--- manual/s_overview/text/manual.tex	2001/10/25 15:24:01	1.8
+++ manual/s_overview/text/manual.tex	2001/11/19 19:58:20	1.13
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.8 2001/10/25 15:24:01 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.13 2001/11/19 19:58:20 cnh Exp $
 % $Name:  $
 
 %tci%\documentclass[12pt]{book}
@@ -34,7 +34,7 @@
 
 % Section: Overview
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.8 2001/10/25 15:24:01 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.13 2001/11/19 19:58:20 cnh Exp $
 % $Name:  $
 
 \section{Introduction}
@@ -83,13 +83,57 @@
 computational platforms.
 \end{itemize}
 
-Key publications reporting on and charting the development of the model are
-listed in an Appendix.
+Key publications reporting on and charting the development of the model are:
+
+\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 Eight ECMWF Workshop on the Use of Parallel Processors
+in Meteorology
+
+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.
 
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+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.13 2001/11/19 19:58:20 cnh Exp $
 % $Name:  $
 
 \section{Illustrations of the model in action}
@@ -102,7 +146,7 @@
 numerical algorithm and implementation that lie behind these calculations is
 given later. Indeed many of the illustrative examples shown below can be
 easily reproduced: simply download the model (the minimum you need is a PC
-running linux, together with a FORTRAN\ 77 compiler) and follow the examples
+running Linux, together with a FORTRAN\ 77 compiler) and follow the examples
 described in detail in the documentation.
 
 \subsection{Global atmosphere: `Held-Suarez' benchmark}
@@ -126,7 +170,7 @@
 %% CNHend
 
 As described in Adcroft (2001), a `cubed sphere' is used to discretize the
-globe permitting a uniform gridding and obviated the need to Fourier filter.
+globe permitting a uniform griding and obviated the need to Fourier filter.
 The `vector-invariant' form of MITgcm supports any orthogonal curvilinear
 grid, of which the cubed sphere is just one of many choices.
 
@@ -163,7 +207,7 @@
 visible.
 
 %% CNHbegin
-\input{part1/ocean_gyres_figure}
+\input{part1/atl6_figure}
 %% CNHend
 
 
@@ -191,7 +235,7 @@
 ocean may be influenced by rotation when the deformation radius is smaller
 than the width of the cooling region. Rather than gravity plumes, the
 mechanism for moving dense fluid down the shelf is then through geostrophic
-eddies. The simulation shown in the figure \ref{fig::convect-and-topo}
+eddies. The simulation shown in the figure \ref{fig:convect-and-topo}
 (blue is cold dense fluid, red is
 warmer, lighter fluid) employs the non-hydrostatic capability of MITgcm to
 trigger convection by surface cooling. The cold, dense water falls down the
@@ -231,7 +275,7 @@
 
 As one example of application of the MITgcm adjoint, Figure \ref{fig:hf-sensitivity}
 maps the gradient $\frac{\partial J}{\partial \mathcal{H}}$where $J$ is the magnitude
-of the overturning streamfunction shown in figure \ref{fig:large-scale-circ}
+of the overturning stream-function shown in figure \ref{fig:large-scale-circ}
 at 60$^{\circ }$N and $
 \mathcal{H}(\lambda,\varphi)$ is the mean, local air-sea heat flux over
 a 100 year period. We see that $J$ is
@@ -248,7 +292,7 @@
 An important application of MITgcm is in state estimation of the global
 ocean circulation. An appropriately defined `cost function', which measures
 the departure of the model from observations (both remotely sensed and
-insitu) over an interval of time, is minimized by adjusting `control
+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
@@ -256,7 +300,7 @@
 1992-1997. {\bf CHANGE THIS TEXT - FIG FROM PATRICK/CARL/DETLEF}
 
 %% CNHbegin
-\input{part1/globes_figure}
+\input{part1/assim_figure}
 %% CNHend
 
 \subsection{Ocean biogeochemical cycles}
@@ -277,7 +321,7 @@
 \subsection{Simulations of laboratory experiments}
 
 Figure \ref{fig:lab-simulation} shows MITgcm being used to simulate a 
-laboratory experiment enquiring in to the dynamics of the Antarctic Circumpolar Current (ACC). An
+laboratory experiment inquiring in to 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 +333,7 @@
 \input{part1/lab_figure}
 %%CNHend
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.8 2001/10/25 15:24:01 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.13 2001/11/19 19:58:20 cnh Exp $
 % $Name:  $
 
 \section{Continuous equations in `r' coordinates}
@@ -351,7 +395,7 @@
 
 \begin{equation}
 \frac{DS}{Dt}=\mathcal{Q}_{S}\text{ humidity/salinity}
-\label{eq:humidtity_salt}
+\label{eq:humidity_salt}
 \end{equation}
 
 Here:
@@ -432,7 +476,7 @@
 
 \begin{equation}
 \dot{r}=\frac{Dr}{Dt}atr=R_{moving}\text{ \
-(oceansurface,bottomoftheatmosphere)}  \label{eq:movingbc}
+(ocean surface,bottom of the atmosphere)}  \label{eq:movingbc}
 \end{equation}
 
 Here
@@ -525,7 +569,7 @@
 atmosphere)}  \label{eq:moving-bc-atmos}
 \end{eqnarray}
 
-Then the (hydrostatic form of) equations (\ref{eq:horizontal_mtm}-\ref{eq:humidity_slainty}) 
+Then the (hydrostatic form of) equations (\ref{eq:horizontal_mtm}-\ref{eq:humidity_salt}) 
 yields a consistent set of atmospheric equations which, for convenience, are written out in $p$
 coordinates in Appendix Atmosphere - see eqs(\ref{eq:atmos-prime}).
 
@@ -562,7 +606,7 @@
 \end{eqnarray}
 where $\eta $ is the elevation of the free surface.
 
-Then equations (\ref{eq:horizontal_mtm}-\ref{eq:humidity_slainty}) yield a consistent set 
+Then equations (\ref{eq:horizontal_mtm}-\ref{eq:humidity_salt}) yield a consistent set 
 of oceanic equations
 which, for convenience, are written out in $z$ coordinates in Appendix Ocean
 - see eqs(\ref{eq:ocean-mom}) to (\ref{eq:ocean-salt}).
@@ -1028,7 +1072,7 @@
 Tangent linear and adjoint counterparts of the forward model are described
 in Chapter 5.
 
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+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.13 2001/11/19 19:58:20 cnh Exp $
 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1155,7 +1199,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.8 2001/10/25 15:24:01 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.13 2001/11/19 19:58:20 cnh Exp $
 % $Name:  $
 
 \section{Appendix OCEAN}
@@ -1178,7 +1222,7 @@
 \label{eq:non-boussinesq}
 \end{eqnarray}
 These equations permit acoustics modes, inertia-gravity waves,
-non-hydrostatic motions, a geostrophic (Rossby) mode and a thermo-haline
+non-hydrostatic motions, a geostrophic (Rossby) mode and a thermohaline
 mode. As written, they cannot be integrated forward consistently - if we
 step $\rho $ forward in (\ref{eq-zns-cont}), the answer will not be
 consistent with that obtained by stepping (\ref{eq-zns-heat}) and (\ref
@@ -1371,7 +1415,7 @@
 _{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 1.8 2001/10/25 15:24:01 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.13 2001/11/19 19:58:20 cnh Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}