1 |
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\appendix |
2 |
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\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} |
3 |
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|
4 |
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Designing object-oriented software is hard, and designing reusable |
5 |
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object-oriented scientific software is even harder. Absence of |
6 |
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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 |
4 |
> |
The absence of modern software development practices has been a |
5 |
> |
bottleneck limiting progress in the Scientific Computing |
6 |
> |
community. In the last 20 years, a large number of |
7 |
> |
few MD packages\cite{Brooks1983, Vincent1995, Kale1999} were |
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|
developed to solve common MD problems and perform robust simulations |
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< |
. However, many of the codes are legacy programs that are either |
10 |
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poorly organized or extremely complex. Usually, these packages were |
11 |
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contributed by scientists without official computer science |
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training. The development of most MD applications are lack of strong |
13 |
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coordination to enforce design and programming guidelines. Moreover, |
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most MD programs also suffer from missing design and implement |
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documents which is crucial to the maintenance and extensibility. |
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Along the way of studying structural and dynamic processes in |
18 |
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condensed phase systems like biological membranes and nanoparticles, |
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we developed and maintained an Object-Oriented Parallel Simulation |
20 |
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Engine ({\sc OOPSE}). This new molecular dynamics package has some |
21 |
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unique features |
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. Most of these are commercial programs that are either poorly |
10 |
> |
written or extremely complicated to use correctly. This situation |
11 |
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prevents researchers from reusing or extending those packages to do |
12 |
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cutting-edge research effectively. In the process of studying |
13 |
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structural and dynamic processes in condensed phase systems like |
14 |
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biological membranes and nanoparticles, we developed an open source |
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Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new |
16 |
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molecular dynamics package has some unique features |
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\begin{enumerate} |
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\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
19 |
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atom types (transition metals, point dipoles, sticky potentials, |
20 |
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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 |
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\item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap |
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Beowulf clusters to obtain very efficient parallelism. |
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|
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\section{\label{appendixSection:architecture }Architecture} |
35 |
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|
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Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE} |
37 |
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uses C++ Standard Template Library (STL) and fortran modules as the |
38 |
< |
foundation. As an extensive set of the STL and Fortran90 modules, |
39 |
< |
{\sc Base Classes} provide generic implementations of mathematical |
40 |
< |
objects (e.g., matrices, vectors, polynomials, random number |
41 |
< |
generators) and advanced data structures and algorithms(e.g., tuple, |
42 |
< |
bitset, generic data, string manipulation). The molecular data |
43 |
< |
structures for the representation of atoms, bonds, bends, torsions, |
44 |
< |
rigid bodies and molecules \textit{etc} are contained in the {\sc |
45 |
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Kernel} which is implemented with {\sc Base Classes} and are |
46 |
< |
carefully designed to provide maximum extensibility and flexibility. |
47 |
< |
The functionality required for applications is provide by the third |
