118 |
|
OOPSE}. |
119 |
|
|
120 |
|
\subsection{\label{appendixSection:singleton}Singleton} |
121 |
< |
The Singleton pattern ensures that only one instance of a class is |
122 |
< |
created. All objects that use an instance of that class use the same |
123 |
< |
instance. |
121 |
> |
The Singleton pattern not only provides a mechanism to restrict |
122 |
> |
instantiation of a class to one object, but also provides a global |
123 |
> |
point of access to the object. Currently implemented as a global |
124 |
> |
variable, the logging utility which reports error and warning |
125 |
> |
messages to the console in {\sc OOPSE} is a good candidate for |
126 |
> |
applying the Singleton pattern to avoid the global namespace |
127 |
> |
pollution.Although the singleton pattern can be implemented in |
128 |
> |
various ways to account for different aspects of the software |
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}] |
133 |
|
|
134 |
+ |
class IntegratorFactory { |
135 |
+ |
public: |
136 |
+ |
static IntegratorFactory* getInstance(); |
137 |
+ |
protected: |
138 |
+ |
IntegratorFactory(); |
139 |
+ |
private: |
140 |
+ |
static IntegratorFactory* instance_; |
141 |
+ |
}; |
142 |
+ |
|
143 |
+ |
\end{lstlisting} |
144 |
+ |
The corresponding implementation is |
145 |
+ |
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}] |
146 |
+ |
|
147 |
+ |
IntegratorFactory::instance_ = NULL; |
148 |
+ |
|
149 |
+ |
IntegratorFactory* getInstance() { |
150 |
+ |
if (instance_ == NULL){ |
151 |
+ |
instance_ = new IntegratorFactory; |
152 |
+ |
} |
153 |
+ |
return instance_; |
154 |
+ |
} |
155 |
+ |
|
156 |
+ |
\end{lstlisting} |
157 |
+ |
Since constructor is declared as {\tt protected}, a client can not |
158 |
+ |
instantiate {\tt IntegratorFactory} directly. Moreover, since the |
159 |
+ |
member function {\tt getInstance} serves as the only entry of access |
160 |
+ |
to {\tt IntegratorFactory}, this approach fulfills the basic |
161 |
+ |
requirement, a single instance. Another consequence of this approach |
162 |
+ |
is the automatic destruction since static data are destroyed upon |
163 |
+ |
program termination. |
164 |
+ |
|
165 |
|
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
126 |
– |
The Factory Method pattern is a creational pattern which deals with |
127 |
– |
the problem of creating objects without specifying the exact class |
128 |
– |
of object that will be created. Factory Method solves this problem |
129 |
– |
by defining a separate method for creating the objects, which |
130 |
– |
subclasses can then override to specify the derived type of product |
131 |
– |
that will be created. |
166 |
|
|
167 |
< |
\subsection{\label{appendixSection:visitorPattern}Visitor} |
168 |
< |
The purpose of the Visitor Pattern is to encapsulate an operation |
169 |
< |
that you want to perform on the elements of a data structure. In |
170 |
< |
this way, you can change the operation being performed on a |
171 |
< |
structure without the need of changing the classes of the elements |
172 |
< |
that you are operating on. |
167 |
> |
Categoried as a creational pattern, the Factory Method pattern deals |
168 |
> |
with the problem of creating objects without specifying the exact |
169 |
> |
class of object that will be created. Factory Method is typically |
170 |
> |
implemented by delegating the creation operation to the subclasses. |
171 |
> |
|
172 |
> |
Registers a creator with a type identifier. Looks up the type |
173 |
> |
identifier in the internal map. If it is found, it invokes the |
174 |
> |
corresponding creator for the type identifier and returns its |
175 |
> |
result. |
176 |
> |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}] |
177 |
> |
|
178 |
> |
class IntegratorFactory { |
179 |
> |
public: |
180 |
> |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
181 |
> |
|
182 |
> |
bool registerIntegrator(IntegratorCreator* creator); |
183 |
> |
|
184 |
> |
Integrator* createIntegrator(const string& id, SimInfo* info); |
185 |
> |
|
186 |
> |
private: |
187 |
> |
CreatorMapType creatorMap_; |
188 |
> |
}; |
189 |
> |
|
190 |
> |
\end{lstlisting} |
191 |
> |
|
192 |
> |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}] |
193 |
> |
|
194 |
> |
bool IntegratorFactory::unregisterIntegrator(const string& id) { |
195 |
> |
return creatorMap_.erase(id) == 1; |
196 |
> |
} |
197 |
> |
|
198 |
> |
Integrator* IntegratorFactory::createIntegrator(const string& id, |
199 |
> |
SimInfo* info) { |
200 |
> |
CreatorMapType::iterator i = creatorMap_.find(id); |
201 |
> |
if (i != creatorMap_.end()) { |
202 |
> |
return (i->second)->create(info); |
203 |
> |
} else { |
204 |
> |
return NULL; |
205 |
> |
} |
206 |
> |
} |
207 |
> |
|
208 |
> |
\end{lstlisting} |
209 |
> |
|
210 |
> |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}] |
211 |
> |
|
212 |
> |
class IntegratorCreator { |
213 |
> |
public: |
214 |
> |
IntegratorCreator(const string& ident) : ident_(ident) {} |
215 |
> |
|
216 |
> |
const string& getIdent() const { return ident_; } |
217 |
> |
|
218 |
> |
virtual Integrator* create(SimInfo* info) const = 0; |
219 |
> |
|
220 |
> |
private: |
221 |
> |
string ident_; |
222 |
> |
}; |
223 |
> |
|
224 |
> |
template<class ConcreteIntegrator> |
225 |
> |
class IntegratorBuilder : public IntegratorCreator { |
226 |
> |
public: |
227 |
> |
IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {} |
228 |
> |
virtual Integrator* create(SimInfo* info) const { |
229 |
> |
return new ConcreteIntegrator(info); |
230 |
> |
} |
231 |
> |
}; |
232 |
> |
\end{lstlisting} |
233 |
|
|
234 |
+ |
\subsection{\label{appendixSection:visitorPattern}Visitor} |
235 |
+ |
|
236 |
+ |
The purpose of the Visitor Pattern is to encapsulate an operation |
237 |
+ |
that you want to perform on the elements. The operation being |
238 |
+ |
performed on a structure can be switched without changing the |
239 |
+ |
interfaces of the elements. In other words, one can add virtual |
240 |
+ |
functions into a set of classes without modifying their interfaces. |
241 |
+ |
The UML class diagram of Visitor patten is shown in |
242 |
+ |
Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
243 |
+ |
Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
244 |
+ |
extensively. |
245 |
+ |
|
246 |
+ |
\begin{figure} |
247 |
+ |
\centering |
248 |
+ |
\includegraphics[width=\linewidth]{visitor.eps} |
249 |
+ |
\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
250 |
+ |
of {\sc OOPSE}} \label{appendixFig:visitorUML} |
251 |
+ |
\end{figure} |
252 |
+ |
|
253 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
254 |
+ |
|
255 |
+ |
class BaseVisitor{ |
256 |
+ |
public: |
257 |
+ |
virtual void visit(Atom* atom); |
258 |
+ |
virtual void visit(DirectionalAtom* datom); |
259 |
+ |
virtual void visit(RigidBody* rb); |
260 |
+ |
}; |
261 |
+ |
|
262 |
+ |
\end{lstlisting} |
263 |
+ |
|
264 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
265 |
+ |
|
266 |
+ |
class StuntDouble { |
267 |
+ |
public: |
268 |
+ |
virtual void accept(BaseVisitor* v) = 0; |
269 |
+ |
}; |
270 |
+ |
|
271 |
+ |
class Atom: public StuntDouble { |
272 |
+ |
public: |
273 |
+ |
virtual void accept{BaseVisitor* v*} { |
274 |
+ |
v->visit(this); |
275 |
+ |
} |
276 |
+ |
}; |
277 |
+ |
|
278 |
+ |
class DirectionalAtom: public Atom { |
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*} { |
288 |
+ |
v->visit(this); |
289 |
+ |
} |
290 |
+ |
}; |
291 |
+ |
|
292 |
+ |
\end{lstlisting} |
293 |
|
\section{\label{appendixSection:concepts}Concepts} |
294 |
+ |
|
295 |
+ |
\begin{figure} |
296 |
+ |
\centering |
297 |
+ |
\includegraphics[width=\linewidth]{heirarchy.eps} |
298 |
+ |
\caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class |
299 |
+ |
heirarchy of StuntDoubles in {\sc OOPSE}.} |
300 |
+ |
\label{oopseFig:heirarchy} |
301 |
+ |
\end{figure} |
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: |
306 |
> |
freedom. A diagram of the class heirarchy is illustrated in |
307 |
> |
Fig.~\ref{oopseFig:heirarchy}. |
308 |
|
|
147 |
– |
%\begin{figure} |
148 |
– |
%\centering |
149 |
– |
%\includegraphics[width=3in]{heirarchy.eps} |
150 |
– |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
151 |
– |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
152 |
– |
%selection syntax allows the user to select any of the objects that |
153 |
– |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
154 |
– |
%\end{figure} |
309 |
|
|
310 |
|
\begin{itemize} |
311 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
531 |
|
\centering |
532 |
|
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
533 |
|
\caption[A representation of the three-stage correlations in |
534 |
< |
\texttt{StaticProps}]{Three-stage processing in |
535 |
< |
\texttt{StaticProps}. $S_1$ and $S_2$ are the numbers of selected |
536 |
< |
stuntdobules from {\tt -{}-sele1} and {\tt -{}-sele2} respectively, |
537 |
< |
while $C$ is the number of stuntdobules appearing at both sets. The |
538 |
< |
first stage($S_1-C$ and $S_2$) and second stages ($S_1$ and $S_2-C$) |
539 |
< |
are completely non-overlapping. On the contrary, the third stage($C$ |
540 |
< |
and $C$) are completely overlapping} |
541 |
< |
\label{oopseFig:staticPropsProcess} |
534 |
> |
\texttt{StaticProps}]{This diagram illustrates three-stage |
535 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
536 |
> |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
537 |
> |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
538 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
539 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
540 |
> |
the contrary, the third stage($C$ and $C$) are completely |
541 |
> |
overlapping} \label{oopseFig:staticPropsProcess} |
542 |
|
\end{figure} |
543 |
|
|
544 |
|
The options available for {\tt StaticProps} are as follows: |
616 |
|
incremented and the process repeated until the end of the |
617 |
|
trajectory. Once the end is reached, the first block is freed then |
618 |
|
incremented, until all frame pairs have been correlated in time. |
619 |
+ |
This process is illustrated in |
620 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
621 |
|
|
622 |
+ |
\begin{figure} |
623 |
+ |
\centering |
624 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
625 |
+ |
\caption[A representation of the block correlations in |
626 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
627 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
628 |
+ |
the self correlation of the block, and the open blocks are read one |
629 |
+ |
at a time and the cross correlations between blocks are calculated.} |
630 |
+ |
\label{oopseFig:dynamicPropsProcess} |
631 |
+ |
\end{figure} |
632 |
+ |
|
633 |
|
The options available for DynamicProps are as follows: |
634 |
|
\begin{longtable}[c]{|EFG|} |
635 |
|
\caption{DynamicProps Command-line Options} |
656 |
|
|
657 |
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
658 |
|
|
659 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
660 |
< |
be opened by other molecular dynamics viewers such as Jmol and |
661 |
< |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
662 |
< |
follows: |
659 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
660 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
661 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
662 |
> |
as follows: |
663 |
|
|
664 |
|
|
665 |
|
\begin{longtable}[c]{|EFG|} |
690 |
|
\end{longtable} |
691 |
|
|
692 |
|
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
693 |
< |
The options available for Hydro are as follows: |
693 |
> |
|
694 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
695 |
> |
center of resistance. Both tensors at the center of diffusion can |
696 |
> |
also be reported from the program, as well as the coordinates for |
697 |
> |
the beads which are used to approximate the arbitrary shapes. The |
698 |
> |
options available for Hydro are as follows: |
699 |
|
\begin{longtable}[c]{|EFG|} |
700 |
|
\caption{Hydrodynamics Command-line Options} |
701 |
|
\\ \hline |