1 |
|
\appendix |
2 |
|
\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} |
3 |
|
|
4 |
< |
Designing object-oriented software is hard, and designing reusable |
5 |
< |
object-oriented scientific software is even harder. Absence of |
6 |
< |
applying modern software development practices is the bottleneck of |
7 |
< |
Scientific Computing community\cite{Wilson2006}. For instance, in |
8 |
< |
the last 20 years , there are quite a few MD packages that were |
9 |
< |
developed to solve common MD problems and perform robust simulations |
10 |
< |
. However, many of the codes are legacy programs that are either |
11 |
< |
poorly organized or extremely complex. Usually, these packages were |
12 |
< |
contributed by scientists without official computer science |
13 |
< |
training. The development of most MD applications are lack of strong |
14 |
< |
coordination to enforce design and programming guidelines. Moreover, |
15 |
< |
most MD programs also suffer from missing design and implement |
16 |
< |
documents which is crucial to the maintenance and extensibility. |
17 |
< |
Along the way of studying structural and dynamic processes in |
18 |
< |
condensed phase systems like biological membranes and nanoparticles, |
19 |
< |
we developed and maintained an Object-Oriented Parallel Simulation |
20 |
< |
Engine ({\sc OOPSE}). This new molecular dynamics package has some |
21 |
< |
unique features |
4 |
> |
Absence of applying modern software development practices is the |
5 |
> |
bottleneck of Scientific Computing community\cite{Wilson2006}. In |
6 |
> |
the last 20 years , there are quite a few MD |
7 |
> |
packages\cite{Brooks1983, Vincent1995, Kale1999} that were developed |
8 |
> |
to solve common MD problems and perform robust simulations . |
9 |
> |
Unfortunately, most of them are commercial programs that are either |
10 |
> |
poorly written or extremely complicate. Consequently, it prevents |
11 |
> |
the researchers to reuse or extend those packages to do cutting-edge |
12 |
> |
research effectively. Along the way of studying structural and |
13 |
> |
dynamic processes in condensed phase systems like biological |
14 |
> |
membranes and nanoparticles, we developed an open source |
15 |
> |
Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new |
16 |
> |
molecular dynamics package has some unique features |
17 |
|
\begin{enumerate} |
18 |
|
\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
19 |
|
atom types (transition metals, point dipoles, sticky potentials, |
59 |
|
program of the package, \texttt{oopse} and it corresponding parallel |
60 |
|
version \texttt{oopse\_MPI}, as well as other useful utilities, such |
61 |
|
as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}), |
62 |
< |
\texttt{DynamicProps} (see |
63 |
< |
Sec.~\ref{appendixSection:appendixSection:DynamicProps}), |
64 |
< |
\texttt{Dump2XYZ} (see |
70 |
< |
Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro} |
71 |
< |
(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics}) |
62 |
> |
\texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}), |
63 |
> |
\texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}), |
64 |
> |
\texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics}) |
65 |
|
\textit{etc}. |
66 |
|
|
67 |
|
\begin{figure} |
106 |
|
As one of the latest advanced techniques emerged from |
107 |
|
object-oriented community, design patterns were applied in some of |
108 |
|
the modern scientific software applications, such as JMol, {\sc |
109 |
< |
OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. |
110 |
< |
The following sections enumerates some of the patterns used in {\sc |
111 |
< |
OOPSE}. |
109 |
> |
OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2005} |
110 |
> |
\textit{etc}. The following sections enumerates some of the patterns |
111 |
> |
used in {\sc OOPSE}. |
112 |
|
|
113 |
|
\subsection{\label{appendixSection:singleton}Singleton} |
114 |
+ |
|
115 |
|
The Singleton pattern not only provides a mechanism to restrict |
116 |
|
instantiation of a class to one object, but also provides a global |
117 |
|
point of access to the object. Currently implemented as a global |
121 |
|
pollution.Although the singleton pattern can be implemented in |
122 |
|
various ways to account for different aspects of the software |
123 |
|
designs, such as lifespan control \textit{etc}, we only use the |
124 |
< |
static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class |
125 |
< |
is declared as |
132 |
< |
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}] |
124 |
> |
