main_document.tex

\documentclass[11pt,%
               letter,%
               oneside,%
               openright,%
               titlepage,%
               fleqn,%
               headinclude,%
               footinclude,%
               BCOR=5mm,%
               numbers=noenddot,%
               cleardoublepage=empty,%
               tablecaptionabove]{scrreprt}

\usepackage{cmap}
\usepackage[english]{babel}
\addto\captionsenglish{%
  \renewcommand{\contentsname}{Table of Contents}%
}
%\usepackage[applemac]{inputenc}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{amsmath,amssymb,amsthm}
\usepackage{amssymb}% http://ctan.org/pkg/amssymb
\usepackage{pifont}% http://ctan.org/pkg/pifont
\usepackage{varioref}
\usepackage{chngpage}
\usepackage{calc}
\usepackage{listings}
\usepackage{graphicx}
\usepackage{multirow}
\usepackage{multicol}
\usepackage{makeidx}



% \usepackage{subfigure}
% \usepackage{subfig}
% \usepackage{fixltx2e}
% \usepackage{lgrind}
\usepackage{array}
\usepackage{subcaption}
\usepackage{caption}
\usepackage[hidelinks]{hyperref}

% \pagestyle{plain}
\usepackage{soul,colortbl}
\usepackage{float}
\newcolumntype{Y}{>{\centering\arraybackslash}X} %
\renewcommand{\arraystretch}{1} % f
\definecolor{Gray}{gray}{0.9}

\usepackage{arydshln}  % For dashed line in tables
\usepackage{booktabs}
\usepackage[singlespacing=true]{scrlayer-scrpage}
% ============================================================



\RequirePackage{silence}
\WarningFilter{remreset}{The remreset package}
% \WarningFilter{titlesec}{The titlesec package}
\usepackage{relsize}
\usepackage{lipsum}
\usepackage[beramono,eulermath,pdfspacing,listings,dottedtoc]{classicthesis}
\usepackage{boldline}
\renewcommand{\cftdot}{}

\usepackage{arsclassica}
% \RequirePackage[letterpaper, top=1in, bottom=1.5in,
%   left=1.5in, right=1.5in,showframe=false]{geometry}
\usepackage[letterpaper, margin=1in]{geometry}
\usepackage[doublespacing]{setspace}
\usepackage{algorithm}
\usepackage{algpseudocode}
\usepackage{wasysym}
\usepackage{bbm}
\usepackage{tcolorbox}
\usepackage{tabularx}
%\usepackage[backend=bibtex]{biblatex}
\usepackage{cite}
\usepackage{chngcntr}
\counterwithin{figure}{chapter}
\counterwithin{table}{chapter}
\counterwithin{equation}{chapter}
\counterwithin{algorithm}{chapter}

\input{arsclassica-settings}

\usepackage{tocloft}

% ==================================================================
% ==================================================================
% Override the hyperlink settings:
\hypersetup{%
    colorlinks=false,
    linktocpage=false,
    citecolor=webgreen%
    }
% ----------------------------------------------------------------------
% Override page number font
\renewcommand{\pnumfont}{\normalfont}
% ----------------------------------------------------------------------

\makeatletter
% -- for chapters --
\newcommand\myformatchapter[1]{%
    \vbox to \ht\strutbox{
    \setbox0=\hbox{\chapterNumber\thechapter\hspace{10pt}\vline\ }
    \advance\hsize-\wd0 \advance\hsize-10pt\raggedright
    \spacedallcaps{#1}\vss}}
    \titleformat{\chapter}[block]
       {\normalfont\Large}
       {\textcolor{halfgray}{\chapterNumber\thechapter} % color of Chapter number
       \hspace{10pt}\vline\ }{10pt}
    {\formatchapter}



% ----------------------------------------------------------------------
\makeatletter
\renewcommand\formatchapter[1]{%
  \begin{minipage}[b]{0.15\linewidth}
    \chapterNumber
  \end{minipage}%
  \begin{minipage}[b]{0.6\linewidth}
    \raggedright\normalsize\spacedallcaps{#1}
  \end{minipage}
}
\makeatother
% ------------------------------------------------------------------------

\renewcommand{\cftchapfont}{\normalfont\normalsize}
\renewcommand{\cftchappresnum}{\normalfont\normalsize}


% -- for sections --
\titleformat{\section}
{\normalfont}{\thesection}{1em}{}
\renewcommand{\cftsecfont}{}

% -- for subsections --
\titleformat{\subsection}
{\normalfont\itshape}{\thesubsection}{1em}{}
\renewcommand{\cftsubsecfont}{\itshape}
\makeatother




% ==================================================================
% ==================================================================


% -- dotted lines in toc --
\renewcommand{\cftchapleader}{\leaders\hbox to1em{\hss.\hss}\hskip 2.9mm plus1fill}
\renewcommand\cftsecleader{\leaders\hbox to1em{\hss.\hss}\hskip 2.9mm plus1fill}
\renewcommand\cftsubsecleader{\leaders\hbox to1em{\hss.\hss}\hskip 2.9mm plus1fill}
\renewcommand\cftfigleader{\leaders\hbox to1em{\hss.\hss}\hskip 2.9mm plus1fill}
\renewcommand\cfttableader{\leaders\hbox to1em{\hss.\hss}\hskip 2.9mm plus1fill}


\usepackage{etoolbox}

% Fix to put section numbers on sections
\makeatletter
\patchcmd{\ttlh@hang}{\parindent\z@}{\parindent\z@\leavevmode}{}{}
\patchcmd{\ttlh@hang}{\noindent}{}{}{}
\makeatother

% custom arg min/max commands
\newcommand{\argmin}{\operatornamewithlimits{argmin}}
\newcommand{\argmax}{\operatornamewithlimits{argmax}}
\algdef{SE}[DOWHILE]{Do}{doWhile}{\algorithmicdo}[1]{\algorithmicwhile\ #1}%

% declaration of parallel for block
\algblock{ParFor}{EndParFor}
% customization of the parallel for block
\algnewcommand\algorithmicparfor{\textbf{for}}
\algnewcommand\algorithmicpardo{\textbf{do in parallel}}
\algnewcommand\algorithmicendparfor{\textbf{end\ for}}
\algrenewtext{ParFor}[1]{\algorithmicparfor\ #1\ \algorithmicpardo}
\algrenewtext{EndParFor}{\algorithmicendparfor}

\renewcommand{\algorithmicrequire}{\textbf{Input:}}
\renewcommand{\algorithmicensure}{\textbf{Output:}}

% thick line for table
\makeatletter
 \def\hlinewd#1{%
    \noalign{\ifnum0=`}\fi\hrule \@height #1 \futurelet
    \reserved@a\@xhline
 }
\makeatother


\clearscrheadfoot
\cfoot{\pagemark}



%******************************************************************
%******************************************************************
%**********************                ****************************
%********************** BEGIN DOCUMENT ****************************
%**********************                ****************************
%******************************************************************
%******************************************************************
\begin{document}
\pagenumbering{roman}
\pagestyle{plain}

%******************************************************************
% Frontmatter
%******************************************************************
\input{FrontMatter/Titlepage}
\setcounter{page}{1}
\input{FrontMatter/AbstractPage}
\input{FrontMatter/Titleback}
\input{FrontMatter/ApprovedForm}

\pagestyle{scrheadings}
\input{FrontMatter/Dedication}
\input{FrontMatter/Acknowledgements}
\clearpage

\clearpage

\clearscrheadfoot
\cfoot[\pagemark]{\pagemark}
\input{FrontMatter/Contents}
\cleardoublepage
%******************************************************************
% Mainmatter
%******************************************************************
\pagenumbering{arabic}
\input{Dissertation/src/Chapters/chapter_1}
\input{Dissertation/src/Chapters/chapter_3}
\input{Dissertation/src/Chapters/chapter_4}
\input{Dissertation/src/Chapters/chapter_5}
\input{Dissertation/src/Chapters/chapter_10}
% *****************************************************************
% Backmatter
%******************************************************************
\clearpage
%----------------------------------------------------------------------------------------
%   BIBLIOGRAPHY
%----------------------------------------------------------------------------------------
\phantomsection
\addcontentsline{toc}{chapter}{\tocEntry{References}}
\renewcommand{\refname}{{References}} % For modifying the bibliography heading
% \singlespacing
% \section{References}
\small
\bibliographystyle{unsrt}
\bibliography{bibfile} % The file containing the bibliography

\end{document}