3 |
|
|
4 |
|
The absence of modern software development practices has been a |
5 |
|
bottleneck limiting progress in the Scientific Computing |
6 |
< |
community\cite{Wilson2006}. In the last 20 years , a large number of |
7 |
< |
few MD packages\cite{Brooks1983, Vincent1995, Kale1999} were |
6 |
> |
community. In the last 20 years, a large number of |
7 |
> |
MD packages\cite{Brooks1983, Vincent1995, Kale1999} were |
8 |
|
developed to solve common MD problems and perform robust simulations |
9 |
|
. Most of these are commercial programs that are either poorly |
10 |
|
written or extremely complicated to use correctly. This situation |
17 |
|
\begin{enumerate} |
18 |
|
\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
19 |
|
atom types (transition metals, point dipoles, sticky potentials, |
20 |
< |
Gay-Berne ellipsoids, or other "lumpy"atoms with orientational |
20 |
> |
Gay-Berne ellipsoids, or other "lumpy" atoms with orientational |
21 |
|
degrees of freedom), as well as rigid bodies. |
22 |
|
\item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap |
23 |
|
Beowulf clusters to obtain very efficient parallelism. |
35 |
|
|
36 |
|
Mainly written by C++ and Fortran90, {\sc OOPSE} uses C++ Standard |
37 |
|
Template Library (STL) and fortran modules as a foundation. As an |
38 |
< |
extensive set of the STL and Fortran90 modules, {\sc Base Classes} |
39 |
< |
provide generic implementations of mathematical objects (e.g., |
40 |
< |
matrices, vectors, polynomials, random number generators) and |
38 |
> |
extensive set of the STL and Fortran90 modules, the {\sc Base |
39 |
> |
Classes} provide generic implementations of mathematical objects |
40 |
> |
(e.g., matrices, vectors, polynomials, random number generators) and |
41 |
|
advanced data structures and algorithms(e.g., tuple, bitset, generic |
42 |
|
data and string manipulation). The molecular data structures for the |
43 |
|
representation of atoms, bonds, bends, torsions, rigid bodies and |
52 |
|
meta-data files, which has been implemented using the ANother Tool |
53 |
|
for Language Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. |
54 |
|
The Molecular Mechanics module consists of energy minimization and a |
55 |
< |
wide varieties of integration methods(see |
55 |
> |
wide variety of integration methods(see |
56 |
|
Chap.~\ref{chapt:methodology}). The structure module contains a |
57 |
|
flexible and powerful selection library which syntax is elaborated |
58 |
|
in Sec.~\ref{appendixSection:syntax}. The top layer is made of the |
59 |
|
main program of the package, \texttt{oopse} and it corresponding |
60 |
|
parallel version \texttt{oopse\_MPI}, as well as other useful |
61 |
< |
utilities, such as \texttt{StatProps} (see |
61 |
> |
utilities, such as \texttt{StaticProps} (see |
62 |
|
Sec.~\ref{appendixSection:StaticProps}), \texttt{DynamicProps} (see |
63 |
|
Sec.~\ref{appendixSection:DynamicProps}), \texttt{Dump2XYZ} (see |
64 |
|
Sec.~\ref{appendixSection:Dump2XYZ}), \texttt{Hydro} (see |
74 |
|
\section{\label{appendixSection:desginPattern}Design Patterns} |
75 |
|
|
76 |
|
Design patterns are optimal solutions to commonly-occurring problems |
77 |
< |
in software design. Although originated as an architectural concept |
78 |
< |
for buildings and towns by Christopher Alexander |
79 |
< |
\cite{Alexander1987}, software patterns first became popular with |
80 |
< |
the wide acceptance of the book, Design Patterns: Elements of |
81 |
< |
Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
82 |
< |
the experience, knowledge and insights of developers who have |
83 |
< |
successfully used these patterns in their own work. Patterns are |
84 |
< |
reusable. They provide a ready-made solution that can be adapted to |
85 |
< |
different problems as necessary. As one of the latest advanced |
86 |
< |
techniques to emerge from object-oriented community, design patterns |
