/[MITgcm]/manual/s_examples/text/model_examples.tex

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-revision 1.16 by jmc,
Tue Jan 15 19:59:51 2008 UTC
+revision 1.26 by jmc,
Fri Aug 29 17:08:21 2014 UTC
 Line 2
  % $Name$
  \section[MITgcm Example Experiments]{Example experiments}
- \label{sect:modelExamples}
+ \label{sec:modelExamples}
  \begin{rawhtml}
  <!-- CMIREDIR:modelExamples: -->
  \end{rawhtml}
 Line 13 
 The full MITgcm distribution comes with
  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} -
+ and are documented in sections \ref{sec:eg-baro} -
- \ref{sect:eg-tank}. The other examples follow the same general
+ \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}.
 Line 23 
 Each example is briefly described below.
  \subsection{Full list of model examples}
  \begin{enumerate}
- \item \texttt{advection\_in\_gyre\_circulation} - test of various
+ \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}.
+   \ref{sec:eg-adv-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\_baroclinic\_gyre} - Four layer, ocean double
    gyre. This experiment is described in detail in section
-   \ref{sect:eg-fourlayer}.
+   \ref{sec:eg-fourlayer}.
- \item \texttt{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean
+ \item \texttt{tutorial\_barotropic\_gyre} - Single layer, ocean double
-   simulation with steady climatological forcing. This experiment is
+   gyre (barotropic with free-surface).
-   described in detail in section \ref{sect:eg-global}.
+   This experiment is described in detail in section \ref{sec:eg-baro}.
- \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
+ \item \texttt{tutorial\_cfc\_offline} - Offline form of the MITgcm to
-   channel with open boundaries.
+   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
+ \item \texttt{tutorial\_deep\_convection} - Non-uniformly forced
    ocean convection in a doubly periodic box. This experiment is
-   described in detail in section \ref{sect:eg-bconv}.
+   described in detail in section \ref{sec:eg-bconv}.
- \item \texttt{front\_relax} - Relaxation of an ocean thermal front
+ \item \texttt{tutorial\_dic\_adoffline} - Offline form of MITgcm
-   (test for Gent/McWilliams scheme). 2D (Y-Z).
+   dynamics coupled to the dissolved inorganic carbon biogeochemistry model;
+   adjoint set-up.
- \item \texttt{internal\_wave} - Ocean internal wave forced by open
+ \item \texttt{tutorial\_global\_oce\_biogeo} - Ocean model coupled to
-   boundary conditions.
+   the dissolved inorganic carbon biogeochemistry model. This
+   experiment is described in detail in section
- \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
+   \ref{sec:eg-biogeochem_tutorial}.
-   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{adjustment.128x64x1} Barotropic adjustment problem on
+ \item \texttt{tutorial\_global\_oce\_in\_p} - Global ocean simulation in
-   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
+   pressure coordinate (non-Boussinesq ocean model). Described in
+   detail in section \ref{sec:eg-globalpressure}.
- \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\_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{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean
+   simulation with steady climatological forcing. This experiment is
- \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
+   described in detail in section \ref{sec:eg-global}.
-   boundary conditions and poles.
- \item \texttt{tutorial\_global\_oce\_in\_p} Global circulation in
+ \item \texttt{tutorial\_global\_oce\_optim} - Global ocean state
-   pressure coordinate (non-Boussinesq ocean model). Described in
+   estimation at $4^\circ$ resolution.  This experiment is described in
-   detail in section \ref{sect:eg-globalpressure}.
+   detail in section \ref{sec:eg-global_state_estimate}.
- \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
+ \item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics
-   sphere grid.
+   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
+ \item \texttt{tutorial\_plume\_on\_slope} - Gravity Plume on a
    continental slope.  This experiment is described in detail in
-   section \ref{sect:eg-gravityplume}.
+   section \ref{sec:eg-gravityplume}.
- \item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to
+ \item \texttt{tutorial\_tracer\_adjsens} - Simple passive tracer
-   the dissolved inorganic carbon biogeochemistry model. This
+   experiment. Includes derivative calculation. This experiment is
-   experiment is described in detail in section
+   described in detail in section \ref{sec:eg-simple-tracer-adjoint}.\\
-   \ref{sect:eg-biogeochem_tutorial}.
+   Also contains an additional set-up using Secon Order Moment (SOM) advection
+   scheme ({\it input\_ad.som81/}).
- \item \texttt{tutorial\_global\_oce\_optim} Global ocean state
+ \item \texttt{1D\_ocean\_ice\_column} - Oceanic column with seaice on top.
-   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
+ \item \texttt{adjustment.128x64x1} - Barotropic adjustment problem on
-   advection of a passive tracer.  This experiment is described in
+   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
-   detail in section \ref{sect:eg-offline}.
- \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
+ \item \texttt{adjustment.cs-32x32x1} - Barotropic adjustment problem on
-   coordinates.  This experiment is described in detail in section
+   cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
-   \ref{sect:eg-tank}.