static data approach in {\sc OOPSE}. IntegratorFactory class is |
125 |
> |
declared as |
126 |
|
|
127 |
+ |
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
128 |
+ |
|
129 |
|
class IntegratorFactory { |
130 |
< |
public: |
131 |
< |
static IntegratorFactory* getInstance(); |
132 |
< |
protected: |
133 |
< |
IntegratorFactory(); |
134 |
< |
private: |
135 |
< |
static IntegratorFactory* instance_; |
130 |
> |
public: |
131 |
> |
static IntegratorFactory* |
132 |
> |
getInstance(); |
133 |
> |
protected: |
134 |
> |
IntegratorFactory(); |
135 |
> |
private: |
136 |
> |
static IntegratorFactory* instance_; |
137 |
|
}; |
138 |
|
|
139 |
|
\end{lstlisting} |
140 |
+ |
|
141 |
|
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}] |
142 |
|
|
143 |
+ |
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] |
144 |
+ |
|
145 |
|
IntegratorFactory::instance_ = NULL; |
146 |
|
|
147 |
|
IntegratorFactory* getInstance() { |
152 |
|
} |
153 |
|
|
154 |
|
\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. |
155 |
|
|
156 |
+ |
Since constructor is declared as protected, a client can not |
157 |
+ |
instantiate IntegratorFactory directly. Moreover, since the member |
158 |
+ |
function getInstance serves as the only entry of access to |
159 |
+ |
IntegratorFactory, this approach fulfills the basic requirement, a |
160 |
+ |
single instance. Another consequence of this approach is the |
161 |
+ |
automatic destruction since static data are destroyed upon program |
162 |
+ |
termination. |
163 |
+ |
|
164 |
|
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
165 |
|
|
166 |
|
Categoried as a creational pattern, the Factory Method pattern deals |
167 |
|
with the problem of creating objects without specifying the exact |
168 |
|
class of object that will be created. Factory Method is typically |
169 |
|
implemented by delegating the creation operation to the subclasses. |
170 |
+ |
Parameterized Factory pattern where factory method ( |
171 |
+ |
createIntegrator member function) creates products based on the |
172 |
+ |
identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If |
173 |
+ |
the identifier has been already registered, the factory method will |
174 |
+ |
invoke the corresponding creator (see List.~\ref{integratorCreator}) |
175 |
+ |
which utilizes the modern C++ template technique to avoid excess |
176 |
+ |
subclassing. |
177 |
|
|
178 |
< |
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}] |
178 |
> |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
179 |
|
|
180 |
|
class IntegratorFactory { |
181 |
< |
public: |
182 |
< |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
181 |
> |
public: |
182 |
> |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
183 |
|
|
184 |
< |
bool registerIntegrator(IntegratorCreator* creator); |
184 |
> |
bool registerIntegrator(IntegratorCreator* creator) { |
185 |
> |
return creatorMap_.insert(creator->getIdent(), creator).second; |
186 |
> |
} |
187 |
|
|
188 |
< |
Integrator* createIntegrator(const string& id, SimInfo* info); |
188 |
> |
Integrator* createIntegrator(const string& id, SimInfo* info) { |
189 |
> |
Integrator* result = NULL; |
190 |
> |
CreatorMapType::iterator i = creatorMap_.find(id); |
191 |
> |
if (i != creatorMap_.end()) { |
192 |
> |
result = (i->second)->create(info); |
193 |
> |
} |
194 |
> |
return result; |
195 |
> |
} |
196 |
|
|
197 |
< |
private: |
198 |
< |
CreatorMapType creatorMap_; |
197 |
> |
private: |
198 |
> |
CreatorMapType creatorMap_; |
199 |
|
}; |
189 |
– |
|
200 |
|
\end{lstlisting} |
201 |
|
|
202 |
< |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}] |
202 |
> |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
203 |
|
|
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 |
– |
|
204 |
|
class IntegratorCreator { |
205 |
< |
public: |
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: |
212 |
> |
private: |
213 |
|
string ident_; |
214 |
|
}; |
215 |
|
|
216 |
|
template<class ConcreteIntegrator> |
217 |
|
class IntegratorBuilder : public IntegratorCreator { |
218 |
< |
public: |
219 |
< |
IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {} |
220 |
< |
virtual Integrator* create(SimInfo* info) const { |
221 |
< |
return new ConcreteIntegrator(info); |
222 |
< |
} |
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. 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 |
< |
The UML class diagram of Visitor patten is shown in |
235 |
< |
Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
236 |
< |
Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
237 |
< |
extensively. |
229 |
> |
The visitor pattern is designed to decouple the data structure and |
230 |
> |
algorithms used upon them by collecting related operation from |
231 |
> |
element classes into other visitor classes, which is equivalent to |
232 |
> |
adding virtual functions into a set of classes without modifying |
233 |
> |
their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
234 |
> |
structure of Visitor pattern which is used extensively in {\tt |
235 |
> |
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
236 |
> |
distinct operations are performed on different StuntDoubles (See the |
237 |
> |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
238 |
> |
in List.~\ref{appendixScheme:element}). Since the hierarchies |
239 |
> |
remains stable, it is easy to define a visit operation (see |
240 |
> |
List.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
241 |
> |
Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
242 |
> |
manages a priority visitor list and handles the execution of every |
243 |
> |
visitor in the priority list on different StuntDoubles. |
244 |
|
|
245 |
|
\begin{figure} |
246 |
|
\centering |
247 |
< |
\includegraphics[width=\linewidth]{architecture.eps} |
248 |
< |
\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
249 |
< |
of {\sc OOPSE}} \label{appendixFig:visitorUML} |
247 |
> |
\includegraphics[width=\linewidth]{visitor.eps} |
248 |
> |
\caption[The UML class diagram of Visitor patten] {The UML class |
249 |
> |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
250 |
|
\end{figure} |
251 |
|
|
252 |
< |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
252 |
> |
\begin{figure} |
253 |
> |
\centering |
254 |
> |
\includegraphics[width=\linewidth]{hierarchy.eps} |
255 |
> |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
256 |
> |
the class hierarchy. } \label{oopseFig:hierarchy} |
257 |
> |
\end{figure} |
258 |
|
|
259 |
< |
class BaseVisitor{ |
260 |
< |
public: |
261 |
< |
virtual void visit(Atom* atom); |
262 |
< |
virtual void visit(DirectionalAtom* datom); |
259 |
< |
virtual void visit(RigidBody* rb); |
259 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
260 |
> |
|
261 |
> |
class StuntDouble { public: |
262 |
> |
virtual void accept(BaseVisitor* v) = 0; |
263 |
|
}; |
264 |
|
|
265 |
+ |
class Atom: public StuntDouble { public: |
266 |
+ |
virtual void accept{BaseVisitor* v*} { |
267 |
+ |
v->visit(this); |
268 |
+ |
} |
269 |
+ |
}; |
270 |
+ |
|
271 |
+ |
class DirectionalAtom: public Atom { public: |
272 |
+ |
virtual void accept{BaseVisitor* v*} { |
273 |
+ |
v->visit(this); |
274 |
+ |
} |
275 |
+ |
}; |
276 |
+ |
|
277 |
+ |
class RigidBody: public StuntDouble { public: |
278 |
+ |
virtual void accept{BaseVisitor* v*} { |
279 |
+ |
v->visit(this); |
280 |
+ |
} |
281 |
+ |
}; |
282 |
+ |
|
283 |
|
\end{lstlisting} |
284 |
|
|
285 |
< |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
285 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
286 |
|
|
287 |
< |
class StuntDouble { |
288 |
< |
public: |
289 |
< |
virtual void accept(BaseVisitor* v) = 0; |
287 |
> |
class BaseVisitor{ |
288 |
> |
public: |
289 |
> |
virtual void visit(Atom* atom); |
290 |
> |
virtual void visit(DirectionalAtom* datom); |
291 |
> |
virtual void visit(RigidBody* rb); |
292 |
|
}; |
293 |
|
|
294 |
< |
class Atom: public StuntDouble { |
295 |
< |
public: |
296 |
< |
virtual void accept{BaseVisitor* v*} { |
297 |
< |
v->visit(this); |
275 |
< |
} |
294 |
> |
class BaseAtomVisitor:public BaseVisitor{ public: |
295 |
> |
virtual void visit(Atom* atom); |
296 |
> |
virtual void visit(DirectionalAtom* datom); |
297 |
> |
virtual void visit(RigidBody* rb); |
298 |
|
}; |
299 |
|
|
300 |
< |
class DirectionalAtom: public Atom { |
301 |
< |
public: |
302 |
< |
virtual void accept{BaseVisitor* v*} { |
303 |
< |
v->visit(this); |
282 |
< |
} |
300 |
> |
class SSDAtomVisitor:public BaseAtomVisitor{ public: |
301 |
> |
virtual void visit(Atom* atom); |
302 |
> |
virtual void visit(DirectionalAtom* datom); |
303 |
> |
virtual void visit(RigidBody* rb); |
304 |
|
}; |
305 |
|
|
306 |
< |
class RigidBody: public StuntDouble { |
307 |
< |
public: |
308 |
< |
virtual void accept{BaseVisitor* v*} { |
309 |
< |
v->visit(this); |
306 |
> |
class CompositeVisitor: public BaseVisitor { |
307 |
> |
public: |
308 |
> |
|
309 |
> |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
310 |
> |
typedef VistorListType::iterator VisitorListIterator; |
311 |
> |
virtual void visit(Atom* atom) { |
312 |
> |
VisitorListIterator i; |
313 |
> |
BaseVisitor* curVisitor; |
