00-main.tex

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%%                           AUTHOR: BIBEKANANDA DATTA                        %%
%%                               (C) MARCH 2024                               %%
%%                      PhD STUDENT, MECHANICAL ENGINEERING                   %%
%%                           JOHNS HOPKINS UNIVERSITY                         %%
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%%             PLEASE CHECK THE README.md FILE BEFORE YOU PROCEED             %%
%%              it may be convenient to read this file on GitHub              %%
%%   GitHub: https://github.com/bibekananda-datta/JHU-Dissertation-Template   %%
%% template hosted on this GitHub repository is likely to be the most updated %%
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% This is an unofficial dissertation template for Johns Hopkins University.
% As of March 31, 2024, the template follows the dissertation formatting 
% requirements provided by the  Johns Hopkins University Sheridan Library.
% It is the user's responsibility to ensure that the current requirements are 
% followed: https://www.library.jhu.edu/library-services/electronic-theses-dissertations/formatting-requirements/
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% VERSION HISTORY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% The report class-based template was created by R. Jacob Vogelstein in May 2007
% Updated by Noah J. Cowan on March 01, 2010
% Updated by Brian D. Weitzner on April 29, 2014 
% Updated by John Muschelli on January 29, 2016 
% Updated by Leonardo Collado Torres on April 13, 2016 
% Updated by John Clayton in December 2019
% Last Updated by Bibekananda Datta on March 31, 2024
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% VERSION HISTORY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%% REPORT CLASS with 12 pt font and onesided printing (book class also works)
\documentclass[12pt,letterpaper]{report} 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% if possible, make your formatting changes here through the variables 
%%%%%%%%%%%%%%%%%%%%%% LIST OF VARIABLES FOR FORMATTING %%%%%%%%%%%%%%%%%%%%%%%%

%%%% JH Library requirement (DO NOT CHANGE)
\def\GlobalMargin{1.0in}                    % margin on all sides
\def\PrintingOffset{0.5in}                  % additional left margin for the printed copy
\def\MainTextSpacing{\doublespacing}        % double-spaced main text


%%%% ADDITIONAL PATHS and FILES
\def\FigurePath{figures}                    % subdirectory for the figure files
\def\BibFileName{thesis.bib}                % name of BibLaTeX-compatible bib file 


\def\FontPackage{lmodern}                   % default font package


%%%% FONT SIZE and TYPESET for DIFFERENT HEADINGS
%% check here for details: https://en.wikibooks.org/wiki/LaTeX/Fonts

%% font format for thesis title
\def\TitleFont{\Large\bfseries\singlespacing\MakeUppercase}  

%% font for chapter, section, subsection, and subsubsection heading
\def\NoSectionLevel{3}                      % 3 levels => section to subsubsection
\def\ChapterFont{\Large\bfseries\singlespacing} 
\def\SectionFont{\large\bfseries\singlespacing} 
\def\SubsectionFont{\normalsize\bfseries\singlespacing}  
\def\SubsubsectionFont{\normalsize\itshape\singlespacing} 


%%%% PARAGRAPH
\def\ParagraphSpacing{\baselineskip}        % spacing between paragraph
\def\ParagraphIndent{0 pt}                  % indentation at the beginning of the paragraph


%% CAPTION
\def\CaptionFontSize{small}         % caption font size
\def\CaptionLabelFontType{bf}       % boldface label for captions
\def\CaptionSeparator{colon}        % separates caption label from caption text
\def\CaptionSpacing{1.0}            % single-spaced captions
\def\FigureToCaption{0 pt}          % spacing between the figure and the caption


%%%% GLOBAL SPACING for TABLES
\def\GlobalTableSpacing{1.5}                % global spacing parameter for table


%%%% HEADER AND FOOTER SETTING
\def\HeaderHeight{30 pt}                    % height of the chapter header
\def\HeaderSpace{12 pt}                     % space between header and the following text

