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-<
+\chapter{\label{chapt:appendix}APPENDIX}
->
+\appendix
->
+\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine (OOPSE)}
-+
+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{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
-+
+contributed by scientists without official computer science
-+
+training. The development of most MD applications are lack of strong
-+
+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.
-+
-+
+\section{\label{appendixSection:architecture }Architecture}
-+
-+
+\begin{figure}
-+
+\centering
-+
+\includegraphics[width=3in]{architecture.eps}
-+
+\caption[The architecture of {\sc oopse}-3.0] {The architecture
-+
+of{\sc oopse}-3.0.} \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{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.
-<
+\subsection{\label{appendixSection:visitorPattern}Visitor Pattern}
->
+Patterns are usually described using a format that includes the
->
+following information:
->
+\begin{enumerate}
->
+  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
->
+  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
->
+  in the literature. In this case it is common practice to document these nicknames or synonyms under
->
+  the heading of \emph{Aliases} or \emph{Also Known As}.
->
+  \item The \emph{motivation} or \emph{context} that this pattern applies
->
+  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
->
+  \item The \emph{solution} to the problem that the pattern
->
+  addresses. It describes how to construct the necessary work products. The description may include
->
+  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
->
+  collaborations, to show how the problem is solved.
->
+  \item The \emph{consequences} of using the given solution to solve a
->
+  problem, both positive and negative.
->
+\end{enumerate}
-<
+\subsection{\label{appendixSection:templatePattern}Template Pattern}
->
+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}.
-<
+\subsection{\label{appendixSection:factoryPattern}Factory Pattern}
->
+\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.
-<
+\section{\label{appendixSection:hierarchy}Hierarchy}
->
+\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.
-–
+\section{\label{appendixSection:selectionSyntax}Selection Syntax}
-<
+\section{\label{appendixSection:hydrodynamics}Hydrodynamics}
->
+\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.
-+
-+
+\subsection{\label{appendixSection:templateMethod}Template Method}
-+
-+
+\section{\label{appendixSection:concepts}Concepts}
-+
-+
+OOPSE manipulates both traditional atoms as well as some objects
-+
+that {\it behave like atoms}.  These objects can be rigid
-+
+collections of atoms or atoms which have orientational degrees of
-+
+freedom.  Here is a diagram of the class heirarchy:
-+
-+
+%\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}
-+
-+
+\begin{itemize}
-+
+\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
-+
+integrators and minimizers.
-+
+\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
-+
+\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}
-+
-+
+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
-+
+inside the brackets depend on the specifics of the simulation). The
-+
+names of rigid bodies are generated automatically. For example, the
-+
+name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
-+
-+
+\section{\label{appendixSection:syntax}Syntax of the Select Command}
-+
-+
+The most general form of the select command is: {\tt select {\it
-+
+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.
-+
-+
+\subsection{\label{appendixSection:logical}Logical expressions}
-+
-+
+The logical operators allow complex queries to be constructed out of
-+
+simpler ones using the standard boolean connectives {\bf and}, {\bf
-+
+or}, {\bf not}. Parentheses can be used to alter the precedence of
-+
+the operators.
-+
-+
+\begin{center}
-+
+\begin{tabular}{|ll|}
-+
+\hline
-+
+{\bf logical operator} & {\bf equivalent operator}  \\
-+
+\hline
-+
+and & ``\&'', ``\&\&'' \\
-+
+or & ``$|$'', ``$||$'', ``,'' \\
-+
+not & ``!''  \\
-+
+\hline
-+
+\end{tabular}
-+
+\end{center}
-+
-+
+\subsection{\label{appendixSection:name}Name expressions}
-+
-+
+\begin{center}
-+
+\begin{tabular}{|llp{2in}|}
-+
+\hline {\bf type of expression} & {\bf examples} & {\bf translation
-+
+of
-+
+examples} \\
-+
+\hline expression without ``.'' & select DMPC & select all
-+
+StuntDoubles
-+
+belonging to all DMPC molecules \\
-+
+ & select C* & select all atoms which have atom types beginning with C
-+
+\\
-+
+ & select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but
-+
+only select the rigid bodies, and not the atoms belonging to them). \\
-+
+\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the
-+
+O\_TIP3P
-+
+atoms belonging to TIP3P molecules \\
-+
+ & select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to
-+
+the first
-+
+RigidBody in each DMPC molecule \\
-+
+ & select DMPC.20 & select the twentieth StuntDouble in each DMPC
-+
+molecule \\
-+
+\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* &
-+
+select all atoms
-+
+belonging to all rigid bodies within all DMPC molecules \\
-+
+\hline
-+
+\end{tabular}
-+
+\end{center}
-+
-+
+\subsection{\label{appendixSection:index}Index expressions}
-+
-+
+\begin{center}
-+
+\begin{tabular}{|lp{4in}|}
-+
+\hline
-+
+{\bf examples} & {\bf translation of examples} \\
-+
+\hline
-+
+select 20 & select all of the StuntDoubles belonging to Molecule 20 \\
-+
+select 20 to 30 & select all of the StuntDoubles belonging to
-+
+molecules which have global indices between 20 (inclusive) and 30
-+
+(exclusive) \\
-+
+\hline
-+
+\end{tabular}
-+
+\end{center}
-+
-+
+\subsection{\label{appendixSection:predefined}Predefined sets}
-+
-+
+\begin{center}
-+
+\begin{tabular}{|ll|}
-+
+\hline
-+
+{\bf keyword} & {\bf description} \\
-+
+\hline
-+
+all & select all StuntDoubles \\
-+
+none & select none of the StuntDoubles \\
-+
+\hline
-+
+\end{tabular}
-+
+\end{center}
-+
-+
+\subsection{\label{appendixSection:userdefined}User-defined expressions}
-+
-+
+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}}
-+
-+
+Once defined, the user can specify such terms in boolean expressions
-+
-+
+{\tt define SSDWATER SSD or SSD1 or SSDRF}
-+
-+
+{\tt select SSDWATER}
-+
-+
+\subsection{\label{appendixSection:comparison}Comparison expressions}
-+
-+
+StuntDoubles can be selected by using comparision operators on their
-+
+properties. The general form for the comparison command is: a
-+
+property name, followed by a comparision operator and then a number.
-+
-+
+\begin{center}
-+
+\begin{tabular}{|l|l|}
-+
+\hline
-+
+{\bf property} & mass, charge \\
-+
+{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'',
-+
+``$<=$'', ``$!=$'' \\
-+
+\hline
-+
+\end{tabular}
-+
+\end{center}
-+
-+
+For example, the phrase {\tt select mass > 16.0 and charge < -2}
-+
+would select StuntDoubles which have mass greater than 16.0 and
-+
+charges less than -2.
-+
-+
+\subsection{\label{appendixSection:within}Within expressions}
-+
-+
+The ``within'' keyword allows the user to select all StuntDoubles
-+
+within the specified distance (in Angstroms) from a selection,
-+
+including the selected atom itself. The general form for within
-+
+selection is: {\tt select within(distance, expression)}
-+
-+
+For example, the phrase {\tt select within(2.5, PO4 or NC4)} would
-+
+select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
-+
+atoms.
-+
-+
+\section{\label{appendixSection:analysisFramework}Analysis Framework}
-<
+\subsection{\label{appendixSection:staticProps}Factory Properties}
->
+\subsection{\label{appendixSection:StaticProps}StaticProps}
-<
+\subsection{\label{appendixSection:dynamicProps}Dynamics Properties}
->
+{\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.
->
->
+There are five seperate radial distribution functions availiable in
->
+OOPSE. Since every radial distrbution function invlove the
->
+calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
->
+-{}-sele2} must be specified to tell StaticProps which bodies to
->
+include in the calculation.
->
->
+\begin{description}
->
+\item[{\tt -{}-gofr}] Computes the pair distribution function,
->
+\begin{equation*}
->
+g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A}
->
+\sum_{j \in B} \delta(r - r_{ij}) \rangle
->
+\end{equation*}
->
+\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution
->
+function. The angle is defined by the intermolecular vector
->
+$\vec{r}$ and $z$-axis of DirectionalAtom A,
->
+\begin{equation*}
->
+g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle
->
+\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos
->
+\theta_{ij} - \cos \theta)\rangle
->
+\end{equation*}
->
+\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution
->
+function. The angle is defined by the $z$-axes of the two
->
+DirectionalAtoms A and B.
->
+\begin{equation*}
->
+g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle
->
+\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos
->
+\omega_{ij} - \cos \omega)\rangle
->
+\end{equation*}
->
+\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular
->
+space $\theta, \omega$ defined by the two angles mentioned above.
->
+\begin{equation*}
->
+g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A}
->
+\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos
->
+\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos
->
+\omega)\rangle
->
+\end{equation*}
->
+\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type
->
+B in the body frame of particle A. Therefore, {\tt -{}-originsele}
->
+and {\tt -{}-refsele} must be given to define A's internal
->
+coordinate set as the reference frame for the calculation.
->
+\end{description}
->
->
+The vectors (and angles) associated with these angular pair
->
+distribution functions are most easily seen in the figure below:
->
->
+\begin{figure}
->
+\centering
->
+\includegraphics[width=3in]{definition.eps}
->
+\caption[Definitions of the angles between directional objects]{ \\
->
+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}
->
->
+The options available for {\tt StaticProps} are as follows:
->
+\begin{longtable}[c]{|EFG|}
->
+\caption{StaticProps 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 -{}-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
->
+    &  {\tt -{}-gofr}                    &  $g(r)$ \\
->
+    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
->
+    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
->
+    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
->
+    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
->
+    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
->
+    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
->
+    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
->
+    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
->
+\end{longtable}
->
->
+\subsection{\label{appendixSection:DynamicProps}DynamicProps}
->
->
+{\tt DynamicProps} computes time correlation functions from the
->
+configurations stored in a dump file.  Typical examples of time
->
+correlation functions are the mean square displacement and the
->
+velocity autocorrelation functions.   Once again, the selection
->
+syntax can be used to specify the StuntDoubles that will be used for
->
+the calculation.  A general time correlation function can be thought
->
+of as:
->
+\begin{equation}
->
+C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle
->
+\end{equation}
->
+where $\vec{u}_A(t)$ is a vector property associated with an atom of
->
+type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different
->
+vector property associated with an atom of type $B$ at a different
->
+time $t^{\prime}$.  In most autocorrelation functions, the vector
->
+properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and
->
+$B$) are identical, and the three calculations built in to {\tt
->
+DynamicProps} make these assumptions.  It is possible, however, to
->
+make simple modifications to the {\tt DynamicProps} code to allow
->
+the use of {\it cross} time correlation functions (i.e. with
->
+different vectors).  The ability to use two selection scripts to
->
+select different types of atoms is already present in the code.
->
->
+The options available for DynamicProps are as follows:
->
+\begin{longtable}[c]{|EFG|}
->
+\caption{DynamicProps 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 \\
->
+    & {\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
->
+  -r& {\tt -{}-rcorr}                  & compute mean square displacement \\
->
+  -v& {\tt -{}-vcorr}                  & compute velocity correlation function \\
->
+  -d& {\tt -{}-dcorr}                  & compute dipole correlation function
->
+\end{longtable}
->
->
+\section{\label{appendixSection:tools}Other Useful Utilities}
->
->
+\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:
->
->
->
+\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}Hydrodynamics}
->
->
+\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 (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
->
+\end{longtable}

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Comparing trunk/tengDissertation/Appendix.tex (file contents): Revision 2685 by tim, Mon Apr 3 18:07:54 2006 UTC vs. Revision 2812 by tim, Wed Jun 7 02:40:32 2006 UTC

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Comparing trunk/tengDissertation/Appendix.tex (file contents):
Revision 2685 by tim, Mon Apr 3 18:07:54 2006 UTC vs.
Revision 2812 by tim, Wed Jun 7 02:40:32 2006 UTC