--- trunk/tengDissertation/Appendix.tex	2006/06/09 02:54:01	2840
+++ trunk/tengDissertation/Appendix.tex	2006/06/25 17:39:42	2883
@@ -1,22 +1,19 @@
 \appendix
 \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
 
-Absence of applying modern software development practices is the
-bottleneck of Scientific Computing community\cite{Wilson2006}. In
-the last 20 years , there are quite a few MD packages that were
+The absence of modern software development practices has been a
+bottleneck limiting progress in the Scientific Computing
+community\cite{Wilson2006}. In the last 20 years , a large number of
+few MD packages\cite{Brooks1983, Vincent1995, Kale1999} were
 developed to solve common MD problems and perform robust simulations
-. However, many of the codes are legacy programs that are either
-poorly organized or extremely complex. Usually, these packages were
-contributed by scientists without official computer science
-training. The development of most MD applications are lack of strong
-coordination to enforce design and programming guidelines. Moreover,
-most MD programs also suffer from missing design and implement
-documents which is crucial to the maintenance and extensibility.
-Along the way of studying structural and dynamic processes in
-condensed phase systems like biological membranes and nanoparticles,
-we developed and maintained an Object-Oriented Parallel Simulation
-Engine ({\sc OOPSE}). This new molecular dynamics package has some
-unique features
+. Most of these are commercial programs that are either poorly
+written or extremely complicated to use correctly. This situation
+prevents researchers from reusing or extending those packages to do
+cutting-edge research effectively. In the process of studying
+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
 \begin{enumerate}
   \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
 atom types (transition metals, point dipoles, sticky potentials,
@@ -36,36 +33,36 @@ Mainly written by \texttt{C/C++} and \texttt{Fortran90
 
 \section{\label{appendixSection:architecture }Architecture}
 
-Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
-uses C++ Standard Template Library (STL) and fortran modules as the
-foundation. As an extensive set of the STL and Fortran90 modules,
-{\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 data, 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 implemented with {\sc Base Classes} and are
-carefully designed to provide maximum extensibility and flexibility.
-The functionality required for applications is provide by the third
-layer which contains Input/Output, Molecular Mechanics and Structure
-modules. Input/Output module not only implements general methods for
-file handling, but also defines a generic force field interface.
-Another important component of Input/Output module is the meta-data
-file parser, which is rewritten using ANother Tool for Language
-Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
-Mechanics module consists of energy minimization and a wide
-varieties of integration methods(see Chap.~\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 parallel
-version \texttt{oopse\_MPI}, as well as other useful utilities, such
-as \texttt{StatProps} (see 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}.
+Mainly written by C++ and Fortran90, {\sc OOPSE} uses C++ Standard
+Template Library (STL) and fortran modules as a foundation. As an
+extensive set of the STL and Fortran90 modules, {\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
+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
+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
+contains Input/Output, Molecular Mechanics and Structure modules.
+The Input/Output module not only implements general methods for file
+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.
+The Molecular Mechanics module consists of energy minimization and a
+wide varieties of integration methods(see
+Chap.~\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
+parallel version \texttt{oopse\_MPI}, as well as other useful
+utilities, such as \texttt{StatProps} (see
+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}.
 
 \begin{figure}
 \centering
@@ -74,7 +71,7 @@ of {\sc OOPSE}} \label{appendixFig:architecture}
 of {\sc OOPSE}} \label{appendixFig:architecture}
 \end{figure}
 
-\section{\label{appendixSection:desginPattern}Design Pattern}
+\section{\label{appendixSection:desginPattern}Design Patterns}
 
 Design patterns are optimal solutions to commonly-occurring problems
 in software design. Although originated as an architectural concept
@@ -85,55 +82,68 @@ different problems as necessary. Pattern are expressiv
 the experience, knowledge and insights of developers who have
 successfully used these patterns in their own work. Patterns are
 reusable. They provide a ready-made solution that can be adapted to
-different problems as necessary. Pattern are expressive. they
-provide a common vocabulary of solutions that can express large
-solutions succinctly.
+different problems as necessary. As 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 used in {\sc OOPSE}.
 
-Patterns are usually described using a format that includes the
-following information:
-\begin{enumerate}
-  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
-  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
-  in the literature. In this case it is common practice to document these nicknames or synonyms under
-  the heading of \emph{Aliases} or \emph{Also Known As}.
-  \item The \emph{motivation} or \emph{context} that this pattern applies
-  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
-  \item The \emph{solution} to the problem that the pattern
-  addresses. It describes how to construct the necessary work products. The description may include
-  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
-  collaborations, to show how the problem is solved.
-  \item The \emph{consequences} of using the given solution to solve a
-  problem, both positive and negative.
-\end{enumerate}
+\subsection{\label{appendixSection:singleton}Singletons}
 
-As one of the latest advanced techniques emerged 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{Matthey2005}
-\textit{etc}. The following sections enumerates some of the patterns
-used in {\sc OOPSE}.
-
-\subsection{\label{appendixSection:singleton}Singleton}
-
 The Singleton pattern not only provides a mechanism to restrict
 instantiation of a class to one object, but also provides a global
-point of access to the object. Currently implemented as a global
-variable, the logging utility which reports error and warning
-messages to the console in {\sc OOPSE} is a good candidate for
-applying the Singleton pattern to avoid the global namespace
-pollution.Although the singleton pattern can be implemented in
-various ways  to account for different aspects of the software
-designs, such as lifespan control \textit{etc}, we only use the
-static data approach in {\sc OOPSE}. IntegratorFactory class is
-declared as
+point of access to the object. Although the singleton pattern can be
+implemented in various ways  to account for different aspects of the
+software designs, such as lifespan control \textit{etc}, 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
+Scheme.~\ref{appendixScheme:singletonImplementation} respectively.
+Since the constructor is declared as protected, a client can not
+instantiate IntegratorFactory directly. Moreover, since the member
+function getInstance serves as the only entry of access to
+IntegratorFactory, this approach fulfills the basic requirement, a
+single instance. Another consequence of this approach is the
+automatic destruction since static data are destroyed upon program
+termination.
 
+\subsection{\label{appendixSection:factoryMethod}Factory Methods}
+
+The Factory Method pattern is a creational pattern and deals with
+the problem of creating objects without specifying the exact class
+of object that will be created. Factory method is typically
+implemented by delegating the creation operation to the subclasses.
+One of the most popular Factory pattern is Parameterized Factory
+pattern which creates products based on their identifiers (see
+Scheme.~\ref{appendixScheme:factoryDeclaration}). If the identifier
+has been already registered, the factory method will invoke the
+corresponding creator (see
+Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the
+modern C++ template technique to avoid excess subclassing.
+
+\subsection{\label{appendixSection:visitorPattern}Visitor}
+
+The visitor pattern is designed to decouple the data structure and
+algorithms used upon them by collecting related operation from
+element classes into other visitor classes, which is equivalent to
+adding virtual functions into a set of classes without modifying
+their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
+structure of a Visitor pattern which is used extensively in {\tt
+Dump2XYZ}. In order to convert an OOPSE dump file, a series of
+distinct operations are performed on different StuntDoubles (See the
+class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration
+in Scheme.~\ref{appendixScheme:element}). Since the hierarchies
+remain stable, it is easy to define a visit operation (see
+Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble.
+Note that using Composite pattern\cite{Gamma1994}, CompositeVisitor
+manages a priority visitor list and handles the execution of every
+visitor in the priority list on different StuntDoubles.
+
 \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
 
-class IntegratorFactory {
-public:
-  static IntegratorFactory*
-  getInstance();
-protected:
+class IntegratorFactory { public:
+  static IntegratorFactory* getInstance(); protected:
   IntegratorFactory();
 private:
   static IntegratorFactory* instance_;
@@ -141,8 +151,6 @@ The corresponding implementation is
 
 \end{lstlisting}
 
-The corresponding implementation is
-
 \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
 
 IntegratorFactory::instance_ = NULL;
@@ -156,32 +164,9 @@ Since constructor is declared as protected, a client c
 
