main.tex

\documentclass[12pt,a4paper]{report}
\usepackage[utf8]{inputenc}
% \usepackage[T1]{fontenc}
% For two column text, add "twocolumn" as an option to the document
% class. Also uncomment the two "onecolumn" and "twocolumn" lines
% around the title page below.

% Variables that controls behaviour
\usepackage{ifthen} % for conditional statements
\newboolean{pdflatex}
\setboolean{pdflatex}{true} % False for eps figures 

\newboolean{articletitles}
\setboolean{articletitles}{true} % False removes titles in references

\newboolean{uprightparticles}
\setboolean{uprightparticles}{false} %True for upright particle symbols

\newboolean{inbibliography}
\setboolean{inbibliography}{false} %True once you enter the bibliography

\input{preamble}

% ============================================================================
% my commands and defs
\usepackage{float}
\usepackage{subfigure}
\usepackage{caption}
\usepackage{multicol}
\usepackage{booktabs}
\usepackage{rotating}  %
\usepackage{graphpap}  %
\usepackage{mathrsfs}
\usepackage{multirow}  %
\usepackage{cancel}    %
\usepackage{bm}
% \usepackage{tabularx}
\usepackage{verbatim}
\usepackage[percent]{overpic}
\usepackage{longtable} % only for template; not usually to be used in PAPERs
\usepackage{cleveref}
\usepackage[toc,page]{appendix}
\usepackage[chapter]{tocbibind}
\input{symbols-def}

\newcommand{\systpol}{\ensuremath{\mathrm{\,(syst.pol)}}\xspace}

\def\tesla {\ensuremath{\rm \,T}\xspace}
\newcommand\iamp{{Intel\textsuperscript{\textregistered} VTune\texttrademark Amplifier XE} }
\newcommand\amp{{VTune\texttrademark Amplifier XE} }
\newcommand\intel{{Intel\textsuperscript{\textregistered}} }
\newcommand\google{{Google\textsuperscript{\textregistered} }}
\def\mmu        {\ensuremath{\Pmu}\xspace}
% ============================================================================


\hypersetup{
  colorlinks = true,
  urlcolor = blue,
  pdfauthor = {Alexander Mazurov},
  pdfkeywords = {scientific computing, system and distributing programming},
  pdftitle = {Thesis},
  pdfsubject = {Thesis},
  pdfpagemode = UseNone
}
% =============================================================================
% Customize page headers
\usepackage{fancyhdr}
\pagestyle{fancy}
% \fancyhead{} % clear all header fields
% \fancyhead[LE,RO]{\small \slshape \rightmark}
% \fancyhead[LO,RE]{\small \slshape \leftmark}
\renewcommand{\headrulewidth}{0.4pt}
\fancyfoot[L]{\today}
\fancyfoot[C]{Version 2.0}
\fancyfoot[R]{\thepage}
\renewcommand{\footrulewidth}{0.4pt}

\begin{document}
%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% Title     %%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%
\renewcommand{\thefootnote}{\fnsymbol{footnote}}
\setcounter{footnote}{1}

% %%%%%%% CHOOSE TITLE PAGE--------
\input{title}

\renewcommand{\thefootnote}{\arabic{footnote}}
\setcounter{footnote}{0}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%  Table of Content   %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Uncomment next 2 lines if desired
\lhead{\leftmark}
\rhead{\rightmark}

\makeatletter
\renewcommand\tableofcontents{%
    \section*{\contentsname
        \@mkboth{%
%           \MakeUppercase\contentsname}{\MakeUppercase\contentsname}}% DELETED
           \MakeUppercase\contentsname}{}}% ADDED
    \@starttoc{toc}%
    } 
\makeatother
\tableofcontents
%\cleardoublepage


%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% Main text %%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%

% \pagestyle{plain} % restore page numbers for the main text
\setcounter{page}{1}
\pagenumbering{arabic}

%% Uncomment during review phase. 
%% Comment before a final submission.
\linenumbers

% You can include short sections directly in the main tex file.
% However, for larger papers it is desirable to split the text into
% several semiautonomous files, which can be revised independently.
% This is especially useful when developing a document in
% collaboration with several people, since then different parts can be
% edited independently.  This type of file organization is shown here.
% 

\input{introduction}
\input{review}
\input{lhcb}
\input{profiler}
\chapter{Study of \texorpdfstring{$\chi_{b}$}{xb} production}
\input{csintroduction}
\input{datasets}
\input{upsilon}
\input{chib}
\input{ratio}
\input{mc}
\input{fraction}
\input{systematic}
\input{results}
\input{conclusion}
\input{appendix}

% \renewcommand{\bibname}{References}%  Change the section name from "Bibliography" to "References"
\setboolean{inbibliography}{true}
\bibliographystyle{bib/LHCb}
\renewcommand{\headrulewidth}{0pt}
\fancyhead{}
\bibliography{bib/main,bib/perf,bib/LHCb-PAPER,bib/LHCb-CONF,bib/LHCb-DP}

\input{acknowledgements}
\end{document}