--- manual/manual.tex	2001/10/21 04:19:40	1.9
+++ manual/manual.tex	2002/03/01 20:03:35	1.12
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.9 2001/10/21 04:19:40 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.12 2002/03/01 20:03:35 cnh Exp $
 % $Name:  $
 
 \documentclass[12pt]{book}
@@ -9,11 +9,22 @@
 %aja%\usepackage{amsfonts}
 \usepackage{amsmath}
 \usepackage{html}
-\usepackage{graphics}
+\usepackage{graphicx}
 
 %cnh%\usepackage{array}
 %cnh%\usepackage{multirow}
 
+% Command to reference entries in either "code" or "names"
+% directories of browseable code tree.
+\newcommand{\proclink}[2]{
+\htmladdnormallink{\em #1()}{../../code_reference/vdb/names/#2_docref.html}
+}
+\newcommand{\varlink}[2]{
+\htmladdnormallink{\bf \tt #1}{../../code_reference/vdb/names/#2_docref.html}
+}
+
+
+
 %ph%\usepackage{epsfig}
 %ph%\usepackage{psfrag}
 %ph%\usepackage{oldgerm}
@@ -34,12 +45,13 @@
 %cnh%\renewcommand{\footrulewidth}{0.4pt}
 
 % bibtex stuff
-\newcommand{\BIBPATH}{.}
-\usepackage{natbib}
-\bibliographystyle{\BIBPATH/jmr_my}
-\gdef\harvardleft{[}
-\gdef\harvardright{]}
-\bibpunct{[}{]}{,}{a}{}{,}
+%aja%\newcommand{\BIBPATH}{.}
+%aja%\usepackage{natbib}
+%aja%\bibliographystyle{\BIBPATH/jmr_my}
+%aja%\gdef\harvardleft{[}
+%aja%\gdef\harvardright{]}
+%aja%\bibpunct{[}{]}{,}{a}{}{,}
+\bibliographystyle{plain}
 
 % referencing
 %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
@@ -59,14 +71,32 @@
 %\renewcommand{\chaptername}{Section}
 
 
+% This allows hyperlinks in PDF
+% hyperref package and colors for hyperref package 
+\usepackage{color} 
+\usepackage[dvips]{hyperref} 
+\definecolor{darkgreen}{rgb}{0,0.4,0} 
+\definecolor{darkblue}{rgb}{0,0,0.4} 
+\definecolor{darkred}{rgb}{0.5,0,0} 
+\hypersetup{breaklinks=true, 
+  colorlinks=true, 
+  linkcolor=darkgreen,
+  citecolor=darkblue,
+  pagecolor=darkred,
+  pdftitle={MITgcm Release 1 Documentation}, 
+  pdfauthor={support@mitgcm.org}, 
+  pdfkeywords={oceanography, ocean model, general circulation model,
+    non-hydrostatic, finite volume, inverse methods, adjoint method} 
+  } 
+
 \begin{document}
 
 \bodytext{bgcolor="#FFFFFFFF"} 
 
 \tableofcontents
-\pagebreak
+%\pagebreak
 
-\part{MIT GCM basics}
+%\part{MIT GCM basics}
 
 % Section: Overview
 \input{part1/part1}
@@ -85,14 +115,14 @@
 %\pagebreak
 
 
-\part{Adjoint of the MIT GCM}
+%\part{Adjoint of the MIT GCM}
 
 % Section: Automatic Differentiation
 \input{part5/part5}
 %\pagebreak
 
 
-\part{Additional features}
+%\part{Additional features}
 
 % Section: Physical Packages
 \input{part6/part6}
@@ -107,8 +137,9 @@
 %\pagebreak
 
 % Section: References:
-\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
+%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
 \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
-\bibliography{\BIBPATH/manual_references}
+%aja%\bibliography{\BIBPATH/manual_references}
+\bibliography{manual_references}
 
 \end{document}