--- manual/s_examples/text/model_examples.tex	2006/06/27 22:34:09	1.13
+++ manual/s_examples/text/model_examples.tex	2008/01/15 21:14:34	1.17
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.13 2006/06/27 22:34:09 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.17 2008/01/15 21:14:34 jmc Exp $
 % $Name:  $
 
 \section[MITgcm Example Experiments]{Example experiments}
@@ -24,60 +24,58 @@
 
 \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_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\_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\_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.
 
-\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{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 circulation 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{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\_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}.
 
 \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
@@ -87,7 +85,7 @@
   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.
@@ -95,44 +93,17 @@
 \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{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{MLAdjust} Simple test for different viscosity formulations.
+\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 $2.8^\circ$). 
 
 \item \texttt{bottom\_ctrl\_5x5} Adjoint test using the bottom
   topography as the control parameter.
@@ -144,9 +115,12 @@
 
 \item \texttt{exp2} Old version of the global ocean experiment.
 
+\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-32x32x10} Global atmospheric simulation with
+\item \texttt{fizhi-cs-32x32x40} Global atmospheric simulation with
   realistic topography, 10 vertical levels, a cubed sphere grid and
   the full atmospheric physics package.
 
@@ -159,6 +133,14 @@
   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{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
   cubed sphere grid, using thermodynamic sea ice and bulk force
   packages.
@@ -171,12 +153,21 @@
   grid using the exf package. Similar to global\_ocean.90x40x15
   experiment.
 
+\item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
+  Suarez '94 forcing.
+  
+\item \texttt{hs94.1x64x5} - Zonal averaged atmosphere 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.
 
@@ -186,8 +177,17 @@
 \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{MLAdjust} Simple test for different viscosity formulations.
+
+\item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
+  scheme; 1 month integration
+  
+\item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
+  coordinates.  This experiment is described in detail in section
+  \ref{sect:eg-tank}.
+
+\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.
@@ -249,12 +249,16 @@
   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
@@ -268,6 +272,9 @@
 \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
@@ -283,9 +290,6 @@
 \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