314 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) { |
315 |
> |
atom->accept(*i); |
316 |
|
} |
317 |
+ |
} |
318 |
+ |
|
319 |
+ |
virtual void visit(DirectionalAtom* datom) { |
320 |
+ |
VisitorListIterator i; |
321 |
+ |
BaseVisitor* curVisitor; |
322 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
323 |
+ |
atom->accept(*i); |
324 |
+ |
} |
325 |
+ |
} |
326 |
+ |
|
327 |
+ |
virtual void visit(RigidBody* rb) { |
328 |
+ |
VisitorListIterator i; |
329 |
+ |
std::vector<Atom*> myAtoms; |
330 |
+ |
std::vector<Atom*>::iterator ai; |
331 |
+ |
myAtoms = rb->getAtoms(); |
332 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) {{ |
333 |
+ |
rb->accept(*i); |
334 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
335 |
+ |
(*ai)->accept(*i); |
336 |
+ |
} |
337 |
+ |
} |
338 |
+ |
|
339 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
340 |
+ |
|
341 |
+ |
protected: |
342 |
+ |
VistorListType visitorList; |
343 |
|
}; |
344 |
|
|
345 |
|
\end{lstlisting} |
346 |
+ |
|
347 |
|
\section{\label{appendixSection:concepts}Concepts} |
348 |
|
|
349 |
|
OOPSE manipulates both traditional atoms as well as some objects |
350 |
|
that {\it behave like atoms}. These objects can be rigid |
351 |
|
collections of atoms or atoms which have orientational degrees of |
352 |
< |
freedom. Here is a diagram of the class heirarchy: |
353 |
< |
|
354 |
< |
\begin{figure} |
355 |
< |
\centering |
356 |
< |
\includegraphics[width=3in]{heirarchy.eps} |
357 |
< |
\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
358 |
< |
The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
359 |
< |
selection syntax allows the user to select any of the objects that |
360 |
< |
are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
307 |
< |
\end{figure} |
308 |
< |
|
352 |
> |
freedom. A diagram of the class hierarchy is illustrated in |
353 |
> |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
354 |
> |
DirectionalAtom in {\sc OOPSE} have their own names which are |
355 |
> |
specified in the {\tt .md} file. In contrast, RigidBodies are |
356 |
> |
denoted by their membership and index inside a particular molecule: |
357 |
> |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
358 |
> |
on the specifics of the simulation). The names of rigid bodies are |
359 |
> |
generated automatically. For example, the name of the first rigid |
360 |
> |
body in a DMPC molecule is DMPC\_RB\_0. |
361 |
|
\begin{itemize} |
362 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
363 |
|
integrators and minimizers. |
366 |
|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
367 |
|
DirectionalAtom}s which behaves as a single unit. |
368 |
|
\end{itemize} |
317 |
– |
|
318 |
– |
Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
319 |
– |
own names which are specified in the {\tt .md} file. In contrast, |
320 |
– |
RigidBodies are denoted by their membership and index inside a |
321 |
– |
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
322 |
– |
inside the brackets depend on the specifics of the simulation). The |
323 |
– |
names of rigid bodies are generated automatically. For example, the |
324 |
– |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
369 |
|
|
370 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
371 |
|
|
372 |
< |
The most general form of the select command is: {\tt select {\it |
373 |
< |
expression}}. This expression represents an arbitrary set of |
330 |
< |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
331 |
< |
composed of either name expressions, index expressions, predefined |
332 |
< |
sets, user-defined expressions, comparison operators, within |
333 |
< |
expressions, or logical combinations of the above expression types. |
334 |
< |
Expressions can be combined using parentheses and the Boolean |
335 |
< |
operators. |
372 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
373 |
> |
StuntDoubles. The most general form of the select command is: |
374 |
|
|
375 |
+ |
{\tt select {\it expression}}. |
376 |
+ |
|
377 |
+ |
This expression represents an arbitrary set of StuntDoubles (Atoms |
378 |
+ |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
379 |
+ |
name expressions, index expressions, predefined sets, user-defined |
380 |
+ |
expressions, comparison operators, within expressions, or logical |
381 |
+ |
combinations of the above expression types. Expressions can be |
382 |
+ |
combined using parentheses and the Boolean operators. |
383 |
+ |
|
384 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
385 |
|
|
386 |
|
The logical operators allow complex queries to be constructed out of |