--- manual/manual.tex	2002/04/24 11:01:46	1.13
+++ manual/manual.tex	2006/06/30 05:58:03	1.40
@@ -1,7 +1,7 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.13 2002/04/24 11:01:46 heimbach Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.40 2006/06/30 05:58:03 edhill Exp $
 % $Name:  $
 
-\documentclass[12pt]{book}
+\documentclass[10pt]{book}
 
 %To help cross-reference
 %\usepackage{showlabels}
@@ -9,20 +9,64 @@
 %aja%\usepackage{amsfonts}
 \usepackage{amsmath}
 \usepackage{html}
+\usepackage{hthtml}
 \usepackage{graphicx}
+\usepackage{rotating}
+
+% CNH playing around with page widths
+\usepackage{anysize}
 
 %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}
-}
-
+%eh3  Commands to reference either files or symbols within the "HTML-ized"
+%eh3  ("vdb") code.
+%eh3  
+%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}}
+\newcommand{\sectiontitle}[1]{\textsl{#1}}
+\newcommand{\code}[1]{\texttt{#1}}
+
+%%  EH3 : try out the epsfig package
+\usepackage[dvips]{epsfig}
+\def\scalefig#1{\epsfxsize #1\textwidth}
+
+%EH3% ==========================================================
+%EH3%  ***   PRIVATE SECTIONS   ******   PRIVATE SECTIONS   ***
+%EH3%
+%EH3%  Directions: To build the ``private'' or ``local-only'' 
+%EH3%    version of this manual, then edit the following so 
+%EH3%    they appear as:
+%EH3%
+%EH3%    % \includecomment{versionprivate}
+%EH3%    \excludecoment{versionprivate}
+%EH3%
+%EH3%    The default is to include everything which is:
+%EH3%
+%EH3%    \includecomment{versionprivate}
+%EH3%    % \excludecoment{versionprivate}
+
+%\includecomment{versionprivate}
+\excludecomment{versionprivate}
+
+%EH3%
+%EH3%    To use this comment, simply bracket any part of the 
+%EH3%    manual with two lines that contain ONLY the following
+%EH3%    pair:
+%EH3%
+%EH3%      \begin{versionprivate}
+%EH3%      \end{versionprivate}
+%EH3%
+%EH3%    with NO additional comments or other commands on the
+%EH3%    lines containing the \begin{...}\end{...} statements.
+%EH3%
+%EH3%  ***   PRIVATE SECTIONS   ******   PRIVATE SECTIONS   ***
+%EH3% ==========================================================
 
 
 %ph%\usepackage{epsfig}
@@ -51,7 +95,12 @@
 %aja%\gdef\harvardleft{[}
 %aja%\gdef\harvardright{]}
 %aja%\bibpunct{[}{]}{,}{a}{}{,}
-\bibliographystyle{plain}
+%\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})}
@@ -74,7 +123,8 @@
 % This allows hyperlinks in PDF
 % hyperref package and colors for hyperref package 
 \usepackage{color} 
-\usepackage[dvips]{hyperref} 
+\usepackage{hyperref} 
+%\usepackage[dvips]
 \definecolor{darkgreen}{rgb}{0,0.4,0} 
 \definecolor{darkblue}{rgb}{0,0,0.4} 
 \definecolor{darkred}{rgb}{0.5,0,0} 
@@ -84,15 +134,73 @@
   citecolor=darkblue,
   pagecolor=darkred,
   pdftitle={MITgcm Release 1 Documentation}, 
-  pdfauthor={support@mitgcm.org}, 
+  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\bq{\begin{equation}}
+\def\bqa{\begin{eqnarray}}
+\def\eq{\end{equation}}
+\def\eqa{\end{eqnarray}}
+
+\def\h{ {1\over2} }
+\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{
+  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
+  \\
+  \\
+  \\
+  MIT Department of EAPS  \\
+  77 Massachusetts Ave. \\
+  Cambridge, MA \ 02139-4307
+}
+
+\date{August 19, 2004}
+
+\maketitle
+
 \tableofcontents
 %\pagebreak
 
@@ -128,14 +236,22 @@
 \input{part6/part6}
 %\pagebreak
 
-% Section: Diagnostics
+% Section: Pre-processing and Post-processing Tools
 \input{part7/part7}
 %\pagebreak
 
+% Section: ECCO
+\input{part8/part8}
+%\pagebreak
+
+% Section: Model Uses
+\input{model_uses}
+%\pagebreak
+
 % Section: References:
 %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
 \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
 %aja%\bibliography{\BIBPATH/manual_references}
-\bibliography{manual_references}
+\bibliography{manual_references,baylor_biblio}
 
 \end{document}
