--- manual/s_examples/text/model_examples.tex	2006/06/28 17:20:51	1.14
+++ manual/s_examples/text/model_examples.tex	2010/08/27 18:21:43	1.22
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.14 2006/06/28 17:20:51 molod Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.22 2010/08/27 18:21:43 jmc Exp $
 % $Name:  $
 
 \section[MITgcm Example Experiments]{Example experiments}
@@ -24,173 +24,260 @@
 
 \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.
+  This experiment is described in detail in section \ref{sect:eg-offline-cfc}.
 
-\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 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{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
+  using Held and Suarez (1994) forcing on cubed sphere grid.  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-adjoint}.
 
-\item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
+\item \texttt{adjustment.128x64x1} - Barotropic adjustment problem on
   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
   
-\item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
+\item \texttt{adjustment.cs-32x32x1} - Barotropic adjustment problem on
   cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
-  resolution).
+  resolution).\\
+  Also contains a non-linear free-surface adjustment version ({\it input.nlfs/}).
   
 \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.
+\item \texttt{advect\_xy} - Two-dimensional (horizontal plane) passive
+  advection test on Cartesian grid.\\
+  Also contains an additional set-up using Adams-Bashforth 3 ({\it input.ab3\_c4/}).
   
-\item \texttt{advect\_xz} 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 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 $2.8^\circ$).\\
+  Also contains an additional set-up with an ocean mixed layer and thermodynamics
+  sea-ice ({\it input.thSI/}).
 
-\item \texttt{bottom\_ctrl\_5x5} Adjoint test using the bottom
+\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
+\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.
-
-\item \texttt{exp2} Old version of the global ocean experiment.
+\item \texttt{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic 
+  configuration on cubed-sphere cs32 horizontal grid, 
+  using Intermediate Atmospheric physics ({\it pkg/aim\_v23})
+  thermodynamics seaice ({\it pkg/thsice}) and land packages.
+  on cubed-sphere cs32 in a realistics configuration.
+
+\item \texttt{cpl\_atm2d+ocn} - Coupled Ocean - Atmosphere realistic 
+  configuration using 2-D Atmospheric Model ({\it pkg/atm2d}).
+
+\item \texttt{deep\_anelastic} - Convection simulation on a giant planet:
+  relax both the Boussinesq approximation (anelastic) and the thin atmosphere
+  approximation (deep atmosphere).
+
+\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 ({\it input.rigidLid/}).
 
-\item \texttt{exp5} Deep convection.
+\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
-  realistic topography, 10 vertical levels, a cubed sphere grid and
+\item \texttt{fizhi-cs-32x32x40} - Global atmospheric simulation with
+  realistic topography, 40 vertical levels, a cubed sphere grid and
   the full atmospheric physics package.
 
-\item \texttt{fizhi-cs-aqualev20} Global atmospheric simulation on an
+\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
+\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{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).\\
+  Also contains an additional set-up with Mixed-Layer Eddy parameterization
+  (Ferrari \& McWilliams, 2007) ({\it input.mxl/}).
+
+\item \texttt{global1x1\_tot} - ECCO-GODAE production configuration
+ version 1, 2 \& 3
+
+\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 ({\it 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 ({\it input.viscA4/})
+   \item using thermodynamic sea ice and bulk force ({\it input.thsice/})
+   \item using thermodynamic ({\it pkg/thsice}) dynamics ({\it pkg/seaice}) sea-ice
+         and EXF package ({\it input.icedyn/})
+  \end{enumerate}
 
-\item \texttt{global\_ocean\_ebm} Global ocean experiment on a lat-lon
+\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.
+  global\_ocean.90x40x15 experiment.\\
+  Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
 
-\item \texttt{global\_with\_exf} Global ocean experiment on a lat-lon
+\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{hs94.128x64x5} - 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.\\
+  Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
+  
+\item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
+  Suarez (1994) forcing on the cubed sphere. 5 vertical levels.\\
+  Also contains an additional set-up with Implicit Internal gravity waves
+  treatment ({\it input.impIGW/}).
 
-\item \texttt{ideal\_2D\_oce} Idealized 2D global ocean simulation on
+\item \texttt{ideal\_2D\_oce} - Idealized 2D global ocean simulation on
   an aqua planet.
 
