PhD_thesis_FCUL_template.tex

%% Set the page dimensions, font dimensions, and tells LaTeX to use the class "mythesis.cls" which contains your particular stylistic choices for the thesis.
\documentclass[12pt]{mythesis}

%\usepackage{showframe}  %% just for demo; it shows page frames
%\usepackage[switch, modulo, pagewise]{lineno}  %% Show line numbers
%\linenumbers  %% turn line numbers on
%\usepackage{kantlipsum} %% just for demo; adds blindtext
%\usepackage[hpos={\ifodd\thepage \dimexpr0.92\paperwidth\else \dimexpr0.07\paperwidth\fi}, vpos=0.5\paperheight, angle=90, vanchor=m, hanchor=c, fontsize=0.8\marginparwidth, text={\normalfont DRAFT - {\today}\, - DRAFT}]{draftwatermark}  %% Add watermark

% To help with breaking lines in paragraph (overfull \hbox)
\setlength{\emergencystretch}{3em}

\usepackage{breakcites}  % references do not go through margins
\usepackage{csquotes}  % Quotation marks management
\usepackage{doi}  % Add good DOI styling to bibliography
\renewcommand{\doitext}{} % to make doi addresses links

\usepackage{graphicx}
\graphicspath{{figures/}} % include all folders with images

%% The following two lines ensure that you set your page dimensions and margins *exactly* as for University requirements.
\usepackage{geometry}
\geometry{margin=2.5cm, headheight=0.75cm}

\usepackage{aas_macros}  % Journals naming
\usepackage{adjustbox}
\usepackage{array}
\usepackage{color}
\usepackage[shortlabels]{enumitem}
% Indentation for first line of Chapter
\usepackage{indentfirst}

% Bibliography (and not ToC) to the ToC
\usepackage[nottoc]{tocbibind}
\usepackage{afterpage}
% To add to-do notes and comment blocks
\setlength{\marginparwidth}{2cm}
\usepackage[colorinlistoftodos]{todonotes}
\usepackage{comment}
% To make pretty tables
\usepackage{tabularx}
\usepackage{booktabs}
\usepackage{multirow}
\usepackage{longtable}
\usepackage{rotating}
\usepackage{pdflscape}
\usepackage{threeparttable}  % Notes in tables
\usepackage{threeparttablex}  % Notes in longtables
\hfuzz=6.001pt
\usepackage{etoolbox}
\appto\TPTnoteSettings{\fontsize{9pt}{11pt}\selectfont}  % Font size notes in tables
% Floats
\usepackage{float}
\restylefloat{figure}
\usepackage{wrapfig}

% To obtain dates in Roman numerals (only if needed)
\usepackage{datetime}
\makeatletter
\newcommand\Romanyear{\@Roman{\year}}
\makeatother

% To show subsubsections in ToC
\setcounter{tocdepth}{3}

\newcommand\blankpage{%
    \null
    \thispagestyle{empty}%
    \addtocounter{page}{-1}%
    \newpage
}

% Load glossaries
\makeglossaries
\loadglsentries{./preambles/glossaries}
\glsaddall

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%          Start the document          %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{document}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%               FRONTPAGE              %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newgeometry{hmargin=3cm, top=1cm, headsep=0.1cm, bmargin=1.5cm}
\include{./preambles/frontpage}
%\newpage

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%              COVER PAGE              %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\frontmatter % What it does is to set the page numbering to Roman numbering (I. II. etc.)
\include{./preambles/coverpage}
\restoregeometry % Revert to original geometry formatting

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%              DEDICATION              %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\include{./preambles/dedication}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%           ACKNOWLEDGEMENTS           %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\include{./preambles/acknowledgments}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%           ABSTRACT - RESUMO          %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\include{./preambles/resumo}

\cleardoublepage

\include{./preambles/abstract}

\cleardoublepage

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%       COMMUNICATION OF OUTPUTS       %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\include{./preambles/output_communication}

\cleardoublepage

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%           TABLE OF CONTENTS          %
%             LIST OF TABLES           %
%            LIST OF FIGURES           %
%                GLOSSARY              %
%           LIST OF ACRONYMS           %
%            LIST OF SYMBOLS           %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\pagestyle{plain}

\pdfbookmark{\contentsname}{toc}
\tableofcontents

\CAPinToC % All entries in ToC will be CAPITALIZED from here on
\phantomsection \label{listoftables}
\listoftables

\phantomsection \label{listoffigures}
\listoffigures

\phantomsection \label{glossary}
\printglossary[type=acronym,style=long,title={List of acronyms}]
\printglossary[type=symbols,style=long4col,title={List of symbols}]
\noCAPinToC % Revert to original \addcontentsline formatting
\cleardoublepage

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%           TEXT  OF  THESIS           %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%Switch to chapters, which means it switch back to standard arabic page numbering (1, 2, etc.)
\newpage
\mainmatter

%% Include the chapters (which have to have the same filename plus the .tex extension)
\include{./chapters/chapter_01}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  DATA AND SOFTWARE ACKNOWLEDGEMENTS  %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\include{./preambles/data_software}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%               REFERENCES             %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\cleardoublepage
\input{./preambles/references}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%              APPENDICES              %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{appendices} % It is like a chapter, so each appendix (A, B, C...) must to be considered as a section

\input{./chapters/appendix_01}

\end{appendices}

\cleardoublepage

\end{document}