--- manual/s_getstarted/text/getting_started.tex	2001/11/13 20:13:54	1.10
+++ 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 1.10 2001/11/13 20:13:54 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}
@@ -18,31 +18,42 @@
 \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}
+http://mitgcm.org/mailman/listinfo/mitgcm-support/
+http://mitgcm.org/pipermail/mitgcm-support/
+\end{verbatim}
+\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}
-news://mitgcm.org/mitgcm.support
+http://mitgcm.org/htdig/
 \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}
+%%% 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:support@mitgcm.org> \end{rawhtml}
-support@mitgcm.org
+\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:
@@ -72,30 +83,52 @@
 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/gcmpack
+\end{verbatim}
+in your .cshrc or .tcshrc file.  For bash or sh shells, put:
 \begin{verbatim}
-% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
 \end{verbatim}
+in your .profile or .bashrc file.
 
-To start using CVS, register with the MITgcm CVS server using command:
+
+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 sources for release1 type:
+To obtain the latest sources type:
+\begin{verbatim}
+% cvs co MITgcm
+\end{verbatim}
+or to get a specific release type:
 \begin{verbatim}
-% cvs co -d directory -P -r release1 MITgcmUV
+% cvs co -d directory -P -r release1_beta1 MITgcm
 \end{verbatim}
+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}
+http://mitgcm.org/source_code.html
+\end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
+
 
-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}!
-You can also use CVS to download code updates.  More extensive
-information on using CVS for maintaining MITgcm code can be found 
+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} 
@@ -106,7 +139,7 @@
 \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/
@@ -114,19 +147,84 @@
 \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%
@@ -160,7 +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.
@@ -180,95 +278,102 @@
 \section{Example experiments}
 \label{sect:modelExamples}
 
-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.
+%% a set of twenty-four pre-configured numerical experiments
+
+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.
 
 \subsection{Full list of model examples}
 
 \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}.
+  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. 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.
+  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{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{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.
-
+  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. Global 
-Zonal Mean configuration, 1x64x5 resolution.
-
-\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric
-physics, 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. 3D Equatorial Channel configuration.
-
+  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).
-
+  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}.
+  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.
+  
+\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.
 
 \end{enumerate}
 
@@ -281,35 +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 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.
+  ``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
@@ -804,43 +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}
 
@@ -1073,3 +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: