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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
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 48 | 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}
55 – The Singleton pattern ensures that only one instance of a class is
56 – created. All objects that use an instance of that class use the same
57 – 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}
60 – The Factory Method pattern is a creational pattern which deals with
61 – the problem of creating objects without specifying the exact class
62 – of object that will be created. Factory Method solves this problem
63 – by defining a separate method for creating the objects, which
64 – subclasses can then override to specify the derived type of product
65 – 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 + \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 +  bool registerIntegrator(IntegratorCreator* creator) {
192 +    return creatorMap_.insert(creator->getIdent(), creator).second;
193 +  }
194 +
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 + private:
205 +  CreatorMapType creatorMap_;
206 + };
207 + \end{lstlisting}
208 +
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}
69 – The purpose of the Visitor Pattern is to encapsulate an operation
70 – that you want to perform on the elements of a data structure. In
71 – this way, you can change the operation being performed on a
72 – structure without the need of changing the classes of the elements
73 – that you are operating on.
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 < \subsection{\label{appendixSection:templateMethod}Template Method}
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 < \section{\label{appendixSection:analysisFramework}Analysis Framework}
259 > \begin{figure}
260 > \centering
261 > \includegraphics[width=\linewidth]{hierarchy.eps}
262 > \caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
263 > the class hierarchy. } \label{oopseFig:hierarchy}
264 > \end{figure}
265  
266 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
267 +
268 + class StuntDouble { public:
269 +  virtual void accept(BaseVisitor* v) = 0;
270 + };
271 +
272 + class Atom: public StuntDouble { public:
273 +  virtual void accept{BaseVisitor* v*} {
274 +    v->visit(this);
275 +  }
276 + };
277 +
278 + class DirectionalAtom: public Atom { public:
279 +  virtual void accept{BaseVisitor* v*} {
280 +    v->visit(this);
281 +  }
282 + };
283 +
284 + class RigidBody: public StuntDouble { public:
285 +  virtual void accept{BaseVisitor* v*} {
286 +    v->visit(this);
287 +  }
288 + };
289 +
290 + \end{lstlisting}
291 +
292 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
293 +
294 + class BaseVisitor{
295 + public:
296 +  virtual void visit(Atom* atom);
297 +  virtual void visit(DirectionalAtom* datom);
298 +  virtual void visit(RigidBody* rb);
299 + };
300 +
301 + class BaseAtomVisitor:public BaseVisitor{ public:
302 +  virtual void visit(Atom* atom);
303 +  virtual void visit(DirectionalAtom* datom);
304 +  virtual void visit(RigidBody* rb);
305 + };
306 +
307 + class SSDAtomVisitor:public BaseAtomVisitor{ public:
308 +  virtual void visit(Atom* atom);
309 +  virtual void visit(DirectionalAtom* datom);
310 +  virtual void visit(RigidBody* rb);
311 + };
312 +
313 + class CompositeVisitor: public BaseVisitor {
314 + public:
315 +
316 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
317 +  typedef VistorListType::iterator VisitorListIterator;
318 +  virtual void visit(Atom* atom) {
319 +    VisitorListIterator i;
320 +    BaseVisitor* curVisitor;
321 +    for(i = visitorList.begin();i != visitorList.end();++i) {
322 +      atom->accept(*i);
323 +    }
324 +  }
325 +
326 +  virtual void visit(DirectionalAtom* datom) {
327 +    VisitorListIterator i;
328 +    BaseVisitor* curVisitor;
329 +    for(i = visitorList.begin();i != visitorList.end();++i) {
330 +      atom->accept(*i);
331 +    }
332 +  }
333 +
334 +  virtual void visit(RigidBody* rb) {
335 +    VisitorListIterator i;
336 +    std::vector<Atom*> myAtoms;
337 +    std::vector<Atom*>::iterator ai;
338 +    myAtoms = rb->getAtoms();
339 +    for(i = visitorList.begin();i != visitorList.end();++i) {{
340 +      rb->accept(*i);
341 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
342 +        (*ai)->accept(*i);
343 +    }
344 +  }
345 +
346 +  void addVisitor(BaseVisitor* v, int priority);
347 +
348 +  protected:
349 +    VistorListType visitorList;
350 + };
351 +
352 + \end{lstlisting}
353 +
354   \section{\label{appendixSection:concepts}Concepts}
355  
356   OOPSE manipulates both traditional atoms as well as some objects
357   that {\it behave like atoms}.  These objects can be rigid
358   collections of atoms or atoms which have orientational degrees of
359 < freedom.  Here is a diagram of the class heirarchy:
360 <
361 < %\begin{figure}
362 < %\centering
363 < %\includegraphics[width=3in]{heirarchy.eps}
364 < %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
365 < %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
366 < %selection syntax allows the user to select any of the objects that
367 < %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
94 < %\end{figure}
95 <
359 > freedom.  A diagram of the class hierarchy is illustrated in
360 > Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
361 > DirectionalAtom in {\sc OOPSE} have their own names which are
362 > specified in the {\tt .md} file. In contrast, RigidBodies are
363 > denoted by their membership and index inside a particular molecule:
364 > [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
365 > on the specifics of the simulation). The names of rigid bodies are
366 > generated automatically. For example, the name of the first rigid
367 > body in a DMPC molecule is DMPC\_RB\_0.
368   \begin{itemize}
369   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
370   integrators and minimizers.
# Line 102 | Line 374 | Every Molecule, Atom and DirectionalAtom in {\sc oopse
374   DirectionalAtom}s which behaves as a single unit.
375   \end{itemize}
376  
105 – Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
106 – own names which are specified in the {\tt .md} file. In contrast,
107 – RigidBodies are denoted by their membership and index inside a
108 – particular molecule: [MoleculeName]\_RB\_[index] (the contents
109 – inside the brackets depend on the specifics of the simulation). The
110 – names of rigid bodies are generated automatically. For example, the
111 – name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
112 –
377   \section{\label{appendixSection:syntax}Syntax of the Select Command}
378  
379 < The most general form of the select command is: {\tt select {\it
380 < expression}}
379 > {\sc OOPSE} provides a powerful selection utility to select
380 > StuntDoubles. The most general form of the select command is:
381  
382 + {\tt select {\it expression}}.
383 +
384   This expression represents an arbitrary set of StuntDoubles (Atoms
385 < or RigidBodies) in {\sc oopse}. Expressions are composed of either
385 > or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
386   name expressions, index expressions, predefined sets, user-defined
387   expressions, comparison operators, within expressions, or logical
388   combinations of the above expression types. Expressions can be
# Line 203 | Line 469 | expression}}
469   Users can define arbitrary terms to represent groups of
470   StuntDoubles, and then use the define terms in select commands. The
471   general form for the define command is: {\bf define {\it term
472 < expression}}
472 > expression}}. Once defined, the user can specify such terms in
473 > boolean expressions
474  
208 – Once defined, the user can specify such terms in boolean expressions
209 –
475   {\tt define SSDWATER SSD or SSD1 or SSDRF}
476  
477   {\tt select SSDWATER}
# Line 242 | Line 507 | atoms.
507   select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
508   atoms.
509  
245 – \section{\label{appendixSection:tools}Tools which use the selection command}
510  
511 < \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
511 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
512  
249 – Dump2XYZ can transform an OOPSE dump file into a xyz file which can
250 – be opened by other molecular dynamics viewers such as Jmol and VMD.
251 – The options available for Dump2XYZ are as follows:
252 –
253 –
254 – \begin{longtable}[c]{|EFG|}
255 – \caption{Dump2XYZ Command-line Options}
256 – \\ \hline
257 – {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
258 – \endhead
259 – \hline
260 – \endfoot
261 –  -h & {\tt -{}-help} &                        Print help and exit \\
262 –  -V & {\tt -{}-version} &                     Print version and exit \\
263 –  -i & {\tt -{}-input=filename}  &             input dump file \\
264 –  -o & {\tt -{}-output=filename} &             output file name \\
265 –  -n & {\tt -{}-frame=INT}   &                 print every n frame  (default=`1') \\
266 –  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
267 –  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
268 –  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
269 –  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
270 –  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
271 –  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
272 –     & {\tt -{}-repeatX=INT}  &                 The number of images to repeat in the x direction  (default=`0') \\
273 –     & {\tt -{}-repeatY=INT} &                 The number of images to repeat in the y direction  (default=`0') \\
274 –     &  {\tt -{}-repeatZ=INT}  &                The number of images to repeat in the z direction  (default=`0') \\
275 –  -s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
276 – converted. \\
277 –     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
278 –     & {\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}.
279 – \end{longtable}
280 –
281 –
513   \subsection{\label{appendixSection:StaticProps}StaticProps}
514  
515   {\tt StaticProps} can compute properties which are averaged over
516   some or all of the configurations that are contained within a dump
517   file. The most common example of a static property that can be
518   computed is the pair distribution function between atoms of type $A$
519 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
520 < used to compute the density distributions of other molecules in a
521 < reference frame {\it fixed to the body-fixed reference frame} of a
522 < selected atom or rigid body.
519 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
520 > also be used to compute the density distributions of other molecules
521 > in a reference frame {\it fixed to the body-fixed reference frame}
522 > of a selected atom or rigid body.
523  
524   There are five seperate radial distribution functions availiable in
525   OOPSE. Since every radial distrbution function invlove the
# Line 344 | Line 575 | The options available for {\tt StaticProps} are as fol
575   their body-fixed frames.} \label{oopseFig:gofr}
576   \end{figure}
577  
578 + Due to the fact that the selected StuntDoubles from two selections
579 + may be overlapped, {\tt StaticProps} performs the calculation in
580 + three stages which are illustrated in
581 + Fig.~\ref{oopseFig:staticPropsProcess}.
582 +
583 + \begin{figure}
584 + \centering
585 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
586 + \caption[A representation of the three-stage correlations in
587 + \texttt{StaticProps}]{This diagram illustrates three-stage
588 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
589 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
590 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
591 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
592 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
593 + the contrary, the third stage($C$ and $C$) are completely
594 + overlapping} \label{oopseFig:staticPropsProcess}
595 + \end{figure}
596 +
597   The options available for {\tt StaticProps} are as follows:
598   \begin{longtable}[c]{|EFG|}
599   \caption{StaticProps Command-line Options}
# Line 354 | Line 604 | The options available for {\tt StaticProps} are as fol
604   \endfoot
605    -h& {\tt -{}-help}                    &  Print help and exit \\
606    -V& {\tt -{}-version}                 &  Print version and exit \\
607 <  -i& {\tt -{}-input=filename}          &  input dump file \\
608 <  -o& {\tt -{}-output=filename}         &  output file name \\
609 <  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
610 <  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
611 <  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
612 <  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
613 <    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
614 <    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
615 <    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
616 <    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
617 <    & {\tt -{}-molname=STRING}           & molecule name \\
618 <    & {\tt -{}-begin=INT}                & begin internal index \\
619 <    & {\tt -{}-end=INT}                  & end internal index \\
607 >  -i& {\tt -{}-input}          &  input dump file \\
608 >  -o& {\tt -{}-output}         &  output file name \\
609 >  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
610 >  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
611 >  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
612 >  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
613 >    & {\tt -{}-sele1}   & select the first StuntDouble set \\
614 >    & {\tt -{}-sele2}   & select the second StuntDouble set \\
615 >    & {\tt -{}-sele3}   & select the third StuntDouble set \\
616 >    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
617 >    & {\tt -{}-molname}           & molecule name \\
618 >    & {\tt -{}-begin}                & begin internal index \\
619 >    & {\tt -{}-end}                  & end internal index \\
620   \hline
621   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
622   \hline
# Line 405 | Line 655 | The options available for DynamicProps are as follows:
655   different vectors).  The ability to use two selection scripts to
656   select different types of atoms is already present in the code.
657  
658 + For large simulations, the trajectory files can sometimes reach
659 + sizes in excess of several gigabytes. In order to effectively
660 + analyze that amount of data. In order to prevent a situation where
661 + the program runs out of memory due to large trajectories,
662 + \texttt{dynamicProps} will estimate the size of free memory at
663 + first, and determine the number of frames in each block, which
664 + allows the operating system to load two blocks of data
665 + simultaneously without swapping. Upon reading two blocks of the
666 + trajectory, \texttt{dynamicProps} will calculate the time
667 + correlation within the first block and the cross correlations
668 + between the two blocks. This second block is then freed and then
669 + incremented and the process repeated until the end of the
670 + trajectory. Once the end is reached, the first block is freed then
671 + incremented, until all frame pairs have been correlated in time.
672 + This process is illustrated in
673 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
674 +
675 + \begin{figure}
676 + \centering
677 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
678 + \caption[A representation of the block correlations in
679 + \texttt{dynamicProps}]{This diagram illustrates block correlations
680 + processing in \texttt{dynamicProps}. The shaded region represents
681 + the self correlation of the block, and the open blocks are read one
682 + at a time and the cross correlations between blocks are calculated.}
683 + \label{oopseFig:dynamicPropsProcess}
684 + \end{figure}
685 +
686   The options available for DynamicProps are as follows:
687   \begin{longtable}[c]{|EFG|}
688   \caption{DynamicProps Command-line Options}
# Line 415 | Line 693 | The options available for DynamicProps are as follows:
693   \endfoot
694    -h& {\tt -{}-help}                   & Print help and exit \\
695    -V& {\tt -{}-version}                & Print version and exit \\
696 <  -i& {\tt -{}-input=filename}         & input dump file \\
697 <  -o& {\tt -{}-output=filename}        & output file name \\
698 <    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
699 <    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
696 >  -i& {\tt -{}-input}         & input dump file \\
697 >  -o& {\tt -{}-output}        & output file name \\
698 >    & {\tt -{}-sele1} & select first StuntDouble set \\
699 >    & {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
700   \hline
701   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
702   \hline
# Line 427 | Line 705 | The options available for DynamicProps are as follows:
705    -d& {\tt -{}-dcorr}                  & compute dipole correlation function
706   \end{longtable}
707  
708 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
708 > \section{\label{appendixSection:tools}Other Useful Utilities}
709 >
710 > \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
711 >
712 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
713 > which can be opened by other molecular dynamics viewers such as Jmol
714 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
715 > as follows:
716 >
717 >
718 > \begin{longtable}[c]{|EFG|}
719 > \caption{Dump2XYZ Command-line Options}
720 > \\ \hline
721 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
722 > \endhead
723 > \hline
724 > \endfoot
725 >  -h & {\tt -{}-help} &                        Print help and exit \\
726 >  -V & {\tt -{}-version} &                     Print version and exit \\
727 >  -i & {\tt -{}-input}  &             input dump file \\
728 >  -o & {\tt -{}-output} &             output file name \\
729 >  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
730 >  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
731 >  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
732 >  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
733 >  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
734 >  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
735 >  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
736 >     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
737 >     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
738 >     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
739 >  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
740 > converted. \\
741 >     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
742 >     & {\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}.
743 > \end{longtable}
744 >
745 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
746 >
747 > {\tt Hydro} can calculate resistance and diffusion tensors at the
748 > center of resistance. Both tensors at the center of diffusion can
749 > also be reported from the program, as well as the coordinates for
750 > the beads which are used to approximate the arbitrary shapes. The
751 > options available for Hydro are as follows:
752 > \begin{longtable}[c]{|EFG|}
753 > \caption{Hydrodynamics Command-line Options}
754 > \\ \hline
755 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
756 > \endhead
757 > \hline
758 > \endfoot
759 >  -h & {\tt -{}-help} &                        Print help and exit \\
760 >  -V & {\tt -{}-version} &                     Print version and exit \\
761 >  -i & {\tt -{}-input}  &             input dump file \\
762 >  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
763 >  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
764 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
765 > \end{longtable}

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