48 |
< |
layer which contains Input/Output, Molecular Mechanics and Structure |
49 |
< |
modules. Input/Output module not only implements general methods for |
50 |
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file handling, but also defines a generic force field interface. |
51 |
< |
Another important component of Input/Output module is the meta-data |
52 |
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file parser, which is rewritten using ANother Tool for Language |
53 |
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Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular |
54 |
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Mechanics module consists of energy minimization and a wide |
55 |
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varieties of integration methods(see Chap.~\ref{chapt:methodology}). |
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The structure module contains a flexible and powerful selection |
57 |
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library which syntax is elaborated in |
58 |
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Sec.~\ref{appendixSection:syntax}. The top layer is made of the main |
59 |
< |
program of the package, \texttt{oopse} and it corresponding parallel |
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version \texttt{oopse\_MPI}, as well as other useful utilities, such |
61 |
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as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}), |
62 |
< |
\texttt{DynamicProps} (see |
63 |
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Sec.~\ref{appendixSection:appendixSection:DynamicProps}), |
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\texttt{Dump2XYZ} (see |
65 |
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Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro} |
71 |
< |
(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics}) |
72 |
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\textit{etc}. |
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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, 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 |
44 |
> |
molecules \textit{etc} are contained in the {\sc Kernel} which is |
45 |
> |
implemented with {\sc Base Classes} and are carefully designed to |
46 |
> |
provide maximum extensibility and flexibility. The functionality |
47 |
> |
required for applications is provided by the third layer which |
48 |
> |
contains Input/Output, Molecular Mechanics and Structure modules. |
49 |
> |
The Input/Output module not only implements general methods for file |
50 |
> |
handling, but also defines a generic force field interface. Another |
51 |
> |
important component of Input/Output module is the parser for |
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 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{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 |
65 |
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Sec.~\ref{appendixSection:hydrodynamics}) \textit{etc}. |
66 |
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|
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\begin{figure} |
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\centering |
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of {\sc OOPSE}} \label{appendixFig:architecture} |
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\end{figure} |
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|
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\section{\label{appendixSection:desginPattern}Design Pattern} |
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\section{\label{appendixSection:desginPattern}Design Patterns} |
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|
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Design patterns are optimal solutions to commonly-occurring problems |
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in software design. Although originated as an architectural concept |
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for buildings and towns by Christopher Alexander |
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< |
\cite{Alexander1987}, software patterns first became popular with |
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the wide acceptance of the book, Design Patterns: Elements of |
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Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
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the experience, knowledge and insights of developers who have |
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successfully used these patterns in their own work. Patterns are |
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reusable. They provide a ready-made solution that can be adapted to |
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different problems as necessary. Pattern are expressive. they |
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provide a common vocabulary of solutions that can express large |
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< |
solutions succinctly. |
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in software design. Although they originated as an architectural |
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concept for buildings and towns by Christopher Alexander |
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> |
\cite{Alexander1987}, design patterns first became popular in |
80 |
> |
software engineering with the wide acceptance of the book, Design |
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Patterns: Elements of Reusable Object-Oriented Software |
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> |
\cite{Gamma1994}. Patterns reflect the experience, knowledge and |
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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 |
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scientific software applications, such as JMol, {\sc |
89 |
> |
OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004} |
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> |
\textit{etc}. The following sections enumerates some of the patterns |
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used in {\sc OOPSE}. |
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|
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Patterns are usually described using a format that includes the |
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following information: |
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\begin{enumerate} |
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\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
100 |
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discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
101 |
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in the literature. In this case it is common practice to document these nicknames or synonyms under |
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the heading of \emph{Aliases} or \emph{Also Known As}. |
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\item The \emph{motivation} or \emph{context} that this pattern applies |
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to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
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\item The \emph{solution} to the problem that the pattern |
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addresses. It describes how to construct the necessary work products. The description may include |
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< |
pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
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< |
collaborations, to show how the problem is solved. |
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< |
\item The \emph{consequences} of using the given solution to solve a |
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problem, both positive and negative. |
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\end{enumerate} |
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\subsection{\label{appendixSection:singleton}Singletons} |
94 |
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|
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As one of the latest advanced techniques emerged from |
114 |
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object-oriented community, design patterns were applied in some of |
115 |
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the modern scientific software applications, such as JMol, {\sc |
116 |
– |
OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. |
117 |
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The following sections enumerates some of the patterns used in {\sc |
118 |
– |
OOPSE}. |
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|
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\subsection{\label{appendixSection:singleton}Singleton} |
95 |
|
The Singleton pattern not only provides a mechanism to restrict |
96 |
|
instantiation of a class to one object, but also provides a global |
97 |
< |
point of access to the object. Currently implemented as a global |
98 |
< |
variable, the logging utility which reports error and warning |
99 |
< |
messages to the console in {\sc OOPSE} is a good candidate for |
100 |
< |
applying the Singleton pattern to avoid the global namespace |
101 |
< |
pollution.Although the singleton pattern can be implemented in |
102 |
< |
various ways to account for different aspects of the software |
103 |
< |
designs, such as lifespan control \textit{etc}, we only use the |
104 |
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static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class |
105 |
< |
is declared as |
106 |
< |
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}] |
97 |
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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 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 |
103 |
> |
Scheme.~\ref{appendixScheme:singletonImplementation} respectively. |
104 |
> |
Since the constructor is declared as protected, a client can not |
105 |
> |
instantiate IntegratorFactory directly. Moreover, since the member |
106 |
> |
function getInstance serves as the only entry of access to |
107 |
> |
IntegratorFactory, this approach fulfills the basic requirement, a |
108 |
> |
single instance. Another consequence of this approach is the |