\def\FootnoteSpacing{\baselineskip}         % spacing between footnotes


%%%% BIBLIOGRAPHY ITEMS
\def\BibTextSpacing{\singlespacing}         % single-spaced bibliography
\def\BibItemSpacing{\baselineskip}          % spacing between bibliographic items in reference


%%%% CHAPTER QUOTE (EPIGRAPH PACKAGE)
\def\ChapQuoteFontSize{\small}              % font size of chapter quotes
\def\ChapQuoteLocation{flushright}          % location of chapter quote
\def\ChapQuoteTextShape{\itshape}           % font shape for quotes
\def\ChapQuoteAuthorTextShape{\scshape}     % font shape for quote author
\def\MaxQuoteWidth{0.65\textwidth}          % width epigraph-based quotes in chapter



%%%% SECTION LEVELS and TOC APPEARANCE
\def\NoTocLevel{2}                          % no of levels showed in the table of contents
\def\TocIndent{0 pt}                        % indentation in the list of figs and tables
%% 3 levels mean: section to subsubsection.. decrease if you want to show less in TOC

%%%% TOC SPACING of different section levels (chapter to subsubsection)
\def\TOCTextSpacing{\singlespacing}         % single spacing for TOC texts
\def\ChapTOCSpacing{\baselineskip}          % spacing between chapters
\def\SecTOCSpacing{0.5\baselineskip}        % spacing between sections
\def\SubsecTOCSpacing{0.3\baselineskip}     % ... between subsections
\def\SubsubsecTOCSpacing{0.3\baselineskip}  % ... between subsubsections
\def\LOTItemSpacing{\baselineskip}          % spacing between LOT/LOF items


%%%% ADHOC HEIGHT ADJUSTMENT VARIABLES for consistent typesettings
%% following numbers are found by trial and error to compensate 
%% for default spacing around default LaTeX environments
\def\TitleTopSpacing{-\HeaderHeight-\HeaderSpace}   % top height adjustment for thesis title
\def\BeforeTOCTitleSpacing{-42 pt}          % space before TOC title
\def\AfterTOCTitleSpacing{34 pt}            % space after TOC title
\def\AfterLOTTitleSpacing{34 pt}            % space after LOT/ LOF title

\def\NumChapterTopMargin{-64 pt}            % space before numbered chapter label
\def\UnNumChapterTopMargin{-85 pt}          % space before unnumbered chapter label
\def\ChapLabelToTitle{-27 pt}               % space between chapter label to title 
\def\ChapTitleToText{24 pt}                 % space between the chapter title and the following text
\def\SpaceBeforeQuote{-20 pt}               % white space before quote

%%%% if you want to change any of the heights, adjust using a ruler:
% \usepackage[unit=in,type=upperleftT,color=red,showframe]{fgruler}

%%%%%%%%%%%%%%%%%%%% END LIST OF VARIABLES FOR FORMATTING %%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% add packages as needed but sometimes the order of the packages matters.
%% you may have to change the options of the biblatex package for the bibliography.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LaTeX PACKAGES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%% SOME PRE-REQUISITE PACKAGES
\usepackage[utf8]{inputenc}                 % for encoding input character (required)
\usepackage[american]{babel}                % for different language typography
\usepackage[T1]{fontenc}                    % for font encoding


%%%% COMMON MATH PACKAGES
\usepackage{amsfonts,amssymb,amsmath,amsthm,autobreak,
cancel,dsfont,mathtools,mathbbol,mathrsfs,siunitx,upgreek}


%%%% DEFAULT FONT (you can specify other fonts - compatibility could be an issue)
\usepackage{\FontPackage}


%%%% BIBLIOGRAPHIC PACKAGE (change the style or other options if you need to)
%% Nature style bibliography
\usepackage[backend=biber, defernumbers=true, style=nature, maxnames=99,
     date=year, isbn=false, url=false, doi=true]{biblatex}

%% APA style
% \usepackage[backend=biber, defernumbers=true, style=apa, maxnames=99,
%     isbn=false, url=false, doi=true]{biblatex}

