--- manual/s_overview/text/manual.tex	2003/08/07 18:27:51	1.17
+++ manual/s_overview/text/manual.tex	2004/10/17 04:15:13	1.22
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 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 1.17 2003/08/07 18:27:51 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 This document provides the reader with the information necessary to
@@ -48,6 +48,10 @@
 also presented.
 
 \section{Introduction}
+\begin{rawhtml}
+<!-- CMIREDIR:innovations: -->
+\end{rawhtml}
+
 
 MITgcm has a number of novel aspects:
 
@@ -133,7 +137,7 @@
 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 1.17 2003/08/07 18:27:51 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 \section{Illustrations of the model in action}
@@ -150,6 +154,11 @@
 described in detail in the documentation.
 
 \subsection{Global atmosphere: `Held-Suarez' benchmark}
+\begin{rawhtml}
+<!-- CMIREDIR:atmospheric_example: -->
+\end{rawhtml}
+
+
 
 A novel feature of MITgcm is its ability to simulate, using one basic algorithm, 
 both atmospheric and oceanographic flows at both small and large scales.
@@ -186,6 +195,12 @@
 %% CNHend
 
 \subsection{Ocean gyres}
+\begin{rawhtml}
+<!-- CMIREDIR:oceanic_example: -->
+\end{rawhtml}
+\begin{rawhtml}
+<!-- CMIREDIR:ocean_gyres: -->
+\end{rawhtml}
 
 Baroclinic instability is a ubiquitous process in the ocean, as well as the
 atmosphere. Ocean eddies play an important role in modifying the
@@ -212,6 +227,9 @@
 
 
 \subsection{Global ocean circulation}
+\begin{rawhtml}
+<!-- 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$^{\circ }$
@@ -230,6 +248,10 @@
 %%CNHend
 
 \subsection{Convection and mixing over topography}
+\begin{rawhtml}
+<!-- CMIREDIR:mixing_over_topography: -->
+\end{rawhtml}
+
 
 Dense plumes generated by localized cooling on the continental shelf of the
 ocean may be influenced by rotation when the deformation radius is smaller
@@ -249,6 +271,9 @@
 %%CNHend
 
 \subsection{Boundary forced internal waves}
+\begin{rawhtml}
+<!-- CMIREDIR:boundary_forced_internal_waves: -->
+\end{rawhtml}
 
 The unique ability of MITgcm to treat non-hydrostatic dynamics in the
 presence of complex geometry makes it an ideal tool to study internal wave
@@ -268,6 +293,9 @@
 %%CNHend
 
 \subsection{Parameter sensitivity using the adjoint of MITgcm}
+\begin{rawhtml}
+<!-- CMIREDIR:parameter_sensitivity: -->
+\end{rawhtml}
 
 Forward and tangent linear counterparts of MITgcm are supported using an
 `automatic adjoint compiler'. These can be used in parameter sensitivity and
@@ -288,6 +316,10 @@
 %%CNHend
 
 \subsection{Global state estimation of the ocean}
+\begin{rawhtml}
+<!-- CMIREDIR:global_state_estimation: -->
+\end{rawhtml}
+
 
 An important application of MITgcm is in state estimation of the global
 ocean circulation. An appropriately defined `cost function', which measures
@@ -305,6 +337,9 @@
 %% CNHend
 
 \subsection{Ocean biogeochemical cycles}
+\begin{rawhtml}
+<!-- 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
@@ -320,6 +355,9 @@
 %%CNHend
 
 \subsection{Simulations of laboratory experiments}
+\begin{rawhtml}
+<!-- CMIREDIR:classroom_exp: -->
+\end{rawhtml}
 
 Figure \ref{fig:lab-simulation} shows MITgcm being used to simulate a 
 laboratory experiment inquiring into the dynamics of the Antarctic Circumpolar Current (ACC). An
@@ -334,10 +372,13 @@
 \input{part1/lab_figure}
 %%CNHend
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 \section{Continuous equations in `r' coordinates}
+\begin{rawhtml}
+<!-- CMIREDIR:z-p_isomorphism: -->
+\end{rawhtml}
 
 To render atmosphere and ocean models from one dynamical core we exploit
 `isomorphisms' between equation sets that govern the evolution of the
@@ -368,11 +409,11 @@
 \input{part1/vertcoord_figure.tex}
 %%CNHend
 
-\begin{equation*}
+\begin{equation}
 \frac{D\vec{\mathbf{v}_{h}}}{Dt}+\left( 2\vec{\Omega}\times \vec{\mathbf{v}}
 \right) _{h}+\mathbf{\nabla }_{h}\phi =\mathcal{F}_{\vec{\mathbf{v}_{h}}}
 \text{ horizontal mtm} \label{eq:horizontal_mtm}
-\end{equation*}
+\end{equation}
 
 \begin{equation}
 \frac{D\dot{r}}{Dt}+\widehat{k}\cdot \left( 2\vec{\Omega}\times \vec{\mathbf{
@@ -570,9 +611,11 @@
 atmosphere)}  \label{eq:moving-bc-atmos}
 \end{eqnarray}
 
-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}).
+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}).
 
 \subsection{Ocean}
 
@@ -614,6 +657,10 @@
 
 \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
 Non-hydrostatic forms}
+\begin{rawhtml}
+<!-- CMIREDIR:non_hydrostatic: -->
+\end{rawhtml}
+
 
 Let us separate $\phi $ in to surface, hydrostatic and non-hydrostatic terms:
 
@@ -621,7 +668,9 @@
 \phi (x,y,r)=\phi _{s}(x,y)+\phi _{hyd}(x,y,r)+\phi _{nh}(x,y,r)
 \label{eq:phi-split}
 \end{equation}
-and write eq(\ref{eq:incompressible}) in the form:
+%and write eq(\ref{eq:incompressible}) in the form: 
+%                  ^- this eq is missing (jmc) ; replaced with:
+and write eq( \ref{eq:horizontal_mtm}) in the form:
 
 \begin{equation}
 \frac{\partial \vec{\mathbf{v}_{h}}}{\partial t}+\mathbf{\nabla }_{h}\phi
@@ -1051,8 +1100,9 @@
 
 \subsection{Vector invariant form}
 
-For some purposes it is advantageous to write momentum advection in eq(\ref
-{eq:horizontal_mtm}) and (\ref{eq:vertical_mtm}) in the (so-called) `vector invariant' form:
+For some purposes it is advantageous to write momentum advection in
+eq(\ref {eq:horizontal_mtm}) and (\ref{eq:vertical_mtm}) in the
+(so-called) `vector invariant' form:
 
 \begin{equation}
 \frac{D\vec{\mathbf{v}}}{Dt}=\frac{\partial \vec{\mathbf{v}}}{\partial t}
@@ -1073,7 +1123,7 @@
 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 1.17 2003/08/07 18:27:51 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1163,6 +1213,7 @@
 surface ($\phi $ is imposed and $\omega \neq 0$).
 
 \subsubsection{Splitting the geo-potential}
+\label{sec:hpe-p-geo-potential-split}
 
 For the purposes of initialization and reducing round-off errors, the model
 deals with perturbations from reference (or ``standard'') profiles. For
@@ -1192,7 +1243,8 @@
 The final form of the HPE's in p coordinates is then: 
 \begin{eqnarray}
 \frac{D\vec{\mathbf{v}}_{h}}{Dt}+f\hat{\mathbf{k}}\times \vec{\mathbf{v}}
-_{h}+\mathbf{\nabla }_{p}\phi ^{\prime } &=&\vec{\mathbf{\mathcal{F}}} \label{eq:atmos-prime} \\
+_{h}+\mathbf{\nabla }_{p}\phi ^{\prime } &=&\vec{\mathbf{\mathcal{F}}} 
+\label{eq:atmos-prime} \\
 \frac{\partial \phi ^{\prime }}{\partial p}+\alpha ^{\prime } &=&0 \\
 \mathbf{\nabla }_{p}\cdot \vec{\mathbf{v}}_{h}+\frac{\partial \omega }{
 \partial p} &=&0 \\
@@ -1200,7 +1252,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } 
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.17 2003/08/07 18:27:51 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 \section{Appendix OCEAN}
@@ -1238,8 +1290,9 @@
 _{\theta ,S}\frac{Dp}{Dt}  \label{EOSexpansion}
 \end{equation}
 
-Note that $\frac{\partial \rho }{\partial p}=\frac{1}{c_{s}^{2}}$ is the
-reciprocal of the sound speed ($c_{s}$) squared. Substituting into \ref{eq-zns-cont} gives: 
+Note that $\frac{\partial \rho }{\partial p}=\frac{1}{c_{s}^{2}}$ is
+the reciprocal of the sound speed ($c_{s}$) squared. Substituting into
+\ref{eq-zns-cont} gives:
 \begin{equation}
 \frac{1}{\rho c_{s}^{2}}\frac{Dp}{Dt}+\mathbf{\nabla }_{z}\cdot \vec{\mathbf{
 v}}+\partial _{z}w\approx 0  \label{eq-zns-pressure}
@@ -1416,7 +1469,7 @@
 _{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 1.17 2003/08/07 18:27:51 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.22 2004/10/17 04:15:13 jmc Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}
