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1 < \chapter{\label{chapt:appendix}APPENDIX}
1 > \appendix
2 > \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
3  
4 < Designing object-oriented software is hard, and designing reusable
5 < object-oriented scientific software is even harder. Absence of
6 < applying modern software development practices is the bottleneck of
7 < Scientific Computing community\cite{wilson}. For instance, in the
8 < last 20 years , there are quite a few MD packages that were
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
12 < contributed by scientists without official computer science
13 < training. The development of most MD applications are lack of strong
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.
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
7 > packages\cite{Brooks1983, Vincent1995, Kale1999} that were developed
8 > to solve common MD problems and perform robust simulations .
9 > Unfortunately, most of them are commercial programs that are either
10 > poorly written or extremely complicate. Consequently, it prevents
11 > the researchers to reuse or extend those packages to do cutting-edge
12 > research effectively. Along the way of studying structural and
13 > dynamic processes in condensed phase systems like biological
14 > 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 \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
37 + uses C++ Standard Template Library (STL) and fortran modules as the
38 + foundation. As an extensive set of the STL and Fortran90 modules,
39 + {\sc Base Classes} provide generic implementations of mathematical
40 + objects (e.g., matrices, vectors, polynomials, random number
41 + generators) and advanced data structures and algorithms(e.g., tuple,
42 + bitset, generic data, string manipulation). The molecular data
43 + structures for the representation of atoms, bonds, bends, torsions,
44 + rigid bodies and molecules \textit{etc} are contained in the {\sc
45 + Kernel} which is implemented with {\sc Base Classes} and are
46 + carefully designed to provide maximum extensibility and flexibility.
47 + The functionality required for applications is provide by the third
48 + layer which contains Input/Output, Molecular Mechanics and Structure
49 + modules. Input/Output module not only implements general methods for
50 + file handling, but also defines a generic force field interface.
51 + Another important component of Input/Output module is the meta-data
52 + file parser, which is rewritten using ANother Tool for Language
53 + Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
54 + Mechanics module consists of energy minimization and a wide
55 + varieties of integration methods(see Chap.~\ref{chapt:methodology}).
56 + The structure module contains a flexible and powerful selection
57 + library which syntax is elaborated in
58 + Sec.~\ref{appendixSection:syntax}. The top layer is made of the main
59 + program of the package, \texttt{oopse} and it corresponding parallel
60 + version \texttt{oopse\_MPI}, as well as other useful utilities, such
61 + as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}),
62 + \texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}),
63 + \texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}),
64 + \texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics})
65 + \textit{etc}.
66 +
67 + \begin{figure}
68 + \centering
69 + \includegraphics[width=\linewidth]{architecture.eps}
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}
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 \cite{alexander},
79 < software patterns first became popular with the wide acceptance of
80 < the book, Design Patterns: Elements of Reusable Object-Oriented
81 < Software \cite{gamma94}. Patterns reflect the experience, knowledge
82 < and insights of developers who have successfully used these patterns
83 < in their own work. Patterns are reusable. They provide a ready-made
84 < solution that can be adapted to different problems as necessary.
85 < Pattern are expressive. they provide a common vocabulary of
86 < solutions that can express large solutions succinctly.
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.
88  
89   Patterns are usually described using a format that includes the
90   following information:
# Line 47 | Line 105 | the modern scientific software applications, such as J
105  
106   As one of the latest advanced techniques emerged from
107   object-oriented community, design patterns were applied in some of
108 < the modern scientific software applications, such as JMol, OOPSE
109 < \cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}.
108 > the modern scientific software applications, such as JMol, {\sc
109 > OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2005}
110 > \textit{etc}. The following sections enumerates some of the patterns
111 > used in {\sc OOPSE}.
112  
113   \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.
