--- 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 19:59:51	1.16
@@ -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 1.16 2008/01/15 19:59:51 jmc Exp $
 % $Name:  $
 
 \section[MITgcm Example Experiments]{Example experiments}
@@ -9,37 +9,47 @@
 
 %% 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{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{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{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.
@@ -53,9 +63,9 @@
 \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{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.
@@ -70,7 +80,7 @@
   Global configuration, on latitude longitude grid with 128x64x5 grid
   points ($2.8^\circ$ resolution).
   
-\item \texttt{aim.5l_cs}
+\item \texttt{aim.5l\_cs}
 
 \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
@@ -88,45 +98,50 @@
 \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{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{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{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{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{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.
 
@@ -134,43 +149,51 @@
 
 \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-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{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{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{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{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{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{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{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{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.
+\item \texttt{vermix} Simple test in a small domain (3 columns) for
+  ocean vertical mixing schemes.
 
 \end{enumerate}
 
@@ -229,12 +252,16 @@
   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
@@ -242,6 +269,9 @@
 
 
 \newpage
+\input{part3/case_studies/advection_in_gyre_circulation/adv_gyre.tex}
+
+\newpage
 \input{part3/case_studies/barotropic_gyre/baro.tex}
 
 \newpage
@@ -263,9 +293,6 @@
 \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
