ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/tengDissertation/Appendix.tex
(Generate patch)

Comparing trunk/tengDissertation/Appendix.tex (file contents):
Revision 2789 by tim, Mon Jun 5 21:00:46 2006 UTC vs.
Revision 2835 by tim, Thu Jun 8 22:39:54 2006 UTC

# Line 1 | Line 1
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
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 13 | 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 47 | 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}
121 < The Singleton pattern ensures that only one instance of a class is
122 < created. All objects that use an instance of that class use the same
123 < instance.
121 > The Singleton pattern not only provides a mechanism to restrict
122 > instantiation of a class to one object, but also provides a global
123 > point of access to the object. Currently implemented as a global
124 > variable, the logging utility which reports error and warning
125 > messages to the console in {\sc OOPSE} is a good candidate for
126 > applying the Singleton pattern to avoid the global namespace
127 > pollution.Although the singleton pattern can be implemented in
128 > various ways  to account for different aspects of the software
129 > designs, such as lifespan control \textit{etc}, we only use the
130 > static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class
131 > is declared as
132 > \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
133  
134 + class IntegratorFactory {
135 + public:
136 +  static IntegratorFactory*
137 +  getInstance();
138 + protected:
139 +  IntegratorFactory();
140 + private:
141 +  static IntegratorFactory* instance_;
142 + };
143 +
144 + \end{lstlisting}
145 + The corresponding implementation is
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 + Since constructor is declared as {\tt protected}, a client can not
159 + instantiate {\tt IntegratorFactory} directly. Moreover, since the
160 + member function {\tt getInstance} serves as the only entry of access
161 + to {\tt IntegratorFactory}, this approach fulfills the basic
162 + requirement, a single instance. Another consequence of this approach
163 + is the automatic destruction since static data are destroyed upon
164 + program termination.
165 +
166   \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.
167  
168 + Categoried as a creational pattern, the Factory Method pattern deals
169 + with the problem of creating objects without specifying the exact
170 + class of object that will be created. Factory Method is typically
171 + implemented by delegating the creation operation to the subclasses.
172 + {\tt Integrator} class Parameterized Factory pattern where factory
173 + method ({\tt createIntegrator} member function) creates products
174 + based on the identifier (see
175 + List.~\ref{appendixScheme:factoryDeclaration}). If the identifier
176 + has been already registered, the factory method will invoke the
177 + corresponding creator (see List.~\ref{integratorCreator}) which
178 + utilizes the modern C++ template technique to avoid subclassing.
179 + \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of {\tt IntegratorFactory} class.},label={appendixScheme:factoryDeclaration}]
180  
181 < \subsection{\label{appendixSection:visitorPattern}Visitor}
182 < The purpose of the Visitor Pattern is to encapsulate an operation
183 < 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 > class IntegratorFactory {
182 > public:
183 >  typedef std::map<string, IntegratorCreator*> CreatorMapType;
184  
185 +  bool registerIntegrator(IntegratorCreator* creator) {
186 +    return creatorMap_.insert(creator->getIdent(), creator).second;
187 +  }
188  
189 < \subsection{\label{appendixSection:templateMethod}Template Method}
189 >  Integrator* createIntegrator(const string& id, SimInfo* info) {
190 >    Integrator* result = NULL;
191 >    CreatorMapType::iterator i = creatorMap_.find(id);
192 >    if (i != creatorMap_.end()) {
193 >      result = (i->second)->create(info);
194 >    }
195 >    return result;
196 >  }
197  
198 < \section{\label{appendixSection:analysisFramework}Analysis Framework}
198 > private:
199 >  CreatorMapType creatorMap_;
200 > };
201 > \end{lstlisting}
202 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
203  
204 < \section{\label{appendixSection:concepts}Concepts}
204 > class IntegratorCreator {
205 > public:
206 >    IntegratorCreator(const string& ident) : ident_(ident) {}
207  
208 < 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:
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 purpose of the Visitor Pattern is to encapsulate an operation
230 + that you want to perform on the elements. The operation being
231 + performed on a structure can be switched without changing the
232 + interfaces of the elements. In other words, one can add virtual
233 + functions into a set of classes without modifying their interfaces.
234 + Fig.~\ref{appendixFig:visitorUML} demonstrates the structure of
235 + Visitor pattern which is used extensively in {\tt Dump2XYZ}. In
236 + order to convert an OOPSE dump file, a series of distinct and
237 + unrelated operations are performed on different StuntDoubles.