114  
115 + The Singleton pattern not only provides a mechanism to restrict
116 + instantiation of a class to one object, but also provides a global
117 + point of access to the object. Currently implemented as a global
118 + variable, the logging utility which reports error and warning
119 + messages to the console in {\sc OOPSE} is a good candidate for
120 + applying the Singleton pattern to avoid the global namespace
121 + pollution.Although the singleton pattern can be implemented in
122 + various ways  to account for different aspects of the software
123 + designs, such as lifespan control \textit{etc}, we only use the
124 + static data approach in {\sc OOPSE}. IntegratorFactory class is
125 + declared as
126 +
127 + \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
128 +
129 + class IntegratorFactory {
130 + public:
131 +  static IntegratorFactory*
132 +  getInstance();
133 + protected:
134 +  IntegratorFactory();
135 + private:
136 +  static IntegratorFactory* instance_;
137 + };
138 +
139 + \end{lstlisting}
140 +
141 + The corresponding implementation is
142 +
143 + \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
144 +
145 + IntegratorFactory::instance_ = NULL;
146 +
147 + IntegratorFactory* getInstance() {
148 +  if (instance_ == NULL){
149 +    instance_ = new IntegratorFactory;
150 +  }
151 +  return instance_;
152 + }
153 +
154 + \end{lstlisting}
155 +
156 + Since constructor is declared as protected, a client can not
157 + instantiate IntegratorFactory directly. Moreover, since the member
158 + function getInstance serves as the only entry of access to
159 + IntegratorFactory, this approach fulfills the basic requirement, a
160 + single instance. Another consequence of this approach is the
161 + automatic destruction since static data are destroyed upon program
162 + termination.
163 +
164   \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.
165  
166 + Categoried as a creational pattern, the Factory Method pattern deals
167 + with the problem of creating objects without specifying the exact
168 + class of object that will be created. Factory Method is typically
169 + implemented by delegating the creation operation to the subclasses.
170 + Parameterized Factory pattern where factory method (
171 + createIntegrator member function) creates products based on the
172 + identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If
173 + the identifier has been already registered, the factory method will
174 + invoke the corresponding creator (see List.~\ref{integratorCreator})
175 + which utilizes the modern C++ template technique to avoid excess
176 + subclassing.
177  
178 < \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.
178 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
179  
180 + class IntegratorFactory {
181 + public:
182 +  typedef std::map<string, IntegratorCreator*> CreatorMapType;
183  
184 < \subsection{\label{appendixSection:templateMethod}Template Method}
184 >  bool registerIntegrator(IntegratorCreator* creator) {
185 >    return creatorMap_.insert(creator->getIdent(), creator).second;
186 >  }
187  
188 < \section{\label{appendixSection:analysisFramework}Analysis Framework}
188 >  Integrator* createIntegrator(const string& id, SimInfo* info) {
189 >    Integrator* result = NULL;
190 >    CreatorMapType::iterator i = creatorMap_.find(id);
191 >    if (i != creatorMap_.end()) {
192 >      result = (i->second)->create(info);
193 >    }
194 >    return result;
195 >  }
196  
197 < \section{\label{appendixSection:concepts}Concepts}
197 > private:
198 >  CreatorMapType creatorMap_;
199 > };
200 > \end{lstlisting}
201  
202 < 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:
202 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
203  
204 + class IntegratorCreator {
205 + public:
206 +    IntegratorCreator(const string& ident) : ident_(ident) {}
207 +
208 +    const string& getIdent() const { return ident_; }
209 +
210 +    virtual Integrator* create(SimInfo* info) const = 0;
211 +
212 + private:
213 +    string ident_;
214 + };
215 +
216 + template<class ConcreteIntegrator>
217 + class IntegratorBuilder : public IntegratorCreator {
218 + public:
219 +  IntegratorBuilder(const string& ident)
220 +                   : IntegratorCreator(ident) {}
221 +  virtual  Integrator* create(SimInfo* info) const {
222 +    return new ConcreteIntegrator(info);
223 +  }
224 + };
225 + \end{lstlisting}
226 +
227 + \subsection{\label{appendixSection:visitorPattern}Visitor}
228 +
229 + The visitor pattern is designed to decouple the data structure and
230 + algorithms used upon them by collecting related operation from
231 + element classes into other visitor classes, which is equivalent to
232 + adding virtual functions into a set of classes without modifying
233 + their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
234 + structure of Visitor pattern which is used extensively in {\tt
235 + Dump2XYZ}. In order to convert an OOPSE dump file, a series of
236 + distinct operations are performed on different StuntDoubles (See the
237 + class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration
238 + in List.~\ref{appendixScheme:element}). Since the hierarchies
239 + remains stable, it is easy to define a visit operation (see
240 + List.~\ref{appendixScheme:visitor}) for each class of StuntDouble.
