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* |
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}] |
147 |
+ |
|
148 |
+ |
IntegratorFactory::instance_ = NULL; |
149 |
+ |
|
150 |
+ |
IntegratorFactory* getInstance() { |
151 |
+ |
if (instance_ == NULL){ |
152 |
+ |
instance_ = new IntegratorFactory; |
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 |
160 |
+ |
member function {\tt getInstance} serves as the only entry of access |
161 |
+ |
to {\tt IntegratorFactory}, this approach fulfills the basic |
162 |
+ |
requirement, a single instance. Another consequence of this approach |
163 |
+ |
is the automatic destruction since static data are destroyed upon |
164 |
+ |
program termination. |
165 |
+ |
|
166 |
|
\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. |
167 |
|
|
168 |
+ |
Categoried as a creational pattern, the Factory Method pattern deals |
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 |
+ |
|
173 |
+ |
Registers a creator with a type identifier. Looks up the type |
174 |
+ |
identifier in the internal map. If it is found, it invokes the |
175 |
+ |
corresponding creator for the type identifier and returns its |
176 |
+ |
result. |
177 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}] |
178 |
+ |
|
179 |
+ |
class IntegratorFactory { |
180 |
+ |
public: |
181 |
+ |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
182 |
+ |
|
183 |
+ |
bool registerIntegrator(IntegratorCreator* creator) { |
184 |
+ |
return creatorMap_.insert(creator->getIdent(), creator).second; |
185 |
+ |
} |
186 |
+ |
|
187 |
+ |
Integrator* createIntegrator(const string& id, SimInfo* info) { |
188 |
+ |
Integrator* result = NULL; |
189 |
+ |
CreatorMapType::iterator i = creatorMap_.find(id); |
190 |
+ |
if (i != creatorMap_.end()) { |
191 |
+ |
result = (i->second)->create(info); |
192 |
+ |
} |
193 |
+ |
return result; |
194 |
+ |
} |
195 |
+ |
|
196 |
+ |
private: |
197 |
+ |
CreatorMapType creatorMap_; |
198 |
+ |
}; |
199 |
+ |
\end{lstlisting} |
200 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)]Souce code of creator classes.},label={appendixScheme:integratorCreator}] |
201 |
+ |
|
202 |
+ |
class IntegratorCreator { |
203 |
+ |
public: |
204 |
+ |
IntegratorCreator(const string& ident) : ident_(ident) {} |
205 |
+ |
|
206 |
+ |
const string& getIdent() const { return ident_; } |
207 |
+ |
|
208 |
+ |
virtual Integrator* create(SimInfo* info) const = 0; |
209 |
+ |
|
210 |
+ |
private: |
211 |
+ |
string ident_; |
212 |
+ |
}; |
213 |
+ |
|
214 |
+ |
template<class ConcreteIntegrator> class IntegratorBuilder : public |
215 |
+ |
IntegratorCreator { |
216 |
+ |
public: |
217 |
+ |
IntegratorBuilder(const string& ident) |
218 |
+ |
: IntegratorCreator(ident) {} |
219 |
+ |
virtual Integrator* create(SimInfo* info) const { |
220 |
+ |
return new ConcreteIntegrator(info); |
221 |
+ |
} |
222 |
+ |
}; |
223 |
+ |
\end{lstlisting} |
224 |
+ |
|
225 |
|
\subsection{\label{appendixSection:visitorPattern}Visitor} |
226 |
+ |
|
227 |
|
The purpose of the Visitor Pattern is to encapsulate an operation |
228 |
< |
that you want to perform on the elements of a data structure. In |
229 |
< |
this way, you can change the operation being performed on a |
230 |
< |
structure without the need of changing the classes of the elements |
231 |
< |
that you are operating on. |
228 |
> |
that you want to perform on the elements. The operation being |
229 |
> |
performed on a structure can be switched without changing the |
230 |
> |
interfaces of the elements. In other words, one can add virtual |
231 |
> |
functions into a set of classes without modifying their interfaces. |
232 |
> |
The UML class diagram of Visitor patten is shown in |
233 |
> |
Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
234 |
> |
Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
235 |
> |
extensively. |
236 |
> |
|
237 |
> |
\begin{figure} |
238 |
> |
\centering |
239 |
> |
\includegraphics[width=\linewidth]{visitor.eps} |
240 |
> |
\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
241 |
> |
of {\sc OOPSE}} \label{appendixFig:visitorUML} |
242 |
> |
\end{figure} |
243 |
|
|
244 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
245 |
+ |
|
246 |
+ |
class BaseVisitor{ |
247 |
+ |
public: |
248 |
+ |
virtual void visit(Atom* atom); |
249 |
+ |
virtual void visit(DirectionalAtom* datom); |
250 |
+ |
virtual void visit(RigidBody* rb); |
251 |
+ |
}; |
252 |
+ |
|
253 |
+ |
\end{lstlisting} |
254 |
+ |
|
255 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
256 |
+ |
|
257 |
+ |
class StuntDouble { |
258 |
+ |
public: |
259 |
+ |
virtual void accept(BaseVisitor* v) = 0; |
260 |
+ |
}; |
261 |
+ |
|
262 |
+ |
class Atom: public StuntDouble { |
263 |
+ |
public: |
264 |
+ |
virtual void accept{BaseVisitor* v*} { |
265 |
+ |
v->visit(this); |
266 |
+ |
} |
267 |
+ |
}; |
268 |
+ |
|
269 |
+ |
class DirectionalAtom: public Atom { |
270 |
+ |
public: |
271 |
+ |
virtual void accept{BaseVisitor* v*} { |
272 |
+ |
v->visit(this); |
273 |
+ |
} |
274 |
+ |
}; |
275 |
+ |
|
276 |
+ |
class RigidBody: public StuntDouble { |
277 |
+ |
public: |
278 |
+ |
virtual void accept{BaseVisitor* v*} { |
279 |
+ |
v->visit(this); |
280 |
+ |
} |
281 |
+ |
}; |
282 |
+ |
|
283 |
+ |
\end{lstlisting} |
284 |
+ |
|
285 |
|
\section{\label{appendixSection:concepts}Concepts} |
286 |
|
|
287 |
|
OOPSE manipulates both traditional atoms as well as some objects |
288 |
|
that {\it behave like atoms}. These objects can be rigid |
289 |
|
collections of atoms or atoms which have orientational degrees of |
290 |
< |
freedom. Here is a diagram of the class heirarchy: |
291 |
< |
|
292 |
< |
%\begin{figure} |
293 |
< |
%\centering |
294 |
< |
%\includegraphics[width=3in]{heirarchy.eps} |
295 |
< |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
296 |
< |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
297 |
< |
%selection syntax allows the user to select any of the objects that |
298 |
< |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
299 |
< |
%\end{figure} |
300 |
< |
|
290 |
> |
freedom. A diagram of the class heirarchy is illustrated in |
291 |
> |
Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and |
292 |
> |
DirectionalAtom in {\sc OOPSE} have their own names which are |
293 |
> |
specified in the {\tt .md} file. In contrast, RigidBodies are |
294 |
> |
denoted by their membership and index inside a particular molecule: |
295 |
> |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
296 |
> |
on the specifics of the simulation). The names of rigid bodies are |
297 |
> |
generated automatically. For example, the name of the first rigid |
298 |
> |
body in a DMPC molecule is DMPC\_RB\_0. |
299 |
> |
\begin{figure} |
300 |
> |
\centering |
301 |
> |
\includegraphics[width=\linewidth]{heirarchy.eps} |
302 |
> |
\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of |
303 |
> |
the class heirarchy. |
304 |
|
\begin{itemize} |
305 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
306 |
|
integrators and minimizers. |
309 |
|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
310 |
|
DirectionalAtom}s which behaves as a single unit. |
311 |
|
\end{itemize} |
312 |
+ |
} \label{oopseFig:heirarchy} |
313 |
+ |
\end{figure} |
314 |
|
|
165 |
– |
Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
166 |
– |
own names which are specified in the {\tt .md} file. In contrast, |
167 |
– |
RigidBodies are denoted by their membership and index inside a |
168 |
– |
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
169 |
– |
inside the brackets depend on the specifics of the simulation). The |
170 |
