--- manual/s_getstarted/text/getting_started.tex	2001/10/18 18:44:14	1.6
+++ manual/s_getstarted/text/getting_started.tex	2004/01/28 20:50:14	1.15
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.6 2001/10/18 18:44:14 adcroft Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.15 2004/01/28 20:50:14 edhill Exp $
 % $Name:  $
 
 %\section{Getting started}
@@ -18,87 +18,213 @@
 \section{Where to find information}
 \label{sect:whereToFindInfo}
 
-A web site is maintained for release 1 (Sealion) of MITgcm:
+A web site is maintained for release 2 (``Pelican'') of MITgcm:
+\begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
 \begin{verbatim}
-http://mitgcm.org/sealion
+http://mitgcm.org/pelican
 \end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
 Here you will find an on-line version of this document, a
 ``browsable'' copy of the code and a searchable database of the model
 and site, as well as links for downloading the model and
-documentation, to data-sources and other related sites.
+documentation, to data-sources, and other related sites.
 
-There is also a support news group for the model that you can email at
-\texttt{support@mitgcm.org} or browse at:
+There is also a web-archived support mailing list for the model that
+you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
+\begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
 \begin{verbatim}
-news://mitgcm.org/mitgcm.support
+http://mitgcm.org/mailman/listinfo/mitgcm-support/
+http://mitgcm.org/pipermail/mitgcm-support/
 \end{verbatim}
-A mail to the email list will reach all the developers and be archived
-on the newsgroup. A users email list will be established at some time
-in the future.
+\begin{rawhtml} </A> \end{rawhtml}
+Essentially all of the MITgcm web pages can be searched using a
+popular web crawler such as Google or through our own search facility:
+\begin{verbatim}
+http://mitgcm.org/htdig/
+\end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
+%%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
+
 
 
 \section{Obtaining the code}
 \label{sect:obtainingCode}
 
+MITgcm can be downloaded from our system by following
+the instructions below. As a courtesy we ask that you send e-mail to us at
+\begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml}
+MITgcm-support@mitgcm.org
+\begin{rawhtml} </A> \end{rawhtml}
+to enable us to keep track of who's using the model and in what application.
+You can download the model two ways:
+
+\begin{enumerate}
+\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
+\begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml}
+cvshome.org
+\begin{rawhtml} </A> \end{rawhtml}
+and
+\begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml}
+wincvs.org
+\begin{rawhtml} </A> \end{rawhtml}
+.
+
+\item Using a tar file. This method is simple and does not
+require any special software. However, this method does not
+provide easy support for maintenance updates.
+
+\end{enumerate}
+
 If CVS is available on your system, we strongly encourage you to use it. CVS
 provides an efficient and elegant way of organizing your code and keeping
 track of your changes. If CVS is not available on your machine, you can also
 download a tar file.
 
-Before you can use CVS, the following environment variable has to be set in
-your .cshrc or .tcshrc:
+Before you can use CVS, the following environment variable(s) should
+be set within your shell.  For a csh or tcsh shell, put the following 
 \begin{verbatim}
-% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
 \end{verbatim}
+in your .cshrc or .tcshrc file.  For bash or sh shells, put:
+\begin{verbatim}
+% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
+\end{verbatim}
+in your .profile or .bashrc file.
+
 
-To start using CVS, "login" to the server using:
+To get MITgcm through CVS, first register with the MITgcm CVS server
+using command:
 \begin{verbatim}
 % cvs login ( CVS password: cvsanon )
 \end{verbatim}
-You only need to do ``cvs login'' once.
+You only need to do a ``cvs login'' once.
 
-To obtain the source for the release:
+To obtain the latest sources type:
 \begin{verbatim}
-% cvs co -d directory -P -r release1 MITgcmUV
+% cvs co MITgcm
 \end{verbatim}
-
-This creates a directory called \textit{directory}. If \textit{directory}
-exists this command updates your code based on the repository. Each
-directory in the source tree contains a directory \textit{CVS}. This
-information is required by CVS to keep track of your file versions with
-respect to the repository. Don't edit the files in \textit{CVS}! To obtain a
-different \textit{version} that is not the latest source:
+or to get a specific release type:
 \begin{verbatim}
-% cvs co -d directory -P -r version MITgcm
+% cvs co -d directory -P -r release1_beta1 MITgcm
 \end{verbatim}
-or the latest development version:
+The MITgcm web site contains further directions concerning the source
+code and CVS.  It also contains a web interface to our CVS archive so
+that one may easily view the state of files, revisions, and other
+development milestones:
+\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
 \begin{verbatim}
-% cvs co -d directory -P MITgcm
+http://mitgcm.org/source_code.html
 \end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
+
+
+The checkout process creates a directory called \textit{MITgcm}. If
+the directory \textit{MITgcm} exists this command updates your code
+based on the repository. Each directory in the source tree contains a
+directory \textit{CVS}. This information is required by CVS to keep
+track of your file versions with respect to the repository. Don't edit
+the files in \textit{CVS}!  You can also use CVS to download code
+updates.  More extensive information on using CVS for maintaining
+MITgcm code can be found
+\begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}
+here
+\begin{rawhtml} </A> \end{rawhtml} 
+.
+
 
