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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 |
15 |
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Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new |
16 |
< |
molecular dynamics package has some unique features |
16 |
> |
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 |
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|
atom types (transition metals, point dipoles, sticky potentials, |
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|
extensive set of the STL and Fortran90 modules, the {\sc Base |
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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 |
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 |
44 |
> |
molecules 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 |
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|
required for applications is provided by the third layer which |
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|
handling, but also defines a generic force field interface. Another |
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|
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. |
53 |
> |
for Language Recognition (ANTLR)\cite{Parr1995, Schaps1999} syntax. |
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|
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 |
56 |
> |
Chapter.~\ref{chapt:methodology}). The structure module contains a |
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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 |
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 |
< |
Sec.~\ref{appendixSection:hydrodynamics}) \textit{etc}. |
65 |
> |
Sec.~\ref{appendixSection:hydrodynamics}). |
66 |
|
|
67 |
|
\begin{figure} |
68 |
|
\centering |
75 |
|
|
76 |
|
Design patterns are optimal solutions to commonly-occurring problems |
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|
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 |
78 |
> |
concept for buildings and towns by Christopher |
79 |
> |
Alexander,\cite{Alexander1987} design patterns first became popular |
80 |
> |
in software engineering with the wide acceptance of the book, Design |
81 |
> |
Patterns: Elements of Reusable Object-Oriented |
82 |
> |
Software.\cite{Gamma1994} Patterns reflect the experience, knowledge |
83 |
> |
and insights of developers who have successfully used these patterns |
84 |
> |
in 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}. |
89 |
> |
OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}. The |
90 |
> |
following sections enumerates some of the patterns used in {\sc |
91 |
> |
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 design, such as lifespan control \textit{etc}, we only use |
99 |
> |
software design, such as lifespan control, 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 |
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. |
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 by using the Composite pattern,\cite{Gamma1994} |
141 |
> |
CompositeVisitor manages a priority visitor list and handles the |
142 |
> |
execution of every visitor in the priority list on different |
143 |
> |
StuntDoubles. |
144 |
|
|
145 |
|
\begin{figure} |
146 |
|
\centering |
668 |
|
|
669 |
|
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
670 |
|
which can be opened by other molecular dynamics viewers such as Jmol |
671 |
< |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
671 |
> |
and VMD.\cite{Humphrey1996} The options available for Dump2XYZ are |
672 |
|
as follows: |
673 |
|
|
674 |
|
\begin{longtable}[c]{|EFG|} |