--- manual/s_getstarted/text/getting_started.tex 2006/04/20 22:09:08 1.35 +++ manual/s_getstarted/text/getting_started.tex 2006/06/27 19:08:22 1.36 @@ -1,4 +1,4 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.35 2006/04/20 22:09:08 molod Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.36 2006/06/27 19:08:22 molod Exp $ % $Name: $ %\section{Getting started} @@ -334,177 +334,6 @@ \end{itemize} -\section[MITgcm Example Experiments]{Example experiments} -\label{sect:modelExamples} -\begin{rawhtml} - -\end{rawhtml} - -%% a set of twenty-four pre-configured numerical experiments - -The full 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 \texttt{verification}. -Each example is briefly described below. - -\subsection{Full list of model examples} - -\begin{enumerate} - -\item \texttt{exp0} - single layer, ocean double gyre (barotropic with - free-surface). This experiment is described in detail in section - \ref{sect:eg-baro}. - -\item \texttt{exp1} - Four layer, ocean double gyre. This experiment - is described in detail in section \ref{sect:eg-baroc}. - -\item \texttt{exp2} - 4x4 degree global ocean simulation with steady - climatological forcing. This experiment is described in detail in - section \ref{sect:eg-global}. - -\item \texttt{exp4} - Flow over a Gaussian bump in open-water or - channel with open boundaries. - -\item \texttt{exp5} - Inhomogenously forced ocean convection in a - doubly periodic box. - -\item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for -Gent/McWilliams scheme). 2D (Y-Z). - -\item \texttt{internal wave} - Ocean internal wave forced by open - boundary conditions. - -\item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP - scheme; 1 month integration - -\item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and - Suarez '94 forcing. - -\item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and - Suarez '94 forcing. - -\item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and - Suarez '94 forcing on the cubed sphere. - -\item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics. - Global Zonal Mean configuration, 1x64x5 resolution. - -\item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate - Atmospheric physics, equatorial Slice configuration. 2D (X-Z). - -\item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric - physics. 3D Equatorial Channel configuration. - -\item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics. - Global configuration, on latitude longitude grid with 128x64x5 grid - points ($2.8^\circ$ resolution). - -\item \texttt{adjustment.128x64x1} Barotropic adjustment problem on - latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution). - -\item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on - cube sphere grid with 32x32 points per face (roughly $2.8^\circ$ - resolution). - -\item \texttt{advect\_cs} Two-dimensional passive advection test on - cube sphere grid. - -\item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive - advection test on Cartesian grid. - -\item \texttt{advect\_yz} Two-dimensional (vertical plane) passive - advection test on Cartesian grid. - -\item \texttt{carbon} Simple passive tracer experiment. Includes - derivative calculation. Described in detail in section - \ref{sect:eg-carbon-ad}. - -\item \texttt{flt\_example} Example of using float package. - -\item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux - boundary conditions and poles. - -\item \texttt{global\_ocean\_pressure} Global circulation in pressure - coordinate (non-Boussinesq ocean model). Described in detail in - section \ref{sect:eg-globalpressure}. - -\item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube - sphere grid. - -\end{enumerate} - -\subsection{Directory structure of model examples} - -Each example directory has the following subdirectories: - -\begin{itemize} -\item \texttt{code}: contains the code particular to the example. At a - minimum, this directory includes the following files: - - \begin{itemize} - \item \texttt{code/packages.conf}: declares the list of packages or - package groups to be used. If not included, the default version - is located in \texttt{pkg/pkg\_default}. Package groups are - simply convenient collections of commonly used packages which are - defined in \texttt{pkg/pkg\_default}. Some packages may require - other packages or may require their absence (that is, they are - incompatible) and these package dependencies are listed in - \texttt{pkg/pkg\_depend}. - - \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to - the ``execution environment'' part of the code. The default - version is located in \texttt{eesupp/inc}. - - \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to - the ``numerical model'' part of the code. The default version is - located in \texttt{model/inc}. - - \item \texttt{code/SIZE.h}: declares size of underlying - computational grid. The default version is located in - \texttt{model/inc}. - \end{itemize} - - In addition, other include files and subroutines might be present in - \texttt{code} depending on the particular experiment. See Section 2 - for more details. - -\item \texttt{input}: contains the input data files required to run - the example. At a minimum, the \texttt{input} directory contains the - following files: - - \begin{itemize} - \item \texttt{input/data}: this file, written as a namelist, - specifies the main parameters for the experiment. - - \item \texttt{input/data.pkg}: contains parameters relative to the - packages used in the experiment. - - \item \texttt{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 files as well as the files describing the initial state - of the experiment. This varies from experiment to experiment. See - section 2 for more details. - -\item \texttt{results}: this directory contains the output file - \texttt{output.txt} produced by the simulation example. This file is - useful for comparison with your own output when you run the - experiment. -\end{itemize} - -Once you have chosen the example you want to run, you are ready to -compile the code. - \section[Building MITgcm]{Building the code} \label{sect:buildingCode} \begin{rawhtml}