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 |
|
|
122 |
+ |
The Singleton pattern not only provides a mechanism to restrict |
123 |
+ |
instantiation of a class to one object, but also provides a global |
124 |
+ |
point of access to the object. Currently implemented as a global |
125 |
+ |
variable, the logging utility which reports error and warning |
126 |
+ |
messages to the console in {\sc OOPSE} is a good candidate for |
127 |
+ |
applying the Singleton pattern to avoid the global namespace |
128 |
+ |
pollution.Although the singleton pattern can be implemented in |
129 |
+ |
various ways to account for different aspects of the software |
130 |
+ |
designs, such as lifespan control \textit{etc}, we only use the |
131 |
+ |
static data approach in {\sc OOPSE}. IntegratorFactory class is |
132 |
+ |
declared as |
133 |
+ |
|
134 |
+ |
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
135 |
+ |
|
136 |
+ |
class IntegratorFactory { |
137 |
+ |
public: |
138 |
+ |
static IntegratorFactory* |
139 |
+ |
getInstance(); |
140 |
+ |
protected: |
141 |
+ |
IntegratorFactory(); |
142 |
+ |
private: |
143 |
+ |
static IntegratorFactory* instance_; |
144 |
+ |
}; |
145 |
+ |
|
146 |
+ |
\end{lstlisting} |
147 |
+ |
|
148 |
+ |
The corresponding implementation is |
149 |
+ |
|
150 |
+ |
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] |
151 |
+ |
|
152 |
+ |
IntegratorFactory::instance_ = NULL; |
153 |
+ |
|
154 |
+ |
IntegratorFactory* getInstance() { |
155 |
+ |
if (instance_ == NULL){ |
156 |
+ |
instance_ = new IntegratorFactory; |
157 |
+ |
} |
158 |
+ |
return instance_; |
159 |
+ |
} |
160 |
+ |
|
161 |
+ |
\end{lstlisting} |
162 |
+ |
|
163 |
+ |
Since constructor is declared as protected, a client can not |
164 |
+ |
instantiate IntegratorFactory directly. Moreover, since the member |
165 |
+ |
function getInstance serves as the only entry of access to |
166 |
+ |
IntegratorFactory, this approach fulfills the basic requirement, a |
167 |
+ |
single instance. Another consequence of this approach is the |
168 |
+ |
automatic destruction since static data are destroyed upon program |
169 |
+ |
termination. |
170 |
+ |
|
171 |
|
\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. |
172 |
|
|
173 |
+ |
Categoried as a creational pattern, the Factory Method pattern deals |
174 |
+ |
with the problem of creating objects without specifying the exact |
175 |
+ |
class of object that will be created. Factory Method is typically |
176 |
+ |
implemented by delegating the creation operation to the subclasses. |
177 |
+ |
Parameterized Factory pattern where factory method ( |
178 |
+ |
createIntegrator member function) creates products based on the |
179 |
+ |
identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If |
180 |
+ |
the identifier has been already registered, the factory method will |
181 |
+ |
invoke the corresponding creator (see List.~\ref{integratorCreator}) |
182 |
+ |
which utilizes the modern C++ template technique to avoid excess |
183 |
+ |
subclassing. |
184 |
+ |
|
185 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
186 |
+ |
|
187 |
+ |
class IntegratorFactory { |
188 |
+ |
public: |
189 |
+ |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
190 |
+ |
|
191 |
+ |
bool registerIntegrator(IntegratorCreator* creator) { |
192 |
+ |
return creatorMap_.insert(creator->getIdent(), creator).second; |
193 |
+ |
} |
194 |
+ |
|
195 |
+ |
Integrator* createIntegrator(const string& id, SimInfo* info) { |
196 |
+ |
Integrator* result = NULL; |
197 |
+ |
CreatorMapType::iterator i = creatorMap_.find(id); |
198 |
+ |
if (i != creatorMap_.end()) { |
199 |
+ |
result = (i->second)->create(info); |
200 |
+ |
} |
201 |
+ |
return result; |
202 |
+ |
} |
203 |
+ |
|
204 |
+ |
private: |
205 |
+ |
CreatorMapType creatorMap_; |
206 |
+ |
}; |
207 |
+ |
\end{lstlisting} |
208 |
+ |
|
209 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
210 |
+ |
|
211 |
+ |
class IntegratorCreator { |
212 |
+ |
public: |
213 |
+ |
IntegratorCreator(const string& ident) : ident_(ident) {} |
214 |
+ |
|
215 |
+ |
const string& getIdent() const { return ident_; } |
216 |
+ |
|
217 |
+ |
virtual Integrator* create(SimInfo* info) const = 0; |
218 |
+ |
|
219 |
+ |
private: |
220 |
+ |
string ident_; |
221 |
+ |
}; |
222 |
+ |
|
223 |
+ |
template<class ConcreteIntegrator> |
224 |
+ |
class IntegratorBuilder : public IntegratorCreator { |
225 |
+ |
public: |
226 |
+ |
IntegratorBuilder(const string& ident) |
227 |
+ |
: 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 |
< |
The purpose of the Visitor Pattern is to encapsulate an operation |
236 |
< |
that you want to perform on the elements of a data structure. In |
237 |
< |
this way, you can change the operation being performed on a |
238 |
< |
structure without the need of changing the classes of the elements |
239 |
< |
that you are operating on. |
235 |
> |
|
236 |
> |
The visitor pattern is designed to decouple the data structure and |
237 |
> |
algorithms used upon them by collecting related operation from |
238 |
> |
element classes into other visitor classes, which is equivalent to |
239 |
> |
adding virtual functions into a set of classes without modifying |
240 |
> |
their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
241 |
> |
structure of Visitor pattern which is used extensively in {\tt |
242 |
> |
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
243 |
> |
distinct operations are performed on different StuntDoubles (See the |
244 |
> |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
245 |
> |
in List.~\ref{appendixScheme:element}). Since the hierarchies |
246 |
> |
remains stable, it is easy to define a visit operation (see |
247 |
> |
List.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
248 |
> |
Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
249 |
> |
manages a priority visitor list and handles the execution of every |
250 |
> |
visitor in the priority list on different StuntDoubles. |
251 |
> |
|
252 |
> |
\begin{figure} |
253 |
> |
\centering |
254 |
> |
\includegraphics[width=\linewidth]{visitor.eps} |
255 |
> |
\caption[The UML class diagram of Visitor patten] {The UML class |
256 |
> |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
257 |
> |
\end{figure} |
258 |
> |
|
259 |
> |
\begin{figure} |
260 |
> |
\centering |
261 |
> |
\includegraphics[width=\linewidth]{hierarchy.eps} |
262 |
> |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
263 |
> |
the class hierarchy. } \label{oopseFig:hierarchy} |
264 |
> |
\end{figure} |
265 |
|
|
266 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
267 |
+ |
|
268 |
+ |
class StuntDouble { public: |
269 |
+ |
virtual void accept(BaseVisitor* v) = 0; |
270 |
+ |
}; |
271 |
+ |
|
272 |
+ |
class Atom: public StuntDouble { public: |
273 |
+ |
virtual void accept{BaseVisitor* v*} { |
274 |
+ |
v->visit(this); |
275 |
+ |
} |
276 |
+ |
}; |
277 |
+ |
|
278 |
+ |
class DirectionalAtom: public Atom { public: |
279 |
+ |
virtual void accept{BaseVisitor* v*} { |
280 |
+ |
v->visit(this); |
281 |
+ |
} |
282 |
+ |
}; |
283 |
+ |
|
284 |
+ |
class RigidBody: public StuntDouble { public: |
285 |
+ |
virtual void accept{BaseVisitor* v*} { |
286 |
+ |
v->visit(this); |
287 |
+ |
} |
288 |
+ |
}; |
289 |
+ |
|
290 |
+ |
\end{lstlisting} |
291 |
+ |
|
292 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
293 |
+ |
|
294 |
+ |
class BaseVisitor{ |
295 |
+ |
public: |
296 |
+ |
virtual void visit(Atom* atom); |
297 |
+ |
virtual void visit(DirectionalAtom* datom); |
298 |
+ |
virtual void visit(RigidBody* rb); |
299 |
+ |
}; |
300 |
+ |
|
301 |
+ |
class BaseAtomVisitor:public BaseVisitor{ public: |
302 |
+ |
virtual void visit(Atom* atom); |
303 |
+ |
virtual void visit(DirectionalAtom* datom); |
304 |
+ |
virtual void visit(RigidBody* rb); |
305 |
+ |
}; |
306 |
+ |
|
307 |
+ |
class SSDAtomVisitor:public BaseAtomVisitor{ public: |
308 |
+ |
virtual void visit(Atom* atom); |
309 |
+ |
virtual void visit(DirectionalAtom* datom); |
310 |
+ |
virtual void visit(RigidBody* rb); |
311 |
+ |
}; |
312 |
+ |
|
313 |
+ |
class CompositeVisitor: public BaseVisitor { |
314 |
+ |
public: |
315 |
+ |
|
316 |
+ |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
317 |
+ |
typedef VistorListType::iterator VisitorListIterator; |
318 |
+ |
virtual void visit(Atom* atom) { |
319 |
+ |
VisitorListIterator i; |
320 |
+ |
BaseVisitor* curVisitor; |
321 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
322 |
+ |
atom->accept(*i); |
323 |
+ |
} |
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
virtual void visit(DirectionalAtom* datom) { |
327 |
+ |
VisitorListIterator i; |
328 |
+ |
BaseVisitor* curVisitor; |
329 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
330 |
+ |
atom->accept(*i); |
331 |
+ |
} |
332 |
+ |
} |
333 |
+ |
|
334 |
+ |
virtual void visit(RigidBody* rb) { |
335 |
+ |
VisitorListIterator i; |
336 |
+ |
std::vector<Atom*> myAtoms; |
337 |
+ |
std::vector<Atom*>::iterator ai; |
338 |
+ |
myAtoms = rb->getAtoms(); |
339 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) {{ |
340 |
+ |
rb->accept(*i); |