-\item \texttt{inverted\_barometer} Simple test of ocean response to
+\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{lab\_sea} Regional Labrador Sea simulation on a lat-lon
-  grid. Coupled to the sea ice model.
+\item \texttt{isomip} - ISOMIP like set-up including ice-shelf cavities
+  ({\it pkg/shelfice}).\\
+  Also contains an additional set-up with ({\it input.htd/})
+  but only Martin knows what "htd" stands for.
+
+\item \texttt{lab\_sea} - Regional Labrador Sea simulation on a lat-lon
+  grid using the sea ice package.\\
+  Also contains additional set-ups:
+  \begin{enumerate}
+   \item using the LSR solver (instead of EVP dynamics) ({\it input.lsr/})
+   \item using Hibler and Bryan (1987) sea-ice ocean stress ({\it input.hb87/})
+   \item using package {\it salt\_plume} ({\it input.salt\_plume/})
+  \end{enumerate}
+  and also 3 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.noseaicedyn/,
+  input\_ad.noseaice/}).
 
-\item \texttt{matrix\_example} Test of experimental method to
+\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 tests for different viscosity formulations.\\
+  Also contains additional set-ups:
+  \begin{enumerate}
+   \item ({\it input.0.leith/})
+   \item ({\it input.0.leithD/})
+   \item ({\it input.0.smag/})
+   \item ({\it input.1.leith/})
+  \end{enumerate}
+
+\item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
+  scheme; 1 month integration
+
+\item \texttt{natl\_box\_adjoint} - Eastern subtropical North Atlantic with KPP
+  scheme; adjoint set-up.
+
+\item \texttt{offline\_exf\_seaice} - oceanic surface forcing computed
+  by bulk-formulae ({\it pkg/exf}) and inposed SST (offline ocean).\\
+  Also contains additional set-ups:
+  \begin{enumerate}
+   \item with sea-ice ({\it pkg/seaice}) thermodynamics ({\it input.seaicetd/})
+   \item an adjoint test ({\it code\_ad/, input\_ad/}).
+  \end{enumerate}
+  
+\item \texttt{OpenAD} simple Adjoint experiement (used also to test 
+  open-AD compiler)
+
+\item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
+  coordinates.  This experiment is described in detail in section
+  \ref{sect:eg-tank}.
+
+\item \texttt{seaice\_obcs} similar to "lab\_sea" ({\it input.salt\_plume/})
+  experiment with only a fraction of the domain and open-boundary conditions
+  derived from "lab\_sea" experiment.
+
+\item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
+  sphere grid.
+
+\item \texttt{tidal\_basin\_2d} 2-D vertical section (X-Z) with tidal forcing
 
 \item \texttt{vermix} Simple test in a small domain (3 columns) for
-  ocean vertical mixing schemes.
+  ocean vertical mixing schemes. The standard set-up ({\it input/}) uses
+  KPP scheme.\\
+  Also contains additional set-ups:
+  \begin{enumerate}
+   \item with Gaspar et al. (1990) ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
+   \item with Mellor \& Yamada (1982) level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
+   \item with Paluszkiewicz \& Romea (1997) ({\it pkg/opps}) scheme ({\it input.opps/})
+   \item with Pacanowski \& Philander (1981) ({\it pkg/pp81}) scheme ({\it input.pp81/})
+  \end{enumerate}
 
 \end{enumerate}
 
@@ -264,42 +351,3 @@
 Once you have chosen the example you want to run, you are ready to
 compile the code.
 
-
-\newpage
-\input{part3/case_studies/barotropic_gyre/baro.tex}
-
-\newpage
-\input{part3/case_studies/fourlayer_gyre/fourlayer.tex}
-
-\newpage
-\input{part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex}
-
-\newpage
-\input{part3/case_studies/ogcm_in_pressure/ogcm_in_pressure.tex}
-
-\newpage
-\input{part3/case_studies/held_suarez_cs/held_suarez_cs.tex}
-
-\newpage
-\input{part3/case_studies/doubly_periodic_convection/convection.tex}
-
-\newpage
-\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
-\input{part3/case_studies/global_oce_estimation/global_oce_estimation.tex}
-
-\newpage
-\input{part3/case_studies/sens_airsea_tracer/doc_ad_examples.tex}
-
-\newpage
-\input{part3/case_studies/offline/offline_tutorial.tex}
-
-\newpage
-\input{part3/case_studies/rotating_tank/tank.tex}
