% Main Thesis File: This is the main file and it connects all the different parts of the thesis and compiles it into a single outcome file.
\documentclass[onecolumn, 12 pt, doublespace, fullpage, a4paper]{report}
\renewcommand{\baselinestretch}{1.75} % baseline stretch
% Packages
\usepackage{amssymb}
\usepackage{amsthm}
\usepackage[cmex10]{amsmath}
\usepackage{adjustbox}
\usepackage{arabtex}
\usepackage{academicons}
\usepackage{breakcites}
\usepackage{color}
\usepackage{epsfig}
\usepackage{epstopdf}
\usepackage{etoolbox}
\usepackage{enumitem}
\usepackage{float}
\usepackage{fancyhdr}
\usepackage{graphicx}
\usepackage{graphics}
%\usepackage{hyperref} % if you want to highlight the links
\usepackage[hidelinks]{hyperref}
\usepackage{latexsym,amsfonts}
\usepackage{longtable}
\usepackage{listings}
\usepackage{lscape}
\usepackage{lipsum}
\usepackage{multirow}
\usepackage{pdfpages}
\usepackage[figuresright]{rotating}
\usepackage{sectsty}
\usepackage{setspace}
\usepackage{subfigure}
\usepackage{textcomp}
\usepackage{utf8}
\usepackage{url}
\usepackage{wrapfig}
\usepackage{wasysym}
\usepackage{xcolor}
% you can define your most used synonyms/acronyms
\def\KAUST {King Abdullah University of Science and Technology}
\def\dg{$^\circ$} % for degree celcius
\def\2{$^2$} % for raised to power 2
\def\3{$^3$} % for raised to power 3
\def\-2{$^{-2}$} % for raised to power -2
\def\-3{$^{-3}$} % for raised to power -2
\def\-1{$^{-1}$} % for raised to power -1
\def\h{W.m$^{-2}$K$^{-1}$}
\def\hh{kJ.kg$^{-1}$}
\def\hfg{kJ.kg$^{-1}$}
\def\ss{kJ.kg$^{-1}$K$^{-1}$}
\def\Q{W.m$^{-2}$}
\def\mone {$^{-1}$}
\def\mtwo {$^{-2}$}
\def\um{$\mu m$}
\def\kwhm{kWh.m$ ^{-3} $}
\def\LMH{kg.m$^{-2}$h$^{-1}$}
% Changing chapters' headings and subheadings to size 14
\chapterfont{\fontsize{14}{15}\selectfont} % font size and baseline stretch
\sectionfont{\fontsize{14}{15}\selectfont}
\subsectionfont{\fontsize{14}{15}\selectfont}
\subsubsectionfont{\fontsize{14}{15}\selectfont}
\pagestyle{fancy} % adds a line at the top of every page, except title-page
\fancyhead{} \fancyfoot{} % for header and footer
\fancyhead[CO,CE]{\thepage} % center odd and even page number
%centering the page numbers with text body
\fancyheadoffset[L]{0.01mm}
\renewcommand{\headrulewidth}{0pt}
%The following code changes the empty vertical space above a new chapter title. It sets it from 50pt to 20pt
\makeatletter
\patchcmd{\@makechapterhead}{50\p@}{20pt}{}{}
\patchcmd{\@makeschapterhead}{50\p@}{20pt}{}{}
\makeatother
%end of modification
% The following code redefines the plain pagestyle with the objective of moving the page number from the bottom to the top of the page. This only affects new chapter pages.
\fancypagestyle{plain}{
\fancyhf{} %clear all header and footer fields
\fancyhead[C]{\thepage} %puts number on top center of the page
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}}
%ending of plain pagestyle modification.
% ### Nomenclature, List of Abbreviations and List of Symbols
\usepackage{ifthen,xkeyval,xfor,amsgen}
\usepackage[acronym,toc, nogroupskip]{glossaries}
\newglossary[slg]{symbols}{syi}{sbl}{List of Symbols}
\makeglossaries
\include{Lists}
% Run the following three lines in the command line to get the lists
%makeindex -s Thesis.ist -t Thesis.alg -o Thesis.acr Thesis.acn
%makeindex -s Thesis.ist -t Thesis.slg -o Thesis.syi Thesis.sbl
%makeindex -s Thesis.ist -t Thesis.glg -o Thesis.gls Thesis.glo
% ### End of addition
% Modified commands
\newcommand{\Tab}{\hspace{2ex}}
\usepackage[lmargin=40mm, rmargin=25mm, vmargin=25mm, headsep=2.5mm]{geometry}
\newcommand{\mathsym}[1]{{}}
\newcommand{\unicode}[1]{{}}
\renewcommand{\thechapter}{\arabic{chapter}}
\renewcommand\bibname{\centering BIBLIOGRAPHY}
%\newcommand{\orcid}[1]{\href{https://orcid.org/#1}{\textcolor[HTML]{A6CE39}{\aiOrcid}}}
\newcommand{\orcid}{\includegraphics[width=8pt]{ORCID}} % ORCID ID
\begin{document}
% $$$$$$$$$$$$$$$$$ Start of Thesis Front matter $$$$$$$$$$$$$$
%\vspace{10mm} % vertical space
\thispagestyle{empty}
\addvspace{5mm} % vertical space until length
%$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
% make the title page
\begin{center}
\begin{doublespace}
{\textbf{{\large Thesis/Dissertation Title}}}%\vfill % Write your thesis title
\end{doublespace}
\vspace{10mm}
{Thesis/Dissertation by}\\
{Student Name} %\vfill
\vspace{30mm}
{ In Partial Fulfillment of the Requirements}\\[12pt]
{ For the Degree of}\\[12pt]
{Doctor of Philosophy/Masters of Science} \vfill
{King Abdullah University of Science and Technology }\\
{Thuwal, Kingdom of Saudi Arabia}
\vfill
%\maketitle
\begin{onehalfspace}
{\copyright Month, Year}\\
Student Name\\ % write your First name second name
All rights reserved\\
\orcid{} \small \href{https://orcid.org/0000-0001-2345-6789}{https://orcid.org/0000-0001-2345-6789}\\
\end{onehalfspace}
\end{center}
% end of title page
%$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
\newpage
%$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
%
\chaptertitlefont{\fontsize{14}{15}\selectfont\centering}
\include{Abstract} % include your abstract file
\include{Acknowledgment} % include your Acknowledgement file
\begin{onehalfspacing}%To make the table of contents, figures, and tables single spaced, as required by the formatting guidelines, pg. 24.
%\renewcommand{\contentsname}{\textbf{{\large TABLE OF CONTENTS}}}
\tableofcontents
% Maybe we don't need this blank page.
\cleardoublepage
\printglossary[type=\acronymtype,style=long3col, title=\centerline{LIST OF ABBREVIATIONS}, toctitle=List of Abbreviations, nonumberlist=true]
\printglossary[type=symbols,style=long3col, title=\centerline{LIST OF SYMBOLS}, toctitle=List of Symbols, nonumberlist=true]
% adding list of figures
% adding list of figures
\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{\listfigurename} % <--- change here
\renewcommand*\listfigurename{LIST OF FIGURES}
\listoffigures
% adding list of tables
\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{\listtablename} % <---- and change here too.
\renewcommand*\listtablename{LIST OF TABLES}
\listoftables
```
\end{onehalfspacing}
% \printglossary[style=altlist,title=Nomenclature, toctitle=Nomenclature, nonumberlist=true]
% $$$$$$$$$$$$$$$$$ Thesis front matter ends $$$$$$$$$$$$$$
% $$$$$$$$$$$$$$$$$ include your separate chapters $$$$$$$$$$$$$$
% Remove the centering of chapter name.
\chaptertitlefont{\fontsize{14}{15}\selectfont} % <------ Add this line
\include{Chapter_1}
\include{Chapter_2}
\include{Chapter_3}
\include{Chapter_4}
\include{Chapter_5}
\include{Conclusion}
% $$$$$$$$$$$$$$$$$ Reference style Starts $$$$$$$$$$$$$$
\begin{onehalfspacing}
\renewcommand*\bibname{\centerline{REFERENCES}}
\phantomsection
\addcontentsline{toc}{chapter}{References}
\newcommand{\BIBdecl}{\setlength{\itemsep}{0pt}}%To control space between bibliography entries
\bibliographystyle{IEEEtran}
\bibliography{References}
\end{onehalfspacing}
% $$$$$$$$$$$$$$$$$ Reference style Ends $$$$$$$$$$$$$$
% $$$$$$$$$$$$$$$$$ include Appendices $$$$$$$$$$$$$$
\appendix
\newpage
\begingroup
\let\clearpage\relax
\begin{center}
\vspace*{2\baselineskip}
{ \textbf{{\large APPENDICES}}}
% Fixes the numbering of "new" section created with "\addcontentsline."
% You need to add the "\phantomsection" before *every* "\addcontentsline."
\phantomsection
\addcontentsline{toc}{chapter}{Appendices}
\end{center}
\include{Appendix_A}
\include{Appendix_B}
\include{Papers}
\endgroup
% $$$$$$$$$$$$$$$$$ Appendix ends $$$$$$$$$$$$$$
\end{document}