--- manual/s_algorithm/text/spatial-discrete.tex	2001/11/13 18:15:26	1.11
+++ manual/s_algorithm/text/spatial-discrete.tex	2004/10/13 18:50:54	1.16
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_algorithm/text/spatial-discrete.tex,v 1.11 2001/11/13 18:15:26 adcroft Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_algorithm/text/spatial-discrete.tex,v 1.16 2004/10/13 18:50:54 jmc Exp $
 % $Name:  $
 
 \section{Spatial discretization of the dynamical equations}
@@ -14,6 +14,11 @@
 
 
 \subsection{The finite volume method: finite volumes versus finite difference}
+\begin{rawhtml}
+<!-- CMIREDIR:finite_volume: -->
+\end{rawhtml}
+
+
 
 The finite volume method is used to discretize the equations in
 space. The expression ``finite volume'' actually has two meanings; one
@@ -361,15 +366,23 @@
 
 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. An alternative, the
-vertex or interface centered approach, is shown in
+centers are mid-way between the cell interfaces. 
+This discretisation 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
 Fig.~\ref{fig:vgrid}b. Here, the interior interfaces are positioned
 mid-way between the tracer nodes (no longer cell centers). This
 approach is formally more accurate for evaluation of hydrostatic
 pressure and vertical advection but historically the cell centered
 approach has been used. An alternative form of subroutine {\em
 INI\_VERTICAL\_GRID} is used to select the interface centered approach
-but no run time option is currently available.
+This form requires to specify $Nr+1$ vertical distances {\bf delRc} 
+(parameter file {\em data}, namelist {\em PARM04}, e.g. 
+{\em verification/ideal\_2D\_oce/input/data})
+corresponding to surface to center, $Nr-1$ center to center, and center to 
+bottom distances.
+%but no run time option is currently available.
 
 \fbox{ \begin{minipage}{4.75in}
 {\em S/R INI\_VERTICAL\_GRID} ({\em
@@ -387,6 +400,9 @@
 
 
 \subsection{Topography: partially filled cells}
+\begin{rawhtml}
+<!-- CMIREDIR:topo_partial_cells: -->
+\end{rawhtml}
 
 \begin{figure}
 \begin{center}
@@ -471,7 +487,7 @@
 \end{eqnarray}
 where the continuity equation has been most naturally discretized by
 staggering the three components of velocity as shown in
-Fig.~\ref{fig-cgrid3d}. The grid lengths $\Delta x_c$ and $\Delta y_c$
+Fig.~\ref{fig:cgrid3d}. The grid lengths $\Delta x_c$ and $\Delta y_c$
 are the lengths between tracer points (cell centers). The grid lengths
 $\Delta x_g$, $\Delta y_g$ are the grid lengths between cell
 corners. $\Delta r_f$ and $\Delta r_c$ are the distance (in units of