--- manual/s_examples/deep_convection/convection.tex	2001/12/19 14:34:39	1.1
+++ manual/s_examples/deep_convection/convection.tex	2002/05/16 15:54:37	1.3
@@ -1,4 +1,5 @@
-\section{Example: Surface driven convection}
+\section{Surface Driven Convection}
+\label{www:tutorials}
 \label{sect:eg-bconv}
 
 \bodytext{bgcolor="#FFFFFFFF"}
@@ -22,10 +23,10 @@
 for the surface driven convection experiment. The domain is doubly periodic
 with an initially uniform temperature of 20 $^oC$. 
 }
-\label{FIG:simulation_config}
+\label{FIG:eg-bconv-simulation_config}
 \end{figure}
 
-This experiment, figure \ref{FIG:simulation_config}, showcasing MITgcm's non-hydrostatic capability, was designed to explore 
+This experiment, figure \ref{FIG:eg-bconv-simulation_config}, showcasing MITgcm's non-hydrostatic capability, was designed to explore 
 the temporal and spatial characteristics of convection plumes as they might exist during a 
 period of oceanic deep convection. It is
 
@@ -39,6 +40,7 @@
 \end{itemize}
 
 \subsection{Overview}
+\label{www:tutorials}
 
 The model domain consists of an approximately 3
 km square by 1 km deep box of initially
@@ -50,14 +52,14 @@
 used in this experiment is linear
 
 \begin{equation}
-\label{EQ:linear1_eos}
+\label{EQ:eg-bconv-linear1_eos}
 \rho = \rho_{0} ( 1 - \alpha_{\theta}\theta^{'} )
 \end{equation}
 
 \noindent which is implemented in the model as a density anomaly equation
 
 \begin{equation}
-\label{EQ:linear1_eos_pert}
+\label{EQ:eg-bconv-linear1_eos_pert}
 \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}
 \end{equation}
 
@@ -72,9 +74,10 @@
 As the fluid in the surface layer is cooled (at a mean rate of 800 Wm$^2$), it becomes 
 convectively unstable and 
 overturns, at first close to the grid-scale, but, as the flow matures, on larger scales 
-(figures \ref{FIG:vertsection} and \ref{FIG:horizsection}), under the influence of 
+(figures \ref{FIG:eg-bconv-vertsection} and \ref{FIG:eg-bconv-horizsection}), under the influence of 
 rotation ($f_o = 10^{-4}$ s$^{-1}$) .
 
+\begin{rawhtml}MITGCM_INSERT_FIGURE_BEGIN surf-convection-vertsection\end{rawhtml}
 \begin{figure}
 \begin{center}
  \resizebox{15cm}{10cm}{
@@ -83,9 +86,12 @@
 \end{center}
 \caption{
 }
-\label{FIG:vertsection}
+\label{FIG:eg-bconv-vertsection}
+\label{fig:surf-convection-vertsection}
 \end{figure}
+\begin{rawhtml}MITGCM_INSERT_FIGURE_END\end{rawhtml}
 
+\begin{rawhtml}MITGCM_INSERT_FIGURE_BEGIN surf-convection-horizsection\end{rawhtml}
 \begin{figure}
 \begin{center}
  \resizebox{10cm}{10cm}{
@@ -94,14 +100,17 @@
 \end{center}
 \caption{
 }
-\label{FIG:horizsection}
+\label{FIG:eg-bconv-horizsection}
+\label{fig:surf-convection-horizsection}
 \end{figure}
+\begin{rawhtml}MITGCM_INSERT_FIGURE_END\end{rawhtml}
 
 Model parameters are specified in file {\it input/data}. The grid dimensions are
 prescribed in {\it code/SIZE.h}. The forcing (file {\it input/Qsurf.bin}) is specified 
 in a binary data file generated using the Matlab script {\it input/gendata.m}.
 
 \subsection{Equations solved}
+\label{www:tutorials}
 
 The model is configured in nonhydrostatic form, that is, all terms in the Navier 
 Stokes equations are retained and the pressure field is found, subject to appropriate
@@ -111,11 +120,11 @@
 pressure equation described in Marshall et. al \cite{marshall:97a} is
 employed. A horizontal Laplacian operator $\nabla_{h}^2$ provides viscous
 dissipation. The thermodynamic forcing appears as a sink in the potential temperature, 
-$\theta$, equation (\ref{EQ:global_forcing_ft}). This produces a set of equations 
+$\theta$, equation (\ref{EQ:eg-bconv-global_forcing_ft}). This produces a set of equations 
 solved in this configuration as follows:
 
 \begin{eqnarray}
-\label{EQ:model_equations}
+\label{EQ:eg-bconv-model_equations}
 \frac{Du}{Dt} - fv + 
   \frac{1}{\rho}\frac{\partial p^{'}}{\partial x} - 
   \nabla_{h}\cdot A_{h}\nabla_{h}u - 
@@ -171,12 +180,14 @@
 \\
 
 \subsection{Discrete numerical configuration}
+\label{www:tutorials}
 
 The domain is discretised with a uniform grid spacing in each direction. There are 64
 grid cells in directions $x$ and $y$ and 20 vertical levels thus the domain
 comprises a total of just over 80 000 gridpoints.
 
 \subsection{Numerical stability criteria and other considerations}
+\label{www:tutorials}
 
 For a heat flux of 800 Wm$^2$ and a rotation rate of $10^{-4}$ s$^{-1}$ the
 plume-scale can be expected to be a few hundred meters guiding our choice of grid
@@ -190,7 +201,7 @@
 50 m, the implied maximum timestep for stability, $\delta t_u$ is 
 
 \begin{eqnarray}
-\label{EQ:advectiveCFLcondition}
+\label{EQ:eg-bconv-advectiveCFLcondition}
 %\delta t_u = \frac{\Delta x}{| \vec{u} \} = 50 s
 \end{eqnarray}
 
@@ -202,6 +213,7 @@
 correlated over 50 m.  
 
 \subsection{Experiment configuration}
+\label{www:tutorials}
 
 The model configuration for this experiment resides under the directory
 {\it verification/convection/}. The experiment files
@@ -218,16 +230,19 @@
 experiment. Below we describe these experiment-specific customisations.
 
 \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
+\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 \subsubsection{File {\it code/CPP\_OPTIONS.h}}
+\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 \subsubsection{File {\it code/SIZE.h}}
+\label{www:tutorials}
 
 Three lines are customized in this file. These prescribe the domain grid dimensions.
 \begin{itemize}
@@ -255,6 +270,7 @@
 \begin{rawhtml}</PRE>\end{rawhtml}
 
 \subsubsection{File {\it input/data}}
+\label{www:tutorials}
 
 This file, reproduced completely below, specifies the main parameters 
 for the experiment. The parameters that are significant for this configuration
@@ -669,7 +685,7 @@
 \end{verbatim}
 Sets the tolerance which the three-dimensional, conjugate
 gradient solver will use to test for convergence in equation 
-\ref{EQ:congrad_3d_resid} to $1 \times 10^{-9}$.
+\ref{EQ:eg-bconv-congrad_3d_resid} to $1 \times 10^{-9}$.
 The solver will iterate until the 
 tolerance falls below this value or until the maximum number of
 solver iterations is reached. Used in routine
@@ -772,17 +788,20 @@
 
 
 \subsubsection{File {\it input/data.pkg}}
+\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 \subsubsection{File {\it input/eedata}}
+\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 
 \subsubsection{File {\it input/Qsurf.bin}}
+\label{www:tutorials}
 
 The file {\it input/Qsurf.bin} specifies a two-dimensional ($x,y$) 
 map of heat flux values where 
@@ -801,17 +820,20 @@
 \end{center}
 \caption{
 }
-\label{FIG:Qsurf}
+\label{FIG:eg-bconv-Qsurf}
 \end{figure}
 
 \subsection{Running the example}
+\label{www:tutorials}
 
 \subsubsection{Code download}
+\label{www:tutorials}
 
 In order to run the examples you must first download the code distribution.
 Instructions for downloading the code can be found in \ref{sect:obtainingCode}.
 
 \subsubsection{Experiment Location}
+\label{www:tutorials}
 
  This example experiments is located under the release sub-directory
 
@@ -819,6 +841,7 @@
 {\it verification/convection/ }
 
 \subsubsection{Running the Experiment}
+\label{www:tutorials}
 
  To run the experiment
 
