| 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} |
| 166 |
< |
The Factory Method pattern is a creational pattern which deals with |
| 167 |
< |
the problem of creating objects without specifying the exact class |
| 168 |
< |
of object that will be created. Factory Method solves this problem |
| 169 |
< |
by defining a separate method for creating the objects, which |
| 170 |
< |
subclasses can then override to specify the derived type of product |
| 171 |
< |
that will be created. |
| 166 |
> |
|
| 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 of a data structure. In |
| 238 |
< |
this way, you can change the operation being performed on a |
| 239 |
< |
structure without the need of changing the classes of the elements |
| 240 |
< |
that you are operating on. |
| 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 |
+ |
|
| 294 |
|
\section{\label{appendixSection:concepts}Concepts} |
| 295 |
|
|
| 296 |
|
OOPSE manipulates both traditional atoms as well as some objects |
| 297 |
|
that {\it behave like atoms}. These objects can be rigid |
| 298 |
|
collections of atoms or atoms which have orientational degrees of |
| 299 |
< |
freedom. Here is a diagram of the class heirarchy: |
| 300 |
< |
|
| 301 |
< |
%\begin{figure} |
| 302 |
< |
%\centering |
| 303 |
< |
%\includegraphics[width=3in]{heirarchy.eps} |
| 304 |
< |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
| 305 |
< |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
| 306 |
< |
%selection syntax allows the user to select any of the objects that |
| 307 |
< |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
| 308 |
< |
%\end{figure} |
| 309 |
< |
|
| 299 |
> |
freedom. A diagram of the class heirarchy is illustrated in |
| 300 |
> |
Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and |
| 301 |
> |
DirectionalAtom in {\sc OOPSE} have their own names which are |
| 302 |
> |
specified in the {\tt .md} file. In contrast, RigidBodies are |
| 303 |
> |
denoted by their membership and index inside a particular molecule: |
| 304 |
> |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
| 305 |
> |
on the specifics of the simulation). The names of rigid bodies are |
| 306 |
> |
generated automatically. For example, the name of the first rigid |
| 307 |
> |
body in a DMPC molecule is DMPC\_RB\_0. |
| 308 |
> |
\begin{figure} |
| 309 |
> |
\centering |
| 310 |
> |
\includegraphics[width=\linewidth]{heirarchy.eps} |
| 311 |
> |
\caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class |
| 312 |
> |
heirarchy of StuntDoubles in {\sc OOPSE}. |
| 313 |
|
\begin{itemize} |
| 314 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
| 315 |
|
integrators and minimizers. |
| 318 |
|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
| 319 |
|
DirectionalAtom}s which behaves as a single unit. |
| 320 |
|
\end{itemize} |
| 321 |
< |
|
| 322 |
< |
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. |
| 321 |
> |
} \label{oopseFig:heirarchy} |
| 322 |
> |
\end{figure} |
| 323 |
|
|
| 324 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
| 325 |
|
|
| 653 |
|
|
| 654 |
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
| 655 |
|
|
| 656 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
| 657 |
< |
be opened by other molecular dynamics viewers such as Jmol and |
| 658 |
< |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
| 659 |
< |
follows: |
| 656 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
| 657 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
| 658 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
| 659 |
> |
as follows: |
| 660 |
|
|
| 661 |
|
|
| 662 |
|
\begin{longtable}[c]{|EFG|} |
| 687 |
|
\end{longtable} |
| 688 |
|
|
| 689 |
|
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
| 690 |
< |
The options available for Hydro are as follows: |
| 690 |
> |
|
| 691 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
| 692 |
> |
center of resistance. Both tensors at the center of diffusion can |
| 693 |
> |
also be reported from the program, as well as the coordinates for |
| 694 |
> |
the beads which are used to approximate the arbitrary shapes. The |
| 695 |
> |
options available for Hydro are as follows: |
| 696 |
|
\begin{longtable}[c]{|EFG|} |
| 697 |
|
\caption{Hydrodynamics Command-line Options} |
| 698 |
|
\\ \hline |