241 + Note that using Composite pattern\cite{Gamma1994}, CompositVisitor
242 + manages a priority visitor list and handles the execution of every
243 + visitor in the priority list on different StuntDoubles.
244 +
245   \begin{figure}
246   \centering
247 < \includegraphics[width=3in]{heirarchy.eps}
248 < \caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
249 < 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}
247 > \includegraphics[width=\linewidth]{visitor.eps}
248 > \caption[The UML class diagram of Visitor patten] {The UML class
249 > diagram of Visitor patten.} \label{appendixFig:visitorUML}
250   \end{figure}
251  
252 + \begin{figure}
253 + \centering
254 + \includegraphics[width=\linewidth]{hierarchy.eps}
255 + \caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
256 + the class hierarchy. } \label{oopseFig:hierarchy}
257 + \end{figure}
258 +
259 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
260 +
261 + class StuntDouble { public:
262 +  virtual void accept(BaseVisitor* v) = 0;
263 + };
264 +
265 + class Atom: public StuntDouble { public:
266 +  virtual void accept{BaseVisitor* v*} {
267 +    v->visit(this);
268 +  }
269 + };
270 +
271 + class DirectionalAtom: public Atom { public:
272 +  virtual void accept{BaseVisitor* v*} {
273 +    v->visit(this);
274 +  }
275 + };
276 +
277 + class RigidBody: public StuntDouble { public:
278 +  virtual void accept{BaseVisitor* v*} {
279 +    v->visit(this);
280 +  }
281 + };
282 +
283 + \end{lstlisting}
284 +
285 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
286 +
287 + class BaseVisitor{
288 + public:
289 +  virtual void visit(Atom* atom);
290 +  virtual void visit(DirectionalAtom* datom);
291 +  virtual void visit(RigidBody* rb);
292 + };
293 +
294 + class BaseAtomVisitor:public BaseVisitor{ public:
295 +  virtual void visit(Atom* atom);
296 +  virtual void visit(DirectionalAtom* datom);
297 +  virtual void visit(RigidBody* rb);
298 + };
299 +
300 + class SSDAtomVisitor:public BaseAtomVisitor{ public:
301 +  virtual void visit(Atom* atom);
302 +  virtual void visit(DirectionalAtom* datom);
303 +  virtual void visit(RigidBody* rb);
304 + };
305 +
306 + class CompositeVisitor: public BaseVisitor {
307 + public:
308 +
309 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
310 +  typedef VistorListType::iterator VisitorListIterator;
311 +  virtual void visit(Atom* atom) {
312 +    VisitorListIterator i;
313 +    BaseVisitor* curVisitor;
314 +    for(i = visitorList.begin();i != visitorList.end();++i) {
315 +      atom->accept(*i);
316 +    }
317 +  }
318 +
319 +  virtual void visit(DirectionalAtom* datom) {
320 +    VisitorListIterator i;
321 +    BaseVisitor* curVisitor;
322 +    for(i = visitorList.begin();i != visitorList.end();++i) {
323 +      atom->accept(*i);
324 +    }
325 +  }
326 +
327 +  virtual void visit(RigidBody* rb) {
328 +    VisitorListIterator i;
329 +    std::vector<Atom*> myAtoms;
330 +    std::vector<Atom*>::iterator ai;
331 +    myAtoms = rb->getAtoms();
332 +    for(i = visitorList.begin();i != visitorList.end();++i) {{
333 +      rb->accept(*i);
334 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
335 +        (*ai)->accept(*i);
336 +    }
337 +  }
338 +
339 +  void addVisitor(BaseVisitor* v, int priority);
340 +
341 +  protected:
342 +    VistorListType visitorList;
343 + };
344 +
