\documentclass{book}

\usepackage{graphicx}
\usepackage{moreverb}    % Defines {listing} environment.
\usepackage{amsmath, amsthm, amssymb, amsbsy, mathtools}
\usepackage{alltt}
\usepackage{rotating}
\usepackage[TABBOTCAP]{subfigure}
\usepackage{toc}
\usepackage{xspace}
%%\usepackage{makeidx}
\usepackage[section]{placeins}   % For preventing floats from floating to end of chapter.
\usepackage{longtable}  % For splitting long vertical tables into pieces
\usepackage{index}
\usepackage{multirow}
\usepackage{booktabs}   % For table layouts
\usepackage{yhmath}     % For widehat

\usepackage[T1]{fontenc}   % so _, <, and > print correctly in text.
\usepackage[strings]{underscore}    % to use "_" in text
\usepackage[pdftex,colorlinks=true]{hyperref}   % Must be last package!

%----------------------------------------------------------------

\input{macros.tex}

\setlength{\textwidth}{6.25in}
\setlength{\hoffset}{0.0in}
\setlength{\oddsidemargin}{0.25in}
\setlength{\evensidemargin}{0.0in}
\setlength{\textheight}{8.5in}
\setlength{\topmargin}{0in}

\makeindex
\newindex{routine}{rdx}{rnd}{Routine Index}

\begin{document}

\index{coordinates!reference|see{reference orbit}}
\index{coordinates!global|see{global coordinates}}
\index{coordinates!phase space|see{phase space coordinates}}
\index{floor coordinates|see{global coordinates}}
\index{canonical coordinates|see{phase space coordinates}}
\index{FPP|see{PTC/FPP}}
\index{Forest, Etienne|see{PTC/FPP}}
\index{Bmad!lattice format|see{lattice file format}}
\index{radiation damping and excitation|see{\hfill\break synchrotron radiation}}
\index{coupling|see{normal mode}}
\index{variables|see{lattice file format, variables}}
\index{transfer map!Taylor map|see{Taylor map}}
\index{transfer map!mat6_calc_method|see{mat6_calc_method}}
\index{map|see{transfer map}}
\index{beam line|see{line}}
\index{replacement list|see{list}}
\index{functions|see{intrinsic functions}}
\index{arithmetic expressions!intrinsic functions|see{intrinsic functions}}
\index{lat_struct!\%param|see{lat_param_struct}}
\index{lattice files!XSIF|see{XSIF}}
\index{an|see{multipole, an}}
\index{bn|see{multipole, ban}}
\index{knl|see{multipole, knl}}
\index{tn|see{multipole, tn}}
\index{coherent synchrotron radiation|see{CSR}}

%----------------------------------------------------------------

\renewcommand{\textfraction}{0.1}
\renewcommand{\topfraction}{1.0}

%----------------------------------------------------------------
%\include{cover-page}

%----------------------------------------------------------------
{
\setlength{\parskip}{\dPar}
\setlength{\parindent}{0ex}
%\include{overview}
%\include{introduction}
}

%----------------------------------------------------------------

%\cleardoublepage
%\phantomsection 
%\pdfbookmark[0]{Contents}{Contents}
%\pdfbookmark[1]{Table of Contents}{toc} 
%\tableofcontents

%\cleardoublepage
%\phantomsection 
%\pdfbookmark[1]{List of Figures}{LoF} 
%\listoffigures

%\cleardoublepage
%\phantomsection 
%\pdfbookmark[1]{List of Tables}{LoT} 
%\listoftables

%----------------------------------------------------------------
\setlength{\parskip}{\dPar}
\setlength{\parindent}{0ex}

%----------------------------------------------------------------
%\part{Language Reference}
%--------------------------------------------------------------
%\chapter{Overview}
\include{overview}
\label{c:overview}
\include{m5}
\label{c:m5}
%\chapter{Field Map}
\label{c:field-map}
\include{InjectionChannel}
\label{c:muon_distribution}
\include{Muon distribution}
\label{c:electrostatic_quadrupoles}
\include{Electrostatic quadrupoles}
%\include{attributes}
%\include{methods}
%\include{lines-and-lists}
%\include{superimpose-and-multipass}
%\include{param-statements}
%\include{param-structs}
%\include{lattice-examples}
%%\include{list-of-element-attributes}

%----------------------------------------------------------------
%\part{Conventions and Physics}
%----------------------------------------------------------------
%\include{coordinates}
%\include{physics}
%\include{charged-tracking}
%\include{xray-tracking}
%\include{simulation-modules}

%----------------------------------------------------------------
%\part{Programmer's Guide}
%----------------------------------------------------------------
%\include{programming}
%\include{example-program}
%\include{ele-struct}
%\include{lat-struct}
%\include{reading-and-writing-lattices}
%\include{normal-modes}
%\include{tracking}
%\include{misc-programming}
%\include{ptc}
%\include{opal}
%\include{cpp-interface}
%\include{quick-plot}
%\include{helper-routines}
%\include{subroutines}


%----------------------------------------------------------------
%\part{Bibliography and Index}
%----------------------------------------------------------------

%\cleardoublepage
%\phantomsection
%\addcontentsline{toc}{chapter}{Bibliography}
%\include{bibliography}

%\cleardoublepage
%\phantomsection
%\addcontentsline{toc}{chapter}{Routine Index}
%\printindex[routine]

%\cleardoublepage
%\phantomsection
%\addcontentsline{toc}{chapter}{Index}
%\printindex

\end{document}