109 |
> |
automatic destruction since static data are destroyed upon program |
110 |
> |
termination. |
111 |
|
|
112 |
+ |
\subsection{\label{appendixSection:factoryMethod}Factory Methods} |
113 |
+ |
|
114 |
+ |
The Factory Method pattern is a creational pattern and deals with |
115 |
+ |
the problem of creating objects without specifying the exact class |
116 |
+ |
of object that will be created. Factory method is typically |
117 |
+ |
implemented by delegating the creation operation to the subclasses. |
118 |
+ |
One of the most popular Factory pattern is Parameterized Factory |
119 |
+ |
pattern which creates products based on their identifiers (see |
120 |
+ |
Scheme.~\ref{appendixScheme:factoryDeclaration}). If the identifier |
121 |
+ |
has been already registered, the factory method will invoke the |
122 |
+ |
corresponding creator (see |
123 |
+ |
Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the |
124 |
+ |
modern C++ template technique to avoid excess subclassing. |
125 |
+ |
|
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 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 |
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{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 |
+ |
\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_; |
141 |
< |
}; |
165 |
> |
static IntegratorFactory* getInstance(); |
166 |
> |
protected: |
167 |
> |
IntegratorFactory(); |
168 |
> |
private: |
169 |
> |
static IntegratorFactory* instance_; }; |
170 |
|
|
171 |
|
\end{lstlisting} |
144 |
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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}] |
172 |
|
|
173 |
+ |
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] |
174 |
+ |
|
175 |
|
IntegratorFactory::instance_ = NULL; |
176 |
|
|
177 |
|
IntegratorFactory* getInstance() { |
182 |
|
} |
183 |
|
|
184 |
|
\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. |
185 |
|
|
186 |
< |
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
186 |
> |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
187 |
|
|
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 |
– |
|
188 |
|
class IntegratorFactory { |
189 |
|
public: |
190 |
< |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
190 |
> |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
191 |
|
|
192 |
< |
bool registerIntegrator(IntegratorCreator* creator) { |
193 |
< |
return creatorMap_.insert(creator->getIdent(), creator).second; |
194 |
< |
} |
192 |
> |
bool registerIntegrator(IntegratorCreator* creator){ |
193 |
> |
return creatorMap_.insert(creator->getIdent(),creator).second; |
194 |
> |
} |
195 |
|
|
196 |
< |
Integrator* createIntegrator(const string& id, SimInfo* info) { |
197 |
< |
Integrator* result = NULL; |
198 |
< |
CreatorMapType::iterator i = creatorMap_.find(id); |
199 |
< |
if (i != creatorMap_.end()) { |
200 |
< |
result = (i->second)->create(info); |
191 |
< |
} |
192 |
< |
return result; |
196 |
> |
Integrator* createIntegrator(const string& id, SimInfo* info) { |
197 |
> |
Integrator* result = NULL; |
198 |
> |
CreatorMapType::iterator i = creatorMap_.find(id); |
199 |
> |
if (i != creatorMap_.end()) { |
200 |
> |
result = (i->second)->create(info); |
201 |
|
} |
202 |
+ |
return result; |
203 |
+ |
} |
204 |
|
|
205 |
< |
private: |
206 |
< |
CreatorMapType creatorMap_; |
205 |
> |
private: |
206 |
> |
CreatorMapType creatorMap_; |
207 |
|
}; |
208 |
|
\end{lstlisting} |
199 |
– |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)]Souce code of creator classes.},label={appendixScheme:integratorCreator}] |
209 |
|
|
210 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
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_; |
221 |
> |
string ident_; |
222 |
|
}; |
223 |
|
|
224 |
< |
template<class ConcreteIntegrator> |
225 |
< |
class IntegratorBuilder : public IntegratorCreator { |
224 |
> |
template<class ConcreteIntegrator> class IntegratorBuilder : |
225 |
> |
public IntegratorCreator { |
226 |
|
public: |
227 |
< |
IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {} |
228 |
< |
virtual Integrator* create(SimInfo* info) const { |
229 |
< |
return new ConcreteIntegrator(info); |
230 |
< |
} |
227 |
> |
IntegratorBuilder(const string& ident) |
228 |
> |
: IntegratorCreator(ident) {} |
229 |
> |
virtual Integrator* create(SimInfo* info) const { |
230 |
> |
return new ConcreteIntegrator(info); |
231 |
> |
} |
232 |
|
}; |
233 |
|
\end{lstlisting} |
234 |
|
|
223 |
– |
\subsection{\label{appendixSection:visitorPattern}Visitor} |
224 |
– |
|
225 |
– |
The purpose of the Visitor Pattern is to encapsulate an operation |
226 |
– |
that you want to perform on the elements. The operation being |
227 |
– |
performed on a structure can be switched without changing the |
228 |
– |
interfaces of the elements. In other words, one can add virtual |
229 |
– |
functions into a set of classes without modifying their interfaces. |
230 |
– |
The UML class diagram of Visitor patten is shown in |
231 |
– |
Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
232 |
– |
Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
233 |
– |
extensively. |
234 |
– |
|
235 |
– |
\begin{figure} |
236 |
– |
\centering |
237 |
– |
\includegraphics[width=\linewidth]{visitor.eps} |
238 |
– |
\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
239 |
– |
of {\sc OOPSE}} \label{appendixFig:visitorUML} |
240 |
– |
\end{figure} |
241 |
– |
|
242 |
– |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
243 |
– |
|
244 |
– |
class BaseVisitor{ |
245 |
– |
public: |
246 |
– |
virtual void visit(Atom* atom); |
247 |
– |
virtual void visit(DirectionalAtom* datom); |
248 |
– |
virtual void visit(RigidBody* rb); |
249 |
– |
}; |
250 |
– |
|
251 |
– |
\end{lstlisting} |
252 |
– |
|
235 |
|
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
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}] |
266 |
+ |
class BaseVisitor{ |
267 |
+ |
public: |
268 |
+ |
virtual void visit(Atom* atom); |
269 |
+ |
virtual void visit(DirectionalAtom* datom); |
270 |
+ |
virtual void visit(RigidBody* rb); |
271 |
+ |
}; |
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); |
277 |
+ |
}; |
278 |
+ |
class CompositeVisitor: public BaseVisitor { |
279 |
+ |
public: |
280 |
+ |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
281 |
+ |
typedef VistorListType::iterator VisitorListIterator; |
282 |
+ |
virtual void visit(Atom* atom) { |
283 |
+ |
VisitorListIterator i; |
284 |
+ |
BaseVisitor* curVisitor; |
285 |
+ |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) |
286 |
+ |
atom->accept(*i); |
287 |
+ |
} |
288 |
+ |
virtual void visit(DirectionalAtom* datom) { |
289 |
+ |
VisitorListIterator i; |
290 |
+ |
BaseVisitor* curVisitor; |
291 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) |
292 |
+ |
atom->accept(*i); |
293 |
+ |
} |
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 = visitorList.begin();i != visitorList.end();++i) { |
300 |
+ |
rb->accept(*i); |
301 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai) |
302 |
+ |
(*ai)->accept(*i); |
303 |
+ |
} |
304 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
305 |
+ |
protected: |
306 |
+ |
VistorListType visitorList; |
307 |
+ |
}; |
308 |
+ |
\end{lstlisting} |
309 |
+ |
|
310 |
|
\section{\label{appendixSection:concepts}Concepts} |
311 |
|
|
312 |
|
OOPSE manipulates both traditional atoms as well as some objects |
313 |
|
that {\it behave like atoms}. These objects can be rigid |
314 |
|
collections of atoms or atoms which have orientational degrees of |
315 |
< |
freedom. A diagram of the class heirarchy is illustrated in |
316 |
< |
Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and |
315 |
> |
freedom. A diagram of the class hierarchy is illustrated in |
316 |
> |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
317 |
|
DirectionalAtom in {\sc OOPSE} have their own names which are |
318 |
< |
specified in the {\tt .md} file. In contrast, RigidBodies are |
318 |
> |
specified in the meta data file. In contrast, RigidBodies are |
319 |
|
denoted by their membership and index inside a particular molecule: |
320 |
|
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
321 |
|
on the specifics of the simulation). The names of rigid bodies are |
322 |
|
generated automatically. For example, the name of the first rigid |
323 |
|
body in a DMPC molecule is DMPC\_RB\_0. |
297 |
– |
\begin{figure} |
298 |
– |
\centering |
299 |
– |
\includegraphics[width=\linewidth]{heirarchy.eps} |
300 |
– |
\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of |
301 |
– |
the class heirarchy. |
324 |
|
\begin{itemize} |
325 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
326 |
|
integrators and minimizers. |
329 |
|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
330 |
|
DirectionalAtom}s which behaves as a single unit. |
331 |
|
\end{itemize} |
310 |
– |
} \label{oopseFig:heirarchy} |
311 |
– |
\end{figure} |
332 |
|
|
333 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
334 |
|
|
335 |
< |
The most general form of the select command is: {\tt select {\it |
336 |
< |
expression}}. This expression represents an arbitrary set of |
317 |
< |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
318 |
< |
composed of either name expressions, index expressions, predefined |
319 |
< |
sets, user-defined expressions, comparison operators, within |
320 |
< |
expressions, or logical combinations of the above expression types. |
321 |
< |
Expressions can be combined using parentheses and the Boolean |
322 |
< |
operators. |
335 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
336 |
> |
StuntDoubles. The most general form of the select command is: |
337 |
|
|
338 |
+ |
{\tt select {\it expression}}. |
339 |
+ |
|
340 |
+ |
This expression represents an arbitrary set of StuntDoubles (Atoms |
341 |
+ |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
342 |
+ |
name expressions, index expressions, predefined sets, user-defined |
343 |
+ |
expressions, comparison operators, within expressions, or logical |
344 |
+ |
combinations of the above expression types. Expressions can be |
345 |
+ |
combined using parentheses and the Boolean operators. |
346 |
+ |
|
347 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
348 |
|
|
349 |
|
The logical operators allow complex queries to be constructed out of |
475 |
|
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
476 |
|
also be used to compute the density distributions of other molecules |
477 |
|
in a reference frame {\it fixed to the body-fixed reference frame} |
478 |
< |
of a selected atom or rigid body. |
478 |
> |
of a selected atom or rigid body. Due to the fact that the selected |
479 |
> |
StuntDoubles from two selections may be overlapped, {\tt |
480 |
> |
StaticProps} performs the calculation in three stages which are |
481 |
> |
illustrated in Fig.~\ref{oopseFig:staticPropsProcess}. |
482 |
> |
|
483 |
> |
\begin{figure} |
484 |
> |
\centering |
485 |
> |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
486 |
> |
\caption[A representation of the three-stage correlations in |
487 |
> |
\texttt{StaticProps}]{This diagram illustrates three-stage |
488 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
489 |
> |
numbers of selected StuntDobules from {\tt -{}-sele1} and {\tt |
490 |
> |
-{}-sele2} respectively, while $C$ is the number of StuntDobules |
491 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
492 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
493 |
> |
the contrary, the third stage($C$ and $C$) are completely |
494 |
> |
overlapping} \label{oopseFig:staticPropsProcess} |
495 |
> |
\end{figure} |
496 |
|
|
497 |
+ |
\begin{figure} |
498 |
+ |
\centering |
499 |
+ |
\includegraphics[width=3in]{definition.eps} |
500 |
+ |
\caption[Definitions of the angles between directional objects]{Any |
501 |
+ |
two directional objects (DirectionalAtoms and RigidBodies) have a |
502 |
+ |
set of two angles ($\theta$, and $\omega$) between the z-axes of |
503 |
+ |
their body-fixed frames.} \label{oopseFig:gofr} |
504 |
+ |
\end{figure} |
505 |
+ |
|
506 |
|
There are five seperate radial distribution functions availiable in |
507 |
|
OOPSE. Since every radial distrbution function invlove the |
508 |
|
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
546 |
|
\end{description} |
547 |
|
|
548 |
|
The vectors (and angles) associated with these angular pair |
549 |
< |
distribution functions are most easily seen in the figure below: |
549 |
> |
distribution functions are most easily seen in |
550 |
> |
Fig.~\ref{oopseFig:gofr}. The options available for {\tt |
551 |
> |
StaticProps} are showed in Table.~\ref{appendix:staticPropsOptions}. |
552 |
|
|
502 |
– |
\begin{figure} |
503 |
– |
\centering |
504 |
– |
\includegraphics[width=3in]{definition.eps} |
505 |
– |
\caption[Definitions of the angles between directional objects]{ \\ |
506 |
– |
Any two directional objects (DirectionalAtoms and RigidBodies) have |
507 |
– |
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
508 |
– |
their body-fixed frames.} \label{oopseFig:gofr} |
509 |
– |
\end{figure} |
510 |
– |
|
511 |
– |
Due to the fact that the selected StuntDoubles from two selections |
512 |
– |
may be overlapped, {\tt StaticProps} performs the calculation in |
513 |
– |
three stages which are illustrated in |
514 |
– |
Fig.~\ref{oopseFig:staticPropsProcess}. |
515 |
– |
|
516 |
– |
\begin{figure} |
517 |
– |
\centering |
518 |
– |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
519 |
– |
\caption[A representation of the three-stage correlations in |
520 |
– |
\texttt{StaticProps}]{This diagram illustrates three-stage |
521 |
– |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
522 |
– |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
523 |
– |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
524 |
– |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
525 |
– |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
526 |
– |
the contrary, the third stage($C$ and $C$) are completely |
527 |
– |
overlapping} \label{oopseFig:staticPropsProcess} |
528 |
– |
\end{figure} |
529 |
– |
|
530 |
– |
The options available for {\tt StaticProps} are as follows: |
531 |
– |
\begin{longtable}[c]{|EFG|} |
532 |
– |
\caption{StaticProps Command-line Options} |
533 |
– |
\\ \hline |
534 |
– |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
535 |
– |
\endhead |
536 |
– |
\hline |
537 |
– |
\endfoot |
538 |
– |
-h& {\tt -{}-help} & Print help and exit \\ |
539 |
– |
-V& {\tt -{}-version} & Print version and exit \\ |
540 |
– |
-i& {\tt -{}-input} & input dump file \\ |
541 |
– |
-o& {\tt -{}-output} & output file name \\ |
542 |
– |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
543 |
– |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
544 |
– |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
545 |
– |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
546 |
– |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
547 |
– |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
548 |
– |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
549 |
– |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
550 |
– |
& {\tt -{}-molname} & molecule name \\ |
551 |
– |
& {\tt -{}-begin} & begin internal index \\ |
552 |
– |
& {\tt -{}-end} & end internal index \\ |
553 |
– |
\hline |
554 |
– |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
555 |
– |
\hline |
556 |
– |
& {\tt -{}-gofr} & $g(r)$ \\ |
557 |
– |
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
558 |
– |
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
559 |
– |
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
560 |
– |
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
561 |
– |
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
562 |
– |
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
563 |
– |
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
564 |
– |
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
565 |
– |
\end{longtable} |
566 |
– |
|
553 |
|
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
554 |
|
|
555 |
|
{\tt DynamicProps} computes time correlation functions from the |
575 |
|
select different types of atoms is already present in the code. |
576 |
|
|
577 |
|
For large simulations, the trajectory files can sometimes reach |
578 |
< |
sizes in excess of several gigabytes. In order to effectively |
579 |
< |
analyze that amount of data. In order to prevent a situation where |
580 |
< |
the program runs out of memory due to large trajectories, |
581 |
< |
\texttt{dynamicProps} will estimate the size of free memory at |
582 |
< |
first, and determine the number of frames in each block, which |
597 |
< |
allows the operating system to load two blocks of data |
578 |
> |
sizes in excess of several gigabytes. In order to prevent a |
579 |
> |
situation where the program runs out of memory due to large |
580 |
> |
trajectories, \texttt{dynamicProps} will first estimate the size of |
581 |
> |
free memory, and determine the number of frames in each block, which |
582 |
> |
will allow the operating system to load two blocks of data |
583 |
|
simultaneously without swapping. Upon reading two blocks of the |
584 |
|
trajectory, \texttt{dynamicProps} will calculate the time |
585 |
|
correlation within the first block and the cross correlations |
588 |
|
trajectory. Once the end is reached, the first block is freed then |
589 |
|
incremented, until all frame pairs have been correlated in time. |
590 |
|
This process is illustrated in |
591 |
< |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
591 |
> |
Fig.~\ref{oopseFig:dynamicPropsProcess} and the options available |
592 |
> |
for DynamicProps are showed in |
593 |
> |
Table.~\ref{appendix:dynamicPropsOptions} |
594 |
|
|
595 |
|
\begin{figure} |
596 |
|
\centering |
603 |
|
\label{oopseFig:dynamicPropsProcess} |
604 |
|
\end{figure} |
605 |
|
|
619 |
– |
The options available for DynamicProps are as follows: |
606 |
|
\begin{longtable}[c]{|EFG|} |
607 |
< |
\caption{DynamicProps Command-line Options} |
607 |
> |
\caption{STATICPROPS COMMAND-LINE OPTIONS} |
608 |
> |
\label{appendix:staticPropsOptions} |
609 |
|
\\ \hline |
610 |
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
611 |
|
\endhead |
612 |
|
\hline |
613 |
|
\endfoot |
614 |
+ |
-h& {\tt -{}-help} & Print help and exit \\ |
615 |
+ |
-V& {\tt -{}-version} & Print version and exit \\ |
616 |
+ |
-i& {\tt -{}-input} & input dump file \\ |
617 |
+ |
-o& {\tt -{}-output} & output file name \\ |
618 |
+ |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
619 |
+ |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
620 |
+ |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
621 |
+ |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
622 |
+ |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
623 |
+ |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
624 |
+ |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
625 |
+ |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
626 |
+ |
& {\tt -{}-molname} & molecule name \\ |
627 |
+ |
& {\tt -{}-begin} & begin internal index \\ |
628 |
+ |
& {\tt -{}-end} & end internal index \\ |
629 |
+ |
\hline |
630 |
+ |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
631 |
+ |
\hline |
632 |
+ |
& {\tt -{}-gofr} & $g(r)$ \\ |
633 |
+ |
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
634 |
+ |
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
635 |
+ |
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
636 |
+ |
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
637 |
+ |
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
638 |
+ |
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
639 |
+ |
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
640 |
+ |
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
641 |
+ |
\end{longtable} |
642 |
+ |
|
643 |
+ |
\begin{longtable}[c]{|EFG|} |
644 |
+ |
\caption{DYNAMICPROPS COMMAND-LINE OPTIONS} |
645 |
+ |
\label{appendix:dynamicPropsOptions} |
646 |
+ |
\\ \hline |
647 |
+ |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
648 |
+ |
\endhead |
649 |
+ |
\hline |
650 |
+ |
\endfoot |
651 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
652 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
653 |
|
-i& {\tt -{}-input} & input dump file \\ |
671 |
|
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
672 |
|
as follows: |
673 |
|
|
650 |
– |
|
674 |
|
\begin{longtable}[c]{|EFG|} |
675 |
< |
\caption{Dump2XYZ Command-line Options} |
675 |
> |
\caption{DUMP2XYZ COMMAND-LINE OPTIONS} |
676 |
|
\\ \hline |
677 |
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
678 |
|
\endhead |
706 |
|
the beads which are used to approximate the arbitrary shapes. The |
707 |
|
options available for Hydro are as follows: |
708 |
|
\begin{longtable}[c]{|EFG|} |
709 |
< |
\caption{Hydrodynamics Command-line Options} |
709 |
> |
\caption{HYDRODYNAMICS COMMAND-LINE OPTIONS} |
710 |
|
\\ \hline |
711 |
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
712 |
|
\endhead |