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1   \appendix
2 < \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine (OOPSE)}
2 > \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
3  
4 < Designing object-oriented software is hard, and designing reusable
5 < object-oriented scientific software is even harder. Absence of
6 < applying modern software development practices is the bottleneck of
7 < Scientific Computing community\cite{Wilson2006}. For instance, in
8 < the last 20 years , there are quite a few MD packages that were
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 > few MD packages\cite{Brooks1983, Vincent1995, Kale1999} were
8   developed to solve common MD problems and perform robust simulations
9 < . However, many of the codes are legacy programs that are either
10 < poorly organized or extremely complex. Usually, these packages were
11 < contributed by scientists without official computer science
12 < training. The development of most MD applications are lack of strong
13 < coordination to enforce design and programming guidelines. Moreover,
14 < most MD programs also suffer from missing design and implement
15 < documents which is crucial to the maintenance and extensibility.
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
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.
24 >  \item {\sc OOPSE} integrates the equations of motion using advanced methods for
25 > orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T
26 > ensembles.
27 >  \item {\sc OOPSE} can carry out simulations on metallic systems using the
28 > Embedded Atom Method (EAM) as well as the Sutton-Chen potential.
29 >  \item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals.
30 >  \item  {\sc OOPSE} can simulate systems containing the extremely efficient
31 > extended-Soft Sticky Dipole (SSD/E) model for water.
32 > \end{enumerate}
33  
34   \section{\label{appendixSection:architecture }Architecture}
35  
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
69   \includegraphics[width=\linewidth]{architecture.eps}
70 < \caption[The architecture of {\sc oopse}-3.0] {The architecture of
71 < {\sc oopse}-3.0.} \label{appendixFig:architecture}
70 > \caption[The architecture of {\sc OOPSE}] {Overview of the structure
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.
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 < Patterns are usually described using a format that includes the
43 < following information:
44 < \begin{enumerate}
45 <  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
46 <  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
47 <  in the literature. In this case it is common practice to document these nicknames or synonyms under
48 <  the heading of \emph{Aliases} or \emph{Also Known As}.
49 <  \item The \emph{motivation} or \emph{context} that this pattern applies
50 <  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
51 <  \item The \emph{solution} to the problem that the pattern
52 <  addresses. It describes how to construct the necessary work products. The description may include
53 <  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
54 <  collaborations, to show how the problem is solved.
55 <  \item The \emph{consequences} of using the given solution to solve a
56 <  problem, both positive and negative.
57 < \end{enumerate}
93 > \subsection{\label{appendixSection:singleton}Singletons}
94  
95 < As one of the latest advanced techniques emerged from
96 < object-oriented community, design patterns were applied in some of
97 < the modern scientific software applications, such as JMol, OOPSE
98 < \cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}.
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. 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 > 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.
111  
112 < \subsection{\label{appendixSection:singleton}Singleton}
65 < The Singleton pattern ensures that only one instance of a class is
66 < created. All objects that use an instance of that class use the same
67 < instance.
112 > \subsection{\label{appendixSection:factoryMethod}Factory Methods}
113  
114 < \subsection{\label{appendixSection:factoryMethod}Factory Method}
70 < The Factory Method pattern is a creational pattern which deals with
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 solves this problem
117 < by defining a separate method for creating the objects, which
118 < subclasses can then override to specify the derived type of product
119 < that will be created.
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  
77 –
126   \subsection{\label{appendixSection:visitorPattern}Visitor}
79 – The purpose of the Visitor Pattern is to encapsulate an operation
80 – that you want to perform on the elements of a data structure. In
81 – this way, you can change the operation being performed on a
82 – structure without the need of changing the classes of the elements
83 – that you are operating on.
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 Scheme.~\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 < \subsection{\label{appendixSection:templateMethod}Template Method}
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* getInstance();
166 >  protected:
167 >  IntegratorFactory();
168 >  private:
169 >  static IntegratorFactory* instance_; };
170 >
171 > \end{lstlisting}
172 >
173 > \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
174 >
175 > IntegratorFactory::instance_ = NULL;
176 >
177 > IntegratorFactory* getInstance() {
178 >  if (instance_ == NULL){
179 >    instance_ = new IntegratorFactory;
180 >  }
181 >  return instance_;
182 > }
183 >
184 > \end{lstlisting}
185 >
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:
190 >  typedef std::map<string, IntegratorCreator*> CreatorMapType;
191 >
192 >  bool registerIntegrator(IntegratorCreator* creator){
193 >    return creatorMap_.insert(creator->getIdent(),creator).second;
194 >  }
195 >
196 >  Integrator* createIntegrator(const string& id, SimInfo* info) {
197 >    Integrator* result = NULL;
198 >    CreatorMapType::iterator i = creatorMap_.find(id);
199 >    if (i != creatorMap_.end()) {
200 >      result = (i->second)->create(info);
201 >    }
202 >    return result;
203 >  }
204 >
205 > private:
206 >  CreatorMapType creatorMap_;
207 > };
208 > \end{lstlisting}
209 >
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) {}
215 >
216 >  const string& getIdent() const { return ident_; }
217 >
218 >  virtual Integrator* create(SimInfo* info) const = 0;
219 >
220 >  private:
221 >  string ident_;
222 > };
223 >
224 > template<class ConcreteIntegrator> class IntegratorBuilder :
225 > public IntegratorCreator {
226 >  public:
227 >  IntegratorBuilder(const string& ident)
228 >                     : IntegratorCreator(ident) {}
229 >  virtual  Integrator* create(SimInfo* info) const {
230 >    return new ConcreteIntegrator(info);
231 >  }
232 > };
233 > \end{lstlisting}
234  
235 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
236 +
237 + class StuntDouble {
238 +  public:
239 +  virtual void accept(BaseVisitor* v) = 0;
240 + };
241 +
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 {
250 +  public:
251 +  virtual void accept{BaseVisitor* v*} {
252 +    v->visit(this);
253 +  }
254 + };
255 +
256 + class RigidBody: public StuntDouble {
257 +  public:
258 +  virtual void accept{BaseVisitor* v*} {
259 +    v->visit(this);
260 +  }
261 + };
262 +
263 + \end{lstlisting}
264 +
265 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
266 + class BaseVisitor{
267 +  public:
268 +  virtual void visit(Atom* atom);
269 +  virtual void visit(DirectionalAtom* datom);
270 +  virtual void visit(RigidBody* rb);
271 + };
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 + };
278 + class CompositeVisitor: public BaseVisitor {
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 = visitorScheme.begin();i != visitorScheme.end();++i)
286 +      atom->accept(*i);
287 +  }
288 +  virtual void visit(DirectionalAtom* datom) {
289 +    VisitorListIterator i;
290 +    BaseVisitor* curVisitor;
291 +    for(i = visitorList.begin();i != visitorList.end();++i)
292 +      atom->accept(*i);
293 +  }
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) {
300 +      rb->accept(*i);
301 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai)
302 +        (*ai)->accept(*i);
303 +    }
304 +  void addVisitor(BaseVisitor* v, int priority);
305 +  protected:
306 +  VistorListType visitorList;
307 + };
308 + \end{lstlisting}
309 +
310   \section{\label{appendixSection:concepts}Concepts}
311  
312   OOPSE manipulates both traditional atoms as well as some objects
313   that {\it behave like atoms}.  These objects can be rigid
314   collections of atoms or atoms which have orientational degrees of
315 < freedom.  Here is a diagram of the class heirarchy:
316 <
317 < %\begin{figure}
318 < %\centering
319 < %\includegraphics[width=3in]{heirarchy.eps}
320 < %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
321 < %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
322 < %selection syntax allows the user to select any of the objects that
323 < %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
102 < %\end{figure}
103 <
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 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
322 > generated automatically. For example, the name of the first rigid
323 > body in a DMPC molecule is DMPC\_RB\_0.
324   \begin{itemize}
325   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
326   integrators and minimizers.
# Line 110 | Line 330 | Every Molecule, Atom and DirectionalAtom in {\sc oopse
330   DirectionalAtom}s which behaves as a single unit.
331   \end{itemize}
332  
113 – Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
114 – own names which are specified in the {\tt .md} file. In contrast,
115 – RigidBodies are denoted by their membership and index inside a
116 – particular molecule: [MoleculeName]\_RB\_[index] (the contents
117 – inside the brackets depend on the specifics of the simulation). The
118 – names of rigid bodies are generated automatically. For example, the
119 – name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
120 –
333   \section{\label{appendixSection:syntax}Syntax of the Select Command}
334  
335 < The most general form of the select command is: {\tt select {\it
336 < expression}}
335 > {\sc OOPSE} provides a powerful selection utility to select
336 > StuntDoubles. The most general form of the select command is:
337  
338 + {\tt select {\it expression}}.
339 +
340   This expression represents an arbitrary set of StuntDoubles (Atoms
341 < or RigidBodies) in {\sc oopse}. Expressions are composed of either
341 > or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
342   name expressions, index expressions, predefined sets, user-defined
343   expressions, comparison operators, within expressions, or logical
344   combinations of the above expression types. Expressions can be
# Line 211 | Line 425 | expression}}
425   Users can define arbitrary terms to represent groups of
426   StuntDoubles, and then use the define terms in select commands. The
427   general form for the define command is: {\bf define {\it term
428 < expression}}
428 > expression}}. Once defined, the user can specify such terms in
429 > boolean expressions
430  
216 – Once defined, the user can specify such terms in boolean expressions
217 –
431   {\tt define SSDWATER SSD or SSD1 or SSDRF}
432  
433   {\tt select SSDWATER}
# Line 259 | Line 472 | and other atoms of type $B$, $g_{AB}(r)$.  StaticProps
472   some or all of the configurations that are contained within a dump
473   file. The most common example of a static property that can be
474   computed is the pair distribution function between atoms of type $A$
475 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
476 < used to compute the density distributions of other molecules in a
477 < reference frame {\it fixed to the body-fixed reference frame} of a
478 < selected atom or rigid body.
475 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
476 > also be used to compute the density distributions of other molecules
477 > in a reference frame {\it fixed to the body-fixed reference frame}
478 > of a selected atom or rigid body. Due to the fact that the selected
479 > StuntDoubles from two selections may be overlapped, {\tt
480 > StaticProps} performs the calculation in three stages which are
481 > illustrated in Fig.~\ref{oopseFig:staticPropsProcess}.
482  
483 + \begin{figure}
484 + \centering
485 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
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
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 307 | Line 546 | distribution functions are most easily seen in the fig
546   \end{description}
547  
548   The vectors (and angles) associated with these angular pair
549 < distribution functions are most easily seen in the figure below:
549 > distribution functions are most easily seen in
550 > Fig.~\ref{oopseFig:gofr}. The options available for {\tt
551 > StaticProps} are showed in Table.~\ref{appendix:staticPropsOptions}.
552  
553 + \subsection{\label{appendixSection:DynamicProps}DynamicProps}
554 +
555 + {\tt DynamicProps} computes time correlation functions from the
556 + configurations stored in a dump file.  Typical examples of time
557 + correlation functions are the mean square displacement and the
558 + velocity autocorrelation functions.   Once again, the selection
559 + syntax can be used to specify the StuntDoubles that will be used for
560 + the calculation.  A general time correlation function can be thought
561 + of as:
562 + \begin{equation}
563 + C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle
564 + \end{equation}
565 + where $\vec{u}_A(t)$ is a vector property associated with an atom of
566 + type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different
567 + vector property associated with an atom of type $B$ at a different
568 + time $t^{\prime}$.  In most autocorrelation functions, the vector
569 + properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and
570 + $B$) are identical, and the three calculations built in to {\tt
571 + DynamicProps} make these assumptions.  It is possible, however, to
572 + make simple modifications to the {\tt DynamicProps} code to allow
573 + the use of {\it cross} time correlation functions (i.e. with
574 + different vectors).  The ability to use two selection scripts to
575 + select different types of atoms is already present in the code.
576 +
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 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
586 + between the two blocks. This second block is then freed and then
587 + incremented and the process repeated until the end of the
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} and the options available
592 + for DynamicProps are showed in
593 + Table.~\ref{appendix:dynamicPropsOptions}
594 +
595   \begin{figure}
596   \centering
597 < \includegraphics[width=3in]{definition.eps}
598 < \caption[Definitions of the angles between directional objects]{ \\
599 < Any two directional objects (DirectionalAtoms and RigidBodies) have
600 < a set of two angles ($\theta$, and $\omega$) between the z-axes of
601 < their body-fixed frames.} \label{oopseFig:gofr}
597 > \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
598 > \caption[A representation of the block correlations in
599 > \texttt{dynamicProps}]{This diagram illustrates block correlations
600 > processing in \texttt{dynamicProps}. The shaded region represents
601 > the self correlation of the block, and the open blocks are read one
602 > at a time and the cross correlations between blocks are calculated.}
603 > \label{oopseFig:dynamicPropsProcess}
604   \end{figure}
605  
321 – The options available for {\tt StaticProps} are as follows:
606   \begin{longtable}[c]{|EFG|}
607 < \caption{StaticProps 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
# Line 355 | Line 640 | The options available for {\tt StaticProps} are as fol
640      &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
641   \end{longtable}
642  
358 – \subsection{\label{appendixSection:DynamicProps}DynamicProps}
359 –
360 – {\tt DynamicProps} computes time correlation functions from the
361 – configurations stored in a dump file.  Typical examples of time
362 – correlation functions are the mean square displacement and the
363 – velocity autocorrelation functions.   Once again, the selection
364 – syntax can be used to specify the StuntDoubles that will be used for
365 – the calculation.  A general time correlation function can be thought
366 – of as:
367 – \begin{equation}
368 – C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle
369 – \end{equation}
370 – where $\vec{u}_A(t)$ is a vector property associated with an atom of
371 – type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different
372 – vector property associated with an atom of type $B$ at a different
373 – time $t^{\prime}$.  In most autocorrelation functions, the vector
374 – properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and
375 – $B$) are identical, and the three calculations built in to {\tt
376 – DynamicProps} make these assumptions.  It is possible, however, to
377 – make simple modifications to the {\tt DynamicProps} code to allow
378 – the use of {\it cross} time correlation functions (i.e. with
379 – different vectors).  The ability to use two selection scripts to
380 – select different types of atoms is already present in the code.
381 –
382 – The options available for DynamicProps are as follows:
643   \begin{longtable}[c]{|EFG|}
644 < \caption{DynamicProps Command-line Options}
644 > \caption{DYNAMICPROPS COMMAND-LINE OPTIONS}
645 > \label{appendix:dynamicPropsOptions}
646   \\ \hline
647   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
648   \endhead
# Line 405 | Line 666 | Dump2XYZ can transform an OOPSE dump file into a xyz f
666  
667   \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
668  
669 < Dump2XYZ can transform an OOPSE dump file into a xyz file which can
670 < be opened by other molecular dynamics viewers such as Jmol and VMD.
671 < The options available for Dump2XYZ are as follows:
669 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
670 > which can be opened by other molecular dynamics viewers such as Jmol
671 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
672 > as follows:
673  
412 –
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 437 | Line 698 | converted. \\
698       & {\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}.
699   \end{longtable}
700  
701 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
701 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
702  
703 + {\tt Hydro} can calculate resistance and diffusion tensors at the
704 + center of resistance. Both tensors at the center of diffusion can
705 + also be reported from the program, as well as the coordinates for
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
# Line 451 | Line 717 | converted. \\
717    -i & {\tt -{}-input}  &             input dump file \\
718    -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
719    -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
720 <     & {\tt -{}-model}  &                 hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
720 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
721   \end{longtable}

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