--- manual/s_examples/global_oce_latlon/climatalogical_ogcm.tex	2008/01/15 20:04:06	1.16
+++ manual/s_examples/global_oce_latlon/climatalogical_ogcm.tex	2015/11/25 10:57:41	1.25
@@ -1,9 +1,9 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/global_oce_latlon/climatalogical_ogcm.tex,v 1.16 2008/01/15 20:04:06 jmc Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/global_oce_latlon/climatalogical_ogcm.tex,v 1.25 2015/11/25 10:57:41 mlosch Exp $
 % $Name:  $
 
-\section[Global Ocean MITgcm Exmaple]{Global Ocean Simulation at $4^\circ$ Resolution}
-\label{www:tutorials}
-\label{sect:eg-global}
+\section[Global Ocean MITgcm Example]{Global Ocean Simulation at $4^\circ$ Resolution}
+%\label{www:tutorials}
+\label{sec:eg-global}
 \begin{rawhtml}
 <!-- CMIREDIR:eg-global: -->
 \end{rawhtml}
@@ -13,7 +13,10 @@
 
 \bodytext{bgcolor="#FFFFFFFF"}
 
-%\begin{center} 
+\noindent {\bf WARNING: the description of this experiment is not complete.
+ In particular, many parameters are not yet described.}\\
+
+%\begin{center}
 %{\Large \bf Using MITgcm to Simulate Global Climatological Ocean Circulation
 %At Four Degree Resolution with Asynchronous Time Stepping}
 %
@@ -23,48 +26,47 @@
 %{\large May 2001}
 %\end{center}
 
-
-This example experiment demonstrates using the MITgcm to simulate
-the planetary ocean circulation. The simulation is configured
-with realistic geography and bathymetry on a
-$4^{\circ} \times 4^{\circ}$ spherical polar grid.
-The files for this experiment are in the verification directory
-under tutorial\_global\_oce\_latlon.
-Twenty levels are used in the vertical, ranging in thickness
-from $50\,{\rm m}$ at the surface to $815\,{\rm m}$ at depth,
-giving a maximum model depth of $6\,{\rm km}$.
-At this resolution, the configuration
-can be integrated forward for thousands of years on a single 
-processor desktop computer.
+This example experiment demonstrates using the MITgcm to simulate the
+planetary ocean circulation. The simulation is configured with
+realistic geography and bathymetry on a $4^{\circ} \times 4^{\circ}$
+spherical polar grid. The files for this experiment are in the
+verification directory under tutorial\_global\_oce\_latlon. Fifteen
+levels are used in the vertical, ranging in thickness from $50\,{\rm
+  m}$ at the surface to $690\,{\rm m}$ at depth, giving a maximum
+model depth of $5200\,{\rm m}$.
+Different time-steps are used to accelerate the convergence to
+equilibrium \cite[]{bryan:84} so that, at this resolution,
+the configuration can be integrated forward for thousands of years
+on a single processor desktop computer.
 \\
 \subsection{Overview}
-\label{www:tutorials}
+%\label{www:tutorials}
 
-The model is forced with climatological wind stress data and surface
-flux data from DaSilva \cite{DaSilva94}. Climatological data
-from Levitus \cite{Levitus94} is used to initialize the model hydrography.
-Levitus seasonal climatology data is also used throughout the calculation
-to provide additional air-sea fluxes.
-These fluxes are combined with the DaSilva climatological estimates of
-surface heat flux and fresh water, resulting in a mixed boundary
-condition of the style described in Haney \cite{Haney}.
-Altogether, this yields the following forcing applied
-in the model surface layer.
+The model is forced with climatological wind stress data from
+\citet{trenberth90} and NCEP surface flux data from
+\citet{kalnay96}. Climatological data \citep{Levitus94} is
+used to initialize the model hydrography. \citeauthor{Levitus94} seasonal
+climatology data is also used throughout the calculation to provide
+additional air-sea fluxes.  These fluxes are combined with the NCEP
+climatological estimates of surface heat flux, resulting in a mixed
+boundary condition of the style described in \citet{Haney}.
+Altogether, this yields the following forcing applied in the model
+surface layer.
 
 \begin{eqnarray}
-\label{EQ:eg-global-global_forcing}
-\label{EQ:eg-global-global_forcing_fu}
+\label{eq:eg-global-global_forcing}
+\label{eq:eg-global-global_forcing_fu}
 {\cal F}_{u} & = & \frac{\tau_{x}}{\rho_{0} \Delta z_{s}}
 \\
-\label{EQ:eg-global-global_forcing_fv}
+\label{eq:eg-global-global_forcing_fv}
 {\cal F}_{v} & = & \frac{\tau_{y}}{\rho_{0} \Delta z_{s}}
 \\
-\label{EQ:eg-global-global_forcing_ft}
-{\cal F}_{\theta} & = & - \lambda_{\theta} ( \theta - \theta^{\ast} ) 
+\label{eq:eg-global-global_forcing_ft}
+{\cal F}_{\theta} & = & - \lambda_{\theta} ( \theta - \theta^{\ast} )
  - \frac{1}{C_{p} \rho_{0} \Delta z_{s}}{\cal Q}
 \\
-\label{EQ:eg-global-global_forcing_fs}
-{\cal F}_{s} & = & - \lambda_{s} ( S - S^{\ast} ) 
+\label{eq:eg-global-global_forcing_fs}
+{\cal F}_{s} & = & - \lambda_{s} ( S - S^{\ast} )
  + \frac{S_{0}}{\Delta z_{s}}({\cal E} - {\cal P} - {\cal R})
 \end{eqnarray}
 
