--- manual/s_examples/rotating_tank/tank.tex	2004/10/16 03:40:15	1.11
+++ manual/s_examples/rotating_tank/tank.tex	2005/06/14 20:09:04	1.12
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/rotating_tank/tank.tex,v 1.11 2004/10/16 03:40:15 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/rotating_tank/tank.tex,v 1.12 2005/06/14 20:09:04 afe Exp $
 % $Name:  $
 
 \bodytext{bgcolor="#FFFFFFFF"}
@@ -27,16 +27,16 @@
 
 \subsection{Overview}
 \label{www:tutorials}
-                                                                                
-                                                                                
-This example configuration demonstrates using the MITgcm to simulate
-a laboratory demonstration using a rotating tank of water with an ice
-bucket in the center. The simulation is configured for a laboratory
-scale on a
-$3^{\circ}$ $\times$ 20cm
-cyclindrical grid with twenty-nine vertical
-levels.
+                                                                          
+This example configuration demonstrates using the MITgcm to simulate a
+laboratory demonstration using a differentially heated rotating
+annulus of water.  The simulation is configured for a laboratory scale
+on a $3^{\circ}$ $\times$ 1cm cyclindrical grid with twenty-nine
+vertical levels of 0.5cm each.  This is a typical laboratory setup for
+illustration principles of GFD, as well as for a laboratory data
+assimilation project.
 \\
+
 example illustration from GFD lab here
 \\
 
@@ -51,11 +51,14 @@
 \subsection{Discrete Numerical Configuration}
 \label{www:tutorials}
 
- The domain is discretised with 
-a uniform cylindrical grid spacing in the horizontal set to
- $\Delta a=1$~cm and $\Delta \phi=3^{\circ}$, so 
-that there are 120 grid cells in the azimuthal direction and thirty-one grid cells in the radial. Vertically the 
-model is configured with twenty-nine layers of uniform 0.5cm thickness.
+ The domain is discretised with a uniform cylindrical grid spacing in
+the horizontal set to $\Delta a=1$~cm and $\Delta \phi=3^{\circ}$, so
+that there are 120 grid cells in the azimuthal direction and
+thirty-one grid cells in the radial, representing a tank 62cm in
+diameter.  The bathymetry file sets the depth=0 in the nine lowest
+radial rows to represent the central of the annulus.  Vertically the
+model is configured with twenty-nine layers of uniform 0.5cm
+thickness.
 \\
 something about heat flux
 
@@ -89,75 +92,99 @@
 
 \begin{itemize}
 
-\item Line 10, \begin{verbatim} viscAh=5.0E-6, \end{verbatim} this line sets
-the Laplacian friction coefficient to $6 \times 10^{-6} m^2s^{-1}$, 
-which is ususally 
-low because of the small scale, presumably.... qqq
-
-\item Line 19, \begin{verbatim}f0=0.5 , \end{verbatim} this line sets the 
-coriolis term, and represents a tank spinning at 2/s
-\item Line 20, \begin{verbatim} beta=1.E-11, \end{verbatim} this line sets
-$\beta$ (the gradient of the coriolis parameter, $f$) to $10^{-11} s^{-1}m^{-1}$
+\item Lines 9-10, \begin{verbatim} 
+viscAh=5.0E-6, 
+viscAz=5.0E-6,
+\end{verbatim} 
+
+
+These lines set the Laplacian friction coefficient in the horizontal
+and vertical, respectively.  Note that they are several orders of
+magnitude smaller than the other examples due to the small scale of
+this example.
+
+\item Lines 13-16, \begin{verbatim} 
+ diffKhT=2.5E-6,
+ diffKzT=2.5E-6,
+ diffKhS=1.0E-6,
+ diffKzS=1.0E-6,
+
+\end{verbatim} 
+
+
+These lines set horizontal and vertical diffusion coefficients for
+temperature and salinity.  Similarly to the friction coefficients, the
+values are a couple of orders of magnitude less than most
+ configurations.
+
 
-\item Lines 27 and 28
+\item Line 17, \begin{verbatim}f0=0.5 , \end{verbatim} this line sets the 
+coriolis term, and represents a tank spinning at about 2.4 rpm.
+
+\item Lines 23 and 24
 \begin{verbatim}
 rigidLid=.TRUE.,
 implicitFreeSurface=.FALSE.,
 \end{verbatim}
 
-qqq these lines do the opposite of the following: 
-suppress the rigid lid formulation of the surface
-pressure inverter and activate the implicit free surface form
+These lines activate  the rigid lid formulation of the surface
+pressure inverter and suppress the implicit free surface form
 of the pressure inverter.
 
