--- manual/s_examples/deep_convection/convection.tex	2002/02/28 19:32:19	1.2
+++ manual/s_examples/deep_convection/convection.tex	2003/07/30 13:42:52	1.4
@@ -1,4 +1,5 @@
 \section{Surface Driven Convection}
+\label{www:tutorials}
 \label{sect:eg-bconv}
 
 \bodytext{bgcolor="#FFFFFFFF"}
@@ -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
@@ -108,6 +110,7 @@
 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
@@ -177,12 +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
@@ -208,6 +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
@@ -224,16 +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}
@@ -261,6 +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
@@ -280,19 +290,19 @@
 $x$ and $y$. The values specified are read into the
 variable 
 {\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/OK.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/OK.htm> \end{rawhtml}
 tRef
 \begin{rawhtml} </A>\end{rawhtml}
 } 
 in the model code, by procedure 
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}.
 }
 The temperature field is initialised, by procedure 
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/OK.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/OK.htm> \end{rawhtml}
 S/R INI\_THETA ({\it ini\_theta.F})
 \begin{rawhtml} </A>\end{rawhtml}.
 }
@@ -310,19 +320,19 @@
 $x$ and $y$. The values specified are read into the
 variable 
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/OK.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/OK.htm> \end{rawhtml}
 sRef
 \begin{rawhtml} </A>\end{rawhtml}
 } 
 in the model code, by procedure 
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 }
 \begin{rawhtml} </A>\end{rawhtml}.
 The salinity field is initialised, by procedure 
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/OK.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/OK.htm> \end{rawhtml}
 S/R INI\_SALT ({\it ini\_salt.F})
 \begin{rawhtml} </A>\end{rawhtml}.
 }
@@ -337,23 +347,23 @@
 for this operator are specified later. 
 The variable 
 {\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/SI.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/SI.htm> \end{rawhtml}
 viscAh
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_params.F})
 \begin{rawhtml} </A>\end{rawhtml}
 } and applied in routines 
 {\it 
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_MOM\_RHS ({\it calc\_mom\_rhs.F})
 \begin{rawhtml} </A>\end{rawhtml}
 } and 
 {\it 
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_GW ({\it calc\_gw.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -368,25 +378,25 @@
 for this operator are specified later.
 The variable 
 {\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/ZQ.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/ZQ.htm> \end{rawhtml}
 viscAz
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }
 and is copied into model general vertical coordinate variable 
 {\bf 
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/PF.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/PF.htm> \end{rawhtml}
 viscAr
 \begin{rawhtml} </A>\end{rawhtml}
 }. At each time step, the viscous term contribution to the momentum equations
 is calculated in routine
 {\it 
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_DIFFUSIVITY ({\it calc\_diffusivity.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -402,18 +412,18 @@
 $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/UT.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/UT.htm> \end{rawhtml}
 no\_slip\_sides
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 } and the boundary condition is evaluated in routine
 {\it 
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_MOM\_RHS ({\it calc\_mom\_rhs.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -428,18 +438,18 @@
 e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/UK.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/UK.htm> \end{rawhtml}
 no\_slip\_bottom
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 } and is applied in the routine 
 {\it 
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_MOM\_RHS ({\it calc\_mom\_rhs.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -454,18 +464,18 @@
 all boundaries.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/RC.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/RC.htm> \end{rawhtml}
 diffKhT
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 } and used in routine 
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_GT ({\it calc\_gt.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -479,24 +489,24 @@
 operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/ZT.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/ZT.htm> \end{rawhtml}
 diffKzT
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
 It is copied into model general vertical coordinate variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/PD.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/PD.htm> \end{rawhtml}
 diffKrT
 \begin{rawhtml} </A>\end{rawhtml}
 } which is used in routine 
 {\it 
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_DIFFUSIVITY ({\it calc\_diffusivity.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -512,18 +522,18 @@
 all boundaries.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/RC.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/RC.htm> \end{rawhtml}
 diffKsT
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 } and used in routine 
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_GS ({\it calc\_gs.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -538,24 +548,24 @@
 operator is $\frac{\partial}{\partial z}$ = 0 on all boundaries.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/ZT.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/ZT.htm> \end{rawhtml}
 diffKzS
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
 It is copied into model general vertical coordinate variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/PD.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/PD.htm> \end{rawhtml}
 diffKrS
 \begin{rawhtml} </A>\end{rawhtml}
 } which is used in routine 
 {\it 
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CALC\_DIFFUSIVITY ({\it calc\_diffusivity.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }.
@@ -584,19 +594,19 @@
 to $2 \times 10^{-4}$ $^o$ C$^{-1}$.
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/ZV.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/ZV.htm> \end{rawhtml}
 tAlpha 
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }. 
 The routine 
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R FIND\_RHO ({\it find\_rho.F})
 \begin{rawhtml} </A>\end{rawhtml}
 } makes use of {\bf tAlpha}.
@@ -662,7 +672,7 @@
 gradient solver will use to 40, {\bf irrespective of the convergence 
 criteria being met}. Used in routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CG3D ({\it cg3d.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }. 
@@ -680,7 +690,7 @@
 tolerance falls below this value or until the maximum number of
 solver iterations is reached. Used in routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R CG3D ({\it cg3d.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }. 
@@ -749,19 +759,19 @@
 surface heat flux file used in the example. 
 The variable
 {\bf
-\begin{rawhtml} <A href=../../../code_reference/vdb/names/179.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/names/179.htm> \end{rawhtml}
 Qsurf 
 \begin{rawhtml} </A>\end{rawhtml}
 }
 is read in the routine
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R INI\_PARMS ({\it ini\_parms.F})
 \begin{rawhtml} </A>\end{rawhtml}
 }
 and applied in  
 {\it
-\begin{rawhtml} <A href=../../../code_reference/vdb/code/94.htm> \end{rawhtml}
+\begin{rawhtml} <A href=../code_reference/vdb/code/94.htm> \end{rawhtml}
 S/R EXTERNAL\_FORCING\_SURF ({\it external\_forcing\_surf.F})
 \begin{rawhtml} </A>\end{rawhtml}
 } where the flux is converted to a temperature tendency.
@@ -778,17 +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 
@@ -811,13 +824,16 @@
 \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
 
@@ -825,6 +841,7 @@
 {\it verification/convection/ }
 
 \subsubsection{Running the Experiment}
+\label{www:tutorials}
 
  To run the experiment
 