@@ -88,90 +90,79 @@
 $\cal{Q}$ and $\cal{E}-\cal{P}-\cal{R}$. The wind stress fields ($\tau_x$, $\tau_y$)
 have units of ${\rm N}~{\rm m}^{-2}$. The temperature forcing fields
 ($\theta^{\ast}$ and $Q$) have units of $^{\circ}{\rm C}$ and ${\rm W}~{\rm m}^{-2}$
-respectively. The salinity forcing fields ($S^{\ast}$ and 
+respectively. The salinity forcing fields ($S^{\ast}$ and
 $\cal{E}-\cal{P}-\cal{R}$) have units of ${\rm ppt}$ and ${\rm m}~{\rm s}^{-1}$
 respectively. The source files and procedures for ingesting this data into the
 simulation are described in the experiment configuration discussion in section
-\ref{SEC:eg-global-clim_ocn_examp_exp_config}.
+\ref{sec:eg-global-clim_ocn_examp_exp_config}.
 
 
 \subsection{Discrete Numerical Configuration}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 
- The model is configured in hydrostatic form.  The domain is discretised with 
-a uniform grid spacing in latitude and longitude on the sphere
- $\Delta \phi=\Delta \lambda=4^{\circ}$, so 
-that there are ninety grid cells in the zonal and forty in the 
-meridional direction. The internal model coordinate variables
-$x$ and $y$ are initialized according to
+The model is configured in hydrostatic form.  The domain is
+discretised with a uniform grid spacing in latitude and longitude on
+the sphere $\Delta \phi=\Delta \lambda=4^{\circ}$, so that there are
+ninety grid cells in the zonal and forty in the meridional
+direction. The internal model coordinate variables $x$ and $y$ are
+initialized according to
 \begin{eqnarray}
 x=r\cos(\phi),~\Delta x & = &r\cos(\Delta \phi) \\
-y=r\lambda,~\Delta y &= &r\Delta \lambda 
+y=r\lambda,~\Delta y &= &r\Delta \lambda
 \end{eqnarray}
 
 Arctic polar regions are not
 included in this experiment. Meridionally the model extends from
 $80^{\circ}{\rm S}$ to $80^{\circ}{\rm N}$.
-Vertically the model is configured with twenty layers with the 
-following thicknesses
-$\Delta z_{1} = 50\,{\rm m},\,
- \Delta z_{2} = 50\,{\rm m},\,
- \Delta z_{3} = 55\,{\rm m},\,
- \Delta z_{4} = 60\,{\rm m},\,
- \Delta z_{5} = 65\,{\rm m},\,
-$
-$
- \Delta z_{6}~=~70\,{\rm m},\,
- \Delta z_{7}~=~80\,{\rm m},\,
- \Delta z_{8}~=95\,{\rm m},\,
- \Delta z_{9}=120\,{\rm m},\,
- \Delta z_{10}=155\,{\rm m},\,
-$
-$
- \Delta z_{11}=200\,{\rm m},\,
- \Delta z_{12}=260\,{\rm m},\,
- \Delta z_{13}=320\,{\rm m},\,
- \Delta z_{14}=400\,{\rm m},\,
- \Delta z_{15}=480\,{\rm m},\,
-$
-$
- \Delta z_{16}=570\,{\rm m},\,
- \Delta z_{17}=655\,{\rm m},\,
- \Delta z_{18}=725\,{\rm m},\,
- \Delta z_{19}=775\,{\rm m},\,
- \Delta z_{20}=815\,{\rm m}
-$ (here the numeric subscript indicates the model level index number, ${\tt k}$) to
-give a total depth, $H$, of $-5450{\rm m}$.
-The implicit free surface form of the pressure equation described in Marshall et. al 
-\cite{marshall:97a} is employed. A Laplacian operator, $\nabla^2$, provides viscous
+Vertically the model is configured with fifteen layers with the
+following thicknesses:
+$\Delta z_{1} = 50\,{\rm m},$\\
+$\Delta z_{2} = 70\,{\rm m},\,
+ \Delta z_{3} = 100\,{\rm m},\,
+ \Delta z_{4} = 140\,{\rm m},\,
+ \Delta z_{5} = 190\,{\rm m},\,
+ \Delta z_{6} = 240\,{\rm m},\,
+ \Delta z_{7} = 290\,{\rm m},\,
+ \Delta z_{8} = 340\,{\rm m},$\\
+$\Delta z_{9} = 390\,{\rm m},\,
+ \Delta z_{10}= 440\,{\rm m},\,
+ \Delta z_{11}= 490\,{\rm m},\,
+ \Delta z_{12}= 540\,{\rm m},\,
+ \Delta z_{13}= 590\,{\rm m},\,
+ \Delta z_{14}= 640\,{\rm m},\,
+ \Delta z_{15}= 690\,{\rm m}$\\
+(here the numeric subscript indicates the model level index number, ${\tt k}$) to
+give a total depth, $H$, of $-5200{\rm m}$.
+The implicit free surface form of the pressure equation described in
+\citet{marshall:97a} is employed. A Laplacian operator, $\nabla^2$, provides viscous
 dissipation. Thermal and haline diffusion is also represented by a Laplacian operator.
 
