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1   \appendix
2   \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
3  
4 < Designing object-oriented software is hard, and designing reusable
5 < object-oriented scientific software is even harder. Absence of
6 < 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
9 < developed to solve common MD problems and perform robust simulations
10 < . However, many of the codes are legacy programs that are either
11 < poorly organized or extremely complex. Usually, these packages were
12 < contributed by scientists without official computer science
13 < training. The development of most MD applications are lack of strong
14 < coordination to enforce design and programming guidelines. Moreover,
15 < most MD programs also suffer from missing design and implement
16 < documents which is crucial to the maintenance and extensibility.
17 < Along the way of studying structural and dynamic processes in
18 < condensed phase systems like biological membranes and nanoparticles,
19 < we developed and maintained an Object-Oriented Parallel Simulation
20 < Engine ({\sc OOPSE}). This new molecular dynamics package has some
21 < unique features
4 > Absence of applying modern software development practices is the
5 > bottleneck of Scientific Computing community\cite{Wilson2006}. In
6 > the last 20 years , there are quite a few MD
7 > packages\cite{Brooks1983, Vincent1995, Kale1999} that were developed
8 > to solve common MD problems and perform robust simulations .
9 > Unfortunately, most of them are commercial programs that are either
10 > poorly written or extremely complicate. Consequently, it prevents
11 > the researchers to reuse or extend those packages to do cutting-edge
12 > research effectively. Along the way of studying structural and
13 > dynamic processes in condensed phase systems like biological
14 > 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
17   \begin{enumerate}
18    \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
19   atom types (transition metals, point dipoles, sticky potentials,
# Line 64 | Line 59 | as \texttt{StatProps} (see Sec.~\ref{appendixSection:S
59   program of the package, \texttt{oopse} and it corresponding parallel
60   version \texttt{oopse\_MPI}, as well as other useful utilities, such
61   as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}),
62 < \texttt{DynamicProps} (see
63 < Sec.~\ref{appendixSection:appendixSection:DynamicProps}),
64 < \texttt{Dump2XYZ} (see
70 < Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro}
71 < (see Sec.~\ref{appendixSection:appendixSection:hydrodynamics})
62 > \texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}),
63 > \texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}),
64 > \texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics})
65   \textit{etc}.
66  
67   \begin{figure}
# Line 91 | Line 84 | solutions succinctly.
84   reusable. They provide a ready-made solution that can be adapted to
85   different problems as necessary. Pattern are expressive. they
86   provide a common vocabulary of solutions that can express large
87 < solutions succinctly.
87 > solutions succinctly. As one of the latest advanced techniques
88 > emerged from object-oriented community, design patterns were applied
89 > in some of the modern scientific software applications, such as
90 > JMol, {\sc OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}
91 > \textit{etc}. The following sections enumerates some of the patterns
92 > used in {\sc OOPSE}.
93  
96 – Patterns are usually described using a format that includes the
97 – following information:
98 – \begin{enumerate}
99 –  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
100 –  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
101 –  in the literature. In this case it is common practice to document these nicknames or synonyms under
102 –  the heading of \emph{Aliases} or \emph{Also Known As}.
103 –  \item The \emph{motivation} or \emph{context} that this pattern applies
104 –  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
105 –  \item The \emph{solution} to the problem that the pattern
106 –  addresses. It describes how to construct the necessary work products. The description may include
107 –  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
108 –  collaborations, to show how the problem is solved.
109 –  \item The \emph{consequences} of using the given solution to solve a
110 –  problem, both positive and negative.
111 – \end{enumerate}
112 –
113 – As one of the latest advanced techniques emerged from
114 – object-oriented community, design patterns were applied in some of
115 – the modern scientific software applications, such as JMol, {\sc
116 – OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}.
117 – The following sections enumerates some of the patterns used in {\sc
118 – OOPSE}.
119 –
94   \subsection{\label{appendixSection:singleton}Singleton}
95 +
96   The Singleton pattern not only provides a mechanism to restrict
97   instantiation of a class to one object, but also provides a global
98   point of access to the object. Currently implemented as a global
99   variable, the logging utility which reports error and warning
100   messages to the console in {\sc OOPSE} is a good candidate for
101   applying the Singleton pattern to avoid the global namespace
102 < pollution.Although the singleton pattern can be implemented in
102 > pollution. Although the singleton pattern can be implemented in
103   various ways  to account for different aspects of the software
104   designs, such as lifespan control \textit{etc}, we only use the
105 < static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class
106 < is declared as
107 < \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}]
105 > static data approach in {\sc OOPSE}. The declaration and
106 > implementation of IntegratorFactory class are given by declared in
107 > List.~\ref{appendixScheme:singletonDeclaration} and
108 > List.~\ref{appendixScheme:singletonImplementation} respectively.
109 > Since constructor is declared as protected, a client can not
110 > instantiate IntegratorFactory directly. Moreover, since the member
111 > function getInstance serves as the only entry of access to
112 > IntegratorFactory, this approach fulfills the basic requirement, a
113 > single instance. Another consequence of this approach is the
114 > automatic destruction since static data are destroyed upon program
115 > termination.
116 > \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
117  
118   class IntegratorFactory {
119 <  public:
120 <    static IntegratorFactory* getInstance();
121 <    protected:
122 <      IntegratorFactory();
123 <    private:
124 <      static IntegratorFactory* instance_;
119 > public:
120 >  static IntegratorFactory*
121 >  getInstance();
122 > protected:
123 >  IntegratorFactory();
124 > private:
125 >  static IntegratorFactory* instance_;
126   };
127  
128   \end{lstlisting}
144 – 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}]
129  
130 + \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
131 +
132   IntegratorFactory::instance_ = NULL;
133  
134   IntegratorFactory* getInstance() {
# Line 154 | Line 139 | Since constructor is declared as {\tt protected}, a cl
139   }
140  
141   \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.
142  
143 +
144   \subsection{\label{appendixSection:factoryMethod}Factory Method}
145  
146   Categoried as a creational pattern, the Factory Method pattern deals
147   with the problem of creating objects without specifying the exact
148   class of object that will be created. Factory Method is typically
149   implemented by delegating the creation operation to the subclasses.
150 + Parameterized Factory pattern where factory method (
151 + createIntegrator member function) creates products based on the
152 + identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If
153 + the identifier has been already registered, the factory method will
154 + invoke the corresponding creator (see
155 + List.~\ref{appendixScheme:integratorCreator}) which utilizes the
156 + modern C++ template technique to avoid excess subclassing.
157  
158 < 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}]
158 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
159  
160   class IntegratorFactory {
161 <  public:
162 <    typedef std::map<string, IntegratorCreator*> CreatorMapType;
161 > public:
162 >  typedef std::map<string, IntegratorCreator*> CreatorMapType;
163  
164 <    bool registerIntegrator(IntegratorCreator* creator);
164 >  bool registerIntegrator(IntegratorCreator* creator) {
165 >    return creatorMap_.insert(creator->getIdent(), creator).second;
166 >  }
167  
168 <    Integrator* createIntegrator(const string& id, SimInfo* info);
168 >  Integrator* createIntegrator(const string& id, SimInfo* info) {
169 >    Integrator* result = NULL;
170 >    CreatorMapType::iterator i = creatorMap_.find(id);
171 >    if (i != creatorMap_.end()) {
172 >      result = (i->second)->create(info);
173 >    }
174 >    return result;
175 >  }
176  
177 <  private:
178 <    CreatorMapType creatorMap_;
177 > private:
178 >  CreatorMapType creatorMap_;
179   };
189 –
180   \end{lstlisting}
181  
182 < \begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}]
182 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
183  
194 – bool IntegratorFactory::unregisterIntegrator(const string& id) {
195 –  return creatorMap_.erase(id) == 1;
196 – }
197 –
198 – Integrator* IntegratorFactory::createIntegrator(const string& id,
199 –                                                SimInfo* info) {
200 –  CreatorMapType::iterator i = creatorMap_.find(id);
201 –  if (i != creatorMap_.end()) {
202 –    return (i->second)->create(info);
203 –  } else {
204 –    return NULL;
205 –  }
206 – }
207 –
208 – \end{lstlisting}
209 –
210 – \begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}]
211 –
184   class IntegratorCreator {
185 <  public:
185 > public:
186      IntegratorCreator(const string& ident) : ident_(ident) {}
187  
188      const string& getIdent() const { return ident_; }
189  
190      virtual Integrator* create(SimInfo* info) const = 0;
191  
192 <  private:
192 > private:
193      string ident_;
194   };
195  
196   template<class ConcreteIntegrator>
197   class IntegratorBuilder : public IntegratorCreator {
198 <  public:
199 <    IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {}
200 <    virtual  Integrator* create(SimInfo* info) const {
201 <      return new ConcreteIntegrator(info);
202 <    }
198 > public:
199 >  IntegratorBuilder(const string& ident)
200 >                   : IntegratorCreator(ident) {}
201 >  virtual  Integrator* create(SimInfo* info) const {
202 >    return new ConcreteIntegrator(info);
203 >  }
204   };
205   \end{lstlisting}
206  
207   \subsection{\label{appendixSection:visitorPattern}Visitor}
208  
209 < The purpose of the Visitor Pattern is to encapsulate an operation
210 < that you want to perform on the elements. The operation being
211 < performed on a structure can be switched without changing the
212 < interfaces  of the elements. In other words, one can add virtual
213 < functions into a set of classes without modifying their interfaces.