238 + Visitor allows one to keep related operations together by packing
239 + them into one class. {\tt BaseAtomVisitor} is a typical example of
240 + visitor in {\tt Dump2XYZ} program{see
241 + List.~\ref{appendixScheme:visitor}}. In contrast to the operations,
242 + the object structure or element classes rarely change(See
243 + Fig.~\ref{oopseFig:heirarchy} and
244 + List.~\ref{appendixScheme:element}).
245 +
246 +
247   \begin{figure}
248   \centering
249 < \includegraphics[width=3in]{heirarchy.eps}
250 < \caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
251 < 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}
249 > \includegraphics[width=\linewidth]{visitor.eps}
250 > \caption[The UML class diagram of Visitor patten] {The UML class
251 > diagram of Visitor patten.} \label{appendixFig:visitorUML}
252   \end{figure}
253  
254 < \begin{itemize}
96 < \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
97 < integrators and minimizers.
98 < \item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
99 < \item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
100 < \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
101 < DirectionalAtom}s which behaves as a single unit.
102 < \end{itemize}
254 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
255  
256 < Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
257 < own names which are specified in the {\tt .md} file. In contrast,
258 < RigidBodies are denoted by their membership and index inside a
259 < particular molecule: [MoleculeName]\_RB\_[index] (the contents
260 < inside the brackets depend on the specifics of the simulation). The
261 < 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.
256 > class BaseVisitor{
257 > public:
258 >  virtual void visit(Atom* atom);
259 >  virtual void visit(DirectionalAtom* datom);
260 >  virtual void visit(RigidBody* rb);
261 > };
262  
263 + class BaseAtomVisitor:public BaseVisitor{ public:
264 +  virtual void visit(Atom* atom);
265 +  virtual void visit(DirectionalAtom* datom);
266 +  virtual void visit(RigidBody* rb);
267 + };
268 +
269 + \end{lstlisting}
270 +
271 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
272 +
273 + class StuntDouble {
274 + public:
275 +  virtual void accept(BaseVisitor* v) = 0;
276 + };
277 +
278 + class Atom: public StuntDouble {
279 + public:
280 +  virtual void accept{BaseVisitor* v*} {
281 +    v->visit(this);
282 +  }
283 + };
284 +
285 + class DirectionalAtom: public Atom {
286 + public:
287 +  virtual void accept{BaseVisitor* v*} {
288 +    v->visit(this);
289 +  }
290 + };
291 +
292 + class RigidBody: public StuntDouble {
293 + public:
294 +  virtual void accept{BaseVisitor* v*} {
295 +    v->visit(this);
296 +  }
297 + };
298 +
299 + \end{lstlisting}
300 +
301 + \section{\label{appendixSection:concepts}Concepts}
302 +
303 + OOPSE manipulates both traditional atoms as well as some objects
304 + that {\it behave like atoms}.  These objects can be rigid
305 + collections of atoms or atoms which have orientational degrees of
306 + freedom.  A diagram of the class heirarchy is illustrated in
307 + Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and
308 + DirectionalAtom in {\sc OOPSE} have their own names which are
309 + specified in the {\tt .md} file. In contrast, RigidBodies are
310 + denoted by their membership and index inside a particular molecule:
311 + [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
312 + on the specifics of the simulation). The names of rigid bodies are
313 + generated automatically. For example, the name of the first rigid
314 + body in a DMPC molecule is DMPC\_RB\_0.
315 + %\begin{figure}
316 + %\centering
317 + %\includegraphics[width=\linewidth]{heirarchy.eps}
318 + %\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of
319 + %the class heirarchy.
320 + %\begin{itemize}
321 + %\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
322 + %integrators and minimizers.
323 + %\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
324 + %\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
325 + %\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
326 + %DirectionalAtom}s which behaves as a single unit.
327 + %\end{itemize}
328 + %} \label{oopseFig:heirarchy}
329 + %\end{figure}
330 +
331   \section{\label{appendixSection:syntax}Syntax of the Select Command}
332  
333   The most general form of the select command is: {\tt select {\it
334 < expression}}
334 > expression}}. This expression represents an arbitrary set of
335 > StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
336 > composed of either name expressions, index expressions, predefined
337 > sets, user-defined expressions, comparison operators, within
338 > expressions, or logical combinations of the above expression types.
339 > Expressions can be combined using parentheses and the Boolean
340 > operators.
341  
117 – This expression represents an arbitrary set of StuntDoubles (Atoms
118 – or RigidBodies) in {\sc oopse}. Expressions are composed of either
119 – name expressions, index expressions, predefined sets, user-defined
120 – expressions, comparison operators, within expressions, or logical
121 – combinations of the above expression types. Expressions can be
122 – combined using parentheses and the Boolean operators.