341 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
342 |
+ |
(*ai)->accept(*i); |
343 |
+ |
} |
344 |
+ |
} |
345 |
+ |
|
346 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
347 |
+ |
|
348 |
+ |
protected: |
349 |
+ |
VistorListType visitorList; |
350 |
+ |
}; |
351 |
+ |
|
352 |
+ |
\end{lstlisting} |
353 |
+ |
|
354 |
|
\section{\label{appendixSection:concepts}Concepts} |
355 |
|
|
356 |
|
OOPSE manipulates both traditional atoms as well as some objects |
357 |
|
that {\it behave like atoms}. These objects can be rigid |
358 |
|
collections of atoms or atoms which have orientational degrees of |
359 |
< |
freedom. Here is a diagram of the class heirarchy: |
360 |
< |
|
361 |
< |
%\begin{figure} |
362 |
< |
%\centering |
363 |
< |
%\includegraphics[width=3in]{heirarchy.eps} |
364 |
< |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
365 |
< |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
366 |
< |
%selection syntax allows the user to select any of the objects that |
367 |
< |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
154 |
< |
%\end{figure} |
155 |
< |
|
359 |
> |
freedom. A diagram of the class hierarchy is illustrated in |
360 |
> |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
361 |
> |
DirectionalAtom in {\sc OOPSE} have their own names which are |
362 |
> |
specified in the {\tt .md} file. In contrast, RigidBodies are |
363 |
> |
denoted by their membership and index inside a particular molecule: |
364 |
> |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
365 |
> |
on the specifics of the simulation). The names of rigid bodies are |
366 |
> |
generated automatically. For example, the name of the first rigid |
367 |
> |
body in a DMPC molecule is DMPC\_RB\_0. |
368 |
|
\begin{itemize} |
369 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
370 |
|
integrators and minimizers. |
374 |
|
DirectionalAtom}s which behaves as a single unit. |
375 |
|
\end{itemize} |
376 |
|
|
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 |
– |
|
377 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
378 |
|
|
379 |
< |
The most general form of the select command is: {\tt select {\it |
380 |
< |
expression}}. This expression represents an arbitrary set of |
177 |
< |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
178 |
< |
composed of either name expressions, index expressions, predefined |
179 |
< |
sets, user-defined expressions, comparison operators, within |
180 |
< |
expressions, or logical combinations of the above expression types. |
181 |
< |
Expressions can be combined using parentheses and the Boolean |
182 |
< |
operators. |
379 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
380 |
> |
StuntDoubles. The most general form of the select command is: |
381 |
|
|
382 |
+ |
{\tt select {\it expression}}. |
383 |
+ |
|
384 |
+ |
This expression represents an arbitrary set of StuntDoubles (Atoms |
385 |
+ |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
386 |
+ |
name expressions, index expressions, predefined sets, user-defined |
387 |
+ |
expressions, comparison operators, within expressions, or logical |
388 |
+ |
combinations of the above expression types. Expressions can be |
389 |
+ |
combined using parentheses and the Boolean operators. |
390 |
+ |
|
391 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
392 |
|
|
393 |
|
The logical operators allow complex queries to be constructed out of |
709 |
|
|
710 |
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
711 |
|
|
712 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
713 |
< |
be opened by other molecular dynamics viewers such as Jmol and |
714 |
< |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
715 |
< |
follows: |
712 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
713 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
714 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
715 |
> |
as follows: |
716 |
|
|
717 |
|
|
718 |
|
\begin{longtable}[c]{|EFG|} |
743 |
|
\end{longtable} |
744 |
|
|
745 |
|
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
746 |
< |
The options available for Hydro are as follows: |
746 |
> |
|
747 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
748 |
> |
center of resistance. Both tensors at the center of diffusion can |
749 |
> |
also be reported from the program, as well as the coordinates for |
750 |
> |
the beads which are used to approximate the arbitrary shapes. The |
751 |
> |
options available for Hydro are as follows: |
752 |
|
\begin{longtable}[c]{|EFG|} |
753 |
|
\caption{Hydrodynamics Command-line Options} |
754 |
|
\\ \hline |