 \paragraph*{Conventional download method}
 \label{sect:conventionalDownload}
 
 If you do not have CVS on your system, you can download the model as a
-tar file from the reference web site at:
+tar file from the web site at:
+\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
 \begin{verbatim}
 http://mitgcm.org/download/
 \end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
 The tar file still contains CVS information which we urge you not to
 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.
+us if you should need to send us your copy of the code.  If a recent
+tar file does not exist, then please contact the developers through
+the MITgcm-support list.
+
+\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 such as:
+\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%
@@ -111,7 +237,7 @@
 
 \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.
@@ -132,7 +258,7 @@
 in detail in section 3.
 
 \item \textit{tools}: this directory contains various useful tools. For
-example, \textit{genmake} is a script written in csh (C-shell) that should
+example, \textit{genmake2} is a script written in csh (C-shell) that should
 be used to generate your makefile. The directory \textit{adjoint} contains
 the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that
 generates the adjoint code. The latter is described in details in part V.
@@ -152,66 +278,104 @@
 \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):
+%% a set of twenty-four pre-configured numerical experiments
 
-\subsection{List of model examples}
+The MITgcm distribution comes with more than a dozen pre-configured
+numerical experiments. Some of these example 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.
 
-\begin{itemize}
-\item \textit{exp0} - single layer, ocean double gyre (barotropic with
-free-surface).
+\subsection{Full list of model examples}
 
-\item \textit{exp1} - 4 layers, ocean double gyre.
+\begin{enumerate}
+\item \textit{exp0} - single layer, ocean double gyre (barotropic with
+  free-surface). This experiment is described in detail in section
+  \ref{sect:eg-baro}.
 
+\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 with open boundaries.
+  
+\item \textit{exp5} - Inhomogenously forced ocean convection in a
+  doubly periodic box.
 
-\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
-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
-conditions.
-
-\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
-'94 forcing.
-
-\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez
-'94 forcing.
-
+\item \textit{internal wave} - Ocean internal wave forced by open
+  boundary conditions.
+  
+\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 '94 forcing.
+  
+\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
+  Suarez '94 forcing.
+  
 \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\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. Equatorial Slice configuration.
-2D (X-Z).
-
+  Suarez '94 forcing on the cubed sphere.
+  
+\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, 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.
+  Global configuration, on latitude longitude grid with 128x64x5 grid
+  points ($2.8^\circ{\rm degree}$ resolution).
+  
+\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} 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{global\_ocean\_pressure} Global circulation in pressure
+  coordinate (non-Boussinesq ocean model). Described in detail in
+  section \ref{sect:eg-globalpressure}.
+  
+\item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
+  sphere grid.
 
-\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global configuration, 128x64x5 resolution.
-
-\item \textit{adjustment.128x64x1}
-
-\item \textit{adjustment.cs-32x32x1}
-\end{itemize}
+\end{enumerate}
 
 \subsection{Directory structure of model examples}
 
@@ -222,35 +386,37 @@
 minimum, this directory includes the following files:
 
 \begin{itemize}
-\item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the
-``execution environment'' part of the code. The default version is located
-in \textit{eesupp/inc}.
-
+\item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+  the ``execution environment'' part of the code. The default version
+  is located in \textit{eesupp/inc}.
+  
 \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the
-``numerical model'' part of the code. The default version is located in 
-\textit{model/inc}.
-
-\item \textit{code/SIZE.h}: declares size of underlying computational grid.
-The default version is located in \textit{model/inc}.
-\end{itemize}
-
-In addition, other include files and subroutines might be present in \textit{%
-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
-files:
-
-\begin{itemize}
-\item \textit{input/data}: this file, written as a namelist, specifies the
-main parameters for the experiment.
-
-\item \textit{input/data.pkg}: contains parameters relative to the packages
-used in the experiment.
-
-\item \textit{input/eedata}: this file contains ``execution environment''
-data. At present, this consists of a specification of the number of threads
-to use in $X$ and $Y$ under multithreaded execution.
+  ``numerical model'' part of the code. The default version is located
+  in \textit{model/inc}.
+  
+\item \textit{code/SIZE.h}: declares size of underlying computational
+  grid.  The default version is located in \textit{model/inc}.
+\end{itemize}
+
+In addition, other include files and subroutines might be present in
+\textit{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 minimum, the \textit{input} directory contains the
+  following files:
+
+\begin{itemize}
+\item \textit{input/data}: this file, written as a namelist, specifies
+  the main parameters for the experiment.
+  
+\item \textit{input/data.pkg}: contains parameters relative to the
+  packages used in the experiment.
+  
+\item \textit{input/eedata}: this file contains ``execution
+  environment'' data. At present, this consists of a specification of
+  the number of threads to use in $X$ and $Y$ under multithreaded
+  execution.
 \end{itemize}
 
 In addition, you will also find in this directory the forcing and topography
@@ -271,9 +437,9 @@
 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
@@ -295,7 +461,7 @@
 % ../../../tools/genmake  -mods=../code
 \end{verbatim}
 
-Next, create the dependancies:
+Next, create the dependencies:
 \begin{verbatim}
 % make depend
 \end{verbatim}
@@ -347,7 +513,7 @@
 % 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
@@ -359,7 +525,7 @@
 \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
@@ -745,43 +911,70 @@
 \item time-discretization
 \end{itemize}
 
-The time steps are set through the real variables \textbf{deltaTMom }and 
-\textbf{deltaTtracer }(in s) which represent the time step for the momentum
-and tracer equations, respectively. For synchronous integrations, simply set
-the two variables to the same value (or you can prescribe one time step only
-through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing
-parameter is set through the variable \textbf{abEps }(dimensionless). The
-stagger baroclinic time stepping can be activated by setting the logical
-variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.
+The time steps are set through the real variables \textbf{deltaTMom}
+and \textbf{deltaTtracer} (in s) which represent the time step for the
+momentum and tracer equations, respectively. For synchronous
+integrations, simply set the two variables to the same value (or you
+can prescribe one time step only through the variable
+\textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
+through the variable \textbf{abEps} (dimensionless). The stagger
+baroclinic time stepping can be activated by setting the logical
+variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
 
 \subsection{Equation of state}
 
-First, because the model equations are written in terms of perturbations, a
-reference thermodynamic state needs to be specified. This is done through
-the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }%
-specifies the reference potential temperature profile (in $^{o}$C for
-the ocean and $^{o}$K for the atmosphere) starting from the level
-k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity
-profile (in ppt) for the ocean or the reference specific humidity profile
-(in g/kg) for the atmosphere.
-
-The form of the equation of state is controlled by the character variables 
-\textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%
-buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and
-needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In
-this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.
-For the ocean, two forms of the equation of state are available: linear (set 
-\textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial
-approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\ 
-}to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the
-thermal and haline expansion coefficients represented by the variables 
-\textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$%
-^{-1}$). For the nonlinear case, you need to generate a file of polynomial
-coefficients called \textit{POLY3.COEFFS. }To do this, use the program 
-\textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is
-available in the same directory and you will need to edit the number and the
-values of the vertical levels in \textit{knudsen2.f }so that they match
-those of your configuration). \textit{\ }
+First, because the model equations are written in terms of
+perturbations, a reference thermodynamic state needs to be specified.
+This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
+\textbf{tRef} specifies the reference potential temperature profile
+(in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
+from the level k=1. Similarly, \textbf{sRef} specifies the reference
+salinity profile (in ppt) for the ocean or the reference specific
+humidity profile (in g/kg) for the atmosphere.
+
+The form of the equation of state is controlled by the character
+variables \textbf{buoyancyRelation} and \textbf{eosType}.
+\textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
+needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
+In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'.
+For the ocean, two forms of the equation of state are available:
+linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
+approximation to the full nonlinear equation ( set
+\textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
+case, you need to specify the thermal and haline expansion
+coefficients represented by the variables \textbf{tAlpha}\textit{\ 
+  }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
+case, you need to generate a file of polynomial coefficients called
+\textit{POLY3.COEFFS}. To do this, use the program
+\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
+available in the same directory and you will need to edit the number
+and the values of the vertical levels in \textit{knudsen2.f} so that
+they match those of your configuration).
+
+There there are also higher polynomials for the equation of state:
+\begin{description}
+\item['\texttt{UNESCO}':] The UNESCO equation of state formula of
+  Fofonoff and Millard \cite{fofonoff83}. This equation of state
+  assumes in-situ temperature, which is not a model variable; \emph{its use
+  is therefore discouraged, and it is only listed for completeness}.
+\item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and
+  McDougall \cite{jackett95}, which uses the model variable potential
+  temperature as input. The '\texttt{Z}' indicates that this equation
+  of state uses a horizontally and temporally constant pressure
+  $p_{0}=-g\rho_{0}z$. 
+\item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and
+  McDougall \cite{jackett95}, which uses the model variable potential
+  temperature as input. The '\texttt{P}' indicates that this equation
+  of state uses the actual hydrostatic pressure of the last time
+  step. Lagging the pressure in this way requires an additional pickup
+  file for restarts.
+\item['\texttt{MDJWF}':] The new, more accurate and less expensive
+  equation of state by McDougall et~al. \cite{mcdougall03}. It also
+  requires lagging the pressure and therefore an additional pickup
+  file for restarts.
+\end{description}
+For none of these options an reference profile of temperature or
+salinity is required.
 
 \subsection{Momentum equations}
 
@@ -1014,3 +1207,8 @@
 The precision with which to write the binary data is controlled by the
 integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
 64}).
+
+%%% Local Variables: 
+%%% mode: latex
+%%% TeX-master: t
+%%% End: