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

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-revision 1.11 by molod,
Tue Jun 27 19:08:22 2006 UTC
+revision 1.19 by jmc,
Tue Jan 15 23:24:59 2008 UTC
 Line 9
  %% a set of pre-configured numerical experiments
- The full MITgcm distribution comes with a set of pre-configured numerical experiments.
+ The full MITgcm distribution comes with a set of pre-configured
- Some of these example experiments are tests of individual parts of the model code, but many
+ numerical experiments.  Some of these example experiments are tests of
- are fully fledged numerical simulations. Full tutorials exist for a few of the examples,
+ individual parts of the model code, but many are fully fledged
- and are documented in sections \ref{sect:eg-baro} - \ref{sect:eg-tank}. The other examples
+ numerical simulations. Full tutorials exist for a few of the examples,
- follow the same general structure as the tutorial examples. However, they only include brief
+ and are documented in sections \ref{sect:eg-baro} -
- instructions in a text file called {\it README}.  The examples are located in subdirectories
+ \ref{sect:eg-tank}. The other examples follow the same general
- under the directory \texttt{verification}.  Each example is briefly described below.
+ 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{tutorial\_barotropic\_gyre} - single layer, ocean double gyre
+ \item \texttt{tutorial\_advection\_in\_gyre} - test of various
-   (barotropic with free-surface). This experiment is described in detail in section
+   advection schemes in a single-layer double-gyre experiment.
-   \ref{sect:eg-baro}.
+   This experiment is described in detail in section
+   \ref{sect: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}.
+ \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\_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{sect: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}.
+ \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\_in\_p} Global ocean simulation in
+   pressure coordinate (non-Boussinesq ocean model). Described in
+   detail in section \ref{sect: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}.
+ \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\_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{sect: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{sect:eg-offline}.
+ \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\_tracer\_adjsens} Simple passive tracer
+   experiment. Includes derivative calculation. This experiment is
+   described in detail in section \ref{sect:eg-simple-tracer-adjoint}.
- \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{hs94.cs-32x32x5} - 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{adjustment.128x64x1} Barotropic adjustment problem on
    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
-Line 76 
 Gent/McWilliams scheme). 2D (Y-Z).
+Line 86 
 Gent/McWilliams scheme). 2D (Y-Z).
    resolution).
  \item \texttt{advect\_cs} Two-dimensional passive advection test on
-   cube sphere grid.
+   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.
+   advection test on Cartesian grid.\\
+   Also contains an additional set-up iusing Adams-Bashforth 3 (input.ab3\_c4).
- \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
+ \item \texttt{advect\_xz} Two-dimensional (vertical plane) passive
    advection test on Cartesian grid.
- \item \texttt{tutorial\_tracer\_adjsens} Simple passive tracer experiment. Includes
+ \item \texttt{aim.5l\_Equatorial\_Channel}
-   derivative calculation. This experiment is described in detail in section
+   - 5-levels Intermediate Atmospheric physics,
-   \ref{sect:eg-simple-tracer}.
+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 (input.thSI).
+ \item \texttt{biogeo} (to be removed)
+ \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{cpl\_aim+ocn}
+ \item \texttt{cpl\_atm2d+ocn}
+ \item \texttt{deep\_anelastic}
+ \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 (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
+   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{flt\_example} Example of using float package.
- \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
+ \item \texttt{front\_relax} - Relaxation of an ocean thermal front
-   boundary conditions and poles.
+   (test for Gent/McWilliams scheme). 2D (Y-Z).
- \item \texttt{tutorial\_global\_oce\_in\_p} Global circulation in pressure
+ \item \texttt{global1x1\_tot} ECCO-GODAE production configuration
-   coordinate (non-Boussinesq ocean model). Described in detail in
+  version 1, 2 \& 3
-   section \ref{sect:eg-globalpressure}.
- \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
+ \item \texttt{global2x2\_tot} ECCO production configuration version 0
-   sphere grid.
+ \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 (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 (input.viscA4)
+    \item using thermodynamic sea ice and bulk force (input.thsice)
+    \item using thermodynamic (pkg/thsice) dynamics (pkg/seaice) sea-ice
+          and exf pkg (input.icedyn)
+   \end{enumerate}
+ \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{hs94.128x64x5} - 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.
+ \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{internal\_wave} - Ocean internal wave forced by open
+   boundary conditions.
+ \item \texttt{inverted\_barometer} Simple test of ocean response to
+   atmospheric pressure loading.
+ \item \texttt{isomip}
- \item \texttt{tutorial\_plume\_on\_slope} Gravity Plume on a continental slope.
+ \item \texttt{lab\_sea} Regional Labrador Sea simulation on a lat-lon
-   This experiment is described in detail in section \ref{sect:eg-gravityplume}.
+   grid. Coupled to the sea ice model.
- \item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to the dissolved
+ \item \texttt{matrix\_example} Test of experimental method to
-   inorganic carbon biogeochemistry model. This experiment is described in detail in section
+   accelerated convergence towards equillibrium.
-   \ref{sect:eg-biogeochem\_tutorial}.
- \item \texttt{tutorial\_global\_oce\_optim} Global ocean state estimation at $4^\circ$ resolution.
+ \item \texttt{MLAdjust} Simple test for different viscosity formulations.
-   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
+ \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
-   tracer.  This experiment is described in detail in section \ref{sect:eg-offline}.
+   scheme; 1 month integration
+ \item \texttt{natl\_box\_adjoint}
+ \item \texttt{offline\_exf\_seaice}
+ \item \texttt{OpenAD}
- \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical coordinates.
+ \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
-   This experiment is described in detail in section \ref{sect:eg-tank}.
+   coordinates.  This experiment is described in detail in section
+   \ref{sect:eg-tank}.
+ \item \texttt{seaice\_obcs}
+ \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
+   sphere grid.
+ \item \texttt{tidal\_basin\_2d}
+ \item \texttt{vermix} Simple test in a small domain (3 columns) for
+   ocean vertical mixing schemes.
  \end{enumerate}
-Line 173 
 Each example directory has the following
+Line 288 
 Each example directory has the following
    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.
+   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
-Line 192 
 compile the code.
+Line 311 
 compile the code.
  \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
-Line 207 
 compile the code.
+Line 329 
 compile the code.
  \input{part3/case_studies/plume_on_slope/plume_on_slope.tex}
  \newpage
- \input{part3/case_studies/carbon_outgassing_sensitivity/co2sens.tex}
- \newpage
  \input{part3/case_studies/biogeochem_tutorial/biogeochem.tex}
  \newpage

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