87 |
< |
were applied in some of the modern scientific software applications, |
88 |
< |
such as JMol, {\sc OOPSE}\cite{Meineke2005} and |
89 |
< |
PROTOMOL\cite{Matthey2004} \textit{etc}. The following sections |
90 |
< |
enumerates some of the patterns used in {\sc OOPSE}. |
77 |
> |
in software design. Although they originated as an architectural |
78 |
> |
concept for buildings and towns by Christopher Alexander |
79 |
> |
\cite{Alexander1987}, design patterns first became popular in |
80 |
> |
software engineering with the wide acceptance of the book, Design |
81 |
> |
Patterns: Elements of Reusable Object-Oriented Software |
82 |
> |
\cite{Gamma1994}. Patterns reflect the experience, knowledge and |
83 |
> |
insights of developers who have successfully used these patterns in |
84 |
> |
their own work. Patterns are reusable. They provide a ready-made |
85 |
> |
solution that can be adapted to different problems as necessary. As |
86 |
> |
one of the latest advanced techniques to emerge from object-oriented |
87 |
> |
community, design patterns were applied in some of the modern |
88 |
> |
scientific software applications, such as JMol, {\sc |
89 |
> |
OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004} |
90 |
> |
\textit{etc}. The following sections enumerates some of the patterns |
91 |
> |
used in {\sc OOPSE}. |
92 |
|
|
93 |
|
\subsection{\label{appendixSection:singleton}Singletons} |
94 |
|
|
96 |
|
instantiation of a class to one object, but also provides a global |
97 |
|
point of access to the object. Although the singleton pattern can be |
98 |
|
implemented in various ways to account for different aspects of the |
99 |
< |
software designs, such as lifespan control \textit{etc}, we only use |
99 |
> |
software design, such as lifespan control \textit{etc}, we only use |
100 |
|
the static data approach in {\sc OOPSE}. The declaration and |
101 |
|
implementation of IntegratorFactory class are given by declared in |
102 |
|
List.~\ref{appendixScheme:singletonDeclaration} and |
126 |
|
\subsection{\label{appendixSection:visitorPattern}Visitor} |
127 |
|
|
128 |
|
The visitor pattern is designed to decouple the data structure and |
129 |
< |
algorithms used upon them by collecting related operation from |
129 |
> |
algorithms used upon them by collecting related operations from |
130 |
|
element classes into other visitor classes, which is equivalent to |
131 |
|
adding virtual functions into a set of classes without modifying |
132 |
|
their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
133 |
|
structure of a Visitor pattern which is used extensively in {\tt |
134 |
|
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
135 |
|
distinct operations are performed on different StuntDoubles (See the |
136 |
< |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
137 |
< |
in Scheme.~\ref{appendixScheme:element}). Since the hierarchies |
138 |
< |
remain stable, it is easy to define a visit operation (see |
139 |
< |
Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
140 |
< |
Note that using Composite pattern\cite{Gamma1994}, CompositeVisitor |
141 |
< |
manages a priority visitor list and handles the execution of every |
142 |
< |
visitor in the priority list on different StuntDoubles. |
136 |
> |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the |
137 |
> |
declaration in Scheme.~\ref{appendixScheme:element}). Since the |
138 |
> |
hierarchies remain stable, it is easy to define a visit operation |
139 |
> |
(see Scheme.~\ref{appendixScheme:visitor}) for each class of |
140 |
> |
StuntDouble. Note that by using the Composite |
141 |
> |
pattern\cite{Gamma1994}, CompositeVisitor manages a priority visitor |
142 |
> |
list and handles the execution of every visitor in the priority list |
143 |
> |
on different StuntDoubles. |
144 |
|
|
145 |
< |
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
145 |
