% Template file for a standard thesis
\documentclass[11pt,notitlepage]{isuthesis}
% notitlepage is used because \begin{abstract} uses titlepage by default, which resets the page numbers
\usepackage[pdftex]{graphicx}
% Standard, old-style thesis
\usepackage{isutraditional}
\chaptertitle
% Old-style, thesis numbering down to subsubsection
\alternate
\usepackage{rotating}
% Bibliography without numbers or labels
\usepackage{natbib}
% Use the following line if you want square brackets and numbering system
%\usepackage[square, numbers]{natbib}
\renewcommand{\bibfont}{\setstretch{1}\selectfont}
\setlength{\bibsep}{13.2pt}
\usepackage{chapterbib}
%\renewcommand\bibsection{\section*{\ref name}}
%\renewcommand\bibsection{\section*}
\renewcommand{\bibsection}{\section{References}}
%\bibliographystyle{apa} % changed from apa, abbrv, unsrtnat
%\includeonly{titletoc,chapter1}
%Optional Package to add PDF bookmarks and hypertext links
\usepackage[pdftex,hypertexnames=false,linktocpage=true]{hyperref}
\hypersetup{colorlinks=true,linkcolor=blue,anchorcolor=blue,citecolor=blue,filecolor=blue,urlcolor=blue,bookmarksnumbered=true,pdfview=FitB}
%\usepackage{titletoc}
\usepackage{hyperref}
% \usepackage{subfig} %% Use this package instead of the subcaptions package for subfigures. Please see at the end of this file, an example of how to use the package.
\overfullrule=0pt
%%%%%%%%%%%%%%%%%%%%%
% The following piece of code removes extra space on the top of each chapter
% that is default of latex report class documents
\usepackage{etoolbox}
\makeatletter
\patchcmd{\@makechapterhead}{50\p@}{0pt}{}{}
\patchcmd{\@makeschapterhead}{50\p@}{0pt}{}{}
\setlength{\@fptop}{0pt} %command added to ensure images always float on top of the page
\makeatother
%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%
% Removing Bold characters in the Table of Contents
% % Alternatively to this the isuthesis.cls file has been changed by default in the
% % line section \renewcommand{\l@chapter}[2]{\addpenalty{-\@highpenalty}....
%\titlecontents{chapter}
%[0pt] % left margin
%{}%
%{\contentsmargin{0pt} % numbered entry format
% \thecontentslabel\enspace%
% \large}
%{\contentsmargin{0pt}\large} % unnumbered entry format
%{\titlerule*[.5pc]{.}\contentspage} % filler-page format (e.g dots)
%[] % below code (e.g vertical space)
%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% In order to change space between the Table of contents items go to isuthesis.cls
% line \renewcommand{\l@chapter}[2]{\addpenalty{-\@highpenalty}....
% change \vkip values
%%%%%%%%%%%%%%%%%%%%%%%%%%
%% This is to minimize orphan lines. Might not be possible to entirely remove them
% Method 1 of doing this
\widowpenalty100000
\clubpenalty100000
% Method 2 of doing this
\usepackage[all]{nowidow}
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% control bibliography spacings
% \newlength{\bibitemsep}\setlength{\bibitemsep}{\baselineskip}
% % plus .05\baselineskip minus .05\baselineskip}
% \newlength{\bibparskip}\setlength{\bibparskip}{0pt}
% \let\oldthebibliography\thebibliography
% \renewcommand\thebibliography[1]{%
% \oldthebibliography{#1}%
% \setlength{\parskip}{\bibitemsep}%
% \setlength{\itemsep}{\bibparskip}%
% }
% \usepackage{setspace}
% \setlength{\bibsep}{2sp}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %% aligning lof captions
% \usepackage{tocloft}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set the margins in the whole document
\geometry{letterpaper, left=1in, top=1in, right=1in, bottom=1in, includehead=true}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{amssymb}
\usepackage[intoc, english]{nomencl}
\begin{document}
\DeclareGraphicsExtensions{.jpg,.pdf,.mps,.png}
%\begin{singlespace}
\def\@makechapterheada{\vspace*{-2cm}\titlepage} % in order to reduce the space between margin and heading in titlepage
\include{Preface/titlepage}
%\end{singlespace}
% Left-justified setting for all sections including
% dedication, nomenclature, acknowledgement, abstract and all chapters
% Re-position the two lines below will change all the section
% being compiled after those two lines
\raggedright
\parindent 0.25 in % set all paragraphs in the document to have indent
% Optional thesis dedication
\include{Preface/dedication}
% Table of Contents, List of Tables and List of Figures
{
\pdfbookmark[1]{TABLE OF CONTENTS}{table}
\tableofcontents
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% The line below adds the word "Page" over the page numbers in TOC, LOT, LOF
\addtocontents{toc}{~\hfill\textbf{Page}\par}
\addtocontents{lot}{~\hfill\textbf{Page}\par}
\addtocontents{lof}{~\hfill\textbf{Page}\par}
%%
\addtocontents{toc}{\def\protect\@chapapp{}} \cleardoublepage \phantomsection
\pagebreak
\addcontentsline{toc}{chapter}{LIST OF TABLES}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\listoftables
\cleardoublepage \phantomsection \addcontentsline{toc}{chapter}{LIST OF FIGURES}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\listoffigures
%Optional Nomenclature
\cleardoublepage \phantomsection
\include{Preface/nomenclature}
% Comment out the next line if NOT using chaptertitle
\addtocontents{toc}{\def\protect\@chapapp{CHAPTER\ }}
%Optional Acknowledgements
\cleardoublepage \phantomsection
\include{Preface/acknowl}
%Optional thesis abstract
\cleardoublepage \phantomsection
\include{Preface/abstract}
\newpage
\pagenumbering{arabic}
\include{Body/ch1/ch1_main}
\include{Body/ch2/ch2_main}
\include{Body/ch3/ch3_main}
\include{Body/ch4/ch4_main}
\include{Body/ch5/ch5_main}
\include{Body/ch6/ch6_future_and_conclusions}
%%%%%% bibliographies
%\clearpage
%% \nocite{*}
%\unappendixtitle
%\newpage
%% % \phantomsection
%\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
%\section*{BIBLIOGRAPHY}
%\bibliographystyle{apa}
%\vspace{-20pt}
%\begingroup
% \setlength{\bibsep}{14.5pt}
% \linespread{1}\selectfont
% \bibliography{master_bib}
%\endgroup
% Renders the citations but does not show the bibliography at the end of the thesis
%\newsavebox\mytempbib
%\savebox\mytempbib{\parbox{\textwidth}{\bibliography{master_bib}}}
\clearpage
\pagebreak
%% Only within chapter appendix is allowed for Journal style writing
%\include{Appendix/appendix1} % Instruction for single appendix look below
%\include{Appendix/appendix2}
\end{document}
% use \isucaption{} for all captions of figures and tables, where the captions are not too long.
% Use \isucaption[]{} with the square brackets for short caption of figure or table that goes into the list of tables and list of figures, and the curly brackets can have long captions which go with the figure/ table.
% IMPORTANT NOTES
% TABLE OF CONTENTS :
% TOPIC 1: If you need a page break follow the steps below
% step1
% check before which chapter in the table of contents you want a page break
% step 2
% go the folder "body". There open the chapter tex file that you noted needed page break in the table of contents..
% step 3
% insert \addtocontents{toc}{\protect\newpage} before the first line i.e. before the line \chapter{RESULTS}.
%%%%%%%%%%%%%%
% use \isucaption{} for all captions of figures and tables, where the captions are not too long.
% Use \isucaption[]{} with the square brackets for short caption of figure or table that goes into the list of tables and list of figures, and the curly brackets can have long captions which go with the figure/ table.
%%%%%% Using sub figures
% %%% In preamble include : \usepackage{subfig}
% \begin{figure}[htbp]
% \centering
% \subfloat[first caption.\label{fig:2a}]{\includegraphics[width=0.2\textwidth]{Images/dc5.jpg}}\hfill
% \subfloat[second caption.\label{fig:2b}] {\includegraphics[width=0.2\textwidth]{Images/dc5.jpg}}\hfill
% \isucaption{Sub-figure test}
% \label{fig:subfigure-test}
% \end{figure}
% Subfloat reference: Fig \ref{fig:2a}
% Figure reference: Fig \ref{fig:subfigure-test}