+   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 (32x32 grid points per face, roughly $2.8^\circ$ 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{advect\_xz} - Two-dimensional (vertical plane) passive
+   advection test on Cartesian grid.\\
+   Also contains an additional set-up using non-linear free-surface
+    with divergent barotropic flow and implicit vertical advection ({\it input.nlfs/}).
+ \item \texttt{aim.5l\_Equatorial\_Channel} -
+-levels Intermediate Atmospheric physics,
+D 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{MLAdjust} Simple test for different viscosity formulations.
+ \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 a slab-ocean and thermodynamic
+   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{cheapAML\_box} - Example using cheap atmospheric mixed layer
+    (cheapAML) package.
- \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})
+   thermodynamic seaice ({\it pkg/thsice}) and land packages.
+   on cubed-sphere cs32 in a realistic 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 rigid-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.\\
+   Also contains an additional set-up using non-linear free-surface ({\it input.nlfs/}).
- \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
+   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
+ \item \texttt{flt\_example} - Example of using float package.
-   cubed sphere grid, using thermodynamic sea ice and bulk force
-   packages.
- \item \texttt{global\_ocean\_ebm} Global ocean experiment on a lat-lon
+ \item \texttt{front\_relax} - Relaxation of an ocean thermal front
-   grid coupled to an atmospheric energy balance model. Similar to
+   (test for Gent/McWilliams scheme). 2D (y-z).\\
-   global\_ocean.90x40x15 experiment.
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item using the Boundary-Value Problem method
+           (Ferrari et al., 2010) ({\it input.bvp/}).
+    \item with Mixed-Layer Eddy parameterization
+           (Ferrari \& McWilliams, 2007) ({\it input.mxl/}).
+   \end{enumerate}
+ \item \texttt{global\_ocean.90x40x15} - Global ocean simulation at 4x4
+   degree resolution. Similar to tutorial\_global\_oce\_latlon, but using
+   $z^*$ coordinates with quasi-non-hydrostatic and non-hydrostatic metric terms.
+   This experiment also illustrate the use of SBO package.
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item using down-slope package ({\it pkg/down\_slope}) ({\it input.dwnslp/})
+    \item an Open-AD adjoint set-up ({\it code\_oad/, input\_oad/}).
+    \item four TAF adjoint set-ups ({\it code\_ad/}):
+    \begin{enumerate}
+      \item standard experiment ({\it input\_ad/}).
+      \item with bottom drag as a control ({\it input\_ad.bottomdrag/}).
+      \item with kappa GM as a control ({\it input\_ad.kapgm/}).
+      \item with kappa Redi as a control ({\it input\_ad.kapredi/}).
+    \end{enumerate}
+   \end{enumerate}
+ \item \texttt{global\_ocean.cs32x15} - Global ocean experiment on the
+   cubed sphere grid.\\
+   Also contains additional forward set-ups:
+   \begin{enumerate}
+    \item non-hydrostatic with biharmonic viscosity ({\it input.viscA4/})
+    \item using thermodynamic sea ice and bulk force ({\it input.thsice/})
+    \item using thermodynamic ({\it pkg/thsice}) dynamic ({\it pkg/seaice}) sea-ice
+          and {\it exf} package ({\it input.icedyn/})
+    \item using thermodynamic - dynamic ({\it pkg/seaice}) sea-ice
+          with {\it exf} package ({\it input.seaice/})
+   \end{enumerate}
+   and few additional adjoint set-ups ({\it code\_ad/}):
+   \begin{enumerate}
+    \item standard experiment without sea-ice ({\it input\_ad/}).
+    \item using thermodynamic - dynamic sea-ice ({\it input\_ad.seaice/})
+    \item same as above without adjoint sea-ice dynamics ({\it input\_ad.seaice\_dynmix/})
+    \item using thermodynamic sea-ice from {\it thsice} package ({\it input\_ad.thsice/})
+   \end{enumerate}
- \item \texttt{global\_with\_exf} Global ocean experiment on a lat-lon
+ \item \texttt{global\_ocean\_ebm} - Global ocean experiment on a lat-lon
-   grid using the exf package. Similar to global\_ocean.90x40x15
+   grid coupled to an atmospheric energy balance model. Similar to
-   experiment.
+   global\_ocean.90x40x15 experiment.\\
+   Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
- \item \texttt{hs94.cs-32x32x5} 3D atmosphere dynamics using Held and
+ \item \texttt{global\_with\_exf} - Global ocean experiment on a lat-lon
-   Suarez (1994) forcing on the cubed sphere. 5 vertical levels.
+   grid using the {\it exf} package. Similar to tutorial\_global\_oce\_latlon
+   experiment.\\
+   Also contains a secondary set-up with yearly {\it exf} fields ({\it input\_ad.yearly/}).
+ \item \texttt{halfpipe\_streamice} - Example using package "streamice".\\
+   Also contains adjoint set-ups using TAF ({\it code\_ad/, input\_ad/})
+    and using Open-AD ({\it code\_oad/, input\_oad/}).
