84 |
|
reusable. They provide a ready-made solution that can be adapted to |
85 |
|
different problems as necessary. Pattern are expressive. they |
86 |
|
provide a common vocabulary of solutions that can express large |
87 |
< |
solutions succinctly. |
88 |
< |
|
89 |
< |
Patterns are usually described using a format that includes the |
90 |
< |
following information: |
91 |
< |
\begin{enumerate} |
92 |
< |
\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
93 |
< |
discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
94 |
< |
in the literature. In this case it is common practice to document these nicknames or synonyms under |
95 |
< |
the heading of \emph{Aliases} or \emph{Also Known As}. |
96 |
< |
\item The \emph{motivation} or \emph{context} that this pattern applies |
97 |
< |
to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
98 |
< |
\item The \emph{solution} to the problem that the pattern |
99 |
< |
addresses. It describes how to construct the necessary work products. The description may include |
100 |
< |
pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
101 |
< |
collaborations, to show how the problem is solved. |
102 |
< |
\item The \emph{consequences} of using the given solution to solve a |
103 |
< |
problem, both positive and negative. |
104 |
< |
\end{enumerate} |
105 |
< |
|
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{Meineke2005} and PROTOMOL\cite{Matthey2005} |
87 |
> |
solutions succinctly. As one of the latest advanced techniques |
88 |
> |
emerged from object-oriented community, design patterns were applied |
89 |
> |
in some of the modern scientific software applications, such as |
90 |
> |
JMol, {\sc OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004} |
91 |
|
\textit{etc}. The following sections enumerates some of the patterns |
92 |
|
used in {\sc OOPSE}. |
93 |
|
|
99 |
|
variable, the logging utility which reports error and warning |
100 |
|
messages to the console in {\sc OOPSE} is a good candidate for |
101 |
|
applying the Singleton pattern to avoid the global namespace |
102 |
< |
pollution.Although the singleton pattern can be implemented in |
102 |
> |
pollution. Although the singleton pattern can be implemented in |
103 |
|
various ways to account for different aspects of the software |
104 |
|
designs, such as lifespan control \textit{etc}, we only use the |
105 |
< |
static data approach in {\sc OOPSE}. IntegratorFactory class is |
106 |
< |
declared as |
107 |
< |
|
105 |
> |
static data approach in {\sc OOPSE}. The declaration and |
106 |
> |
implementation of IntegratorFactory class are given by declared in |
107 |
> |
List.~\ref{appendixScheme:singletonDeclaration} and |
108 |
> |
List.~\ref{appendixScheme:singletonImplementation} respectively. |
109 |
> |
Since constructor is declared as protected, a client can not |
110 |
> |
instantiate IntegratorFactory directly. Moreover, since the member |
111 |
> |
function getInstance serves as the only entry of access to |
112 |
> |
IntegratorFactory, this approach fulfills the basic requirement, a |
113 |
> |
single instance. Another consequence of this approach is the |
114 |
> |
automatic destruction since static data are destroyed upon program |
115 |
> |
termination. |
116 |
|
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
117 |
|
|
118 |
|
class IntegratorFactory { |
127 |
|
|
128 |
|
\end{lstlisting} |
129 |
|
|
141 |
– |
The corresponding implementation is |
142 |
– |
|
130 |
|
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] |
131 |
|
|
132 |
|
IntegratorFactory::instance_ = NULL; |
140 |
|
|
141 |
|
\end{lstlisting} |
142 |
|
|
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. |
143 |
|
|
144 |
|
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
145 |
|
|
151 |
|
createIntegrator member function) creates products based on the |
152 |
|
identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If |
153 |
|
the identifier has been already registered, the factory method will |
154 |
< |
invoke the corresponding creator (see List.~\ref{integratorCreator}) |
155 |
< |
which utilizes the modern C++ template technique to avoid excess |
156 |
< |
subclassing. |
154 |
> |
invoke the corresponding creator (see |
155 |
> |
List.~\ref{appendixScheme:integratorCreator}) which utilizes the |
156 |
> |
modern C++ template technique to avoid excess subclassing. |
157 |
|
|
158 |
|
