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1   \appendix
2 < \chapter{\label{chapt:appendix}APPENDIX}
2 > \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
3  
4 < Designing object-oriented software is hard, and designing reusable
5 < object-oriented scientific software is even harder. Absence of
6 < applying modern software development practices is the bottleneck of
7 < Scientific Computing community\cite{wilson}. For instance, in the
8 < last 20 years , there are quite a few MD packages that were
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. 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
33 < following information:
34 < \begin{enumerate}
35 <  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
36 <  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
37 <  in the literature. In this case it is common practice to document these nicknames or synonyms under
38 <  the heading of \emph{Aliases} or \emph{Also Known As}.
39 <  \item The \emph{motivation} or \emph{context} that this pattern applies
40 <  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
41 <  \item The \emph{solution} to the problem that the pattern
42 <  addresses. It describes how to construct the necessary work products. The description may include
43 <  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
44 <  collaborations, to show how the problem is solved.
45 <  \item The \emph{consequences} of using the given solution to solve a
46 <  problem, both positive and negative.
47 < \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 > List.~\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}
60 – The Factory Method pattern is a creational pattern which deals with
61 – the problem of creating objects without specifying the exact class
62 – of object that will be created. Factory Method solves this problem
63 – by defining a separate method for creating the objects, which
64 – subclasses can then override to specify the derived type of product
65 – that will be created.
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 List.~\ref{appendixScheme:factoryDeclaration}). If
153 + the identifier has been already registered, the factory method will
154 + invoke the corresponding creator (see
155 + List.~\ref{appendixScheme:integratorCreator}) which utilizes the
156 + modern C++ template technique to avoid excess subclassing.
157  
158 < \subsection{\label{appendixSection:visitorPattern}Visitor}
69 < The purpose of the Visitor Pattern is to encapsulate an operation
70 < that you want to perform on the elements of a data structure. In
71 < this way, you can change the operation being performed on a
72 < structure without the need of changing the classes of the elements
73 < that you are operating on.
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 < \subsection{\label{appendixSection:templateMethod}Template Method}
164 >  bool registerIntegrator(IntegratorCreator* creator) {
165 >    return creatorMap_.insert(creator->getIdent(), creator).second;
166 >  }
167  
168 < \section{\label{appendixSection:analysisFramework}Analysis Framework}
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 < \section{\label{appendixSection:concepts}Concepts}
177 > private:
178 >  CreatorMapType creatorMap_;
179 > };
180 > \end{lstlisting}
181  
182 < OOPSE manipulates both traditional atoms as well as some objects
83 < that {\it behave like atoms}.  These objects can be rigid
84 < collections of atoms or atoms which have orientational degrees of
85 < freedom.  Here is a diagram of the class heirarchy:
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}
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 List.~\ref{appendixScheme:element}). Since the hierarchies
219 + remains stable, it is easy to define a visit operation (see
220 + List.~\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   \begin{figure}
226   \centering
227 < \includegraphics[width=3in]{heirarchy.eps}
228 < \caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
229 < The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
92 < selection syntax allows the user to select any of the objects that
93 < are descended from a StuntDouble.} \label{oopseFig:heirarchy}
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 + \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 SSDAtomVisitor:public BaseAtomVisitor{ public:
281 +  virtual void visit(Atom* atom);
282 +  virtual void visit(DirectionalAtom* datom);
283 +  virtual void visit(RigidBody* rb);
284 + };
285 +
286 + class CompositeVisitor: public BaseVisitor {
287 + public:
288 +
289 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
290 +  typedef VistorListType::iterator VisitorListIterator;
291 +  virtual void visit(Atom* atom) {
292 +    VisitorListIterator i;
293 +    BaseVisitor* curVisitor;
294 +    for(i = visitorList.begin();i != visitorList.end();++i) {
295 +      atom->accept(*i);
296 +    }
297 +  }
298 +
299 +  virtual void visit(DirectionalAtom* datom) {
300 +    VisitorListIterator i;
301 +    BaseVisitor* curVisitor;
302 +    for(i = visitorList.begin();i != visitorList.end();++i) {
303 +      atom->accept(*i);
304 +    }
305 +  }
306 +
307 +  virtual void visit(RigidBody* rb) {
308 +    VisitorListIterator i;
309 +    std::vector<Atom*> myAtoms;
310 +    std::vector<Atom*>::iterator ai;
311 +    myAtoms = rb->getAtoms();
312 +    for(i = visitorList.begin();i != visitorList.end();++i) {{
313 +      rb->accept(*i);
314 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
315 +        (*ai)->accept(*i);
316 +    }
317 +  }
318 +
319 +  void addVisitor(BaseVisitor* v, int priority);
320 +
321 +  protected:
322 +    VistorListType visitorList;
323 + };
324 +
325 + \end{lstlisting}
326 +
327 + \section{\label{appendixSection:concepts}Concepts}
328 +
329 + OOPSE manipulates both traditional atoms as well as some objects
330 + that {\it behave like atoms}.  These objects can be rigid
331 + collections of atoms or atoms which have orientational degrees of
332 + freedom.  A diagram of the class hierarchy is illustrated in
333 + Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
334 + DirectionalAtom in {\sc OOPSE} have their own names which are
335 + specified in the {\tt .md} file. In contrast, RigidBodies are
336 + denoted by their membership and index inside a particular molecule:
337 + [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
338 + on the specifics of the simulation). The names of rigid bodies are
339 + generated automatically. For example, the name of the first rigid
340 + body in a DMPC molecule is DMPC\_RB\_0.
341   \begin{itemize}
342   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
343   integrators and minimizers.
# Line 102 | Line 347 | Every Molecule, Atom and DirectionalAtom in {\sc oopse
347   DirectionalAtom}s which behaves as a single unit.
348   \end{itemize}
349  
105 – Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
106 – own names which are specified in the {\tt .md} file. In contrast,
107 – RigidBodies are denoted by their membership and index inside a
108 – particular molecule: [MoleculeName]\_RB\_[index] (the contents
109 – inside the brackets depend on the specifics of the simulation). The
110 – names of rigid bodies are generated automatically. For example, the
111 – name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
112 –
350   \section{\label{appendixSection:syntax}Syntax of the Select Command}
351  
352 < The most general form of the select command is: {\tt select {\it
353 < expression}}
352 > {\sc OOPSE} provides a powerful selection utility to select
353 > StuntDoubles. The most general form of the select command is:
354  
355 + {\tt select {\it expression}}.
356 +
357   This expression represents an arbitrary set of StuntDoubles (Atoms
358 < or RigidBodies) in {\sc oopse}. Expressions are composed of either
358 > or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
359   name expressions, index expressions, predefined sets, user-defined
360   expressions, comparison operators, within expressions, or logical
361   combinations of the above expression types. Expressions can be
# Line 203 | Line 442 | expression}}
442   Users can define arbitrary terms to represent groups of
443   StuntDoubles, and then use the define terms in select commands. The
444   general form for the define command is: {\bf define {\it term
445 < expression}}
445 > expression}}. Once defined, the user can specify such terms in
446 > boolean expressions
447  
208 – Once defined, the user can specify such terms in boolean expressions
209 –
448   {\tt define SSDWATER SSD or SSD1 or SSDRF}
449  
450   {\tt select SSDWATER}
# Line 242 | Line 480 | atoms.
480   select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
481   atoms.
482  
245 – \section{\label{appendixSection:tools}Tools which use the selection command}
483  
484 < \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
484 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
485  
249 – Dump2XYZ can transform an OOPSE dump file into a xyz file which can
250 – be opened by other molecular dynamics viewers such as Jmol and VMD.
251 – The options available for Dump2XYZ are as follows:
252 –
253 –
254 – \begin{longtable}[c]{|EFG|}
255 – \caption{Dump2XYZ Command-line Options}
256 – \\ \hline
257 – {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
258 – \endhead
259 – \hline
260 – \endfoot
261 –  -h & {\tt -{}-help} &                        Print help and exit \\
262 –  -V & {\tt -{}-version} &                     Print version and exit \\
263 –  -i & {\tt -{}-input=filename}  &             input dump file \\
264 –  -o & {\tt -{}-output=filename} &             output file name \\
265 –  -n & {\tt -{}-frame=INT}   &                 print every n frame  (default=`1') \\
266 –  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
267 –  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
268 –  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
269 –  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
270 –  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
271 –  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
272 –     & {\tt -{}-repeatX=INT}  &                 The number of images to repeat in the x direction  (default=`0') \\
273 –     & {\tt -{}-repeatY=INT} &                 The number of images to repeat in the y direction  (default=`0') \\
274 –     &  {\tt -{}-repeatZ=INT}  &                The number of images to repeat in the z direction  (default=`0') \\
275 –  -s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
276 – converted. \\
277 –     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
278 –     & {\tt -{}-refsele} &  In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}.
279 – \end{longtable}
280 –
281 –
486   \subsection{\label{appendixSection:StaticProps}StaticProps}
487  
488   {\tt StaticProps} can compute properties which are averaged over
489   some or all of the configurations that are contained within a dump
490   file. The most common example of a static property that can be
491   computed is the pair distribution function between atoms of type $A$
492 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
493 < used to compute the density distributions of other molecules in a
494 < reference frame {\it fixed to the body-fixed reference frame} of a
495 < selected atom or rigid body.
492 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
493 > also be used to compute the density distributions of other molecules
494 > in a reference frame {\it fixed to the body-fixed reference frame}
495 > of a selected atom or rigid body. Due to the fact that the selected
496 > StuntDoubles from two selections may be overlapped, {\tt
497 > StaticProps} performs the calculation in three stages which are
498 > illustrated in Fig.~\ref{oopseFig:staticPropsProcess}.
499  
500 + \begin{figure}
501 + \centering
502 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
503 + \caption[A representation of the three-stage correlations in
504 + \texttt{StaticProps}]{This diagram illustrates three-stage
505 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
506 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
507 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
508 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
509 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
510 + the contrary, the third stage($C$ and $C$) are completely
511 + overlapping} \label{oopseFig:staticPropsProcess}
512 + \end{figure}
513 +
514   There are five seperate radial distribution functions availiable in
515   OOPSE. Since every radial distrbution function invlove the
516   calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
# Line 333 | Line 554 | distribution functions are most easily seen in the fig
554   \end{description}
555  
556   The vectors (and angles) associated with these angular pair
557 < distribution functions are most easily seen in the figure below:
557 > distribution functions are most easily seen in
558 > Fig.~\ref{oopseFig:gofr}
559  
560   \begin{figure}
561   \centering
# Line 354 | Line 576 | The options available for {\tt StaticProps} are as fol
576   \endfoot
577    -h& {\tt -{}-help}                    &  Print help and exit \\
578    -V& {\tt -{}-version}                 &  Print version and exit \\
579 <  -i& {\tt -{}-input=filename}          &  input dump file \\
580 <  -o& {\tt -{}-output=filename}         &  output file name \\
581 <  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
582 <  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
583 <  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
584 <  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
585 <    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
586 <    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
587 <    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
588 <    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
589 <    & {\tt -{}-molname=STRING}           & molecule name \\
590 <    & {\tt -{}-begin=INT}                & begin internal index \\
591 <    & {\tt -{}-end=INT}                  & end internal index \\
579 >  -i& {\tt -{}-input}          &  input dump file \\
580 >  -o& {\tt -{}-output}         &  output file name \\
581 >  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
582 >  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
583 >  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
584 >  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
585 >    & {\tt -{}-sele1}   & select the first StuntDouble set \\
586 >    & {\tt -{}-sele2}   & select the second StuntDouble set \\
587 >    & {\tt -{}-sele3}   & select the third StuntDouble set \\
588 >    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
589 >    & {\tt -{}-molname}           & molecule name \\
590 >    & {\tt -{}-begin}                & begin internal index \\
591 >    & {\tt -{}-end}                  & end internal index \\
592   \hline
593   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
594   \hline
# Line 405 | Line 627 | The options available for DynamicProps are as follows:
627   different vectors).  The ability to use two selection scripts to
628   select different types of atoms is already present in the code.
629  
630 + For large simulations, the trajectory files can sometimes reach
631 + sizes in excess of several gigabytes. In order to prevent a
632 + situation where the program runs out of memory due to large
633 + trajectories, \texttt{dynamicProps} will estimate the size of free
634 + memory at first, and determine the number of frames in each block,
635 + which allows the operating system to load two blocks of data
636 + simultaneously without swapping. Upon reading two blocks of the
637 + trajectory, \texttt{dynamicProps} will calculate the time
638 + correlation within the first block and the cross correlations
639 + between the two blocks. This second block is then freed and then
640 + incremented and the process repeated until the end of the
641 + trajectory. Once the end is reached, the first block is freed then
642 + incremented, until all frame pairs have been correlated in time.
643 + This process is illustrated in
644 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
645 +
646 + \begin{figure}
647 + \centering
648 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
649 + \caption[A representation of the block correlations in
650 + \texttt{dynamicProps}]{This diagram illustrates block correlations
651 + processing in \texttt{dynamicProps}. The shaded region represents
652 + the self correlation of the block, and the open blocks are read one
653 + at a time and the cross correlations between blocks are calculated.}
654 + \label{oopseFig:dynamicPropsProcess}
655 + \end{figure}
656 +
657   The options available for DynamicProps are as follows:
658   \begin{longtable}[c]{|EFG|}
659   \caption{DynamicProps Command-line Options}
# Line 415 | Line 664 | The options available for DynamicProps are as follows:
664   \endfoot
665    -h& {\tt -{}-help}                   & Print help and exit \\
666    -V& {\tt -{}-version}                & Print version and exit \\
667 <  -i& {\tt -{}-input=filename}         & input dump file \\
668 <  -o& {\tt -{}-output=filename}        & output file name \\
669 <    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
670 <    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
667 >  -i& {\tt -{}-input}         & input dump file \\
668 >  -o& {\tt -{}-output}        & output file name \\
669 >    & {\tt -{}-sele1} & select first StuntDouble set \\
670 >    & {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
671   \hline
672   \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
673   \hline
# Line 427 | Line 676 | The options available for DynamicProps are as follows:
676    -d& {\tt -{}-dcorr}                  & compute dipole correlation function
677   \end{longtable}
678  
679 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
679 > \section{\label{appendixSection:tools}Other Useful Utilities}
680 >
681 > \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
682 >
683 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
684 > which can be opened by other molecular dynamics viewers such as Jmol
685 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
686 > as follows:
687 >
688 >
689 > \begin{longtable}[c]{|EFG|}
690 > \caption{Dump2XYZ Command-line Options}
691 > \\ \hline
692 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
693 > \endhead
694 > \hline
695 > \endfoot
696 >  -h & {\tt -{}-help} &                        Print help and exit \\
697 >  -V & {\tt -{}-version} &                     Print version and exit \\
698 >  -i & {\tt -{}-input}  &             input dump file \\
699 >  -o & {\tt -{}-output} &             output file name \\
700 >  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
701 >  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
702 >  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
703 >  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
704 >  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
705 >  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
706 >  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
707 >     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
708 >     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
709 >     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
710 >  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
711 > converted. \\
712 >     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
713 >     & {\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}.
714 > \end{longtable}
715 >
716 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
717 >
718 > {\tt Hydro} can calculate resistance and diffusion tensors at the
719 > center of resistance. Both tensors at the center of diffusion can
720 > also be reported from the program, as well as the coordinates for
721 > the beads which are used to approximate the arbitrary shapes. The
722 > options available for Hydro are as follows:
723 > \begin{longtable}[c]{|EFG|}
724 > \caption{Hydrodynamics Command-line Options}
725 > \\ \hline
726 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
727 > \endhead
728 > \hline
729 > \endfoot
730 >  -h & {\tt -{}-help} &                        Print help and exit \\
731 >  -V & {\tt -{}-version} &                     Print version and exit \\
732 >  -i & {\tt -{}-input}  &             input dump file \\
733 >  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
734 >  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
735 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
736 > \end{longtable}

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