13 |
|
structural and dynamic processes in condensed phase systems like |
14 |
|
biological 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 |
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, |
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 |
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 |
47 |
|
required for applications is provided by the third layer which |
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. |
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 |
56 |
> |
Chapter.~\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 |
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 |
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 |
89 |
> |
OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}. |
90 |
> |
The following sections enumerates some of the patterns |
91 |
|
used in {\sc OOPSE}. |
92 |
|
|
93 |
|
\subsection{\label{appendixSection:singleton}Singletons} |
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 |