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1 < \chapter{\label{chapt:appendix}APPENDIX}
1 > \appendix
2 > \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
3  
4 < Designing object-oriented software is hard, and designing reusable
5 < object-oriented scientific software is even harder. Absence of
6 < applying modern software development practices is the bottleneck of
7 < Scientific Computing community\cite{wilson}. For instance, in the
8 < last 20 years , there are quite a few MD packages that were
9 < developed to solve common MD problems and perform robust simulations
10 < . However, many of the codes are legacy programs that are either
11 < poorly organized or extremely complex. Usually, these packages were
12 < contributed by scientists without official computer science
13 < training. The development of most MD applications are lack of strong
14 < coordination to enforce design and programming guidelines. Moreover,
15 < most MD programs also suffer from missing design and implement
16 < documents which is crucial to the maintenance and extensibility.
4 > Absence of applying modern software development practices is the
5 > bottleneck of Scientific Computing community\cite{Wilson2006}. In
6 > the last 20 years , there are quite a few MD
7 > packages\cite{Brooks1983, Vincent1995, Kale1999} that were developed
8 > to solve common MD problems and perform robust simulations .
9 > Unfortunately, most of them are commercial programs that are either
10 > poorly written or extremely complicate. Consequently, it prevents
11 > the researchers to reuse or extend those packages to do cutting-edge
12 > research effectively. Along the way of studying structural and
13 > dynamic processes in condensed phase systems like biological
14 > membranes and nanoparticles, we developed an open source
15 > Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new
16 > molecular dynamics package has some unique features
17 > \begin{enumerate}
18 >  \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
19 > atom types (transition metals, point dipoles, sticky potentials,
20 > Gay-Berne ellipsoids, or other "lumpy"atoms with orientational
21 > degrees of freedom), as well as rigid bodies.
22 >  \item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap
23 > Beowulf clusters to obtain very efficient parallelism.
24 >  \item {\sc OOPSE} integrates the equations of motion using advanced methods for
25 > orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T
26 > ensembles.
27 >  \item {\sc OOPSE} can carry out simulations on metallic systems using the
28 > Embedded Atom Method (EAM) as well as the Sutton-Chen potential.
29 >  \item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals.
30 >  \item  {\sc OOPSE} can simulate systems containing the extremely efficient
31 > extended-Soft Sticky Dipole (SSD/E) model for water.
32 > \end{enumerate}
33  
34 + \section{\label{appendixSection:architecture }Architecture}
35 +
36 + Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
37 + uses C++ Standard Template Library (STL) and fortran modules as the
38 + foundation. As an extensive set of the STL and Fortran90 modules,
39 + {\sc Base Classes} provide generic implementations of mathematical
40 + objects (e.g., matrices, vectors, polynomials, random number
41 + generators) and advanced data structures and algorithms(e.g., tuple,
42 + bitset, generic data, string manipulation). The molecular data
43 + structures for the representation of atoms, bonds, bends, torsions,
44 + rigid bodies and molecules \textit{etc} are contained in the {\sc
45 + Kernel} which is implemented with {\sc Base Classes} and are
46 + carefully designed to provide maximum extensibility and flexibility.
47 + The functionality required for applications is provide by the third
48 + layer which contains Input/Output, Molecular Mechanics and Structure
49 + modules. Input/Output module not only implements general methods for
50 + file handling, but also defines a generic force field interface.
51 + Another important component of Input/Output module is the meta-data
52 + file parser, which is rewritten using ANother Tool for Language
53 + Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
54 + Mechanics module consists of energy minimization and a wide
55 + varieties of integration methods(see Chap.~\ref{chapt:methodology}).
56 + The structure module contains a flexible and powerful selection
57 + library which syntax is elaborated in
58 + Sec.~\ref{appendixSection:syntax}. The top layer is made of the main
59 + program of the package, \texttt{oopse} and it corresponding parallel
60 + version \texttt{oopse\_MPI}, as well as other useful utilities, such
61 + as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}),
62 + \texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}),
63 + \texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}),
64 + \texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics})
65 + \textit{etc}.
66 +
67 + \begin{figure}
68 + \centering
69 + \includegraphics[width=\linewidth]{architecture.eps}
70 + \caption[The architecture of {\sc OOPSE}] {Overview of the structure
71 + of {\sc OOPSE}} \label{appendixFig:architecture}
72 + \end{figure}
73 +
74   \section{\label{appendixSection:desginPattern}Design Pattern}
75  
76   Design patterns are optimal solutions to commonly-occurring problems
77   in software design. Although originated as an architectural concept
78 < for buildings and towns by Christopher Alexander \cite{alexander},
79 < software patterns first became popular with the wide acceptance of
80 < the book, Design Patterns: Elements of Reusable Object-Oriented
81 < Software \cite{gamma94}. Patterns reflect the experience, knowledge
82 < and insights of developers who have successfully used these patterns
83 < in their own work. Patterns are reusable. They provide a ready-made
84 < solution that can be adapted to different problems as necessary.
85 < Pattern are expressive. they provide a common vocabulary of
86 < solutions that can express large solutions succinctly.
78 > for buildings and towns by Christopher Alexander
79 > \cite{Alexander1987}, software patterns first became popular with
80 > the wide acceptance of the book, Design Patterns: Elements of
81 > Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect
82 > the experience, knowledge and insights of developers who have
83 > successfully used these patterns in their own work. Patterns are
84 > reusable. They provide a ready-made solution that can be adapted to
85 > different problems as necessary. Pattern are expressive. they
86 > provide a common vocabulary of solutions that can express large
87 > solutions succinctly. 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
32 < following information:
33 < \begin{enumerate}
34 <  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
35 <  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
36 <  in the literature. In this case it is common practice to document these nicknames or synonyms under
37 <  the heading of \emph{Aliases} or \emph{Also Known As}.
38 <  \item The \emph{motivation} or \emph{context} that this pattern applies
39 <  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
40 <  \item The \emph{solution} to the problem that the pattern
41 <  addresses. It describes how to construct the necessary work products. The description may include
42 <  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
43 <  collaborations, to show how the problem is solved.
44 <  \item The \emph{consequences} of using the given solution to solve a
45 <  problem, both positive and negative.
46 < \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}
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.
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 + \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}
68 – The purpose of the Visitor Pattern is to encapsulate an operation
69 – that you want to perform on the elements of a data structure. In
70 – this way, you can change the operation being performed on a
71 – structure without the need of changing the classes of the elements
72 – that you are operating on.
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 < \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 < \section{\label{appendixSection:hierarchy}Hierarchy}
239 > \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
240  
241 < \subsection{\label{appendixSection:selectionSyntax}Selection Syntax}
241 > class StuntDouble { public:
242 >  virtual void accept(BaseVisitor* v) = 0;
243 > };
244  
245 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
245 > class Atom: public StuntDouble { public:
246 >  virtual void accept{BaseVisitor* v*} {
247 >    v->visit(this);
248 >  }
249 > };
250  
251 < \subsection{\label{appendixSection:staticProps}Static Properties}
251 > class DirectionalAtom: public Atom { public:
252 >  virtual void accept{BaseVisitor* v*} {
253 >    v->visit(this);
254 >  }
255 > };
256  
257 < \subsection{\label{appendixSection:dynamicProps}Dynamics Properties}
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.
344 > \item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
345 > \item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
346 > \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
347 > DirectionalAtom}s which behaves as a single unit.
348 > \end{itemize}
349 >
350 > \section{\label{appendixSection:syntax}Syntax of the Select Command}
351 >
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
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
362 > combined using parentheses and the Boolean operators.
363 >
364 > \subsection{\label{appendixSection:logical}Logical expressions}
365 >
366 > The logical operators allow complex queries to be constructed out of
367 > simpler ones using the standard boolean connectives {\bf and}, {\bf
368 > or}, {\bf not}. Parentheses can be used to alter the precedence of
369 > the operators.
370 >
371 > \begin{center}
372 > \begin{tabular}{|ll|}
373 > \hline
374 > {\bf logical operator} & {\bf equivalent operator}  \\
375 > \hline
376 > and & ``\&'', ``\&\&'' \\
377 > or & ``$|$'', ``$||$'', ``,'' \\
378 > not & ``!''  \\
379 > \hline
380 > \end{tabular}
381 > \end{center}
382 >
383 > \subsection{\label{appendixSection:name}Name expressions}
384 >
385 > \begin{center}
386 > \begin{tabular}{|llp{2in}|}
387 > \hline {\bf type of expression} & {\bf examples} & {\bf translation
388 > of
389 > examples} \\
390 > \hline expression without ``.'' & select DMPC & select all
391 > StuntDoubles
392 > belonging to all DMPC molecules \\
393 > & select C* & select all atoms which have atom types beginning with C
394 > \\
395 > & select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but
396 > only select the rigid bodies, and not the atoms belonging to them). \\
397 > \hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the
398 > O\_TIP3P
399 > atoms belonging to TIP3P molecules \\
400 > & select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to
401 > the first
402 > RigidBody in each DMPC molecule \\
403 > & select DMPC.20 & select the twentieth StuntDouble in each DMPC
404 > molecule \\
405 > \hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* &
406 > select all atoms
407 > belonging to all rigid bodies within all DMPC molecules \\
408 > \hline
409 > \end{tabular}
410 > \end{center}
411 >
412 > \subsection{\label{appendixSection:index}Index expressions}
413 >
414 > \begin{center}
415 > \begin{tabular}{|lp{4in}|}
416 > \hline
417 > {\bf examples} & {\bf translation of examples} \\
418 > \hline
419 > select 20 & select all of the StuntDoubles belonging to Molecule 20 \\
420 > select 20 to 30 & select all of the StuntDoubles belonging to
421 > molecules which have global indices between 20 (inclusive) and 30
422 > (exclusive) \\
423 > \hline
424 > \end{tabular}
425 > \end{center}
426 >
427 > \subsection{\label{appendixSection:predefined}Predefined sets}
428 >
429 > \begin{center}
430 > \begin{tabular}{|ll|}
431 > \hline
432 > {\bf keyword} & {\bf description} \\
433 > \hline
434 > all & select all StuntDoubles \\
435 > none & select none of the StuntDoubles \\
436 > \hline
437 > \end{tabular}
438 > \end{center}
439 >
440 > \subsection{\label{appendixSection:userdefined}User-defined expressions}
441 >
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}}. Once defined, the user can specify such terms in
446 > boolean expressions
447 >
448 > {\tt define SSDWATER SSD or SSD1 or SSDRF}
449 >
450 > {\tt select SSDWATER}
451 >
452 > \subsection{\label{appendixSection:comparison}Comparison expressions}
453 >
454 > StuntDoubles can be selected by using comparision operators on their
455 > properties. The general form for the comparison command is: a
456 > property name, followed by a comparision operator and then a number.
457 >
458 > \begin{center}
459 > \begin{tabular}{|l|l|}
460 > \hline
461 > {\bf property} & mass, charge \\
462 > {\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'',
463 > ``$<=$'', ``$!=$'' \\
464 > \hline
465 > \end{tabular}
466 > \end{center}
467 >
468 > For example, the phrase {\tt select mass > 16.0 and charge < -2}
469 > would select StuntDoubles which have mass greater than 16.0 and
470 > charges less than -2.
471 >
472 > \subsection{\label{appendixSection:within}Within expressions}
473 >
474 > The ``within'' keyword allows the user to select all StuntDoubles
475 > within the specified distance (in Angstroms) from a selection,
476 > including the selected atom itself. The general form for within
477 > selection is: {\tt select within(distance, expression)}
478 >
479 > For example, the phrase {\tt select within(2.5, PO4 or NC4)} would
480 > select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
481 > atoms.
482 >
483 >
484 > \section{\label{appendixSection:analysisFramework}Analysis Framework}
485 >
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 $B$, $g_{AB}(r)$.  {\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
517 > -{}-sele2} must be specified to tell StaticProps which bodies to
518 > include in the calculation.
519 >
520 > \begin{description}
521 > \item[{\tt -{}-gofr}] Computes the pair distribution function,
522 > \begin{equation*}
523 > g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A}
524 > \sum_{j \in B} \delta(r - r_{ij}) \rangle
525 > \end{equation*}
526 > \item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution
527 > function. The angle is defined by the intermolecular vector
528 > $\vec{r}$ and $z$-axis of DirectionalAtom A,
529 > \begin{equation*}
530 > g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle
531 > \sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos
532 > \theta_{ij} - \cos \theta)\rangle
533 > \end{equation*}
534 > \item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution
535 > function. The angle is defined by the $z$-axes of the two
536 > DirectionalAtoms A and B.
537 > \begin{equation*}
538 > g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle
539 > \sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos
540 > \omega_{ij} - \cos \omega)\rangle
541 > \end{equation*}
542 > \item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular
543 > space $\theta, \omega$ defined by the two angles mentioned above.
544 > \begin{equation*}
545 > g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A}
546 > \langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos
547 > \theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos
548 > \omega)\rangle
549 > \end{equation*}
550 > \item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type
551 > B in the body frame of particle A. Therefore, {\tt -{}-originsele}
552 > and {\tt -{}-refsele} must be given to define A's internal
553 > coordinate set as the reference frame for the calculation.
554 > \end{description}
555 >
556 > The vectors (and angles) associated with these angular pair
557 > distribution functions are most easily seen in
558 > Fig.~\ref{oopseFig:gofr}
559 >
560 > \begin{figure}
561 > \centering
562 > \includegraphics[width=3in]{definition.eps}
563 > \caption[Definitions of the angles between directional objects]{ \\
564 > Any two directional objects (DirectionalAtoms and RigidBodies) have
565 > a set of two angles ($\theta$, and $\omega$) between the z-axes of
566 > their body-fixed frames.} \label{oopseFig:gofr}
567 > \end{figure}
568 >
569 > The options available for {\tt StaticProps} are as follows:
570 > \begin{longtable}[c]{|EFG|}
571 > \caption{StaticProps Command-line Options}
572 > \\ \hline
573 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
574 > \endhead
575 > \hline
576 > \endfoot
577 >  -h& {\tt -{}-help}                    &  Print help and exit \\
578 >  -V& {\tt -{}-version}                 &  Print version and exit \\
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
595 >    &  {\tt -{}-gofr}                    &  $g(r)$ \\
596 >    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
597 >    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
598 >    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
599 >    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
600 >    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
601 >    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
602 >    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
603 >    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
604 > \end{longtable}
605 >
606 > \subsection{\label{appendixSection:DynamicProps}DynamicProps}
607 >
608 > {\tt DynamicProps} computes time correlation functions from the
609 > configurations stored in a dump file.  Typical examples of time
610 > correlation functions are the mean square displacement and the
611 > velocity autocorrelation functions.   Once again, the selection
612 > syntax can be used to specify the StuntDoubles that will be used for
613 > the calculation.  A general time correlation function can be thought
614 > of as:
615 > \begin{equation}
616 > C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle
617 > \end{equation}
618 > where $\vec{u}_A(t)$ is a vector property associated with an atom of
619 > type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different
620 > vector property associated with an atom of type $B$ at a different
621 > time $t^{\prime}$.  In most autocorrelation functions, the vector
622 > properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and
623 > $B$) are identical, and the three calculations built in to {\tt
624 > DynamicProps} make these assumptions.  It is possible, however, to
625 > make simple modifications to the {\tt DynamicProps} code to allow
626 > the use of {\it cross} time correlation functions (i.e. with
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}
660 > \\ \hline
661 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
662 > \endhead
663 > \hline
664 > \endfoot
665 >  -h& {\tt -{}-help}                   & Print help and exit \\
666 >  -V& {\tt -{}-version}                & Print version and exit \\
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
674 >  -r& {\tt -{}-rcorr}                  & compute mean square displacement \\
675 >  -v& {\tt -{}-vcorr}                  & compute velocity correlation function \\
676 >  -d& {\tt -{}-dcorr}                  & compute dipole correlation function
677 > \end{longtable}
678 >
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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