\documentclass[a4paper,10pt]{book}

\usepackage[usenames]{color}
\usepackage{bm}
\usepackage{amsmath}
\usepackage{xspace}
\usepackage{a4wide}
\usepackage{wrapfig}
\usepackage[numbers,comma,sort&compress]{natbib}
\usepackage{graphicx}
\usepackage{xstring}
\usepackage{listings,courier}
%\usepackage{draftcopy}
\usepackage{longtable}
\usepackage{paralist}
%\usepackage{fancyvrb}
\usepackage{listings}
\usepackage{array}
\usepackage[table]{xcolor}
\usepackage{units}
\usepackage[toc,page]{appendix}
\usepackage{lineno}
\usepackage{makeidx}
\usepackage{palatino}
\usepackage{sidecap}




\usepackage[tikz]{bclogo}
\usepackage[framemethod=tikz]{mdframed}
\usepackage{lipsum}




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\usepackage
[ps2pdf, %dvips, %dvipdf, %or dvips or pdftex 
pagebackref, %or backref
breaklinks,
colorlinks=true,
linkcolor=webgreen, %defined below
filecolor=webbrown, %defined below
citecolor=webgreen, %defined below
urlcolor=magenta,
pdftitle={VOTCA-XTP manual},
pdfauthor={},
pdfsubject={VOTCA-XTP},
pdfkeywords={exciton transport organic semiconductors},
bookmarksopen=false,
pdfpagemode=UseNone]{hyperref}
\usepackage[all]{hypcap}
\usepackage[hyphenbreaks]{breakurl}
%\pdfcompresslevel=9

\usepackage[T1]{fontenc}
%\usepackage{times}
\usepackage{type1cm}
%\usepackage{showidx}
\usepackage[draft,color,notref,notcite]{showkeys}

\usepackage{braket}
\usepackage{amssymb}

%%%%%%%% TESTING


\usepackage{tikz}
\usetikzlibrary{shapes,shadows,arrows}
\usetikzlibrary{positioning}





\makeindex

\input{newcommands}

\begin{document}

\addtolength{\oddsidemargin}{0cm}
\addtolength{\evensidemargin}{0cm}
\addtolength{\textwidth}{0cm}
\addtolength{\topmargin}{0cm}
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  morekeywords={xmlns,version,type}% list your attributes here
}


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        keywordstyle=\color{keywords},
        commentstyle=\color{comments},
        stringstyle=\color{red},
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        identifierstyle=\color{green}}


\setlength\parindent{0pt}
\frontmatter
\include{titlepage}
\thispagestyle{empty}
\cleardoublepage

\tableofcontents
\cleardoublepage
\mainmatter

\printindex
\vfill

\linenumbers

\input{theory/introduction}

\chapter{Theoretical background}
\label{sec:theory}

\input{theory/workflow}	
\input{theory/morphology}
\input{theory/fragments}
\input{theory/neighborlist}
\input{theory/reorganization_energy}
\input{theory/energetic_disorder}
\input{theory/gdma}
\input{theory/thole}
\input{theory/electronic_couplings}
\input{theory/rate}
\input{theory/kmc}
\input{theory/nondispersive}
\input{theory/stochastic}
\input{theory/analysis}
\input{theory/correlations}
%\input{theory/idft}
\input{RandomFacts}
\chapter{Input and output files}
\label{sec:io}
\input{input/topology_atomistic}
\input{input/topology_coarsegrained}

%\input{input/topology_conjseg}
\input{input/orbitals_zindo}
\input{input/header_edft}
\input{input/header_idft}
\input{input/output_dft}
\input{input/statefile}

\input{reference/reference}



%\appendix
%\input{appendix/xtp_standalone}

\nolinenumbers

\bibliographystyle{short}
{\footnotesize \bibliography{xtp-manual} }

\end{document} 
