--- manual/manual.tex	2005/08/02 17:13:01	1.33
+++ manual/manual.tex	2010/08/27 13:31:32	1.44
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.33 2005/08/02 17:13:01 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.44 2010/08/27 13:31:32 jmc Exp $
 % $Name:  $
 
 \documentclass[10pt]{book}
@@ -11,6 +11,7 @@
 \usepackage{html}
 \usepackage{hthtml}
 \usepackage{graphicx}
+\usepackage{rotating}
 
 % CNH playing around with page widths
 \usepackage{anysize}
@@ -24,6 +25,7 @@
 %afe seems like these need to be long, sorry
 \newcommand{\varlink}[2]{\htmladdnormallink{\tt #1}{../code_reference/vdb/byname/#2.html}}
 \newcommand{\filelink}[2]{\htmladdnormallink{\bf \tt #1}{../code_reference/vdb/byname/#2.html}}
+\newcommand{\myhref}[2]{\htmladdnormallink{#2}{#1}}
 
 % afe  Commands to standardize typesetting 
 \newcommand{\file}[1]{\texttt{#1}}
@@ -95,8 +97,10 @@
 %aja%\bibpunct{[}{]}{,}{a}{}{,}
 %\bibliographystyle{plain}
 %-jmc: try agu bib-style (give author names & year instead of just a number)
+%% \usepackage[square]
 \usepackage[square]{natbib}
 \bibliographystyle{agu}
+%% \bibliographystyle{aguurl}
 
 % referencing
 %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
@@ -150,54 +154,100 @@
 
 \def\blankpage{ \vspace*{\fill} \vspace{5in} \vfill \newpage}
 
+% Some definitions modified from the ones provided by Baylor
+\def\BFKav#1{\overline{#1}}
+\def\BFKpd#1#2{{\frac{\partial{#2}}{\partial{#1}}}}
+\def\BFKpds#1#2{{\frac{\partial^2{#2}}{{\partial{#1}}^2}}}
+\def\BFKDt#1{\frac{D{#1}}{Dt}}
+\def\BFKaDt#1{\frac{\BFKav D{#1}}{\BFKav{Dt}}}
+\def\BFKd#1{{\,\rm d#1}}
+\def\BFKRo{{\rm Ro}}
+\def\BFKRe{{\rm Re}}
+\def\BFKFr{{\rm Fr}}
+\def\BFKPr{{\rm Pr}}
+\def\BFKMr{{M_{Ro}}}
+\def\BFKtu{{\tilde u}}
+\def\BFKtv{{\tilde v}}
+\def\BFKatu{{\tilde {\BFKav u}}}
+\def\BFKatv{{\tilde {\BFKav v}}}
+\def\BFKlesssim{{<\atop\sim}}
+
+%  Definitions from EH3:
+\def\CC{C\raise.3ex\hbox{{\footnotesize
+      +}}\raise.3ex\hbox{\footnotesize +}\ }
 
 \begin{document}
 
 \bodytext{bgcolor="#FFFFFFFF"} 
 
+\title{ \textsc{MITgcm User Manual} }
+
+\author{
+  Alistair Adcroft \and Jean-Michel Campin \and Stephanie Dutkiewicz
+  \and Constantinos Evangelinos \and David Ferreira %\and Mick Follows 
+  \and Gael Forget \and Baylor Fox-Kemper \and Patrick Heimbach 
+  \and Chris Hill \and Ed Hill \and Helen Hill 
+  \and Oliver Jahn \and Martin Losch \and John Marshall
+  \and Guillaume Maze \and Dimitris Menemenlis \and Andrea Molod
+  \\
+  \\
+  \\
+  MIT Department of EAPS  \\
+  77 Massachusetts Ave. \\
+  Cambridge, MA \ 02139-4307
+}
+
+%\date{August 19, 2004}
+\date{\today}
+
+\maketitle
+
 \tableofcontents
 %\pagebreak
 
 %\part{MIT GCM basics}
 
 % Section: Overview
-\input{part1/part1}
+\input{s_overview/text/top_section}
 %\pagebreak
 
 % Section: Discretization and Algorithm
-\input{part2/part2}
+\input{s_algorithm/text/top_section}
 %\pagebreak
 
 % Section: Getting started
-\input{part3/part3}
+\input{s_getstarted/text/top_section}
 %\pagebreak
 
 % Section: Software Architecture
-\input{part4/part4}
+\input{s_software/text/top_section}
 %\pagebreak
 
 
 %\part{Adjoint of the MIT GCM}
 
 % Section: Automatic Differentiation
-\input{part5/part5}
+\input{s_autodiff/text/top_section}
 %\pagebreak
 
 
 %\part{Additional features}
 
 % Section: Physical Packages
-\input{part6/part6}
+\input{s_phys_pkgs/text/top_section}
 %\pagebreak
 
 % Section: Pre-processing and Post-processing Tools
-\input{part7/part7}
+\input{s_outp_pkgs/text/top_section}
 %\pagebreak
 
 % Section: ECCO
-\input{part8/part8}
+\input{s_ecco/text/top_section}
 %\pagebreak
 
+% Section: Under Development
+\input{s_under_dvlp/text/top_section}
+
 % Section: Model Uses
 \input{model_uses}
 %\pagebreak
@@ -206,6 +256,6 @@
 %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
 \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
 %aja%\bibliography{\BIBPATH/manual_references}
-\bibliography{manual_references}
+\bibliography{manual_references,baylor_biblio}
 
 \end{document}