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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 > Scheme.~\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_;
125 <  };
118 > class IntegratorFactory {
119 > public:
120 >  static IntegratorFactory*
121 >  getInstance();
122 > protected:
123 >  IntegratorFactory();
124 > private:
125 >  static IntegratorFactory* instance_;
126 > };
127 >
128   \end{lstlisting}
143 – The corresponding implementation is
144 – \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(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 151 | Line 137 | IntegratorFactory* getInstance() {
137    }
138    return instance_;
139   }
140 +
141   \end{lstlisting}
155 – Since constructor is declared as {\tt protected}, a client can not
156 – instantiate {\tt IntegratorFactory} directly. Moreover, since the
157 – member function {\tt getInstance} serves as the only entry of access
158 – to {\tt IntegratorFactory}, this approach fulfills the basic
159 – requirement, a single instance. Another consequence of this approach
160 – is the automatic destruction since static data are destroyed upon
161 – 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 Scheme.~\ref{appendixScheme:factoryDeclaration}). If
153 + the identifier has been already registered, the factory method will
154 + invoke the corresponding creator (see
155 + Scheme.~\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
171 < identifier in the internal map. If it is found, it invokes the
172 < corresponding creator for the type identifier and returns its
173 < result.
174 < \begin{lstlisting}[float,caption={[].},label={appendixScheme:factoryDeclaration}]
175 <  class IntegratorCreator;
176 <  class IntegratorFactory {
177 <    public:
178 <      typedef std::map<std::string, IntegratorCreator*> CreatorMapType;
158 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
159  
160 <      bool registerIntegrator(IntegratorCreator* creator);
160 > class IntegratorFactory {
161 > public:
162 >  typedef std::map<string, IntegratorCreator*> CreatorMapType;
163  
164 <      Integrator* createIntegrator(const std::string& id, SimInfo* info);
165 <
184 <    private:
185 <      CreatorMapType creatorMap_;
186 <  };
187 < \end{lstlisting}
188 <
189 < \begin{lstlisting}[float,caption={[].},label={appendixScheme:factoryDeclarationImplementation}]
190 <  bool IntegratorFactory::unregisterIntegrator(const std::string& id) {
191 <    return creatorMap_.erase(id) == 1;
164 >  bool registerIntegrator(IntegratorCreator* creator) {
165 >    return creatorMap_.insert(creator->getIdent(), creator).second;
166    }
167  
168 <  Integrator*
169 <  IntegratorFactory::createIntegrator(const std::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 <      //invoke functor to create object
199 <      return (i->second)->create(info);
200 <    } else {
201 <      return NULL;
172 >      result = (i->second)->create(info);
173      }
174 +    return result;
175    }
176 +
177 + private:
178 +  CreatorMapType creatorMap_;
179 + };
180   \end{lstlisting}
181  
182 < \begin{lstlisting}[float,caption={[].},label={appendixScheme:integratorCreator}]
182 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
183  
184 <  class IntegratorCreator {
185 <  public:
186 <    IntegratorCreator(const std::string& ident) : ident_(ident) {}
184 > class IntegratorCreator {
185 > public:
186 >    IntegratorCreator(const string& ident) : ident_(ident) {}
187  
188 <    const std::string& getIdent() const { return ident_; }
188 >    const string& getIdent() const { return ident_; }
189  
190      virtual Integrator* create(SimInfo* info) const = 0;
191  
192 <  private:
193 <    std::string ident_;
194 <  };
192 > private:
193 >    string ident_;
194 > };
195  
196 <  template<class ConcreteIntegrator>
197 <  class IntegratorBuilder : public IntegratorCreator {
198 <  public:
199 <    IntegratorBuilder(const std::string& ident) : IntegratorCreator(ident) {}
200 <    virtual  Integrator* create(SimInfo* info) const {
201 <      return new ConcreteIntegrator(info);
202 <    }
203 <  };
196 > template<class ConcreteIntegrator>
197 > class IntegratorBuilder : public IntegratorCreator {
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 of a data structure. In
211 < this way, you can change the operation being performed on a
212 < structure without the need of changing the class heirarchy of the
213 < elements that you are operating on.