> |
\begin{figure} |
146 |
> |
\centering |
147 |
> |
\includegraphics[width=\linewidth]{visitor.eps} |
148 |
> |
\caption[The UML class diagram of Visitor patten] {The UML class |
149 |
> |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
150 |
> |
\end{figure} |
151 |
|
|
152 |
< |
class IntegratorFactory { public: |
153 |
< |
static IntegratorFactory* getInstance(); protected: |
152 |
> |
\begin{figure} |
153 |
> |
\centering |
154 |
> |
\includegraphics[width=\linewidth]{hierarchy.eps} |
155 |
> |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
156 |
> |
the class hierarchy. Objects below others on the diagram inherit |
157 |
> |
data structures and functions from their parent classes above them.} |
158 |
> |
\label{oopseFig:hierarchy} |
159 |
> |
\end{figure} |
160 |
> |
|
161 |
> |
\begin{lstlisting}[float,basicstyle=\ttfamily,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
162 |
> |
|
163 |
> |
class IntegratorFactory { |
164 |
> |
public: |
165 |
> |
static IntegratorFactory* getInstance(); |
166 |
> |
protected: |
167 |
|
IntegratorFactory(); |
168 |
< |
private: |
169 |
< |
static IntegratorFactory* instance_; |
150 |
< |
}; |
168 |
> |
private: |
169 |
> |
static IntegratorFactory* instance_; }; |
170 |
|
|
171 |
|
\end{lstlisting} |
172 |
|
|
185 |
|
|
186 |
|
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
187 |
|
|
188 |
< |
class IntegratorFactory { public: |
188 |
> |
class IntegratorFactory { |
189 |
> |
public: |
190 |
|
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
191 |
|
|
192 |
< |
bool registerIntegrator(IntegratorCreator* creator) { |
193 |
< |
return creatorMap_.insert(creator->getIdent(), creator).second; |
192 |
> |
bool registerIntegrator(IntegratorCreator* creator){ |
193 |
> |
return creatorMap_.insert(creator->getIdent(),creator).second; |
194 |
|
} |
195 |
|
|
196 |
|
Integrator* createIntegrator(const string& id, SimInfo* info) { |
211 |
|
|
212 |
|
class IntegratorCreator { |
213 |
|
public: |
214 |
< |
IntegratorCreator(const string& ident) : ident_(ident) {} |
214 |
> |
IntegratorCreator(const string& ident) : ident_(ident) {} |
215 |
|
|
216 |
< |
const string& getIdent() const { return ident_; } |
216 |
> |
const string& getIdent() const { return ident_; } |
217 |
|
|
218 |
< |
virtual Integrator* create(SimInfo* info) const = 0; |
218 |
> |
virtual Integrator* create(SimInfo* info) const = 0; |
219 |
|
|
220 |
< |
private: |
221 |
< |
string ident_; |
220 |
> |
private: |
221 |
> |
string ident_; |
222 |
|
}; |
223 |
|
|
224 |
< |
template<class ConcreteIntegrator> class IntegratorBuilder : public |
225 |
< |
IntegratorCreator { |
224 |
> |
template<class ConcreteIntegrator> class IntegratorBuilder : |
225 |
> |
public IntegratorCreator { |
226 |
|
public: |
227 |
< |
IntegratorBuilder(const string& ident) |
227 |
> |
IntegratorBuilder(const string& ident) |
228 |
|
: IntegratorCreator(ident) {} |
229 |
< |
virtual Integrator* create(SimInfo* info) const { |
230 |
< |
return new ConcreteIntegrator(info); |
231 |
< |
} |
229 |
> |
virtual Integrator* create(SimInfo* info) const { |
230 |
> |
return new ConcreteIntegrator(info); |
231 |
> |
} |
232 |
|
}; |
233 |
|
\end{lstlisting} |
234 |
|
|
236 |
|
|
237 |
|
class StuntDouble { |
238 |
|
public: |
239 |
< |
virtual void accept(BaseVisitor* v) = 0; |
239 |
> |
virtual void accept(BaseVisitor* v) = 0; |
240 |
|
}; |
241 |
|
|
242 |
|
class Atom: public StuntDouble { |
243 |
|
public: |
244 |
< |
virtual void accept{BaseVisitor* v*} { |
245 |
< |
v->visit(this); |
246 |
< |
} |
244 |
> |
virtual void accept{BaseVisitor* v*} { |
245 |
> |
v->visit(this); |
246 |
> |
} |
247 |
|
}; |
248 |
|
|
249 |
|
class DirectionalAtom: public Atom { |
250 |
|
public: |
251 |
< |
virtual void accept{BaseVisitor* v*} { |
252 |
< |
v->visit(this); |
253 |
< |
} |
251 |
> |
virtual void accept{BaseVisitor* v*} { |
252 |
> |
v->visit(this); |
253 |
