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)] The declaration of of simple Singleton pattern.},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)] The implementation of simple Singleton pattern.},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 |
+ |
{\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 |
+ |
class IntegratorFactory { |
182 |
+ |
public: |
183 |
+ |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
184 |
+ |
|
185 |
+ |
bool registerIntegrator(IntegratorCreator* creator) { |
186 |
+ |
return creatorMap_.insert(creator->getIdent(), creator).second; |
187 |
+ |
} |
188 |
+ |
|
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 |
+ |
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 |
+ |
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: |
213 |
+ |
string ident_; |
214 |
+ |
}; |
215 |
+ |
|
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 classes of the elements |
233 |
< |
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 |
+ |
|
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} |
270 |
+ |
|
271 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
272 |
+ |
|
273 |
+ |
class StuntDouble { |
274 |
+ |
public: |
275 |
+ |
virtual void accept(BaseVisitor* v) = 0; |
276 |
+ |
}; |
277 |
+ |
|
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} |
330 |
|
|
156 |
– |
\begin{itemize} |
157 |
– |
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
158 |
– |
integrators and minimizers. |
159 |
– |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
160 |
– |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
161 |
– |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
162 |
– |
DirectionalAtom}s which behaves as a single unit. |
163 |
– |
\end{itemize} |
164 |
– |
|
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 |
– |
|
331 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
332 |
|
|
333 |
|
The most general form of the select command is: {\tt select {\it |
660 |
|
|
661 |
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
662 |
|
|
663 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
664 |
< |
be opened by other molecular dynamics viewers such as Jmol and |
665 |
< |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
666 |
< |
follows: |
663 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
664 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
665 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
666 |
> |
as follows: |
667 |
|
|
668 |
|
|
669 |
|
\begin{longtable}[c]{|EFG|} |
694 |
|
\end{longtable} |
695 |
|
|
696 |
|
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
697 |
< |
The options available for Hydro are as follows: |
697 |
> |
|
698 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
699 |
> |
center of resistance. Both tensors at the center of diffusion can |
700 |
> |
also be reported from the program, as well as the coordinates for |
701 |
> |
the beads which are used to approximate the arbitrary shapes. The |
702 |
> |
options available for Hydro are as follows: |
703 |
|
\begin{longtable}[c]{|EFG|} |
704 |
|
\caption{Hydrodynamics Command-line Options} |
705 |
|
\\ \hline |