123 –
342   \subsection{\label{appendixSection:logical}Logical expressions}
343  
344   The logical operators allow complex queries to be constructed out of
# Line 143 | Line 361 | not & ``!''  \\
361   \subsection{\label{appendixSection:name}Name expressions}
362  
363   \begin{center}
364 < \begin{tabular}{|llp{3in}|}
364 > \begin{tabular}{|llp{2in}|}
365   \hline {\bf type of expression} & {\bf examples} & {\bf translation
366   of
367   examples} \\
# Line 202 | Line 420 | expression}}
420   Users can define arbitrary terms to represent groups of
421   StuntDoubles, and then use the define terms in select commands. The
422   general form for the define command is: {\bf define {\it term
423 < expression}}
423 > expression}}. Once defined, the user can specify such terms in
424 > boolean expressions
425  
207 – Once defined, the user can specify such terms in boolean expressions
208 –
426   {\tt define SSDWATER SSD or SSD1 or SSDRF}
427  
428   {\tt select SSDWATER}
# Line 227 | Line 444 | wouldselect StuntDoubles which have mass greater than
444   \end{center}
445  
446   For example, the phrase {\tt select mass > 16.0 and charge < -2}
447 < wouldselect StuntDoubles which have mass greater than 16.0 and
447 > would select StuntDoubles which have mass greater than 16.0 and
448   charges less than -2.
449  
450   \subsection{\label{appendixSection:within}Within expressions}
# Line 241 | Line 458 | atoms.
458   select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
459   atoms.
460  
244 – \section{\label{appendixSection:tools}Tools which use the selection command}
461  
462 < \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
462 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
463  
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 –
464   \subsection{\label{appendixSection:StaticProps}StaticProps}
465  
466   {\tt StaticProps} can compute properties which are averaged over
467   some or all of the configurations that are contained within a dump
468   file. The most common example of a static property that can be
469   computed is the pair distribution function between atoms of type $A$
470 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
471 < used to compute the density distributions of other molecules in a
472 < reference frame {\it fixed to the body-fixed reference frame} of a
473 < selected atom or rigid body.
470 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
471 > also be used to compute the density distributions of other molecules
472 > in a reference frame {\it fixed to the body-fixed reference frame}
473 > of a selected atom or rigid body.
474  
475   There are five seperate radial distribution functions availiable in
476   OOPSE. Since every radial distrbution function invlove the
# Line 336 | Line 519 | distribution functions are most easily seen in the fig
519  
520   \begin{figure}
521   \centering
522 < \includegraphics[width=3in]{definition.pdf}
522 > \includegraphics[width=3in]{definition.eps}
523   \caption[Definitions of the angles between directional objects]{ \\
524   Any two directional objects (DirectionalAtoms and RigidBodies) have
525   a set of two angles ($\theta$, and $\omega$) between the z-axes of
526   their body-fixed frames.} \label{oopseFig:gofr}
527 + \end{figure}
528 +
529 + Due to the fact that the selected StuntDoubles from two selections
530 + may be overlapped, {\tt StaticProps} performs the calculation in
531 + three stages which are illustrated in
532 + Fig.~\ref{oopseFig:staticPropsProcess}.
533 +
534 + \begin{figure}
535 + \centering
536 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
537 + \caption[A representation of the three-stage correlations in
538 + \texttt{StaticProps}]{This diagram illustrates three-stage
539 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
540 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
541 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
542 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
543 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
544 + the contrary, the third stage($C$ and $C$) are completely
545 + overlapping} \label{oopseFig:staticPropsProcess}
546   \end{figure}
547  
548   The options available for {\tt StaticProps} are as follows:
# Line 353 | Line 555 | The options available for {\tt StaticProps} are as fol
555   \endfoot
556    -h& {\tt -{}-help}                    &  Print help and exit \\
557    -V& {\tt -{}-version}                 &  Print version and exit \\
558 <  -i& {\tt -{}-input=filename}          &  input dump file \\
559 <  -o& {\tt -{}-output=filename}         &  output file name \\
560 <  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
561 <  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
562 <  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
563 <  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
564 <    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
565 <    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
566 <    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
567 <    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
568 <    & {\tt -{}-molname=STRING}           & molecule name \\
569 <    & {\tt -{}-begin=INT}                & begin internal index \\
570 <    & {\tt -{}-end=INT}                  & end internal index \\
558 >  -i& {\tt -{}-input}          &  input dump file \\
559 >  -o& {\tt -{}-output}         &  output file name \\
560 >  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
561 >  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
562 >  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
563 >  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
564 >    & {\tt -{}-sele1}   & select the first StuntDouble set \\
565 >    & {\tt -{}-sele2}   & select the second StuntDouble set \\
566 >    & {\tt -{}-sele3}   & select the third StuntDouble set \\
567 >    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
568 >    & {\tt -{}-molname}           & molecule name \\
569 >    & {\tt -{}-begin}                & begin internal index \\
570 >    & {\tt -{}-end}                  & end internal index \\
571   \hline
572   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
573   \hline
# Line 404 | Line 606 | The options available for DynamicProps are as follows:
606   different vectors).  The ability to use two selection scripts to
607   select different types of atoms is already present in the code.
