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1   \appendix
2   \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
3  
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
4 > The absence of modern software development practices has been a
5 > bottleneck limiting progress in the Scientific Computing
6 > community. In the last 20 years, a large number of
7 > MD packages\cite{Brooks1983, Vincent1995, Kale1999} were
8 > developed to solve common MD problems and perform robust simulations
9 > . Most of these are commercial programs that are either poorly
10 > written or extremely complicated to use correctly. This situation
11 > prevents researchers from reusing or extending those packages to do
12 > cutting-edge research effectively. In the process of studying
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
17   \begin{enumerate}
18    \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
19   atom types (transition metals, point dipoles, sticky potentials,
20 < Gay-Berne ellipsoids, or other "lumpy"atoms with orientational
20 > Gay-Berne ellipsoids, or other "lumpy" atoms with orientational
21   degrees of freedom), as well as rigid bodies.
22    \item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap
23   Beowulf clusters to obtain very efficient parallelism.
# Line 33 | Line 33 | Mainly written by \texttt{C/C++} and \texttt{Fortran90
33  
34   \section{\label{appendixSection:architecture }Architecture}
35  
36 < Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
37 < uses C++ Standard Template Library (STL) and fortran modules as the
38 < foundation. As an extensive set of the STL and Fortran90 modules,
39 < {\sc Base Classes} provide generic implementations of mathematical
40 < objects (e.g., matrices, vectors, polynomials, random number
41 < generators) and advanced data structures and algorithms(e.g., tuple,
42 < bitset, generic data, string manipulation). The molecular data
43 < structures for the representation of atoms, bonds, bends, torsions,
44 < rigid bodies and molecules \textit{etc} are contained in the {\sc
45 < Kernel} which is implemented with {\sc Base Classes} and are
46 < carefully designed to provide maximum extensibility and flexibility.
47 < The functionality required for applications is provide by the third
48 < layer which contains Input/Output, Molecular Mechanics and Structure
49 < modules. Input/Output module not only implements general methods for
50 < file handling, but also defines a generic force field interface.
51 < Another important component of Input/Output module is the meta-data
52 < file parser, which is rewritten using ANother Tool for Language
53 < Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
54 < Mechanics module consists of energy minimization and a wide
55 < varieties of integration methods(see Chap.~\ref{chapt:methodology}).
56 < The structure module contains a flexible and powerful selection
57 < library which syntax is elaborated in
58 < Sec.~\ref{appendixSection:syntax}. The top layer is made of the main
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 Sec.~\ref{appendixSection:DynamicProps}),
63 < \texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}),
64 < \texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics})
65 < \textit{etc}.
36 > Mainly written by C++ and Fortran90, {\sc OOPSE} uses C++ Standard
37 > Template Library (STL) and fortran modules as a foundation. As an
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
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
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
48 > contains Input/Output, Molecular Mechanics and Structure modules.
49 > The Input/Output module not only implements general methods for file
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.
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
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
60 > parallel version \texttt{oopse\_MPI}, as well as other useful
61 > utilities, such as \texttt{StaticProps} (see
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}.
66  
67   \begin{figure}
68   \centering
# Line 71 | Line 71 | of {\sc OOPSE}} \label{appendixFig:architecture}
71   of {\sc OOPSE}} \label{appendixFig:architecture}
72   \end{figure}
73  
74 < \section{\label{appendixSection:desginPattern}Design Pattern}
74 > \section{\label{appendixSection:desginPattern}Design Patterns}
75  
76   Design patterns are optimal solutions to commonly-occurring problems
77 < in software design. Although originated as an architectural concept
78 < for buildings and towns by Christopher Alexander
79 < \cite{Alexander1987}, software patterns first became popular with
80 < the wide acceptance of the book, Design Patterns: Elements of
81 < Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect
82 < the experience, knowledge and insights of developers who have
83 < successfully used these patterns in their own work. Patterns are
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. 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}
77 > in software design. Although they originated as an architectural
78 > concept for buildings and towns by Christopher Alexander
79 > \cite{Alexander1987}, design patterns first became popular in
80 > software engineering with the wide acceptance of the book, Design
81 > Patterns: Elements of Reusable Object-Oriented Software
82 > \cite{Gamma1994}. Patterns reflect the experience, knowledge and
83 > insights of developers who have successfully used these patterns in
84 > their own work. Patterns are reusable. They provide a ready-made
85 > solution that can be adapted to different problems as necessary. As
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
91   used in {\sc OOPSE}.
