--- manual/s_examples/text/model_examples.tex	2006/06/27 20:47:05	1.12
+++ manual/s_examples/text/model_examples.tex	2008/01/15 23:24:59	1.19
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.12 2006/06/27 20:47:05 molod Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.19 2008/01/15 23:24:59 jmc Exp $
 % $Name:  $
 
 \section[MITgcm Example Experiments]{Example experiments}
@@ -9,68 +9,74 @@
 
 %% 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.
+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{tutorial\_barotropic\_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{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}.
+
+\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{adjustment.128x64x1} Barotropic adjustment problem on
   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
@@ -80,97 +86,150 @@
   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\_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{aim.5l\_Equatorial\_Channel}
+  - 5-levels Intermediate Atmospheric physics, 
+  3D Equatorial Channel configuration.
   
-\item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
-  boundary conditions and poles.
+\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{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{biogeo} (to be removed)
 
-\item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
-  sphere grid.
+\item \texttt{bottom\_ctrl\_5x5} Adjoint test using the bottom
+  topography as the control parameter.
 
-\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{cfc\_example} Global ocean with online computation and
+  advection of CFC11 and CFC12.
 
-\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{cpl\_aim+ocn}
 
-\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{cpl\_atm2d+ocn}
 
-\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{deep\_anelastic}
 
-\item \texttt{rotating\_tank} Rotating tank simulation in cylindrical coordinates.
-  This experiment is described in detail in section \ref{sect:eg-tank}.
+\item \texttt{dome} Idealized 3D test of a density-driven bottom current.
 
-\item \texttt{MLAdjust} Simple test for different viscosity formulations.
+\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{bottom_ctrl_5x5} Adjoint test using the bottom topography as the
-  control parameter.
+\item \texttt{exp4} - Flow over a Gaussian bump in open-water or
+  channel with open boundaries.
+  
+\item \texttt{exp5} Deep convection.
 
-\item \texttt{cfc_example} Global ocean with online computation and advection of
-CFC11 and CFC12.
+\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{dome} Idealized 3D test of a density-driven bottom current.
+\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{exp2} Old version of the global ocean experiment.
+\item \texttt{global1x1\_tot} ECCO-GODAE production configuration
+ version 1, 2 \& 3
 
-\item \texttt{exp5} Deep convection.
+\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 (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{fizhi-cs-32x32x10} Global atmospheric simulation with realistic topography,
-  10 vertical levels, a cubed sphere grid and the full atmospheric physics package.
+\item \texttt{internal\_wave} - Ocean internal wave forced by open
+  boundary conditions.
 
-\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{inverted\_barometer} Simple test of ocean response to
+  atmospheric pressure loading.
 
-\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{isomip}
 
-\item \texttt{global_ocean.cs32x15} Global ocean experiment on the cubed sphere grid, using
-thermodynamic sea ice and bulk force packages.
+\item \texttt{lab\_sea} Regional Labrador Sea simulation on a lat-lon
+  grid. Coupled to the sea ice model.
 
-\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{matrix\_example} Test of experimental method to
+  accelerated convergence towards equillibrium.
 
-\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{MLAdjust} Simple test for different viscosity formulations.
 
-\item \texttt{hs94.cs-32x32x5} 3D atmosphere dynamics using Held and Suarez
-  (1994) forcing on the cubed sphere. 5 vertical levels.
+\item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
+  scheme; 1 month integration
 
-\item \texttt{ideal_2D_oce} Idealized 2D global ocean simulation on an aqua planet.
+\item \texttt{natl\_box\_adjoint}
 
-\item \texttt{inverted_barometer} Simple test of ocean response to atmospheric pressure
-loading.
+\item \texttt{offline\_exf\_seaice}
+  
+\item \texttt{OpenAD}
 
-\item \texttt{lab_sea} Regional Labrador Sea simulation on a lat-lon grid. Coupled to
-the sea ice model.
+\item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
+  coordinates.  This experiment is described in detail in section
+  \ref{sect:eg-tank}.
 
-\item \texttt{matrix_example} Test of experimental method to accelerated convergence towards
-equillibrium.
+\item \texttt{seaice\_obcs}
 
-\item \texttt{tutorial_cfc_offline} Offline form of the MITgcm to study advection of a passive
-  tracer and CFCs.
+\item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
+  sphere grid.
 
-\item \texttt{vermix} Simple test in a small domain (3 columns) for ocean vertical mixing schemes.
+\item \texttt{tidal\_basin\_2d}
+
+\item \texttt{vermix} Simple test in a small domain (3 columns) for
+  ocean vertical mixing schemes.
 
 \end{enumerate}
 
@@ -229,12 +288,16 @@
   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
@@ -248,6 +311,9 @@
 \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
@@ -263,9 +329,6 @@
 \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