--- manual/s_algorithm/text/spatial-discrete.tex	2004/10/13 18:50:54	1.16
+++ manual/s_algorithm/text/spatial-discrete.tex	2010/08/30 23:09:19	1.24
@@ -1,7 +1,10 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_algorithm/text/spatial-discrete.tex,v 1.16 2004/10/13 18:50:54 jmc Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_algorithm/text/spatial-discrete.tex,v 1.24 2010/08/30 23:09:19 jmc Exp $
 % $Name:  $
 
 \section{Spatial discretization of the dynamical equations}
+\begin{rawhtml}
+<!-- CMIREDIR:spatial_discretization_of_dyn_eq: -->
+\end{rawhtml}
 
 Spatial discretization is carried out using the finite volume
 method. This amounts to a grid-point method (namely second-order
@@ -10,8 +13,6 @@
 representation of the position of the boundary. We treat the
 horizontal and vertical directions as separable and differently.
 
-\input{part2/notation}
-
 
 \subsection{The finite volume method: finite volumes versus finite difference}
 \begin{rawhtml}
@@ -73,7 +74,7 @@
 
 \begin{figure}
 \begin{center}
-\resizebox{!}{2in}{ \includegraphics{part2/cgrid3d.eps}}
+\resizebox{!}{2in}{ \includegraphics{s_algorithm/figs/cgrid3d.eps}}
 \end{center}
 \caption{Three dimensional staggering of velocity components. This
 facilitates the natural discretization of the continuity and tracer
@@ -125,11 +126,11 @@
 \begin{figure}
 \begin{center}
 \begin{tabular}{cc}
-  \raisebox{1.5in}{a)}\resizebox{!}{2in}{ \includegraphics{part2/hgrid-Ac.eps}}
-& \raisebox{1.5in}{b)}\resizebox{!}{2in}{ \includegraphics{part2/hgrid-Az.eps}}
+  \raisebox{1.5in}{a)}\resizebox{!}{2in}{ \includegraphics{s_algorithm/figs/hgrid-Ac.eps}}
+& \raisebox{1.5in}{b)}\resizebox{!}{2in}{ \includegraphics{s_algorithm/figs/hgrid-Az.eps}}
 \\
-  \raisebox{1.5in}{c)}\resizebox{!}{2in}{ \includegraphics{part2/hgrid-Au.eps}}
-& \raisebox{1.5in}{d)}\resizebox{!}{2in}{ \includegraphics{part2/hgrid-Av.eps}}
+  \raisebox{1.5in}{c)}\resizebox{!}{2in}{ \includegraphics{s_algorithm/figs/hgrid-Au.eps}}
+& \raisebox{1.5in}{d)}\resizebox{!}{2in}{ \includegraphics{s_algorithm/figs/hgrid-Av.eps}}
 \end{tabular}
 \end{center}
 \caption{
@@ -138,8 +139,8 @@
 grid for all panels. a) The area of a tracer cell, $A_c$, is bordered
 by the lengths $\Delta x_g$ and $\Delta y_g$. b) The area of a
 vorticity cell, $A_\zeta$, is bordered by the lengths $\Delta x_c$ and
-$\Delta y_c$. c) The area of a u cell, $A_c$, is bordered by the
-lengths $\Delta x_v$ and $\Delta y_f$. d) The area of a v cell, $A_c$,
+$\Delta y_c$. c) The area of a u cell, $A_w$, is bordered by the
+lengths $\Delta x_v$ and $\Delta y_f$. d) The area of a v cell, $A_s$,
 is bordered by the lengths $\Delta x_f$ and $\Delta y_u$.}
 \label{fig:hgrid}
 \end{figure}
@@ -147,8 +148,8 @@
 The model domain is decomposed into tiles and within each tile a
 quasi-regular grid is used. A tile is the basic unit of domain
 decomposition for parallelization but may be used whether parallelized
-or not; see section \ref{sect:tiles} for more details. Although the
-tiles may be patched together in an unstructured manner
+or not; see section \ref{sec:domain_decomposition} for more details. 
+Although the tiles may be patched together in an unstructured manner
 (i.e. irregular or non-tessilating pattern), the interior of tiles is
 a structured grid of quadrilateral cells. The horizontal coordinate
 system is orthogonal curvilinear meaning we can not necessarily treat
@@ -185,7 +186,7 @@
 Fig.~\ref{fig:hgrid}b shows the vorticity cell. The length of the
 southern edge, $\Delta x_c$, western edge, $\Delta y_c$ and surface
 area, $A_\zeta$, presented in the vertical are stored in arrays {\bf
-DXg}, {\bf DYg} and {\bf rAz}.
+DXc}, {\bf DYc} and {\bf rAz}.
 \marginpar{$A_\zeta$: {\bf rAz}}
 \marginpar{$\Delta x_c$: {\bf DXc}}
 \marginpar{$\Delta y_c$: {\bf DYc}}
@@ -326,8 +327,8 @@
 \begin{center}
   \begin{tabular}{cc}
   \raisebox{4in}{a)} \resizebox{!}{4in}{
-  \includegraphics{part2/vgrid-cellcentered.eps}} & \raisebox{4in}{b)}
-  \resizebox{!}{4in}{ \includegraphics{part2/vgrid-accurate.eps}}
+  \includegraphics{s_algorithm/figs/vgrid-cellcentered.eps}} & \raisebox{4in}{b)}
+  \resizebox{!}{4in}{ \includegraphics{s_algorithm/figs/vgrid-accurate.eps}}
 \end{tabular} 
 \end{center}
 \caption{Two versions of the vertical grid. a) The cell centered
@@ -367,7 +368,7 @@
 The above grid (Fig.~\ref{fig:vgrid}a) is known as the cell centered
 approach because the tracer points are at cell centers; the cell
 centers are mid-way between the cell interfaces. 
-This discretisation is selected when the thickness of the
+This discretization is selected when the thickness of the
 levels are provided ({\bf delR}, parameter file {\em data}, 
 namelist {\em PARM04})
 An alternative, the vertex or interface centered approach, is shown in
@@ -406,7 +407,7 @@
 
 \begin{figure}
 \begin{center}
-\resizebox{4.5in}{!}{\includegraphics{part2/vgrid-xz.eps}}
+\resizebox{4.5in}{!}{\includegraphics{s_algorithm/figs/vgrid-xz.eps}}
 \end{center}
 \caption{
 A schematic of the x-r plane showing the location of the
@@ -473,6 +474,10 @@
 
 
 \section{Continuity and horizontal pressure gradient terms}
+\begin{rawhtml}
+<!-- CMIREDIR:continuity_and_horizontal_pressure: -->
+\end{rawhtml}
+
 
 The core algorithm is based on the ``C grid'' discretization of the
 continuity equation which can be summarized as:
@@ -511,6 +516,9 @@
 evaporation and only enters the top-level of the {\em ocean} model.
 
 \section{Hydrostatic balance}
+\begin{rawhtml}
+<!-- CMIREDIR:hydrostatic_balance: -->
+\end{rawhtml}
 
 The vertical momentum equation has the hydrostatic or
 quasi-hydrostatic balance on the right hand side. This discretization
