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1   \appendix
2 < \chapter{\label{chapt:appendix}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 14 | 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
# Line 49 | 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}
56 – The Singleton pattern ensures that only one instance of a class is
57 – created. All objects that use an instance of that class use the same
58 – instance.
121  
122 + The Singleton pattern not only provides a mechanism to restrict
123 + instantiation of a class to one object, but also provides a global
124 + point of access to the object. Currently implemented as a global
125 + variable, the logging utility which reports error and warning
126 + messages to the console in {\sc OOPSE} is a good candidate for
127 + applying the Singleton pattern to avoid the global namespace
128 + pollution.Although the singleton pattern can be implemented in
129 + various ways  to account for different aspects of the software
130 + designs, such as lifespan control \textit{etc}, we only use the
131 + static data approach in {\sc OOPSE}. IntegratorFactory class is
132 + declared as
133 +
134 + \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
135 +
136 + class IntegratorFactory {
137 + public:
138 +  static IntegratorFactory*
139 +  getInstance();
140 + protected:
141 +  IntegratorFactory();
142 + private:
143 +  static IntegratorFactory* instance_;
144 + };
145 +
146 + \end{lstlisting}
147 +
148 + The corresponding implementation is
149 +
150 + \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
151 +
152 + IntegratorFactory::instance_ = NULL;
153 +
154 + IntegratorFactory* getInstance() {
155 +  if (instance_ == NULL){
156 +    instance_ = new IntegratorFactory;
157 +  }
158 +  return instance_;
159 + }
160 +
161 + \end{lstlisting}
162 +
163 + Since constructor is declared as protected, a client can not
164 + instantiate IntegratorFactory directly. Moreover, since the member
165 + function getInstance serves as the only entry of access to
166 + IntegratorFactory, this approach fulfills the basic requirement, a
167 + single instance. Another consequence of this approach is the
168 + automatic destruction since static data are destroyed upon program
169 + termination.
170 +
171   \subsection{\label{appendixSection:factoryMethod}Factory Method}
61 – The Factory Method pattern is a creational pattern which deals with
62 – the problem of creating objects without specifying the exact class
63 – of object that will be created. Factory Method solves this problem
64 – by defining a separate method for creating the objects, which
65 – subclasses can then override to specify the derived type of product
66 – that will be created.
172  
173 + Categoried as a creational pattern, the Factory Method pattern deals
174 + with the problem of creating objects without specifying the exact
175 + class of object that will be created. Factory Method is typically
176 + implemented by delegating the creation operation to the subclasses.
177 + Parameterized Factory pattern where factory method (
178 + createIntegrator member function) creates products based on the
179 + identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If
180 + the identifier has been already registered, the factory method will
181 + invoke the corresponding creator (see List.~\ref{integratorCreator})
182 + which utilizes the modern C++ template technique to avoid excess
183 + subclassing.
184  
185 < \subsection{\label{appendixSection:visitorPattern}Visitor}
70 < The purpose of the Visitor Pattern is to encapsulate an operation
71 < that you want to perform on the elements of a data structure. In
72 < this way, you can change the operation being performed on a
73 < structure without the need of changing the classes of the elements
74 < that you are operating on.
185 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
186  
187 + class IntegratorFactory {
188 + public:
189 +  typedef std::map<string, IntegratorCreator*> CreatorMapType;
190  
191 < \subsection{\label{appendixSection:templateMethod}Template Method}
191 >  bool registerIntegrator(IntegratorCreator* creator) {
192 >    return creatorMap_.insert(creator->getIdent(), creator).second;
193 >  }
194  
195 < \section{\label{appendixSection:analysisFramework}Analysis Framework}
195 >  Integrator* createIntegrator(const string& id, SimInfo* info) {
196 >    Integrator* result = NULL;
197 >    CreatorMapType::iterator i = creatorMap_.find(id);
198 >    if (i != creatorMap_.end()) {
199 >      result = (i->second)->create(info);
200 >    }
201 >    return result;
202 >  }
203  
204 < \section{\label{appendixSection:concepts}Concepts}
204 > private:
205 >  CreatorMapType creatorMap_;
206 > };
207 > \end{lstlisting}
208  
209 < OOPSE manipulates both traditional atoms as well as some objects
84 < that {\it behave like atoms}.  These objects can be rigid
85 < collections of atoms or atoms which have orientational degrees of
86 < freedom.  Here is a diagram of the class heirarchy:
209 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
210  
211 + class IntegratorCreator {
212 + public:
213 +    IntegratorCreator(const string& ident) : ident_(ident) {}
214 +
215 +    const string& getIdent() const { return ident_; }
216 +
217 +    virtual Integrator* create(SimInfo* info) const = 0;
218 +
219 + private:
220 +    string ident_;
221 + };
222 +
223 + template<class ConcreteIntegrator>
224 + class IntegratorBuilder : public IntegratorCreator {
225 + public:
226 +  IntegratorBuilder(const string& ident)
227 +                   : IntegratorCreator(ident) {}
228 +  virtual  Integrator* create(SimInfo* info) const {
229 +    return new ConcreteIntegrator(info);
230 +  }
231 + };
232 + \end{lstlisting}
233 +
234 + \subsection{\label{appendixSection:visitorPattern}Visitor}
235 +
236 + The visitor pattern is designed to decouple the data structure and
237 + algorithms used upon them by collecting related operation from
238 + element classes into other visitor classes, which is equivalent to
239 + adding virtual functions into a set of classes without modifying
240 + their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
241 + structure of Visitor pattern which is used extensively in {\tt
242 + Dump2XYZ}. In order to convert an OOPSE dump file, a series of
243 + distinct operations are performed on different StuntDoubles (See the
244 + class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration
245 + in List.~\ref{appendixScheme:element}). Since the hierarchies
246 + remains stable, it is easy to define a visit operation (see
247 + List.~\ref{appendixScheme:visitor}) for each class of StuntDouble.
248 + Note that using Composite pattern\cite{Gamma1994}, CompositVisitor
249 + manages a priority visitor list and handles the execution of every
250 + visitor in the priority list on different StuntDoubles.
251 +
252 + \begin{figure}
253 + \centering
254 + \includegraphics[width=\linewidth]{visitor.eps}
255 + \caption[The UML class diagram of Visitor patten] {The UML class
256 + diagram of Visitor patten.} \label{appendixFig:visitorUML}
257 + \end{figure}
258 +
259   %\begin{figure}
260   %\centering
261 < %\includegraphics[width=3in]{heirarchy.eps}
262 < %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
263 < %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
264 < %selection syntax allows the user to select any of the objects that
265 < %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
261 > %\includegraphics[width=\linewidth]{hierarchy.eps}
262 > %\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
263 > %the class hierarchy.
264 > %\begin{itemize}
265 > %\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
266 > %integrators and minimizers.
267 > %\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
268 > %\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
269 > %\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
270 > %DirectionalAtom}s which behaves as a single unit.
271 > %\end{itemize}
272 > %} \label{oopseFig:hierarchy}
273   %\end{figure}
274  
275 < \begin{itemize}
98 < \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
99 < integrators and minimizers.
100 < \item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
101 < \item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
102 < \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
103 < DirectionalAtom}s which behaves as a single unit.
104 < \end{itemize}
275 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
276  
277 < Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
278 < own names which are specified in the {\tt .md} file. In contrast,
279 < RigidBodies are denoted by their membership and index inside a
280 < particular molecule: [MoleculeName]\_RB\_[index] (the contents
281 < inside the brackets depend on the specifics of the simulation). The
282 < names of rigid bodies are generated automatically. For example, the
283 < name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
277 > class StuntDouble { public:
278 >  virtual void accept(BaseVisitor* v) = 0;
279 > };
280 >
281 > class Atom: public StuntDouble { public:
282 >  virtual void accept{BaseVisitor* v*} {
283 >    v->visit(this);
284 >  }
285 > };
286  
287 + class DirectionalAtom: public Atom { public:
288 +  virtual void accept{BaseVisitor* v*} {
289 +    v->visit(this);
290 +  }
291 + };
292 +
293 + class RigidBody: public StuntDouble { public:
294 +  virtual void accept{BaseVisitor* v*} {
295 +    v->visit(this);
296 +  }
297 + };
298 +
299 + \end{lstlisting}
300 +
301 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
302 +
303 + class BaseVisitor{
304 + public:
305 +  virtual void visit(Atom* atom);
306 +  virtual void visit(DirectionalAtom* datom);
307 +  virtual void visit(RigidBody* rb);
308 + };
309 +
310 + class BaseAtomVisitor:public BaseVisitor{ public:
311 +  virtual void visit(Atom* atom);
312 +  virtual void visit(DirectionalAtom* datom);
313 +  virtual void visit(RigidBody* rb);
314 + };
315 +
316 + class SSDAtomVisitor:public BaseAtomVisitor{ public:
317 +  virtual void visit(Atom* atom);
318 +  virtual void visit(DirectionalAtom* datom);
319 +  virtual void visit(RigidBody* rb);
320 + };
321 +
322 + class CompositeVisitor: public BaseVisitor {
323 + public:
324 +
325 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
326 +  typedef VistorListType::iterator VisitorListIterator;
327 +  virtual void visit(Atom* atom) {
328 +    VisitorListIterator i;
329 +    BaseVisitor* curVisitor;
330 +    for(i = visitorList.begin();i != visitorList.end();++i) {
331 +      atom->accept(*i);
332 +    }
333 +  }
334 +
335 +  virtual void visit(DirectionalAtom* datom) {
336 +    VisitorListIterator i;
337 +    BaseVisitor* curVisitor;
338 +    for(i = visitorList.begin();i != visitorList.end();++i) {
339 +      atom->accept(*i);
340 +    }
341 +  }
342 +
343 +  virtual void visit(RigidBody* rb) {
344 +    VisitorListIterator i;
345 +    std::vector<Atom*> myAtoms;
346 +    std::vector<Atom*>::iterator ai;
347 +    myAtoms = rb->getAtoms();
348 +    for(i = visitorList.begin();i != visitorList.end();++i) {{
349 +      rb->accept(*i);
350 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
351 +        (*ai)->accept(*i);
352 +    }
353 +  }
354 +
355 +  void addVisitor(BaseVisitor* v, int priority);
356 +
357 +  protected:
358 +    VistorListType visitorList;
359 + };
360 +
361 + \end{lstlisting}
362 +
363 + \section{\label{appendixSection:concepts}Concepts}
364 +
365 + OOPSE manipulates both traditional atoms as well as some objects
366 + that {\it behave like atoms}.  These objects can be rigid
367 + collections of atoms or atoms which have orientational degrees of
368 + freedom.  A diagram of the class hierarchy is illustrated in
369 + Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
370 + DirectionalAtom in {\sc OOPSE} have their own names which are
371 + specified in the {\tt .md} file. In contrast, RigidBodies are
372 + denoted by their membership and index inside a particular molecule:
373 + [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
374 + on the specifics of the simulation). The names of rigid bodies are
375 + generated automatically. For example, the name of the first rigid
376 + body in a DMPC molecule is DMPC\_RB\_0.
377 +
378   \section{\label{appendixSection:syntax}Syntax of the Select Command}
379  
380   The most general form of the select command is: {\tt select {\it
381 < expression}}
381 > expression}}. This expression represents an arbitrary set of
382 > StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
383 > composed of either name expressions, index expressions, predefined
384 > sets, user-defined expressions, comparison operators, within
385 > expressions, or logical combinations of the above expression types.
386 > Expressions can be combined using parentheses and the Boolean
387 > operators.
388  
119 – This expression represents an arbitrary set of StuntDoubles (Atoms
120 – or RigidBodies) in {\sc oopse}. Expressions are composed of either
121 – name expressions, index expressions, predefined sets, user-defined
122 – expressions, comparison operators, within expressions, or logical
123 – combinations of the above expression types. Expressions can be
124 – combined using parentheses and the Boolean operators.
125 –
389   \subsection{\label{appendixSection:logical}Logical expressions}
390  
391   The logical operators allow complex queries to be constructed out of
# Line 204 | Line 467 | expression}}
467   Users can define arbitrary terms to represent groups of
468   StuntDoubles, and then use the define terms in select commands. The
469   general form for the define command is: {\bf define {\it term
470 < expression}}
470 > expression}}. Once defined, the user can specify such terms in
471 > boolean expressions
472  
209 – Once defined, the user can specify such terms in boolean expressions
210 –
473   {\tt define SSDWATER SSD or SSD1 or SSDRF}
474  
475   {\tt select SSDWATER}
# Line 243 | Line 505 | atoms.
505   select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
506   atoms.
507  
246 – \section{\label{appendixSection:tools}Tools which use the selection command}
508  
509 < \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
249 <
250 < Dump2XYZ can transform an OOPSE dump file into a xyz file which can
251 < be opened by other molecular dynamics viewers such as Jmol and VMD.
252 < The options available for Dump2XYZ are as follows:
253 <
254 <
255 < \begin{longtable}[c]{|EFG|}
256 < \caption{Dump2XYZ Command-line Options}
257 < \\ \hline
258 < {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
259 < \endhead
260 < \hline
261 < \endfoot
262 <  -h & {\tt -{}-help} &                        Print help and exit \\
263 <  -V & {\tt -{}-version} &                     Print version and exit \\
264 <  -i & {\tt -{}-input}  &             input dump file \\
265 <  -o & {\tt -{}-output} &             output file name \\
266 <  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
267 <  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
268 <  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
269 <  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
270 <  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
271 <  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
272 <  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
273 <     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
274 <     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
275 <     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
276 <  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
277 < converted. \\
278 <     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
279 <     & {\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}.
280 < \end{longtable}
509 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
510  
282 –
511   \subsection{\label{appendixSection:StaticProps}StaticProps}
512  
513   {\tt StaticProps} can compute properties which are averaged over
514   some or all of the configurations that are contained within a dump
515   file. The most common example of a static property that can be
516   computed is the pair distribution function between atoms of type $A$
517 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
518 < used to compute the density distributions of other molecules in a
519 < reference frame {\it fixed to the body-fixed reference frame} of a
520 < selected atom or rigid body.
517 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
518 > also be used to compute the density distributions of other molecules
519 > in a reference frame {\it fixed to the body-fixed reference frame}
520 > of a selected atom or rigid body.
521  
522   There are five seperate radial distribution functions availiable in
523   OOPSE. Since every radial distrbution function invlove the
# Line 345 | Line 573 | The options available for {\tt StaticProps} are as fol
573   their body-fixed frames.} \label{oopseFig:gofr}
574   \end{figure}
575  
576 + Due to the fact that the selected StuntDoubles from two selections
577 + may be overlapped, {\tt StaticProps} performs the calculation in
578 + three stages which are illustrated in
579 + Fig.~\ref{oopseFig:staticPropsProcess}.
580 +
581 + \begin{figure}
582 + \centering
583 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
584 + \caption[A representation of the three-stage correlations in
585 + \texttt{StaticProps}]{This diagram illustrates three-stage
586 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
587 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
588 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
589 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
590 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
591 + the contrary, the third stage($C$ and $C$) are completely
592 + overlapping} \label{oopseFig:staticPropsProcess}
593 + \end{figure}
594 +
595   The options available for {\tt StaticProps} are as follows:
596   \begin{longtable}[c]{|EFG|}
597   \caption{StaticProps Command-line Options}
# Line 406 | Line 653 | The options available for DynamicProps are as follows:
653   different vectors).  The ability to use two selection scripts to
654   select different types of atoms is already present in the code.
655  
656 + For large simulations, the trajectory files can sometimes reach
657 + sizes in excess of several gigabytes. In order to effectively
658 + analyze that amount of data. In order to prevent a situation where
659 + the program runs out of memory due to large trajectories,
660 + \texttt{dynamicProps} will estimate the size of free memory at
661 + first, and determine the number of frames in each block, which
662 + allows the operating system to load two blocks of data
663 + simultaneously without swapping. Upon reading two blocks of the
664 + trajectory, \texttt{dynamicProps} will calculate the time
665 + correlation within the first block and the cross correlations
666 + between the two blocks. This second block is then freed and then
667 + incremented and the process repeated until the end of the
668 + trajectory. Once the end is reached, the first block is freed then
669 + incremented, until all frame pairs have been correlated in time.
670 + This process is illustrated in
671 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
672 +
673 + \begin{figure}
674 + \centering
675 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
676 + \caption[A representation of the block correlations in
677 + \texttt{dynamicProps}]{This diagram illustrates block correlations
678 + processing in \texttt{dynamicProps}. The shaded region represents
679 + the self correlation of the block, and the open blocks are read one
680 + at a time and the cross correlations between blocks are calculated.}
681 + \label{oopseFig:dynamicPropsProcess}
682 + \end{figure}
683 +
684   The options available for DynamicProps are as follows:
685   \begin{longtable}[c]{|EFG|}
686   \caption{DynamicProps Command-line Options}
# Line 428 | Line 703 | The options available for DynamicProps are as follows:
703    -d& {\tt -{}-dcorr}                  & compute dipole correlation function
704   \end{longtable}
705  
706 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
706 > \section{\label{appendixSection:tools}Other Useful Utilities}
707 >
708 > \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
709 >
710 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
711 > which can be opened by other molecular dynamics viewers such as Jmol
712 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
713 > as follows:
714 >
715 >
716 > \begin{longtable}[c]{|EFG|}
717 > \caption{Dump2XYZ Command-line Options}
718 > \\ \hline
719 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
720 > \endhead
721 > \hline
722 > \endfoot
723 >  -h & {\tt -{}-help} &                        Print help and exit \\
724 >  -V & {\tt -{}-version} &                     Print version and exit \\
725 >  -i & {\tt -{}-input}  &             input dump file \\
726 >  -o & {\tt -{}-output} &             output file name \\
727 >  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
728 >  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
729 >  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
730 >  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
731 >  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
732 >  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
733 >  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
734 >     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
735 >     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
736 >     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
737 >  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
738 > converted. \\
739 >     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
740 >     & {\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}.
741 > \end{longtable}
742 >
743 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
744 >
745 > {\tt Hydro} can calculate resistance and diffusion tensors at the
746 > center of resistance. Both tensors at the center of diffusion can
747 > also be reported from the program, as well as the coordinates for
748 > the beads which are used to approximate the arbitrary shapes. The
749 > options available for Hydro are as follows:
750 > \begin{longtable}[c]{|EFG|}
751 > \caption{Hydrodynamics Command-line Options}
752 > \\ \hline
753 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
754 > \endhead
755 > \hline
756 > \endfoot
757 >  -h & {\tt -{}-help} &                        Print help and exit \\
758 >  -V & {\tt -{}-version} &                     Print version and exit \\
759 >  -i & {\tt -{}-input}  &             input dump file \\
760 >  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
761 >  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
762 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
763 > \end{longtable}

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