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
159 |
|
|
492 |
|
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
493 |
|
also be used to compute the density distributions of other molecules |
494 |
|
in a reference frame {\it fixed to the body-fixed reference frame} |
495 |
< |
of a selected atom or rigid body. |
495 |
> |
of a selected atom or rigid body. Due to the fact that the selected |
496 |
> |
StuntDoubles from two selections may be overlapped, {\tt |
497 |
> |
StaticProps} performs the calculation in three stages which are |
498 |
> |
illustrated in Fig.~\ref{oopseFig:staticPropsProcess}. |
499 |
|
|
500 |
+ |
\begin{figure} |
501 |
+ |
\centering |
502 |
+ |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
503 |
+ |
\caption[A representation of the three-stage correlations in |
504 |
+ |
\texttt{StaticProps}]{This diagram illustrates three-stage |
505 |
+ |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
506 |
+ |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
507 |
+ |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
508 |
+ |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
509 |
+ |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
510 |
+ |
the contrary, the third stage($C$ and $C$) are completely |
511 |
+ |
overlapping} \label{oopseFig:staticPropsProcess} |
512 |
+ |
\end{figure} |
513 |
+ |
|
514 |
|
There are five seperate radial distribution functions availiable in |
515 |
|
OOPSE. Since every radial distrbution function invlove the |
516 |
|
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
554 |
|
\end{description} |
555 |
|
|
556 |
|
The vectors (and angles) associated with these angular pair |
557 |
< |
distribution functions are most easily seen in the figure below: |
557 |
> |
distribution functions are most easily seen in |
558 |
> |
Fig.~\ref{oopseFig:gofr} |
559 |
|
|
560 |
|
\begin{figure} |
561 |
|
\centering |
564 |
|
Any two directional objects (DirectionalAtoms and RigidBodies) have |
565 |
|
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
566 |
|
their body-fixed frames.} \label{oopseFig:gofr} |
569 |
– |
\end{figure} |
570 |
– |
|
571 |
– |
Due to the fact that the selected StuntDoubles from two selections |
572 |
– |
may be overlapped, {\tt StaticProps} performs the calculation in |
573 |
– |
three stages which are illustrated in |
574 |
– |
Fig.~\ref{oopseFig:staticPropsProcess}. |
575 |
– |
|
576 |
– |
\begin{figure} |
577 |
– |
\centering |
578 |
– |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
579 |
– |
\caption[A representation of the three-stage correlations in |
580 |
– |
\texttt{StaticProps}]{This diagram illustrates three-stage |
581 |
– |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
582 |
– |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
583 |
– |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
584 |
– |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
585 |
– |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
586 |
– |
the contrary, the third stage($C$ and $C$) are completely |
587 |
– |
overlapping} \label{oopseFig:staticPropsProcess} |
567 |
|
\end{figure} |
568 |
|
|
569 |
|
The options available for {\tt StaticProps} are as follows: |
628 |
|
select different types of atoms is already present in the code. |
629 |
|
|
630 |
|
For large simulations, the trajectory files can sometimes reach |
631 |
< |
sizes in excess of several gigabytes. In order to effectively |
632 |
< |
analyze that amount of data. In order to prevent a situation where |
633 |
< |
the program runs out of memory due to large trajectories, |
634 |
< |
\texttt{dynamicProps} will estimate the size of free memory at |
635 |
< |
first, and determine the number of frames in each block, which |
657 |
< |
allows the operating system to load two blocks of data |
631 |
> |
sizes in excess of several gigabytes. In order to prevent a |
632 |
> |
situation where the program runs out of memory due to large |
633 |
> |
trajectories, \texttt{dynamicProps} will estimate the size of free |
634 |
> |
memory at first, and determine the number of frames in each block, |
635 |
> |
which allows the operating system to load two blocks of data |
636 |
|
simultaneously without swapping. Upon reading two blocks of the |
637 |
|
trajectory, \texttt{dynamicProps} will calculate the time |
638 |
|
correlation within the first block and the cross correlations |