345 + \end{lstlisting}
346 +
347 + \section{\label{appendixSection:concepts}Concepts}
348 +
349 + OOPSE manipulates both traditional atoms as well as some objects
350 + that {\it behave like atoms}.  These objects can be rigid
351 + collections of atoms or atoms which have orientational degrees of
352 + freedom.  A diagram of the class hierarchy is illustrated in
353 + Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
354 + DirectionalAtom in {\sc OOPSE} have their own names which are
355 + specified in the {\tt .md} file. In contrast, RigidBodies are
356 + denoted by their membership and index inside a particular molecule:
357 + [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
358 + on the specifics of the simulation). The names of rigid bodies are
359 + generated automatically. For example, the name of the first rigid
360 + body in a DMPC molecule is DMPC\_RB\_0.
361   \begin{itemize}
362   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
363   integrators and minimizers.
# Line 101 | Line 367 | Every Molecule, Atom and DirectionalAtom in {\sc oopse
367   DirectionalAtom}s which behaves as a single unit.
368   \end{itemize}
369  
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 –
370   \section{\label{appendixSection:syntax}Syntax of the Select Command}
371  
372 < The most general form of the select command is: {\tt select {\it
373 < expression}}
372 > {\sc OOPSE} provides a powerful selection utility to select
373 > StuntDoubles. The most general form of the select command is:
374  
375 + {\tt select {\it expression}}.
376 +
377   This expression represents an arbitrary set of StuntDoubles (Atoms
378 < or RigidBodies) in {\sc oopse}. Expressions are composed of either
378 > or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
379   name expressions, index expressions, predefined sets, user-defined
380   expressions, comparison operators, within expressions, or logical
381   combinations of the above expression types. Expressions can be
# Line 143 | Line 403 | not & ``!''  \\
403   \subsection{\label{appendixSection:name}Name expressions}
404  
405   \begin{center}
406 < \begin{tabular}{|llp{3in}|}
406 > \begin{tabular}{|llp{2in}|}
407   \hline {\bf type of expression} & {\bf examples} & {\bf translation
408   of
409   examples} \\
# Line 202 | Line 462 | expression}}
462   Users can define arbitrary terms to represent groups of
463   StuntDoubles, and then use the define terms in select commands. The
464   general form for the define command is: {\bf define {\it term
465 < expression}}
465 > expression}}. Once defined, the user can specify such terms in
466 > boolean expressions
467  
207 – Once defined, the user can specify such terms in boolean expressions
208 –
468   {\tt define SSDWATER SSD or SSD1 or SSDRF}
469  
470   {\tt select SSDWATER}
# Line 227 | Line 486 | wouldselect StuntDoubles which have mass greater than
486   \end{center}
487  
488   For example, the phrase {\tt select mass > 16.0 and charge < -2}
489 < wouldselect StuntDoubles which have mass greater than 16.0 and
489 > would select StuntDoubles which have mass greater than 16.0 and
490   charges less than -2.
491  
492   \subsection{\label{appendixSection:within}Within expressions}
# Line 241 | Line 500 | atoms.
500   select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
501   atoms.
