--- manual/s_examples/text/model_examples.tex	2010/08/27 13:25:32	1.21
+++ manual/s_examples/text/model_examples.tex	2013/03/26 13:21:28	1.25
@@ -1,8 +1,8 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/text/model_examples.tex,v 1.21 2010/08/27 13:25:32 jmc 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}
@@ -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}.
@@ -23,89 +23,89 @@
 \subsection{Full list of model examples}
 
 \begin{enumerate}
-  
+
 \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}.
+  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{sect:eg-offline-cfc}.
+  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{sect:eg-bconv}.
+  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{sect:eg-biogeochem_tutorial}.
+  \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{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
   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 cubed sphere grid.  This
-  experiment is described in detail in section \ref{sect:eg-hs}.
-  
+  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
   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
   experiment. Includes derivative calculation. This experiment is
-  described in detail in section \ref{sect:eg-simple-tracer-adjoint}.
+  described in detail in section \ref{sec:eg-simple-tracer-adjoint}.
 
 \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).\\
   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 $2.8^\circ$)
-  
+
 \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{aim.5l\_Equatorial\_Channel}
-  - 5-levels Intermediate Atmospheric physics, 
+  - 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 
+  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/}).
@@ -116,13 +116,13 @@
 \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, 
+\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 
+\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:
@@ -131,13 +131,13 @@
 
 \item \texttt{dome} - Idealized 3D test of a density-driven bottom current.
 
-\item \texttt{exp2} - Old version of the global ocean experiment (no GM, 
+\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
@@ -154,7 +154,7 @@
   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
@@ -165,13 +165,13 @@
 
 \item \texttt{global2x2\_tot} - ECCO production configuration version 0
 
-\item \texttt{global\_ocean.90x40x15} Global ocean simulation at 4x4 
+\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.\\ 
+  cubed sphere grid.\\
   Also contains additional set-ups:
   \begin{enumerate}
    \item non-hydrostratic with biharmonic viscosity ({\it input.viscA4/})
@@ -191,11 +191,11 @@
 
 \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 
+
+\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
@@ -251,13 +251,13 @@
    \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 
+
+\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}.
+  \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
@@ -270,13 +270,13 @@
 
 \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.\\
+  KPP scheme \cite[]{lar-eta:94}.\\
   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/})
+   \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}
@@ -302,20 +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:
@@ -323,16 +323,16 @@
   \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
     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
@@ -343,50 +343,14 @@
   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{s_examples/barotropic_gyre/baro.tex}
-
-\newpage
-\input{s_examples/baroclinic_gyre/fourlayer.tex}
-
-\newpage
-\input{s_examples/advection_in_gyre/adv_gyre.tex}
-
-\newpage
-\input{s_examples/global_oce_latlon/climatalogical_ogcm.tex}
-
-\newpage
-\input{s_examples/global_oce_in_p/ogcm_in_pressure.tex}
-
-\newpage
-\input{s_examples/held_suarez_cs/held_suarez_cs.tex}
-
-\newpage
-\input{s_examples/deep_convection/convection.tex}
-
-\newpage
-\input{s_examples/plume_on_slope/plume_on_slope.tex}
-
-\newpage
-\input{s_examples/global_oce_biogeo/biogeochem.tex}
-
-\newpage
-\input{s_examples/global_oce_optim/global_oce_estimation.tex}
-
-\newpage
-\input{s_examples/tracer_adjsens/doc_ad_examples.tex}
-
-\newpage
-\input{s_examples/cfc_offline/offline_tutorial.tex}
-
-\newpage
-\input{s_examples/rotating_tank/tank.tex}
