--- manual/s_overview/text/manual.tex	2001/11/21 16:33:17	1.15
+++ manual/s_overview/text/manual.tex	2003/08/07 18:27:51	1.17
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.15 2001/11/21 16:33:17 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
 % $Name:  $
 
 %tci%\documentclass[12pt]{book}
@@ -34,12 +34,10 @@
 
 % Section: Overview
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.15 2001/11/21 16:33:17 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
 % $Name:  $
 
-\section{Introduction}
-
-This documentation provides the reader with the information necessary to
+This document provides the reader with the information necessary to
 carry out numerical experiments using MITgcm. It gives a comprehensive
 description of the continuous equations on which the model is based, the
 numerical algorithms the model employs and a description of the associated
@@ -49,6 +47,8 @@
 both process and general circulation studies of the atmosphere and ocean are
 also presented.
 
+\section{Introduction}
+
 MITgcm has a number of novel aspects:
 
 \begin{itemize}
@@ -83,10 +83,10 @@
 computational platforms.
 \end{itemize}
 
-Key publications reporting on and charting the development of the model are:
+Key publications reporting on and charting the development of the model are
+\cite{hill:95,marshall:97a,marshall:97b,adcroft:97,marshall:98,adcroft:99,hill:99,maro-eta:99}:
 
 \begin{verbatim}
-
 Hill, C. and J. Marshall, (1995)
 Application of a Parallel Navier-Stokes Model to Ocean Circulation in 
 Parallel Computational Fluid Dynamics
@@ -95,7 +95,7 @@
 Elsevier Science B.V.: New York
 
 Marshall, J., C. Hill, L. Perelman, and A. Adcroft, (1997)
-Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modeling,
+Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modeling
 J. Geophysical Res., 102(C3), 5733-5752.
 
 Marshall, J., A. Adcroft, C. Hill, L. Perelman, and C. Heisey, (1997)
@@ -128,13 +128,12 @@
 application to Atlantic heat transport variability
 J. Geophysical Res., 104(C12), 29,529-29,547.
 
-
 \end{verbatim}
 
 We begin by briefly showing some of the results of the model in action to
 give a feel for the wide range of problems that can be addressed using it.
 
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+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
 % $Name:  $
 
 \section{Illustrations of the model in action}
@@ -323,7 +322,7 @@
 \subsection{Simulations of laboratory experiments}
 
 Figure \ref{fig:lab-simulation} shows MITgcm being used to simulate a 
-laboratory experiment inquiring in to the dynamics of the Antarctic Circumpolar Current (ACC). An
+laboratory experiment inquiring into the dynamics of the Antarctic Circumpolar Current (ACC). An
 initially homogeneous tank of water ($1m$ in diameter) is driven from its
 free surface by a rotating heated disk. The combined action of mechanical
 and thermal forcing creates a lens of fluid which becomes baroclinically
@@ -335,7 +334,7 @@
 \input{part1/lab_figure}
 %%CNHend
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.15 2001/11/21 16:33:17 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
 % $Name:  $
 
 \section{Continuous equations in `r' coordinates}
@@ -347,8 +346,8 @@
 and encoded. The model variables have different interpretations depending on
 whether the atmosphere or ocean is being studied. Thus, for example, the
 vertical coordinate `$r$' is interpreted as pressure, $p$, if we are
-modeling the atmosphere (left hand side of figure \ref{fig:isomorphic-equations})
-and height, $z$, if we are modeling the ocean (right hand side of figure
+modeling the atmosphere (right hand side of figure \ref{fig:isomorphic-equations})
+and height, $z$, if we are modeling the ocean (left hand side of figure
 \ref{fig:isomorphic-equations}).
 
 %%CNHbegin
@@ -472,12 +471,12 @@
 at fixed and moving $r$ surfaces we set (see figure \ref{fig:zandp-vert-coord}):
 
 \begin{equation}
-\dot{r}=0atr=R_{fixed}(x,y)\text{ (ocean bottom, top of the atmosphere)}
+\dot{r}=0 \text{\ at\ } r=R_{fixed}(x,y)\text{ (ocean bottom, top of the atmosphere)}
 \label{eq:fixedbc}
 \end{equation}
 
 \begin{equation}
-\dot{r}=\frac{Dr}{Dt}atr=R_{moving}\text{ \
+\dot{r}=\frac{Dr}{Dt} \text{\ at\ } r=R_{moving}\text{ \
 (ocean surface,bottom of the atmosphere)}  \label{eq:movingbc}
 \end{equation}
 
@@ -1074,7 +1073,7 @@
 Tangent linear and adjoint counterparts of the forward model are described
 in Chapter 5.
 
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 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1201,7 +1200,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
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+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
 % $Name:  $
 
 \section{Appendix OCEAN}
@@ -1417,7 +1416,7 @@
 _{nh}=0$ form of these equations that are used throughout the ocean modeling
 community and referred to as the primitive equations (HPE).
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.15 2001/11/21 16:33:17 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}