 \end{lstlisting}
 
-Since constructor is declared as protected, a client can not
-instantiate IntegratorFactory directly. Moreover, since the member
-function getInstance serves as the only entry of access to
-IntegratorFactory, this approach fulfills the basic requirement, a
-single instance. Another consequence of this approach is the
-automatic destruction since static data are destroyed upon program
-termination.
-
-\subsection{\label{appendixSection:factoryMethod}Factory Method}
-
-Categoried as a creational pattern, the Factory Method pattern deals
-with the problem of creating objects without specifying the exact
-class of object that will be created. Factory Method is typically
-implemented by delegating the creation operation to the subclasses.
-Parameterized Factory pattern where factory method (
-createIntegrator member function) creates products based on the
-identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If
-the identifier has been already registered, the factory method will
-invoke the corresponding creator (see List.~\ref{integratorCreator})
-which utilizes the modern C++ template technique to avoid excess
-subclassing.
-
 \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
 
-class IntegratorFactory {
-public:
+class IntegratorFactory { public:
   typedef std::map<string, IntegratorCreator*> CreatorMapType;
 
   bool registerIntegrator(IntegratorCreator* creator) {
@@ -205,7 +190,7 @@ class IntegratorCreator { (public)
 \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
 
 class IntegratorCreator {
-public:
+  public:
     IntegratorCreator(const string& ident) : ident_(ident) {}
 
     const string& getIdent() const { return ident_; }
@@ -216,71 +201,43 @@ template<class ConcreteIntegrator>
     string ident_;
 };
 
-template<class ConcreteIntegrator>
-class IntegratorBuilder : public IntegratorCreator {
-public:
-  IntegratorBuilder(const string& ident)
-                   : IntegratorCreator(ident) {}
-  virtual  Integrator* create(SimInfo* info) const {
-    return new ConcreteIntegrator(info);
-  }
+template<class ConcreteIntegrator> class IntegratorBuilder : public
+IntegratorCreator {
+  public:
+    IntegratorBuilder(const string& ident)
+                     : IntegratorCreator(ident) {}
+    virtual  Integrator* create(SimInfo* info) const {
+      return new ConcreteIntegrator(info);
+    }
 };
 \end{lstlisting}
 
-\subsection{\label{appendixSection:visitorPattern}Visitor}
-
-The visitor pattern is designed to decouple the data structure and
-algorithms used upon them by collecting related operation from
-element classes into other visitor classes, which is equivalent to
-adding virtual functions into a set of classes without modifying
-their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
-structure of Visitor pattern which is used extensively in {\tt
-Dump2XYZ}. In order to convert an OOPSE dump file, a series of
-distinct operations are performed on different StuntDoubles (See the
-class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration
-in List.~\ref{appendixScheme:element}). Since the hierarchies
-remains stable, it is easy to define a visit operation (see
-List.~\ref{appendixScheme:visitor}) for each class of StuntDouble.
-Note that using Composite pattern\cite{Gamma1994}, CompositVisitor
-manages a priority visitor list and handles the execution of every
-visitor in the priority list on different StuntDoubles.
-
-\begin{figure}
-\centering
-\includegraphics[width=\linewidth]{visitor.eps}
-\caption[The UML class diagram of Visitor patten] {The UML class
-diagram of Visitor patten.} \label{appendixFig:visitorUML}
-\end{figure}
-
-\begin{figure}
-\centering
-\includegraphics[width=\linewidth]{hierarchy.eps}
-\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
-the class hierarchy. } \label{oopseFig:hierarchy}
-\end{figure}
-
 \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
 
-class StuntDouble { public:
-  virtual void accept(BaseVisitor* v) = 0;
+class StuntDouble {
+  public:
+    virtual void accept(BaseVisitor* v) = 0;
 };
 
-class Atom: public StuntDouble { public:
-  virtual void accept{BaseVisitor* v*} {
-    v->visit(this);
-  }
+class Atom: public StuntDouble {
+  public:
+    virtual void accept{BaseVisitor* v*} {
+      v->visit(this);
+    }
 };
 
