--- manual/manual.tex	2006/04/07 15:40:07	1.37
+++ 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 1.37 2006/04/07 15:40:07 edhill 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}
@@ -25,6 +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}}
@@ -96,8 +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})}
@@ -169,6 +172,10 @@
 \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"} 
@@ -176,12 +183,12 @@
 \title{ \textsc{MITgcm User Manual} }
 
 \author{
-  John Marshall \and Alistair Adcroft \and Jean-Michel Campin 
-  \and Patrick Heimbach \and Andrea Molod \and Stephanie Dutkiewicz
-  \and Helen Hill \and Martin Losch \and Baylor Fox-Kemper
-  \and Dimitris Menemenlis \and David Ferreira \and Ed Hill 
-  \and Mick Follows \and Chris Hill \and Constantinos Evangelinos
-  \and Gael Forget
+  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
   \\
   \\
   \\
@@ -190,7 +197,8 @@
   Cambridge, MA \ 02139-4307
 }
 
-\date{August 19, 2004}
+%\date{August 19, 2004}
+\date{\today}
 
 \maketitle
 
@@ -200,43 +208,46 @@
 %\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