--- manual/manual.tex	2004/03/15 22:39:28	1.22
+++ manual/manual.tex	2005/08/01 22:14:19	1.32
@@ -1,7 +1,7 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.22 2004/03/15 22:39:28 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/manual.tex,v 1.32 2005/08/01 22:14:19 jmc Exp $
 % $Name:  $
 
-\documentclass[12pt]{book}
+\documentclass[10pt]{book}
 
 %To help cross-reference
 %\usepackage{showlabels}
@@ -18,32 +18,51 @@
 %eh3  Commands to reference either files or symbols within the "HTML-ized"
 %eh3  ("vdb") code.
 %eh3  
-\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 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{\file}[1]{\texttt{#1}}
+\newcommand{\sectiontitle}[1]{\textsl{#1}}
+\newcommand{\code}[1]{\texttt{#1}}
 
-\newcommand{\sectiontitle}[1]{
-\textsl{#1}
-}
-
-\newcommand{\code}[1]{
-\texttt{#1}
-}
-
-
-
-%eh3 try out the epsfig package
+%%  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}
@@ -71,7 +90,10 @@
 %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]{natbib}
+\bibliographystyle{agu}
 
 % referencing
 %ph%\newcommand{\refequ}[1]{equation (\ref{equ:#1})}
@@ -94,7 +116,8 @@
 % 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} 
@@ -164,7 +187,7 @@
 \input{part6/part6}
 %\pagebreak
 
-% Section: Diagnostics
+% Section: Pre-processing and Post-processing Tools
 \input{part7/part7}
 %\pagebreak
 
@@ -172,6 +195,10 @@
 \input{part8/part8}
 %\pagebreak
 
+% Section: Model Uses
+\input{model_uses}
+%\pagebreak
+
 % Section: References:
 %\markboth{BIBLIOGRAPHY}{BIBLIOGRAPHY}
 \addcontentsline{toc}{chapter}{BIBLIOGRAPHY}