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

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-revision 1.24 by jmc,
Wed May 11 19:17:52 2011 UTC
+revision 1.25 by jmc,
Tue Mar 26 13:21:28 2013 UTC
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 Each example is briefly described below.
  \subsection{Full list of model examples}
  \begin{enumerate}
  \item \texttt{tutorial\_advection\_in\_gyre} - Test of various
    advection schemes in a single-layer double-gyre experiment.
    This experiment is described in detail in section
 Line 34 
 Each example is briefly described below.
    \ref{sec:eg-fourlayer}.
  \item \texttt{tutorial\_barotropic\_gyre} - Single layer, ocean double
    gyre (barotropic with free-surface).
    This experiment is described in detail in section \ref{sec:eg-baro}.
  \item \texttt{tutorial\_cfc\_offline} - Offline form of the MITgcm to
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 Each example is briefly described below.
  \item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics
    using Held and Suarez (1994) forcing on cubed sphere grid.  This
    experiment is described in detail in section \ref{sec:eg-hs}.
  \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{sec:eg-offline}.
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 Each example is briefly described below.
  \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).\\
    Also contains a non-linear free-surface adjustment version ({\it input.nlfs/}).
  \item \texttt{advect\_cs} Two-dimensional passive advection test on
    cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$)
  \item \texttt{advect\_xy} - Two-dimensional (horizontal plane) passive
    advection test on Cartesian grid.\\
    Also contains an additional set-up using Adams-Bashforth 3 ({\it input.ab3\_c4/}).
  \item \texttt{advect\_xz} - Two-dimensional (vertical plane) passive
    advection test on Cartesian grid.
  \item \texttt{aim.5l\_Equatorial\_Channel}
    - 5-levels Intermediate Atmospheric physics,
 D Equatorial Channel configuration.
  \item \texttt{aim.5l\_LatLon} - 5-levels Intermediate Atmospheric physics,
    Global configuration, on latitude longitude grid with 128x64x5 grid
    points ($2.8^\circ$ resolution).
  \item \texttt{aim.5l\_cs} - 5-levels Intermediate Atmospheric physics,
    Global configuration on cube sphere grid
    (32x32 grid points per face, roughly $2.8^\circ$).\\
    Also contains an additional set-up with an ocean mixed layer and thermodynamics
    sea-ice ({\it input.thSI/}).
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 Each example is briefly described below.
  \item \texttt{cfc\_example} - Global ocean with online computation and
    advection of CFC11 and CFC12.
  \item \texttt{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic
    configuration on cubed-sphere cs32 horizontal grid,
    using Intermediate Atmospheric physics ({\it pkg/aim\_v23})
    thermodynamics seaice ({\it pkg/thsice}) and land packages.
    on cubed-sphere cs32 in a realistics configuration.
  \item \texttt{cpl\_atm2d+ocn} - Coupled Ocean - Atmosphere realistic
    configuration using 2-D Atmospheric Model ({\it pkg/atm2d}).
  \item \texttt{deep\_anelastic} - Convection simulation on a giant planet:
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 Each example is briefly described below.
  \item \texttt{dome} - Idealized 3D test of a density-driven bottom current.
  \item \texttt{exp2} - Old version of the global ocean experiment (no GM,
        no partial-cells).\\
    Also contains an additional set-up with ridid-lid ({\it input.rigidLid/}).
  \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
    channel with open boundaries.
  \item \texttt{exp5} - Deep convection.
  \item \texttt{fizhi-cs-32x32x40} - Global atmospheric simulation with
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 Each example is briefly described below.
    dynamical forcing running on different vertical grids.
  \item \texttt{flt\_example} - Example of using float package.
  \item \texttt{front\_relax} - Relaxation of an ocean thermal front
    (test for Gent/McWilliams scheme). 2D (Y-Z).\\
    Also contains an additional set-up with Mixed-Layer Eddy parameterization
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 Each example is briefly described below.
  \item \texttt{global2x2\_tot} - ECCO production configuration version 0
  \item \texttt{global\_ocean.90x40x15} Global ocean simulation at 4x4
    degree resolution. Similar to tutorial\_global\_oce\_latlon, with
    quasi-non-hydrostatics and non-hydrostatic metric terms.\\
    Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
  \item \texttt{global\_ocean.cs32x15} - Global ocean experiment on the
    cubed sphere grid.\\
    Also contains additional set-ups:
    \begin{enumerate}
     \item non-hydrostratic with biharmonic viscosity ({\it input.viscA4/})
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 Each example is briefly described below.
  \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics on lat-lon grid,
    using Held and Suarez '94 forcing.
  \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere dynamics
    using Held and Suarez '94 forcing.\\
    Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
  \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
    Suarez (1994) forcing on the cubed sphere. 5 vertical levels.\\
    Also contains an additional set-up with Implicit Internal gravity waves
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 Each example is briefly described below.
     \item with sea-ice ({\it pkg/seaice}) thermodynamics ({\it input.seaicetd/})
     \item an adjoint test ({\it code\_ad/, input\_ad/}).
    \end{enumerate}
  \item \texttt{OpenAD} simple Adjoint experiement (used also to test
    open-AD compiler)
  \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
 Line 270 
 Each example is briefly described below.
  \item \texttt{vermix} Simple test in a small domain (3 columns) for
    ocean vertical mixing schemes. The standard set-up ({\it input/}) uses
-   KPP scheme.\\
+   KPP scheme \cite[]{lar-eta:94}.\\
    Also contains additional set-ups:
    \begin{enumerate}
-    \item with Gaspar et al. (1990) ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
+    \item with \cite{gas-eta:90} ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
-    \item with Mellor \& Yamada (1982) level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
+    \item with \cite{Mellor:Yamada1982} level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
-    \item with Paluszkiewicz \& Romea (1997) ({\it pkg/opps}) scheme ({\it input.opps/})
+    \item with \cite{pal-rom:97} ({\it pkg/opps}) scheme ({\it input.opps/})
-    \item with Pacanowski \& Philander (1981) ({\it pkg/pp81}) scheme ({\it input.pp81/})
+    \item with \cite{Pacanowski:Philander1981} ({\it pkg/pp81}) scheme ({\it input.pp81/})
    \end{enumerate}
  \end{enumerate}
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 Each example directory has the following
    \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:
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 Each example directory has the following
    \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

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