--- trunk/tengDissertation/Appendix.tex	2006/07/16 02:48:00	2937
+++ trunk/tengDissertation/Appendix.tex	2006/07/17 15:28:44	2938
@@ -13,7 +13,7 @@ molecular dynamics package has some unique features
 structural and dynamic processes in condensed phase systems like
 biological membranes and nanoparticles, we developed an open source
 Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new
-molecular dynamics package has some unique features
+molecular dynamics package has some unique features:
 \begin{enumerate}
   \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
 atom types (transition metals, point dipoles, sticky potentials,
@@ -38,10 +38,10 @@ advanced data structures and algorithms(e.g., tuple, b
 extensive set of the STL and Fortran90 modules, the {\sc Base
 Classes} provide generic implementations of mathematical objects
 (e.g., matrices, vectors, polynomials, random number generators) and
-advanced data structures and algorithms(e.g., tuple, bitset, generic
+advanced data structures and algorithms (e.g., tuple, bitset, generic
 data and string manipulation). The molecular data structures for the
 representation of atoms, bonds, bends, torsions, rigid bodies and
-molecules \textit{etc} are contained in the {\sc Kernel} which is
+molecules are contained in the {\sc Kernel} which is
 implemented with {\sc Base Classes} and are carefully designed to
 provide maximum extensibility and flexibility. The functionality
 required for applications is provided by the third layer which
@@ -50,10 +50,10 @@ for Language Recognition(ANTLR)\cite{Parr1995, Schaps1
 handling, but also defines a generic force field interface. Another
 important component of Input/Output module is the parser for
 meta-data files, which has been implemented using the ANother Tool
-for Language Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax.
+for Language Recognition (ANTLR)\cite{Parr1995, Schaps1999} syntax.
 The Molecular Mechanics module consists of energy minimization and a
 wide variety of integration methods(see
-Chap.~\ref{chapt:methodology}). The structure module contains a
+Chapter.~\ref{chapt:methodology}). The structure module contains a
 flexible and powerful selection library which syntax is elaborated
 in Sec.~\ref{appendixSection:syntax}. The top layer is made of the
 main program of the package, \texttt{oopse} and it corresponding
@@ -62,7 +62,7 @@ Sec.~\ref{appendixSection:hydrodynamics}) \textit{etc}
 Sec.~\ref{appendixSection:StaticProps}), \texttt{DynamicProps} (see
 Sec.~\ref{appendixSection:DynamicProps}), \texttt{Dump2XYZ} (see
 Sec.~\ref{appendixSection:Dump2XYZ}), \texttt{Hydro} (see
-Sec.~\ref{appendixSection:hydrodynamics}) \textit{etc}.
+Sec.~\ref{appendixSection:hydrodynamics}).
 
 \begin{figure}
 \centering
@@ -86,8 +86,8 @@ OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004
 one of the latest advanced techniques to emerge from object-oriented
 community, design patterns were applied in some of the modern
 scientific software applications, such as JMol, {\sc
-OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}
-\textit{etc}. The following sections enumerates some of the patterns
+OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}. 
+The following sections enumerates some of the patterns
 used in {\sc OOPSE}.
 
 \subsection{\label{appendixSection:singleton}Singletons}
@@ -96,7 +96,7 @@ software design, such as lifespan control \textit{etc}
 instantiation of a class to one object, but also provides a global
 point of access to the object. Although the singleton pattern can be
 implemented in various ways  to account for different aspects of the
-software design, such as lifespan control \textit{etc}, we only use
+software design, such as lifespan control, we only use
 the static data approach in {\sc OOPSE}. The declaration and
 implementation of IntegratorFactory class are given by declared in
 List.~\ref{appendixScheme:singletonDeclaration} and