-class DirectionalAtom: public Atom { public:
-  virtual void accept{BaseVisitor* v*} {
-    v->visit(this);
-  }
+class DirectionalAtom: public Atom {
+  public:
+    virtual void accept{BaseVisitor* v*} {
+      v->visit(this);
+    }
 };
 
-class RigidBody: public StuntDouble { public:
-  virtual void accept{BaseVisitor* v*} {
-    v->visit(this);
-  }
+class RigidBody: public StuntDouble {
+  public:
+    virtual void accept{BaseVisitor* v*} {
+      v->visit(this);
+    }
 };
 
 \end{lstlisting}
@@ -288,33 +245,27 @@ class BaseVisitor{ (public)
 \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
 
 class BaseVisitor{
-public:
-  virtual void visit(Atom* atom);
-  virtual void visit(DirectionalAtom* datom);
-  virtual void visit(RigidBody* rb);
+  public:
+    virtual void visit(Atom* atom);
+    virtual void visit(DirectionalAtom* datom);
+    virtual void visit(RigidBody* rb);
 };
 
-class BaseAtomVisitor:public BaseVisitor{ public:
-  virtual void visit(Atom* atom);
-  virtual void visit(DirectionalAtom* datom);
-  virtual void visit(RigidBody* rb);
-};
-
-class SSDAtomVisitor:public BaseAtomVisitor{ public:
-  virtual void visit(Atom* atom);
-  virtual void visit(DirectionalAtom* datom);
-  virtual void visit(RigidBody* rb);
+class BaseAtomVisitor:public BaseVisitor{
+  public:
+    virtual void visit(Atom* atom);
+    virtual void visit(DirectionalAtom* datom);
+    virtual void visit(RigidBody* rb);
 };
 
 class CompositeVisitor: public BaseVisitor {
-public:
-
+  public:
   typedef list<pair<BaseVisitor*, int> > VistorListType;
   typedef VistorListType::iterator VisitorListIterator;
   virtual void visit(Atom* atom) {
     VisitorListIterator i;
     BaseVisitor* curVisitor;
-    for(i = visitorList.begin();i != visitorList.end();++i) {
+    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
       atom->accept(*i);
     }
   }
@@ -322,7 +273,7 @@ class CompositeVisitor: public BaseVisitor { (public)
   virtual void visit(DirectionalAtom* datom) {
     VisitorListIterator i;
     BaseVisitor* curVisitor;
-    for(i = visitorList.begin();i != visitorList.end();++i) {
+    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
       atom->accept(*i);
     }
   }
@@ -332,21 +283,35 @@ class CompositeVisitor: public BaseVisitor { (public)
     std::vector<Atom*> myAtoms;
     std::vector<Atom*>::iterator ai;
     myAtoms = rb->getAtoms();
-    for(i = visitorList.begin();i != visitorList.end();++i) {{
+    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
       rb->accept(*i);
       for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
         (*ai)->accept(*i);
+      }
     }
-  }
 
   void addVisitor(BaseVisitor* v, int priority);
-
   protected:
     VistorListType visitorList;
 };
-
 \end{lstlisting}
 
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{visitor.eps}
+\caption[The UML class diagram of Visitor patten] {The UML class
+diagram of Visitor patten.} \label{appendixFig:visitorUML}
+\end{figure}
+
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{hierarchy.eps}
+\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
+the class hierarchy. Objects below others on the diagram inherit
+data structures and functions from their parent classes above them.}
+\label{oopseFig:hierarchy}
+\end{figure}
+
 \section{\label{appendixSection:concepts}Concepts}
 