92  
93 < \subsection{\label{appendixSection:singleton}Singleton}
93 > \subsection{\label{appendixSection:singleton}Singletons}
94  
95   The Singleton pattern not only provides a mechanism to restrict
96   instantiation of a class to one object, but also provides a global
97 < point of access to the object. Currently implemented as a global
98 < variable, the logging utility which reports error and warning
99 < messages to the console in {\sc OOPSE} is a good candidate for
100 < applying the Singleton pattern to avoid the global namespace
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}. The declaration and
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
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
103 < List.~\ref{appendixScheme:singletonImplementation} respectively.
104 < Since constructor is declared as protected, a client can not
103 > Scheme.~\ref{appendixScheme:singletonImplementation} respectively.
104 > Since the constructor is declared as protected, a client can not
105   instantiate IntegratorFactory directly. Moreover, since the member
106   function getInstance serves as the only entry of access to
107   IntegratorFactory, this approach fulfills the basic requirement, a
108   single instance. Another consequence of this approach is the
109   automatic destruction since static data are destroyed upon program
110   termination.
116 – \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
111  
112 + \subsection{\label{appendixSection:factoryMethod}Factory Methods}
113 +
114 + The Factory Method pattern is a creational pattern and deals with
115 + the problem of creating objects without specifying the exact class
116 + of object that will be created. Factory method is typically
117 + implemented by delegating the creation operation to the subclasses.
118 + One of the most popular Factory pattern is Parameterized Factory
119 + pattern which creates products based on their identifiers (see
120 + Scheme.~\ref{appendixScheme:factoryDeclaration}). If the identifier
121 + has been already registered, the factory method will invoke the
122 + corresponding creator (see
123 + Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the
124 + modern C++ template technique to avoid excess subclassing.
125 +
126 + \subsection{\label{appendixSection:visitorPattern}Visitor}
127 +
128 + The visitor pattern is designed to decouple the data structure and
129 + algorithms used upon them by collecting related operations from
130 + element classes into other visitor classes, which is equivalent to
131 + adding virtual functions into a set of classes without modifying
132 + their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
133 + structure of a Visitor pattern which is used extensively in {\tt
134 + Dump2XYZ}. In order to convert an OOPSE dump file, a series of
135 + distinct operations are performed on different StuntDoubles (See the
136 + class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the
137 + declaration in Scheme.~\ref{appendixScheme:element}). Since the
138 + hierarchies remain stable, it is easy to define a visit operation
139 + (see Scheme.~\ref{appendixScheme:visitor}) for each class of
140 + StuntDouble. Note that by using the Composite
141 + pattern\cite{Gamma1994}, CompositeVisitor manages a priority visitor
142 + list and handles the execution of every visitor in the priority list
143 + on different StuntDoubles.
144 +
145 + \begin{figure}
146 + \centering
147 + \includegraphics[width=\linewidth]{visitor.eps}
148 + \caption[The UML class diagram of Visitor patten] {The UML class
149 + diagram of Visitor patten.} \label{appendixFig:visitorUML}
150 + \end{figure}
151 +
152 + \begin{figure}
153 + \centering
154 + \includegraphics[width=\linewidth]{hierarchy.eps}
155 + \caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
156 + the class hierarchy. Objects below others on the diagram inherit
157 + data structures and functions from their parent classes above them.}
158 + \label{oopseFig:hierarchy}
159 + \end{figure}
160 +
161 + \begin{lstlisting}[float,basicstyle=\ttfamily,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
162 +
163   class IntegratorFactory {
164 < public:
165 <  static IntegratorFactory*
166 <  getInstance();
122 < protected:
164 >  public:
165 >  static IntegratorFactory* getInstance();
166 >  protected:
167    IntegratorFactory();
168 < private:
169 <  static IntegratorFactory* instance_;
126 < };
168 >  private:
169 >  static IntegratorFactory* instance_; };
170  
171   \end{lstlisting}
172  
# Line 140 | Line 183 | IntegratorFactory* getInstance() {
183  
184   \end{lstlisting}
185  
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 –
186   \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
187  
188   class IntegratorFactory {
189 < public:
189 >  public:
190    typedef std::map<string, IntegratorCreator*> CreatorMapType;
191  
192 <  bool registerIntegrator(IntegratorCreator* creator) {
193 <    return creatorMap_.insert(creator->getIdent(), creator).second;
192 >  bool registerIntegrator(IntegratorCreator* creator){
193 >    return creatorMap_.insert(creator->getIdent(),creator).second;
194    }
195  
196    Integrator* createIntegrator(const string& id, SimInfo* info) {
# Line 182 | Line 210 | class IntegratorCreator { (public)
210   \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
211  
212   class IntegratorCreator {
213 < public:
214 <    IntegratorCreator(const string& ident) : ident_(ident) {}
213 >  public:
214 >  IntegratorCreator(const string& ident) : ident_(ident) {}
215  
216 <    const string& getIdent() const { return ident_; }
216 >  const string& getIdent() const { return ident_; }
217  
218 <    virtual Integrator* create(SimInfo* info) const = 0;
218 >  virtual Integrator* create(SimInfo* info) const = 0;
219  
220 < private:
221 <    string ident_;
220 >  private:
221 >  string ident_;
222   };
223  
224 < template<class ConcreteIntegrator>
225 < class IntegratorBuilder : public IntegratorCreator {
226 < public:
224 > template<class ConcreteIntegrator> class IntegratorBuilder :
225 > public IntegratorCreator {
226 >  public:
227    IntegratorBuilder(const string& ident)
228 <                   : IntegratorCreator(ident) {}
228 >                     : IntegratorCreator(ident) {}
229    virtual  Integrator* create(SimInfo* info) const {
230      return new ConcreteIntegrator(info);
231    }
232   };
233   \end{lstlisting}
234  
207 – \subsection{\label{appendixSection:visitorPattern}Visitor}
208 –
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 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 –
235   \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
236  
237 < class StuntDouble { public:
237 > class StuntDouble {
238 >  public:
239    virtual void accept(BaseVisitor* v) = 0;
240   };
241  
242 < class Atom: public StuntDouble { public:
242 > class Atom: public StuntDouble {
243 >  public:
244    virtual void accept{BaseVisitor* v*} {
245      v->visit(this);
246    }
247   };
248  
249 < class DirectionalAtom: public Atom { public:
249 > class DirectionalAtom: public Atom {
250 >  public:
251    virtual void accept{BaseVisitor* v*} {
252      v->visit(this);
253    }
254   };
255  
256 < class RigidBody: public StuntDouble { public:
256 > class RigidBody: public StuntDouble {
257 >  public:
258    virtual void accept{BaseVisitor* v*} {
259      v->visit(this);
260    }
# Line 263 | Line 263 | class RigidBody: public StuntDouble { public:
263   \end{lstlisting}
264  
265   \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
266 –
266   class BaseVisitor{
267 < public:
269 <  virtual void visit(Atom* atom);
270 <  virtual void visit(DirectionalAtom* datom);
271 <  virtual void visit(RigidBody* rb);
272 < };
273 <
274 < class BaseAtomVisitor:public BaseVisitor{ public:
267 >  public:
268    virtual void visit(Atom* atom);
269    virtual void visit(DirectionalAtom* datom);
270    virtual void visit(RigidBody* rb);
271   };
272 <
273 < class SSDAtomVisitor:public BaseAtomVisitor{ public:
272 > class BaseAtomVisitor:public BaseVisitor{
273 >  public:
274    virtual void visit(Atom* atom);
275    virtual void visit(DirectionalAtom* datom);
276    virtual void visit(RigidBody* rb);
277   };
285 –
278   class CompositeVisitor: public BaseVisitor {
279 < public:
288 <
279 >  public:
280    typedef list<pair<BaseVisitor*, int> > VistorListType;
281    typedef VistorListType::iterator VisitorListIterator;
282    virtual void visit(Atom* atom) {
283      VisitorListIterator i;
284      BaseVisitor* curVisitor;
285 <    for(i = visitorList.begin();i != visitorList.end();++i) {
285 >    for(i = visitorList.begin();i != visitorList.end();++i)
286        atom->accept(*i);
296 –    }
287    }
298 –
288    virtual void visit(DirectionalAtom* datom) {
289      VisitorListIterator i;
290      BaseVisitor* curVisitor;
291 <    for(i = visitorList.begin();i != visitorList.end();++i) {
291 >    for(i = visitorList.begin();i != visitorList.end();++i)
292        atom->accept(*i);
304 –    }
293    }
306 –
294    virtual void visit(RigidBody* rb) {
295      VisitorListIterator i;
296      std::vector<Atom*> myAtoms;
297      std::vector<Atom*>::iterator ai;
298      myAtoms = rb->getAtoms();
299 <    for(i = visitorList.begin();i != visitorList.end();++i) {{
299 >    for(i = visitorList.begin();i != visitorList.end();++i) {
300        rb->accept(*i);
301 <      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
301 >      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai)
302          (*ai)->accept(*i);
303      }
304 <  }
318 <
319 <  void addVisitor(BaseVisitor* v, int priority);
320 <
304 >  void addVisitor(BaseVisitor* v, int priority);
305    protected:
306 <    VistorListType visitorList;
306 >  VistorListType visitorList;
307   };
324 –
308   \end{lstlisting}
309  
310   \section{\label{appendixSection:concepts}Concepts}
# Line 332 | Line 315 | specified in the {\tt .md} file. In contrast, RigidBod
315   freedom.  A diagram of the class hierarchy is illustrated in
316   Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
317   DirectionalAtom in {\sc OOPSE} have their own names which are
318 < specified in the {\tt .md} file. In contrast, RigidBodies are
318 > specified in the meta data file. In contrast, RigidBodies are
319   denoted by their membership and index inside a particular molecule:
320   [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
321   on the specifics of the simulation). The names of rigid bodies are
# Line 397 | Line 380 | atoms belonging to TIP3P molecules \\
380   \hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the
381   O\_TIP3P
382   atoms belonging to TIP3P molecules \\
383 < & select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to
383 > & select DMPC\_RB\_0.PO4 & select the PO4 atoms belonging to
384   the first
385   RigidBody in each DMPC molecule \\
386   & select DMPC.20 & select the twentieth StuntDouble in each DMPC
# Line 503 | Line 486 | numbers of selected stuntdobules from {\tt -{}-sele1}
486   \caption[A representation of the three-stage correlations in
487   \texttt{StaticProps}]{This diagram illustrates three-stage
488   processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
489 < numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
490 < -{}-sele2} respectively, while $C$ is the number of stuntdobules
489 > numbers of selected StuntDobules from {\tt -{}-sele1} and {\tt
490 > -{}-sele2} respectively, while $C$ is the number of StuntDobules
491   appearing at both sets. The first stage($S_1-C$ and $S_2$) and
492   second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
493   the contrary, the third stage($C$ and $C$) are completely
494   overlapping} \label{oopseFig:staticPropsProcess}
495   \end{figure}
496  
497 + \begin{figure}
498 + \centering
499 + \includegraphics[width=3in]{definition.eps}
500 + \caption[Definitions of the angles between directional objects]{Any
501 + two directional objects (DirectionalAtoms and RigidBodies) have a
502 + set of two angles ($\theta$, and $\omega$) between the z-axes of
503 + their body-fixed frames.} \label{oopseFig:gofr}
504 + \end{figure}
505 +
506   There are five seperate radial distribution functions availiable in
507   OOPSE. Since every radial distrbution function invlove the
508   calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
# Line 555 | Line 547 | Fig.~\ref{oopseFig:gofr}
547  
548   The vectors (and angles) associated with these angular pair
549   distribution functions are most easily seen in
550 < Fig.~\ref{oopseFig:gofr}
550 > Fig.~\ref{oopseFig:gofr}. The options available for {\tt
551 > StaticProps} are showed in Table.~\ref{appendix:staticPropsOptions}.
552  
560 – \begin{figure}
561 – \centering
562 – \includegraphics[width=3in]{definition.eps}
563 – \caption[Definitions of the angles between directional objects]{ \\
564 – Any two directional objects (DirectionalAtoms and RigidBodies) have
565 – a set of two angles ($\theta$, and $\omega$) between the z-axes of
566 – their body-fixed frames.} \label{oopseFig:gofr}
567 – \end{figure}
568 –
569 – The options available for {\tt StaticProps} are as follows:
570 – \begin{longtable}[c]{|EFG|}
571 – \caption{StaticProps Command-line Options}
572 – \\ \hline
573 – {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
574 – \endhead
575 – \hline
576 – \endfoot
577 –  -h& {\tt -{}-help}                    &  Print help and exit \\
578 –  -V& {\tt -{}-version}                 &  Print version and exit \\
579 –  -i& {\tt -{}-input}          &  input dump file \\
580 –  -o& {\tt -{}-output}         &  output file name \\
581 –  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
582 –  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
583 –  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
584 –  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
585 –    & {\tt -{}-sele1}   & select the first StuntDouble set \\
586 –    & {\tt -{}-sele2}   & select the second StuntDouble set \\
587 –    & {\tt -{}-sele3}   & select the third StuntDouble set \\
588 –    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
589 –    & {\tt -{}-molname}           & molecule name \\
590 –    & {\tt -{}-begin}                & begin internal index \\
591 –    & {\tt -{}-end}                  & end internal index \\
592 – \hline
593 – \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
594 – \hline
595 –    &  {\tt -{}-gofr}                    &  $g(r)$ \\
596 –    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
597 –    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
598 –    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
599 –    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
600 –    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
601 –    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
602 –    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
603 –    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
604 – \end{longtable}
605 –
553   \subsection{\label{appendixSection:DynamicProps}DynamicProps}
554  
555   {\tt DynamicProps} computes time correlation functions from the
# Line 630 | Line 577 | trajectories, \texttt{dynamicProps} will estimate the
577   For large simulations, the trajectory files can sometimes reach
578   sizes in excess of several gigabytes. In order to prevent a
579   situation where the program runs out of memory due to large
580 < trajectories, \texttt{dynamicProps} will estimate the size of free
581 < memory at first, and determine the number of frames in each block,
582 < which allows the operating system to load two blocks of data
580 > trajectories, \texttt{dynamicProps} will first estimate the size of
581 > free memory, and determine the number of frames in each block, which
582 > will allow the operating system to load two blocks of data
583   simultaneously without swapping. Upon reading two blocks of the
584   trajectory, \texttt{dynamicProps} will calculate the time
585   correlation within the first block and the cross correlations
# Line 641 | Line 588 | Fig.~\ref{oopseFig:dynamicPropsProcess}.
588   trajectory. Once the end is reached, the first block is freed then
589   incremented, until all frame pairs have been correlated in time.
590   This process is illustrated in
591 < Fig.~\ref{oopseFig:dynamicPropsProcess}.
591 > Fig.~\ref{oopseFig:dynamicPropsProcess} and the options available
592 > for DynamicProps are showed in
593 > Table.~\ref{appendix:dynamicPropsOptions}
594  
595   \begin{figure}
596   \centering
# Line 654 | Line 603 | The options available for DynamicProps are as follows:
603   \label{oopseFig:dynamicPropsProcess}
604   \end{figure}
605  
657 – The options available for DynamicProps are as follows:
606   \begin{longtable}[c]{|EFG|}
607 < \caption{DynamicProps Command-line Options}
607 > \caption{STATICPROPS COMMAND-LINE OPTIONS}
608 > \label{appendix:staticPropsOptions}
609   \\ \hline
610   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
611   \endhead
612   \hline
613   \endfoot
614 +  -h& {\tt -{}-help}                    &  Print help and exit \\
615 +  -V& {\tt -{}-version}                 &  Print version and exit \\
616 +  -i& {\tt -{}-input}          &  input dump file \\
617 +  -o& {\tt -{}-output}         &  output file name \\
618 +  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
619 +  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
620 +  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
621 +  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
622 +    & {\tt -{}-sele1}   & select the first StuntDouble set \\
623 +    & {\tt -{}-sele2}   & select the second StuntDouble set \\
624 +    & {\tt -{}-sele3}   & select the third StuntDouble set \\
625 +    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
626 +    & {\tt -{}-molname}           & molecule name \\
627 +    & {\tt -{}-begin}                & begin internal index \\
628 +    & {\tt -{}-end}                  & end internal index \\
629 + \hline
630 + \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
631 + \hline
632 +    &  {\tt -{}-gofr}                    &  $g(r)$ \\
633 +    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
634 +    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
635 +    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
636 +    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
637 +    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
638 +    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
639 +    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
640 +    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
641 + \end{longtable}
642 +
643 + \begin{longtable}[c]{|EFG|}
644 + \caption{DYNAMICPROPS COMMAND-LINE OPTIONS}
645 + \label{appendix:dynamicPropsOptions}
646 + \\ \hline
647 + {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
648 + \endhead
649 + \hline
650 + \endfoot
651    -h& {\tt -{}-help}                   & Print help and exit \\
652    -V& {\tt -{}-version}                & Print version and exit \\
653    -i& {\tt -{}-input}         & input dump file \\
# Line 685 | Line 671 | as follows:
671   and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
672   as follows:
673  
688 –
674   \begin{longtable}[c]{|EFG|}
675 < \caption{Dump2XYZ Command-line Options}
675 > \caption{DUMP2XYZ COMMAND-LINE OPTIONS}
676   \\ \hline
677   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
678   \endhead
# Line 721 | Line 706 | options available for Hydro are as follows:
706   the beads which are used to approximate the arbitrary shapes. The
707   options available for Hydro are as follows:
708   \begin{longtable}[c]{|EFG|}
709 < \caption{Hydrodynamics Command-line Options}
709 > \caption{HYDRODYNAMICS COMMAND-LINE OPTIONS}
710   \\ \hline
711   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
712   \endhead

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