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

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-revision 1.17 by jmc,
Tue Jan 15 21:14:34 2008 UTC
+revision 1.25 by jmc,
Tue Mar 26 13:21:28 2013 UTC
 Line 2
  % $Name$
  \section[MITgcm Example Experiments]{Example experiments}
- \label{sect:modelExamples}
+ \label{sec:modelExamples}
  \begin{rawhtml}
  <!-- CMIREDIR:modelExamples: -->
  \end{rawhtml}
 Line 13 
 The full MITgcm distribution comes with
  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} -
+ and are documented in sections \ref{sec:eg-baro} -
- \ref{sect:eg-tank}. The other examples follow the same general
+ \ref{sec: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}.
 Line 23 
 Each example is briefly described below.
  \subsection{Full list of model examples}
  \begin{enumerate}
- \item \texttt{tutorial_advection\_in\_gyre} - test of various
+ \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
-   \ref{sect:eg-adv-gyre}.
+   \ref{sec:eg-adv-gyre}.
  \item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double
    gyre. This experiment is described in detail in section
-   \ref{sect:eg-fourlayer}.
+   \ref{sec:eg-fourlayer}.
- \item \texttt{tutorial\_barotropic\_gyre} - single layer, ocean double
+ \item \texttt{tutorial\_barotropic\_gyre} - Single layer, ocean double
-   gyre (barotropic with free-surface). This experiment is described in
+   gyre (barotropic with free-surface).
-   detail in section \ref{sect:eg-baro}.
+   This experiment is described in detail in section \ref{sec:eg-baro}.
- \item \texttt{tutorial\_cfc\_offline} Offline form of the MITgcm to
+ \item \texttt{tutorial\_cfc\_offline} - Offline form of the MITgcm to
    study advection of a passive tracer and CFCs.
+   This experiment is described in detail in section \ref{sec:eg-offline-cfc}.
  \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}.
+   described in detail in section \ref{sec:eg-bconv}.
- \item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to
+ \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}.
+   \ref{sec:eg-biogeochem_tutorial}.
- \item \texttt{tutorial\_global\_oce\_in\_p} Global circulation in
+ \item \texttt{tutorial\_global\_oce\_in\_p} - Global ocean simulation in
    pressure coordinate (non-Boussinesq ocean model). Described in
-   detail in section \ref{sect:eg-globalpressure}.
+   detail in section \ref{sec:eg-globalpressure}.
  \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}.
+   described in detail in section \ref{sec:eg-global}.
- \item \texttt{tutorial\_global\_oce\_optim} Global ocean state
+ \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}.
+   detail in section \ref{sec:eg-global_state_estimate}.
  \item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics
-   using Held and Suarez (1994) forcing on the cubed sphere.  This
+   using Held and Suarez (1994) forcing on cubed sphere grid.  This
-   experiment is described in detail in section \ref{sect:eg-hs}.
+   experiment is described in detail in section \ref{sec:eg-hs}.
- \item \texttt{tutorial\_offline} Offline form of the MITgcm to study
+ \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}.
+   detail in section \ref{sec:eg-offline}.
- \item \texttt{tutorial\_plume\_on\_slope} Gravity Plume on a
+ \item \texttt{tutorial\_plume\_on\_slope} - Gravity Plume on a
    continental slope.  This experiment is described in detail in
-   section \ref{sect:eg-gravityplume}.
+   section \ref{sec:eg-gravityplume}.
- \item \texttt{tutorial\_tracer\_adjsens} Simple passive tracer
+ \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}.
+   described in detail in section \ref{sec:eg-simple-tracer-adjoint}.
- \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
+ \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
+ \item \texttt{adjustment.cs-32x32x1} - Barotropic adjustment problem on
    cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
-   resolution).
+   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
+ \item \texttt{advect\_xy} - Two-dimensional (horizontal plane) passive
-   advection test on Cartesian grid.
+   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
+ \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 $2.8^\circ$).
+   (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/}).
- \item \texttt{bottom\_ctrl\_5x5} Adjoint test using the bottom
+ \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
+ \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{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic
+   configuration on cubed-sphere cs32 horizontal grid,
- \item \texttt{exp2} Old version of the global ocean experiment.
+   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:
+   relax both the Boussinesq approximation (anelastic) and the thin atmosphere
+   approximation (deep atmosphere).
+ \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
+ \item \texttt{exp5} - Deep convection.
-   realistic topography, 10 vertical levels, a cubed sphere grid and
+ \item \texttt{fizhi-cs-32x32x40} - Global atmospheric simulation with
+   realistic topography, 40 vertical levels, a cubed sphere grid and
    the full atmospheric physics package.
- \item \texttt{fizhi-cs-aqualev20} Global atmospheric simulation on an
+ \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
+ \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{flt\_example} Example of using float package.
+ \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).
- \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
-   boundary conditions and poles.
- \item \texttt{global\_ocean.cs32x15} Global ocean experiment on the
+ \item \texttt{front\_relax} - Relaxation of an ocean thermal front
-   cubed sphere grid, using thermodynamic sea ice and bulk force
+   (test for Gent/McWilliams scheme). 2D (Y-Z).\\
-   packages.
+   Also contains an additional set-up with Mixed-Layer Eddy parameterization
+   (Ferrari \& McWilliams, 2007) ({\it input.mxl/}).
+ \item \texttt{global1x1\_tot} - ECCO-GODAE production configuration
+  version 1, 2 \& 3
+ \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/})
+    \item using thermodynamic sea ice and bulk force ({\it input.thsice/})
+    \item using thermodynamic ({\it pkg/thsice}) dynamics ({\it pkg/seaice}) sea-ice
+          and EXF package ({\it input.icedyn/})
+   \end{enumerate}
- \item \texttt{global\_ocean\_ebm} Global ocean experiment on a lat-lon
+ \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.
+   global\_ocean.90x40x15 experiment.\\
+   Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
- \item \texttt{global\_with\_exf} Global ocean experiment on a lat-lon
+ \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{hs94.128x64x5} - 3D atmosphere dynamics using Held and
+ \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics on lat-lon grid,
-   Suarez '94 forcing.
+   using Held and Suarez '94 forcing.
- \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
+ \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere dynamics
-   Suarez '94 forcing.
+   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.
+ \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
+   treatment ({\it input.impIGW/}).
- \item \texttt{ideal\_2D\_oce} Idealized 2D global ocean simulation on
+ \item \texttt{ideal\_2D\_oce} - Idealized 2D global ocean simulation on
    an aqua planet.
  \item \texttt{internal\_wave} - Ocean internal wave forced by open
    boundary conditions.
- \item \texttt{inverted\_barometer} Simple test of ocean response to
+ \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
+ \item \texttt{isomip} - ISOMIP like set-up including ice-shelf cavities
-   grid. Coupled to the sea ice model.
+   ({\it pkg/shelfice}).\\
+   Also contains an additional set-up with ({\it input.htd/})
+   but only Martin knows what "htd" stands for.
+ \item \texttt{lab\_sea} - Regional Labrador Sea simulation on a lat-lon
+   grid using the sea ice package.\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item using the LSR solver (instead of EVP dynamics) ({\it input.lsr/})
+    \item using Hibler and Bryan (1987) sea-ice ocean stress ({\it input.hb87/})
+    \item using package {\it salt\_plume} ({\it input.salt\_plume/})
+   \end{enumerate}
+   and also 3 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.noseaicedyn/,
+   input\_ad.noseaice/}).
- \item \texttt{matrix\_example} Test of experimental method to
+ \item \texttt{matrix\_example} - Test of experimental method to
    accelerated convergence towards equillibrium.
- \item \texttt{MLAdjust} Simple test for different viscosity formulations.
+ \item \texttt{MLAdjust} - Simple tests for different viscosity formulations.\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item ({\it input.0.leith/})
+    \item ({\it input.0.leithD/})
+    \item ({\it input.0.smag/})
+    \item ({\it input.1.leith/})
+   \end{enumerate}
  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
    scheme; 1 month integration
+ \item \texttt{natl\_box\_adjoint} - Eastern subtropical North Atlantic with KPP
+   scheme; adjoint set-up.
+ \item \texttt{offline\_exf\_seaice} - oceanic surface forcing computed
+   by bulk-formulae ({\it pkg/exf}) and inposed SST (offline ocean).\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \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
    coordinates.  This experiment is described in detail in section
-   \ref{sect:eg-tank}.
+   \ref{sec:eg-tank}.
+ \item \texttt{seaice\_obcs} similar to "lab\_sea" ({\it input.salt\_plume/})
+   experiment with only a fraction of the domain and open-boundary conditions
+   derived from "lab\_sea" experiment.
  \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
    sphere grid.
+ \item \texttt{tidal\_basin\_2d} 2-D vertical section (X-Z) with tidal forcing
  \item \texttt{vermix} Simple test in a small domain (3 columns) for
-   ocean vertical mixing schemes.
+   ocean vertical mixing schemes. The standard set-up ({\it input/}) uses
+   KPP scheme \cite[]{lar-eta:94}.\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item with \cite{gas-eta:90} ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
+    \item with \cite{Mellor:Yamada1982} level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
+    \item with \cite{pal-rom:97} ({\it pkg/opps}) scheme ({\it input.opps/})
+    \item with \cite{Pacanowski:Philander1981} ({\it pkg/pp81}) scheme ({\it input.pp81/})
+   \end{enumerate}
  \end{enumerate}
-Line 215 
 Each example directory has the following
+Line 302 
 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:
-Line 236 
 Each example directory has the following
+Line 323 
 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
-Line 256 
 Each example directory has the following
+Line 343 
 Each example directory has the following
    useful for comparison with your own output when you run the
    experiment.
- \item \texttt{build}: this directory is where the model is compiled
+ \item \texttt{build}: this directory is initially empty and is used
-   and loaded, and where the executable resides.
+   to compile and load the model, and to generate the executable.
+ \item \texttt{run}: this directory is initially empty and is used
+   to run the executable.
  \end{itemize}
  Once you have chosen the example you want to run, you are ready to
  compile the code.
- \newpage
- \input{part3/case_studies/barotropic_gyre/baro.tex}
- \newpage
- \input{part3/case_studies/fourlayer_gyre/fourlayer.tex}
- \newpage
- \input{part3/case_studies/advection_in_gyre_circulation/adv_gyre.tex}
- \newpage
- \input{part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex}
- \newpage
- \input{part3/case_studies/ogcm_in_pressure/ogcm_in_pressure.tex}
- \newpage
- \input{part3/case_studies/held_suarez_cs/held_suarez_cs.tex}
- \newpage
- \input{part3/case_studies/doubly_periodic_convection/convection.tex}
- \newpage
- \input{part3/case_studies/plume_on_slope/plume_on_slope.tex}
- \newpage
- \input{part3/case_studies/biogeochem_tutorial/biogeochem.tex}
- \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}

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