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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  
96 – 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}
112 –
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 –
94   \subsection{\label{appendixSection:singleton}Singleton}
95 +
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
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}. {\tt IntegratorFactory} class
106 < is declared as
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   class IntegratorFactory {
# Line 142 | Line 126 | The corresponding implementation is
126   };
127  
128   \end{lstlisting}
129 < The corresponding implementation is
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;
# Line 155 | Line 139 | Since constructor is declared as {\tt protected}, a cl
139   }
140  
141   \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.
142  
143 +
144   \subsection{\label{appendixSection:factoryMethod}Factory Method}
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 < {\tt Integrator} class Parameterized Factory pattern where factory
151 < method ({\tt createIntegrator} member function) creates products
152 < based on the identifier (see
153 < List.~\ref{appendixScheme:factoryDeclaration}). If the identifier
154 < has been already registered, the factory method will invoke the
155 < corresponding creator (see List.~\ref{integratorCreator}) which
156 < 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}]
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;
# Line 199 | Line 178 | class IntegratorFactory { (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 {
# Line 226 | Line 206 | The purpose of the Visitor Pattern is to encapsulate a
206  
207   \subsection{\label{appendixSection:visitorPattern}Visitor}
208  
209 < The purpose of the Visitor Pattern is to encapsulate an operation
210 < that you want to perform on the elements. The operation being
211 < performed on a structure can be switched without changing the
212 < interfaces of the elements. In other words, one can add virtual
213 < functions into a set of classes without modifying their interfaces.
214 < Fig.~\ref{appendixFig:visitorUML} demonstrates the structure of
215 < Visitor pattern which is used extensively in {\tt Dump2XYZ}. In
216 < order to convert an OOPSE dump file, a series of distinct and
217 < unrelated operations are performed on different StuntDoubles.
218 < Visitor allows one to keep related operations together by packing
219 < them into one class. {\tt BaseAtomVisitor} is a typical example of
220 < visitor in {\tt Dump2XYZ} program{see
221 < List.~\ref{appendixScheme:visitor}}. In contrast to the operations,
222 < the object structure or element classes rarely change(See
223 < Fig.~\ref{oopseFig:heirarchy} and
244 < List.~\ref{appendixScheme:element}).
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  
246 –
225   \begin{figure}
226   \centering
227   \includegraphics[width=\linewidth]{visitor.eps}
# Line 251 | Line 229 | diagram of Visitor patten.} \label{appendixFig:visitor
229   diagram of Visitor patten.} \label{appendixFig:visitorUML}
230   \end{figure}
231  
232 < \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
233 <
234 < class BaseVisitor{
235 < public:
236 <  virtual void visit(Atom* atom);
237 <  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}
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 {
274 < public:
241 > class StuntDouble { public:
242    virtual void accept(BaseVisitor* v) = 0;
243   };
244  
245 < class Atom: public StuntDouble {
279 < public:
245 > class Atom: public StuntDouble { public:
246    virtual void accept{BaseVisitor* v*} {
247      v->visit(this);
248    }
249   };
250  
251 < class DirectionalAtom: public Atom {
286 < public:
251 > class DirectionalAtom: public Atom { public:
252    virtual void accept{BaseVisitor* v*} {
253      v->visit(this);
254    }
255   };
256  
257 < class RigidBody: public StuntDouble {
293 < public:
257 > class RigidBody: public StuntDouble { 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 +
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.  A diagram of the class heirarchy is illustrated in
326 < Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and
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:
# Line 312 | Line 331 | body in a DMPC molecule is DMPC\_RB\_0.
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{figure}
335 < %\centering
336 < %\includegraphics[width=\linewidth]{heirarchy.eps}
337 < %\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of
338 < %the class heirarchy.
339 < %\begin{itemize}
340 < %\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
341 < %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}
334 > \begin{itemize}
335 > \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
336 > integrators and minimizers.
337 > \item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
338 > \item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
339 > \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
340 > DirectionalAtom}s which behaves as a single unit.
341 > \end{itemize}
342  
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
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.
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 470 | 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
# Line 515 | 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 526 | Line 559 | Due to the fact that the selected StuntDoubles from tw
559   their body-fixed frames.} \label{oopseFig:gofr}
560   \end{figure}
561  
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 –
562   The options available for {\tt StaticProps} are as follows:
563   \begin{longtable}[c]{|EFG|}
564   \caption{StaticProps Command-line Options}
# Line 607 | 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
615 < 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

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