--- manual/s_overview/text/manual.tex	2006/04/05 02:27:32	1.24
+++ manual/s_overview/text/manual.tex	2010/08/30 23:09:21	1.29
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.29 2010/08/30 23:09:21 jmc 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 1.24 2006/04/05 02:27:32 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.29 2010/08/30 23:09:21 jmc Exp $
 % $Name:  $
 
 This document provides the reader with the information necessary to
@@ -61,14 +61,14 @@
 models - see fig \ref{fig:onemodel}
 
 %% CNHbegin
-\input{part1/one_model_figure}
+\input{s_overview/text/one_model_figure}
 %% CNHend
 
 \item it has a non-hydrostatic capability and so can be used to study both
 small-scale and large scale processes - see fig \ref{fig:all-scales}
 
 %% CNHbegin
-\input{part1/all_scales_figure}
+\input{s_overview/text/all_scales_figure}
 %% CNHend
 
 \item finite volume techniques are employed yielding an intuitive
@@ -76,7 +76,7 @@
 orthogonal curvilinear grids and shaved cells - see fig \ref{fig:finite-volumes}
 
 %% CNHbegin
-\input{part1/fvol_figure}
+\input{s_overview/text/fvol_figure}
 %% CNHend
 
 \item tangent linear and adjoint counterparts are automatically maintained
@@ -87,8 +87,10 @@
 computational platforms.
 \end{itemize}
 
+
 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,adcroft:04a,adcroft:04b,marshall:04}:
+\cite{hill:95,marshall:97a,marshall:97b,adcroft:97,mars-eta:98,adcroft:99,hill:99,maro-eta:99,adcroft:04a,adcroft:04b,marshall:04}
+(an overview on the model formulation can also be found in \cite{adcroft:04c}):
 
 \begin{verbatim}
 Hill, C. and J. Marshall, (1995)
@@ -137,7 +139,7 @@
 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 1.24 2006/04/05 02:27:32 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.29 2010/08/30 23:09:21 jmc Exp $
 % $Name:  $
 
 \section{Illustrations of the model in action}
@@ -165,7 +167,7 @@
 
 Figure \ref{fig:eddy_cs} shows an instantaneous plot of the 500$mb$
 temperature field obtained using the atmospheric isomorph of MITgcm run at
-2.8$^{\circ }$ resolution on the cubed sphere. We see cold air over the pole
+$2.8^{\circ }$ resolution on the cubed sphere. We see cold air over the pole
 (blue) and warm air along an equatorial band (red). Fully developed
 baroclinic eddies spawned in the northern hemisphere storm track are
 evident. There are no mountains or land-sea contrast in this calculation,
@@ -175,7 +177,7 @@
 there are no mountains or land-sea contrast.
 
 %% CNHbegin
-\input{part1/cubic_eddies_figure}
+\input{s_overview/text/cubic_eddies_figure}
 %% CNHend
 
 As described in Adcroft (2001), a `cubed sphere' is used to discretize the
@@ -191,7 +193,7 @@
 latitude-longitude grid. Both grids are supported within the model.
 
 %% CNHbegin
-\input{part1/hs_zave_u_figure}
+\input{s_overview/text/hs_zave_u_figure}
 %% CNHend
 
 \subsection{Ocean gyres}
@@ -210,19 +212,19 @@
 increased until the baroclinic instability process is resolved, numerical
 solutions of a different and much more realistic kind, can be obtained.
 
-Figure \ref{fig:ocean-gyres} shows the surface temperature and velocity 
-field obtained from MITgcm run at $\frac{1}{6}^{\circ }$ horizontal 
-resolution on a $lat-lon$
-grid in which the pole has been rotated by 90$^{\circ }$ on to the equator
-(to avoid the converging of meridian in northern latitudes). 21 vertical
-levels are used in the vertical with a `lopped cell' representation of
-topography. The development and propagation of anomalously warm and cold
-eddies can be clearly seen in the Gulf Stream region. The transport of
-warm water northward by the mean flow of the Gulf Stream is also clearly
-visible.
+Figure \ref{fig:ocean-gyres} shows the surface temperature and
+velocity field obtained from MITgcm run at $\frac{1}{6}^{\circ }$
+horizontal resolution on a \textit{lat-lon} grid in which the pole has
+been rotated by $90^{\circ }$ on to the equator (to avoid the
+converging of meridian in northern latitudes). 21 vertical levels are
+used in the vertical with a `lopped cell' representation of
+topography. The development and propagation of anomalously warm and
+cold eddies can be clearly seen in the Gulf Stream region. The
+transport of warm water northward by the mean flow of the Gulf Stream
+is also clearly visible.
 
 %% CNHbegin
-\input{part1/atl6_figure}
+\input{s_overview/text/atl6_figure}
 %% CNHend
 
 
@@ -231,20 +233,20 @@
 <!-- CMIREDIR:global_ocean_circulation: -->
 \end{rawhtml}
 
-Figure \ref{fig:large-scale-circ} (top) shows the pattern of ocean currents at 
-the surface of a 4$^{\circ }$
-global ocean model run with 15 vertical levels. Lopped cells are used to
-represent topography on a regular $lat-lon$ grid extending from 70$^{\circ
-}N $ to 70$^{\circ }S$. The model is driven using monthly-mean winds with
-mixed boundary conditions on temperature and salinity at the surface. The
-transfer properties of ocean eddies, convection and mixing is parameterized
-in this model.
+Figure \ref{fig:large-scale-circ} (top) shows the pattern of ocean
+currents at the surface of a $4^{\circ }$ global ocean model run with
+15 vertical levels. Lopped cells are used to represent topography on a
+regular \textit{lat-lon} grid extending from $70^{\circ }N$ to
+$70^{\circ }S$. The model is driven using monthly-mean winds with
+mixed boundary conditions on temperature and salinity at the surface.
+The transfer properties of ocean eddies, convection and mixing is
+parameterized in this model.
 
 Figure \ref{fig:large-scale-circ} (bottom) shows the meridional overturning 
 circulation of the global ocean in Sverdrups.
 
 %%CNHbegin
-\input{part1/global_circ_figure}
+\input{s_overview/text/global_circ_figure}
 %%CNHend
 
 \subsection{Convection and mixing over topography}
@@ -267,7 +269,7 @@
 instability of the along-slope current.
 
 %%CNHbegin
-\input{part1/convect_and_topo}
+\input{s_overview/text/convect_and_topo}
 %%CNHend
 
 \subsection{Boundary forced internal waves}
@@ -289,7 +291,7 @@
 nonhydrostatic dynamics.
 
 %%CNHbegin
-\input{part1/boundary_forced_waves}
+\input{s_overview/text/boundary_forced_waves}
 %%CNHend
 
 \subsection{Parameter sensitivity using the adjoint of MITgcm}
@@ -301,18 +303,18 @@
 `automatic adjoint compiler'. These can be used in parameter sensitivity and
 data assimilation studies.
 
-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 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
-sensitive to heat fluxes over the Labrador Sea, one of the important sources
-of deep water for the thermohaline circulations. This calculation also
+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
+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 sensitive
+to heat fluxes over the Labrador Sea, one of the important sources of
+deep water for the thermohaline circulations. This calculation also
 yields sensitivities to all other model parameters.
 
 %%CNHbegin
-\input{part1/adj_hf_ocean_figure}
+\input{s_overview/text/adj_hf_ocean_figure}
 %%CNHend
 
 \subsection{Global state estimation of the ocean}
@@ -333,7 +335,7 @@
 1992-1997.
 
 %% CNHbegin
-\input{part1/assim_figure}
+\input{s_overview/text/assim_figure}
 %% CNHend
 
 \subsection{Ocean biogeochemical cycles}
@@ -341,17 +343,19 @@
 <!-- CMIREDIR:ocean_biogeo_cycles: -->
 \end{rawhtml}
 
-MITgcm is being used to study global biogeochemical cycles in the ocean. For
-example one can study the effects of interannual changes in meteorological
-forcing and upper ocean circulation on the fluxes of carbon dioxide and
-oxygen between the ocean and atmosphere. Figure \ref{fig:biogeo} shows 
-the annual air-sea flux of oxygen and its relation to density outcrops in 
-the southern oceans from a single year of a global, interannually varying 
-simulation. The simulation is run at $1^{\circ}\times1^{\circ}$ resolution
-telescoping to $\frac{1}{3}^{\circ}\times\frac{1}{3}^{\circ}$ in the tropics (not shown).
+MITgcm is being used to study global biogeochemical cycles in the
+ocean. For example one can study the effects of interannual changes in
+meteorological forcing and upper ocean circulation on the fluxes of
+carbon dioxide and oxygen between the ocean and atmosphere. Figure
+\ref{fig:biogeo} shows the annual air-sea flux of oxygen and its
+relation to density outcrops in the southern oceans from a single year
+of a global, interannually varying simulation. The simulation is run
+at $1^{\circ}\times1^{\circ}$ resolution telescoping to
+$\frac{1}{3}^{\circ}\times\frac{1}{3}^{\circ}$ in the tropics (not
+shown).
 
 %%CNHbegin
-\input{part1/biogeo_figure}
+\input{s_overview/text/biogeo_figure}
 %%CNHend
 
 \subsection{Simulations of laboratory experiments}
@@ -369,10 +373,10 @@
 stratification of the ACC.
 
 %%CNHbegin
-\input{part1/lab_figure}
+\input{s_overview/text/lab_figure}
 %%CNHend
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.29 2010/08/30 23:09:21 jmc Exp $
 % $Name:  $
 
 \section{Continuous equations in `r' coordinates}
@@ -392,7 +396,7 @@
 \ref{fig:isomorphic-equations}).
 
 %%CNHbegin
-\input{part1/zandpcoord_figure.tex}
+\input{s_overview/text/zandpcoord_figure.tex}
 %%CNHend
 
 The state of the fluid at any time is characterized by the distribution of
@@ -406,7 +410,7 @@
 see figure \ref{fig:zandp-vert-coord}.
 
 %%CNHbegin
-\input{part1/vertcoord_figure.tex}
+\input{s_overview/text/vertcoord_figure.tex}
 %%CNHend
 
 \begin{equation}
@@ -657,6 +661,7 @@
 
 \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
 Non-hydrostatic forms}
+\label{sec:all_hydrostatic_forms}
 \begin{rawhtml}
 <!-- CMIREDIR:non_hydrostatic: -->
 \end{rawhtml}
@@ -765,7 +770,7 @@
 OPERATORS.
 
 %%CNHbegin
-\input{part1/sphere_coord_figure.tex}
+\input{s_overview/text/sphere_coord_figure.tex}
 %%CNHend
 
 \subsubsection{Shallow atmosphere approximation}
@@ -886,7 +891,7 @@
 stepping forward the vertical momentum equation.
 
 %%CNHbegin
-\input{part1/solution_strategy_figure.tex}
+\input{s_overview/text/solution_strategy_figure.tex}
 %%CNHend
 
 There is no penalty in implementing \textbf{QH} over \textbf{HPE} except, of
@@ -1075,7 +1080,7 @@
 
 The mixing terms for the temperature and salinity equations have a similar
 form to that of momentum except that the diffusion tensor can be
-non-diagonal and have varying coefficients. $\qquad $
+non-diagonal and have varying coefficients.
 \begin{equation}
 D_{T,S}=\nabla .[\underline{\underline{K}}\nabla (T,S)]+K_{4}\nabla
 _{h}^{4}(T,S)  \label{eq:diffusion}
@@ -1124,7 +1129,7 @@
 Tangent linear and adjoint counterparts of the forward model are described
 in Chapter 5.
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.29 2010/08/30 23:09:21 jmc Exp $
 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1253,7 +1258,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.24 2006/04/05 02:27:32 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.29 2010/08/30 23:09:21 jmc Exp $
 % $Name:  $
 
 \section{Appendix OCEAN}
@@ -1470,7 +1475,7 @@
 _{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 1.24 2006/04/05 02:27:32 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.29 2010/08/30 23:09:21 jmc Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}
@@ -1487,9 +1492,8 @@
 \end{equation*}
 
 \begin{equation*}
-v=r\frac{D\varphi }{Dt}\qquad
+v=r\frac{D\varphi }{Dt}
 \end{equation*}
-$\qquad \qquad \qquad \qquad $
 
 \begin{equation*}
 \dot{r}=\frac{Dr}{Dt}
@@ -1499,7 +1503,7 @@
 distance of the particle from the center of the earth, $\Omega $ is the
 angular speed of rotation of the Earth and $D/Dt$ is the total derivative.
 
-The `grad' ($\nabla $) and `div' ($\nabla $.) operators are defined by, in
+The `grad' ($\nabla $) and `div' ($\nabla\cdot$) operators are defined by, in
 spherical coordinates:
 
 \begin{equation*}
@@ -1509,7 +1513,7 @@
 \end{equation*}
 
 \begin{equation*}
-\nabla .v\equiv \frac{1}{r\cos \varphi }\left\{ \frac{\partial u}{\partial
+\nabla\cdot v\equiv \frac{1}{r\cos \varphi }\left\{ \frac{\partial u}{\partial
 \lambda }+\frac{\partial }{\partial \varphi }\left( v\cos \varphi \right) \right\}
 +\frac{1}{r^{2}}\frac{\partial \left( r^{2}\dot{r}\right) }{\partial r}
 \end{equation*}