--- manual/s_examples/text/model_examples.tex	2006/06/27 20:47:05	1.12
+++ manual/s_examples/text/model_examples.tex	2006/06/27 22:34:09	1.13
@@ -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 1.13 2006/06/27 22:34:09 edhill Exp $
 % $Name:  $
 
 \section[MITgcm Example Experiments]{Example experiments}
@@ -9,13 +9,16 @@
 
 %% 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}
 
@@ -23,23 +26,27 @@
   
 \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\_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\_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 +60,9 @@
 \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 +77,7 @@
   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 +95,50 @@
 \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 +146,51 @@
 
 \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-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-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{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.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\_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}
 
