\documentclass[12pt]{report}
\topmargin=0in
\headheight=0in
\headsep=0in
\oddsidemargin=0in
\evensidemargin=0in
\textwidth=6.5in
\textheight=9in

\usepackage{acronym}
\usepackage{setspace}
\usepackage{graphicx}
\usepackage{listings,cite,footmisc,multirow,url,amsmath}
\usepackage{color}
\usepackage{pslatex}
\usepackage{fullpage}
\usepackage{alltt}
\usepackage{rotating}
\usepackage{float}
\usepackage{pifont}
\usepackage{wasysym}
\usepackage{makeidx}
\usepackage{glossary}
\usepackage[noauto]{chappg}
\usepackage{textcomp}
\usepackage{boxedminipage}
\usepackage[subfigure]{tocloft}
\usepackage{subfigure}
\usepackage{tocloft}
%\usepackage[printonlyused,withpage]{acronym}



%index
\makeindex

%glossary
\makeglossary

%calculations
\newcommand{\listcalculationsname}{List of Calculations}
\newlistof[chapter]{calculations}{loc}{\listcalculationsname}
\newfloat{calculations}{htpb}{loc}[chapter]
\floatname{calculations}{Calculations}

%samples
\newcommand{\listsamplename}{List of Samples}
\newlistof[chapter]{sample}{los}{\listsamplename}
\newfloat{sample}{htpb}{los}[chapter]
\floatname{sample}{Sample}

%listings
\renewcommand{\lstlistlistingname}{List of Code}
\renewcommand{\lstlistingname}{Code}
\lstset{tabsize=2,frame=single,basicstyle=\tiny,lineskip=3pt}

\lstdefinelanguage{nova}[AUTO]{lisp}{morekeywords=NOVA-USER>}

%custom commands
\newcommand{\fig}[1]{(Figure~\ref{fig:#1})}
\newcommand{\eq}[1]{(Equation~\ref{eq:#1})}
\newcommand{\code}[1]{(Code~\ref{code:#1})}
\newcommand{\calc}[1]{(Calculations~\ref{calc:#1})}
\newcommand{\tab}[1]{Table~(\ref{tab:#1})}
\newcommand{\subsec}[1]{(\ref{subsec:#1})}


\newcommand{\nova}{NOVA}
\newcommand{\xomo}{XOMO}

\singlespacing

\begin{document}
\thispagestyle{empty}

\title{\large NOVA: Search based \ldots}
\author{\normalsize Phillip Green II \\ \\
\normalsize Thesis submitted to the \\
\normalsize College of Engineering and Mineral Resources \\
\normalsize at West Virginia University \\
\normalsize in partial fulfillment of the requirements \\
\normalsize for the degree of \\ \\
\normalsize Master of Science \\
\normalsize in \\
\normalsize Computer Science \\ \\
\normalsize Tim Menzies, Ph.D., Chair \\
\normalsize Elaine Eschen, Ph.D. \\
\normalsize Afzel Noore, Ph.D. \\ \\
\normalsize Lane Department of Computer Science and Electrical Engineering \\ \\
\normalsize Morgantown, West Virginia \\
\normalsize 2008 \\ \\
\normalsize Keywords: TODO: add keywords\\ \\
\normalsize Copyright \copyright~2008 Phillip Green II
}

\date{}
\maketitle

\label{abstract}
\input{abstract}

\doublespacing

\renewcommand{\thepage}{\roman{page}}
\setcounter{page}{3}

\chapter*{Dedication}
\label{dedication}
\input{dedication}

\chapter*{Acknowledgments}
\label{acknowledgments}
\input{acknowledgments}

\singlespacing

\tableofcontents
\listoffigures
\listoftables
\lstlistoflistings
\listofcalculations
\listofsample
\pagebreak

\doublespacing

\setcounter{page}{1}
\pagenumbering{arabic}

\chapter{Introduction}
\label{introduction}
\input{introduction}

\chapter{Related Work}
\label{related-work}
\input{related-work}

\chapter{NOVA: The walkthrough (User)}
\label{nova-user-interface}
\input{nova-user-interface}

\chapter{NOVA: The walkthrough (Programmer)}
\label{nova-programmer-interface}
\input{nova-programmer-interface}

\chapter{NOVA: Under the Hood}
\label{nova-implementation}
\input{nova-implementation}

\chapter{Applications}
\label{nova-applications}
\input{nova-applications}

\pagebreak

\singlespacing

\addcontentsline{toc}{chapter}{Acronyms}
%FIXME why error occurs when defining acronym envirment.
%\begin{acronym}[MRE]
% \acro{MRE}{Magnitude of Relative Error}
%\end{acronym}
\pagebreak

\addcontentsline{toc}{chapter}{Glossary}
\printglossary
\pagebreak

\addcontentsline{toc}{chapter}{Index}
\printindex
\pagebreak

\appendix
\pagenumbering{bychapter}

\doublespacing

\chapter{Setup}
\label{setup}
\input{setup}

\chapter{Code}
\label{code}
%\input{code}

\chapter{Scripts}
\label{scripts}
%\input{scripts}

\pagebreak

\singlespacing

\bibliography{refs,myrefs}
\bibliographystyle{plain}

\pagebreak
\thispagestyle{empty}

\end{document}
