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I am preparing my thesis. It consists of an introduction plus some articles. I am using the following template. Visually in the .pdf, everything seems fine. However, the problem appears when clicking in the table of contents.

When I click in introduction, it remains at the table of contents. Except section 1. and "references for the introduction", the remaining sections do not work well. And concerning the articles, when I click in the table of contents, I go to "references for the introduction", instead of the articles.

Moreover, when I open the pdf, the toolbar of contents that appears to the left of the screen does not reflect correctly the structure of the table of contents.

Remark: I want the \clearpage commands not to be removed.

\documentclass[12pt,reqno]{report}

\usepackage{hyperref}
\usepackage[usenames]{color}
\usepackage[latin1]{inputenc} 
\usepackage{float}
\usepackage{bbm}
\usepackage[english]{babel} 
\usepackage{amssymb, amsmath}
\usepackage{geometry,graphicx}
\usepackage[final]{pdfpages}

\addto\captionsenglish{%
  \renewcommand{\bibname}{\centerline{{\Large References for the introduction}}}
}

\newtheorem{theorem}{Theorem}
\newtheorem{lemma}[theorem]{Lemma} 
\newtheorem{definition}[theorem]{Definition}
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{fact}[theorem]{Fact}
\newtheorem{remark}[theorem]{Remark}
\newtheorem{notation}[theorem]{Notation}
\newtheorem{example}[theorem]{Example}
\geometry{a4paper,twoside,top=3.5cm,bottom=3.5cm,left=3cm,right=3cm,headsep=1cm}

\setlength{\parskip}{0.5em}

\begin{document}

\includepdf[pages=-]{./coverthesis.pdf}

\newpage\null\thispagestyle{empty}\newpage

\begin{center}
\textbf{Abstract}
\end{center}

This is my abstract.

\tableofcontents

\clearpage

\begin{center}
\Large \textbf{Introduction} \normalsize
\addcontentsline{toc}{chapter}{Introduction}
\end{center}

\clearpage

\begin{center}
\textbf{1. First part introduction} 
\addcontentsline{toc}{section}{1. First part introduction}
\end{center}

Something...

\clearpage

\noindent \textbf{1.1. Subsection 1 in the first part} 
\addcontentsline{toc}{subsection}{1.1. Subsection 1 in the first part}

Something...

\clearpage

\noindent \textbf{1.2. Subsection 2 in the first part} 
\addcontentsline{toc}{subsection}{1.2. Subsection 2 in the first part}

Something...

\clearpage

\begin{center}
\textbf{2. Second part introduction} 
\addcontentsline{toc}{section}{2. Second part introduction}
\end{center}

\clearpage

\noindent \textbf{2.1. Subsection 1 in the second part} 
\addcontentsline{toc}{subsection}{1.1. Subsection 1 in the second part}

Something...

\clearpage

\noindent \textbf{2.2. Subsection 2 in the second part} 
\addcontentsline{toc}{subsection}{1.2. Subsection 2 in the second part}

Something...

\clearpage

\begin{thebibliography}{a}
\addcontentsline{toc}{section}{References for the introduction}

\bibitem{Author}
Author. \textit{Title}. Edition and year.

\end{thebibliography}

\clearpage

\begin{center}
\textbf{Article 1.} 
\addcontentsline{toc}{chapter}{Article 1}
\end{center}

\includepdf[pages=-]{./art1.pdf}

\clearpage

\begin{center}
\textbf{Article 2.} 
\addcontentsline{toc}{chapter}{Article 2}
\end{center}

\includepdf[pages=-]{./art2.pdf}

\end{document}
3
  • 4
    Well, you are missing the sections themselves in your document. So, if you instead of \textbf{1. First part introduction} and so on use, e.g. \section{First part introduction} or some equivalent level/variant of your choice, it should work.
    – gusbrs
    Feb 18, 2018 at 11:27
  • 1
    Welcome to TeX SX! Normally, hyperref should be loaded as the last package, with very dew exceptions.
    – Bernard
    Feb 18, 2018 at 11:27
  • Why are using sections only in a report - like document? Wouldn't article be much more suited for this? Your document is not compilable at all, since it misses the relevant included files
    – user31729
    Feb 18, 2018 at 11:32

2 Answers 2

3

I would go with the regular sectioning commands:

\documentclass[12pt,reqno]{report}

\usepackage[usenames]{color}
\usepackage[latin1]{inputenc} 
\usepackage{float}
\usepackage{bbm}
\usepackage[english]{babel} 
\usepackage{amssymb, amsmath}
\usepackage{geometry,graphicx}
\usepackage[final]{pdfpages}
\usepackage{hyperref}

\addto\captionsenglish{%
  \renewcommand{\bibname}{References for the introduction}
}

\newtheorem{theorem}{Theorem}
\newtheorem{lemma}[theorem]{Lemma} 
\newtheorem{definition}[theorem]{Definition}
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{fact}[theorem]{Fact}
\newtheorem{remark}[theorem]{Remark}
\newtheorem{notation}[theorem]{Notation}
\newtheorem{example}[theorem]{Example}
\geometry{a4paper,twoside,top=3.5cm,bottom=3.5cm,left=3cm,right=3cm,headsep=1cm}

\setlength{\parskip}{0.5em}

\renewcommand{\thesection}{\arabic{section}}

\begin{document}

%\includepdf[pages=-]{./coverthesis.pdf}

\newpage\null\thispagestyle{empty}\newpage

\begin{center}
\textbf{Abstract}
\end{center}

This is my abstract.

\tableofcontents

\clearpage


\chapter*{Introduction}
\addcontentsline{toc}{chapter}{Introduction}

\clearpage



\section{First part introduction} 



Something...

\clearpage

\subsection{Subsection 1 in the first part} 


Something...

\clearpage

\subsection{Subsection 2 in the first part} 


Something...

\clearpage

\section{Second part introduction} 

\clearpage

\subsection{Subsection 1 in the second part} 


Something...

\clearpage

\subsection{Subsection 2 in the second part} 


Something...

\clearpage

\begin{thebibliography}{a}
\addcontentsline{toc}{section}{References for the introduction}

\bibitem{Author}
Author. \textit{Title}. Edition and year.

\end{thebibliography}

\clearpage

\chapter*{Article 1.} 
\addcontentsline{toc}{chapter}{Article 1.}

%\includepdf[pages=-]{./art1.pdf}

\clearpage

\chapter*{Article 2.}
\addcontentsline{toc}{chapter}{Article 2.}

%\includepdf[pages=-]{./art2.pdf}

\end{document}

enter image description here

2

The weird usage of \textbf{1.1 Subsection} etc. does not provide hyperanchors that can be grabbed by \addcontentsline.

If this usage should persist, a \phantomsection macro is needed to generate hyperanchors, but I don't recommend this manual and error prone \textbf{...} style.

\documentclass[12pt,reqno]{report}

\usepackage[usenames]{color}
\usepackage[latin1]{inputenc} 
\usepackage{float}
\usepackage{bbm}
\usepackage[english]{babel} 
\usepackage{amssymb, amsmath}
\usepackage{geometry,graphicx}
\usepackage[final]{pdfpages}

\addto\captionsenglish{%
  \renewcommand{\bibname}{\centerline{{\Large References for the introduction}}}
}

\newtheorem{theorem}{Theorem}
\newtheorem{lemma}[theorem]{Lemma} 
\newtheorem{definition}[theorem]{Definition}
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{fact}[theorem]{Fact}
\newtheorem{remark}[theorem]{Remark}
\newtheorem{notation}[theorem]{Notation}
\newtheorem{example}[theorem]{Example}
\geometry{a4paper,twoside,top=3.5cm,bottom=3.5cm,left=3cm,right=3cm,headsep=1cm}

\setlength{\parskip}{0.5em}


\usepackage{hyperref}

\begin{document}

%\includepdf[pages=-]{./coverthesis.pdf}

\newpage\null\thispagestyle{empty}\newpage

\begin{center}
\textbf{Abstract}
\end{center}

This is my abstract.

\tableofcontents

\clearpage

\begin{center}
\Large \textbf{Introduction} \normalsize
\phantomsection
\addcontentsline{toc}{chapter}{Introduction}
\end{center}

\clearpage

\begin{center}
\textbf{1. First part introduction} 
\phantomsection
\addcontentsline{toc}{section}{1. First part introduction}
\end{center}

Something...

\clearpage

\noindent \textbf{1.1. Subsection 1 in the first part} 
\addcontentsline{toc}{subsection}{1.1. Subsection 1 in the first part}

Something...

\clearpage

\noindent \textbf{1.2. Subsection 2 in the first part} 
\addcontentsline{toc}{subsection}{1.2. Subsection 2 in the first part}

Something...

\clearpage

\begin{center}
\textbf{2. Second part introduction} 
\addcontentsline{toc}{section}{2. Second part introduction}
\end{center}

\clearpage

\noindent \textbf{2.1. Subsection 1 in the second part} 
\addcontentsline{toc}{subsection}{1.1. Subsection 1 in the second part}

Something...

\clearpage

\noindent \textbf{2.2. Subsection 2 in the second part} 
\addcontentsline{toc}{subsection}{1.2. Subsection 2 in the second part}

Something...

\clearpage

\begin{thebibliography}{a}
\addcontentsline{toc}{section}{References for the introduction}

\bibitem{Author}
Author. \textit{Title}. Edition and year.

\end{thebibliography}

\clearpage

\begin{center}
\textbf{Article 1.} 
\addcontentsline{toc}{chapter}{Article 1}
\end{center}

%\includepdf[pages=-]{./art1.pdf}

\clearpage

\begin{center}
\textbf{Article 2.} 
\addcontentsline{toc}{chapter}{Article 2}
\end{center}

%\includepdf[pages=-]{./art2.pdf}

\end{document}

Improvement with centered sections (only sections, not \subsections) etc. This solves the problem with the bookmarks as well.

\documentclass[12pt,reqno]{report}

\usepackage[usenames]{color}
\usepackage[latin1]{inputenc} 
\usepackage{float}
\usepackage{bbm}
\usepackage[english]{babel} 
\usepackage{amssymb, amsmath}
\usepackage{geometry,graphicx}
\usepackage[final]{pdfpages}

%\addto\captionsenglish{%
%  \renewcommand{\bibname}{\begingroup\protect\centering \protect\Large References for the introduction\endgroup}
%}

\newtheorem{theorem}{Theorem}
\newtheorem{lemma}[theorem]{Lemma} 
\newtheorem{definition}[theorem]{Definition}
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{fact}[theorem]{Fact}
\newtheorem{remark}[theorem]{Remark}
\newtheorem{notation}[theorem]{Notation}
\newtheorem{example}[theorem]{Example}
\geometry{a4paper,twoside,top=3.5cm,bottom=3.5cm,left=3cm,right=3cm,headsep=1cm}

\setlength{\parskip}{0.5em}


\usepackage[nottoc]{tocbibind}
\usepackage{xpatch}


\renewcommand{\thesection}{\arabic{section}}

\makeatletter


%\AtBeginDocument{%


  \xpatchcmd{\@sect}{%
    \def\@svsechd{%
      #6{\hskip #3\relax
        \@svsec #8}}%
  }{%
    \def\@svsechd{%
      #6{\hskip #3\relax
        \begingroup\centering \@svsec #8 \endgroup}}%
  }{\typeout{Patch success}}{\typeout{first patch failed}}
  \xpatchcmd{\@sect}{%
    \begingroup
    #6{%
      \@hangfrom{\hskip #3\relax\@svsec}%
      \interlinepenalty \@M #8\@@par}%
    \endgroup%
  }{\begingroup
    #6{%
      \@hangfrom{\hskip #3\relax\@svsec}%
      \ifnum0=\pdfstrcmp{#1}{section}%
         \begingroup\centering
         \interlinepenalty \@M #8 \@@par\endgroup
         \else
         \interlinepenalty \@M #8 \@@par% Non - section types
      \fi
    }%
    \endgroup%
  }{}{\typeout{Second patch failed}}%
\makeatother

\usepackage{hyperref}

\begin{document}

%\includepdf[pages=-]{./coverthesis.pdf}

\newpage\null\thispagestyle{empty}\newpage

\begin{center}
\textbf{Abstract}
\end{center}

This is my abstract.

\tableofcontents

\clearpage



\phantomsection
\chapter*{\centering Introduction}
\addcontentsline{toc}{chapter}{Introduction}

\clearpage

\section{First part introduction} 
%\addcontentsline{toc}{section}{1. First part introduction}

Something...

\clearpage

\subsection{Subsection 1 in the first part} 
%\addcontentsline{toc}{subsection}{1.1. Subsection 1 in the first part}

Something...

\clearpage

\subsection{Subsection 2 in the first part}

Something...

\clearpage


\section{Second part introduction}

\clearpage

\subsection{Subsection 1 in the second part} 

Something...

\clearpage

\subsection{Subsection 2 in the second part} 

Something...

\clearpage

\begin{thebibliography}{a}
%\addcontentsline{toc}{section}{References for the introduction}

\bibitem{Author}
Author. \textit{Title}. Edition and year.

\end{thebibliography}

\clearpage

\chapter*{\centering Article 1}
\addcontentsline{toc}{chapter}{Article 1}

%\includepdf[pages=-]{./art1.pdf}

\clearpage

\chapter*{\centering Article 2}
\addcontentsline{toc}{chapter}{Article 2}

%\includepdf[pages=-]{./art2.pdf}

\end{document}

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