--- manual/manual.tex	2005/10/05 19:52:47	1.35
+++ manual/manual.tex	2017/06/19 20:07:25	1.47
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.35 2005/10/05 19:52:47 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.47 2017/06/19 20:07:25 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})}
@@ -130,76 +133,126 @@
   linkcolor=darkgreen,
   citecolor=darkblue,
   pagecolor=darkred,
-  pdftitle={MITgcm Release 1 Documentation}, 
+  pdftitle={MITgcm Documentation}, 
   pdfauthor={MITgcm-support@mitgcm.org}, 
   pdfkeywords={oceanography, ocean model, general circulation model,
     non-hydrostatic, finite volume, inverse methods, adjoint method} 
   } 
 
 % Some definitions (AMM)
-\def\p#1{{\partial \over {\partial #1}}}
-\def\pp#1#2{{\partial #1 \over {\partial #2}}}
-\def\dd#1#2{{d #1 \over {d #2}}}
+\def\p#1{\frac{\partial }{\partial #1}}
+\def\pp#1#2{\frac{\partial #1}{\partial #2}}
+\def\dd#1#2{\frac{d #1}{d #2}}
 \def\bq{\begin{equation}}
 \def\bqa{\begin{eqnarray}}
 \def\eq{\end{equation}}
 \def\eqa{\end{eqnarray}}
 
-\def\h{ {1\over2} }
+\def\h{ \frac{1}{2} }
 \def\txt{\mbox{$2^\circ$ x $2.5^\circ \,$}}
 \def\fxf{\mbox{$4^\circ$ x $5^\circ \,$}}
 
 \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}
+% Section: Overview of MITgcm
+\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}
+% Section: Getting started with MITgcm
+\input{s_getstarted/text/top_section}
+%\pagebreak
+
+% Section: Model Example <- not yet a section
+\input{s_examples/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}
+% Section: Physical Parameterization - Packages I
+\input{s_phys_pkgs/text/top_section}
 %\pagebreak
 
-% Section: Pre-processing and Post-processing Tools
-\input{part7/part7}
+% Section: Diagnostics and I/O - Packages II, and Post-Processing Utilities
+\input{s_outp_pkgs/text/top_section}
 %\pagebreak
 
-% Section: ECCO
-\input{part8/part8}
+% Section: Interface with ECCO
+\input{s_ecco/text/top_section}
 %\pagebreak
 
-% Section: Model Uses
+% Section: Under Development
+\input{s_under_dvlp/text/top_section}
+
+% Section: Previous applications of MITgcm
 \input{model_uses}
 %\pagebreak