-\item Line 44,
+\item Line 40,
 \begin{verbatim}
 nIter=0,
 \end{verbatim}
-this line indicates that the experiment should start from $t=0$
-and implicitly suppresses searching for checkpoint files associated
-with restarting an numerical integration from a previously saved state.
+This line indicates that the experiment should start from $t=0$ and
+implicitly suppresses searching for checkpoint files associated with
+restarting an numerical integration from a previously saved state.
+Instead, the file thetaPol.bin will be loaded to initialized the
+temperature fields as indicated below, and other variables will be
+initialized to their defaults.
+
 
-\item Line 47,
+\item Line 43,
 \begin{verbatim}
 deltaT=0.1,
 \end{verbatim}
-This line sets the integration timestep to $0.1s$.  This is an unsually
-small value among the examples due to the small physical scale of the 
-experiment.
+This line sets the integration timestep to $0.1s$.  This is an
+unsually small value among the examples due to the small physical
+scale of the experiment.  Using the ensemble Kalman filter to produce
+input fields can necessitate even shorter timesteps.
 
-\item Line 58,
+\item Line 56,
 \begin{verbatim}
 usingCylindricalGrid=.TRUE.,
 \end{verbatim}
 This line requests that the simulation be performed in a 
 cylindrical coordinate system.
 
-\item Line 60,
+\item Line 57,
 \begin{verbatim}
 dXspacing=3,
 \end{verbatim}
 This line sets the azimuthal grid spacing between each $x$-coordinate line
 in the discrete grid. The syntax indicates that the discrete grid
-should be comprise of $120$ grid lines each separated by $3^{\circ}$.
-                                                                                
-
+should be comprised of $120$ grid lines each separated by $3^{\circ}$.
+                                                                               
 
-\item Line 61,
+\item Line 58,
 \begin{verbatim}
 dYspacing=0.01,
 \end{verbatim}
-This line sets the radial cylindrical grid spacing between each $a$-coordinate line
-in the discrete grid to $1cm$.
 
-\item Line 62,
+This line sets the radial cylindrical grid spacing between each
+$a$-coordinate line in the discrete grid to $1cm$.
+
+\item Line 59,
 \begin{verbatim}
 delZ=29*0.005,
 \end{verbatim}
-This line sets the vertical grid spacing between each z-coordinate line
-in the discrete grid to $5000m$ ($5$~km).
 
-\item Line 68,
+This line sets the vertical grid spacing between each of 29
+z-coordinate lines in the discrete grid to $0.005m$ ($5$~mm).
+
+\item Line 64,
 \begin{verbatim}
 bathyFile='bathyPol.bin',
 \end{verbatim}
@@ -173,7 +200,7 @@
 and a depth
 f $-0.145m$ indicates the tank itself. 
 
-\item Line 67,
+\item Line 65,
 \begin{verbatim}
 hydrogThetaFile='thetaPol.bin',
 \end{verbatim}
@@ -183,17 +210,19 @@
 ($x,y,z$) map and is enumerated and formatted in the same manner as the 
 bathymetry file. 
 
-\item Line qqq
+\item Lines 66 and 57
 \begin{verbatim}
- tCyl  = 0
+ tCylIn  = 0
+ tCylOut  = 20
 \end{verbatim}
-This line specifies the temperature in degrees Celsius of the interior
-wall of the tank -- usually a bucket of ice water.
+These line specify the temperatures in degrees Celsius of the interior
+and exterior walls of the tank -- typically taken to be icewater on
+the inside and room temperature on the inside.
 
 
 \end{itemize}
 
-\noindent other lines in the file {\it input/data} are standard values
+\noindent Other lines in the file {\it input/data} are standard values
 that are described in the MITgcm Getting Started and MITgcm Parameters
 notes.