214 < The UML class diagram of Visitor patten is shown in
215 < Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in
216 < Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern
217 < extensively.
209 > The visitor pattern is designed to decouple the data structure and
210 > algorithms used upon them by collecting related operation from
211 > element classes into other visitor classes, which is equivalent to
212 > adding virtual functions into a set of classes without modifying
213 > their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
214 > structure of Visitor pattern which is used extensively in {\tt
215 > Dump2XYZ}. In order to convert an OOPSE dump file, a series of
216 > distinct operations are performed on different StuntDoubles (See the
217 > class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration
218 > in List.~\ref{appendixScheme:element}). Since the hierarchies
219 > remains stable, it is easy to define a visit operation (see
220 > List.~\ref{appendixScheme:visitor}) for each class of StuntDouble.
221 > Note that using Composite pattern\cite{Gamma1994}, CompositVisitor
222 > manages a priority visitor list and handles the execution of every
223 > visitor in the priority list on different StuntDoubles.
224  
225   \begin{figure}
226   \centering
227   \includegraphics[width=\linewidth]{visitor.eps}
228 < \caption[The architecture of {\sc OOPSE}] {Overview of the structure
229 < of {\sc OOPSE}} \label{appendixFig:visitorUML}
228 > \caption[The UML class diagram of Visitor patten] {The UML class
229 > diagram of Visitor patten.} \label{appendixFig:visitorUML}
230   \end{figure}
231  
232 < \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
232 > \begin{figure}
233 > \centering
234 > \includegraphics[width=\linewidth]{hierarchy.eps}
235 > \caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
236 > the class hierarchy. } \label{oopseFig:hierarchy}
237 > \end{figure}
238  
239 < class BaseVisitor{
240 <  public:
241 <    virtual void visit(Atom* atom);
242 <    virtual void visit(DirectionalAtom* datom);
259 <    virtual void visit(RigidBody* rb);
239 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
240 >
241 > class StuntDouble { public:
242 >  virtual void accept(BaseVisitor* v) = 0;
243   };
244  
245 + class Atom: public StuntDouble { public:
246 +  virtual void accept{BaseVisitor* v*} {
247 +    v->visit(this);
248 +  }
249 + };
250 +
251 + class DirectionalAtom: public Atom { public:
252 +  virtual void accept{BaseVisitor* v*} {
253 +    v->visit(this);
254 +  }
255 + };
256 +
257 + class RigidBody: public StuntDouble { public:
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 (II)]Source code of the element classes.},label={appendixScheme:element}]
265 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
266  
267 < class StuntDouble {
268 <  public:
269 <    virtual void accept(BaseVisitor* v) = 0;
267 > class BaseVisitor{
268 > public:
269 >  virtual void visit(Atom* atom);
270 >  virtual void visit(DirectionalAtom* datom);
271 >  virtual void visit(RigidBody* rb);
272   };
273  
274 < class Atom: public StuntDouble {
275 <  public:
276 <    virtual void accept{BaseVisitor* v*} {
277 <      v->visit(this);
275 <    }
274 > class BaseAtomVisitor:public BaseVisitor{ public:
275 >  virtual void visit(Atom* atom);
276 >  virtual void visit(DirectionalAtom* datom);
277 >  virtual void visit(RigidBody* rb);
278   };
279  
280 < class DirectionalAtom: public Atom {
281 <  public:
282 <    virtual void accept{BaseVisitor* v*} {
283 <      v->visit(this);
282 <    }
280 > class SSDAtomVisitor:public BaseAtomVisitor{ public:
281 >  virtual void visit(Atom* atom);
282 >  virtual void visit(DirectionalAtom* datom);
283 >  virtual void visit(RigidBody* rb);
284   };
285  
286 < class RigidBody: public StuntDouble {
287 <  public:
288 <    virtual void accept{BaseVisitor* v*} {
289 <      v->visit(this);
286 > class CompositeVisitor: public BaseVisitor {
287 > public:
288 >
289 >  typedef list<pair<BaseVisitor*, int> > VistorListType;
290 >  typedef VistorListType::iterator VisitorListIterator;
291 >  virtual void visit(Atom* atom) {
292 >    VisitorListIterator i;
293 >    BaseVisitor* curVisitor;
294 >    for(i = visitorList.begin();i != visitorList.end();++i) {
295 >      atom->accept(*i);
296 >    }
297 >  }
298 >
299 >  virtual void visit(DirectionalAtom* datom) {
300 >    VisitorListIterator i;
301 >    BaseVisitor* curVisitor;
302 >    for(i = visitorList.begin();i != visitorList.end();++i) {
303 >      atom->accept(*i);
304 >    }
305 >  }
306 >
307 >  virtual void visit(RigidBody* rb) {
308 >    VisitorListIterator i;
309 >    std::vector<Atom*> myAtoms;
310 >    std::vector<Atom*>::iterator ai;
311 >    myAtoms = rb->getAtoms();
312 >    for(i = visitorList.begin();i != visitorList.end();++i) {{
313 >      rb->accept(*i);
314 >      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
315 >        (*ai)->accept(*i);
316      }
317 +  }
318 +
319 +  void addVisitor(BaseVisitor* v, int priority);
320 +
321 +  protected:
322 +    VistorListType visitorList;
323   };
324  
325   \end{lstlisting}
# Line 296 | Line 329 | freedom.  A diagram of the class heirarchy is illustra
329   OOPSE manipulates both traditional atoms as well as some objects
330   that {\it behave like atoms}.  These objects can be rigid
331   collections of atoms or atoms which have orientational degrees of
332 < freedom.  A diagram of the class heirarchy is illustrated in
333 < Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and
332 > freedom.  A diagram of the class hierarchy is illustrated in
333 > Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
334   DirectionalAtom in {\sc OOPSE} have their own names which are
335   specified in the {\tt .md} file. In contrast, RigidBodies are
336   denoted by their membership and index inside a particular molecule:
# Line 305 | Line 338 | body in a DMPC molecule is DMPC\_RB\_0.
338   on the specifics of the simulation). The names of rigid bodies are
339   generated automatically. For example, the name of the first rigid
340   body in a DMPC molecule is DMPC\_RB\_0.
308 – \begin{figure}
309 – \centering
310 – \includegraphics[width=\linewidth]{heirarchy.eps}
311 – \caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class
312 – heirarchy of StuntDoubles in {\sc OOPSE}.
341   \begin{itemize}
342   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
343   integrators and minimizers.
# Line 318 | Line 346 | DirectionalAtom}s which behaves as a single unit.
346   \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
347   DirectionalAtom}s which behaves as a single unit.
348   \end{itemize}
321 – } \label{oopseFig:heirarchy}
322 – \end{figure}
349  
350   \section{\label{appendixSection:syntax}Syntax of the Select Command}
351  
352 < The most general form of the select command is: {\tt select {\it
353 < expression}}. This expression represents an arbitrary set of
328 < StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
329 < composed of either name expressions, index expressions, predefined
330 < sets, user-defined expressions, comparison operators, within
331 < expressions, or logical combinations of the above expression types.
332 < Expressions can be combined using parentheses and the Boolean
333 < operators.
352 > {\sc OOPSE} provides a powerful selection utility to select
353 > StuntDoubles. The most general form of the select command is:
354  
355 + {\tt select {\it expression}}.
356 +
357 + This expression represents an arbitrary set of StuntDoubles (Atoms
358 + or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
359 + name expressions, index expressions, predefined sets, user-defined
360 + expressions, comparison operators, within expressions, or logical
361 + combinations of the above expression types. Expressions can be
362 + combined using parentheses and the Boolean operators.
363 +
364   \subsection{\label{appendixSection:logical}Logical expressions}
365  
366   The logical operators allow complex queries to be constructed out of
# Line 463 | Line 492 | of a selected atom or rigid body.
492   and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
493   also be used to compute the density distributions of other molecules
494   in a reference frame {\it fixed to the body-fixed reference frame}
495 < of a selected atom or rigid body.
495 > of a selected atom or rigid body. Due to the fact that the selected
496 > StuntDoubles from two selections may be overlapped, {\tt
497 > StaticProps} performs the calculation in three stages which are
498 > illustrated in Fig.~\ref{oopseFig:staticPropsProcess}.
499  
500 + \begin{figure}
501 + \centering
502 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
503 + \caption[A representation of the three-stage correlations in
504 + \texttt{StaticProps}]{This diagram illustrates three-stage
505 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
506 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
507 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
508 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
509 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
510 + the contrary, the third stage($C$ and $C$) are completely
511 + overlapping} \label{oopseFig:staticPropsProcess}
512 + \end{figure}
513 +
514   There are five seperate radial distribution functions availiable in
515   OOPSE. Since every radial distrbution function invlove the
516   calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
# Line 508 | Line 554 | distribution functions are most easily seen in the fig
554   \end{description}
555  
556   The vectors (and angles) associated with these angular pair
557 < distribution functions are most easily seen in the figure below:
557 > distribution functions are most easily seen in
558 > Fig.~\ref{oopseFig:gofr}
559  
560   \begin{figure}
561   \centering
# Line 519 | Line 566 | Due to the fact that the selected StuntDoubles from tw
566   their body-fixed frames.} \label{oopseFig:gofr}
567   \end{figure}
568  
522 – Due to the fact that the selected StuntDoubles from two selections
523 – may be overlapped, {\tt StaticProps} performs the calculation in
524 – three stages which are illustrated in
525 – Fig.~\ref{oopseFig:staticPropsProcess}.
526 –
527 – \begin{figure}
528 – \centering
529 – \includegraphics[width=\linewidth]{staticPropsProcess.eps}
530 – \caption[A representation of the three-stage correlations in
531 – \texttt{StaticProps}]{This diagram illustrates three-stage
532 – processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
533 – numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
534 – -{}-sele2} respectively, while $C$ is the number of stuntdobules
535 – appearing at both sets. The first stage($S_1-C$ and $S_2$) and
536 – second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
537 – the contrary, the third stage($C$ and $C$) are completely
538 – overlapping} \label{oopseFig:staticPropsProcess}
539 – \end{figure}
540 –
569   The options available for {\tt StaticProps} are as follows:
570   \begin{longtable}[c]{|EFG|}
571   \caption{StaticProps Command-line Options}
# Line 600 | Line 628 | sizes in excess of several gigabytes. In order to effe
628   select different types of atoms is already present in the code.
629  
630   For large simulations, the trajectory files can sometimes reach
631 < sizes in excess of several gigabytes. In order to effectively
632 < analyze that amount of data. In order to prevent a situation where
633 < the program runs out of memory due to large trajectories,
634 < \texttt{dynamicProps} will estimate the size of free memory at
635 < first, and determine the number of frames in each block, which
608 < allows the operating system to load two blocks of data
631 > sizes in excess of several gigabytes. In order to prevent a
632 > situation where the program runs out of memory due to large
633 > trajectories, \texttt{dynamicProps} will estimate the size of free
634 > memory at first, and determine the number of frames in each block,
635 > which allows the operating system to load two blocks of data
636   simultaneously without swapping. Upon reading two blocks of the
637   trajectory, \texttt{dynamicProps} will calculate the time
638   correlation within the first block and the cross correlations

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