– |
names of rigid bodies are generated automatically. For example, the |
171 |
– |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
172 |
– |
|
315 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
316 |
|
|
317 |
|
The most general form of the select command is: {\tt select {\it |
519 |
|
\centering |
520 |
|
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
521 |
|
\caption[A representation of the three-stage correlations in |
522 |
< |
\texttt{StaticProps}]{Three-stage processing in |
523 |
< |
\texttt{StaticProps}. $S_1$ and $S_2$ are the numbers of selected |
524 |
< |
stuntdobules from {\tt -{}-sele1} and {\tt -{}-sele2} respectively, |
525 |
< |
while $C$ is the number of stuntdobules appearing at both sets. The |
526 |
< |
first stage($S_1-C$ and $S_2$) and second stages ($S_1$ and $S_2-C$) |
527 |
< |
are completely non-overlapping. On the contrary, the third stage($C$ |
528 |
< |
and $C$) are completely overlapping} |
529 |
< |
\label{oopseFig:staticPropsProcess} |
522 |
> |
\texttt{StaticProps}]{This diagram illustrates three-stage |
523 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
524 |
> |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
525 |
> |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
526 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
527 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
528 |
> |
the contrary, the third stage($C$ and $C$) are completely |
529 |
> |
overlapping} \label{oopseFig:staticPropsProcess} |
530 |
|
\end{figure} |
531 |
|
|
532 |
|
The options available for {\tt StaticProps} are as follows: |
604 |
|
incremented and the process repeated until the end of the |
605 |
|
trajectory. Once the end is reached, the first block is freed then |
606 |
|
incremented, until all frame pairs have been correlated in time. |
607 |
+ |
This process is illustrated in |
608 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
609 |
|
|
610 |
+ |
\begin{figure} |
611 |
+ |
\centering |
612 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
613 |
+ |
\caption[A representation of the block correlations in |
614 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
615 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
616 |
+ |
the self correlation of the block, and the open blocks are read one |
617 |
+ |
at a time and the cross correlations between blocks are calculated.} |
618 |
+ |
\label{oopseFig:dynamicPropsProcess} |
619 |
+ |
\end{figure} |
620 |
+ |
|
621 |
|
The options available for DynamicProps are as follows: |
622 |
|
\begin{longtable}[c]{|EFG|} |
623 |
|
\caption{DynamicProps Command-line Options} |
644 |
|
|
645 |
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
646 |
|
|
647 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
648 |
< |
be opened by other molecular dynamics viewers such as Jmol and |
649 |
< |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
650 |
< |
follows: |
647 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
648 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
649 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
650 |
> |
as follows: |
651 |
|
|
652 |
|
|
653 |
|
\begin{longtable}[c]{|EFG|} |
678 |
|
\end{longtable} |
679 |
|
|
680 |
|
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
681 |
< |
The options available for Hydro are as follows: |
681 |
> |
|
682 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
683 |
> |
center of resistance. Both tensors at the center of diffusion can |
684 |
> |
also be reported from the program, as well as the coordinates for |
685 |
> |
the beads which are used to approximate the arbitrary shapes. The |
686 |
> |
options available for Hydro are as follows: |
687 |
|
\begin{longtable}[c]{|EFG|} |
688 |
|
\caption{Hydrodynamics Command-line Options} |
689 |
|
\\ \hline |