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 2807 by tim, Wed Jun 7 01:49:15 2006 UTC vs.
Revision 2880 by tim, Thu Jun 22 22:19:02 2006 UTC

# Line 1 | Line 1
1   \appendix
2 < \chapter{\label{chapt:appendix}APPENDIX}
2 > \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
3  
4 < Designing object-oriented software is hard, and designing reusable
5 < object-oriented scientific software is even harder. Absence of
6 < applying modern software development practices is the bottleneck of
7 < Scientific Computing community\cite{Wilson}. For instance, in the
8 < last 20 years , there are quite a few MD packages that were
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
# Line 28 | Line 84 | provide a common vocabulary of solutions that can expr
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.
87 > solutions succinctly. As one of the latest advanced techniques
88 > emerged from object-oriented community, design patterns were applied
89 > in some of the modern scientific software applications, such as
90 > JMol, {\sc OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}
91 > \textit{etc}. The following sections enumerates some of the patterns
92 > used in {\sc OOPSE}.
93  
94 < Patterns are usually described using a format that includes the
34 < following information:
35 < \begin{enumerate}
36 <  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
37 <  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
38 <  in the literature. In this case it is common practice to document these nicknames or synonyms under
39 <  the heading of \emph{Aliases} or \emph{Also Known As}.
40 <  \item The \emph{motivation} or \emph{context} that this pattern applies
41 <  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
42 <  \item The \emph{solution} to the problem that the pattern
43 <  addresses. It describes how to construct the necessary work products. The description may include
44 <  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
45 <  collaborations, to show how the problem is solved.
46 <  \item The \emph{consequences} of using the given solution to solve a
47 <  problem, both positive and negative.
48 < \end{enumerate}
94 > \subsection{\label{appendixSection:singleton}Singleton}
95  
96 < As one of the latest advanced techniques emerged from
97 < object-oriented community, design patterns were applied in some of
98 < the modern scientific software applications, such as JMol, OOPSE
99 < \cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}.
96 > The Singleton pattern not only provides a mechanism to restrict
97 > instantiation of a class to one object, but also provides a global
98 > point of access to the object. Currently implemented as a global
99 > variable, the logging utility which reports error and warning
100 > messages to the console in {\sc OOPSE} is a good candidate for
101 > applying the Singleton pattern to avoid the global namespace
102 > pollution. Although the singleton pattern can be implemented in
103 > various ways  to account for different aspects of the software
104 > designs, such as lifespan control \textit{etc}, we only use the
105 > static data approach in {\sc OOPSE}. The declaration and
106 > implementation of IntegratorFactory class are given by declared in
107 > List.~\ref{appendixScheme:singletonDeclaration} and
108 > Scheme.~\ref{appendixScheme:singletonImplementation} respectively.
109 > Since constructor is declared as protected, a client can not
110 > instantiate IntegratorFactory directly. Moreover, since the member
111 > function getInstance serves as the only entry of access to
112 > IntegratorFactory, this approach fulfills the basic requirement, a
113 > single instance. Another consequence of this approach is the
114 > automatic destruction since static data are destroyed upon program
115 > termination.
116 > \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
117  
118 < \subsection{\label{appendixSection:singleton}Singleton}
119 < The Singleton pattern ensures that only one instance of a class is
120 < created. All objects that use an instance of that class use the same
121 < instance.
118 > class IntegratorFactory {
119 > public:
120 >  static IntegratorFactory*
121 >  getInstance();
122 > protected:
123 >  IntegratorFactory();
124 > private:
125 >  static IntegratorFactory* instance_;
126 > };
127  
128 + \end{lstlisting}
129 +
130 + \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
131 +
132 + IntegratorFactory::instance_ = NULL;
133 +
134 + IntegratorFactory* getInstance() {
135 +  if (instance_ == NULL){
136 +    instance_ = new IntegratorFactory;
137 +  }
138 +  return instance_;
139 + }
140 +
141 + \end{lstlisting}
142 +
143 +
144   \subsection{\label{appendixSection:factoryMethod}Factory Method}
61 – The Factory Method pattern is a creational pattern which deals with
62 – the problem of creating objects without specifying the exact class
63 – of object that will be created. Factory Method solves this problem
64 – by defining a separate method for creating the objects, which
65 – subclasses can then override to specify the derived type of product
66 – that will be created.
145  
146 + Categoried as a creational pattern, the Factory Method pattern deals
147 + with the problem of creating objects without specifying the exact
148 + class of object that will be created. Factory Method is typically
149 + implemented by delegating the creation operation to the subclasses.
