--- manual/manual.tex	2001/10/11 19:42:25	1.8
+++ manual/manual.tex	2005/06/15 14:54:58	1.27
@@ -1,7 +1,7 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.8 2001/10/11 19:42:25 adcroft Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.27 2005/06/15 14:54:58 afe Exp $
 % $Name:  $
 
-\documentclass[12pt]{book}
+\documentclass[10pt]{book}
 
 %To help cross-reference
 %\usepackage{showlabels}
@@ -9,11 +9,61 @@
 %aja%\usepackage{amsfonts}
 \usepackage{amsmath}
 \usepackage{html}
-\usepackage{graphics}
+\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}
@@ -34,12 +84,13 @@
 %cnh%\renewcommand{\footrulewidth}{0.4pt}
 
 % bibtex stuff
-\newcommand{\BIBPATH}{.}
-\usepackage{natbib}
-\bibliographystyle{\BIBPATH/jmr_my}
-\gdef\harvardleft{[}
-\gdef\harvardright{]}
-\bibpunct{[}{]}{,}{a}{}{,}
+%aja%\newcommand{\BIBPATH}{.}
+%aja%\usepackage{natbib}
+%aja%\bibliographystyle{\BIBPATH/jmr_my}
+%aja%\gdef\harvardleft{[}
+%aja%\gdef\harvardright{]}
+%aja%\bibpunct{[}{]}{,}{a}{}{,}
+\bibliographystyle{plain}
 
 % referencing
 %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
@@ -59,12 +110,48 @@
 %\renewcommand{\chaptername}{Section}
 
 
+% This allows hyperlinks in PDF
+% hyperref package and colors for hyperref package 
+\usepackage{color} 
+\usepackage[dvips]{hyperref} 
+\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{MIT GCM basics}
+%\part{MIT GCM basics}
 
 % Section: Overview
 \input{part1/part1}
@@ -83,14 +170,14 @@
 %\pagebreak
 
 
-\part{Adjoint of the MIT GCM}
+%\part{Adjoint of the MIT GCM}
 
 % Section: Automatic Differentiation
 \input{part5/part5}
 %\pagebreak
 
 
-\part{Additional features}
+%\part{Additional features}
 
 % Section: Physical Packages
 \input{part6/part6}
@@ -100,13 +187,18 @@
 \input{part7/part7}
 %\pagebreak
 
-% Section: ECCO Interface
+% Section: ECCO
 \input{part8/part8}
 %\pagebreak
 
+% Section: Model Uses
+\input{model_uses}
+%\pagebreak
+
 % Section: References:
-\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
+%\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
 \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}
-\bibliography{\BIBPATH/manual_references}
+%aja%\bibliography{\BIBPATH/manual_references}
+\bibliography{manual_references}
 
 \end{document}