502  
244 – \section{\label{appendixSection:tools}Tools which use the selection command}
503  
504 < \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
504 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
505  
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 –
506   \subsection{\label{appendixSection:StaticProps}StaticProps}
507  
508   {\tt StaticProps} can compute properties which are averaged over
509   some or all of the configurations that are contained within a dump
510   file. The most common example of a static property that can be
511   computed is the pair distribution function between atoms of type $A$
512 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
513 < used to compute the density distributions of other molecules in a
514 < reference frame {\it fixed to the body-fixed reference frame} of a
515 < selected atom or rigid body.
512 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
513 > also be used to compute the density distributions of other molecules
514 > in a reference frame {\it fixed to the body-fixed reference frame}
515 > of a selected atom or rigid body.
516  
517   There are five seperate radial distribution functions availiable in
518   OOPSE. Since every radial distrbution function invlove the
# Line 336 | Line 561 | distribution functions are most easily seen in the fig
561  
562   \begin{figure}
563   \centering
564 < \includegraphics[width=3in]{definition.pdf}
564 > \includegraphics[width=3in]{definition.eps}
565   \caption[Definitions of the angles between directional objects]{ \\
566   Any two directional objects (DirectionalAtoms and RigidBodies) have
567   a set of two angles ($\theta$, and $\omega$) between the z-axes of
568   their body-fixed frames.} \label{oopseFig:gofr}
569   \end{figure}
570  
571 + Due to the fact that the selected StuntDoubles from two selections
572 + may be overlapped, {\tt StaticProps} performs the calculation in
573 + three stages which are illustrated in
574 + Fig.~\ref{oopseFig:staticPropsProcess}.
575 +
576 + \begin{figure}
577 + \centering
578 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
579 + \caption[A representation of the three-stage correlations in
580 + \texttt{StaticProps}]{This diagram illustrates three-stage
581 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
582 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
583 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
584 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
585 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
586 + the contrary, the third stage($C$ and $C$) are completely
587 + overlapping} \label{oopseFig:staticPropsProcess}
588 + \end{figure}
589 +
590   The options available for {\tt StaticProps} are as follows:
591   \begin{longtable}[c]{|EFG|}
592   \caption{StaticProps Command-line Options}
# Line 353 | Line 597 | The options available for {\tt StaticProps} are as fol
597   \endfoot
598    -h& {\tt -{}-help}                    &  Print help and exit \\
599    -V& {\tt -{}-version}                 &  Print version and exit \\
600 <  -i& {\tt -{}-input=filename}          &  input dump file \\
601 <  -o& {\tt -{}-output=filename}         &  output file name \\
602 <  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
603 <  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
604 <  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
605 <  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
606 <    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
607 <    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
608 <    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
609 <    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
610 <    & {\tt -{}-molname=STRING}           & molecule name \\
611 <    & {\tt -{}-begin=INT}                & begin internal index \\
612 <    & {\tt -{}-end=INT}                  & end internal index \\
600 >  -i& {\tt -{}-input}          &  input dump file \\
601 >  -o& {\tt -{}-output}         &  output file name \\
602 >  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
603 >  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
604 >  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
605 >  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
606 >    & {\tt -{}-sele1}   & select the first StuntDouble set \\
607 >    & {\tt -{}-sele2}   & select the second StuntDouble set \\
608 >    & {\tt -{}-sele3}   & select the third StuntDouble set \\
609 >    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
610 >    & {\tt -{}-molname}           & molecule name \\
611 >    & {\tt -{}-begin}                & begin internal index \\
612 >    & {\tt -{}-end}                  & end internal index \\
613   \hline
614   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
615   \hline
# Line 404 | Line 648 | The options available for DynamicProps are as follows:
648   different vectors).  The ability to use two selection scripts to
649   select different types of atoms is already present in the code.
