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1 < \chapter{\label{chapt:appendix}APPENDIX}
1 > \appendix
2 > \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
3  
4 < Designing object-oriented software is hard, and designing reusable
5 < object-oriented scientific software is even harder. Absence of
6 < applying modern software development practices is the bottleneck of
6 < Scientific Computing community\cite{wilson}. For instance, in the
7 < last 20 years , there are quite a few MD packages that were
4 > Absence of applying modern software development practices is the
5 > bottleneck of Scientific Computing community\cite{Wilson2006}. In
6 > the last 20 years , there are quite a few MD packages that were
7   developed to solve common MD problems and perform robust simulations
8   . However, many of the codes are legacy programs that are either
9   poorly organized or extremely complex. Usually, these packages were
# Line 13 | Line 12 | documents which is crucial to the maintenance and exte
12   coordination to enforce design and programming guidelines. Moreover,
13   most MD programs also suffer from missing design and implement
14   documents which is crucial to the maintenance and extensibility.
15 + Along the way of studying structural and dynamic processes in
16 + condensed phase systems like biological membranes and nanoparticles,
17 + we developed and maintained an Object-Oriented Parallel Simulation
18 + Engine ({\sc OOPSE}). This new molecular dynamics package has some
19 + unique features
20 + \begin{enumerate}
21 +  \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
22 + atom types (transition metals, point dipoles, sticky potentials,
23 + Gay-Berne ellipsoids, or other "lumpy"atoms with orientational
24 + degrees of freedom), as well as rigid bodies.
25 +  \item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap
26 + Beowulf clusters to obtain very efficient parallelism.
27 +  \item {\sc OOPSE} integrates the equations of motion using advanced methods for
28 + orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T
29 + ensembles.
30 +  \item {\sc OOPSE} can carry out simulations on metallic systems using the
31 + Embedded Atom Method (EAM) as well as the Sutton-Chen potential.
32 +  \item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals.
33 +  \item  {\sc OOPSE} can simulate systems containing the extremely efficient
34 + extended-Soft Sticky Dipole (SSD/E) model for water.
35 + \end{enumerate}
36  
37 + \section{\label{appendixSection:architecture }Architecture}
38 +
39 + Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
40 + uses C++ Standard Template Library (STL) and fortran modules as the
41 + foundation. As an extensive set of the STL and Fortran90 modules,
42 + {\sc Base Classes} provide generic implementations of mathematical
43 + objects (e.g., matrices, vectors, polynomials, random number
44 + generators) and advanced data structures and algorithms(e.g., tuple,
45 + bitset, generic data, string manipulation). The molecular data
46 + structures for the representation of atoms, bonds, bends, torsions,
47 + rigid bodies and molecules \textit{etc} are contained in the {\sc
48 + Kernel} which is implemented with {\sc Base Classes} and are
49 + carefully designed to provide maximum extensibility and flexibility.
50 + The functionality required for applications is provide by the third
51 + layer which contains Input/Output, Molecular Mechanics and Structure
52 + modules. Input/Output module not only implements general methods for
53 + file handling, but also defines a generic force field interface.
54 + Another important component of Input/Output module is the meta-data
55 + file parser, which is rewritten using ANother Tool for Language
56 + Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
57 + Mechanics module consists of energy minimization and a wide
58 + varieties of integration methods(see Chap.~\ref{chapt:methodology}).
59 + The structure module contains a flexible and powerful selection
60 + library which syntax is elaborated in
61 + Sec.~\ref{appendixSection:syntax}. The top layer is made of the main
62 + program of the package, \texttt{oopse} and it corresponding parallel
63 + version \texttt{oopse\_MPI}, as well as other useful utilities, such
64 + as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}),
65 + \texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}),
66 + \texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}),
67 + \texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics})
68 + \textit{etc}.
69 +
70 + \begin{figure}
71 + \centering
72 + \includegraphics[width=\linewidth]{architecture.eps}
73 + \caption[The architecture of {\sc OOPSE}] {Overview of the structure
74 + of {\sc OOPSE}} \label{appendixFig:architecture}
75 + \end{figure}
76 +
77   \section{\label{appendixSection:desginPattern}Design Pattern}
78  
79   Design patterns are optimal solutions to commonly-occurring problems
80   in software design. Although originated as an architectural concept
81 < for buildings and towns by Christopher Alexander \cite{alexander},
82 < software patterns first became popular with the wide acceptance of
83 < the book, Design Patterns: Elements of Reusable Object-Oriented
84 < Software \cite{gamma94}. Patterns reflect the experience, knowledge
85 < and insights of developers who have successfully used these patterns
86 < in their own work. Patterns are reusable. They provide a ready-made
87 < solution that can be adapted to different problems as necessary.
88 < Pattern are expressive. they provide a common vocabulary of
89 < solutions that can express large solutions succinctly.
81 > for buildings and towns by Christopher Alexander
82 > \cite{Alexander1987}, software patterns first became popular with
83 > the wide acceptance of the book, Design Patterns: Elements of
84 > Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect
85 > the experience, knowledge and insights of developers who have
86 > successfully used these patterns in their own work. Patterns are
87 > reusable. They provide a ready-made solution that can be adapted to
88 > different problems as necessary. Pattern are expressive. they
89 > provide a common vocabulary of solutions that can express large
90 > solutions succinctly.
91  
92   Patterns are usually described using a format that includes the
93   following information:
# Line 47 | Line 108 | the modern scientific software applications, such as J
108  
109   As one of the latest advanced techniques emerged from
110   object-oriented community, design patterns were applied in some of
111 < the modern scientific software applications, such as JMol, OOPSE
112 < \cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}.
111 > the modern scientific software applications, such as JMol, {\sc
112 > OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2005}
113 > \textit{etc}. The following sections enumerates some of the patterns
114 > used in {\sc OOPSE}.
115  
116   \subsection{\label{appendixSection:singleton}Singleton}
54 – The Singleton pattern ensures that only one instance of a class is
55 – created. All objects that use an instance of that class use the same
56 – instance.
117  
118 + The Singleton pattern not only provides a mechanism to restrict
119 + instantiation of a class to one object, but also provides a global
120 + point of access to the object. Currently implemented as a global
121 + variable, the logging utility which reports error and warning
122 + messages to the console in {\sc OOPSE} is a good candidate for
123 + applying the Singleton pattern to avoid the global namespace
124 + pollution.Although the singleton pattern can be implemented in
125 + various ways  to account for different aspects of the software
126 + designs, such as lifespan control \textit{etc}, we only use the
127 + static data approach in {\sc OOPSE}. IntegratorFactory class is
128 + declared as
129 +
130 + \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
131 +
132 + class IntegratorFactory {
133 + public:
134 +  static IntegratorFactory*
135 +  getInstance();
136 + protected:
137 +  IntegratorFactory();
138 + private:
139 +  static IntegratorFactory* instance_;
140 + };
141 +
142 + \end{lstlisting}
143 +
144 + The corresponding implementation is
145 +
146 + \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
147 +
148 + IntegratorFactory::instance_ = NULL;
149 +
150 + IntegratorFactory* getInstance() {
151 +  if (instance_ == NULL){
152 +    instance_ = new IntegratorFactory;
153 +  }
154 +  return instance_;
155 + }
156 +
157 + \end{lstlisting}
158 +
159 + Since constructor is declared as protected, a client can not
160 + instantiate IntegratorFactory directly. Moreover, since the member
161 + function getInstance serves as the only entry of access to
162 + IntegratorFactory, this approach fulfills the basic requirement, a
163 + single instance. Another consequence of this approach is the
164 + automatic destruction since static data are destroyed upon program
165 + termination.
166 +
167   \subsection{\label{appendixSection:factoryMethod}Factory Method}
59 – The Factory Method pattern is a creational pattern which deals with
60 – the problem of creating objects without specifying the exact class
61 – of object that will be created. Factory Method solves this problem
62 – by defining a separate method for creating the objects, which
63 – subclasses can then override to specify the derived type of product
64 – that will be created.
168  
169 + Categoried as a creational pattern, the Factory Method pattern deals
170 + with the problem of creating objects without specifying the exact
171 + class of object that will be created. Factory Method is typically
172 + implemented by delegating the creation operation to the subclasses.
173 + Parameterized Factory pattern where factory method (
174 + createIntegrator member function) creates products based on the
175 + identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If
176 + the identifier has been already registered, the factory method will
177 + invoke the corresponding creator (see List.~\ref{integratorCreator})
178 + which utilizes the modern C++ template technique to avoid excess
179 + subclassing.
180  
181 < \subsection{\label{appendixSection:visitorPattern}Visitor}
68 < The purpose of the Visitor Pattern is to encapsulate an operation
69 < that you want to perform on the elements of a data structure. In
70 < this way, you can change the operation being performed on a
71 < structure without the need of changing the classes of the elements
72 < that you are operating on.
181 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
182  
183 + class IntegratorFactory {
184 + public:
185 +  typedef std::map<string, IntegratorCreator*> CreatorMapType;
186  
187 < \subsection{\label{appendixSection:templateMethod}Template Method}
187 >  bool registerIntegrator(IntegratorCreator* creator) {
188 >    return creatorMap_.insert(creator->getIdent(), creator).second;
189 >  }
190  
191 < \section{\label{appendixSection:analysisFramework}Analysis Framework}
191 >  Integrator* createIntegrator(const string& id, SimInfo* info) {
192 >    Integrator* result = NULL;
193 >    CreatorMapType::iterator i = creatorMap_.find(id);
194 >    if (i != creatorMap_.end()) {
195 >      result = (i->second)->create(info);
196 >    }
197 >    return result;
198 >  }
199  
200 < \section{\label{appendixSection:concepts}Concepts}
200 > private:
201 >  CreatorMapType creatorMap_;
202 > };
203 > \end{lstlisting}
204  
205 < OOPSE manipulates both traditional atoms as well as some objects
82 < that {\it behave like atoms}.  These objects can be rigid
83 < collections of atoms or atoms which have orientational degrees of
84 < freedom.  Here is a diagram of the class heirarchy:
205 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
206  
207 + class IntegratorCreator {
208 + public:
209 +    IntegratorCreator(const string& ident) : ident_(ident) {}
210 +
211 +    const string& getIdent() const { return ident_; }
212 +
213 +    virtual Integrator* create(SimInfo* info) const = 0;
214 +
215 + private:
216 +    string ident_;
217 + };
218 +
219 + template<class ConcreteIntegrator>
220 + class IntegratorBuilder : public IntegratorCreator {
221 + public:
222 +  IntegratorBuilder(const string& ident)
223 +                   : IntegratorCreator(ident) {}
224 +  virtual  Integrator* create(SimInfo* info) const {
225 +    return new ConcreteIntegrator(info);
226 +  }
227 + };
228 + \end{lstlisting}
229 +
230 + \subsection{\label{appendixSection:visitorPattern}Visitor}
231 +
232 + The visitor pattern is designed to decouple the data structure and
233 + algorithms used upon them by collecting related operation from
234 + element classes into other visitor classes, which is equivalent to
235 + adding virtual functions into a set of classes without modifying
236 + their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
237 + structure of Visitor pattern which is used extensively in {\tt
238 + Dump2XYZ}. In order to convert an OOPSE dump file, a series of
239 + distinct operations are performed on different StuntDoubles (See the
240 + class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration
241 + in List.~\ref{appendixScheme:element}). Since the hierarchies
242 + remains stable, it is easy to define a visit operation (see
243 + List.~\ref{appendixScheme:visitor}) for each class of StuntDouble.
244 + Note that using Composite pattern\cite{Gamma1994}, CompositVisitor
245 + manages a priority visitor list and handles the execution of every
246 + visitor in the priority list on different StuntDoubles.
247 +
248   \begin{figure}
249   \centering
250 < \includegraphics[width=3in]{heirarchy.pdf}
251 < \caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
252 < The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
91 < selection syntax allows the user to select any of the objects that
92 < are descended from a StuntDouble.} \label{oopseFig:heirarchy}
250 > \includegraphics[width=\linewidth]{visitor.eps}
251 > \caption[The UML class diagram of Visitor patten] {The UML class
252 > diagram of Visitor patten.} \label{appendixFig:visitorUML}
253   \end{figure}
254 +
255 + \begin{figure}
256 + \centering
257 + \includegraphics[width=\linewidth]{hierarchy.eps}
258 + \caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
259 + the class hierarchy. } \label{oopseFig:hierarchy}
260 + \end{figure}
261 +
262 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
263 +
264 + class StuntDouble { public:
265 +  virtual void accept(BaseVisitor* v) = 0;
266 + };
267 +
268 + class Atom: public StuntDouble { public:
269 +  virtual void accept{BaseVisitor* v*} {
270 +    v->visit(this);
271 +  }
272 + };
273 +
274 + class DirectionalAtom: public Atom { public:
275 +  virtual void accept{BaseVisitor* v*} {
276 +    v->visit(this);
277 +  }
278 + };
279 +
280 + class RigidBody: public StuntDouble { public:
281 +  virtual void accept{BaseVisitor* v*} {
282 +    v->visit(this);
283 +  }
284 + };
285 +
286 + \end{lstlisting}
287 +
288 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
289 +
290 + class BaseVisitor{
291 + public:
292 +  virtual void visit(Atom* atom);
293 +  virtual void visit(DirectionalAtom* datom);
294 +  virtual void visit(RigidBody* rb);
295 + };
296  
297 + class BaseAtomVisitor:public BaseVisitor{ public:
298 +  virtual void visit(Atom* atom);
299 +  virtual void visit(DirectionalAtom* datom);
300 +  virtual void visit(RigidBody* rb);
301 + };
302 +
303 + class SSDAtomVisitor:public BaseAtomVisitor{ public:
304 +  virtual void visit(Atom* atom);
305 +  virtual void visit(DirectionalAtom* datom);
306 +  virtual void visit(RigidBody* rb);
307 + };
308 +
309 + class CompositeVisitor: public BaseVisitor {
310 + public:
311 +
312 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
313 +  typedef VistorListType::iterator VisitorListIterator;
314 +  virtual void visit(Atom* atom) {
315 +    VisitorListIterator i;
316 +    BaseVisitor* curVisitor;
317 +    for(i = visitorList.begin();i != visitorList.end();++i) {
318 +      atom->accept(*i);
319 +    }
320 +  }
321 +
322 +  virtual void visit(DirectionalAtom* datom) {
323 +    VisitorListIterator i;
324 +    BaseVisitor* curVisitor;
325 +    for(i = visitorList.begin();i != visitorList.end();++i) {
326 +      atom->accept(*i);
327 +    }
328 +  }
329 +
330 +  virtual void visit(RigidBody* rb) {
331 +    VisitorListIterator i;
332 +    std::vector<Atom*> myAtoms;
333 +    std::vector<Atom*>::iterator ai;
334 +    myAtoms = rb->getAtoms();
335 +    for(i = visitorList.begin();i != visitorList.end();++i) {{
336 +      rb->accept(*i);
337 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
338 +        (*ai)->accept(*i);
339 +    }
340 +  }
341 +
342 +  void addVisitor(BaseVisitor* v, int priority);
343 +
344 +  protected:
345 +    VistorListType visitorList;
346 + };
347 +
348 + \end{lstlisting}
349 +
350 + \section{\label{appendixSection:concepts}Concepts}
351 +
352 + OOPSE manipulates both traditional atoms as well as some objects
353 + that {\it behave like atoms}.  These objects can be rigid
354 + collections of atoms or atoms which have orientational degrees of
355 + freedom.  A diagram of the class hierarchy is illustrated in
356 + Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
357 + DirectionalAtom in {\sc OOPSE} have their own names which are
358 + specified in the {\tt .md} file. In contrast, RigidBodies are
359 + denoted by their membership and index inside a particular molecule:
360 + [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
361 + on the specifics of the simulation). The names of rigid bodies are
362 + generated automatically. For example, the name of the first rigid
363 + body in a DMPC molecule is DMPC\_RB\_0.
364   \begin{itemize}
365   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
366   integrators and minimizers.
# Line 101 | Line 370 | Every Molecule, Atom and DirectionalAtom in {\sc oopse
370   DirectionalAtom}s which behaves as a single unit.
371   \end{itemize}
372  
104 – Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
105 – own names which are specified in the {\tt .md} file. In contrast,
106 – RigidBodies are denoted by their membership and index inside a
107 – particular molecule: [MoleculeName]\_RB\_[index] (the contents
108 – inside the brackets depend on the specifics of the simulation). The
109 – names of rigid bodies are generated automatically. For example, the
110 – name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
111 –
373   \section{\label{appendixSection:syntax}Syntax of the Select Command}
374  
375 < The most general form of the select command is: {\tt select {\it
376 < expression}}
375 > {\sc OOPSE} provides a powerful selection utility to select
376 > StuntDoubles. The most general form of the select command is:
377  
378 + {\tt select {\it expression}}.
379 +
380   This expression represents an arbitrary set of StuntDoubles (Atoms
381 < or RigidBodies) in {\sc oopse}. Expressions are composed of either
381 > or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
382   name expressions, index expressions, predefined sets, user-defined
383   expressions, comparison operators, within expressions, or logical
384   combinations of the above expression types. Expressions can be
# Line 143 | Line 406 | not & ``!''  \\
406   \subsection{\label{appendixSection:name}Name expressions}
407  
408   \begin{center}
409 < \begin{tabular}{|llp{3in}|}
409 > \begin{tabular}{|llp{2in}|}
410   \hline {\bf type of expression} & {\bf examples} & {\bf translation
411   of
412   examples} \\
# Line 202 | Line 465 | expression}}
465   Users can define arbitrary terms to represent groups of
466   StuntDoubles, and then use the define terms in select commands. The
467   general form for the define command is: {\bf define {\it term
468 < expression}}
468 > expression}}. Once defined, the user can specify such terms in
469 > boolean expressions
470  
207 – Once defined, the user can specify such terms in boolean expressions
208 –
471   {\tt define SSDWATER SSD or SSD1 or SSDRF}
472  
473   {\tt select SSDWATER}
# Line 227 | Line 489 | wouldselect StuntDoubles which have mass greater than
489   \end{center}
490  
491   For example, the phrase {\tt select mass > 16.0 and charge < -2}
492 < wouldselect StuntDoubles which have mass greater than 16.0 and
492 > would select StuntDoubles which have mass greater than 16.0 and
493   charges less than -2.
494  
495   \subsection{\label{appendixSection:within}Within expressions}
# Line 241 | Line 503 | atoms.
503   select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
504   atoms.
505  
244 – \section{\label{appendixSection:tools}Tools which use the selection command}
506  
507 < \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
507 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
508  
248 – Dump2XYZ can transform an OOPSE dump file into a xyz file which can
249 – be opened by other molecular dynamics viewers such as Jmol and VMD.
250 – The options available for Dump2XYZ are as follows:
251 –
252 –
253 – \begin{longtable}[c]{|EFG|}
254 – \caption{Dump2XYZ Command-line Options}
255 – \\ \hline
256 – {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
257 – \endhead
258 – \hline
259 – \endfoot
260 –  -h & {\tt -{}-help} &                        Print help and exit \\
261 –  -V & {\tt -{}-version} &                     Print version and exit \\
262 –  -i & {\tt -{}-input=filename}  &             input dump file \\
263 –  -o & {\tt -{}-output=filename} &             output file name \\
264 –  -n & {\tt -{}-frame=INT}   &                 print every n frame  (default=`1') \\
265 –  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
266 –  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
267 –  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
268 –  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
269 –  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
270 –  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
271 –     & {\tt -{}-repeatX=INT}  &                 The number of images to repeat in the x direction  (default=`0') \\
272 –     & {\tt -{}-repeatY=INT} &                 The number of images to repeat in the y direction  (default=`0') \\
273 –     &  {\tt -{}-repeatZ=INT}  &                The number of images to repeat in the z direction  (default=`0') \\
274 –  -s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
275 – converted. \\
276 –     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
277 –     & {\tt -{}-refsele} &  In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}.
278 – \end{longtable}
279 –
280 –
509   \subsection{\label{appendixSection:StaticProps}StaticProps}
510  
511   {\tt StaticProps} can compute properties which are averaged over
512   some or all of the configurations that are contained within a dump
513   file. The most common example of a static property that can be
514   computed is the pair distribution function between atoms of type $A$
515 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
516 < used to compute the density distributions of other molecules in a
517 < reference frame {\it fixed to the body-fixed reference frame} of a
518 < selected atom or rigid body.
515 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
516 > also be used to compute the density distributions of other molecules
517 > in a reference frame {\it fixed to the body-fixed reference frame}
518 > of a selected atom or rigid body.
519  
520   There are five seperate radial distribution functions availiable in
521   OOPSE. Since every radial distrbution function invlove the
# Line 336 | Line 564 | distribution functions are most easily seen in the fig
564  
565   \begin{figure}
566   \centering
567 < \includegraphics[width=3in]{definition.pdf}
567 > \includegraphics[width=3in]{definition.eps}
568   \caption[Definitions of the angles between directional objects]{ \\
569   Any two directional objects (DirectionalAtoms and RigidBodies) have
570   a set of two angles ($\theta$, and $\omega$) between the z-axes of
571   their body-fixed frames.} \label{oopseFig:gofr}
572   \end{figure}
573  
574 + Due to the fact that the selected StuntDoubles from two selections
575 + may be overlapped, {\tt StaticProps} performs the calculation in
576 + three stages which are illustrated in
577 + Fig.~\ref{oopseFig:staticPropsProcess}.
578 +
579 + \begin{figure}
580 + \centering
581 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
582 + \caption[A representation of the three-stage correlations in
583 + \texttt{StaticProps}]{This diagram illustrates three-stage
584 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
585 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
586 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
587 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
588 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
589 + the contrary, the third stage($C$ and $C$) are completely
590 + overlapping} \label{oopseFig:staticPropsProcess}
591 + \end{figure}
592 +
593   The options available for {\tt StaticProps} are as follows:
594   \begin{longtable}[c]{|EFG|}
595   \caption{StaticProps Command-line Options}
# Line 353 | Line 600 | The options available for {\tt StaticProps} are as fol
600   \endfoot
601    -h& {\tt -{}-help}                    &  Print help and exit \\
602    -V& {\tt -{}-version}                 &  Print version and exit \\
603 <  -i& {\tt -{}-input=filename}          &  input dump file \\
604 <  -o& {\tt -{}-output=filename}         &  output file name \\
605 <  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
606 <  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
607 <  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
608 <  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
609 <    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
610 <    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
611 <    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
612 <    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
613 <    & {\tt -{}-molname=STRING}           & molecule name \\
614 <    & {\tt -{}-begin=INT}                & begin internal index \\
615 <    & {\tt -{}-end=INT}                  & end internal index \\
603 >  -i& {\tt -{}-input}          &  input dump file \\
604 >  -o& {\tt -{}-output}         &  output file name \\
605 >  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
606 >  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
607 >  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
608 >  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
609 >    & {\tt -{}-sele1}   & select the first StuntDouble set \\
610 >    & {\tt -{}-sele2}   & select the second StuntDouble set \\
611 >    & {\tt -{}-sele3}   & select the third StuntDouble set \\
612 >    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
613 >    & {\tt -{}-molname}           & molecule name \\
614 >    & {\tt -{}-begin}                & begin internal index \\
615 >    & {\tt -{}-end}                  & end internal index \\
616   \hline
617   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
618   \hline
# Line 404 | Line 651 | The options available for DynamicProps are as follows:
651   different vectors).  The ability to use two selection scripts to
652   select different types of atoms is already present in the code.
