\documentclass{ruthesis}
\usepackage{cite,latexsym,graphicx,amsmath,epsfig,array}

% PC/Unix settings for non-american encoding.
% Used to get Icelandic characters properly.
\usepackage[T1]{fontenc}
\usepackage[latin1]{inputenc}    

%\fontfamily{ppl}
%\fontseries{b}
%\selectfont
%\renewcommand{\rmdefault}{PS-Palatino-Roman}
\renewcommand{\sfdefault}{cmss}
%\renewcommand{\ttdefault}{cmtt}
\renewcommand{\topfraction}{1.0}

% Include special shortcut commmands 

        \include{commands}

\begin{document}

% Use \draft until you are done
%\draft

% For a  PhD give the command \phd. If you don't do this then the default
% is for a Masters Degree.
% Optional fields are (where normal is for PhD or the default Master
% of Science:
%       \degree (normally Doctor of Philosophy or Master of Science)
%       \initials (normally Ph.D. or M.S.)
%       \draft (this should probably be set  until near the final
%              drafts. Currently it modifies the title page.)
\phd

%  Title and other sections that come before the body  of the document
       \include{title}

% Now lets include the body of the document...

% Chapter 1
       \include{Chapter-1/chap1}
% Chapter 2
       \include{Chapter-2/chap2}
% Chapter 3
       \include{Chapter-3/chap3}
% Chapter 4
       \include{Chapter-4/chap4}
% Chapter 5
       \include{Chapter-5/chap5}
% Chapter 6
       \include{Chapter-6/chap6}
% Chapter 7
       \include{Chapter-7/chap7}
% Chapter 8
       \include{Chapter-8/chap8}
% Chapter 9
       \include{Chapter-9/chap9}

% In the appendix some things should change, so a user should say that
% its starting.
    \appendix

    \include{Appendix/transforms}
    \include{Appendix/betheInt}
    \include{Appendix/fermiLiq}
    \include{Appendix/spectral}
    \include{Appendix/lambin}
    \include{Appendix/lambin2}
    \include{Appendix/palsson}
    \include{Appendix/heildi}

    \bibliography{BibTex/journals,BibTex/articles,BibTex/books,BibTex/thesis}
    \bibliographystyle{unsrt}
    \include{vita}                 

\end{document}










