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1 < \chapter{\label{chapt:appendix}APPENDIX}
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{wilson}. For instance, in the
8 < last 20 years , there are quite a few MD packages that were
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
# Line 13 | Line 14 | documents which is crucial to the maintenance and exte
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
22 + \begin{enumerate}
23 +  \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
24 + atom types (transition metals, point dipoles, sticky potentials,
25 + Gay-Berne ellipsoids, or other "lumpy"atoms with orientational
26 + degrees of freedom), as well as rigid bodies.
27 +  \item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap
28 + Beowulf clusters to obtain very efficient parallelism.
29 +  \item {\sc OOPSE} integrates the equations of motion using advanced methods for
30 + orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T
31 + ensembles.
32 +  \item {\sc OOPSE} can carry out simulations on metallic systems using the
33 + Embedded Atom Method (EAM) as well as the Sutton-Chen potential.
34 +  \item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals.
35 +  \item  {\sc OOPSE} can simulate systems containing the extremely efficient
36 + extended-Soft Sticky Dipole (SSD/E) model for water.
37 + \end{enumerate}
38  
39 + \section{\label{appendixSection:architecture }Architecture}
40 +
41 + Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
42 + uses C++ Standard Template Library (STL) and fortran modules as the
43 + foundation. As an extensive set of the STL and Fortran90 modules,
44 + {\sc Base Classes} provide generic implementations of mathematical
45 + objects (e.g., matrices, vectors, polynomials, random number
46 + generators) and advanced data structures and algorithms(e.g., tuple,
47 + bitset, generic data, string manipulation). The molecular data
48 + structures for the representation of atoms, bonds, bends, torsions,
49 + rigid bodies and molecules \textit{etc} are contained in the {\sc
50 + Kernel} which is implemented with {\sc Base Classes} and are
51 + carefully designed to provide maximum extensibility and flexibility.
52 + The functionality required for applications is provide by the third
53 + layer which contains Input/Output, Molecular Mechanics and Structure
54 + modules. Input/Output module not only implements general methods for
55 + file handling, but also defines a generic force field interface.
56 + Another important component of Input/Output module is the meta-data
57 + file parser, which is rewritten using ANother Tool for Language
58 + Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
59 + Mechanics module consists of energy minimization and a wide
60 + varieties of integration methods(see Chap.~\ref{chapt:methodology}).
61 + The structure module contains a flexible and powerful selection
62 + library which syntax is elaborated in
63 + Sec.~\ref{appendixSection:syntax}. The top layer is made of the main
64 + program of the package, \texttt{oopse} and it corresponding parallel
65 + version \texttt{oopse\_MPI}, as well as other useful utilities, such
66 + as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}),
67 + \texttt{DynamicProps} (see
68 + Sec.~\ref{appendixSection:appendixSection:DynamicProps}),
69 + \texttt{Dump2XYZ} (see
70 + Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro}
71 + (see Sec.~\ref{appendixSection:appendixSection:hydrodynamics})
72 + \textit{etc}.
73 +
74 + \begin{figure}
75 + \centering
76 + \includegraphics[width=\linewidth]{architecture.eps}
77 + \caption[The architecture of {\sc OOPSE}] {Overview of the structure
78 + of {\sc OOPSE}} \label{appendixFig:architecture}
79 + \end{figure}
80 +
81   \section{\label{appendixSection:desginPattern}Design Pattern}
82  
83   Design patterns are optimal solutions to commonly-occurring problems
84   in software design. Although originated as an architectural concept
85 < for buildings and towns by Christopher Alexander \cite{alexander},
86 < software patterns first became popular with the wide acceptance of
87 < the book, Design Patterns: Elements of Reusable Object-Oriented
88 < Software \cite{gamma94}. Patterns reflect the experience, knowledge
89 < and insights of developers who have successfully used these patterns
90 < in their own work. Patterns are reusable. They provide a ready-made
91 < solution that can be adapted to different problems as necessary.
92 < Pattern are expressive. they provide a common vocabulary of
93 < solutions that can express large solutions succinctly.
85 > for buildings and towns by Christopher Alexander
86 > \cite{Alexander1987}, software patterns first became popular with
87 > the wide acceptance of the book, Design Patterns: Elements of
88 > Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect
89 > the experience, knowledge and insights of developers who have
90 > successfully used these patterns in their own work. Patterns are
91 > reusable. They provide a ready-made solution that can be adapted to
92 > different problems as necessary. Pattern are expressive. they
93 > provide a common vocabulary of solutions that can express large
94 > solutions succinctly.
95  
96   Patterns are usually described using a format that includes the
97   following information:
# Line 47 | Line 112 | the modern scientific software applications, such as J
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, OOPSE
116 < \cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}.
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  
120   \subsection{\label{appendixSection:singleton}Singleton}
121 < The Singleton pattern ensures that only one instance of a class is
122 < created. All objects that use an instance of that class use the same
123 < instance.
121 > The Singleton pattern not only provides a mechanism to restrict
122 > instantiation of a class to one object, but also provides a global
123 > point of access to the object. Currently implemented as a global
124 > variable, the logging utility which reports error and warning
125 > messages to the console in {\sc OOPSE} is a good candidate for
126 > applying the Singleton pattern to avoid the global namespace
127 > pollution.Although the singleton pattern can be implemented in
128 > various ways  to account for different aspects of the software
129 > designs, such as lifespan control \textit{etc}, we only use the
130 > static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class
131 > is declared as
132 > \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}]
133  
134 +  class IntegratorFactory {
135 +    public:
136 +      static IntegratorFactory* getInstance();
137 +    protected:
138 +      IntegratorFactory();
139 +    private:
140 +      static IntegratorFactory* instance_;
141 +  };
142 + \end{lstlisting}
143 + The corresponding implementation is
144 + \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}]
145 +
146 + IntegratorFactory::instance_ = NULL;
147 +
148 + IntegratorFactory* getInstance() {
149 +  if (instance_ == NULL){
150 +    instance_ = new IntegratorFactory;
151 +  }
152 +  return instance_;
153 + }
154 + \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.
162 +
163   \subsection{\label{appendixSection:factoryMethod}Factory Method}
59 – The Factory Method pattern is a creational pattern which deals with
60 – the problem of creating objects without specifying the exact class
61 – of object that will be created. Factory Method solves this problem
62 – by defining a separate method for creating the objects, which
63 – subclasses can then override to specify the derived type of product
64 – that will be created.
164  
165 + Categoried as a creational pattern, the Factory Method pattern deals
166 + with the problem of creating objects without specifying the exact
167 + class of object that will be created. Factory Method is typically
168 + implemented by delegating the creation operation to the subclasses.
169  
170 + 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={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}]
175 +  class IntegratorCreator;
176 +  class IntegratorFactory {
177 +    public:
178 +      typedef std::map<string, IntegratorCreator*> CreatorMapType;
179 +
180 +      bool registerIntegrator(IntegratorCreator* creator);
181 +
182 +      Integrator* createIntegrator(const string& id, SimInfo* info);
183 +
184 +    private:
185 +      CreatorMapType creatorMap_;
186 +  };
187 + \end{lstlisting}
188 +
189 + \begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}]
190 +  bool IntegratorFactory::unregisterIntegrator(const string& id) {
191 +    return creatorMap_.erase(id) == 1;
192 +  }
193 +
194 +  Integrator*
195 +  IntegratorFactory::createIntegrator(const string& id, SimInfo* info) {
196 +    CreatorMapType::iterator i = creatorMap_.find(id);
197 +    if (i != creatorMap_.end()) {
198 +      //invoke functor to create object
199 +      return (i->second)->create(info);
200 +    } else {
201 +      return NULL;
202 +    }
203 +  }
204 + \end{lstlisting}
205 +
206 + \begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}]
207 +
208 +  class IntegratorCreator {
209 +  public:
210 +    IntegratorCreator(const string& ident) : ident_(ident) {}
211 +
212 +    const string& getIdent() const { return ident_; }
213 +
214 +    virtual Integrator* create(SimInfo* info) const = 0;
215 +
216 +  private:
217 +    string ident_;
218 +  };
219 +
220 +  template<class ConcreteIntegrator>
221 +  class IntegratorBuilder : public IntegratorCreator {
222 +  public:
223 +    IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {}
224 +    virtual  Integrator* create(SimInfo* info) const {
225 +      return new ConcreteIntegrator(info);
226 +    }
227 +  };
228 + \end{lstlisting}
229 +
230   \subsection{\label{appendixSection:visitorPattern}Visitor}
231 +
232   The purpose of the Visitor Pattern is to encapsulate an operation
233 < that you want to perform on the elements of a data structure. In
234 < this way, you can change the operation being performed on a
235 < structure without the need of changing the classes of the elements
236 < that you are operating on.
233 > that you want to perform on the elements. The operation being
234 > performed on a structure can be switched without changing the
235 > interfaces  of the elements. In other words, one can add virtual
236 > functions into a set of classes without modifying their interfaces.
237 > The UML class diagram of Visitor patten is shown in
238 > Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in
239 > Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern
240 > extensively.
241  
242 + \begin{figure}
243 + \centering
244 + \includegraphics[width=\linewidth]{architecture.eps}
245 + \caption[The architecture of {\sc OOPSE}] {Overview of the structure
246 + of {\sc OOPSE}} \label{appendixFig:visitorUML}
247 + \end{figure}
248  
249 < \subsection{\label{appendixSection:templateMethod}Template Method}
249 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
250 >  class BaseVisitor{
251 >    public:
252 >      virtual void visit(Atom* atom);
253 >      virtual void visit(DirectionalAtom* datom);
254 >      virtual void visit(RigidBody* rb);
255 >  };
256 > \end{lstlisting}
257  
258 < \section{\label{appendixSection:analysisFramework}Analysis Framework}
258 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
259 >  class StuntDouble {
260 >    public:
261 >      virtual void accept(BaseVisitor* v) = 0;
262 >  };
263  
264 +  class Atom: public StuntDouble {
265 +    public:
266 +      virtual void accept{BaseVisitor* v*} {v->visit(this);}
267 +  };
268 +
269 +  class DirectionalAtom: public Atom {
270 +    public:
271 +      virtual void accept{BaseVisitor* v*} {v->visit(this);}
272 +  };
273 +
274 +  class RigidBody: public StuntDouble {
275 +    public:
276 +      virtual void accept{BaseVisitor* v*} {v->visit(this);}
277 +  };
278 +
279 + \end{lstlisting}
280   \section{\label{appendixSection:concepts}Concepts}
281  
282   OOPSE manipulates both traditional atoms as well as some objects
# Line 83 | Line 284 | freedom.  Here is a diagram of the class heirarchy:
284   collections of atoms or atoms which have orientational degrees of
285   freedom.  Here is a diagram of the class heirarchy:
286  
287 < \begin{figure}
288 < \centering
289 < \includegraphics[width=3in]{heirarchy.eps}
290 < \caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
291 < The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
292 < selection syntax allows the user to select any of the objects that
293 < are descended from a StuntDouble.} \label{oopseFig:heirarchy}
294 < \end{figure}
287 > %\begin{figure}
288 > %\centering
289 > %\includegraphics[width=3in]{heirarchy.eps}
290 > %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
291 > %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
292 > %selection syntax allows the user to select any of the objects that
293 > %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
294 > %\end{figure}
295  
296   \begin{itemize}
297   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
# Line 101 | Line 302 | Every Molecule, Atom and DirectionalAtom in {\sc oopse
302   DirectionalAtom}s which behaves as a single unit.
303   \end{itemize}
304  
305 < Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
305 > Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
306   own names which are specified in the {\tt .md} file. In contrast,
307   RigidBodies are denoted by their membership and index inside a
308   particular molecule: [MoleculeName]\_RB\_[index] (the contents
# Line 112 | Line 313 | expression}}
313   \section{\label{appendixSection:syntax}Syntax of the Select Command}
314  
315   The most general form of the select command is: {\tt select {\it
316 < expression}}
316 > expression}}. This expression represents an arbitrary set of
317 > StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
318 > composed of either name expressions, index expressions, predefined
319 > sets, user-defined expressions, comparison operators, within
320 > expressions, or logical combinations of the above expression types.
321 > Expressions can be combined using parentheses and the Boolean
322 > operators.
323  
117 – This expression represents an arbitrary set of StuntDoubles (Atoms
118 – or RigidBodies) in {\sc oopse}. Expressions are composed of either
119 – name expressions, index expressions, predefined sets, user-defined
120 – expressions, comparison operators, within expressions, or logical
121 – combinations of the above expression types. Expressions can be
122 – combined using parentheses and the Boolean operators.
123 –
324   \subsection{\label{appendixSection:logical}Logical expressions}
325  
326   The logical operators allow complex queries to be constructed out of
# Line 143 | Line 343 | not & ``!''  \\
343   \subsection{\label{appendixSection:name}Name expressions}
344  
345   \begin{center}
346 < \begin{tabular}{|llp{3in}|}
346 > \begin{tabular}{|llp{2in}|}
347   \hline {\bf type of expression} & {\bf examples} & {\bf translation
348   of
349   examples} \\
# Line 202 | Line 402 | expression}}
402   Users can define arbitrary terms to represent groups of
403   StuntDoubles, and then use the define terms in select commands. The
404   general form for the define command is: {\bf define {\it term
405 < expression}}
405 > expression}}. Once defined, the user can specify such terms in
406 > boolean expressions
407  
207 – Once defined, the user can specify such terms in boolean expressions
208 –
408   {\tt define SSDWATER SSD or SSD1 or SSDRF}
409  
410   {\tt select SSDWATER}
# Line 227 | Line 426 | wouldselect StuntDoubles which have mass greater than
426   \end{center}
427  
428   For example, the phrase {\tt select mass > 16.0 and charge < -2}
429 < wouldselect StuntDoubles which have mass greater than 16.0 and
429 > would select StuntDoubles which have mass greater than 16.0 and
430   charges less than -2.
431  
432   \subsection{\label{appendixSection:within}Within expressions}
# Line 240 | Line 439 | atoms.
439   For example, the phrase {\tt select within(2.5, PO4 or NC4)} would
440   select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
441   atoms.
243 –
244 – \section{\label{appendixSection:tools}Tools which use the selection command}
245 –
246 – \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
247 –
248 – Dump2XYZ can transform an OOPSE dump file into a xyz file which can
249 – be opened by other molecular dynamics viewers such as Jmol and VMD.
250 – The options available for Dump2XYZ are as follows:
442  
443  
444 < \begin{longtable}[c]{|EFG|}
254 < \caption{Dump2XYZ Command-line Options}
255 < \\ \hline
256 < {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
257 < \endhead
258 < \hline
259 < \endfoot
260 <  -h & {\tt -{}-help} &                        Print help and exit \\
261 <  -V & {\tt -{}-version} &                     Print version and exit \\
262 <  -i & {\tt -{}-input=filename}  &             input dump file \\
263 <  -o & {\tt -{}-output=filename} &             output file name \\
264 <  -n & {\tt -{}-frame=INT}   &                 print every n frame  (default=`1') \\
265 <  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
266 <  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
267 <  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
268 <  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
269 <  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
270 <  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
271 <     & {\tt -{}-repeatX=INT}  &                 The number of images to repeat in the x direction  (default=`0') \\
272 <     & {\tt -{}-repeatY=INT} &                 The number of images to repeat in the y direction  (default=`0') \\
273 <     &  {\tt -{}-repeatZ=INT}  &                The number of images to repeat in the z direction  (default=`0') \\
274 <  -s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
275 < converted. \\
276 <     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
277 <     & {\tt -{}-refsele} &  In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}.
278 < \end{longtable}
444 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
445  
280 –
446   \subsection{\label{appendixSection:StaticProps}StaticProps}
447  
448   {\tt StaticProps} can compute properties which are averaged over
449   some or all of the configurations that are contained within a dump
450   file. The most common example of a static property that can be
451   computed is the pair distribution function between atoms of type $A$
452 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
453 < used to compute the density distributions of other molecules in a
454 < reference frame {\it fixed to the body-fixed reference frame} of a
455 < selected atom or rigid body.
452 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
453 > also be used to compute the density distributions of other molecules
454 > in a reference frame {\it fixed to the body-fixed reference frame}
455 > of a selected atom or rigid body.
456  
457   There are five seperate radial distribution functions availiable in
458   OOPSE. Since every radial distrbution function invlove the
# Line 336 | Line 501 | distribution functions are most easily seen in the fig
501  
502   \begin{figure}
503   \centering
504 < \includegraphics[width=3in]{definition.pdf}
504 > \includegraphics[width=3in]{definition.eps}
505   \caption[Definitions of the angles between directional objects]{ \\
506   Any two directional objects (DirectionalAtoms and RigidBodies) have
507   a set of two angles ($\theta$, and $\omega$) between the z-axes of
508   their body-fixed frames.} \label{oopseFig:gofr}
509   \end{figure}
510  
511 + Due to the fact that the selected StuntDoubles from two selections
512 + may be overlapped, {\tt StaticProps} performs the calculation in
513 + three stages which are illustrated in
514 + Fig.~\ref{oopseFig:staticPropsProcess}.
515 +
516 + \begin{figure}
517 + \centering
518 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
519 + \caption[A representation of the three-stage correlations in
520 + \texttt{StaticProps}]{This diagram illustrates three-stage
521 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
522 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
523 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
524 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
525 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
526 + the contrary, the third stage($C$ and $C$) are completely
527 + overlapping} \label{oopseFig:staticPropsProcess}
528 + \end{figure}
529 +
530   The options available for {\tt StaticProps} are as follows:
531   \begin{longtable}[c]{|EFG|}
532   \caption{StaticProps Command-line Options}
# Line 353 | Line 537 | The options available for {\tt StaticProps} are as fol
537   \endfoot
538    -h& {\tt -{}-help}                    &  Print help and exit \\
539    -V& {\tt -{}-version}                 &  Print version and exit \\
540 <  -i& {\tt -{}-input=filename}          &  input dump file \\
541 <  -o& {\tt -{}-output=filename}         &  output file name \\
542 <  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
543 <  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
544 <  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
545 <  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
546 <    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
547 <    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
548 <    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
549 <    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
550 <    & {\tt -{}-molname=STRING}           & molecule name \\
551 <    & {\tt -{}-begin=INT}                & begin internal index \\
552 <    & {\tt -{}-end=INT}                  & end internal index \\
540 >  -i& {\tt -{}-input}          &  input dump file \\
541 >  -o& {\tt -{}-output}         &  output file name \\
542 >  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
543 >  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
544 >  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
545 >  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
546 >    & {\tt -{}-sele1}   & select the first StuntDouble set \\
547 >    & {\tt -{}-sele2}   & select the second StuntDouble set \\
548 >    & {\tt -{}-sele3}   & select the third StuntDouble set \\
549 >    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
550 >    & {\tt -{}-molname}           & molecule name \\
551 >    & {\tt -{}-begin}                & begin internal index \\
552 >    & {\tt -{}-end}                  & end internal index \\
553   \hline
554   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
555   \hline
# Line 404 | Line 588 | The options available for DynamicProps are as follows:
588   different vectors).  The ability to use two selection scripts to
589   select different types of atoms is already present in the code.
590  
591 + For large simulations, the trajectory files can sometimes reach
592 + sizes in excess of several gigabytes. In order to effectively
593 + analyze that amount of data. In order to prevent a situation where
594 + the program runs out of memory due to large trajectories,
595 + \texttt{dynamicProps} will estimate the size of free memory at
596 + first, and determine the number of frames in each block, which
597 + allows the operating system to load two blocks of data
598 + simultaneously without swapping. Upon reading two blocks of the
599 + trajectory, \texttt{dynamicProps} will calculate the time
600 + correlation within the first block and the cross correlations
601 + between the two blocks. This second block is then freed and then
602 + incremented and the process repeated until the end of the
603 + trajectory. Once the end is reached, the first block is freed then
604 + incremented, until all frame pairs have been correlated in time.
605 + This process is illustrated in
606 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
607 +
608 + \begin{figure}
609 + \centering
610 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
611 + \caption[A representation of the block correlations in
612 + \texttt{dynamicProps}]{This diagram illustrates block correlations
613 + processing in \texttt{dynamicProps}. The shaded region represents
614 + the self correlation of the block, and the open blocks are read one
615 + at a time and the cross correlations between blocks are calculated.}
616 + \label{oopseFig:dynamicPropsProcess}
617 + \end{figure}
618 +
619   The options available for DynamicProps are as follows:
620   \begin{longtable}[c]{|EFG|}
621   \caption{DynamicProps Command-line Options}
# Line 414 | Line 626 | The options available for DynamicProps are as follows:
626   \endfoot
627    -h& {\tt -{}-help}                   & Print help and exit \\
628    -V& {\tt -{}-version}                & Print version and exit \\
629 <  -i& {\tt -{}-input=filename}         & input dump file \\
630 <  -o& {\tt -{}-output=filename}        & output file name \\
631 <    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
632 <    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
629 >  -i& {\tt -{}-input}         & input dump file \\
630 >  -o& {\tt -{}-output}        & output file name \\
631 >    & {\tt -{}-sele1} & select first StuntDouble set \\
632 >    & {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
633   \hline
634   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
635   \hline
# Line 426 | Line 638 | The options available for DynamicProps are as follows:
638    -d& {\tt -{}-dcorr}                  & compute dipole correlation function
639   \end{longtable}
640  
641 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
641 > \section{\label{appendixSection:tools}Other Useful Utilities}
642 >
643 > \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
644 >
645 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
646 > which can be opened by other molecular dynamics viewers such as Jmol
647 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
648 > as follows:
649 >
650 >
651 > \begin{longtable}[c]{|EFG|}
652 > \caption{Dump2XYZ Command-line Options}
653 > \\ \hline
654 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
655 > \endhead
656 > \hline
657 > \endfoot
658 >  -h & {\tt -{}-help} &                        Print help and exit \\
659 >  -V & {\tt -{}-version} &                     Print version and exit \\
660 >  -i & {\tt -{}-input}  &             input dump file \\
661 >  -o & {\tt -{}-output} &             output file name \\
662 >  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
663 >  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
664 >  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
665 >  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
666 >  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
667 >  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
668 >  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
669 >     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
670 >     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
671 >     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
672 >  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
673 > converted. \\
674 >     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
675 >     & {\tt -{}-refsele} &  In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}.
676 > \end{longtable}
677 >
678 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
679 >
680 > {\tt Hydro} can calculate resistance and diffusion tensors at the
681 > center of resistance. Both tensors at the center of diffusion can
682 > also be reported from the program, as well as the coordinates for
683 > the beads which are used to approximate the arbitrary shapes. The
684 > options available for Hydro are as follows:
685 > \begin{longtable}[c]{|EFG|}
686 > \caption{Hydrodynamics Command-line Options}
687 > \\ \hline
688 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
689 > \endhead
690 > \hline
691 > \endfoot
692 >  -h & {\tt -{}-help} &                        Print help and exit \\
693 >  -V & {\tt -{}-version} &                     Print version and exit \\
694 >  -i & {\tt -{}-input}  &             input dump file \\
695 >  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
696 >  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
697 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
698 > \end{longtable}

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