+ \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 adjoint set-ups using TAF ({\it code\_ad/, input\_ad/})
+    and using Open-AD ({\it code\_oad/, input\_oad/}).
+ \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
+   Suarez (1994) forcing on the cubed sphere, similar to tutorial\_held\_suarez\_cs
+   experiment but using linear free-surface and only 5 levels.\\
+   Also contains an additional set-up with Implicit Internal gravity waves
+   treatment and Adams-Bashforth 3 ({\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.\\
+   Also contains an additional set-up using {\it pkg/kl10} (see section
+    \ref{sec:pkg:kl10}, Klymak and Legg, 2010) ({\it input.kl10/}).
+ \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
+ \item \texttt{isomip} - ISOMIP like set-up including ice-shelf cavities
-   grid. Coupled to the sea ice model.
+   ({\it pkg/shelfice}).\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item with "htd" ({\it input.htd/})
+           but only Martin knows what "htd" stands for.
+    \item using package {\it icefront} ({\it input.icefront})
+   \end{enumerate}
+   and also adjoint set-ups using TAF ({\it code\_ad/, input\_ad/, input\_ad.htd/})
+   or using Open-AD ({\it code\_oad/, input\_oad/}).
+ \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 simple "free-drift" assumption for seaice ({\it input.fd/})
+    \item using EVP dynamics (instead of LSR solver) and Hibler \& 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 equilibrium.
+ \item \texttt{MLAdjust} - Simple tests for different viscosity formulations.\\
+   Also contains additional set-ups (see: {\it verification/MLAdjust/README}):
+   \begin{enumerate}
+    \item ({\it input.A4FlxF/})
+    \item ({\it input.AhFlxF/})
+    \item ({\it input.AhVrDv/})
+    \item ({\it input.AhStTn/})
+   \end{enumerate}
+ \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
+   scheme; 1 month integration
+ \item \texttt{obcs\_ctrl} - Adjoint test using Open-Boundary conditions
+   as control parameters.
- \item \texttt{matrix\_example} Test of experimental method to
+ \item \texttt{offline\_exf\_seaice} - Seaice on top of oceanic surface layer
-   accelerated convergence towards equillibrium.
+   in an idealized channel. Forcing is computed by bulk-formulae ({\it pkg/exf})
+   with temperature relaxation to prescribed SST (offline ocean).\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item sea-ice dynamics-only using JFNK solver
+          and {\it pkg/thsice} advection ({\it input.dyn\_jfnk/})
+    \item sea-ice dynamics-only using LSR solver
+          and {\it pkg/seaice} advection ({\it input.dyn\_lsr/})
+    \item sea-ice thermodynamics-only using {\it pkg/seaice} ({\it input.thermo/})
+    \item sea-ice thermodynamics-only using {\it pkg/thsice} ({\it input.thsice/})
+   \end{enumerate}
+   and also 2 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.thsice/}).
- \item \texttt{tutorial\_cfc\_offline} Offline form of the MITgcm to
+ \item \texttt{OpenAD} - Simple Adjoint experiment (used also to test
-   study advection of a passive tracer and CFCs.
+   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{vermix} Simple test in a small domain (3 columns) for
+ \item \texttt{seaice\_itd} - Seaice example using Ice Thickness Distribution (ITD).\\
-   ocean vertical mixing schemes.
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item ({\it input.thermo/})
+    \item ({\it input.lipscomb07/})
+   \end{enumerate}
+ \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.\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item ({\it input.seaiceSponge/})
+    \item ({\it input.tides/})
+   \end{enumerate}
+ \item \texttt{short\_surf\_wave} - Short surface wave adjusment
+    (non-hydrostatic) in homogeneous 2-D vertical section (x-z).
+ \item \texttt{so\_box\_biogeo} - Open-boundary Southern ocean box around
+  Drake passage, using same model parameters and forcing as experiment
+   "tutorial\_global\_oce\_biogeo" from which initial conditions
+  and OB conditions have been extracted.
+ \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
+  (untested)
+ \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 Double Diffusion scheme from KPP ({\it input.dd/})
+    \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}
-Line 218 
 Each example directory has the following
+Line 379 
 Each example directory has the following
    \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:
-Line 239 
 Each example directory has the following
+Line 400 
 Each example directory has the following
    \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
+     of the number of threads to use in $X$ and $Y$ under multi-threaded
      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
-Line 259 
 Each example directory has the following
+Line 420 
 Each example directory has the following
    useful for comparison with your own output when you run the
    experiment.
- \item \texttt{build}: this directory is where the model is compiled
+ \item \texttt{build}: this directory is initially empty and is used
-   and loaded, and where the executable resides.
+   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.
  \end{itemize}
  Once you have chosen the example you want to run, you are ready to
  compile the code.
- \newpage
- \input{part3/case_studies/advection_in_gyre_circulation/adv_gyre.tex}
- \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/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}

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