--- manual/manual.tex	2001/08/08 16:15:12	1.1
+++ manual/manual.tex	2001/10/04 19:30:23	1.5
@@ -1,22 +1,23 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.1 2001/08/08 16:15:12 adcroft Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.5 2001/10/04 19:30:23 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}
 \usepackage{multirow}
 \usepackage{fancyhdr}
 \usepackage{psfrag}
-\usepackage{oldgerm}
-\usepackage{palatcm}              % better PDF 
+%\usepackage{oldgerm}
+% I commented the following because it introduced excessive white space
+%\usepackage{palatcm}              % better PDF 
 
 % page headers and footers
-\pagestyle{fancy}
+%\pagestyle{fancy}
 \fancyhead{}
 \fancyhead[LO]{\slshape \rightmark}
 \fancyhead[RE]{\slshape \leftmark}
@@ -26,6 +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})}
@@ -38,6 +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}
@@ -45,35 +60,45 @@
 \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}
 
+% Section: References:
+\bibliography{\BIBPATH/manual_references}
 \end{document}
