--- manual/manual.tex	2001/08/08 22:14:44	1.2
+++ manual/manual.tex	2001/10/05 22:22:20	1.6
@@ -1,11 +1,11 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.2 2001/08/08 22:14:44 adcroft Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.6 2001/10/05 22:22:20 heimbach Exp $
 % $Name:  $
 
 \documentclass[12pt]{book}
 
 \usepackage{amsfonts}
 \usepackage{amsmath}
-\usepackage{html}
+\usepackage{/usr/local/pkg/latex2html/current/texinputs/html}
 \usepackage{epsfig}
 \usepackage{graphics,subfigure}
 \usepackage{array}
@@ -27,6 +27,14 @@
 \renewcommand{\headrulewidth}{0.4pt}
 \renewcommand{\footrulewidth}{0.4pt}
 
+% bibtex stuff
+\newcommand{\BIBPATH}{.}
+\usepackage{natbib}
+\bibliographystyle{\BIBPATH/jmr_my}
+\gdef\harvardleft{[}
+\gdef\harvardright{]}
+\bibpunct{[}{]}{,}{a}{}{,}
+
 % referencing
 \newcommand{\refequ}[1]{equation (\ref{equ:#1})}
 \newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
@@ -39,6 +47,12 @@
 \newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
 \newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
 
+% This allows numbering of subsubsections
+\setcounter{secnumdepth}{3}
+% This changes the the chapter title
+%\renewcommand{\chaptername}{Section}
+
+\usepackage{showlabels}
 
 
 \begin{document}
@@ -46,35 +60,49 @@
 \tableofcontents
 \pagebreak
 
-% Part: Overview
+\part{The MIT GCM basics}
+
+% Section: Overview
 \input{part1/part1}
 \pagebreak
 
-% Part: Discretization and Algorithm
+% Section: Discretization and Algorithm
 \input{part2/part2}
 \pagebreak
 
-% Part: Getting started
+% Section: Getting started
 \input{part3/part3}
 \pagebreak
 
-% Part: Software Architecture
+% Section: Software Architecture
 \input{part4/part4}
 \pagebreak
 
-% Part: Automatic Differentiation
+
+\part{Adjoint of the MIT GCM}
+
+% Section: Automatic Differentiation
 \input{part5/part5}
 \pagebreak
 
-% Part: Physical Packages
+
+\part{Additional features}
+
+% Section: Physical Packages
 \input{part6/part6}
 \pagebreak
 
-% Part: Diagnostics
+% Section: Diagnostics
 \input{part7/part7}
 \pagebreak
 
-% Part: ECCO Interface
+% Section: ECCO Interface
 \input{part8/part8}
+\pagebreak
+
+% Section: References:
+\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
+\addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
+\bibliography{\BIBPATH/manual_references}
 
 \end{document}