--- manual/s_algorithm/text/spatial-discrete.tex	2004/03/23 16:47:04	1.14
+++ manual/s_algorithm/text/spatial-discrete.tex	2004/10/16 03:40:12	1.17
@@ -1,7 +1,10 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_algorithm/text/spatial-discrete.tex,v 1.14 2004/03/23 16:47:04 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_algorithm/text/spatial-discrete.tex,v 1.17 2004/10/16 03:40:12 edhill 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
@@ -366,15 +369,23 @@
 
 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
@@ -392,6 +403,9 @@
 
 
 \subsection{Topography: partially filled cells}
+\begin{rawhtml}
+<!-- CMIREDIR:topo_partial_cells: -->
+\end{rawhtml}
 
 \begin{figure}
 \begin{center}
@@ -462,6 +476,10 @@
 
 
 \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:
@@ -500,6 +518,9 @@
 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