%% IEEE style
% \usepackage[backend=biber,style=ieee,defernumbers=true,maxnames=99, 
%     date=year, isbn=false, url=false, doi=true]{biblatex}



%%%% TABLE-RELATED PACKAGES
\usepackage{booktabs,longtable,dcolumn,makecell,
multicol,multirow,tabularx,xltabular,rotating}



%%%% package for micro-typography (you can define more settings)
%% see details here: https://www.khirevich.com/latex/microtype/
\usepackage[activate={true,nocompatibility}]{microtype}



%%%% OTHER PACKAGES AND OPTIONS
\usepackage[pagewise,mathlines]{lineno}     % line numbers for drafting
\usepackage[ruled]{algorithm2e}             % to manage algorithm environment
\usepackage[titletoc]{appendix}             % to manage appendix chapters
\usepackage{blindtext}                      % to generate random filler texts
\usepackage{calc}                           % to set arithmetic arguments for spacing
\usepackage{caption}                        % to manage captions
\usepackage{comment}                        % to comment a large amount of text as env
\usepackage{epigraph,varwidth}              % for managing quotes
\usepackage{enumitem}                       % to manage list environment
\usepackage{float}                          % to manage floating environment
% footnote environment management
\usepackage[bottom,multiple,hang,flushmargin]{footmisc}      
\usepackage{graphicx,wrapfig}               % to manage images
\usepackage{geometry}                       % to manage margins and page format
\usepackage{glossaries}                     % to add glossaries
\usepackage{fancyhdr}                       % for header/ footer settings
\usepackage[dvipsnames]{xcolor}             % color-related package
\usepackage[a-1b]{pdfx}                     % to generate PDF/A file (before hyperref)
\usepackage[pdfa]{hyperref}                 % for hyperlink management 
\usepackage[all]{hypcap}                    % for captions on the side of figures
\usepackage{ifthen}                         % if-then statement in LaTeX code
\usepackage{lscape}                         % landscape mode
\usepackage{listings,minted}                % to include codes 
\usepackage{csquotes}                       % yet another package to manage quote
\usepackage{setspace}                       % sets space between lines
\usepackage{seqsplit}                       % splits long character sequence
\usepackage[rightcaption]{sidecap}          % for sideway captions
\usepackage{tocloft}                        % to manage table of contents, etc.
\usepackage{textcomp}                       % text companion fonts in TS1
\usepackage[absolute]{textpos}              % position text at certain location
\usepackage{titlesec}                       % managing different title environments
\usepackage[final]{pdfpages}                % to insert pdf pages
\usepackage{parskip}                        % default spacing around environments
\usepackage{tikz}                           % drawing related package
\usepackage{subcaption}                     % individual panel and caption

%% add more packages and/or change options of the packages as needed

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% END LaTeX PACKAGES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% specifying direct package options related to document formatting
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% PACKAGE OPTIONS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%% GRAPHICX package
\graphicspath{{\FigurePath/}}


%%%% GEOMETRY PACKAGE: margin settings required by JH library 
\geometry{letterpaper, margin=\GlobalMargin, bindingoffset=\PrintingOffset, 
    nomarginpar, includehead, headheight=\HeaderHeight, 
    headsep=\HeaderSpace, includefoot, heightrounded}
%% you can add showframe option to see how the layout looks like


%%%% HYPERREF PACKAGE
\hypersetup{linktocpage, unicode, linktoc=all, colorlinks=true, 
    citecolor=blue, filecolor=blue, linkcolor=blue, urlcolor=blue}
\urlstyle{rm}           % removes default \texttt style for hyperlinks


%%%% CAPTION PACKAGE
\captionsetup{belowskip=\FigureToCaption, font=\CaptionFontSize, 
    labelfont=\CaptionLabelFontType, labelsep=\CaptionSeparator,
    font={stretch=\CaptionSpacing}, hypcap=true} 



%%%% BIBLATEX: bibliography package settings
\addbibresource{\BibFileName}           % name of the bib file 
% \DeclareFieldFormat{titlecase}{\MakeSentenceCase*{#1}}
\AtBeginBibliography{\urlstyle{rm}}     % roman font family for URL (DOI)
\AtBeginBibliography{\vspace*{8pt}}     % add space for single-spaced bib text

%% the following block ensures articles are sentence case 
%% but the journal names are title case 
\DeclareFieldFormat{sentencecase}{\MakeSentenceCase{#1}}
\renewbibmacro*{title}{%
  \ifthenelse{\iffieldundef{title}\AND\iffieldundef{subtitle}}
    {}
    {\ifthenelse{\ifentrytype{article}\OR\ifentrytype{inbook}%
      \OR\ifentrytype{incollection}\OR\ifentrytype{inproceedings}%
      \OR\ifentrytype{inreference}}
      {\printtext[title]{%
        \printfield[sentencecase]{title}%
        \setunit{\subtitlepunct}%
        \printfield[sentencecase]{subtitle}}}%
      {\printtext[title]{%
        \printfield[titlecase]{title}%
        \setunit{\subtitlepunct}%
        \printfield[titlecase]{subtitle}}}%
     \newunit}%
  \printfield{titleaddon}}


%% separate category for papers to be not cited in the bibliography
\DeclareBibliographyCategory{mypapers}             
\newcommand{\mybibexclude}[1]{\addtocategory{mypapers}{#1}}

%%%%%%%%%%%%%%%%%%%%%%%%%%%% END PACKAGE OPTIONS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% further tweaking variables for the current consistent document formatting
%%%%%%%%%%%%%%%%%%%%%%%%%%%%% DOCUMENT FORMATTING %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\setcounter{tocdepth}{\NoTocLevel}                  % list depth in ToC
\setcounter{secnumdepth}{\NoSectionLevel}           % section to ... subsubsection


%%%% font size and spacing around the titles of ToC/ LoT/ LoF
\renewcommand{\cfttoctitlefont}{\ChapterFont}
\renewcommand{\cftlottitlefont}{\ChapterFont}
\renewcommand{\cftloftitlefont}{\ChapterFont}

\setlength{\cftbeforetoctitleskip}{\BeforeTOCTitleSpacing}
\setlength{\cftbeforelottitleskip}{\BeforeTOCTitleSpacing}
\setlength{\cftbeforeloftitleskip}{\BeforeTOCTitleSpacing}
\setlength{\cftaftertoctitleskip}{\AfterTOCTitleSpacing}
\setlength{\cftafterlottitleskip}{\AfterLOTTitleSpacing}
\setlength{\cftafterloftitleskip}{\AfterLOTTitleSpacing}


%% tweak to TOC to add 'chapter' to the chapter name instead of a number only
%% set the width of the box based on the longest label name
\renewcommand{\cftchappresnum}{\chaptername\space}
\renewcommand{\cftchapleader}{\cftdotfill{\cftdotsep}}  % dots for chapters too
\setlength{\cftchapnumwidth}{\widthof{\textbf{Appendix~XXX~}}}


\setlength{\cftbeforechapskip}{\ChapTOCSpacing}
\setlength{\cftbeforesecskip}{\SecTOCSpacing}
\setlength{\cftbeforesubsecskip}{\SubsecTOCSpacing}
\setlength{\cftbeforesubsubsecskip}{\SubsubsecTOCSpacing}


%% tweak to LOT and LOF to add 'Table'/ 'Figure' to the table/ figure caption listing
%% to change the distance to the start of the table/ figure title
\newcommand*{\noaddvspace}{\renewcommand*{\addvspace}[1]{}}

\setlength{\cfttabindent}{\TocIndent}               % indentation from tables in LoT
\renewcommand{\cfttabpresnum}{\bfseries Table }
\setlength{\cfttabnumwidth}{\widthof{\textbf{Table~999.999~}}}
\setlength{\cftbeforetabskip}{\LOTItemSpacing}      % spacing between each item
\addtocontents{lot}{\protect\noaddvspace}


