--- trunk/tengDissertation/Appendix.tex 2006/06/08 20:05:53 2827 +++ trunk/tengDissertation/Appendix.tex 2006/06/08 20:10:36 2828 @@ -291,17 +291,22 @@ class RigidBody: public StuntDouble { \end{lstlisting} \section{\label{appendixSection:concepts}Concepts} + +\begin{figure} +\centering +\includegraphics[width=\linewidth]{heirarchy.eps} +\caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class +heirarchy of StuntDoubles in {\sc OOPSE}.} +\label{oopseFig:heirarchy} +\end{figure} 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: +freedom. A diagram of the class heirarchy is illustrated in +Fig.~\ref{oopseFig: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. + \begin{itemize} \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the integrators and minimizers. @@ -309,8 +314,7 @@ DirectionalAtom}s which behaves as a single unit. \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}} \label{oopseFig:heirarchy} -\end{figure} +\end{itemize} Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their own names which are specified in the {\tt .md} file. In contrast,