--- manual/s_overview/text/manual.tex	2008/01/17 21:28:22	1.27
+++ 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 1.27 2008/01/17 21:28:22 jmc 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 1.27 2008/01/17 21:28:22 jmc 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
@@ -139,7 +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 1.27 2008/01/17 21:28:22 jmc 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}
@@ -177,7 +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
@@ -193,7 +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}
@@ -224,7 +224,7 @@
 is also clearly visible.
 
 %% CNHbegin
-\input{part1/atl6_figure}
+\input{s_overview/text/atl6_figure}
 %% CNHend
 
 
@@ -246,7 +246,7 @@
 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}
@@ -269,7 +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}
@@ -291,7 +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}
@@ -314,7 +314,7 @@
 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}
@@ -335,7 +335,7 @@
 1992-1997.
 
 %% CNHbegin
-\input{part1/assim_figure}
+\input{s_overview/text/assim_figure}
 %% CNHend
 
 \subsection{Ocean biogeochemical cycles}
@@ -355,7 +355,7 @@
 shown).
 
 %%CNHbegin
-\input{part1/biogeo_figure}
+\input{s_overview/text/biogeo_figure}
 %%CNHend
 
 \subsection{Simulations of laboratory experiments}
@@ -373,10 +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 1.27 2008/01/17 21:28:22 jmc 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}
@@ -396,7 +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
@@ -410,7 +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}
@@ -661,6 +661,7 @@
 
 \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
 Non-hydrostatic forms}
+\label{sec:all_hydrostatic_forms}
 \begin{rawhtml}
 <!-- CMIREDIR:non_hydrostatic: -->
 \end{rawhtml}
@@ -769,7 +770,7 @@
 OPERATORS.
 
 %%CNHbegin
-\input{part1/sphere_coord_figure.tex}
+\input{s_overview/text/sphere_coord_figure.tex}
 %%CNHend
 
 \subsubsection{Shallow atmosphere approximation}
@@ -890,7 +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
@@ -1128,7 +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 1.27 2008/01/17 21:28:22 jmc 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}
@@ -1257,7 +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 1.27 2008/01/17 21:28:22 jmc 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}
@@ -1474,7 +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 1.27 2008/01/17 21:28:22 jmc 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}