/[MITgcm]/manual/s_examples/text/model_examples.tex

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-revision 1.6 by edhill,
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+revision 1.15 by jahn,
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  % $Header$
  % $Name$
- \section{Tutorials}
+ \section[MITgcm Example Experiments]{Example experiments}
- \label{sect:tutorials}
+ \label{sect:modelExamples}
- \label{www:tutorials}
+ \begin{rawhtml}
+ <!-- CMIREDIR:modelExamples: -->
+ \end{rawhtml}
+ %% a set of pre-configured numerical experiments
+ The full MITgcm distribution comes with a set of 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. Full tutorials exist for a few of the examples,
+ and are documented in sections \ref{sect:eg-baro} -
+ \ref{sect:eg-tank}. 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{advection\_in\_gyre\_circulation} - test of various
+   advection schemes in a single-layer double-gyre experiment.
+   This experiment is described in detail in section
+   \ref{sect:eg-adv-gyre}.
+ \item \texttt{tutorial\_barotropic\_gyre} - single layer, ocean double
+   gyre (barotropic with free-surface). This experiment is described in
+   detail in section \ref{sect:eg-baro}.
+ \item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double
+   gyre. This experiment is described in detail in section
+   \ref{sect:eg-fourlayer}.
+ \item \texttt{tutorial\_global\_oce\_latlon} - 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{tutorial\_deep\_convection} - Inhomogenously forced
+   ocean convection in a doubly periodic box. This experiment is
+   described in detail in section \ref{sect:eg-bconv}.
+ \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{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics
+   using Held and Suarez (1994) forcing on the cubed sphere.  This
+   experiment is described in detail in section \ref{sect:eg-hs}.
+ \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{aim.5l\_cs}
+ \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\_xz} Two-dimensional (vertical plane) passive
+   advection test on Cartesian grid.
+ \item \texttt{tutorial\_tracer\_adjsens} Simple passive tracer
+   experiment. Includes derivative calculation. This experiment is
+   described in detail in section \ref{sect:eg-simple-tracer}.
+ \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{tutorial\_global\_oce\_in\_p} 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.
+ \item \texttt{tutorial\_plume\_on\_slope} Gravity Plume on a
+   continental slope.  This experiment is described in detail in
+   section \ref{sect:eg-gravityplume}.
+ \item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to
+   the dissolved inorganic carbon biogeochemistry model. This
+   experiment is described in detail in section
+   \ref{sect:eg-biogeochem_tutorial}.
+ \item \texttt{tutorial\_global\_oce\_optim} Global ocean state
+   estimation at $4^\circ$ resolution.  This experiment is described in
+   detail in section \ref{sect:eg-global_state_estimate}.
+ \item \texttt{tutorial\_offline} Offline form of the MITgcm to study
+   advection of a passive tracer.  This experiment is described in
+   detail in section \ref{sect:eg-offline}.
+ \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
+   coordinates.  This experiment is described in detail in section
+   \ref{sect:eg-tank}.
+ \item \texttt{MLAdjust} Simple test for different viscosity formulations.
+ \item \texttt{bottom\_ctrl\_5x5} Adjoint test using the bottom
+   topography as the control parameter.
+ \item \texttt{cfc\_example} Global ocean with online computation and
+   advection of CFC11 and CFC12.
+ \item \texttt{dome} Idealized 3D test of a density-driven bottom current.
+ \item \texttt{exp2} Old version of the global ocean experiment.
+ \item \texttt{exp5} Deep convection.
+ \item \texttt{fizhi-cs-32x32x10} Global atmospheric simulation with
+   realistic topography, 10 vertical levels, a cubed sphere grid and
+   the full atmospheric physics package.
+ \item \texttt{fizhi-cs-aqualev20} Global atmospheric simulation on an
+   aqua planet with full atmospheric physics. Run is perpetual march
+   with an analytical SST distribution.  This is the configuration for
+   the APE (Aqua Planet Experiment) participation experiment.
+ \item \texttt{fizhi-gridalt-hs} Global atmospheric simulation
+   Held-Suarez (1994) forcing, with the physical forcing and the
+   dynamical forcing running on different vertical grids.
+ \item \texttt{global\_ocean.cs32x15} Global ocean experiment on the
+   cubed sphere grid, using thermodynamic sea ice and bulk force
+   packages.
+ \item \texttt{global\_ocean\_ebm} Global ocean experiment on a lat-lon
+   grid coupled to an atmospheric energy balance model. Similar to
+   global\_ocean.90x40x15 experiment.
+ \item \texttt{global\_with\_exf} Global ocean experiment on a lat-lon
+   grid using the exf package. Similar to global\_ocean.90x40x15
+   experiment.
+ \item \texttt{hs94.cs-32x32x5} 3D atmosphere dynamics using Held and
+   Suarez (1994) forcing on the cubed sphere. 5 vertical levels.
+ \item \texttt{ideal\_2D\_oce} Idealized 2D global ocean simulation on
+   an aqua planet.
+ \item \texttt{inverted\_barometer} Simple test of ocean response to
+   atmospheric pressure loading.
+ \item \texttt{lab\_sea} Regional Labrador Sea simulation on a lat-lon
+   grid. Coupled to the sea ice model.
+ \item \texttt{matrix\_example} Test of experimental method to
+   accelerated convergence towards equillibrium.
+ \item \texttt{tutorial\_cfc\_offline} Offline form of the MITgcm to
+   study advection of a passive tracer and CFCs.
+ \item \texttt{vermix} Simple test in a small domain (3 columns) for
+   ocean vertical mixing schemes.
+ \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
+   the verification directories refered to in this chapter 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.
+ \item \texttt{build}: this directory is where the model is compiled
+   and loaded, and where the executable resides.
+ \end{itemize}
+ Once you have chosen the example you want to run, you are ready to
+ compile the code.
+ \newpage
+ \input{part3/case_studies/advection_in_gyre_circulation/adv_gyre.tex}
+ \newpage
  \input{part3/case_studies/barotropic_gyre/baro.tex}
  \newpage
-Line 18
+Line 284
  \input{part3/case_studies/ogcm_in_pressure/ogcm_in_pressure.tex}
  \newpage
- \input{part3/case_studies/hs_atmosphere/hs_atmos.tex}
+ \input{part3/case_studies/held_suarez_cs/held_suarez_cs.tex}
  \newpage
  \input{part3/case_studies/doubly_periodic_convection/convection.tex}
-Line 32
+Line 298
  \newpage
  \input{part3/case_studies/biogeochem_tutorial/biogeochem.tex}
- \begin{versionprivate}
+ \newpage
+ \input{part3/case_studies/global_oce_estimation/global_oce_estimation.tex}
+ \newpage
+ \input{part3/case_studies/sens_airsea_tracer/doc_ad_examples.tex}
+ \newpage
+ \input{part3/case_studies/offline/offline_tutorial.tex}
  \newpage
  \input{part3/case_studies/rotating_tank/tank.tex}
- \end{versionprivate}

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