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. |
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} |
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 |
|
|
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. |
371 |
+ |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
372 |
+ |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
373 |
+ |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
374 |
+ |
DirectionalAtom}s which behaves as a single unit. |
375 |
+ |
\end{itemize} |
376 |
|
|
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 |
382 |
< |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
383 |
< |
composed of either name expressions, index expressions, predefined |
384 |
< |
sets, user-defined expressions, comparison operators, within |
385 |
< |
expressions, or logical combinations of the above expression types. |
386 |
< |
Expressions can be combined using parentheses and the Boolean |
387 |
< |
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 |