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1   \appendix
2 < \chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine (OOPSE)}
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
# Line 14 | Line 14 | documents which is crucial to the maintenance and exte
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
22 + \begin{enumerate}
23 +  \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
24 + atom types (transition metals, point dipoles, sticky potentials,
25 + Gay-Berne ellipsoids, or other "lumpy"atoms with orientational
26 + degrees of freedom), as well as rigid bodies.
27 +  \item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap
28 + Beowulf clusters to obtain very efficient parallelism.
29 +  \item {\sc OOPSE} integrates the equations of motion using advanced methods for
30 + orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T
31 + ensembles.
32 +  \item {\sc OOPSE} can carry out simulations on metallic systems using the
33 + Embedded Atom Method (EAM) as well as the Sutton-Chen potential.
34 +  \item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals.
35 +  \item  {\sc OOPSE} can simulate systems containing the extremely efficient
36 + extended-Soft Sticky Dipole (SSD/E) model for water.
37 + \end{enumerate}
38  
39   \section{\label{appendixSection:architecture }Architecture}
40  
41 + Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
42 + uses C++ Standard Template Library (STL) and fortran modules as the
43 + foundation. As an extensive set of the STL and Fortran90 modules,
44 + {\sc Base Classes} provide generic implementations of mathematical
45 + objects (e.g., matrices, vectors, polynomials, random number
46 + generators) and advanced data structures and algorithms(e.g., tuple,
47 + bitset, generic data, string manipulation). The molecular data
48 + structures for the representation of atoms, bonds, bends, torsions,
49 + rigid bodies and molecules \textit{etc} are contained in the {\sc
50 + Kernel} which is implemented with {\sc Base Classes} and are
51 + carefully designed to provide maximum extensibility and flexibility.
52 + The functionality required for applications is provide by the third
53 + layer which contains Input/Output, Molecular Mechanics and Structure
54 + modules. Input/Output module not only implements general methods for
55 + file handling, but also defines a generic force field interface.
56 + Another important component of Input/Output module is the meta-data
57 + file parser, which is rewritten using ANother Tool for Language
58 + Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
59 + Mechanics module consists of energy minimization and a wide
60 + varieties of integration methods(see Chap.~\ref{chapt:methodology}).
61 + The structure module contains a flexible and powerful selection
62 + library which syntax is elaborated in
63 + Sec.~\ref{appendixSection:syntax}. The top layer is made of the main
64 + program of the package, \texttt{oopse} and it corresponding parallel
65 + version \texttt{oopse\_MPI}, as well as other useful utilities, such
66 + as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}),
67 + \texttt{DynamicProps} (see
68 + Sec.~\ref{appendixSection:appendixSection:DynamicProps}),
69 + \texttt{Dump2XYZ} (see
70 + Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro}
71 + (see Sec.~\ref{appendixSection:appendixSection:hydrodynamics})
72 + \textit{etc}.
73 +
74   \begin{figure}
75   \centering
76 < \includegraphics[width=3in]{architecture.eps}
77 < \caption[The architecture of {\sc oopse}-3.0] {The architecture
78 < of{\sc oopse}-3.0.} \label{appendixFig:architecture}
76 > \includegraphics[width=\linewidth]{architecture.eps}
77 > \caption[The architecture of {\sc OOPSE}] {Overview of the structure
78 > of {\sc OOPSE}} \label{appendixFig:architecture}
79   \end{figure}
80  
81   \section{\label{appendixSection:desginPattern}Design Pattern}
# Line 58 | Line 112 | the modern scientific software applications, such as J
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, OOPSE
116 < \cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}.
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}
121 < The Singleton pattern ensures that only one instance of a class is
122 < created. All objects that use an instance of that class use the same
123 < instance.
121 > The Singleton pattern not only provides a mechanism to restrict
122 > instantiation of a class to one object, but also provides a global
123 > point of access to the object. Currently implemented as a global
124 > variable, the logging utility which reports error and warning
125 > messages to the console in {\sc OOPSE} is a good candidate for
126 > applying the Singleton pattern to avoid the global namespace
127 > pollution.Although the singleton pattern can be implemented in
128 > various ways  to account for different aspects of the software
129 > designs, such as lifespan control \textit{etc}, we only use the
130 > static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class
131 > is declared as
132 > \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}]
133  
134 +  class IntegratorFactory {
135 +    public:
136 +      static IntegratorFactory* getInstance();
137 +    protected:
138 +      IntegratorFactory();
139 +    private:
140 +      static IntegratorFactory* instance_;
141 +  };
142 + \end{lstlisting}
143 + The corresponding implementation is
144 + \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}]
145 +
146 + IntegratorFactory::instance_ = NULL;
147 +
148 + IntegratorFactory* getInstance() {
149 +  if (instance_ == NULL){
150 +    instance_ = new IntegratorFactory;
151 +  }
152 +  return instance_;
153 + }
154 + \end{lstlisting}
155 + Since constructor is declared as {\tt protected}, a client can not
156 + instantiate {\tt IntegratorFactory} directly. Moreover, since the
157 + member function {\tt getInstance} serves as the only entry of access
158 + to {\tt IntegratorFactory}, this approach fulfills the basic
159 + requirement, a single instance. Another consequence of this approach
160 + is the automatic destruction since static data are destroyed upon
161 + program termination.
162 +
163   \subsection{\label{appendixSection:factoryMethod}Factory Method}
164 < The Factory Method pattern is a creational pattern which deals with
165 < the problem of creating objects without specifying the exact class
166 < of object that will be created. Factory Method solves this problem
167 < by defining a separate method for creating the objects, which
168 < subclasses can then override to specify the derived type of product
169 < that will be created.
164 >
165 > Categoried as a creational pattern, the Factory Method pattern deals
166 > with the problem of creating objects without specifying the exact
167 > class of object that will be created. Factory Method is typically
168 > implemented by delegating the creation operation to the subclasses.
169 > \begin{lstlisting}[float,caption={[].},label={appendixScheme:factoryDeclaration}]
170 >  class IntegratorCreator;
171 >  class IntegratorFactory {
172 >    public:
173 >      typedef std::map<std::string, IntegratorCreator*> CreatorMapType;
174 >
175 >      /**
176 >       * Registers a creator with a type identifier
177 >       * @return true if registration is successful, otherwise return false
178 >       * @id the identification of the concrete object
179 >       * @creator the object responsible to create the concrete object
180 >       */
181 >      bool registerIntegrator(IntegratorCreator* creator);
182 >
183 >      /**
184 >       * Looks up the type identifier in the internal map. If it is found, it invokes the
185 >       * corresponding creator for the type identifier and returns its result.
186 >       * @return a pointer of the concrete object, return NULL if no creator is registed for
187 >       * creating this concrete object
188 >       * @param id the identification of the concrete object
189 >       */
190 >      Integrator* createIntegrator(const std::string& id, SimInfo* info);
191 >
192 >    private:
193 >      CreatorMapType creatorMap_;
194 >  };
195 > \end{lstlisting}
196 >
197 > \begin{lstlisting}[float,caption={[].},label={appendixScheme:factoryDeclarationImplementation}]
198 >  bool IntegratorFactory::unregisterIntegrator(const std::string& id) {
199 >    return creatorMap_.erase(id) == 1;
200 >  }
201 >
202 >  Integrator* IntegratorFactory::createIntegrator(const std::string& id, SimInfo* info) {
203 >    CreatorMapType::iterator i = creatorMap_.find(id);
204 >    if (i != creatorMap_.end()) {
205 >      //invoke functor to create object
206 >      return (i->second)->create(info);
207 >    } else {
208 >      return NULL;
209 >    }
210 >  }
211 > \end{lstlisting}
212  
213 + \begin{lstlisting}[float,caption={[].},label={appendixScheme:integratorCreator}]
214  
215 +  class IntegratorCreator {
216 +  public:
217 +    IntegratorCreator(const std::string& ident) : ident_(ident) {}
218 +    virtual ~IntegratorCreator() {}
219 +    const std::string& getIdent() const { return ident_; }
220 +
221 +    virtual Integrator* create(SimInfo* info) const = 0;
222 +
223 +  private:
224 +    std::string ident_;
225 +  };
226 +
227 +  template<class ConcreteIntegrator>
228 +  class IntegratorBuilder : public IntegratorCreator {
229 +  public:
230 +    IntegratorBuilder(const std::string& ident) : IntegratorCreator(ident) {}
231 +    virtual  Integrator* create(SimInfo* info) const {return new ConcreteIntegrator(info);}
232 +  };
233 + \end{lstlisting}
234 +
235   \subsection{\label{appendixSection:visitorPattern}Visitor}
236 +
237   The purpose of the Visitor Pattern is to encapsulate an operation
238   that you want to perform on the elements of a data structure. In
239   this way, you can change the operation being performed on a
240 < structure without the need of changing the classes of the elements
241 < that you are operating on.
