--- manual/s_algorithm/text/spatial-discrete.tex	2006/06/28 16:55:53	1.21
+++ manual/s_algorithm/text/spatial-discrete.tex	2017/06/14 21:05:01	1.25
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_algorithm/text/spatial-discrete.tex,v 1.21 2006/06/28 16:55:53 jmc Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_algorithm/text/spatial-discrete.tex,v 1.25 2017/06/14 21:05:01 jmc Exp $
 % $Name:  $
 
 \section{Spatial discretization of the dynamical equations}
@@ -74,7 +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
@@ -126,11 +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{
@@ -148,7 +148,7 @@
 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:domain_decomposition} for more details. 
+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
@@ -167,7 +167,7 @@
 computational grid using geographic terminology such as points of the
 compass.
 \marginpar{Caution!}
-This is purely for convenience but should note be confused
+This is purely for convenience but should not be confused
 with the actual geographic orientation of model quantities.
 
 Fig.~\ref{fig:hgrid}a shows the tracer cell (synonymous with the
@@ -186,7 +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}}
@@ -194,7 +194,7 @@
 cell centers and the ``$\zeta$'' suffix associates points with the
 vorticity points. The quantities are staggered in space and the
 indexing is such that {\bf DXc(i,j)} is positioned to the north of
-{\bf rAc(i,j)} and {\bf DYc(i,j)} positioned to the east.
+{\bf rAz(i,j)} and {\bf DYc(i,j)} positioned to the east.
 
 Fig.~\ref{fig:hgrid}c shows the ``u'' or western (w) cell. The length of
 the southern edge, $\Delta x_v$, eastern edge, $\Delta y_f$ and
@@ -327,8 +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
@@ -407,7 +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