--- manual/s_overview/text/manual.tex	2006/04/08 01:50:49	1.25
+++ manual/s_overview/text/manual.tex	2016/05/11 18:45:43	1.30
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.25 2006/04/08 01:50:49 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.30 2016/05/11 18:45:43 jmc Exp $
 % $Name:  $
 
 %tci%\documentclass[12pt]{book}
@@ -34,9 +34,6 @@
 
 % Section: Overview
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.25 2006/04/08 01:50:49 edhill Exp $
-% $Name:  $
-
 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
@@ -61,14 +58,14 @@
 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 +73,7 @@
 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 +84,10 @@
 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)
@@ -137,9 +136,6 @@
 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 1.25 2006/04/08 01:50:49 edhill Exp $
-% $Name:  $
-
 \section{Illustrations of the model in action}
 
 MITgcm has been designed and used to model a wide range of phenomena,
@@ -175,7 +171,7 @@
 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 +187,7 @@
 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}
@@ -222,7 +218,7 @@
 is also clearly visible.
 
 %% CNHbegin
-\input{part1/atl6_figure}
+\input{s_overview/text/atl6_figure}
 %% CNHend
 
 
@@ -244,7 +240,7 @@
 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 +263,7 @@
 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 +285,7 @@
 nonhydrostatic dynamics.
 
 %%CNHbegin
-\input{part1/boundary_forced_waves}
+\input{s_overview/text/boundary_forced_waves}
 %%CNHend
 
 \subsection{Parameter sensitivity using the adjoint of MITgcm}
@@ -312,7 +308,7 @@
 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 +329,7 @@
 1992-1997.
 
 %% CNHbegin
-\input{part1/assim_figure}
+\input{s_overview/text/assim_figure}
 %% CNHend
 
 \subsection{Ocean biogeochemical cycles}
@@ -353,7 +349,7 @@
 shown).
 
 %%CNHbegin
-\input{part1/biogeo_figure}
+\input{s_overview/text/biogeo_figure}
 %%CNHend
 
 \subsection{Simulations of laboratory experiments}
@@ -371,12 +367,9 @@
 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 1.25 2006/04/08 01:50:49 edhill Exp $
-% $Name:  $
-
 \section{Continuous equations in `r' coordinates}
 \begin{rawhtml}
 <!-- CMIREDIR:z-p_isomorphism: -->
@@ -394,7 +387,7 @@
 \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
@@ -408,7 +401,7 @@
 see figure \ref{fig:zandp-vert-coord}.
 
 %%CNHbegin
-\input{part1/vertcoord_figure.tex}
+\input{s_overview/text/vertcoord_figure.tex}
 %%CNHend
 
 \begin{equation}
@@ -659,6 +652,7 @@
 
 \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
 Non-hydrostatic forms}
+\label{sec:all_hydrostatic_forms}
 \begin{rawhtml}
 <!-- CMIREDIR:non_hydrostatic: -->
 \end{rawhtml}
@@ -767,7 +761,7 @@
 OPERATORS.
 
 %%CNHbegin
-\input{part1/sphere_coord_figure.tex}
+\input{s_overview/text/sphere_coord_figure.tex}
 %%CNHend
 
 \subsubsection{Shallow atmosphere approximation}
@@ -888,7 +882,7 @@
 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
@@ -1077,7 +1071,7 @@
 
 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}
@@ -1126,9 +1120,6 @@
 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 1.25 2006/04/08 01:50:49 edhill Exp $
-% $Name:  $
-
 \section{Appendix ATMOSPHERE}
 
 \subsection{Hydrostatic Primitive Equations for the Atmosphere in pressure
@@ -1148,14 +1139,14 @@
 c_{v}\frac{DT}{Dt}+p\frac{D\alpha }{Dt} &=&\mathcal{Q}  \label{eq:atmos-heat}
 \end{eqnarray}
 where $\vec{\mathbf{v}}_{h}=(u,v,0)$ is the `horizontal' (on pressure
-surfaces) component of velocity,$\frac{D}{Dt}=\vec{\mathbf{v}}_{h}\cdot 
-\mathbf{\nabla }_{p}+\omega \frac{\partial }{\partial p}$ is the total
-derivative, $f=2\Omega \sin \varphi$ is the Coriolis parameter, $\phi =gz$ is
-the geopotential, $\alpha =1/\rho $ is the specific volume, $\omega =\frac{Dp
-}{Dt}$ is the vertical velocity in the $p-$coordinate. Equation(\ref
-{eq:atmos-heat}) is the first law of thermodynamics where internal energy $
-e=c_{v}T$, $T$ is temperature, $Q$ is the rate of heating per unit mass and $
-p\frac{D\alpha }{Dt}$ is the work done by the fluid in compressing.
+surfaces) component of velocity, $\frac{D}{Dt}=\frac{\partial}{\partial t}
++\vec{\mathbf{v}}_{h}\cdot \mathbf{\nabla }_{p}+\omega \frac{\partial }{\partial p}$
+is the total derivative, $f=2\Omega \sin \varphi$ is the Coriolis parameter,
+$\phi =gz$ is the geopotential, $\alpha =1/\rho $ is the specific volume,
+$\omega =\frac{Dp }{Dt}$ is the vertical velocity in the $p-$coordinate.
+Equation(\ref {eq:atmos-heat}) is the first law of thermodynamics where internal
+energy $e=c_{v}T$, $T$ is temperature, $Q$ is the rate of heating per unit mass
+and $p\frac{D\alpha }{Dt}$ is the work done by the fluid in compressing.
 
 It is convenient to cast the heat equation in terms of potential temperature 
 $\theta $ so that it looks more like a generic conservation law.
@@ -1255,9 +1246,6 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.25 2006/04/08 01:50:49 edhill Exp $
-% $Name:  $
-
 \section{Appendix OCEAN}
 
 \subsection{Equations of motion for the ocean}
@@ -1472,9 +1460,6 @@
 _{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 1.25 2006/04/08 01:50:49 edhill Exp $
-% $Name:  $
-
 \section{Appendix:OPERATORS}
 
 \subsection{Coordinate systems}
@@ -1489,9 +1474,8 @@
 \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}
@@ -1501,7 +1485,7 @@
 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*}
@@ -1511,7 +1495,7 @@
 \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*}