653  
654 + For large simulations, the trajectory files can sometimes reach
655 + sizes in excess of several gigabytes. In order to effectively
656 + analyze that amount of data. In order to prevent a situation where
657 + the program runs out of memory due to large trajectories,
658 + \texttt{dynamicProps} will estimate the size of free memory at
659 + first, and determine the number of frames in each block, which
660 + allows the operating system to load two blocks of data
661 + simultaneously without swapping. Upon reading two blocks of the
662 + trajectory, \texttt{dynamicProps} will calculate the time
663 + correlation within the first block and the cross correlations
664 + between the two blocks. This second block is then freed and then
665 + incremented and the process repeated until the end of the
666 + trajectory. Once the end is reached, the first block is freed then
667 + incremented, until all frame pairs have been correlated in time.
668 + This process is illustrated in
669 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
670 +
671 + \begin{figure}
672 + \centering
673 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
674 + \caption[A representation of the block correlations in
675 + \texttt{dynamicProps}]{This diagram illustrates block correlations
676 + processing in \texttt{dynamicProps}. The shaded region represents
677 + the self correlation of the block, and the open blocks are read one
678 + at a time and the cross correlations between blocks are calculated.}
679 + \label{oopseFig:dynamicPropsProcess}
680 + \end{figure}
681 +
682   The options available for DynamicProps are as follows:
683   \begin{longtable}[c]{|EFG|}
684   \caption{DynamicProps Command-line Options}
# Line 414 | Line 689 | The options available for DynamicProps are as follows:
689   \endfoot
690    -h& {\tt -{}-help}                   & Print help and exit \\
691    -V& {\tt -{}-version}                & Print version and exit \\
692 <  -i& {\tt -{}-input=filename}         & input dump file \\
693 <  -o& {\tt -{}-output=filename}        & output file name \\
694 <    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
695 <    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
692 >  -i& {\tt -{}-input}         & input dump file \\
693 >  -o& {\tt -{}-output}        & output file name \\
694 >    & {\tt -{}-sele1} & select first StuntDouble set \\
695 >    & {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
696   \hline
697   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
698   \hline
# Line 426 | Line 701 | The options available for DynamicProps are as follows:
701    -d& {\tt -{}-dcorr}                  & compute dipole correlation function
702   \end{longtable}
703  
704 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
704 > \section{\label{appendixSection:tools}Other Useful Utilities}
705 >
706 > \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
707 >
708 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
709 > which can be opened by other molecular dynamics viewers such as Jmol
710 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
711 > as follows:
712 >
713 >
714 > \begin{longtable}[c]{|EFG|}
715 > \caption{Dump2XYZ Command-line Options}
716 > \\ \hline
717 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
718 > \endhead
719 > \hline
720 > \endfoot
721 >  -h & {\tt -{}-help} &                        Print help and exit \\
722 >  -V & {\tt -{}-version} &                     Print version and exit \\
723 >  -i & {\tt -{}-input}  &             input dump file \\
724 >  -o & {\tt -{}-output} &             output file name \\
725 >  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
726 >  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
727 >  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
728 >  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
729 >  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
730 >  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
731 >  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
732 >     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
733 >     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
734 >     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
735 >  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
736 > converted. \\
737 >     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
738 >     & {\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}.
739 > \end{longtable}
740 >
741 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
742 >
743 > {\tt Hydro} can calculate resistance and diffusion tensors at the
744 > center of resistance. Both tensors at the center of diffusion can
745 > also be reported from the program, as well as the coordinates for
746 > the beads which are used to approximate the arbitrary shapes. The
747 > options available for Hydro are as follows:
748 > \begin{longtable}[c]{|EFG|}
749 > \caption{Hydrodynamics Command-line Options}
750 > \\ \hline
751 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
752 > \endhead
753 > \hline
754 > \endfoot
755 >  -h & {\tt -{}-help} &                        Print help and exit \\
756 >  -V & {\tt -{}-version} &                     Print version and exit \\
757 >  -i & {\tt -{}-input}  &             input dump file \\
758 >  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
759 >  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
760 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
761 > \end{longtable}

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