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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{Wilson2006}. For instance, in
8 < the last 20 years , there are quite a few MD packages that were
4 > The absence of modern software development practices has been a
5 > bottleneck limiting progress in the Scientific Computing
6 > community. In the last 20 years, a large number of
7 > MD packages\cite{Brooks1983, Vincent1995, Kale1999} were
8   developed to solve common MD problems and perform robust simulations
9 < . However, many of the codes are legacy programs that are either
10 < poorly organized or extremely complex. Usually, these packages were
11 < contributed by scientists without official computer science
12 < training. The development of most MD applications are lack of strong
13 < coordination to enforce design and programming guidelines. Moreover,
14 < most MD programs also suffer from missing design and implement
15 < documents which is crucial to the maintenance and extensibility.
16 < Along the way of studying structural and dynamic processes in
18 < condensed phase systems like biological membranes and nanoparticles,
19 < we developed and maintained an Object-Oriented Parallel Simulation
20 < Engine ({\sc OOPSE}). This new molecular dynamics package has some
21 < unique features
9 > . Most of these are commercial programs that are either poorly
10 > written or extremely complicated to use correctly. This situation
11 > prevents researchers from reusing or extending those packages to do
12 > cutting-edge research effectively. In the process of studying
13 > structural and dynamic processes in condensed phase systems like
14 > biological 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
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.
# Line 38 | Line 33 | extended-Soft Sticky Dipole (SSD/E) model for water.
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
63 < Sec.~\ref{appendixSection:appendixSection:DynamicProps}),
64 < \texttt{Dump2XYZ} (see
65 < Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro}
71 < (see Sec.~\ref{appendixSection:appendixSection:hydrodynamics})
72 < \textit{etc}.
36 > Mainly written by C++ and Fortran90, {\sc OOPSE} uses C++ Standard
37 > Template Library (STL) and fortran modules as a foundation. As an
38 > extensive set of the STL and Fortran90 modules, the {\sc Base
39 > Classes} provide generic implementations of mathematical objects
40 > (e.g., matrices, vectors, polynomials, random number generators) and
41 > advanced data structures and algorithms (e.g., tuple, bitset, generic
42 > data and string manipulation). The molecular data structures for the
43 > representation of atoms, bonds, bends, torsions, rigid bodies and
44 > molecules are contained in the {\sc Kernel} which is
45 > implemented with {\sc Base Classes} and are carefully designed to
46 > provide maximum extensibility and flexibility. The functionality
47 > required for applications is provided by the third layer which
48 > contains Input/Output, Molecular Mechanics and Structure modules.
49 > The Input/Output module not only implements general methods for file
50 > handling, but also defines a generic force field interface. Another
51 > important component of Input/Output module is the parser for
52 > meta-data files, which has been implemented using the ANother Tool
53 > for Language Recognition (ANTLR)\cite{Parr1995, Schaps1999} syntax.
54 > The Molecular Mechanics module consists of energy minimization and a
55 > wide variety of integration methods(see
56 > Chapter.~\ref{chapt:methodology}). The structure module contains a
57 > flexible and powerful selection library which syntax is elaborated
58 > in Sec.~\ref{appendixSection:syntax}. The top layer is made of the
59 > main program of the package, \texttt{oopse} and it corresponding
60 > parallel version \texttt{oopse\_MPI}, as well as other useful
61 > utilities, such as \texttt{StaticProps} (see
62 > Sec.~\ref{appendixSection:StaticProps}), \texttt{DynamicProps} (see
63 > Sec.~\ref{appendixSection:DynamicProps}), \texttt{Dump2XYZ} (see
64 > Sec.~\ref{appendixSection:Dump2XYZ}), \texttt{Hydro} (see
65 > Sec.~\ref{appendixSection:hydrodynamics}).
66  
67   \begin{figure}
68   \centering
# Line 78 | Line 71 | of {\sc OOPSE}} \label{appendixFig:architecture}
71   of {\sc OOPSE}} \label{appendixFig:architecture}
72   \end{figure}
73  
74 < \section{\label{appendixSection:desginPattern}Design Pattern}
74 > \section{\label{appendixSection:desginPattern}Design Patterns}
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
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.
77 > in software design. Although they originated as an architectural
78 > concept for buildings and towns by Christopher Alexander
79 > \cite{Alexander1987}, design patterns first became popular in
80 > software engineering with the wide acceptance of the book, Design
81 > Patterns: Elements of Reusable Object-Oriented Software
82 > \cite{Gamma1994}. Patterns reflect the experience, knowledge and
83 > insights of developers who have successfully used these patterns in
84 > their own work. Patterns are reusable. They provide a ready-made
85 > solution that can be adapted to different problems as necessary. As
86 > one of the latest advanced techniques to emerge from object-oriented
87 > community, design patterns were applied in some of the modern
88 > scientific software applications, such as JMol, {\sc
89 > OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}.
90 > The following sections enumerates some of the patterns
91 > used in {\sc OOPSE}.
92  
93 < Patterns are usually described using a format that includes the
97 < following information:
98 < \begin{enumerate}
99 <  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
100 <  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
101 <  in the literature. In this case it is common practice to document these nicknames or synonyms under
102 <  the heading of \emph{Aliases} or \emph{Also Known As}.
103 <  \item The \emph{motivation} or \emph{context} that this pattern applies
104 <  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
105 <  \item The \emph{solution} to the problem that the pattern
106 <  addresses. It describes how to construct the necessary work products. The description may include
107 <  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
108 <  collaborations, to show how the problem is solved.
109 <  \item The \emph{consequences} of using the given solution to solve a
110 <  problem, both positive and negative.
111 < \end{enumerate}
93 > \subsection{\label{appendixSection:singleton}Singletons}
94  
113 – As one of the latest advanced techniques emerged from
114 – object-oriented community, design patterns were applied in some of
115 – the modern scientific software applications, such as JMol, {\sc
116 – OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}.
117 – The following sections enumerates some of the patterns used in {\sc
118 – OOPSE}.
119 –
120 – \subsection{\label{appendixSection:singleton}Singleton}
95   The Singleton pattern not only provides a mechanism to restrict
96   instantiation of a class to one object, but also provides a global
97 < point of access to the object. Currently implemented as a global
98 < variable, the logging utility which reports error and warning
99 < messages to the console in {\sc OOPSE} is a good candidate for
100 < applying the Singleton pattern to avoid the global namespace
101 < pollution.Although the singleton pattern can be implemented in
102 < various ways  to account for different aspects of the software
103 < designs, such as lifespan control \textit{etc}, we only use the
104 < static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class
105 < is declared as
106 < \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
97 > point of access to the object. Although the singleton pattern can be
98 > implemented in various ways  to account for different aspects of the
99 > software design, such as lifespan control, we only use
100 > the static data approach in {\sc OOPSE}. The declaration and
101 > implementation of IntegratorFactory class are given by declared in
102 > List.~\ref{appendixScheme:singletonDeclaration} and
103 > Scheme.~\ref{appendixScheme:singletonImplementation} respectively.
104 > Since the constructor is declared as protected, a client can not
105 > instantiate IntegratorFactory directly. Moreover, since the member
106 > function getInstance serves as the only entry of access to
107 > IntegratorFactory, this approach fulfills the basic requirement, a
108 > single instance. Another consequence of this approach is the
109 > automatic destruction since static data are destroyed upon program
110 > termination.
111  
112 + \subsection{\label{appendixSection:factoryMethod}Factory Methods}
113 +
114 + The Factory Method pattern is a creational pattern and deals with
115 + the problem of creating objects without specifying the exact class
116 + of object that will be created. Factory method is typically
117 + implemented by delegating the creation operation to the subclasses.
118 + One of the most popular Factory pattern is Parameterized Factory
119 + pattern which creates products based on their identifiers (see
120 + Scheme.~\ref{appendixScheme:factoryDeclaration}). If the identifier
121 + has been already registered, the factory method will invoke the
122 + corresponding creator (see
123 + Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the
124 + modern C++ template technique to avoid excess subclassing.
125 +
126 + \subsection{\label{appendixSection:visitorPattern}Visitor}
127 +
128 + The visitor pattern is designed to decouple the data structure and
129 + algorithms used upon them by collecting related operations from
130 + element classes into other visitor classes, which is equivalent to
131 + adding virtual functions into a set of classes without modifying
132 + their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
133 + structure of a Visitor pattern which is used extensively in {\tt
134 + Dump2XYZ}. In order to convert an OOPSE dump file, a series of
135 + distinct operations are performed on different StuntDoubles (See the
136 + class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the
137 + declaration in Scheme.~\ref{appendixScheme:element}). Since the
138 + hierarchies remain stable, it is easy to define a visit operation
139 + (see Scheme.~\ref{appendixScheme:visitor}) for each class of
140 + StuntDouble. Note that by using the Composite
141 + pattern\cite{Gamma1994}, CompositeVisitor manages a priority visitor
142 + list and handles the execution of every visitor in the priority list
143 + on different StuntDoubles.
144 +
145 + \begin{figure}
146 + \centering
147 + \includegraphics[width=\linewidth]{visitor.eps}
148 + \caption[The UML class diagram of Visitor patten] {The UML class
149 + diagram of Visitor patten.} \label{appendixFig:visitorUML}
150 + \end{figure}
151 +
152 + \begin{figure}
153 + \centering
154 + \includegraphics[width=\linewidth]{hierarchy.eps}
155 + \caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
156 + the class hierarchy. Objects below others on the diagram inherit
157 + data structures and functions from their parent classes above them.}
158 + \label{oopseFig:hierarchy}
159 + \end{figure}
160 +
161 + \begin{lstlisting}[float,basicstyle=\ttfamily,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
162 +
163   class IntegratorFactory {
164 < public:
165 <  static IntegratorFactory*
166 <  getInstance();
138 < protected:
164 >  public:
165 >  static IntegratorFactory* getInstance();
166 >  protected:
167    IntegratorFactory();
168 < private:
169 <  static IntegratorFactory* instance_;
142 < };
168 >  private:
169 >  static IntegratorFactory* instance_; };
170  
171   \end{lstlisting}
172 < The corresponding implementation is
172 >
173   \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
174  
175   IntegratorFactory::instance_ = NULL;
# Line 155 | Line 182 | IntegratorFactory* getInstance() {
182   }
183  
184   \end{lstlisting}
158 – Since constructor is declared as {\tt protected}, a client can not
159 – instantiate {\tt IntegratorFactory} directly. Moreover, since the
160 – member function {\tt getInstance} serves as the only entry of access
161 – to {\tt IntegratorFactory}, this approach fulfills the basic
162 – requirement, a single instance. Another consequence of this approach
163 – is the automatic destruction since static data are destroyed upon
164 – program termination.
185  
186 < \subsection{\label{appendixSection:factoryMethod}Factory Method}
186 > \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
187  
168 – Categoried as a creational pattern, the Factory Method pattern deals
169 – with the problem of creating objects without specifying the exact
170 – class of object that will be created. Factory Method is typically
171 – implemented by delegating the creation operation to the subclasses.
172 – {\tt Integrator} class Parameterized Factory pattern where factory
173 – method ({\tt createIntegrator} member function) creates products
174 – based on the identifier (see
175 – List.~\ref{appendixScheme:factoryDeclaration}). If the identifier
176 – has been already registered, the factory method will invoke the
177 – corresponding creator (see List.~\ref{integratorCreator}) which
178 – utilizes the modern C++ template technique to avoid subclassing.
179 – \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of {\tt IntegratorFactory} class.},label={appendixScheme:factoryDeclaration}]
180 –
188   class IntegratorFactory {
189 < public:
189 >  public:
190    typedef std::map<string, IntegratorCreator*> CreatorMapType;
191  
192 <  bool registerIntegrator(IntegratorCreator* creator) {
193 <    return creatorMap_.insert(creator->getIdent(), creator).second;
192 >  bool registerIntegrator(IntegratorCreator* creator){
193 >    return creatorMap_.insert(creator->getIdent(),creator).second;
194    }
195  
196    Integrator* createIntegrator(const string& id, SimInfo* info) {
# Line 199 | Line 206 | class IntegratorFactory { (private)
206    CreatorMapType creatorMap_;
207   };
208   \end{lstlisting}
209 +
210   \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
211  
212   class IntegratorCreator {
213 < public:
214 <    IntegratorCreator(const string& ident) : ident_(ident) {}
213 >  public:
214 >  IntegratorCreator(const string& ident) : ident_(ident) {}
215  
216 <    const string& getIdent() const { return ident_; }
216 >  const string& getIdent() const { return ident_; }
217  
218 <    virtual Integrator* create(SimInfo* info) const = 0;
218 >  virtual Integrator* create(SimInfo* info) const = 0;
219  
220 < private:
221 <    string ident_;
220 >  private:
221 >  string ident_;
222   };
223  
224 < template<class ConcreteIntegrator>
225 < class IntegratorBuilder : public IntegratorCreator {
226 < public:
224 > template<class ConcreteIntegrator> class IntegratorBuilder :
225 > public IntegratorCreator {
226 >  public:
227    IntegratorBuilder(const string& ident)
228 <                   : IntegratorCreator(ident) {}
228 >                     : IntegratorCreator(ident) {}
229    virtual  Integrator* create(SimInfo* info) const {
230      return new ConcreteIntegrator(info);
231    }
232   };
233   \end{lstlisting}
234  
227 – \subsection{\label{appendixSection:visitorPattern}Visitor}
228 –
229 – The purpose of the Visitor Pattern is to encapsulate an operation
230 – that you want to perform on the elements. The operation being
231 – performed on a structure can be switched without changing the
232 – interfaces of the elements. In other words, one can add virtual
233 – functions into a set of classes without modifying their interfaces.
234 – Fig.~\ref{appendixFig:visitorUML} demonstrates the structure of
235 – Visitor pattern which is used extensively in {\tt Dump2XYZ}. In
236 – order to convert an OOPSE dump file, a series of distinct and
237 – unrelated operations are performed on different StuntDoubles.
238 – Visitor allows one to keep related operations together by packing
239 – them into one class. {\tt BaseAtomVisitor} is a typical example of
240 – visitor in {\tt Dump2XYZ} program{see
241 – List.~\ref{appendixScheme:visitor}}. In contrast to the operations,
242 – the object structure or element classes rarely change(See
243 – Fig.~\ref{oopseFig:heirarchy} and
244 – List.~\ref{appendixScheme:element}).
245 –
246 –
247 – \begin{figure}
248 – \centering
249 – \includegraphics[width=\linewidth]{visitor.eps}
250 – \caption[The UML class diagram of Visitor patten] {The UML class
251 – diagram of Visitor patten.} \label{appendixFig:visitorUML}
252 – \end{figure}
253 –
254 – \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
255 –
256 – class BaseVisitor{
257 – public:
258 –  virtual void visit(Atom* atom);
259 –  virtual void visit(DirectionalAtom* datom);
260 –  virtual void visit(RigidBody* rb);
261 – };
262 –
263 – class BaseAtomVisitor:public BaseVisitor{ public:
264 –  virtual void visit(Atom* atom);
265 –  virtual void visit(DirectionalAtom* datom);
266 –  virtual void visit(RigidBody* rb);
267 – };
268 –
269 – \end{lstlisting}
270 –
235   \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
236  
237   class StuntDouble {
238 < public:
238 >  public:
239    virtual void accept(BaseVisitor* v) = 0;
240   };
241  
242   class Atom: public StuntDouble {
243 < public:
243 >  public:
244    virtual void accept{BaseVisitor* v*} {
245      v->visit(this);
246    }
247   };
248  
249   class DirectionalAtom: public Atom {
250 < public:
250 >  public:
251    virtual void accept{BaseVisitor* v*} {
252      v->visit(this);
253    }
254   };
255  
256   class RigidBody: public StuntDouble {
257 < public:
257 >  public:
258    virtual void accept{BaseVisitor* v*} {
259      v->visit(this);
260    }
# Line 298 | Line 262 | class RigidBody: public StuntDouble { (public)
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 + class BaseVisitor{
267 +  public:
268 +  virtual void visit(Atom* atom);
269 +  virtual void visit(DirectionalAtom* datom);
270 +  virtual void visit(RigidBody* rb);
271 + };
272 + class BaseAtomVisitor:public BaseVisitor{
273 +  public:
274 +  virtual void visit(Atom* atom);
275 +  virtual void visit(DirectionalAtom* datom);
276 +  virtual void visit(RigidBody* rb);
277 + };
278 + class CompositeVisitor: public BaseVisitor {
279 +  public:
280 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
281 +  typedef VistorListType::iterator VisitorListIterator;
282 +  virtual void visit(Atom* atom) {
283 +    VisitorListIterator i;
284 +    BaseVisitor* curVisitor;
285 +    for(i = visitorList.begin();i != visitorList.end();++i)
286 +      atom->accept(*i);
287 +  }
288 +  virtual void visit(DirectionalAtom* datom) {
289 +    VisitorListIterator i;
290 +    BaseVisitor* curVisitor;
291 +    for(i = visitorList.begin();i != visitorList.end();++i)
292 +      atom->accept(*i);
293 +  }
294 +  virtual void visit(RigidBody* rb) {
295 +    VisitorListIterator i;
296 +    std::vector<Atom*> myAtoms;
297 +    std::vector<Atom*>::iterator ai;
298 +    myAtoms = rb->getAtoms();
299 +    for(i = visitorList.begin();i != visitorList.end();++i) {
300 +      rb->accept(*i);
301 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai)
302 +        (*ai)->accept(*i);
303 +    }
304 +  void addVisitor(BaseVisitor* v, int priority);
305 +  protected:
306 +  VistorListType visitorList;
307 + };
308 + \end{lstlisting}
309 +
310   \section{\label{appendixSection:concepts}Concepts}
311  
312   OOPSE manipulates both traditional atoms as well as some objects
313   that {\it behave like atoms}.  These objects can be rigid
314   collections of atoms or atoms which have orientational degrees of
315 < freedom.  A diagram of the class heirarchy is illustrated in
316 < Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and
315 > freedom.  A diagram of the class hierarchy is illustrated in
316 > Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
317   DirectionalAtom in {\sc OOPSE} have their own names which are
318 < specified in the {\tt .md} file. In contrast, RigidBodies are
318 > specified in the meta data file. In contrast, RigidBodies are
319   denoted by their membership and index inside a particular molecule:
320   [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
321   on the specifics of the simulation). The names of rigid bodies are
322   generated automatically. For example, the name of the first rigid
323   body in a DMPC molecule is DMPC\_RB\_0.
324 < %\begin{figure}
325 < %\centering
326 < %\includegraphics[width=\linewidth]{heirarchy.eps}
327 < %\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of
328 < %the class heirarchy.
329 < %\begin{itemize}
330 < %\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
331 < %integrators and minimizers.
323 < %\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
324 < %\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
325 < %\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
326 < %DirectionalAtom}s which behaves as a single unit.
327 < %\end{itemize}
328 < %} \label{oopseFig:heirarchy}
329 < %\end{figure}
324 > \begin{itemize}
325 > \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
326 > integrators and minimizers.
327 > \item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
328 > \item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
329 > \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
330 > DirectionalAtom}s which behaves as a single unit.
331 > \end{itemize}
332  
333   \section{\label{appendixSection:syntax}Syntax of the Select Command}
334  
335 < The most general form of the select command is: {\tt select {\it
336 < expression}}. This expression represents an arbitrary set of
335 < StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
336 < composed of either name expressions, index expressions, predefined
337 < sets, user-defined expressions, comparison operators, within
338 < expressions, or logical combinations of the above expression types.
339 < Expressions can be combined using parentheses and the Boolean
340 < operators.
335 > {\sc OOPSE} provides a powerful selection utility to select
336 > StuntDoubles. The most general form of the select command is:
337  
338 + {\tt select {\it expression}}.
339 +
340 + This expression represents an arbitrary set of StuntDoubles (Atoms
341 + or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
342 + name expressions, index expressions, predefined sets, user-defined
343 + expressions, comparison operators, within expressions, or logical
344 + combinations of the above expression types. Expressions can be
345 + combined using parentheses and the Boolean operators.
346 +
347   \subsection{\label{appendixSection:logical}Logical expressions}
348  
349   The logical operators allow complex queries to be constructed out of
# Line 375 | Line 380 | atoms belonging to TIP3P molecules \\
380   \hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the
381   O\_TIP3P
382   atoms belonging to TIP3P molecules \\
383 < & select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to
383 > & select DMPC\_RB\_0.PO4 & select the PO4 atoms belonging to
384   the first
385   RigidBody in each DMPC molecule \\
386   & select DMPC.20 & select the twentieth StuntDouble in each DMPC
# Line 470 | Line 475 | in a reference frame {\it fixed to the body-fixed refe
475   and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
476   also be used to compute the density distributions of other molecules
477   in a reference frame {\it fixed to the body-fixed reference frame}
478 < of a selected atom or rigid body.
478 > of a selected atom or rigid body. Due to the fact that the selected
479 > StuntDoubles from two selections may be overlapped, {\tt
480 > StaticProps} performs the calculation in three stages which are
481 > illustrated in Fig.~\ref{oopseFig:staticPropsProcess}.
482 >
483 > \begin{figure}
484 > \centering
485 > \includegraphics[width=\linewidth]{staticPropsProcess.eps}
486 > \caption[A representation of the three-stage correlations in
487 > \texttt{StaticProps}]{This diagram illustrates three-stage
488 > processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
489 > numbers of selected StuntDobules from {\tt -{}-sele1} and {\tt
490 > -{}-sele2} respectively, while $C$ is the number of StuntDobules
491 > appearing at both sets. The first stage($S_1-C$ and $S_2$) and
492 > second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
493 > the contrary, the third stage($C$ and $C$) are completely
494 > overlapping} \label{oopseFig:staticPropsProcess}
495 > \end{figure}
496  
497 + \begin{figure}
498 + \centering
499 + \includegraphics[width=3in]{definition.eps}
500 + \caption[Definitions of the angles between directional objects]{Any
501 + two directional objects (DirectionalAtoms and RigidBodies) have a
502 + set of two angles ($\theta$, and $\omega$) between the z-axes of
503 + their body-fixed frames.} \label{oopseFig:gofr}
504 + \end{figure}
505 +
506   There are five seperate radial distribution functions availiable in
507   OOPSE. Since every radial distrbution function invlove the
508   calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
# Line 515 | Line 546 | The vectors (and angles) associated with these angular
546   \end{description}
547  
548   The vectors (and angles) associated with these angular pair
549 < distribution functions are most easily seen in the figure below:
549 > distribution functions are most easily seen in
550 > Fig.~\ref{oopseFig:gofr}. The options available for {\tt
551 > StaticProps} are showed in Table.~\ref{appendix:staticPropsOptions}.
552  
520 – \begin{figure}
521 – \centering
522 – \includegraphics[width=3in]{definition.eps}
523 – \caption[Definitions of the angles between directional objects]{ \\
524 – Any two directional objects (DirectionalAtoms and RigidBodies) have
525 – a set of two angles ($\theta$, and $\omega$) between the z-axes of
526 – their body-fixed frames.} \label{oopseFig:gofr}
527 – \end{figure}
528 –
529 – Due to the fact that the selected StuntDoubles from two selections
530 – may be overlapped, {\tt StaticProps} performs the calculation in
531 – three stages which are illustrated in
532 – Fig.~\ref{oopseFig:staticPropsProcess}.
533 –
534 – \begin{figure}
535 – \centering
536 – \includegraphics[width=\linewidth]{staticPropsProcess.eps}
537 – \caption[A representation of the three-stage correlations in
538 – \texttt{StaticProps}]{This diagram illustrates three-stage
539 – processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
540 – numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
541 – -{}-sele2} respectively, while $C$ is the number of stuntdobules
542 – appearing at both sets. The first stage($S_1-C$ and $S_2$) and
543 – second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
544 – the contrary, the third stage($C$ and $C$) are completely
545 – overlapping} \label{oopseFig:staticPropsProcess}
546 – \end{figure}
547 –
548 – The options available for {\tt StaticProps} are as follows:
549 – \begin{longtable}[c]{|EFG|}
550 – \caption{StaticProps Command-line Options}
551 – \\ \hline
552 – {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
553 – \endhead
554 – \hline
555 – \endfoot
556 –  -h& {\tt -{}-help}                    &  Print help and exit \\
557 –  -V& {\tt -{}-version}                 &  Print version and exit \\
558 –  -i& {\tt -{}-input}          &  input dump file \\
559 –  -o& {\tt -{}-output}         &  output file name \\
560 –  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
561 –  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
562 –  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
563 –  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
564 –    & {\tt -{}-sele1}   & select the first StuntDouble set \\
565 –    & {\tt -{}-sele2}   & select the second StuntDouble set \\
566 –    & {\tt -{}-sele3}   & select the third StuntDouble set \\
567 –    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
568 –    & {\tt -{}-molname}           & molecule name \\
569 –    & {\tt -{}-begin}                & begin internal index \\
570 –    & {\tt -{}-end}                  & end internal index \\
571 – \hline
572 – \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
573 – \hline
574 –    &  {\tt -{}-gofr}                    &  $g(r)$ \\
575 –    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
576 –    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
577 –    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
578 –    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
579 –    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
580 –    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
581 –    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
582 –    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
583 – \end{longtable}
584 –
553   \subsection{\label{appendixSection:DynamicProps}DynamicProps}
554  
555   {\tt DynamicProps} computes time correlation functions from the
# Line 607 | Line 575 | For large simulations, the trajectory files can someti
575   select different types of atoms is already present in the code.
576  
577   For large simulations, the trajectory files can sometimes reach
578 < sizes in excess of several gigabytes. In order to effectively
579 < analyze that amount of data. In order to prevent a situation where
580 < the program runs out of memory due to large trajectories,
581 < \texttt{dynamicProps} will estimate the size of free memory at
582 < first, and determine the number of frames in each block, which
615 < allows the operating system to load two blocks of data
578 > sizes in excess of several gigabytes. In order to prevent a
579 > situation where the program runs out of memory due to large
580 > trajectories, \texttt{dynamicProps} will first estimate the size of
581 > free memory, and determine the number of frames in each block, which
582 > will allow the operating system to load two blocks of data
583   simultaneously without swapping. Upon reading two blocks of the
584   trajectory, \texttt{dynamicProps} will calculate the time
585   correlation within the first block and the cross correlations
# Line 621 | Line 588 | This process is illustrated in
588   trajectory. Once the end is reached, the first block is freed then
589   incremented, until all frame pairs have been correlated in time.
590   This process is illustrated in
591 < Fig.~\ref{oopseFig:dynamicPropsProcess}.
591 > Fig.~\ref{oopseFig:dynamicPropsProcess} and the options available
592 > for DynamicProps are showed in
593 > Table.~\ref{appendix:dynamicPropsOptions}
594  
595   \begin{figure}
596   \centering
# Line 634 | Line 603 | at a time and the cross correlations between blocks ar
603   \label{oopseFig:dynamicPropsProcess}
604   \end{figure}
605  
637 – The options available for DynamicProps are as follows:
606   \begin{longtable}[c]{|EFG|}
607 < \caption{DynamicProps Command-line Options}
607 > \caption{STATICPROPS COMMAND-LINE OPTIONS}
608 > \label{appendix:staticPropsOptions}
609   \\ \hline
610   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
611   \endhead
612   \hline
613   \endfoot
614 +  -h& {\tt -{}-help}                    &  Print help and exit \\
615 +  -V& {\tt -{}-version}                 &  Print version and exit \\
616 +  -i& {\tt -{}-input}          &  input dump file \\
617 +  -o& {\tt -{}-output}         &  output file name \\
618 +  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
619 +  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
620 +  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
621 +  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
622 +    & {\tt -{}-sele1}   & select the first StuntDouble set \\
623 +    & {\tt -{}-sele2}   & select the second StuntDouble set \\
624 +    & {\tt -{}-sele3}   & select the third StuntDouble set \\
625 +    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
626 +    & {\tt -{}-molname}           & molecule name \\
627 +    & {\tt -{}-begin}                & begin internal index \\
628 +    & {\tt -{}-end}                  & end internal index \\
629 + \hline
630 + \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
631 + \hline
632 +    &  {\tt -{}-gofr}                    &  $g(r)$ \\
633 +    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
634 +    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
635 +    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
636 +    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
637 +    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
638 +    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
639 +    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
640 +    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
641 + \end{longtable}
642 +
643 + \begin{longtable}[c]{|EFG|}
644 + \caption{DYNAMICPROPS COMMAND-LINE OPTIONS}
645 + \label{appendix:dynamicPropsOptions}
646 + \\ \hline
647 + {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
648 + \endhead
649 + \hline
650 + \endfoot
651    -h& {\tt -{}-help}                   & Print help and exit \\
652    -V& {\tt -{}-version}                & Print version and exit \\
653    -i& {\tt -{}-input}         & input dump file \\
# Line 665 | Line 671 | as follows:
671   and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
672   as follows:
673  
668 –
674   \begin{longtable}[c]{|EFG|}
675 < \caption{Dump2XYZ Command-line Options}
675 > \caption{DUMP2XYZ COMMAND-LINE OPTIONS}
676   \\ \hline
677   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
678   \endhead
# Line 701 | Line 706 | options available for Hydro are as follows:
706   the beads which are used to approximate the arbitrary shapes. The
707   options available for Hydro are as follows:
708   \begin{longtable}[c]{|EFG|}
709 < \caption{Hydrodynamics Command-line Options}
709 > \caption{HYDRODYNAMICS COMMAND-LINE OPTIONS}
710   \\ \hline
711   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
712   \endhead

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