--- manual/s_getstarted/text/getting_started.tex	2001/10/21 04:19:40	1.7
+++ manual/s_getstarted/text/getting_started.tex	2001/12/05 15:49:39	1.12
@@ -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 1.12 2001/12/05 15:49:39 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
@@ -86,7 +86,7 @@
 
 To obtain the sources for release1 type:
 \begin{verbatim}
-% cvs co -d directory -P -r release1 MITgcmUV
+% cvs co -d directory -P -r release1_beta1 MITgcm
 \end{verbatim}
 
 This creates a directory called \textit{directory}. If \textit{directory}
@@ -116,17 +116,80 @@
 delete; even if you do not use CVS yourself the information can help
 us if you should need to send us your copy of the code.
 
+\paragraph*{Upgrading from an earlier version}
+
+If you already have an earlier version of the code you can ``upgrade''
+your copy instead of downloading the entire repository again. First,
+``cd'' (change directory) to the top of your working copy:
+\begin{verbatim}
+% cd MITgcm
+\end{verbatim}
+and then issue the cvs update command:
+\begin{verbatim}
+% cvs -q update -r release1_beta1 -d -P
+\end{verbatim}
+This will update the ``tag'' to ``release1\_beta1'', add any new
+directories (-d) and remove any empty directories (-P). The -q option
+means be quiet which will reduce the number of messages you'll see in
+the terminal. If you have modified the code prior to upgrading, CVS
+will try to merge your changes with the upgrades. If there is a
+conflict between your modifications and the upgrade, it will report
+that file with a ``C'' in front, e.g.:
+\begin{verbatim}
+C model/src/ini_parms.F
+\end{verbatim}
+If the list of conflicts scrolled off the screen, you can re-issue the
+cvs update command and it will report the conflicts. Conflicts are
+indicated in the code by the delimites ``<<<<<<<'', ``======='' and
+``>>>>>>>''. For example,
+\begin{verbatim}
+<<<<<<< ini_parms.F
+     & bottomDragLinear,myOwnBottomDragCoefficient,
+=======
+     & bottomDragLinear,bottomDragQuadratic,
+>>>>>>> 1.18
+\end{verbatim}
+means that you added ``myOwnBottomDragCoefficient'' to a namelist at
+the same time and place that we added ``bottomDragQuadratic''. You
+need to resolve this conflict and in this case the line should be
+changed to:
+\begin{verbatim}
+     & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
+\end{verbatim}
+and the lines with the delimiters (<<<<<<,======,>>>>>>) be deleted.
+Unless you are making modifications which exactly parallel
+developments we make, these types of conflicts should be rare.
+
+\paragraph*{Upgrading to the current pre-release version}
+
+We don't make a ``release'' for every little patch and bug fix in
+order to keep the frequency of upgrades to a minimum. However, if you
+have run into a problem for which ``we have already fixed in the
+latest code'' and we haven't made a ``tag'' or ``release'' since that
+patch then you'll need to get the latest code:
+\begin{verbatim}
+% cvs -q update -A -d -P
+\end{verbatim}
+Unlike, the ``check-out'' and ``update'' procedures above, there is no
+``tag'' or release name. The -A tells CVS to upgrade to the
+very latest version. As a rule, we don't recommend this since you
+might upgrade while we are in the processes of checking in the code so
+that you may only have part of a patch. Using this method of updating
+also means we can't tell what version of the code you are working
+with. So please be sure you understand what you're doing.
+
 \section{Model and directory structure}
 
-The ``numerical'' model is contained within a execution environment support
-wrapper. This wrapper is designed to provide a general framework for
-grid-point models. MITgcmUV is a specific numerical model that uses the
-framework. Under this structure the model is split into execution
-environment support code and conventional numerical model code. The
-execution environment support code is held under the \textit{eesupp}
-directory. The grid point model code is held under the \textit{model}
-directory. Code execution actually starts in the \textit{eesupp} routines
-and not in the \textit{model} routines. For this reason the top-level 
+The ``numerical'' model is contained within a execution environment
+support wrapper. This wrapper is designed to provide a general
+framework for grid-point models. MITgcmUV is a specific numerical
+model that uses the framework. Under this structure the model is split
+into execution environment support code and conventional numerical
+model code. The execution environment support code is held under the
+\textit{eesupp} directory. The grid point model code is held under the
+\textit{model} directory. Code execution actually starts in the
+\textit{eesupp} routines and not in the \textit{model} routines. For
+this reason the top-level
 \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
 end-users should not need to worry about this level. The top-level routine
 for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
@@ -139,7 +202,7 @@
 
 \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 +243,47 @@
 \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 +292,48 @@
 \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 +360,7 @@
 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 +393,9 @@
 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 +417,7 @@
 % ../../../tools/genmake  -mods=../code
 \end{verbatim}
 
-Next, create the dependancies:
+Next, create the dependencies:
 \begin{verbatim}
 % make depend
 \end{verbatim}
@@ -375,7 +469,7 @@
 % 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 +481,7 @@
 \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
