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} |
134 |
– |
The purpose of the Visitor Pattern is to encapsulate an operation |
135 |
– |
that you want to perform on the elements of a data structure. In |
136 |
– |
this way, you can change the operation being performed on a |
137 |
– |
structure without the need of changing the classes of the elements |
138 |
– |
that you are operating on. |
235 |
|
|
236 |
< |
\section{\label{appendixSection:concepts}Concepts} |
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 |
< |
OOPSE manipulates both traditional atoms as well as some objects |
253 |
< |
that {\it behave like atoms}. These objects can be rigid |
254 |
< |
collections of atoms or atoms which have orientational degrees of |
255 |
< |
freedom. Here is a diagram of the class heirarchy: |
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=3in]{heirarchy.eps} |
262 |
< |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
263 |
< |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
264 |
< |
%selection syntax allows the user to select any of the objects that |
265 |
< |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
261 |
> |
%\includegraphics[width=\linewidth]{hierarchy.eps} |
262 |
> |
%\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
263 |
> |
%the class hierarchy. |
264 |
> |
%\begin{itemize} |
265 |
> |
%\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
266 |
> |
%integrators and minimizers. |
267 |
> |
%\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
268 |
> |
%\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
269 |
> |
%\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
270 |
> |
%DirectionalAtom}s which behaves as a single unit. |
271 |
> |
%\end{itemize} |
272 |
> |
%} \label{oopseFig:hierarchy} |
273 |
|
%\end{figure} |
274 |
|
|
275 |
< |
\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} |
275 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
276 |
|
|
277 |
< |
Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
278 |
< |
own names which are specified in the {\tt .md} file. In contrast, |
279 |
< |
RigidBodies are denoted by their membership and index inside a |
280 |
< |
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
281 |
< |
inside the brackets depend on the specifics of the simulation). The |
282 |
< |
names of rigid bodies are generated automatically. For example, the |
283 |
< |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
277 |
> |
class StuntDouble { public: |
278 |
> |
virtual void accept(BaseVisitor* v) = 0; |
279 |
> |
}; |
280 |
> |
|
281 |
> |
class Atom: public StuntDouble { public: |
282 |
> |
virtual void accept{BaseVisitor* v*} { |
283 |
> |
v->visit(this); |
284 |
> |
} |
285 |
> |
}; |
286 |
> |
|
287 |
> |
class DirectionalAtom: public Atom { public: |
288 |
> |
virtual void accept{BaseVisitor* v*} { |
289 |
> |
v->visit(this); |
290 |
> |
} |
291 |
> |
}; |
292 |
> |
|
293 |
> |
class RigidBody: public StuntDouble { public: |
294 |
> |
virtual void accept{BaseVisitor* v*} { |
295 |
> |
v->visit(this); |
296 |
> |
} |
297 |
> |
}; |
298 |
> |
|
299 |
> |
\end{lstlisting} |
300 |
> |
|
301 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
302 |
> |
|
303 |
> |
class BaseVisitor{ |
304 |
> |
public: |
305 |
> |
virtual void visit(Atom* atom); |
306 |
> |
virtual void visit(DirectionalAtom* datom); |
307 |
> |
virtual void visit(RigidBody* rb); |
308 |
> |
}; |
309 |
> |
|
310 |
> |
class BaseAtomVisitor:public BaseVisitor{ public: |
311 |
> |
virtual void visit(Atom* atom); |
312 |
> |
virtual void visit(DirectionalAtom* datom); |
313 |
> |
virtual void visit(RigidBody* rb); |
314 |
> |
}; |
315 |
> |
|
316 |
> |
class SSDAtomVisitor:public BaseAtomVisitor{ public: |
317 |
> |
virtual void visit(Atom* atom); |
318 |
> |
virtual void visit(DirectionalAtom* datom); |
319 |
> |
virtual void visit(RigidBody* rb); |
320 |
> |
}; |
321 |
> |
|
322 |
> |
class CompositeVisitor: public BaseVisitor { |
323 |
> |
public: |
324 |
> |
|
325 |
> |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
326 |
> |
typedef VistorListType::iterator VisitorListIterator; |
327 |
> |
virtual void visit(Atom* atom) { |
328 |
> |
VisitorListIterator i; |
329 |
> |
BaseVisitor* curVisitor; |
330 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) { |
331 |
> |
atom->accept(*i); |
332 |
> |
} |
333 |
> |
} |
334 |
> |
|
335 |
> |
virtual void visit(DirectionalAtom* datom) { |
336 |
> |
VisitorListIterator i; |
337 |
> |
BaseVisitor* curVisitor; |
338 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) { |
339 |
> |
atom->accept(*i); |
340 |
> |
} |
341 |
> |
} |
342 |
|
|
343 |
+ |
virtual void visit(RigidBody* rb) { |
344 |
+ |
VisitorListIterator i; |
345 |
+ |
std::vector<Atom*> myAtoms; |
346 |
+ |
std::vector<Atom*>::iterator ai; |
347 |
+ |
myAtoms = rb->getAtoms(); |
348 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) {{ |
349 |
+ |
rb->accept(*i); |
350 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
351 |
+ |
(*ai)->accept(*i); |
352 |
+ |
} |
353 |
+ |
} |
354 |
+ |
|
355 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
356 |
+ |
|
357 |
+ |
protected: |
358 |
+ |
VistorListType visitorList; |
359 |
+ |
}; |
360 |
+ |
|
361 |
+ |
\end{lstlisting} |
362 |
+ |
|
363 |
+ |
\section{\label{appendixSection:concepts}Concepts} |
364 |
+ |
|
365 |
+ |
OOPSE manipulates both traditional atoms as well as some objects |
366 |
+ |
that {\it behave like atoms}. These objects can be rigid |
367 |
+ |
collections of atoms or atoms which have orientational degrees of |
368 |
+ |
freedom. A diagram of the class hierarchy is illustrated in |
369 |
+ |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
370 |
+ |
DirectionalAtom in {\sc OOPSE} have their own names which are |
371 |
+ |
specified in the {\tt .md} file. In contrast, RigidBodies are |
372 |
+ |
denoted by their membership and index inside a particular molecule: |
373 |
+ |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
374 |
+ |
on the specifics of the simulation). The names of rigid bodies are |
375 |
+ |
generated automatically. For example, the name of the first rigid |
376 |
+ |
body in a DMPC molecule is DMPC\_RB\_0. |
377 |
+ |
|
378 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
379 |
|
|
380 |
|
The most general form of the select command is: {\tt select {\it |
582 |
|
\centering |
583 |
|
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
584 |
|
\caption[A representation of the three-stage correlations in |
585 |
< |
\texttt{StaticProps}]{Three-stage processing in |
586 |
< |
\texttt{StaticProps}. $S_1$ and $S_2$ are the numbers of selected |
587 |
< |
stuntdobules from {\tt -{}-sele1} and {\tt -{}-sele2} respectively, |
588 |
< |
while $C$ is the number of stuntdobules appearing at both sets. The |
589 |
< |
first stage($S_1-C$ and $S_2$) and second stages ($S_1$ and $S_2-C$) |
590 |
< |
are completely non-overlapping. On the contrary, the third stage($C$ |
591 |
< |
and $C$) are completely overlapping} |
592 |
< |
\label{oopseFig:staticPropsProcess} |
585 |
> |
\texttt{StaticProps}]{This diagram illustrates three-stage |
586 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
587 |
> |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
588 |
> |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
589 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
590 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
591 |
> |
the contrary, the third stage($C$ and $C$) are completely |
592 |
> |
overlapping} \label{oopseFig:staticPropsProcess} |
593 |
|
\end{figure} |
594 |
|
|
595 |
|
The options available for {\tt StaticProps} are as follows: |
667 |
|
incremented and the process repeated until the end of the |
668 |
|
trajectory. Once the end is reached, the first block is freed then |
669 |
|
incremented, until all frame pairs have been correlated in time. |
670 |
+ |
This process is illustrated in |
671 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
672 |
|
|
673 |
+ |
\begin{figure} |
674 |
+ |
\centering |
675 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
676 |
+ |
\caption[A representation of the block correlations in |
677 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
678 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
679 |
+ |
the self correlation of the block, and the open blocks are read one |
680 |
+ |
at a time and the cross correlations between blocks are calculated.} |
681 |
+ |
\label{oopseFig:dynamicPropsProcess} |
682 |
+ |
\end{figure} |
683 |
+ |
|
684 |
|
The options available for DynamicProps are as follows: |
685 |
|
\begin{longtable}[c]{|EFG|} |
686 |
|
\caption{DynamicProps Command-line Options} |
707 |
|
|
708 |
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
709 |
|
|
710 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
711 |
< |
be opened by other molecular dynamics viewers such as Jmol and |
712 |
< |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
713 |
< |
follows: |
710 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
711 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
712 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
713 |
> |
as follows: |
714 |
|
|
715 |
|
|
716 |
|
\begin{longtable}[c]{|EFG|} |
741 |
|
\end{longtable} |
742 |
|
|
743 |
|
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
744 |
< |
The options available for Hydro are as follows: |
744 |
> |
|
745 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
746 |
> |
center of resistance. Both tensors at the center of diffusion can |
747 |
> |
also be reported from the program, as well as the coordinates for |
748 |
> |
the beads which are used to approximate the arbitrary shapes. The |
749 |
> |
options available for Hydro are as follows: |
750 |
|
\begin{longtable}[c]{|EFG|} |
751 |
|
\caption{Hydrodynamics Command-line Options} |
752 |
|
\\ \hline |