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+\appendix
-<
+\chapter{\label{chapt:appendix}APPENDIX}
->
+\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
+Designing object-oriented software is hard, and designing reusable
+object-oriented scientific software is even harder. Absence of
+applying modern software development practices is the bottleneck of
-<
+Scientific Computing community\cite{wilson}. For instance, in the
-<
+last 20 years , there are quite a few MD packages that were
->
+Scientific Computing community\cite{Wilson2006}. For instance, in
->
+the last 20 years , there are quite a few MD packages that were
+developed to solve common MD problems and perform robust simulations
+. However, many of the codes are legacy programs that are either
+poorly organized or extremely complex. Usually, these packages were
+coordination to enforce design and programming guidelines. Moreover,
+most MD programs also suffer from missing design and implement
+documents which is crucial to the maintenance and extensibility.
-+
+Along the way of studying structural and dynamic processes in
-+
+condensed phase systems like biological membranes and nanoparticles,
-+
+we developed and maintained an Object-Oriented Parallel Simulation
-+
+Engine ({\sc OOPSE}). This new molecular dynamics package has some
-+
+unique features
-+
+\begin{enumerate}
-+
+  \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
-+
+atom types (transition metals, point dipoles, sticky potentials,
-+
+Gay-Berne ellipsoids, or other "lumpy"atoms with orientational
-+
+degrees of freedom), as well as rigid bodies.
-+
+  \item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap
-+
+Beowulf clusters to obtain very efficient parallelism.
-+
+  \item {\sc OOPSE} integrates the equations of motion using advanced methods for
-+
+orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T
-+
+ensembles.
-+
+  \item {\sc OOPSE} can carry out simulations on metallic systems using the
-+
+Embedded Atom Method (EAM) as well as the Sutton-Chen potential.
-+
+  \item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals.
-+
+  \item  {\sc OOPSE} can simulate systems containing the extremely efficient
-+
+extended-Soft Sticky Dipole (SSD/E) model for water.
-+
+\end{enumerate}
-+
+\section{\label{appendixSection:architecture }Architecture}
-+
-+
+Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
-+
+uses C++ Standard Template Library (STL) and fortran modules as the
-+
+foundation. As an extensive set of the STL and Fortran90 modules,
-+
+{\sc Base Classes} provide generic implementations of mathematical
-+
+objects (e.g., matrices, vectors, polynomials, random number
-+
+generators) and advanced data structures and algorithms(e.g., tuple,
-+
+bitset, generic data, string manipulation). The molecular data
-+
+structures for the representation of atoms, bonds, bends, torsions,
-+
+rigid bodies and molecules \textit{etc} are contained in the {\sc
-+
+Kernel} which is implemented with {\sc Base Classes} and are
-+
+carefully designed to provide maximum extensibility and flexibility.
-+
+The functionality required for applications is provide by the third
-+
+layer which contains Input/Output, Molecular Mechanics and Structure
-+
+modules. Input/Output module not only implements general methods for
-+
+file handling, but also defines a generic force field interface.
-+
+Another important component of Input/Output module is the meta-data
-+
+file parser, which is rewritten using ANother Tool for Language
-+
+Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
-+
+Mechanics module consists of energy minimization and a wide
-+
+varieties of integration methods(see Chap.~\ref{chapt:methodology}).
-+
+The structure module contains a flexible and powerful selection
-+
+library which syntax is elaborated in
-+
+Sec.~\ref{appendixSection:syntax}. The top layer is made of the main
-+
+program of the package, \texttt{oopse} and it corresponding parallel
-+
+version \texttt{oopse\_MPI}, as well as other useful utilities, such
-+
+as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}),
-+
+\texttt{DynamicProps} (see
-+
+Sec.~\ref{appendixSection:appendixSection:DynamicProps}),
-+
+\texttt{Dump2XYZ} (see
-+
+Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro}
-+
+(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics})
-+
+\textit{etc}.