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 Scheme.~\ref{appendixScheme:element}). Since the hierarchies
219 > remains stable, it is easy to define a visit operation (see
220 > Scheme.~\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{lstlisting}[float,caption={[].},label={appendixScheme:visitor}]
226 <  class BaseVisitor{
227 <    public:
228 <      virtual void visit(Atom* atom);
229 <      virtual void visit(DirectionalAtom* datom);
230 <      virtual void visit(RigidBody* rb);
231 <  };
225 > \begin{figure}
226 > \centering
227 > \includegraphics[width=\linewidth]{visitor.eps}
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{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 > \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}
246 – \begin{lstlisting}[float,caption={[].},label={appendixScheme:element}]
247 –  class StuntDouble {
248 –    public:
249 –      virtual void accept(BaseVisitor* v) = 0;
250 –  };
264  
265 <  class Atom: public StuntDouble {
253 <    public:
254 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
255 <  };
265 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
266  
267 <  class DirectionalAtom: public Atom {
268 <    public:
269 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
270 <  };
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 RigidBody: public StuntDouble {
275 <    public:
276 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
277 <  };
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 CompositeVisitor: public BaseVisitor {
281 + public:
282 +
283 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
284 +  typedef VistorListType::iterator VisitorListIterator;
285 +  virtual void visit(Atom* atom) {
286 +    VisitorListIterator i;
287 +    BaseVisitor* curVisitor;
288 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
289 +      atom->accept(*i);
290 +    }
291 +  }
292 +
293 +  virtual void visit(DirectionalAtom* datom) {
294 +    VisitorListIterator i;
295 +    BaseVisitor* curVisitor;
296 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
297 +      atom->accept(*i);
298 +    }
299 +  }
300 +
301 +  virtual void visit(RigidBody* rb) {
302 +    VisitorListIterator i;
303 +    std::vector<Atom*> myAtoms;
304 +    std::vector<Atom*>::iterator ai;
305 +    myAtoms = rb->getAtoms();
306 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {{
307 +      rb->accept(*i);
308 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
309 +        (*ai)->accept(*i);
310 +    }
311 +  }
312 +
313 +  void addVisitor(BaseVisitor* v, int priority);
314 +
315 +  protected:
316 +    VistorListType visitorList;
317 + };
318   \end{lstlisting}
319 +
320   \section{\label{appendixSection:concepts}Concepts}
321  
322   OOPSE manipulates both traditional atoms as well as some objects
323   that {\it behave like atoms}.  These objects can be rigid
324   collections of atoms or atoms which have orientational degrees of
325 < freedom.  Here is a diagram of the class heirarchy:
326 <
327 < %\begin{figure}
328 < %\centering
329 < %\includegraphics[width=3in]{heirarchy.eps}
330 < %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
331 < %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
332 < %selection syntax allows the user to select any of the objects that
333 < %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
282 < %\end{figure}
283 <
325 > freedom.  A diagram of the class hierarchy is illustrated in
326 > Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
327 > DirectionalAtom in {\sc OOPSE} have their own names which are
328 > specified in the {\tt .md} file. In contrast, RigidBodies are
329 > denoted by their membership and index inside a particular molecule:
330 > [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
331 > on the specifics of the simulation). The names of rigid bodies are
332 > generated automatically. For example, the name of the first rigid
333 > body in a DMPC molecule is DMPC\_RB\_0.
334   \begin{itemize}
335   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
336   integrators and minimizers.
# Line 290 | Line 340 | Every Molecule, Atom and DirectionalAtom in {\sc OOPSE
340   DirectionalAtom}s which behaves as a single unit.
341   \end{itemize}
342  
293 – Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
294 – own names which are specified in the {\tt .md} file. In contrast,
295 – RigidBodies are denoted by their membership and index inside a
296 – particular molecule: [MoleculeName]\_RB\_[index] (the contents
297 – inside the brackets depend on the specifics of the simulation). The
298 – names of rigid bodies are generated automatically. For example, the
299 – name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
300 –
343   \section{\label{appendixSection:syntax}Syntax of the Select Command}
344  
345 < The most general form of the select command is: {\tt select {\it
346 < expression}}. This expression represents an arbitrary set of
305 < StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
306 < composed of either name expressions, index expressions, predefined
307 < sets, user-defined expressions, comparison operators, within
308 < expressions, or logical combinations of the above expression types.
309 < Expressions can be combined using parentheses and the Boolean
310 < operators.
345 > {\sc OOPSE} provides a powerful selection utility to select
346 > StuntDoubles. The most general form of the select command is:
347  
348 + {\tt select {\it expression}}.
349 +
350 + This expression represents an arbitrary set of StuntDoubles (Atoms
351 + or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
352 + name expressions, index expressions, predefined sets, user-defined
353 + expressions, comparison operators, within expressions, or logical
354 + combinations of the above expression types. Expressions can be
355 + combined using parentheses and the Boolean operators.
356 +
357   \subsection{\label{appendixSection:logical}Logical expressions}
358  
359   The logical operators allow complex queries to be constructed out of
# Line 440 | Line 485 | of a selected atom or rigid body.
485   and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
486   also be used to compute the density distributions of other molecules
487   in a reference frame {\it fixed to the body-fixed reference frame}
488 < of a selected atom or rigid body.
488 > of a selected atom or rigid body. Due to the fact that the selected
489 > StuntDoubles from two selections may be overlapped, {\tt
490 > StaticProps} performs the calculation in three stages which are
491 > illustrated in Fig.~\ref{oopseFig:staticPropsProcess}.
492  
493 + \begin{figure}
494 + \centering
495 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
496 + \caption[A representation of the three-stage correlations in
497 + \texttt{StaticProps}]{This diagram illustrates three-stage
498 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
499 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
500 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
501 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
502 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
503 + the contrary, the third stage($C$ and $C$) are completely
504 + overlapping} \label{oopseFig:staticPropsProcess}
505 + \end{figure}
506 +
507   There are five seperate radial distribution functions availiable in
508   OOPSE. Since every radial distrbution function invlove the
509   calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
# Line 485 | Line 547 | distribution functions are most easily seen in the fig
547   \end{description}
548  
549   The vectors (and angles) associated with these angular pair
550 < distribution functions are most easily seen in the figure below:
550 > distribution functions are most easily seen in
551 > Fig.~\ref{oopseFig:gofr}
552  
553   \begin{figure}
554   \centering
# Line 496 | Line 559 | Due to the fact that the selected StuntDoubles from tw
559   their body-fixed frames.} \label{oopseFig:gofr}
560   \end{figure}
561  
499 – Due to the fact that the selected StuntDoubles from two selections
500 – may be overlapped, {\tt StaticProps} performs the calculation in
501 – three stages which are illustrated in
502 – Fig.~\ref{oopseFig:staticPropsProcess}.
503 –
504 – \begin{figure}
505 – \centering
506 – \includegraphics[width=\linewidth]{staticPropsProcess.eps}
507 – \caption[A representation of the three-stage correlations in
508 – \texttt{StaticProps}]{This diagram illustrates three-stage
509 – processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
510 – numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
511 – -{}-sele2} respectively, while $C$ is the number of stuntdobules
512 – appearing at both sets. The first stage($S_1-C$ and $S_2$) and
513 – second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
514 – the contrary, the third stage($C$ and $C$) are completely
515 – overlapping} \label{oopseFig:staticPropsProcess}
516 – \end{figure}
517 –
562   The options available for {\tt StaticProps} are as follows:
563   \begin{longtable}[c]{|EFG|}
564   \caption{StaticProps Command-line Options}
# Line 577 | Line 621 | sizes in excess of several gigabytes. In order to effe
621   select different types of atoms is already present in the code.
622  
623   For large simulations, the trajectory files can sometimes reach
624 < sizes in excess of several gigabytes. In order to effectively
625 < analyze that amount of data. In order to prevent a situation where
626 < the program runs out of memory due to large trajectories,
627 < \texttt{dynamicProps} will estimate the size of free memory at
628 < first, and determine the number of frames in each block, which
585 < allows the operating system to load two blocks of data
624 > sizes in excess of several gigabytes. In order to prevent a
625 > situation where the program runs out of memory due to large
626 > trajectories, \texttt{dynamicProps} will estimate the size of free
627 > memory at first, and determine the number of frames in each block,
628 > which allows the operating system to load two blocks of data
629   simultaneously without swapping. Upon reading two blocks of the
630   trajectory, \texttt{dynamicProps} will calculate the time
631   correlation within the first block and the cross correlations

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