--- manual/manual.tex	2001/08/08 16:15:12	1.1
+++ manual/manual.tex	2005/07/14 19:22:18	1.30
@@ -1,79 +1,204 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.1 2001/08/08 16:15:12 adcroft Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.30 2005/07/14 19:22:18 molod Exp $
 % $Name:  $
 
-\documentclass[12pt]{book}
+\documentclass[10pt]{book}
 
-\usepackage{amsfonts}
+%To help cross-reference
+%\usepackage{showlabels}
+
+%aja%\usepackage{amsfonts}
 \usepackage{amsmath}
 \usepackage{html}
-\usepackage{epsfig}
-\usepackage{graphics,subfigure}
-\usepackage{array}
-\usepackage{multirow}
-\usepackage{fancyhdr}
-\usepackage{psfrag}
-\usepackage{oldgerm}
-\usepackage{palatcm}              % better PDF 
+\usepackage{hthtml}
+\usepackage{graphicx}
+
+%cnh%\usepackage{array}
+%cnh%\usepackage{multirow}
+
+%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}}
+
+% 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}
+%ph%\usepackage{psfrag}
+%ph%\usepackage{oldgerm}
+
+% I commented the following because it introduced excessive white space
+%aja%\usepackage{palatcm}              % better PDF 
 
 % page headers and footers
-\pagestyle{fancy}
-\fancyhead{}
-\fancyhead[LO]{\slshape \rightmark}
-\fancyhead[RE]{\slshape \leftmark}
-\fancyhead[RO,LE]{\thepage}
-\fancyfoot[CO,CE]{\today}
-\fancyfoot[RO,LE]{ }
-\renewcommand{\headrulewidth}{0.4pt}
-\renewcommand{\footrulewidth}{0.4pt}
+%cnh%\usepackage{fancyhdr}
+%\pagestyle{fancy}
+%cnh%\fancyhead{}
+%cnh%\fancyhead[LO]{\slshape \rightmark}
+%cnh%\fancyhead[RE]{\slshape \leftmark}
+%cnh%\fancyhead[RO,LE]{\thepage}
+%cnh%\fancyfoot[CO,CE]{\today}
+%cnh%\fancyfoot[RO,LE]{ }
+%cnh%\renewcommand{\headrulewidth}{0.4pt}
+%cnh%\renewcommand{\footrulewidth}{0.4pt}
+
+% bibtex stuff
+%aja%\newcommand{\BIBPATH}{.}
+%aja%\usepackage{natbib}
+%aja%\bibliographystyle{\BIBPATH/jmr_my}
+%aja%\gdef\harvardleft{[}
+%aja%\gdef\harvardright{]}
+%aja%\bibpunct{[}{]}{,}{a}{}{,}
+\bibliographystyle{plain}
 
 % referencing
-\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
-\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
-\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
-\newcommand{\reftabno}[1]{\ref{tab:#1}}
-\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
-\newcommand{\reffigno}[1]{\ref{fig:#1}}
+%ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
+%ph%\newcommand{\refequbig}[1]{Equation (\ref{equ:#1})}
+%ph%\newcommand{\reftab}[1]{Tab.~\ref{tab:#1}}
+%ph%\newcommand{\reftabno}[1]{\ref{tab:#1}}
+%ph%\newcommand{\reffig}[1]{Fig.~\ref{fig:#1}}
+%ph%\newcommand{\reffigno}[1]{\ref{fig:#1}}
 
 % stuff for psfrag
-\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
-\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
+%ph%\newcommand{\textinfigure}[1]{{\footnotesize\textbf{\textsf{#1}}}}
+%ph%\newcommand{\mathinfigure}[1]{\small\ensuremath{{#1}}}
+
+% This allows numbering of subsubsections
+\setcounter{secnumdepth}{3}
+% This changes the the chapter title
+%\renewcommand{\chaptername}{Section}
+
+
+% This allows hyperlinks in PDF
+% hyperref package and colors for hyperref package 
+\usepackage{color} 
+%\usepackage[dvips]
+\definecolor{darkgreen}{rgb}{0,0.4,0} 
+\definecolor{darkblue}{rgb}{0,0,0.4} 
+\definecolor{darkred}{rgb}{0.5,0,0} 
+\hypersetup{breaklinks=true, 
+  colorlinks=true, 
+  linkcolor=darkgreen,
+  citecolor=darkblue,
+  pagecolor=darkred,
+  pdftitle={MITgcm Release 1 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\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}
 
 
 \begin{document}
 
+\bodytext{bgcolor="#FFFFFFFF"} 
+
 \tableofcontents
-\pagebreak
+%\pagebreak
 
-% Part: Overview
+%\part{MIT GCM basics}
+
+% Section: Overview
 \input{part1/part1}
-\pagebreak
+%\pagebreak
 
-% Part: Discretization and Algorithm
+% Section: Discretization and Algorithm
 \input{part2/part2}
-\pagebreak
+%\pagebreak
 
-% Part: Getting started
+% Section: Getting started
 \input{part3/part3}
-\pagebreak
+%\pagebreak
 
-% Part: Software Architecture
+% Section: Software Architecture
 \input{part4/part4}
-\pagebreak
+%\pagebreak
+
+
+%\part{Adjoint of the MIT GCM}
 
-% Part: Automatic Differentiation
+% Section: Automatic Differentiation
 \input{part5/part5}
-\pagebreak
+%\pagebreak
 
-% Part: Physical Packages
+
+%\part{Additional features}
+
+% Section: Physical Packages
 \input{part6/part6}
-\pagebreak
+%\pagebreak
 
-% Part: Diagnostics
+% Section: Pre-processing and Post-processing Tools
 \input{part7/part7}
-\pagebreak
+%\pagebreak
 
-% Part: ECCO Interface
+% 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}
 
 \end{document}