\setlength{\cftfigindent}{\TocIndent}               % indentation from figures in LoF
\renewcommand{\cftfigpresnum}{\bfseries Figure }
\setlength{\cftfignumwidth}{\widthof{\textbf{Figure~999.999~}}}
\setlength{\cftbeforefigskip}{\LOTItemSpacing}      % spacing between each item
\addtocontents{lof}{\protect\noaddvspace}



%%%% TITLESEC: settings for chapter label and title
\titleformat{\chapter}[display]{\ChapterFont}
    {\chaptertitlename\ \thechapter}{\ChapLabelToTitle}{\ChapterFont}

\titlespacing*{\chapter}{0pt}{\NumChapterTopMargin}{\ChapTitleToText} 

\titlespacing*{name=\chapter,numberless}{0pt}{\UnNumChapterTopMargin}
    {\ChapTitleToText}


%%%% TITLESEC: settings for sections, subsection, ... heading format
\titleformat*{\section}{\SectionFont}
\titleformat*{\subsection}{\SubsectionFont}
\titleformat*{\subsubsection}{\SubsubsectionFont}
%% if you had more levels then add settings for paragraph and subparagraph


%% to customize space around section headings, use the following command:
% \titlespacing*{environment-name}{space-left}{space-before}{space-after}


%%%% PARSKIP: for paragraph (and not title) spacing, roughly speaking
\renewcommand{\arraystretch}{\GlobalTableSpacing}   % spacing inside table
\setlength{\parskip}{\ParagraphSpacing}             % paragraph skip
\setlength{\parindent}{\ParagraphIndent}            % paragraph indentation
\setlength{\bibitemsep}{\BibItemSpacing}            % bib item separation 
\setlength{\footnotesep}{\FootnoteSpacing}          % separation between footnote


%%%% settings for math environment
\allowdisplaybreaks[1]                  % page break for long equations
\numberwithin{equation}{chapter}        % eqn no with chapter label
\setcounter{MaxMatrixCols}{20}          % no of maximum columns in matrix

%%%%%%%%%%%%%%%%%%%%%%%%%%% END DOCUMENT FORMATTING %%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%% TITLE PAGE MACROS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newcommand{\ThesisTitle}[1]{           % thesis title
    \vspace*{\TitleTopSpacing}
    {\TitleFont {#1} \par}
}

\newcommand{\ThesisAuthor}[1]{          % thesis author
    by \\ #1 \\}      


\newcommand{\ThesisStatement}[2]{       %% thesis or dissertation statement 
    A {#1} submitted to The Johns Hopkins University in conformity \\
    with the requirements for the degree of {#2}
}

\newcommand{\Location}{Baltimore, Maryland}     % location

\newcommand{\ThesisDate}[2]{#1 #2}              % thesis submission date 

\newcommand{\ThesisCopyright}[2]{               % optional copyright statement
\begin{textblock*}{\textwidth}(\GlobalMargin +\PrintingOffset,9in)
    \copyright\ {#1} {#2} \\ All rights reserved
\end{textblock*}
\null
}

%%%%%%%%%%%%%%%%%%%%%%%%%%% END TITLE PAGE MACROS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% OTHER MACROS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%% UNNUMBERED CHAPTERS, SECTION, and SUBSECTION COMMAND for ADDING to TOC
%% removes the 'Chapter #' title while keeping it listed in the TOC
\newcommand\chap[1]{%
    \chapter*{#1}%
    \markboth{#1}{}
    \addcontentsline{toc}{chapter}{#1}}
  
%% removes the 'Section #' title while keeping it listed in the TOC
\newcommand\sect[1]{%
    \phantomsection
    \section*{#1}%
    \addcontentsline{toc}{section}{#1}}
  
%% removes the 'Subsection #' title while keeping it listed in the TOC
\newcommand\subsect[1]{%
    \phantomsection
    \subsection*{#1}%
    \addcontentsline{toc}{subsection}{#1}}

%% removes the 'Subsubsection #' title while keeping it listed in the TOC
\newcommand\subsubsect[1]{%
    \phantomsection
    \subsubsection*{#1}%
    \addcontentsline{toc}{subsubsection}{#1}}

%%%% KEYWORDS for abstract
\newcommand{\keywords}[1]{	
    \textbf{Keywords:} {#1}
}

%%%% TOCLOFT: modified macros/ commands for printing ToC, LoF, LoT
\newcommand{\mytableofcontents}{
    \clearpage
    \renewcommand{\contentsname}{Table of Contents}
    \tableofcontents
    \clearpage
}
%
\newcommand{\mylistoffigures}{
    \clearpage \phantomsection
    \addcontentsline{toc}{chapter}{List of Figures}
    \listoffigures
    \clearpage
}
%
\newcommand{\mylistoftables}{
    \clearpage \phantomsection
    \addcontentsline{toc}{chapter}{List of Tables}
    \listoftables
    \clearpage
}

%%%% IN-TEXT MACROS for notes
\newcommand{\COMMENT}{\textcolor{red}}
\newcommand{\ADDCITATION}{\COMMENT{(ADD CITATION)}}

%%%%%%%%%%%%%%%%%%%%%%%%%%%% END OTHER MACROS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% only if you plan on using chapter quotes, you may need epigraph settings
%%%%%%%%%%%%%%%%%%%%%%%%%%%%% EPIGRAPH SETTINGS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\setlength{\epigraphwidth}{\MaxQuoteWidth}              % max width of chapter epigraph
\renewcommand{\epigraphflush}{\ChapQuoteLocation}       % chapter epigraph on right 
\renewcommand{\epigraphsize}{\ChapQuoteFontSize}        % font size for chapter epigraph
\renewcommand{\textflush}{\ChapQuoteLocation}
\renewcommand{\sourceflush}{\ChapQuoteLocation}
\newcommand{\epitextfont}{\ChapQuoteTextShape}          % quote font shape
\newcommand{\episourcefont}{\ChapQuoteAuthorTextShape}  % quote author name shape

%% following settings put variable width underline between quote and author
\makeatletter
\setlength{\beforeepigraphskip}{\SpaceBeforeQuote}
\newsavebox{\epi@textbox}
\newsavebox{\epi@sourcebox}
\newlength\epi@finalwidth
\renewcommand{\epigraph}[2]{%
    \vspace{\beforeepigraphskip}
    {\epigraphsize\begin{\epigraphflush}
    \epi@finalwidth=\z@
    \sbox\epi@textbox{%
        \varwidth{\epigraphwidth}
        \begin{\textflush}\epitextfont#1\end{\textflush}
        \endvarwidth
   }%
    \epi@finalwidth=\wd\epi@textbox
    \sbox\epi@sourcebox{%
        \varwidth{\epigraphwidth}
        \begin{\sourceflush}\episourcefont#2\end{\sourceflush}%
        \endvarwidth
   }%
    \ifdim\wd\epi@sourcebox>\epi@finalwidth 
        \epi@finalwidth=\wd\epi@sourcebox
    \fi
   \leavevmode\vbox{
        \hb@xt@\epi@finalwidth{\hfil\box\epi@textbox}
        \vskip 1ex         % gap between quote and rule
        \hrule height \epigraphrule
        \vskip 1ex         % gap between rule and author
        \hb@xt@\epi@finalwidth{\hfil\box\epi@sourcebox}
   }%
   \end{\epigraphflush}
   \vspace{\afterepigraphskip}}}
\makeatother

%%%%%%%%%%%%%%%%%%%%%%%%%%% END EPIGRAPH SETTINGS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%% define your custom settings for other packages here (algorithm/ listing, etc.)


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% these are just some examples; add more macros for your custom commands
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MATH MACROS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newcommand{\dC}{$^{\circ}$C}           % degree celsius symbol
\newcommand{\vect}[1]{\mathbf{#1}}      % boldface for vectors and tensors
\DeclareMathOperator{\T}{{\top}}        % transpose of a matrix/ tensor
\DeclareMathOperator{\tr}{tr}           % trace of a matrix
\DeclareMathOperator{\divg}{div}        % divergence of vector and tensor
\DeclareMathOperator{\grad}{grad}       % gradient of vector and tensor
\DeclareMathOperator{\curl}{curl}       % curl of vector and tensor

%% theorem-style remark environment
\theoremstyle{definition}
\newtheorem{remark}{Remark}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%% END MATH MACROS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



%%%%%%%%%%%%%%%%%%%%%%%%% DOCUMENT BEGINS HERE %%%%%%%%%%%%%%%%%%%%%%%%%%%


\begin{document}


%%%% TITLE PAGE
\include{01-title}        

%%%%%%%%%%%%%%%%%%%%%%%%%%%% FRONT MATTER %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%% text spacing, page numbering, and header settings
\MainTextSpacing                            % double spacing for the contents
\pagenumbering{roman}                       % pagination style: Roman numeral
\setcounter{page}{2}                        % page counter starts at roman ii
\pagestyle{fancy}
\renewcommand{\chaptermark}[1]{\markboth{#1}{#1}}
\fancyhead[R]{}               
\fancyhead[L]{\nouppercase \leftmark}       % prints header for unnumbered chap


%%%% MUST ADD ABSTRACT (includes committee as well)
\include{02-abstract}


%%%% OPTIONAL but COMMON: preface chapters
\include{03-dedication}
\include{04-acknowledgement}        
\include{05-epigraph}
%% you can have other chapters and the order does not matter



%%%% LISTINGS
\microtypesetup{protrusion=false}
\TOCTextSpacing                             % one-half spacing for the table of contents
\hypersetup{linkcolor=black}                % local black hyperlink for TOC
%
\mytableofcontents                          % MUST
%
\mylistoftables                             % MUST: if you have tables
%
\mylistoffigures                            % MUST: if you have figures
%
%% OPTIONAL: you can add more lists here (but you will have to define those)
%
\microtypesetup{protrusion=true}

%%%%%%%%%%%%%%%%%%%%%%%%%%% END FRONT MATTER %%%%%%%%%%%%%%%%%%%%%%%%%%%%


%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MAIN MATTER %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%% PAGE and TEXT settings 
\MainTextSpacing                        % restores double spacing 
\pagenumbering{arabic}                  % Arabic page numbering
\fancyhead[L]{\chaptername\ \thechapter. \nouppercase \leftmark}


%%%% include all the main text chapters
\include{06-chapter-1}
\include{07-chapter-2}
\include{08-chapter-3}
\include{09-chapter-4}
\include{10-chapter-5}

%% add more main text technical chapters if you have

%%%%%%%%%%%%%%%%%%%%%%%%%%% END MAIN MATTER %%%%%%%%%%%%%%%%%%%%%%%%%%%%



%%%%%%%%%%%%%%%%%%%%%%%%%%%%% BACK MATTER %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%% BIBLIOGRAPHIC REFERENCES
\BibTextSpacing                         % text spacing for each bib item
\fancyhead[L]{\nouppercase \leftmark}
\printbibliography[title={Bibliographic references},
    heading=bibintoc,notcategory=mypapers]
\clearpage                              % flushes out floating header




%%%% OPTIONAL: Appendix chapter (same format as the main chapters)
\MainTextSpacing                    
\fancyhead[L]{\appendixname\ \thechapter. \nouppercase \leftmark}


\include{11-appendix-A}
\include{12-appendix-B}

%% add more appendix chapters if you have

%%%%%%%%%%%%%%%%%%%%%%%%%%% END BACK MATTER %%%%%%%%%%%%%%%%%%%%%%%%%%%%

\end{document}

%%%%%%%%%%%%%%%%%%%%%%%%% DOCUMENT ENDS HERE %%%%%%%%%%%%%%%%%%%%%%%%%%%