--- manual/s_overview/text/manual.tex	2001/10/09 10:48:03	1.2
+++ manual/s_overview/text/manual.tex	2001/10/10 16:48:45	1.3
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.2 2001/10/09 10:48:03 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.3 2001/10/10 16:48:45 cnh Exp $
 % $Name:  $
 %\usepackage{oldgerm}
 % I commented the following because it introduced excessive white space
@@ -57,7 +57,7 @@
 
 % Section: Overview
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.2 2001/10/09 10:48:03 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.3 2001/10/10 16:48:45 cnh Exp $
 % $Name:  $
 
 \section{Introduction}
@@ -77,20 +77,32 @@
 \begin{itemize}
 \item it can be used to study both atmospheric and oceanic phenomena; one
 hydrodynamical kernel is used to drive forward both atmospheric and oceanic
-models - see fig.1%
+models - see fig%
 \marginpar{
 Fig.1 One model}\ref{fig:onemodel}
 
+%% CNHbegin
+\input{part1/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.2%
+small-scale and large scale processes - see fig %
 \marginpar{
 Fig.2 All scales}\ref{fig:all-scales}
 
+%% CNHbegin
+\input{part1/all_scales_figure}
+%% CNHend
+
 \item finite volume techniques are employed yielding an intuitive
 discretization and support for the treatment of irregular geometries using
-orthogonal curvilinear grids and shaved cells - see fig.3%
+orthogonal curvilinear grids and shaved cells - see fig %
 \marginpar{
-Fig.3 Finite volumes}\ref{fig:Finite volumes}
+Fig.3 Finite volumes}\ref{fig:finite-volumes}
+
+%% CNHbegin
+\input{part1/fvol_figure}
+%% CNHend
 
 \item tangent linear and adjoint counterparts are automatically maintained
 along with the forward model, permitting sensitivity and optimization
@@ -107,7 +119,7 @@
 give a feel for the wide range of problems that can be addressed using it.
 \pagebreak
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.2 2001/10/09 10:48:03 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.3 2001/10/10 16:48:45 cnh Exp $
 % $Name:  $
 
 \section{Illustrations of the model in action}
@@ -128,7 +140,7 @@
 A novel feature of MITgcm is its ability to simulate both atmospheric and
 oceanographic flows at both small and large scales.
 
-Fig.E1a.\ref{fig:Held-Suarez} shows an instantaneous plot of the 500$mb$
+Fig.E1a.\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
 (blue) and warm air along an equatorial band (red). Fully developed
@@ -139,6 +151,10 @@
 in Held and Suarez; 1994 designed to test atmospheric hydrodynamical cores -
 there are no mountains or land-sea contrast.
 
+%% CNHbegin
+\input{part1/cubic_eddies_figure}
+%% 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.
 The `vector-invariant' form of MITgcm supports any orthogonal curvilinear
@@ -151,6 +167,10 @@
 
 A regular spherical lat-lon grid can also be used.
 
+%% CNHbegin
+\input{part1/hs_zave_u_figure}
+%% CNHend
+
 \subsection{Ocean gyres}
 
 Baroclinic instability is a ubiquitous process in the ocean, as well as the
@@ -171,6 +191,11 @@
 warm water northward by the mean flow of the Gulf Stream is also clearly
 visible.
 
+%% CNHbegin
+\input{part1/ocean_gyres_figure}
+%% CNHend
+
+
 \subsection{Global ocean circulation}
 
 Fig.E2a shows the pattern of ocean currents at the surface of a 4$^{\circ }$
@@ -184,6 +209,10 @@
 Fig.E2b shows the meridional overturning circulation of the global ocean in
 Sverdrups.
 
+%%CNHbegin
+\input{part1/global_circ_figure}
+%%CNHend
+
 \subsection{Convection and mixing over topography}
 
 Dense plumes generated by localized cooling on the continental shelf of the
@@ -198,6 +227,10 @@
 strong, and replaced by lateral entrainment due to the baroclinic
 instability of the along-slope current.
 
+%%CNHbegin
+\input{part1/convect_and_topo}
+%%CNHend
+
 \subsection{Boundary forced internal waves}
 
 The unique ability of MITgcm to treat non-hydrostatic dynamics in the
@@ -212,6 +245,10 @@
 using MITgcm's finite volume spatial discretization) where they break under
 nonhydrostatic dynamics.
 
+%%CNHbegin
+\input{part1/boundary_forced_waves}
+%%CNHend
+
 \subsection{Parameter sensitivity using the adjoint of MITgcm}
 
 Forward and tangent linear counterparts of MITgcm are supported using an
@@ -226,6 +263,10 @@
 of deep water for the thermohaline circulations. This calculation also
 yields sensitivities to all other model parameters.
 
+%%CNHbegin
+\input{part1/adj_hf_ocean_figure}
+%%CNHend
+
 \subsection{Global state estimation of the ocean}
 
 An important application of MITgcm is in state estimation of the global
@@ -237,6 +278,10 @@
 ocean obtained by bringing the model in to consistency with altimetric and
 in-situ observations over the period 1992-1997.
 
+%% CNHbegin
+\input{part1/globes_figure}
+%% CNHend
+
 \subsection{Ocean biogeochemical cycles}
 
 MITgcm is being used to study global biogeochemical cycles in the ocean. For
@@ -246,8 +291,9 @@
 flux of oxygen and its relation to density outcrops in the southern oceans
 from a single year of a global, interannually varying simulation.
 
-Chris - get figure here: http://puddle.mit.edu/\symbol{126}%
-mick/biogeochem.html
+%%CNHbegin
+\input{part1/biogeo_figure}
+%%CNHend
 
 \subsection{Simulations of laboratory experiments}
 
@@ -260,7 +306,11 @@
 arrested by its instability in a process analogous to that whic sets the
 stratification of the ACC.
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.2 2001/10/09 10:48:03 cnh Exp $
+%%CNHbegin
+\input{part1/lab_figure}
+%%CNHend
+
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.3 2001/10/10 16:48:45 cnh Exp $
 % $Name:  $
 
 \section{Continuous equations in `r' coordinates}
@@ -275,6 +325,10 @@
 vertical coordinate `$r$' is interpreted as pressure, $p$, if we are
 modeling the atmosphere and height, $z$, if we are modeling the ocean.
 
+%%CNHbegin
+\input{part1/zandpcoord_figure.tex}
+%%CNHend
+
 The state of the fluid at any time is characterized by the distribution of
 velocity $\vec{\mathbf{v}}$, active tracers $\theta $ and $S$, a
 `geopotential' $\phi $ and density $\rho =\rho (\theta ,S,p)$ which may
@@ -285,6 +339,10 @@
 \marginpar{
 Fig.5 The vertical coordinate of model}:
 
+%%CNHbegin
+\input{part1/vertcoord_figure.tex}
+%%CNHend
+
 \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}}}%
@@ -630,6 +688,10 @@
 \marginpar{
 Fig.6 Spherical polar coordinate system.}
 
+%%CNHbegin
+\input{part1/sphere_coord_figure.tex}
+%%CNHend
+
 \subsubsection{Shallow atmosphere approximation}
 
 Most models are based on the `hydrostatic primitive equations' (HPE's) in
@@ -746,6 +808,10 @@
 stepping forward the horizontal momentum equations; $\dot{r}$ is found by
 stepping forward the vertical momentum equation.
 
+%%CNHbegin
+\input{part1/solution_strategy_figure.tex}
+%%CNHend
+
 There is no penalty in implementing \textbf{QH} over \textbf{HPE} except, of
 course, some complication that goes with the inclusion of $\cos \phi \ $%
 Coriolis terms and the relaxation of the shallow atmosphere approximation.
@@ -979,7 +1045,7 @@
 Tangent linear and adjoint counterparts of the forward model and described
 in Chapter 5.
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.2 2001/10/09 10:48:03 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.3 2001/10/10 16:48:45 cnh Exp $
 % $Name:  $
 
 \section{Appendix ATMOSPHERE}
@@ -1106,7 +1172,7 @@
 \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi }  \label{eq:atmos-prime}
 \end{eqnarray}
 
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.2 2001/10/09 10:48:03 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.3 2001/10/10 16:48:45 cnh Exp $
 % $Name:  $
 
 \section{Appendix OCEAN}
@@ -1322,7 +1388,7 @@
 _{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 1.2 2001/10/09 10:48:03 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.3 2001/10/10 16:48:45 cnh Exp $
 % $Name:  $
 
 \section{Appendix:OPERATORS}