-+
-+
+\begin{figure}
-+
+\centering
-+
+\includegraphics[width=\linewidth]{architecture.eps}
-+
+\caption[The architecture of {\sc OOPSE}] {Overview of the structure
-+
+of {\sc OOPSE}} \label{appendixFig:architecture}
-+
+\end{figure}
-+
+\section{\label{appendixSection:desginPattern}Design Pattern}
+Design patterns are optimal solutions to commonly-occurring problems
+in software design. Although originated as an architectural concept
-<
+for buildings and towns by Christopher Alexander \cite{alexander},
-<
+software patterns first became popular with the wide acceptance of
-<
+the book, Design Patterns: Elements of Reusable Object-Oriented
-<
+Software \cite{gamma94}. Patterns reflect the experience, knowledge
-<
+and insights of developers who have successfully used these patterns
-<
+in their own work. Patterns are reusable. They provide a ready-made
-<
+solution that can be adapted to different problems as necessary.
-<
+Pattern are expressive. they provide a common vocabulary of
-<
+solutions that can express large solutions succinctly.
->
+for buildings and towns by Christopher Alexander
->
+\cite{Alexander1987}, software patterns first became popular with
->
+the wide acceptance of the book, Design Patterns: Elements of
->
+Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect
->
+the experience, knowledge and insights of developers who have
->
+successfully used these patterns in their own work. Patterns are
->
+reusable. They provide a ready-made solution that can be adapted to
->
+different problems as necessary. Pattern are expressive. they
->
+provide a common vocabulary of solutions that can express large
->
+solutions succinctly.
+Patterns are usually described using a format that includes the
+following information:
+As one of the latest advanced techniques emerged from
+object-oriented community, design patterns were applied in some of
-<
+the modern scientific software applications, such as JMol, OOPSE
-<
+\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}.
->
+the modern scientific software applications, such as JMol, {\sc
->
+OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}.
->
+The following sections enumerates some of the patterns used in {\sc
->
+OOPSE}.
+\subsection{\label{appendixSection:singleton}Singleton}
-<
+The Singleton pattern ensures that only one instance of a class is
-<
+created. All objects that use an instance of that class use the same
-<
+instance.
->
+The Singleton pattern not only provides a mechanism to restrict
->
+instantiation of a class to one object, but also provides a global
->
+point of access to the object. Currently implemented as a global
->
+variable, the logging utility which reports error and warning
->
+messages to the console in {\sc OOPSE} is a good candidate for
->
+applying the Singleton pattern to avoid the global namespace
->
+pollution.Although the singleton pattern can be implemented in
->
+various ways  to account for different aspects of the software
->
+designs, such as lifespan control \textit{etc}, we only use the
->
+static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class
->
+is declared as
->
+\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}]
-+
+class IntegratorFactory {
-+
+  public:
-+
+    static IntegratorFactory* getInstance();
-+
+    protected:
-+
+      IntegratorFactory();
-+
+    private:
-+
+      static IntegratorFactory* instance_;
-+
+};
-+
-+
+\end{lstlisting}
-+
+The corresponding implementation is
-+
+\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}]
-+
-+
+IntegratorFactory::instance_ = NULL;
-+
-+
+IntegratorFactory* getInstance() {
-+
+  if (instance_ == NULL){
-+
+    instance_ = new IntegratorFactory;
-+
+  }
-+
+  return instance_;
-+
+}
-+
-+
+\end{lstlisting}
-+
+Since constructor is declared as {\tt protected}, a client can not
-+
+instantiate {\tt IntegratorFactory} directly. Moreover, since the
-+
+member function {\tt getInstance} serves as the only entry of access
-+
+to {\tt IntegratorFactory}, this approach fulfills the basic
-+
+requirement, a single instance. Another consequence of this approach
-+
+is the automatic destruction since static data are destroyed upon
-+
+program termination.
-+
+\subsection{\label{appendixSection:factoryMethod}Factory Method}
-–
+The Factory Method pattern is a creational pattern which deals with
-–
+the problem of creating objects without specifying the exact class
-–
+of object that will be created. Factory Method solves this problem
-–
+by defining a separate method for creating the objects, which
-–
+subclasses can then override to specify the derived type of product
-–
+that will be created.
-+
+Categoried as a creational pattern, the Factory Method pattern deals
-+
+with the problem of creating objects without specifying the exact
-+
+class of object that will be created. Factory Method is typically
-+
+implemented by delegating the creation operation to the subclasses.
