main.tex

\documentclass[a4paper,12pt,twoside,openright]{book}

\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage{xcolor}
\usepackage{physics}
\usepackage{amssymb}
\usepackage{bbold}
\setlength{\jot}{10pt}
\usepackage{mathtools}
\usepackage{tabularx}
\usepackage{booktabs}
\usepackage{graphicx}
\usepackage{caption}
\usepackage{subcaption}
\usepackage{nccmath}
\usepackage[a4paper,
width=150mm,
top=25mm,
bottom=25mm]{geometry}
\usepackage[
    backend=biber,
    style=numeric,
    sorting=none
]{biblatex}
\usepackage{tcolorbox}
\usepackage{tensor}
\usepackage{slashed}
\usepackage{MnSymbol}
\usepackage{afterpage}
\usepackage{pdflscape}
%Options: Sonny, Lenny, Glenn, Conny, Rejne, Bjarne, Bjornstrup
\usepackage[Bjornstrup]{fncychap}
\usepackage[bottom]{footmisc}
\usepackage{hyperref}

\graphicspath{{images/}{Chapters/Chapter_2/figs/}{Chapters/Chapter_3/figs/}{Chapters/Chapter_4/figs/}}

\bibliography{bibfile.bib, Chapters/Chapter_1/chapter1.bib, Chapters/Chapter_2/chapter2.bib, Chapters/Chapter_3/chapter3.bib, Chapters/Chapter_4/chapter4.bib}

\begin{document}
\newcommand{\T}[1]{\textrm{#1}}
\newcommand{\red}[1]{\textcolor{red}{#1}}
\newcommand{\mb}[1]{\mathbf{#1}}
\newcommand{\secref}[1]{Sec.~\ref{#1}}
\newcommand{\chapref}[1]{Chap.~\ref{#1}}
\newcommand{\tran}[1]{{#1}^{T}}
\newcommand{\quotes}[1]{``#1''}
\setlength{\abovedisplayskip}{6mm}
\setlength{\belowdisplayskip}{6mm}

\frontmatter
\input{Thesis_frontmatter/title-page.tex}
\clearpage
\newpage

\input{acknowledgments.tex}
\clearpage
\newpage
\tableofcontents
\raggedbottom
\mainmatter
\input{Chapters/Chapter_1/chapter_1.tex}
\input{Chapters/Chapter_2/chapter_2.tex}
\input{Chapters/Chapter_3/chapter_3.tex}
\input{Chapters/Chapter_4/chapter_4.tex}
\input{Chapters/Chapter_5/chapter_5.tex}

\afterpage{\null\thispagestyle{empty}\clearpage}

\let\cleardoublepage\clearpage
\appendix
\numberwithin{equation}{chapter}
\setcounter{equation}{0}
%\input{Appendix/spin.tex}
\input{Appendix/linear_systems.tex}
\input{Appendix/exp_err_func.tex}

\afterpage{\null\thispagestyle{empty}\clearpage}
\printbibliography
\end{document}