which behaves as a single unit.
327 > %\end{itemize}
328 > %} \label{oopseFig:heirarchy}
329   %\end{figure}
295 –
296 – \begin{itemize}
297 – \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
298 – integrators and minimizers.
299 – \item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
300 – \item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
301 – \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
302 – DirectionalAtom}s which behaves as a single unit.
303 – \end{itemize}
304 –
305 – Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
306 – own names which are specified in the {\tt .md} file. In contrast,
307 – RigidBodies are denoted by their membership and index inside a
308 – particular molecule: [MoleculeName]\_RB\_[index] (the contents
309 – inside the brackets depend on the specifics of the simulation). The
310 – names of rigid bodies are generated automatically. For example, the
311 – name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
330  
331   \section{\label{appendixSection:syntax}Syntax of the Select Command}
332  

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