-+
+Registers a creator with a type identifier. Looks up the type
-+
+identifier in the internal map. If it is found, it invokes the
-+
+corresponding creator for the type identifier and returns its
-+
+result.
-+
+\begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}]
-+
-+
+class IntegratorFactory {
-+
+  public:
-+
+    typedef std::map<string, IntegratorCreator*> CreatorMapType;
-+
-+
+    bool registerIntegrator(IntegratorCreator* creator);
-+
-+
+    Integrator* createIntegrator(const string& id, SimInfo* info);
-+
-+
+  private:
-+
+    CreatorMapType creatorMap_;
-+
+};
-+
-+
+\end{lstlisting}
-+
-+
+\begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}]
-+
-+
+bool IntegratorFactory::unregisterIntegrator(const string& id) {
-+
+  return creatorMap_.erase(id) == 1;
-+
+}
-+
-+
+Integrator* IntegratorFactory::createIntegrator(const string& id,
-+
+                                                SimInfo* info) {
-+
+  CreatorMapType::iterator i = creatorMap_.find(id);
-+
+  if (i != creatorMap_.end()) {
-+
+    return (i->second)->create(info);
-+
+  } else {
-+
+    return NULL;
-+
+  }
-+
+}
-+
-+
+\end{lstlisting}
-+
-+
+\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}]
-+
-+
+class IntegratorCreator {
-+
+  public:
-+
+    IntegratorCreator(const string& ident) : ident_(ident) {}
-+
-+
+    const string& getIdent() const { return ident_; }
-+
-+
+    virtual Integrator* create(SimInfo* info) const = 0;
-+
-+
+  private:
-+
+    string ident_;
-+
+};
-+
-+
+template<class ConcreteIntegrator>
-+
+class IntegratorBuilder : public IntegratorCreator {
-+
+  public:
-+
+    IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {}
-+
+    virtual  Integrator* create(SimInfo* info) const {
-+
+      return new ConcreteIntegrator(info);
-+
+    }
-+
+};
-+
+\end{lstlisting}
-+
+\subsection{\label{appendixSection:visitorPattern}Visitor}
-+
+The purpose of the Visitor Pattern is to encapsulate an operation
-<
+that you want to perform on the elements of a data structure. In
-<
+this way, you can change the operation being performed on a
-<
+structure without the need of changing the classes of the elements
-<
+that you are operating on.
->
+that you want to perform on the elements. The operation being
->
+performed on a structure can be switched without changing the
->
+interfaces  of the elements. In other words, one can add virtual
->
+functions into a set of classes without modifying their interfaces.
->
+The UML class diagram of Visitor patten is shown in
->
+Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in
->
+Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern
->
+extensively.
-+
+\begin{figure}
-+
+\centering
-+
+\includegraphics[width=\linewidth]{visitor.eps}
-+
+\caption[The architecture of {\sc OOPSE}] {Overview of the structure
-+
+of {\sc OOPSE}} \label{appendixFig:visitorUML}
-+
+\end{figure}
-<
+\subsection{\label{appendixSection:templateMethod}Template Method}
->
+\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
-<
+\section{\label{appendixSection:analysisFramework}Analysis Framework}
->
+class BaseVisitor{
->
+  public:
->
+    virtual void visit(Atom* atom);
->
+    virtual void visit(DirectionalAtom* datom);
->
+    virtual void visit(RigidBody* rb);
->
+};
->
->
+\end{lstlisting}
->
->
+\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
->
->
+class StuntDouble {
->
+  public:
->
+    virtual void accept(BaseVisitor* v) = 0;
->
+};
-+
+class Atom: public StuntDouble {
-+
+  public:
-+
+    virtual void accept{BaseVisitor* v*} {
-+
+      v->visit(this);
-+
+    }
-+
+};
-+
-+
+class DirectionalAtom: public Atom {
-+
+  public:
-+
+    virtual void accept{BaseVisitor* v*} {
-+
+      v->visit(this);
-+
+    }
-+
+};
-+
-+
+class RigidBody: public StuntDouble {
-+
+  public:
-+
+    virtual void accept{BaseVisitor* v*} {
-+
+      v->visit(this);
-+
+    }
-+
+};
-+
-+
+\end{lstlisting}
+\section{\label{appendixSection:concepts}Concepts}
+OOPSE manipulates both traditional atoms as well as some objects
+\begin{figure}
+\centering
+\includegraphics[width=3in]{heirarchy.eps}
-<
+\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
-<
+The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
-<
+selection syntax allows the user to select any of the objects that
-<
+are descended from a StuntDouble.} \label{oopseFig:heirarchy}
-<
+\end{figure}
-<
->
+\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ The
->
+class heirarchy of StuntDoubles in {\sc oopse}-3.0.
+\begin{itemize}
+\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
+integrators and minimizers.
+\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
+\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
+DirectionalAtom}s which behaves as a single unit.
-<
+\end{itemize}
->
+\end{itemize}} \label{oopseFig:heirarchy}
->
+\end{figure}
-<
+Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
->
+Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
+own names which are specified in the {\tt .md} file. In contrast,
+RigidBodies are denoted by their membership and index inside a
+particular molecule: [MoleculeName]\_RB\_[index] (the contents
+\section{\label{appendixSection:syntax}Syntax of the Select Command}
+The most general form of the select command is: {\tt select {\it
-<
+expression}}
->
+expression}}. This expression represents an arbitrary set of
->
+StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
->
+composed of either name expressions, index expressions, predefined
->
+sets, user-defined expressions, comparison operators, within
->
+expressions, or logical combinations of the above expression types.
->
+Expressions can be combined using parentheses and the Boolean
->
+operators.
-–
+This expression represents an arbitrary set of StuntDoubles (Atoms
-–
+or RigidBodies) in {\sc oopse}. Expressions are composed of either
-–
+name expressions, index expressions, predefined sets, user-defined
-–
+expressions, comparison operators, within expressions, or logical
-–
+combinations of the above expression types. Expressions can be
-–
+combined using parentheses and the Boolean operators.
-–
+\subsection{\label{appendixSection:logical}Logical expressions}
+The logical operators allow complex queries to be constructed out of
+Users can define arbitrary terms to represent groups of
+StuntDoubles, and then use the define terms in select commands. The
+general form for the define command is: {\bf define {\it term
-<
+expression}}
->
+expression}}. Once defined, the user can specify such terms in
->
+boolean expressions
-–
+Once defined, the user can specify such terms in boolean expressions
-–
+{\tt define SSDWATER SSD or SSD1 or SSDRF}
+{\tt select SSDWATER}
+select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
+atoms.
-–
+\section{\label{appendixSection:tools}Tools which use the selection command}
-<
+\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
-<
-<
+Dump2XYZ can transform an OOPSE dump file into a xyz file which can
-<
+be opened by other molecular dynamics viewers such as Jmol and VMD.
-<
+The options available for Dump2XYZ are as follows:
->
+\section{\label{appendixSection:analysisFramework}Analysis Framework}
-–
-–
+\begin{longtable}[c]{|EFG|}
-–
+\caption{Dump2XYZ Command-line Options}
-–
+\\ \hline
-–
+{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
-–
+\endhead
-–
+\hline
-–
+\endfoot
-–
+  -h & {\tt -{}-help} &                        Print help and exit \\
-–
+  -V & {\tt -{}-version} &                     Print version and exit \\
-–
+  -i & {\tt -{}-input=filename}  &             input dump file \\
-–
+  -o & {\tt -{}-output=filename} &             output file name \\
-–
+  -n & {\tt -{}-frame=INT}   &                 print every n frame  (default=`1') \\
-–
+  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
-–
+  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
-–
+  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
-–
+  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
-–
+  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
-–
+  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
-–
+     & {\tt -{}-repeatX=INT}  &                 The number of images to repeat in the x direction  (default=`0') \\
-–
+     & {\tt -{}-repeatY=INT} &                 The number of images to repeat in the y direction  (default=`0') \\
-–
+     &  {\tt -{}-repeatZ=INT}  &                The number of images to repeat in the z direction  (default=`0') \\
-–
+  -s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
-–
+converted. \\
-–
+     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
-–
+     & {\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}.
-–
+\end{longtable}
-–
-–
+\subsection{\label{appendixSection:StaticProps}StaticProps}
+{\tt StaticProps} can compute properties which are averaged over
+some or all of the configurations that are contained within a dump
+file. The most common example of a static property that can be
+computed is the pair distribution function between atoms of type $A$
-<
+and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
-<
+used to compute the density distributions of other molecules in a
-<
+reference frame {\it fixed to the body-fixed reference frame} of a
-<
+selected atom or rigid body.
->
+and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
->
+also be used to compute the density distributions of other molecules
->
+in a reference frame {\it fixed to the body-fixed reference frame}
->
+of a selected atom or rigid body.
+There are five seperate radial distribution functions availiable in
+OOPSE. Since every radial distrbution function invlove the
+Any two directional objects (DirectionalAtoms and RigidBodies) have
+a set of two angles ($\theta$, and $\omega$) between the z-axes of
+their body-fixed frames.} \label{oopseFig:gofr}
-+
+\end{figure}
-+
-+
+Due to the fact that the selected StuntDoubles from two selections
-+
+may be overlapped, {\tt StaticProps} performs the calculation in
-+
+three stages which are illustrated in
-+
+Fig.~\ref{oopseFig:staticPropsProcess}.
-+
-+
+\begin{figure}
-+
+\centering
-+
+\includegraphics[width=\linewidth]{staticPropsProcess.eps}
-+
+\caption[A representation of the three-stage correlations in
-+
+\texttt{StaticProps}]{This diagram illustrates three-stage
-+
+processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the
-+
+numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt
-+
+-{}-sele2} respectively, while $C$ is the number of stuntdobules
-+
+appearing at both sets. The first stage($S_1-C$ and $S_2$) and
-+
+second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On
-+
+the contrary, the third stage($C$ and $C$) are completely
-+
+overlapping} \label{oopseFig:staticPropsProcess}
+\end{figure}
+The options available for {\tt StaticProps} are as follows:
+\endfoot
+  -h& {\tt -{}-help}                    &  Print help and exit \\
+  -V& {\tt -{}-version}                 &  Print version and exit \\
-<
+  -i& {\tt -{}-input=filename}          &  input dump file \\
-<
+  -o& {\tt -{}-output=filename}         &  output file name \\
-<
+  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
-<
+  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
-<
+  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
-<
+  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
-<
+    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
-<
+    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
-<
+    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
-<
+    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
-<
+    & {\tt -{}-molname=STRING}           & molecule name \\
-<
+    & {\tt -{}-begin=INT}                & begin internal index \\
-<
+    & {\tt -{}-end=INT}                  & end internal index \\
->
+  -i& {\tt -{}-input}          &  input dump file \\
->
+  -o& {\tt -{}-output}         &  output file name \\
->
+  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
->
+  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
->
+  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
->
+  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
->
+    & {\tt -{}-sele1}   & select the first StuntDouble set \\
->
+    & {\tt -{}-sele2}   & select the second StuntDouble set \\
->
+    & {\tt -{}-sele3}   & select the third StuntDouble set \\
->
+    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
->
+    & {\tt -{}-molname}           & molecule name \\
->
+    & {\tt -{}-begin}                & begin internal index \\
->
+    & {\tt -{}-end}                  & end internal index \\
+\hline
+\multicolumn{3}{|l|}{One option from the following group of options is required:} \\
+\hline
+different vectors).  The ability to use two selection scripts to
+select different types of atoms is already present in the code.
-+
+For large simulations, the trajectory files can sometimes reach
-+
+sizes in excess of several gigabytes. In order to effectively
-+
+analyze that amount of data. In order to prevent a situation where
-+
+the program runs out of memory due to large trajectories,
-+
+\texttt{dynamicProps} will estimate the size of free memory at
-+
+first, and determine the number of frames in each block, which
-+
+allows the operating system to load two blocks of data
-+
+simultaneously without swapping. Upon reading two blocks of the
-+
+trajectory, \texttt{dynamicProps} will calculate the time
-+
+correlation within the first block and the cross correlations
-+
+between the two blocks. This second block is then freed and then
-+
+incremented and the process repeated until the end of the
-+
+trajectory. Once the end is reached, the first block is freed then
-+
+incremented, until all frame pairs have been correlated in time.
-+
+This process is illustrated in
-+
+Fig.~\ref{oopseFig:dynamicPropsProcess}.
-+
-+
+\begin{figure}
-+
+\centering
-+
+\includegraphics[width=\linewidth]{dynamicPropsProcess.eps}
-+
+\caption[A representation of the block correlations in
-+
+\texttt{dynamicProps}]{This diagram illustrates block correlations
-+
+processing in \texttt{dynamicProps}. The shaded region represents
-+
+the self correlation of the block, and the open blocks are read one
-+
+at a time and the cross correlations between blocks are calculated.}
-+
+\label{oopseFig:dynamicPropsProcess}
-+
+\end{figure}
-+
+The options available for DynamicProps are as follows:
+\begin{longtable}[c]{|EFG|}
+\caption{DynamicProps Command-line Options}
+\endfoot
+  -h& {\tt -{}-help}                   & Print help and exit \\
+  -V& {\tt -{}-version}                & Print version and exit \\
-<
+  -i& {\tt -{}-input=filename}         & input dump file \\
-<
+  -o& {\tt -{}-output=filename}        & output file name \\
-<
+    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
-<
+    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
->
+  -i& {\tt -{}-input}         & input dump file \\
->
+  -o& {\tt -{}-output}        & output file name \\
->
+    & {\tt -{}-sele1} & select first StuntDouble set \\
->
+    & {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
+\hline
+\multicolumn{3}{|l|}{One option from the following group of options is required:} \\
+\hline
+  -d& {\tt -{}-dcorr}                  & compute dipole correlation function
+\end{longtable}
-<
+\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
->
+\section{\label{appendixSection:tools}Other Useful Utilities}
->
->
+\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
->
->
+{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file
->
+which can be opened by other molecular dynamics viewers such as Jmol
->
+and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
->
+as follows:
->
->
->
+\begin{longtable}[c]{|EFG|}
->
+\caption{Dump2XYZ Command-line Options}
->
+\\ \hline
->
+{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
->
+\endhead
->
+\hline
->
+\endfoot
->
+  -h & {\tt -{}-help} &                        Print help and exit \\
->
+  -V & {\tt -{}-version} &                     Print version and exit \\
->
+  -i & {\tt -{}-input}  &             input dump file \\
->
+  -o & {\tt -{}-output} &             output file name \\
->
+  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
->
+  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
->
+  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
->
+  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
->
+  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
->
+  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
->
+  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
->
+     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
->
+     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
->
+     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
->
+  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
->
+converted. \\
->
+     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
->
+     & {\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}.
->
+\end{longtable}
->
->
+\subsection{\label{appendixSection:hydrodynamics}Hydro}
->
->
+{\tt Hydro} can calculate resistance and diffusion tensors at the
->
+center of resistance. Both tensors at the center of diffusion can
->
+also be reported from the program, as well as the coordinates for
->
+the beads which are used to approximate the arbitrary shapes. The
->
+options available for Hydro are as follows:
->
+\begin{longtable}[c]{|EFG|}
->
+\caption{Hydrodynamics Command-line Options}
->
+\\ \hline
->
+{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
->
+\endhead
->
+\hline
->
+\endfoot
->
+  -h & {\tt -{}-help} &                        Print help and exit \\
->
+  -V & {\tt -{}-version} &                     Print version and exit \\
->
+  -i & {\tt -{}-input}  &             input dump file \\
->
+  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
->
+  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
->
+     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
->
+\end{longtable}

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Comparing trunk/tengDissertation/Appendix.tex (file contents): Revision 2805 by tim, Tue Jun 6 20:33:28 2006 UTC vs. Revision 2827 by tim, Thu Jun 8 20:05:53 2006 UTC

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Comparing trunk/tengDissertation/Appendix.tex (file contents):
Revision 2805 by tim, Tue Jun 6 20:33:28 2006 UTC vs.
Revision 2827 by tim, Thu Jun 8 20:05:53 2006 UTC