--- manual/s_overview/text/manual.tex	2001/11/13 20:35:51	1.10
+++ 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 1.10 2001/11/13 20:35:51 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 1.10 2001/11/13 20:35:51 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}
@@ -84,12 +84,56 @@
 \end{itemize}
 
 Key publications reporting on and charting the development of the model are
-listed in an Appendix.
+\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
+In Proceedings of Parallel Computational Fluid Dynamics: Implementations 
+and Results Using Parallel Computers, 545-552.
+Elsevier Science B.V.: New York
+
+Marshall, J., C. Hill, L. Perelman, and A. Adcroft, (1997)
+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)
+A finite-volume, incompressible Navier Stokes model for studies of the ocean
+on parallel computers,
+J. Geophysical Res., 102(C3), 5753-5766.
+
+Adcroft, A.J., Hill, C.N. and J. Marshall, (1997)
+Representation of topography by shaved cells in a height coordinate ocean
+model
+Mon Wea Rev, vol 125, 2293-2315
+
+Marshall, J., Jones, H. and C. Hill, (1998)
+Efficient ocean modeling using non-hydrostatic algorithms
+Journal of Marine Systems, 18, 115-134
+
+Adcroft, A., Hill C. and J. Marshall: (1999)
+A new treatment of the Coriolis terms in C-grid models at both high and low
+resolutions,
+Mon. Wea. Rev. Vol 127, pages 1928-1936
+
+Hill, C, Adcroft,A., Jamous,D., and J. Marshall, (1999)
+A Strategy for Terascale Climate Modeling.
+In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors
+in Meteorology, pages 406-425
+World Scientific Publishing Co: UK
+
+Marotzke, J, Giering,R., Zhang, K.Q., Stammer,D., Hill,C., and T.Lee, (1999)
+Construction of the adjoint MIT ocean general circulation model and 
+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.
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.10 2001/11/13 20:35:51 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{Illustrations of the model in action}
@@ -163,7 +207,7 @@
 visible.
 
 %% CNHbegin
-\input{part1/ocean_gyres_figure}
+\input{part1/atl6_figure}
 %% CNHend
 
 
@@ -250,13 +294,14 @@
 the departure of the model from observations (both remotely sensed and
 in-situ) over an interval of time, is minimized by adjusting `control
 parameters' such as air-sea fluxes, the wind field, the initial conditions
-etc. Figure \ref{fig:assimilated-globes} shows an estimate of the time-mean
-surface elevation of the ocean obtained by bringing the model in to
+etc. Figure \ref{fig:assimilated-globes} shows the large scale planetary
+circulation and a Hopf-Muller plot of Equatorial sea-surface height.
+Both are obtained from assimilation bringing the model in to
 consistency with altimetric and in-situ observations over the period
-1992-1997. {\bf CHANGE THIS TEXT - FIG FROM PATRICK/CARL/DETLEF}
+1992-1997.
 
 %% CNHbegin
-\input{part1/globes_figure}
+\input{part1/assim_figure}
 %% CNHend
 
 \subsection{Ocean biogeochemical cycles}
@@ -277,7 +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
@@ -289,7 +334,7 @@
 \input{part1/lab_figure}
 %%CNHend
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.10 2001/11/13 20:35:51 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}
@@ -301,8 +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
@@ -426,12 +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}
 
@@ -1028,7 +1073,7 @@
 Tangent linear and adjoint counterparts of the forward model are described
 in Chapter 5.
 
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 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1155,7 +1200,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.10 2001/11/13 20:35:51 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 OCEAN}
@@ -1371,7 +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 1.10 2001/11/13 20:35:51 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}