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 Singleton design pattern implementation(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 |
|
|
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 |
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={[].},label={appendixScheme:factoryDeclaration}] |
175 |
< |
class IntegratorCreator; |
176 |
< |
class IntegratorFactory { |
177 |
< |
public: |
178 |
< |
typedef std::map<std::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 std::string& id, SimInfo* info); |
183 |
< |
|
184 |
< |
private: |
185 |
< |
CreatorMapType creatorMap_; |
186 |
< |
}; |
187 |
< |
\end{lstlisting} |
188 |
< |
|
189 |
< |
\begin{lstlisting}[float,caption={[].},label={appendixScheme:factoryDeclarationImplementation}] |
190 |
< |
bool IntegratorFactory::unregisterIntegrator(const std::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 std::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={[].},label={appendixScheme:integratorCreator}] |
204 |
> |
class IntegratorCreator { |
205 |
> |
public: |
206 |
> |
IntegratorCreator(const string& ident) : ident_(ident) {} |
207 |
|
|
208 |
< |
class IntegratorCreator { |
209 |
< |
public: |
210 |
< |
IntegratorCreator(const std::string& ident) : ident_(ident) {} |
208 |
> |
const string& getIdent() const { return ident_; } |
209 |
|
|
212 |
– |
const std::string& getIdent() const { return ident_; } |
213 |
– |
|
210 |
|
virtual Integrator* create(SimInfo* info) const = 0; |
211 |
|
|
212 |
< |
private: |
213 |
< |
std::string ident_; |
214 |
< |
}; |
212 |
> |
private: |
213 |
> |
string ident_; |
214 |
> |
}; |
215 |
|
|
216 |
< |
template<class ConcreteIntegrator> |
217 |
< |
class IntegratorBuilder : public IntegratorCreator { |
218 |
< |
public: |
219 |
< |
IntegratorBuilder(const std::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} |
228 |
|
|
229 |
|
The purpose of the Visitor Pattern is to encapsulate an operation |
230 |
< |
that you want to perform on the elements of a data structure. In |
231 |
< |
this way, you can change the operation being performed on a |
232 |
< |
structure without the need of changing the class heirarchy of the |
233 |
< |
elements that you are operating on. |
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 |
233 |
> |
functions into a set of classes without modifying their interfaces. |
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 |
< |
\begin{lstlisting}[float,caption={[].},label={appendixScheme:visitor}] |
247 |
< |
class BaseVisitor{ |
248 |
< |
public: |
249 |
< |
virtual void visit(Atom* atom); |
250 |
< |
virtual void visit(DirectionalAtom* datom); |
251 |
< |
virtual void visit(RigidBody* rb); |
252 |
< |
}; |
246 |
> |
|
247 |
> |
\begin{figure} |
248 |
> |
\centering |
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 |
> |
|
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} |
246 |
– |
\begin{lstlisting}[float,caption={[].},label={appendixScheme:element}] |
247 |
– |
class StuntDouble { |
248 |
– |
public: |
249 |
– |
virtual void accept(BaseVisitor* v) = 0; |
250 |
– |
}; |
270 |
|
|
271 |
< |
class Atom: public StuntDouble { |
253 |
< |
public: |
254 |
< |
virtual void accept{BaseVisitor* v*} {v->visit(this);} |
255 |
< |
}; |
271 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
272 |
|
|
273 |
< |
class DirectionalAtom: public Atom { |
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 RigidBody: public StuntDouble { |
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 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} |
283 |
– |
|
284 |
– |
\begin{itemize} |
285 |
– |
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
286 |
– |
integrators and minimizers. |
287 |
– |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
288 |
– |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
289 |
– |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
290 |
– |
DirectionalAtom}s which behaves as a single unit. |
291 |
– |
\end{itemize} |
330 |
|
|
293 |
– |
Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
294 |
– |
own names which are specified in the {\tt .md} file. In contrast, |
295 |
– |
RigidBodies are denoted by their membership and index inside a |
296 |
– |
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
297 |
– |
inside the brackets depend on the specifics of the simulation). The |
298 |
– |
names of rigid bodies are generated automatically. For example, the |
299 |
– |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
300 |
– |
|
331 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
332 |
|
|
333 |
|
The most general form of the select command is: {\tt select {\it |