--- manual/s_examples/baroclinic_gyre/fourlayer.tex	2001/10/25 18:36:55	1.9
+++ manual/s_examples/baroclinic_gyre/fourlayer.tex	2002/02/28 19:32:19	1.12
@@ -1,8 +1,8 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.9 2001/10/25 18:36:55 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/baroclinic_gyre/fourlayer.tex,v 1.12 2002/02/28 19:32:19 cnh Exp $
 % $Name:  $
 
-\section{Example: Four layer Baroclinic Ocean Gyre In Spherical Coordinates}
-\label{sec:eg-fourlayer}
+\section{Four Layer Baroclinic Ocean Gyre In Spherical Coordinates}
+\label{sect:eg-fourlayer}
 
 \bodytext{bgcolor="#FFFFFFFF"}
 
@@ -19,7 +19,7 @@
 This document describes an example experiment using MITgcm
 to simulate a baroclinic ocean gyre in spherical
 polar coordinates. The barotropic
-example experiment in section \ref{sec:eg-baro}
+example experiment in section \ref{sect:eg-baro}
 illustrated how to configure the code for a single layer 
 simulation in a Cartesian grid. In this example a similar physical problem
 is simulated, but the code is now configured
@@ -43,7 +43,7 @@
 according to latitude, $\varphi$
 
 \begin{equation}
-\label{EQ:fcori}
+\label{EQ:eg-fourlayer-fcori}
 f(\varphi) = 2 \Omega \sin( \varphi )
 \end{equation}
  
@@ -61,9 +61,9 @@
 $\tau_0$ is set to $0.1N m^{-2}$. 
 \\
 
-Figure \ref{FIG:simulation_config}
+Figure \ref{FIG:eg-fourlayer-simulation_config}
 summarizes the configuration simulated.
-In contrast to the example in section \ref{sec:eg-baro}, the 
+In contrast to the example in section \ref{sect:eg-baro}, the 
 current experiment simulates a spherical polar domain. As indicated
 by the axes in the lower left of the figure the model code works internally
 in a locally orthogonal coordinate $(x,y,z)$. For this experiment description 
@@ -82,14 +82,14 @@
 linear
 
 \begin{equation}
-\label{EQ:linear1_eos}
+\label{EQ:eg-fourlayer-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-fourlayer-linear1_eos_pert}
 \rho^{'} = -\rho_{0}\alpha_{\theta}\theta^{'}
 \end{equation}
 
@@ -114,13 +114,13 @@
 imposed by setting the potential temperature, $\theta$, in each layer.
 The vertical spacing, $\Delta z$, is constant and equal to $500$m.
 }
-\label{FIG:simulation_config}
+\label{FIG:eg-fourlayer-simulation_config}
 \end{figure}
 
 \subsection{Equations solved}
 For this problem
-the implicit free surface, {\bf HPE} (see section \ref{sec:hydrostatic_and_quasi-hydrostatic_forms}) form of the 
-equations described in Marshall et. al \cite{Marshall97a} are
+the implicit free surface, {\bf HPE} (see section \ref{sect:hydrostatic_and_quasi-hydrostatic_forms}) form of the 
+equations described in Marshall et. al \cite{marshall:97a} are
 employed. The flow is three-dimensional with just temperature, $\theta$, as 
 an active tracer.  The equation of state is linear.
 A horizontal Laplacian operator $\nabla_{h}^2$ provides viscous
@@ -133,7 +133,7 @@
 follows
 
 \begin{eqnarray}
-\label{EQ:model_equations}
+\label{EQ:eg-fourlayer-model_equations}
 \frac{Du}{Dt} - fv + 
   \frac{1}{\rho}\frac{\partial p^{\prime}}{\partial \lambda} - 
   A_{h}\nabla_{h}^2u - A_{z}\frac{\partial^{2}u}{\partial z^{2}} 
@@ -221,7 +221,7 @@
 
 The procedure for generating a set of internal grid variables from a
 spherical polar grid specification is discussed in section 
-\ref{sec:spatial_discrete_horizontal_grid}.
+\ref{sect:spatial_discrete_horizontal_grid}.
 
 \noindent\fbox{ \begin{minipage}{5.5in}
 {\em S/R INI\_SPHERICAL\_POLAR\_GRID} ({\em
@@ -242,15 +242,15 @@
 
 
 
-As described in \ref{sec:tracer_equations}, the time evolution of potential 
+As described in \ref{sect:tracer_equations}, the time evolution of potential 
 temperature, 
 $\theta$, (equation \ref{eq:eg_fourl_theta})
 is evaluated prognostically. The centered second-order scheme with
 Adams-Bashforth time stepping described in section 
-\ref{sec:tracer_equations_abII} is used to step forward the temperature 
+\ref{sect:tracer_equations_abII} is used to step forward the temperature 
 equation. Prognostic terms in
 the momentum equations are solved using flux form as
-described in section \ref{sec:flux-form_momentum_eqautions}.
+described in section \ref{sect:flux-form_momentum_eqautions}.
 The pressure forces that drive the fluid motions, (
 $\frac{\partial p^{'}}{\partial \lambda}$ and $\frac{\partial p^{'}}{\partial \varphi}$), are found by summing pressure due to surface 
 elevation $\eta$ and the hydrostatic pressure. The hydrostatic part of the 
@@ -258,7 +258,7 @@
 height, $\eta$, is diagnosed using an implicit scheme. The pressure
 field solution method is described in sections
 \ref{sect:pressure-method-linear-backward} and 
-\ref{sec:finding_the_pressure_field}.
+\ref{sect:finding_the_pressure_field}.
 
 \subsubsection{Numerical Stability Criteria}
 
@@ -266,7 +266,7 @@
 This value is chosen to yield a Munk layer width,
 
 \begin{eqnarray}
-\label{EQ:munk_layer}
+\label{EQ:eg-fourlayer-munk_layer}
 M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
 \end{eqnarray}
 
@@ -282,7 +282,7 @@
 parameter to the horizontal Laplacian friction
 
 \begin{eqnarray}
-\label{EQ:laplacian_stability}
+\label{EQ:eg-fourlayer-laplacian_stability}
 S_{l} = 4 \frac{A_{h} \delta t}{{\Delta x}^2}
 \end{eqnarray}
 
@@ -294,7 +294,7 @@
 $1\times10^{-2} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
 
 \begin{eqnarray}
-\label{EQ:laplacian_stability_z}
+\label{EQ:eg-fourlayer-laplacian_stability_z}
 S_{l} = 4 \frac{A_{z} \delta t}{{\Delta z}^2}
 \end{eqnarray}
 
@@ -307,7 +307,7 @@
 \noindent The numerical stability for inertial oscillations
 
 \begin{eqnarray}
-\label{EQ:inertial_stability}
+\label{EQ:eg-fourlayer-inertial_stability}
 S_{i} = f^{2} {\delta t}^2
 \end{eqnarray}
 
@@ -320,7 +320,7 @@
 speed of $ | \vec{u} | = 2 ms^{-1}$
 
 \begin{eqnarray}
-\label{EQ:cfl_stability}
+\label{EQ:eg-fourlayer-cfl_stability}
 C_{a} = \frac{| \vec{u} | \delta t}{ \Delta x}
 \end{eqnarray}
 
@@ -332,7 +332,7 @@
 propagating at $2~{\rm m}~{\rm s}^{-1}$ 
 
 \begin{eqnarray}
-\label{EQ:igw_stability}
+\label{EQ:eg-fourlayer-igw_stability}
 S_{c} = \frac{c_{g} \delta t}{ \Delta x}
 \end{eqnarray}