--- manual/s_examples/text/model_examples.tex	2008/01/15 21:17:19	1.18
+++ manual/s_examples/text/model_examples.tex	2014/08/29 17:08:21	1.26
@@ -1,8 +1,8 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.18 2008/01/15 21:17:19 jmc Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.26 2014/08/29 17:08:21 jmc Exp $
 % $Name:  $
 
 \section[MITgcm Example Experiments]{Example experiments}
-\label{sect:modelExamples}
+\label{sec:modelExamples}
 \begin{rawhtml}
 <!-- CMIREDIR:modelExamples: -->
 \end{rawhtml}
@@ -13,8 +13,8 @@
 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
+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}.
@@ -23,174 +23,338 @@
 \subsection{Full list of model examples}
 
 \begin{enumerate}
-  
-\item \texttt{tutorial\_advection\_in\_gyre} - 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\_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\_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{sec:eg-baro}.
 
-\item \texttt{tutorial\_cfc\_offline} Offline form of the MITgcm to
+\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
+\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{tutorial\_dic\_adoffline} - Offline form of MITgcm
+  dynamics coupled to the dissolved inorganic carbon biogeochemistry model;
+  adjoint set-up.
 
-\item \texttt{tutorial\_global\_oce\_biogeo} Ocean model coupled to
+\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}.
+  \ref{sec:eg-biogeochem_tutorial}.
 
-\item \texttt{tutorial\_global\_oce\_in\_p} Global circulation in
+\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}.
+  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{sect:eg-global}.
+  described in detail in section \ref{sec:eg-global}.
 
-\item \texttt{tutorial\_global\_oce\_optim} Global ocean state
+\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}.
+  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 the cubed sphere.  This
-  experiment is described in detail in section \ref{sect:eg-hs}.
-  
-\item \texttt{tutorial\_offline} Offline form of the MITgcm to study
+  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{sect:eg-offline}.
+  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\_tracer\_adjsens} Simple passive 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}.
+  described in detail in section \ref{sec:eg-simple-tracer-adjoint}.\\
+  Also contains an additional set-up using Secon Order Moment (SOM) advection
+  scheme ({\it input\_ad.som81/}).
 
-\item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
+\item \texttt{1D\_ocean\_ice\_column} - Oceanic column with seaice on top.
+
+\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).
-  
-\item \texttt{advect\_cs} Two-dimensional passive advection test on
-  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\_xz} Two-dimensional (vertical plane) passive
-  advection test on Cartesian grid.
-  
-\item \texttt{aim.5l\_Equatorial\_Channel}
-  - 5-levels Intermediate Atmospheric physics, 
+  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} -
+  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 $2.8^\circ$). 
+  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{exp4} - Flow over a Gaussian bump in open-water or
-  channel with open boundaries.
-  
-\item \texttt{exp5} Deep convection.
+  channel with open boundaries.\\
+  Also contains an additional set-up using non-linear free-surface ({\it input.nlfs/}).
 
-\item \texttt{fizhi-cs-32x32x40} 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{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).
-
-\item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
-  boundary conditions and poles.
+\item \texttt{flt\_example} - Example of using float package.
 
-\item \texttt{global\_ocean.cs32x15} Global ocean experiment on the
-  cubed sphere grid, using thermodynamic sea ice and bulk force
-  packages.
+\item \texttt{front\_relax} - Relaxation of an ocean thermal front
+  (test for Gent/McWilliams scheme). 2D (y-z).\\
+  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\_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.
-
-\item \texttt{global\_with\_exf} Global ocean experiment on a lat-lon
-  grid using the exf package. Similar to global\_ocean.90x40x15
-  experiment.
+  global\_ocean.90x40x15 experiment.\\
+  Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
 
-\item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
-  Suarez '94 forcing.
-  
-\item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
-  Suarez '94 forcing.
-  
-\item \texttt{hs94.cs-32x32x5} 3D atmosphere dynamics using Held and
-  Suarez (1994) forcing on the cubed sphere. 5 vertical levels.
+\item \texttt{global\_with\_exf} - Global ocean experiment on a lat-lon
+  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{internal\_wave} - Ocean internal wave forced by open
-  boundary conditions.
+  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
+\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{matrix\_example} Test of experimental method to
-  accelerated convergence towards equillibrium.
-
-\item \texttt{MLAdjust} Simple test for different viscosity formulations.
+\item \texttt{isomip} - ISOMIP like set-up including ice-shelf cavities
+  ({\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{rotating\_tank} Rotating tank simulation in cylindrical
+
+\item \texttt{obcs\_ctrl} - Adjoint test using Open-Boundary conditions
+  as control parameters.
+
+\item \texttt{offline\_exf\_seaice} - Seaice on top of oceanic surface layer
+  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{OpenAD} - Simple Adjoint experiment (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}.
+  \ref{sec:eg-tank}.
+
+\item \texttt{seaice\_itd} - Seaice example using Ice Thickness Distribution (ITD).\\
+  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
+\item \texttt{solid-body.cs-32x32x1} - Solid body rotation test for cube
   sphere grid.
 
-\item \texttt{vermix} Simple test in a small domain (3 columns) for
-  ocean vertical mixing schemes.
+\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}
 
@@ -215,20 +379,20 @@
   \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:
@@ -236,16 +400,16 @@
   \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
@@ -256,50 +420,14 @@
   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.
+\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.
 
 \end{itemize}
 
 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/advection_in_gyre_circulation/adv_gyre.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}
