--- manual/manual.tex	2006/06/28 21:20:41	1.39
+++ 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 1.39 2006/06/28 21:20:41 cnh 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}
@@ -133,22 +133,22 @@
   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 $5^\circ \,$}}
 
@@ -172,6 +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"} 
@@ -179,12 +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
   \\
   \\
   \\
@@ -193,7 +197,8 @@
   Cambridge, MA \ 02139-4307
 }
 
-\date{August 19, 2004}
+%\date{August 19, 2004}
+\date{\today}
 
 \maketitle
 
@@ -202,45 +207,52 @@
 
 %\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 with MITgcm
+\input{s_getstarted/text/top_section}
 %\pagebreak
 
-% Section: Getting started
-\input{part3/part3}
+% 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