608  
609 + For large simulations, the trajectory files can sometimes reach
610 + sizes in excess of several gigabytes. In order to effectively
611 + analyze that amount of data. In order to prevent a situation where
612 + the program runs out of memory due to large trajectories,
613 + \texttt{dynamicProps} will estimate the size of free memory at
614 + first, and determine the number of frames in each block, which
615 + allows the operating system to load two blocks of data
616 + simultaneously without swapping. Upon reading two blocks of the
617 + trajectory, \texttt{dynamicProps} will calculate the time
618 + correlation within the first block and the cross correlations
619 + between the two blocks. This second block is then freed and then
620 + incremented and the process repeated until the end of the
621 + trajectory. Once the end is reached, the first block is freed then
622 + incremented, until all frame pairs have been correlated in time.
623 + This process is illustrated in
624 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
625 +
626 + \begin{figure}
627 + \centering
628 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
629 + \caption[A representation of the block correlations in
630 + \texttt{dynamicProps}]{This diagram illustrates block correlations
631 + processing in \texttt{dynamicProps}. The shaded region represents
632 + the self correlation of the block, and the open blocks are read one
633 + at a time and the cross correlations between blocks are calculated.}
634 + \label{oopseFig:dynamicPropsProcess}
635 + \end{figure}
636 +
637   The options available for DynamicProps are as follows:
638   \begin{longtable}[c]{|EFG|}
639   \caption{DynamicProps Command-line Options}
# Line 414 | Line 644 | The options available for DynamicProps are as follows:
644   \endfoot
645    -h& {\tt -{}-help}                   & Print help and exit \\
646    -V& {\tt -{}-version}                & Print version and exit \\
647 <  -i& {\tt -{}-input=filename}         & input dump file \\
648 <  -o& {\tt -{}-output=filename}        & output file name \\
649 <    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
650 <    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
647 >  -i& {\tt -{}-input}         & input dump file \\
648 >  -o& {\tt -{}-output}        & output file name \\
649 >    & {\tt -{}-sele1} & select first StuntDouble set \\
650 >    & {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
651   \hline
652   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
653   \hline
# Line 426 | Line 656 | The options available for DynamicProps are as follows:
656    -d& {\tt -{}-dcorr}                  & compute dipole correlation function
657   \end{longtable}
658  
659 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
659 > \section{\label{appendixSection:tools}Other Useful Utilities}
660 >
661 > \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
662 >
663 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
664 > which can be opened by other molecular dynamics viewers such as Jmol
665 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
666 > as follows:
667 >
668 >
669 > \begin{longtable}[c]{|EFG|}
670 > \caption{Dump2XYZ Command-line Options}
671 > \\ \hline
672 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
673 > \endhead
674 > \hline
675 > \endfoot
676 >  -h & {\tt -{}-help} &                        Print help and exit \\
677 >  -V & {\tt -{}-version} &                     Print version and exit \\
678 >  -i & {\tt -{}-input}  &             input dump file \\
679 >  -o & {\tt -{}-output} &             output file name \\
680 >  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
681 >  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
682 >  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
683 >  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
684 >  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
685 >  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
686 >  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
687 >     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
688 >     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
689 >     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
690 >  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
691 > converted. \\
692 >     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
693 >     & {\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}.
694 > \end{longtable}
695 >
696 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
697 >
698 > {\tt Hydro} can calculate resistance and diffusion tensors at the
699 > center of resistance. Both tensors at the center of diffusion can
700 > also be reported from the program, as well as the coordinates for
701 > the beads which are used to approximate the arbitrary shapes. The
702 > options available for Hydro are as follows:
703 > \begin{longtable}[c]{|EFG|}
704 > \caption{Hydrodynamics Command-line Options}
705 > \\ \hline
706 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
707 > \endhead
708 > \hline
709 > \endfoot
710 >  -h & {\tt -{}-help} &                        Print help and exit \\
711 >  -V & {\tt -{}-version} &                     Print version and exit \\
712 >  -i & {\tt -{}-input}  &             input dump file \\
713 >  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
714 >  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
715 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
716 > \end{longtable}

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines