--- manual/s_examples/text/model_examples.tex	2006/06/27 19:08:22	1.11
+++ manual/s_examples/text/model_examples.tex	2013/03/26 13:21:28	1.25
@@ -1,120 +1,283 @@
-% $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 1.25 2013/03/26 13:21:28 jmc Exp $
 % $Name:  $
 
 \section[MITgcm Example Experiments]{Example experiments}
-\label{sect:modelExamples}
+\label{sec:modelExamples}
 \begin{rawhtml}
 <!-- CMIREDIR:modelExamples: -->
 \end{rawhtml}
 
 %% 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{sec:eg-baro} -
+\ref{sec: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\_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{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{sec:eg-adv-gyre}.
+
+\item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double
+  gyre. This experiment is described in detail in section
+  \ref{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec: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{sec:eg-offline}.
+
+\item \texttt{tutorial\_plume\_on\_slope} - Gravity Plume on a
+  continental slope.  This experiment is described in detail in
+  section \ref{sec:eg-gravityplume}.
+
+\item \texttt{tutorial\_tracer\_adjsens} - Simple passive tracer
+  experiment. Includes derivative calculation. This experiment is
+  described in detail in section \ref{sec:eg-simple-tracer-adjoint}.
 
-\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{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{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{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.
-  
-\item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
-  advection test on Cartesian grid.
-  
-\item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
+  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.\\
+  Also contains an additional set-up using Adams-Bashforth 3 ({\it input.ab3\_c4/}).
+
+\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{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{aim.5l\_Equatorial\_Channel}
+  - 5-levels Intermediate Atmospheric physics,
+  3D Equatorial Channel configuration.
+
+\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
+  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{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{tutorial\_plume\_on\_slope} Gravity Plume on a continental slope.
-  This experiment is described in detail in section \ref{sect:eg-gravityplume}.
+\item \texttt{ideal\_2D\_oce} - Idealized 2D global ocean simulation on
+  an aqua planet.
 
-\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{internal\_wave} - Ocean internal wave forced by open
+  boundary conditions.
 
-\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{inverted\_barometer} - Simple test of ocean response to
+  atmospheric pressure loading.
 
-\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{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{rotating\_tank} Rotating tank simulation in cylindrical coordinates.
-  This experiment is described in detail in section \ref{sect:eg-tank}.
+\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{sec: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. The standard set-up ({\it input/}) uses
+  KPP scheme \cite[]{lar-eta:94}.\\
+  Also contains additional set-ups:
+  \begin{enumerate}
+   \item with \cite{gas-eta:90} ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
+   \item with \cite{Mellor:Yamada1982} level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
+   \item with \cite{pal-rom:97} ({\it pkg/opps}) scheme ({\it input.opps/})
+   \item with \cite{Pacanowski:Philander1981} ({\it pkg/pp81}) scheme ({\it input.pp81/})
+  \end{enumerate}
 
 \end{enumerate}
 
@@ -139,20 +302,20 @@
   \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
     the ``execution environment'' part of the code. The default
     version is located in \texttt{eesupp/inc}.
-  
+
   \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
     the ``numerical model'' part of the code. The default version is
     located in \texttt{model/inc}.
-  
+
   \item \texttt{code/SIZE.h}: declares size of underlying
     computational grid.  The default version is located in
     \texttt{model/inc}.
   \end{itemize}
-  
+
   In addition, other include files and subroutines might be present in
   \texttt{code} depending on the particular experiment. See Section 2
   for more details.
-  
+
 \item \texttt{input}: contains the input data files required to run
   the example. At a minimum, the \texttt{input} directory contains the
   following files:
@@ -160,66 +323,34 @@
   \begin{itemize}
   \item \texttt{input/data}: this file, written as a namelist,
     specifies the main parameters for the experiment.
-  
+
   \item \texttt{input/data.pkg}: contains parameters relative to the
     packages used in the experiment.
-  
+
   \item \texttt{input/eedata}: this file contains ``execution
     environment'' data. At present, this consists of a specification
     of the number of threads to use in $X$ and $Y$ under multithreaded
     execution.
   \end{itemize}
-  
+
   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.
-\end{itemize}
 
-Once you have chosen the example you want to run, you are ready to
-compile the code.
+\item \texttt{build}: this directory is initially empty and is used
+  to compile and load the model, and to generate the executable.
 
+\item \texttt{run}: this directory is initially empty and is used
+  to run the executable.
 
-\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}
+\end{itemize}
 
-\newpage
-\input{part3/case_studies/offline/offline_tutorial.tex}
+Once you have chosen the example you want to run, you are ready to
+compile the code.
 
-\newpage
-\input{part3/case_studies/rotating_tank/tank.tex}