> |
} |
254 |
|
}; |
255 |
|
|
256 |
|
class RigidBody: public StuntDouble { |
257 |
|
public: |
258 |
< |
virtual void accept{BaseVisitor* v*} { |
259 |
< |
v->visit(this); |
260 |
< |
} |
258 |
> |
virtual void accept{BaseVisitor* v*} { |
259 |
> |
v->visit(this); |
260 |
> |
} |
261 |
|
}; |
262 |
|
|
263 |
|
\end{lstlisting} |
264 |
|
|
265 |
|
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
246 |
– |
|
266 |
|
class BaseVisitor{ |
267 |
|
public: |
268 |
< |
virtual void visit(Atom* atom); |
269 |
< |
virtual void visit(DirectionalAtom* datom); |
270 |
< |
virtual void visit(RigidBody* rb); |
268 |
> |
virtual void visit(Atom* atom); |
269 |
> |
virtual void visit(DirectionalAtom* datom); |
270 |
> |
virtual void visit(RigidBody* rb); |
271 |
|
}; |
253 |
– |
|
272 |
|
class BaseAtomVisitor:public BaseVisitor{ |
273 |
|
public: |
274 |
< |
virtual void visit(Atom* atom); |
275 |
< |
virtual void visit(DirectionalAtom* datom); |
276 |
< |
virtual void visit(RigidBody* rb); |
274 |
> |
virtual void visit(Atom* atom); |
275 |
> |
virtual void visit(DirectionalAtom* datom); |
276 |
> |
virtual void visit(RigidBody* rb); |
277 |
|
}; |
260 |
– |
|
278 |
|
class CompositeVisitor: public BaseVisitor { |
279 |
|
public: |
280 |
|
typedef list<pair<BaseVisitor*, int> > VistorListType; |
282 |
|
virtual void visit(Atom* atom) { |
283 |
|
VisitorListIterator i; |
284 |
|
BaseVisitor* curVisitor; |
285 |
< |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
285 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) |
286 |
|
atom->accept(*i); |
270 |
– |
} |
287 |
|
} |
272 |
– |
|
288 |
|
virtual void visit(DirectionalAtom* datom) { |
289 |
|
VisitorListIterator i; |
290 |
|
BaseVisitor* curVisitor; |
291 |
< |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
291 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) |
292 |
|
atom->accept(*i); |
278 |
– |
} |
293 |
|
} |
280 |
– |
|
294 |
|
virtual void visit(RigidBody* rb) { |
295 |
|
VisitorListIterator i; |
296 |
|
std::vector<Atom*> myAtoms; |
297 |
|
std::vector<Atom*>::iterator ai; |
298 |
|
myAtoms = rb->getAtoms(); |
299 |
< |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
299 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) { |
300 |
|
rb->accept(*i); |
301 |
< |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
301 |
> |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai) |
302 |
|
(*ai)->accept(*i); |
290 |
– |
} |
303 |
|
} |
292 |
– |
|
304 |
|
void addVisitor(BaseVisitor* v, int priority); |
305 |
|
protected: |
306 |
< |
VistorListType visitorList; |
306 |
> |
VistorListType visitorList; |
307 |
|
}; |
308 |
|
\end{lstlisting} |
309 |
|
|
299 |
– |
\begin{figure} |
300 |
– |
\centering |
301 |
– |
\includegraphics[width=\linewidth]{visitor.eps} |
302 |
– |
\caption[The UML class diagram of Visitor patten] {The UML class |
303 |
– |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
304 |
– |
\end{figure} |
305 |
– |
|
306 |
– |
\begin{figure} |
307 |
– |
\centering |
308 |
– |
\includegraphics[width=\linewidth]{hierarchy.eps} |
309 |
– |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
310 |
– |
the class hierarchy. Objects below others on the diagram inherit |
311 |
– |
data structures and functions from their parent classes above them.} |
312 |
– |
\label{oopseFig:hierarchy} |
313 |
– |
\end{figure} |
314 |
– |
|
310 |
|
\section{\label{appendixSection:concepts}Concepts} |
311 |
|
|
312 |
|
OOPSE manipulates both traditional atoms as well as some objects |
380 |
|
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
381 |
|
O\_TIP3P |
382 |
|
atoms belonging to TIP3P molecules \\ |
383 |
< |
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
383 |
> |
& select DMPC\_RB\_0.PO4 & select the PO4 atoms belonging to |
384 |
|
the first |
385 |
|
RigidBody in each DMPC molecule \\ |
386 |
|
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |