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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
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.
17 < Along the way of studying structural and dynamic processes in
18 < condensed phase systems like biological membranes and nanoparticles,
19 < we developed and maintained an Object-Oriented Parallel Simulation
20 < Engine ({\sc OOPSE}). This new molecular dynamics package has some
21 < unique features
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,
# Line 64 | Line 59 | as \texttt{StatProps} (see Sec.~\ref{appendixSection:S
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
70 < Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro}
71 < (see Sec.~\ref{appendixSection:appendixSection:hydrodynamics})
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}
# Line 91 | Line 84 | solutions succinctly.
84   reusable. They provide a ready-made solution that can be adapted to
85   different problems as necessary. Pattern are expressive. they
86   provide a common vocabulary of solutions that can express large
87 < solutions succinctly.
87 > solutions succinctly. As one of the latest advanced techniques
88 > emerged from object-oriented community, design patterns were applied
89 > in some of the modern scientific software applications, such as
90 > JMol, {\sc OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}
91 > \textit{etc}. The following sections enumerates some of the patterns
92 > used in {\sc OOPSE}.
93  
94 < Patterns are usually described using a format that includes the
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}
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, {\sc
99 < OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}.
100 < The following sections enumerates some of the patterns used in {\sc
101 < OOPSE}.
96 > The Singleton pattern not only provides a mechanism to restrict
97 > instantiation of a class to one object, but also provides a global
98 > point of access to the object. Currently implemented as a global
99 > variable, the logging utility which reports error and warning
100 > messages to the console in {\sc OOPSE} is a good candidate for
101 > applying the Singleton pattern to avoid the global namespace
102 > pollution. Although the singleton pattern can be implemented in
103 > various ways  to account for different aspects of the software
104 > designs, such as lifespan control \textit{etc}, we only use the
105 > static data approach in {\sc OOPSE}. The declaration and
106 > implementation of IntegratorFactory class are given by declared in
107 > List.~\ref{appendixScheme:singletonDeclaration} and
108 > Scheme.~\ref{appendixScheme:singletonImplementation} respectively.
109 > Since constructor is declared as protected, a client can not
110 > instantiate IntegratorFactory directly. Moreover, since the member
111 > function getInstance serves as the only entry of access to
112 > IntegratorFactory, this approach fulfills the basic requirement, a
113 > single instance. Another consequence of this approach is the
114 > automatic destruction since static data are destroyed upon program
115 > termination.
116 > \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}]
117  
118 < \subsection{\label{appendixSection:singleton}Singleton}
119 < The Singleton pattern ensures that only one instance of a class is
120 < created. All objects that use an instance of that class use the same
121 < instance.
118 > class IntegratorFactory {
119 > public:
120 >  static IntegratorFactory*
121 >  getInstance();
122 > protected:
123 >  IntegratorFactory();
124 > private:
125 >  static IntegratorFactory* instance_;
126 > };
127  
128 + \end{lstlisting}
129 +
130 + \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}]
131 +
132 + IntegratorFactory::instance_ = NULL;
133 +
134 + IntegratorFactory* getInstance() {
135 +  if (instance_ == NULL){
136 +    instance_ = new IntegratorFactory;
137 +  }
138 +  return instance_;
139 + }
140 +
141 + \end{lstlisting}
142 +
143 +
144   \subsection{\label{appendixSection:factoryMethod}Factory Method}
126 – The Factory Method pattern is a creational pattern which deals with
127 – the problem of creating objects without specifying the exact class
128 – of object that will be created. Factory Method solves this problem
129 – by defining a separate method for creating the objects, which
130 – subclasses can then override to specify the derived type of product
131 – that will be created.
145  
146 + Categoried as a creational pattern, the Factory Method pattern deals
147 + with the problem of creating objects without specifying the exact
148 + class of object that will be created. Factory Method is typically
149 + implemented by delegating the creation operation to the subclasses.
150 + Parameterized Factory pattern where factory method (
151 + createIntegrator member function) creates products based on the
152 + identifier (see Scheme.~\ref{appendixScheme:factoryDeclaration}). If
153 + the identifier has been already registered, the factory method will
154 + invoke the corresponding creator (see
155 + Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the
156 + modern C++ template technique to avoid excess subclassing.
157 +
158 + \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}]
159 +
160 + class IntegratorFactory {
161 + public:
162 +  typedef std::map<string, IntegratorCreator*> CreatorMapType;
163 +
164 +  bool registerIntegrator(IntegratorCreator* creator) {
165 +    return creatorMap_.insert(creator->getIdent(), creator).second;
166 +  }
167 +
168 +  Integrator* createIntegrator(const string& id, SimInfo* info) {
169 +    Integrator* result = NULL;
170 +    CreatorMapType::iterator i = creatorMap_.find(id);
171 +    if (i != creatorMap_.end()) {
172 +      result = (i->second)->create(info);
173 +    }
174 +    return result;
175 +  }
176 +
177 + private:
178 +  CreatorMapType creatorMap_;
179 + };
180 + \end{lstlisting}
181 +
182 + \begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}]
183 +
184 + class IntegratorCreator {
185 + public:
186 +    IntegratorCreator(const string& ident) : ident_(ident) {}
187 +
188 +    const string& getIdent() const { return ident_; }
189 +
190 +    virtual Integrator* create(SimInfo* info) const = 0;
191 +
192 + private:
193 +    string ident_;
194 + };
195 +
196 + template<class ConcreteIntegrator>
197 + class IntegratorBuilder : public IntegratorCreator {
198 + public:
199 +  IntegratorBuilder(const string& ident)
200 +                   : IntegratorCreator(ident) {}
201 +  virtual  Integrator* create(SimInfo* info) const {
202 +    return new ConcreteIntegrator(info);
203 +  }
204 + };
205 + \end{lstlisting}
206 +
207   \subsection{\label{appendixSection:visitorPattern}Visitor}
208 < The purpose of the Visitor Pattern is to encapsulate an operation
209 < that you want to perform on the elements of a data structure. In
210 < this way, you can change the operation being performed on a
211 < structure without the need of changing the classes of the elements
212 < that you are operating on.
208 >
209 > The visitor pattern is designed to decouple the data structure and
210 > algorithms used upon them by collecting related operation from
211 > element classes into other visitor classes, which is equivalent to
212 > adding virtual functions into a set of classes without modifying
213 > their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the
214 > structure of Visitor pattern which is used extensively in {\tt
215 > Dump2XYZ}. In order to convert an OOPSE dump file, a series of
216 > distinct operations are performed on different StuntDoubles (See the
217 > class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration
218 > in Scheme.~\ref{appendixScheme:element}). Since the hierarchies
219 > remains stable, it is easy to define a visit operation (see
220 > Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble.
221 > Note that using Composite pattern\cite{Gamma1994}, CompositVisitor
222 > manages a priority visitor list and handles the execution of every
223 > visitor in the priority list on different StuntDoubles.
224 >
225 > \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 + \begin{figure}
233 + \centering
234 + \includegraphics[width=\linewidth]{hierarchy.eps}
235 + \caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
236 + the class hierarchy. } \label{oopseFig:hierarchy}
237 + \end{figure}
238 +
239 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
240 +
241 + class StuntDouble { public:
242 +  virtual void accept(BaseVisitor* v) = 0;
243 + };
244 +
245 + class Atom: public StuntDouble { public:
246 +  virtual void accept{BaseVisitor* v*} {
247 +    v->visit(this);
248 +  }
249 + };
250 +
251 + class DirectionalAtom: public Atom { public:
252 +  virtual void accept{BaseVisitor* v*} {
253 +    v->visit(this);
254 +  }
255 + };
256 +
257 + class RigidBody: public StuntDouble { public:
258 +  virtual void accept{BaseVisitor* v*} {
259 +    v->visit(this);
260 +  }
261 + };
262 +
263 + \end{lstlisting}
264 +
265 + \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
266 +
267 + class BaseVisitor{
268 + public:
269 +  virtual void visit(Atom* atom);
270 +  virtual void visit(DirectionalAtom* datom);
271 +  virtual void visit(RigidBody* rb);
272 + };
273 +
274 + class BaseAtomVisitor:public BaseVisitor{ public:
275 +  virtual void visit(Atom* atom);
276 +  virtual void visit(DirectionalAtom* datom);
277 +  virtual void visit(RigidBody* rb);
278 + };
279 +
280 + class CompositeVisitor: public BaseVisitor {
281 + public:
282 +
283 +  typedef list<pair<BaseVisitor*, int> > VistorListType;
284 +  typedef VistorListType::iterator VisitorListIterator;
285 +  virtual void visit(Atom* atom) {
286 +    VisitorListIterator i;
287 +    BaseVisitor* curVisitor;
288 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
289 +      atom->accept(*i);
290 +    }
291 +  }
292 +
293 +  virtual void visit(DirectionalAtom* datom) {
294 +    VisitorListIterator i;
295 +    BaseVisitor* curVisitor;
296 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {
297 +      atom->accept(*i);
298 +    }
299 +  }
300 +
301 +  virtual void visit(RigidBody* rb) {
302 +    VisitorListIterator i;
303 +    std::vector<Atom*> myAtoms;
304 +    std::vector<Atom*>::iterator ai;
305 +    myAtoms = rb->getAtoms();
306 +    for(i = visitorScheme.begin();i != visitorScheme.end();++i) {{
307 +      rb->accept(*i);
308 +      for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){
309 +        (*ai)->accept(*i);
310 +    }
311 +  }
312 +
313 +  void addVisitor(BaseVisitor* v, int priority);
314 +
315 +  protected:
316 +    VistorListType visitorList;
317 + };
318 + \end{lstlisting}
319 +
320   \section{\label{appendixSection:concepts}Concepts}
321  
322   OOPSE manipulates both traditional atoms as well as some objects
323   that {\it behave like atoms}.  These objects can be rigid
324   collections of atoms or atoms which have orientational degrees of
325 < freedom.  Here is a diagram of the class heirarchy:
326 <
327 < %\begin{figure}
328 < %\centering
329 < %\includegraphics[width=3in]{heirarchy.eps}
330 < %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
331 < %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
332 < %selection syntax allows the user to select any of the objects that
333 < %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
154 < %\end{figure}
155 <
325 > freedom.  A diagram of the class hierarchy is illustrated in
326 > Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and
327 > DirectionalAtom in {\sc OOPSE} have their own names which are
328 > specified in the {\tt .md} file. In contrast, RigidBodies are
329 > denoted by their membership and index inside a particular molecule:
330 > [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
331 > on the specifics of the simulation). The names of rigid bodies are
332 > generated automatically. For example, the name of the first rigid
333 > body in a DMPC molecule is DMPC\_RB\_0.
334   \begin{itemize}
335   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
336   integrators and minimizers.
# Line 162 | Line 340 | Every Molecule, Atom and DirectionalAtom in {\sc OOPSE
340   DirectionalAtom}s which behaves as a single unit.
341   \end{itemize}
342  
165 – Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
166 – own names which are specified in the {\tt .md} file. In contrast,
167 – RigidBodies are denoted by their membership and index inside a
168 – particular molecule: [MoleculeName]\_RB\_[index] (the contents
169 – inside the brackets depend on the specifics of the simulation). The
170 – names of rigid bodies are generated automatically. For example, the
171 – name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
172 –
343   \section{\label{appendixSection:syntax}Syntax of the Select Command}
344  
345 < The most general form of the select command is: {\tt select {\it
346 < expression}}. This expression represents an arbitrary set of
177 < StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
178 < composed of either name expressions, index expressions, predefined
179 < sets, user-defined expressions, comparison operators, within
180 < expressions, or logical combinations of the above expression types.
181 < Expressions can be combined using parentheses and the Boolean
182 < operators.
345 > {\sc OOPSE} provides a powerful selection utility to select
346 > StuntDoubles. The most general form of the select command is:
347  
348 + {\tt select {\it expression}}.
349 +
350 + This expression represents an arbitrary set of StuntDoubles (Atoms
351 + or RigidBodies) in {\sc OOPSE}. Expressions are composed of either
352 + name expressions, index expressions, predefined sets, user-defined
353 + expressions, comparison operators, within expressions, or logical
354 + combinations of the above expression types. Expressions can be
355 + combined using parentheses and the Boolean operators.
356 +
357   \subsection{\label{appendixSection:logical}Logical expressions}
358  
359   The logical operators allow complex queries to be constructed out of
# Line 312 | Line 485 | of a selected atom or rigid body.
485   and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
486   also be used to compute the density distributions of other molecules
487   in a reference frame {\it fixed to the body-fixed reference frame}
488 < of a selected atom or rigid body.
488 > of a selected atom or rigid body. Due to the fact that the selected
489 > StuntDoubles from two selections may be overlapped, {\tt
490 > StaticProps} performs the calculation in three stages which are
491 > illustrated in Fig.~\ref{oopseFig:staticPropsProcess}.
492  
493 + \begin{figure}
494 + \centering
495 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
496 + \caption[A representation of the three-stage correlations in
497 + \texttt{StaticProps}]{This diagram illustrates three-stage
498 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
499 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
500 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
501 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
502 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
503 + the contrary, the third stage($C$ and $C$) are completely
504 + overlapping} \label{oopseFig:staticPropsProcess}
505 + \end{figure}
506 +
507   There are five seperate radial distribution functions availiable in
508   OOPSE. Since every radial distrbution function invlove the
509   calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
# Line 357 | Line 547 | distribution functions are most easily seen in the fig
547   \end{description}
548  
549   The vectors (and angles) associated with these angular pair
550 < distribution functions are most easily seen in the figure below:
550 > distribution functions are most easily seen in
551 > Fig.~\ref{oopseFig:gofr}
552  
553   \begin{figure}
554   \centering
# Line 368 | Line 559 | Due to the fact that the selected StuntDoubles from tw
559   their body-fixed frames.} \label{oopseFig:gofr}
560   \end{figure}
561  
371 – Due to the fact that the selected StuntDoubles from two selections
372 – may be overlapped, {\tt StaticProps} performs the calculation in
373 – three stages which are illustrated in
374 – Fig.~\ref{oopseFig:staticPropsProcess}.
375 –
376 – \begin{figure}
377 – \centering
378 – \includegraphics[width=\linewidth]{staticPropsProcess.eps}
379 – \caption[A representation of the three-stage correlations in
380 – \texttt{StaticProps}]{This diagram illustrates three-stage
381 – processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
382 – numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
383 – -{}-sele2} respectively, while $C$ is the number of stuntdobules
384 – appearing at both sets. The first stage($S_1-C$ and $S_2$) and
385 – second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
386 – the contrary, the third stage($C$ and $C$) are completely
387 – overlapping} \label{oopseFig:staticPropsProcess}
388 – \end{figure}
389 –
562   The options available for {\tt StaticProps} are as follows:
563   \begin{longtable}[c]{|EFG|}
564   \caption{StaticProps Command-line Options}
# Line 449 | Line 621 | sizes in excess of several gigabytes. In order to effe
621   select different types of atoms is already present in the code.
622  
623   For large simulations, the trajectory files can sometimes reach
624 < sizes in excess of several gigabytes. In order to effectively
625 < analyze that amount of data. In order to prevent a situation where
626 < the program runs out of memory due to large trajectories,
627 < \texttt{dynamicProps} will estimate the size of free memory at
628 < first, and determine the number of frames in each block, which
457 < allows the operating system to load two blocks of data
624 > sizes in excess of several gigabytes. In order to prevent a
625 > situation where the program runs out of memory due to large
626 > trajectories, \texttt{dynamicProps} will estimate the size of free
627 > memory at first, and determine the number of frames in each block,
628 > which allows the operating system to load two blocks of data
629   simultaneously without swapping. Upon reading two blocks of the
630   trajectory, \texttt{dynamicProps} will calculate the time
631   correlation within the first block and the cross correlations
# Line 502 | Line 673 | Dump2XYZ can transform an OOPSE dump file into a xyz f
673  
674   \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
675  
676 < Dump2XYZ can transform an OOPSE dump file into a xyz file which can
677 < be opened by other molecular dynamics viewers such as Jmol and
678 < VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as
679 < follows:
676 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
677 > which can be opened by other molecular dynamics viewers such as Jmol
678 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
679 > as follows:
680  
681  
682   \begin{longtable}[c]{|EFG|}
# Line 536 | Line 707 | The options available for Hydro are as follows:
707   \end{longtable}
708  
709   \subsection{\label{appendixSection:hydrodynamics}Hydro}
710 < The options available for Hydro are as follows:
710 >
711 > {\tt Hydro} can calculate resistance and diffusion tensors at the
712 > center of resistance. Both tensors at the center of diffusion can
713 > also be reported from the program, as well as the coordinates for
714 > the beads which are used to approximate the arbitrary shapes. The
715 > options available for Hydro are as follows:
716   \begin{longtable}[c]{|EFG|}
717   \caption{Hydrodynamics Command-line Options}
718   \\ \hline

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