--- manual/s_examples/text/model_examples.tex	2006/06/27 19:08:22	1.11
+++ manual/s_examples/text/model_examples.tex	2010/08/27 13:25:32	1.21
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.11 2006/06/27 19:08:22 molod Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.21 2010/08/27 13:25:32 jmc Exp $
 % $Name:  $
 
 \section[MITgcm Example Experiments]{Example experiments}
@@ -9,112 +9,275 @@
 
 %% 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} - 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\_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{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{adjustment.128x64x1} - Barotropic adjustment problem on
+  latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
   
-\item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
-  Suarez '94 forcing.
+\item \texttt{adjustment.cs-32x32x1} - Barotropic adjustment problem on
+  cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
+  resolution).\\
+  Also contains a non-linear free-surface adjustment version ({\it input.nlfs/}).
   
-\item \texttt{hs94.cs-32x32x5} - 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{advect\_cs} Two-dimensional passive advection test on
+  cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$)
   
-\item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
-  Global Zonal Mean configuration, 1x64x5 resolution.
+\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{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
-  Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
+\item \texttt{advect\_xz} - Two-dimensional (vertical plane) passive
+  advection test on Cartesian grid.
   
-\item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-  physics. 3D Equatorial Channel configuration.
+\item \texttt{aim.5l\_Equatorial\_Channel}
+  - 5-levels Intermediate Atmospheric physics, 
+  3D Equatorial Channel configuration.
   
-\item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
+\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{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
-  cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
-  resolution).
-  
-\item \texttt{advect\_cs} Two-dimensional passive advection test on
-  cube sphere grid.
-  
-\item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
-  advection test on Cartesian grid.
-  
-\item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
-  advection test on Cartesian grid.
+\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
+  topography as the control parameter.
+
+\item \texttt{cfc\_example} - Global ocean with online computation and
+  advection of CFC11 and CFC12.
+
+\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{exp4} - Flow over a Gaussian bump in open-water or
+  channel with open boundaries.
+  
+\item \texttt{exp5} - Deep convection.
+
+\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
+  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{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
+  grid coupled to an atmospheric energy balance model. Similar to
+  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
+  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{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{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{solid-body.cs-32x32x1} Solid body rotation test for cube
-  sphere grid.
+\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.
+
+\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
+  accelerated convergence towards equillibrium.
+
+\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{tutorial\_plume\_on\_slope} Gravity Plume on a continental slope.
-  This experiment is described in detail in section \ref{sect:eg-gravityplume}.
+\item \texttt{natl\_box\_adjoint} - Eastern subtropical North Atlantic with KPP
+  scheme; adjoint set-up.
 
-\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{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{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{solid-body.cs-32x32x1} Solid body rotation test for cube
+  sphere grid.
 
-\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{tidal\_basin\_2d} 2-D vertical section (X-Z) with tidal forcing
 
-\item \texttt{rotating\_tank} Rotating tank simulation in cylindrical coordinates.
-  This experiment is described in detail in section \ref{sect:eg-tank}.
+\item \texttt{vermix} Simple test in a small domain (3 columns) for
+  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}
 
@@ -173,12 +336,16 @@
   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
@@ -186,40 +353,40 @@
 
 
 \newpage
-\input{part3/case_studies/barotropic_gyre/baro.tex}
+\input{s_examples/barotropic_gyre/baro.tex}
 
 \newpage
-\input{part3/case_studies/fourlayer_gyre/fourlayer.tex}
+\input{s_examples/baroclinic_gyre/fourlayer.tex}
 
 \newpage
-\input{part3/case_studies/climatalogical_ogcm/climatalogical_ogcm.tex}
+\input{s_examples/advection_in_gyre/adv_gyre.tex}
 
 \newpage
-\input{part3/case_studies/ogcm_in_pressure/ogcm_in_pressure.tex}
+\input{s_examples/global_oce_latlon/climatalogical_ogcm.tex}
 
 \newpage
-\input{part3/case_studies/held_suarez_cs/held_suarez_cs.tex}
+\input{s_examples/global_oce_in_p/ogcm_in_pressure.tex}
 
 \newpage
-\input{part3/case_studies/doubly_periodic_convection/convection.tex}
+\input{s_examples/held_suarez_cs/held_suarez_cs.tex}
 
 \newpage
-\input{part3/case_studies/plume_on_slope/plume_on_slope.tex}
+\input{s_examples/deep_convection/convection.tex}
 
 \newpage
-\input{part3/case_studies/carbon_outgassing_sensitivity/co2sens.tex}
+\input{s_examples/plume_on_slope/plume_on_slope.tex}
 
 \newpage
-\input{part3/case_studies/biogeochem_tutorial/biogeochem.tex}
+\input{s_examples/global_oce_biogeo/biogeochem.tex}
 
 \newpage
-\input{part3/case_studies/global_oce_estimation/global_oce_estimation.tex}
+\input{s_examples/global_oce_optim/global_oce_estimation.tex}
 
 \newpage
-\input{part3/case_studies/sens_airsea_tracer/doc_ad_examples.tex}
+\input{s_examples/tracer_adjsens/doc_ad_examples.tex}
 
 \newpage
-\input{part3/case_studies/offline/offline_tutorial.tex}
+\input{s_examples/cfc_offline/offline_tutorial.tex}
 
 \newpage
-\input{part3/case_studies/rotating_tank/tank.tex}
+\input{s_examples/rotating_tank/tank.tex}