650  
651 + For large simulations, the trajectory files can sometimes reach
652 + sizes in excess of several gigabytes. In order to effectively
653 + analyze that amount of data. In order to prevent a situation where
654 + the program runs out of memory due to large trajectories,
655 + \texttt{dynamicProps} will estimate the size of free memory at
656 + first, and determine the number of frames in each block, which
657 + allows the operating system to load two blocks of data
658 + simultaneously without swapping. Upon reading two blocks of the
659 + trajectory, \texttt{dynamicProps} will calculate the time
660 + correlation within the first block and the cross correlations
661 + between the two blocks. This second block is then freed and then
662 + incremented and the process repeated until the end of the
663 + trajectory. Once the end is reached, the first block is freed then
664 + incremented, until all frame pairs have been correlated in time.
665 + This process is illustrated in
666 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
667 +
668 + \begin{figure}
669 + \centering
670 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
671 + \caption[A representation of the block correlations in
672 + \texttt{dynamicProps}]{This diagram illustrates block correlations
673 + processing in \texttt{dynamicProps}. The shaded region represents
674 + the self correlation of the block, and the open blocks are read one
675 + at a time and the cross correlations between blocks are calculated.}
676 + \label{oopseFig:dynamicPropsProcess}
677 + \end{figure}
678 +
679   The options available for DynamicProps are as follows:
680   \begin{longtable}[c]{|EFG|}
681   \caption{DynamicProps Command-line Options}
# Line 414 | Line 686 | The options available for DynamicProps are as follows:
686   \endfoot
687    -h& {\tt -{}-help}                   & Print help and exit \\
688    -V& {\tt -{}-version}                & Print version and exit \\
689 <  -i& {\tt -{}-input=filename}         & input dump file \\
690 <  -o& {\tt -{}-output=filename}        & output file name \\
691 <    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
692 <    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
689 >  -i& {\tt -{}-input}         & input dump file \\
690 >  -o& {\tt -{}-output}        & output file name \\
691 >    & {\tt -{}-sele1} & select first StuntDouble set \\
692 >    & {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
693   \hline
694   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
695   \hline
# Line 426 | Line 698 | The options available for DynamicProps are as follows:
698    -d& {\tt -{}-dcorr}                  & compute dipole correlation function
699   \end{longtable}
700  
701 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
701 > \section{\label{appendixSection:tools}Other Useful Utilities}
702 >
703 > \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
704 >
705 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
706 > which can be opened by other molecular dynamics viewers such as Jmol
707 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
708 > as follows:
709 >
710 >
711 > \begin{longtable}[c]{|EFG|}
712 > \caption{Dump2XYZ Command-line Options}
713 > \\ \hline
714 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
715 > \endhead
716 > \hline
717 > \endfoot
718 >  -h & {\tt -{}-help} &                        Print help and exit \\
719 >  -V & {\tt -{}-version} &                     Print version and exit \\
720 >  -i & {\tt -{}-input}  &             input dump file \\
721 >  -o & {\tt -{}-output} &             output file name \\
722 >  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
723 >  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
724 >  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
725 >  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
726 >  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
727 >  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
728 >  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
729 >     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
730 >     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
731 >     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
732 >  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
733 > converted. \\
734 >     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
735 >     & {\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}.
736 > \end{longtable}
737 >
738 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
739 >
740 > {\tt Hydro} can calculate resistance and diffusion tensors at the
741 > center of resistance. Both tensors at the center of diffusion can
742 > also be reported from the program, as well as the coordinates for
743 > the beads which are used to approximate the arbitrary shapes. The
744 > options available for Hydro are as follows:
745 > \begin{longtable}[c]{|EFG|}
746 > \caption{Hydrodynamics Command-line Options}
747 > \\ \hline
748 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
749 > \endhead
750 > \hline
751 > \endfoot
752 >  -h & {\tt -{}-help} &                        Print help and exit \\
753 >  -V & {\tt -{}-version} &                     Print version and exit \\
754 >  -i & {\tt -{}-input}  &             input dump file \\
755 >  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
756 >  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
757 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
758 > \end{longtable}

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