 OOPSE manipulates both traditional atoms as well as some objects
@@ -355,7 +320,7 @@ specified in the {\tt .md} file. In contrast, RigidBod
 freedom.  A diagram of the class hierarchy is illustrated in
 Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
 DirectionalAtom in {\sc OOPSE} have their own names which are
-specified in the {\tt .md} file. In contrast, RigidBodies are
+specified in the meta data file. In contrast, RigidBodies are
 denoted by their membership and index inside a particular molecule:
 [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
 on the specifics of the simulation). The names of rigid bodies are
@@ -515,8 +480,34 @@ of a selected atom or rigid body.
 and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
 also be used to compute the density distributions of other molecules
 in a reference frame {\it fixed to the body-fixed reference frame}
-of a selected atom or rigid body.
+of a selected atom or rigid body. Due to the fact that the selected
+StuntDoubles from two selections may be overlapped, {\tt
+StaticProps} performs the calculation in three stages which are
+illustrated in Fig.~\ref{oopseFig:staticPropsProcess}.
+
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{staticPropsProcess.eps}
+\caption[A representation of the three-stage correlations in
+\texttt{StaticProps}]{This diagram illustrates three-stage
+processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
+numbers of selected StuntDobules from {\tt -{}-sele1} and {\tt
+-{}-sele2} respectively, while $C$ is the number of StuntDobules
+appearing at both sets. The first stage($S_1-C$ and $S_2$) and
+second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
+the contrary, the third stage($C$ and $C$) are completely
+overlapping} \label{oopseFig:staticPropsProcess}
+\end{figure}
 
+\begin{figure}
+\centering
+\includegraphics[width=3in]{definition.eps}
+\caption[Definitions of the angles between directional objects]{Any
+two directional objects (DirectionalAtoms and RigidBodies) have a
+set of two angles ($\theta$, and $\omega$) between the z-axes of
+their body-fixed frames.} \label{oopseFig:gofr}
+\end{figure}
+
 There are five seperate radial distribution functions availiable in
 OOPSE. Since every radial distrbution function invlove the
 calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
@@ -560,36 +551,9 @@ distribution functions are most easily seen in the fig
 \end{description}
 
 The vectors (and angles) associated with these angular pair
-distribution functions are most easily seen in the figure below:
+distribution functions are most easily seen in
+Fig.~\ref{oopseFig:gofr}.
 
-\begin{figure}
-\centering
-\includegraphics[width=3in]{definition.eps}
-\caption[Definitions of the angles between directional objects]{ \\
-Any two directional objects (DirectionalAtoms and RigidBodies) have
-a set of two angles ($\theta$, and $\omega$) between the z-axes of
-their body-fixed frames.} \label{oopseFig:gofr}
-\end{figure}
-
-Due to the fact that the selected StuntDoubles from two selections
-may be overlapped, {\tt StaticProps} performs the calculation in
-three stages which are illustrated in
-Fig.~\ref{oopseFig:staticPropsProcess}.
-
-\begin{figure}
-\centering
-\includegraphics[width=\linewidth]{staticPropsProcess.eps}
-\caption[A representation of the three-stage correlations in
-\texttt{StaticProps}]{This diagram illustrates three-stage
-processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
-numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
--{}-sele2} respectively, while $C$ is the number of stuntdobules
-appearing at both sets. The first stage($S_1-C$ and $S_2$) and
-second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
-the contrary, the third stage($C$ and $C$) are completely
-overlapping} \label{oopseFig:staticPropsProcess}
-\end{figure}
-
 The options available for {\tt StaticProps} are as follows:
 \begin{longtable}[c]{|EFG|}
 \caption{StaticProps Command-line Options}
@@ -652,12 +616,11 @@ sizes in excess of several gigabytes. In order to effe
 select different types of atoms is already present in the code.
 
 For large simulations, the trajectory files can sometimes reach
-sizes in excess of several gigabytes. In order to effectively
-analyze that amount of data. In order to prevent a situation where
-the program runs out of memory due to large trajectories,
-\texttt{dynamicProps} will estimate the size of free memory at
-first, and determine the number of frames in each block, which
-allows the operating system to load two blocks of data
+sizes in excess of several gigabytes. In order to prevent a
+situation where the program runs out of memory due to large
+trajectories, \texttt{dynamicProps} will first estimate the size of
+free memory, and determine the number of frames in each block, which
+will allow the operating system to load two blocks of data
 simultaneously without swapping. Upon reading two blocks of the
 trajectory, \texttt{dynamicProps} will calculate the time
 correlation within the first block and the cross correlations