150 + Parameterized Factory pattern where factory method (
151 + createIntegrator member function) creates products based on the
152 + identifier (see Scheme.~\ref{appendixScheme:factoryDeclaration}). If
153 + the identifier has been already registered, the factory method will
154 + invoke the corresponding creator (see
155 + Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the
156 + modern C++ template technique to avoid excess subclassing.
157  
158 + \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
159 +
160 + class IntegratorFactory {
161 + public:
162 +  typedef std::map<string, IntegratorCreator*> CreatorMapType;
163 +
164 +  bool registerIntegrator(IntegratorCreator* creator) {
165 +    return creatorMap_.insert(creator->getIdent(), creator).second;
166 +  }
167 +
168 +  Integrator* createIntegrator(const string& id, SimInfo* info) {
169 +    Integrator* result = NULL;
170 +    CreatorMapType::iterator i = creatorMap_.find(id);
171 +    if (i != creatorMap_.end()) {
172 +      result = (i->second)->create(info);
173 +    }
174 +    return result;
175 +  }
176 +
177 + private:
178 +  CreatorMapType creatorMap_;
179 + };
180 + \end{lstlisting}
181 +
182 + \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
183 +
184 + class IntegratorCreator {
185 + public:
186 +    IntegratorCreator(const string& ident) : ident_(ident) {}
187 +
188 +    const string& getIdent() const { return ident_; }
189 +
190 +    virtual Integrator* create(SimInfo* info) const = 0;
191 +
192 + private:
193 +    string ident_;
194 + };
195 +
196 + template<class ConcreteIntegrator>
197 + class IntegratorBuilder : public IntegratorCreator {
198 + public:
199 +  IntegratorBuilder(const string& ident)
200 +                   : IntegratorCreator(ident) {}
201 +  virtual  Integrator* create(SimInfo* info) const {
202 +    return new ConcreteIntegrator(info);
203 +  }
204 + };
205 + \end{lstlisting}
206 +
207   \subsection{\label{appendixSection:visitorPattern}Visitor}
70 – The purpose of the Visitor Pattern is to encapsulate an operation
71 – that you want to perform on the elements of a data structure. In
72 – this way, you can change the operation being performed on a
73 – structure without the need of changing the classes of the elements
74 – that you are operating on.
208  
209 + The visitor pattern is designed to decouple the data structure and
210 + algorithms used upon them by collecting related operation from
211 + element classes into other visitor classes, which is equivalent to
212 + adding virtual functions into a set of classes without modifying
213 + their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
214 + structure of Visitor pattern which is used extensively in {\tt
215 + Dump2XYZ}. In order to convert an OOPSE dump file, a series of
216 + distinct operations are performed on different StuntDoubles (See the
217 + class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration
218 + in Scheme.~\ref{appendixScheme:element}). Since the hierarchies
219 + remains stable, it is easy to define a visit operation (see
220 + Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble.
221 + Note that using Composite pattern\cite{Gamma1994}, CompositVisitor
222 + manages a priority visitor list and handles the execution of every
223 + visitor in the priority list on different StuntDoubles.
224  
225 < \subsection{\label{appendixSection:templateMethod}Template Method}
225 > \begin{figure}
226 > \centering
227 > \includegraphics[width=\linewidth]{visitor.eps}
228 > \caption[The UML class diagram of Visitor patten] {The UML class
229 > diagram of Visitor patten.} \label{appendixFig:visitorUML}
230 > \end{figure}
231  
232 < \section{\label{appendixSection:analysisFramework}Analysis Framework}
232 > \begin{figure}
233 > \centering
234 > \includegraphics[width=\linewidth]{hierarchy.eps}
235 > \caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
236 > the class hierarchy. } \label{oopseFig:hierarchy}
237 > \end{figure}
238 >
239 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
240 >
241 > class StuntDouble { public:
242 >  virtual void accept(BaseVisitor* v) = 0;
243 > };
244 >
245 > class Atom: public StuntDouble { public:
246 >  virtual void accept{BaseVisitor* v*} {
247 >    v->visit(this);
248 >  }
249 > };
250 >
251 > class DirectionalAtom: public Atom { public:
252 >  virtual void accept{BaseVisitor* v*} {
253 >    v->visit(this);
254 >  }
255 > };
256 >
257 > class RigidBody: public StuntDouble { public:
258 >  virtual void accept{BaseVisitor* v*} {
259 >    v->visit(this);
260 >  }
261 > };
262  
263 + \end{lstlisting}
264 +
265 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
266 +
267 + class BaseVisitor{
268 + public:
269 +  virtual void visit(Atom* atom);
270 +  virtual void visit(DirectionalAtom* datom);
271 +  virtual void visit(RigidBody* rb);
272 + };
273 +
274 + class BaseAtomVisitor:public BaseVisitor{ public:
275 +  virtual void visit(Atom* atom);
276 +  virtual void visit(DirectionalAtom* datom);
277 +  virtual void visit(RigidBody* rb);
278 + };
279 +
280 + class CompositeVisitor: public BaseVisitor {
281 + public:
282 +
283 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
284 +  typedef VistorListType::iterator VisitorListIterator;
285 +  virtual void visit(Atom* atom) {
286 +    VisitorListIterator i;
287 +    BaseVisitor* curVisitor;
288 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
289 +      atom->accept(*i);
290 +    }
291 +  }
292 +
293 +  virtual void visit(DirectionalAtom* datom) {
294 +    VisitorListIterator i;
295 +    BaseVisitor* curVisitor;
296 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
297 +      atom->accept(*i);
298 +    }
299 +  }
300 +
301 +  virtual void visit(RigidBody* rb) {
302 +    VisitorListIterator i;
303 +    std::vector<Atom*> myAtoms;
304 +    std::vector<Atom*>::iterator ai;
305 +    myAtoms = rb->getAtoms();
306 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {{
307 +      rb->accept(*i);
308 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
309 +        (*ai)->accept(*i);
310 +    }
311 +  }
312 +
313 +  void addVisitor(BaseVisitor* v, int priority);
314 +
315 +  protected:
316 +    VistorListType visitorList;
317 + };
318 + \end{lstlisting}
319 +
320   \section{\label{appendixSection:concepts}Concepts}
321  
322   OOPSE manipulates both traditional atoms as well as some objects
323   that {\it behave like atoms}.  These objects can be rigid
324   collections of atoms or atoms which have orientational degrees of
325 < freedom.  Here is a diagram of the class heirarchy:
326 <
327 < %\begin{figure}
328 < %\centering
329 < %\includegraphics[width=3in]{heirarchy.eps}
330 < %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
331 < %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
332 < %selection syntax allows the user to select any of the objects that
333 < %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
95 < %\end{figure}
96 <
325 > freedom.  A diagram of the class hierarchy is illustrated in
326 > Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
327 > DirectionalAtom in {\sc OOPSE} have their own names which are
328 > specified in the {\tt .md} file. In contrast, RigidBodies are
329 > denoted by their membership and index inside a particular molecule:
330 > [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
331 > on the specifics of the simulation). The names of rigid bodies are
332 > generated automatically. For example, the name of the first rigid
333 > body in a DMPC molecule is DMPC\_RB\_0.
334   \begin{itemize}
335   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
336   integrators and minimizers.
# Line 103 | Line 340 | DirectionalAtom}s which behaves as a single unit.
340   DirectionalAtom}s which behaves as a single unit.
341   \end{itemize}
342  
106 – Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
107 – own names which are specified in the {\tt .md} file. In contrast,
108 – RigidBodies are denoted by their membership and index inside a
109 – particular molecule: [MoleculeName]\_RB\_[index] (the contents
110 – inside the brackets depend on the specifics of the simulation). The
111 – names of rigid bodies are generated automatically. For example, the
112 – name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
113 –
343   \section{\label{appendixSection:syntax}Syntax of the Select Command}
344  
345 < The most general form of the select command is: {\tt select {\it
346 < expression}}
345 > {\sc OOPSE} provides a powerful selection utility to select
346 > StuntDoubles. The most general form of the select command is:
347  
348 + {\tt select {\it expression}}.
349 +
350   This expression represents an arbitrary set of StuntDoubles (Atoms
351 < or RigidBodies) in {\sc oopse}. Expressions are composed of either
351 > or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
352   name expressions, index expressions, predefined sets, user-defined
353   expressions, comparison operators, within expressions, or logical
354   combinations of the above expression types. Expressions can be
# Line 204 | Line 435 | general form for the define command is: {\bf define {\
435   Users can define arbitrary terms to represent groups of
436   StuntDoubles, and then use the define terms in select commands. The
437   general form for the define command is: {\bf define {\it term
438 < expression}}
438 > expression}}. Once defined, the user can specify such terms in
439 > boolean expressions
440  
209 – Once defined, the user can specify such terms in boolean expressions
210 –
441   {\tt define SSDWATER SSD or SSD1 or SSDRF}
442  
443   {\tt select SSDWATER}
# Line 243 | Line 473 | atoms.
473   select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
474   atoms.
475  
246 – \section{\label{appendixSection:tools}Tools which use the selection command}
476  
477 < \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
477 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
478  
250 – Dump2XYZ can transform an OOPSE dump file into a xyz file which can
251 – be opened by other molecular dynamics viewers such as Jmol and VMD.
252 – The options available for Dump2XYZ are as follows:
253 –
254 –
255 – \begin{longtable}[c]{|EFG|}
256 – \caption{Dump2XYZ Command-line Options}
257 – \\ \hline
258 – {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
259 – \endhead
260 – \hline
261 – \endfoot
262 –  -h & {\tt -{}-help} &                        Print help and exit \\
263 –  -V & {\tt -{}-version} &                     Print version and exit \\
264 –  -i & {\tt -{}-input=filename}  &             input dump file \\
265 –  -o & {\tt -{}-output=filename} &             output file name \\
266 –  -n & {\tt -{}-frame=INT}   &                 print every n frame  (default=`1') \\
267 –  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
268 –  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
269 –  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
270 –  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
271 –  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
272 –  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
273 –     & {\tt -{}-repeatX=INT}  &                 The number of images to repeat in the x direction  (default=`0') \\
274 –     & {\tt -{}-repeatY=INT} &                 The number of images to repeat in the y direction  (default=`0') \\
275 –     &  {\tt -{}-repeatZ=INT}  &                The number of images to repeat in the z direction  (default=`0') \\
276 –  -s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
277 – converted. \\
278 –     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
279 –     & {\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}.
280 – \end{longtable}
281 –
282 –
479   \subsection{\label{appendixSection:StaticProps}StaticProps}
480  
481   {\tt StaticProps} can compute properties which are averaged over
482   some or all of the configurations that are contained within a dump
483   file. The most common example of a static property that can be
484   computed is the pair distribution function between atoms of type $A$
485 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
486 < used to compute the density distributions of other molecules in a
487 < reference frame {\it fixed to the body-fixed reference frame} of a
488 < selected atom or rigid body.
485 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
486 > also be used to compute the density distributions of other molecules
487 > in a reference frame {\it fixed to the body-fixed reference frame}
488 > of a selected atom or rigid body. Due to the fact that the selected
489 > StuntDoubles from two selections may be overlapped, {\tt
490 > StaticProps} performs the calculation in three stages which are
491 > illustrated in Fig.~\ref{oopseFig:staticPropsProcess}.
492  
493 + \begin{figure}
494 + \centering
495 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
496 + \caption[A representation of the three-stage correlations in
497 + \texttt{StaticProps}]{This diagram illustrates three-stage
498 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
499 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
500 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
501 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
502 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
503 + the contrary, the third stage($C$ and $C$) are completely
504 + overlapping} \label{oopseFig:staticPropsProcess}
505 + \end{figure}
506 +
507   There are five seperate radial distribution functions availiable in
508   OOPSE. Since every radial distrbution function invlove the
509   calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
# Line 334 | Line 547 | The vectors (and angles) associated with these angular
547   \end{description}
548  
549   The vectors (and angles) associated with these angular pair
550 < distribution functions are most easily seen in the figure below:
550 > distribution functions are most easily seen in
551 > Fig.~\ref{oopseFig:gofr}
552  
553   \begin{figure}
554   \centering
# Line 355 | Line 569 | The options available for {\tt StaticProps} are as fol
569   \endfoot
570    -h& {\tt -{}-help}                    &  Print help and exit \\
571    -V& {\tt -{}-version}                 &  Print version and exit \\
572 <  -i& {\tt -{}-input=filename}          &  input dump file \\
573 <  -o& {\tt -{}-output=filename}         &  output file name \\
574 <  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
575 <  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
576 <  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
577 <  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
578 <    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
579 <    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
580 <    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
581 <    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
582 <    & {\tt -{}-molname=STRING}           & molecule name \\
583 <    & {\tt -{}-begin=INT}                & begin internal index \\
584 <    & {\tt -{}-end=INT}                  & end internal index \\
572 >  -i& {\tt -{}-input}          &  input dump file \\
573 >  -o& {\tt -{}-output}         &  output file name \\
574 >  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
575 >  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
576 >  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
577 >  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
578 >    & {\tt -{}-sele1}   & select the first StuntDouble set \\
579 >    & {\tt -{}-sele2}   & select the second StuntDouble set \\
580 >    & {\tt -{}-sele3}   & select the third StuntDouble set \\
581 >    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
582 >    & {\tt -{}-molname}           & molecule name \\
583 >    & {\tt -{}-begin}                & begin internal index \\
584 >    & {\tt -{}-end}                  & end internal index \\
585   \hline
586   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
587   \hline
# Line 406 | Line 620 | select different types of atoms is already present in
620   different vectors).  The ability to use two selection scripts to
621   select different types of atoms is already present in the code.
622  
623 + For large simulations, the trajectory files can sometimes reach
624 + sizes in excess of several gigabytes. In order to prevent a
625 + situation where the program runs out of memory due to large
626 + trajectories, \texttt{dynamicProps} will estimate the size of free
627 + memory at first, and determine the number of frames in each block,
628 + which allows the operating system to load two blocks of data
629 + simultaneously without swapping. Upon reading two blocks of the
630 + trajectory, \texttt{dynamicProps} will calculate the time
631 + correlation within the first block and the cross correlations
632 + between the two blocks. This second block is then freed and then
633 + incremented and the process repeated until the end of the
634 + trajectory. Once the end is reached, the first block is freed then
635 + incremented, until all frame pairs have been correlated in time.
636 + This process is illustrated in
637 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
638 +
639 + \begin{figure}
640 + \centering
641 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
642 + \caption[A representation of the block correlations in
643 + \texttt{dynamicProps}]{This diagram illustrates block correlations
644 + processing in \texttt{dynamicProps}. The shaded region represents
645 + the self correlation of the block, and the open blocks are read one
646 + at a time and the cross correlations between blocks are calculated.}
647 + \label{oopseFig:dynamicPropsProcess}
648 + \end{figure}
649 +
650   The options available for DynamicProps are as follows:
651   \begin{longtable}[c]{|EFG|}
652   \caption{DynamicProps Command-line Options}
# Line 416 | Line 657 | The options available for DynamicProps are as follows:
657   \endfoot
658    -h& {\tt -{}-help}                   & Print help and exit \\
659    -V& {\tt -{}-version}                & Print version and exit \\
660 <  -i& {\tt -{}-input=filename}         & input dump file \\
661 <  -o& {\tt -{}-output=filename}        & output file name \\
662 <    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
663 <    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
660 >  -i& {\tt -{}-input}         & input dump file \\
661 >  -o& {\tt -{}-output}        & output file name \\
662 >    & {\tt -{}-sele1} & select first StuntDouble set \\
663 >    & {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
664   \hline
665   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
666   \hline
# Line 428 | Line 669 | The options available for DynamicProps are as follows:
669    -d& {\tt -{}-dcorr}                  & compute dipole correlation function
670   \end{longtable}
671  
672 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
672 > \section{\label{appendixSection:tools}Other Useful Utilities}
673 >
674 > \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
675 >
676 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
677 > which can be opened by other molecular dynamics viewers such as Jmol
678 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
679 > as follows:
680 >
681 >
682 > \begin{longtable}[c]{|EFG|}
683 > \caption{Dump2XYZ Command-line Options}
684 > \\ \hline
685 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
686 > \endhead
687 > \hline
688 > \endfoot
689 >  -h & {\tt -{}-help} &                        Print help and exit \\
690 >  -V & {\tt -{}-version} &                     Print version and exit \\
691 >  -i & {\tt -{}-input}  &             input dump file \\
692 >  -o & {\tt -{}-output} &             output file name \\
693 >  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
694 >  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
695 >  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
696 >  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
697 >  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
698 >  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
699 >  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
700 >     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
701 >     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
702 >     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
703 >  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
704 > converted. \\
705 >     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
706 >     & {\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}.
707 > \end{longtable}
708 >
709 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
710 >
711 > {\tt Hydro} can calculate resistance and diffusion tensors at the
712 > center of resistance. Both tensors at the center of diffusion can
713 > also be reported from the program, as well as the coordinates for
714 > the beads which are used to approximate the arbitrary shapes. The
715 > options available for Hydro are as follows:
716 > \begin{longtable}[c]{|EFG|}
717 > \caption{Hydrodynamics Command-line Options}
718 > \\ \hline
719 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
720 > \endhead
721 > \hline
722 > \endfoot
723 >  -h & {\tt -{}-help} &                        Print help and exit \\
724 >  -V & {\tt -{}-version} &                     Print version and exit \\
725 >  -i & {\tt -{}-input}  &             input dump file \\
726 >  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
727 >  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
728 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
729 > \end{longtable}

Diff Legend

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