240 > structure without the need of changing the class heirarchy of the
241 > elements that you are operating on.
242  
243 + \begin{lstlisting}[float,caption={[].},label={appendixScheme:visitor}]
244 +  class BaseVisitor{
245 +    public:
246 +      virtual void visit(Atom* atom);
247 +      virtual void visit(DirectionalAtom* datom);
248 +      virtual void visit(RigidBody* rb);
249 +  };
250 + \end{lstlisting}
251 + \begin{lstlisting}[float,caption={[].},label={appendixScheme:element}]
252 +  class StuntDouble {
253 +    public:
254 +      virtual void accept(BaseVisitor* v) = 0;
255 +  };
256  
257 < \subsection{\label{appendixSection:templateMethod}Template Method}
257 >  class Atom: public StuntDouble {
258 >    public:
259 >      virtual void accept{BaseVisitor* v*} {v->visit(this);}
260 >  };
261  
262 +  class DirectionalAtom: public Atom {
263 +    public:
264 +      virtual void accept{BaseVisitor* v*} {v->visit(this);}
265 +  };
266 +
267 +  class RigidBody: public StuntDouble {
268 +    public:
269 +      virtual void accept{BaseVisitor* v*} {v->visit(this);}
270 +  };
271 +
272 + \end{lstlisting}
273   \section{\label{appendixSection:concepts}Concepts}
274  
275   OOPSE manipulates both traditional atoms as well as some objects
# Line 110 | Line 295 | Every Molecule, Atom and DirectionalAtom in {\sc oopse
295   DirectionalAtom}s which behaves as a single unit.
296   \end{itemize}
297  
298 < Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
298 > Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
299   own names which are specified in the {\tt .md} file. In contrast,
300   RigidBodies are denoted by their membership and index inside a
301   particular molecule: [MoleculeName]\_RB\_[index] (the contents
# Line 121 | Line 306 | expression}}
306   \section{\label{appendixSection:syntax}Syntax of the Select Command}
307  
308   The most general form of the select command is: {\tt select {\it
309 < expression}}
309 > expression}}. This expression represents an arbitrary set of
310 > StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
311 > composed of either name expressions, index expressions, predefined
312 > sets, user-defined expressions, comparison operators, within
313 > expressions, or logical combinations of the above expression types.
314 > Expressions can be combined using parentheses and the Boolean
315 > operators.
316  
126 – This expression represents an arbitrary set of StuntDoubles (Atoms
127 – or RigidBodies) in {\sc oopse}. Expressions are composed of either
128 – name expressions, index expressions, predefined sets, user-defined
129 – expressions, comparison operators, within expressions, or logical
130 – combinations of the above expression types. Expressions can be
131 – combined using parentheses and the Boolean operators.
132 –
317   \subsection{\label{appendixSection:logical}Logical expressions}
318  
319   The logical operators allow complex queries to be constructed out of
# Line 211 | Line 395 | expression}}
395   Users can define arbitrary terms to represent groups of
396   StuntDoubles, and then use the define terms in select commands. The
397   general form for the define command is: {\bf define {\it term
398 < expression}}
398 > expression}}. Once defined, the user can specify such terms in
399 > boolean expressions
400  
216 – Once defined, the user can specify such terms in boolean expressions
217 –
401   {\tt define SSDWATER SSD or SSD1 or SSDRF}
402  
403   {\tt select SSDWATER}
# Line 259 | Line 442 | and other atoms of type $B$, $g_{AB}(r)$.  StaticProps
442   some or all of the configurations that are contained within a dump
443   file. The most common example of a static property that can be
444   computed is the pair distribution function between atoms of type $A$
445 < and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
446 < used to compute the density distributions of other molecules in a
447 < reference frame {\it fixed to the body-fixed reference frame} of a
448 < selected atom or rigid body.
445 > and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
446 > also be used to compute the density distributions of other molecules
447 > in a reference frame {\it fixed to the body-fixed reference frame}
448 > of a selected atom or rigid body.
449  
450   There are five seperate radial distribution functions availiable in
451   OOPSE. Since every radial distrbution function invlove the
# Line 318 | Line 501 | The options available for {\tt StaticProps} are as fol
501   their body-fixed frames.} \label{oopseFig:gofr}
502   \end{figure}
503  
504 + Due to the fact that the selected StuntDoubles from two selections
505 + may be overlapped, {\tt StaticProps} performs the calculation in
506 + three stages which are illustrated in
507 + Fig.~\ref{oopseFig:staticPropsProcess}.
508 +
509 + \begin{figure}
510 + \centering
511 + \includegraphics[width=\linewidth]{staticPropsProcess.eps}
512 + \caption[A representation of the three-stage correlations in
513 + \texttt{StaticProps}]{This diagram illustrates three-stage
514 + processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
515 + numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
516 + -{}-sele2} respectively, while $C$ is the number of stuntdobules
517 + appearing at both sets. The first stage($S_1-C$ and $S_2$) and
518 + second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
519 + the contrary, the third stage($C$ and $C$) are completely
520 + overlapping} \label{oopseFig:staticPropsProcess}
521 + \end{figure}
522 +
523   The options available for {\tt StaticProps} are as follows:
524   \begin{longtable}[c]{|EFG|}
525   \caption{StaticProps Command-line Options}
# Line 378 | Line 580 | select different types of atoms is already present in
580   the use of {\it cross} time correlation functions (i.e. with
581   different vectors).  The ability to use two selection scripts to
582   select different types of atoms is already present in the code.
583 +
584 + For large simulations, the trajectory files can sometimes reach
585 + sizes in excess of several gigabytes. In order to effectively
586 + analyze that amount of data. In order to prevent a situation where
587 + the program runs out of memory due to large trajectories,
588 + \texttt{dynamicProps} will estimate the size of free memory at
589 + first, and determine the number of frames in each block, which
590 + allows the operating system to load two blocks of data
591 + simultaneously without swapping. Upon reading two blocks of the
592 + trajectory, \texttt{dynamicProps} will calculate the time
593 + correlation within the first block and the cross correlations
594 + between the two blocks. This second block is then freed and then
595 + incremented and the process repeated until the end of the
596 + trajectory. Once the end is reached, the first block is freed then
597 + incremented, until all frame pairs have been correlated in time.
598 + This process is illustrated in
599 + Fig.~\ref{oopseFig:dynamicPropsProcess}.
600  
601 + \begin{figure}
602 + \centering
603 + \includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
604 + \caption[A representation of the block correlations in
605 + \texttt{dynamicProps}]{This diagram illustrates block correlations
606 + processing in \texttt{dynamicProps}. The shaded region represents
607 + the self correlation of the block, and the open blocks are read one
608 + at a time and the cross correlations between blocks are calculated.}
609 + \label{oopseFig:dynamicPropsProcess}
610 + \end{figure}
611 +
612   The options available for DynamicProps are as follows:
613   \begin{longtable}[c]{|EFG|}
614   \caption{DynamicProps Command-line Options}
# Line 405 | Line 635 | Dump2XYZ can transform an OOPSE dump file into a xyz f
635  
636   \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
637  
638 < Dump2XYZ can transform an OOPSE dump file into a xyz file which can
639 < be opened by other molecular dynamics viewers such as Jmol and VMD.
640 < The options available for Dump2XYZ are as follows:
638 > {\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
639 > which can be opened by other molecular dynamics viewers such as Jmol
640 > and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
641 > as follows:
642  
643  
644   \begin{longtable}[c]{|EFG|}
# Line 437 | Line 668 | converted. \\
668       & {\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}.
669   \end{longtable}
670  
671 < \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
671 > \subsection{\label{appendixSection:hydrodynamics}Hydro}
672  
673 + {\tt Hydro} can calculate resistance and diffusion tensors at the
674 + center of resistance. Both tensors at the center of diffusion can
675 + also be reported from the program, as well as the coordinates for
676 + the beads which are used to approximate the arbitrary shapes. The
677 + options available for Hydro are as follows:
678   \begin{longtable}[c]{|EFG|}
679   \caption{Hydrodynamics Command-line Options}
680   \\ \hline
# Line 451 | Line 687 | converted. \\
687    -i & {\tt -{}-input}  &             input dump file \\
688    -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
689    -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
690 <     & {\tt -{}-model}  &                 hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
690 >     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
691   \end{longtable}

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