--- manual/s_getstarted/text/getting_started.tex	2001/10/21 04:19:40	1.7
+++ manual/s_getstarted/text/getting_started.tex	2001/11/13 20:13:54	1.10
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.7 2001/10/21 04:19:40 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.10 2001/11/13 20:13:54 adcroft Exp $
 % $Name:  $
 
 %\section{Getting started}
@@ -48,7 +48,7 @@
 You can download the model two ways:
 
 \begin{enumerate}
-\item Using CVS software. CVS is a freely available source code managment
+\item Using CVS software. CVS is a freely available source code management
 tool. To use CVS you need to have the software installed. Many systems
 come with CVS pre-installed, otherwise good places to look for
 the software for a particular platform are
@@ -139,7 +139,7 @@
 
 \item \textit{diags}: contains the code relative to time-averaged
 diagnostics. It is subdivided into two subdirectories \textit{inc} and 
-\textit{src} that contain include files (*.\textit{h} files) and fortran
+\textit{src} that contain include files (*.\textit{h} files) and Fortran
 subroutines (*.\textit{F} files), respectively.
 
 \item \textit{doc}: contains brief documentation notes.
@@ -180,40 +180,47 @@
 \section{Example experiments}
 \label{sect:modelExamples}
 
-Now that you have successfully downloaded the model code we recommend that
-you first try to run the examples provided with the base version. You will
-probably want to run the example that is the closest to the configuration
-you will use eventually. The examples are located in subdirectories under
-the directory \textit{verification} and are briefly described below (a full
-description is given in section 2):
+The MITgcm distribution comes with a set of twenty-four pre-configured
+numerical experiments. Some of these examples experiments are tests of 
+individual parts of the model code, but many are fully fledged numerical
+simulations. A few of the examples are used for tutorial documentation
+in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. The other examples
+follow the same general structure as the tutorial examples. However,
+they only include brief instructions in a text file called {\it README}.
+The examples are located in subdirectories under
+the directory \textit{verification}. Each
+example is briefly described below.
 
-\subsection{List of model examples}
+\subsection{Full list of model examples}
 
-\begin{itemize}
+\begin{enumerate}
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with
-free-surface).
+free-surface). This experiment is described in detail in section
+\ref{sect:eg-baro}.
 
-\item \textit{exp1} - 4 layers, ocean double gyre.
+\item \textit{exp1} - Four layer, ocean double gyre. This experiment is described in detail in section
+\ref{sect:eg-baroc}.
 
 \item \textit{exp2} - 4x4 degree global ocean simulation with steady
-climatological forcing.
+climatological forcing. This experiment is described in detail in section
+\ref{sect:eg-global}.
 
-\item \textit{exp4} - flow over a Gaussian bump in open-water or channel
+\item \textit{exp4} - Flow over a Gaussian bump in open-water or channel
 with open boundaries.
 
-\item \textit{exp5} - inhomogenously forced ocean convection in a doubly
+\item \textit{exp5} - Inhomogenously forced ocean convection in a doubly
 periodic box.
 
-\item \textit{front\_relax} - relaxation of an ocean thermal front (test for
+\item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
 Gent/McWilliams scheme). 2D (Y-Z).
 
-\item \textit{internal wave} - ocean internal wave forced by open boundary
+\item \textit{internal wave} - Ocean internal wave forced by open boundary
 conditions.
 
-\item \textit{natl\_box} - eastern subtropical North Atlantic with KPP
+\item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
 scheme; 1 month integration
 
-\item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez
+\item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and Suarez
 '94 forcing.
 
 \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez
@@ -222,24 +229,48 @@
 \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
 Suarez '94 forcing on the cubed sphere.
 
-\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution.
+\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics. Global 
+Zonal Mean configuration, 1x64x5 resolution.
 
 \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. Equatorial Slice configuration.
+physics, equatorial Slice configuration.
 2D (X-Z).
 
 \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. 3D Equatorial Channel
-configuration (not completely tested).
+physics. 3D Equatorial Channel configuration.
 
-\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global configuration, 128x64x5 resolution.
+\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
+Global configuration, on latitude longitude grid with 128x64x5 grid points
+($2.8^\circ{\rm degree}$ resolution).
 
-\item \textit{adjustment.128x64x1}
+\item \textit{adjustment.128x64x1} Barotropic adjustment
+problem on latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm degree}$ resolution).
 
 \item \textit{adjustment.cs-32x32x1}
-\end{itemize}
+Barotropic adjustment
+problem on cube sphere grid with 32x32 points per face ( roughly
+$2.8^\circ{\rm degree}$ resolution).
+
+\item \textit{advect\_cs} Two-dimensional passive advection test on
+cube sphere grid.
+
+\item \textit{advect\_xy} Two-dimensional (horizontal plane) passive advection 
+test on Cartesian grid.
+
+\item \textit{advect\_yz} Two-dimensional (vertical plane) passive advection test on Cartesian grid.
+
+\item \textit{carbon} Simple passive tracer experiment. Includes derivative
+calculation. Described in detail in section \ref{sect:eg-carbon-ad}.
+
+\item \textit{flt\_example} Example of using float package.
+
+\item \textit{global\_ocean.90x40x15} Global circulation with
+GM, flux boundary conditions and poles.
+
+\item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube sphere
+grid.
+
+\end{enumerate}
 
 \subsection{Directory structure of model examples}
 
@@ -266,7 +297,7 @@
 code} depending on the particular experiment. See section 2 for more details.
 
 \item \textit{input}: contains the input data files required to run the
-example. At a mimimum, the \textit{input} directory contains the following
+example. At a minimum, the \textit{input} directory contains the following
 files:
 
 \begin{itemize}
@@ -299,9 +330,9 @@
 To compile the code, we use the {\em make} program. This uses a file
 ({\em Makefile}) that allows us to pre-process source files, specify
 compiler and optimization options and also figures out any file
-dependancies. We supply a script ({\em genmake}), described in section
+dependencies. We supply a script ({\em genmake}), described in section
 \ref{sect:genmake}, that automatically creates the {\em Makefile} for
-you. You then need to build the dependancies and compile the code.
+you. You then need to build the dependencies and compile the code.
 
 As an example, let's assume that you want to build and run experiment
 \textit{verification/exp2}. The are multiple ways and places to actually
@@ -323,7 +354,7 @@
 % ../../../tools/genmake  -mods=../code
 \end{verbatim}
 
-Next, create the dependancies:
+Next, create the dependencies:
 \begin{verbatim}
 % make depend
 \end{verbatim}
@@ -375,7 +406,7 @@
 % cp ../code/mitgcmuv ./
 % ./mitgcmuv > output.txt
 \end{verbatim}
-or if you will be making muliple runs with the same executable:
+or if you will be making multiple runs with the same executable:
 \begin{verbatim}
 % cd ../
 % cp -r input run1
@@ -387,7 +418,7 @@
 \subsubsection{Building from a new directory}
 
 Since the {\em input} directory contains input files it is often more
-useful to keep {\em input} prestine and build in a new directory
+useful to keep {\em input} pristine and build in a new directory
 within {\em verification/exp2/}:
 \begin{verbatim}
 % cd verification/exp2