-Wind-stress forcing is added to the momentum equations in (\ref{EQ:eg-global-model_equations}) 
-for both the zonal flow, $u$ and the meridional flow $v$, according to equations 
-(\ref{EQ:eg-global-global_forcing_fu}) and (\ref{EQ:eg-global-global_forcing_fv}).
-Thermodynamic forcing inputs are added to the equations 
-in (\ref{EQ:eg-global-model_equations}) for
-potential temperature, $\theta$, and salinity, $S$, according to equations 
-(\ref{EQ:eg-global-global_forcing_ft}) and (\ref{EQ:eg-global-global_forcing_fs}).
+Wind-stress forcing is added to the momentum equations in (\ref{eq:eg-global-model_equations})
+for both the zonal flow, $u$ and the meridional flow $v$, according to equations
+(\ref{eq:eg-global-global_forcing_fu}) and (\ref{eq:eg-global-global_forcing_fv}).
+Thermodynamic forcing inputs are added to the equations
+in (\ref{eq:eg-global-model_equations}) for
+potential temperature, $\theta$, and salinity, $S$, according to equations
+(\ref{eq:eg-global-global_forcing_ft}) and (\ref{eq:eg-global-global_forcing_fs}).
 This produces a set of equations solved in this configuration as follows:
 
 \begin{eqnarray}
-\label{EQ:eg-global-model_equations}
-\frac{Du}{Dt} - fv + 
-  \frac{1}{\rho}\frac{\partial p^{'}}{\partial x} - 
-  \nabla_{h}\cdot A_{h}\nabla_{h}u - 
-  \frac{\partial}{\partial z}A_{z}\frac{\partial u}{\partial z} 
+\label{eq:eg-global-model_equations}
+\frac{Du}{Dt} - fv +
+  \frac{1}{\rho}\frac{\partial p^{'}}{\partial x} -
+  \nabla_{h}\cdot A_{h}\nabla_{h}u -
+  \frac{\partial}{\partial z}A_{z}\frac{\partial u}{\partial z}
  & = &
 \begin{cases}
 {\cal F}_u & \text{(surface)} \\
 0 & \text{(interior)}
 \end{cases}
 \\
-\frac{Dv}{Dt} + fu + 
-  \frac{1}{\rho}\frac{\partial p^{'}}{\partial y} - 
-  \nabla_{h}\cdot A_{h}\nabla_{h}v - 
-  \frac{\partial}{\partial z}A_{z}\frac{\partial v}{\partial z} 
+\frac{Dv}{Dt} + fu +
+  \frac{1}{\rho}\frac{\partial p^{'}}{\partial y} -
+  \nabla_{h}\cdot A_{h}\nabla_{h}v -
+  \frac{\partial}{\partial z}A_{z}\frac{\partial v}{\partial z}
 & = &
 \begin{cases}
 {\cal F}_v & \text{(surface)} \\
@@ -184,7 +175,7 @@
 \\
 \frac{D\theta}{Dt} -
  \nabla_{h}\cdot K_{h}\nabla_{h}\theta
- - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial\theta}{\partial z} 
+ - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial\theta}{\partial z}
 & = &
 \begin{cases}
 {\cal F}_\theta & \text{(surface)} \\
@@ -193,7 +184,7 @@
 \\
 \frac{D s}{Dt} -
  \nabla_{h}\cdot K_{h}\nabla_{h}s
- - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial s}{\partial z} 
+ - \frac{\partial}{\partial z}\Gamma(K_{z})\frac{\partial s}{\partial z}
 & = &
 \begin{cases}
 {\cal F}_s & \text{(surface)} \\
@@ -203,529 +194,280 @@
 g\rho_{0} \eta + \int^{0}_{-z}\rho^{'} dz & = & p^{'}
 \end{eqnarray}
 
-\noindent where $u=\frac{Dx}{Dt}=r \cos(\phi)\frac{D \lambda}{Dt}$ and 
-$v=\frac{Dy}{Dt}=r \frac{D \phi}{Dt}$ 
+\noindent where $u=\frac{Dx}{Dt}=r \cos(\phi)\frac{D \lambda}{Dt}$ and
+$v=\frac{Dy}{Dt}=r \frac{D \phi}{Dt}$
 are the zonal and meridional components of the
 flow vector, $\vec{u}$, on the sphere. As described in
-MITgcm Numerical Solution Procedure \ref{chap:discretization}, the time 
+MITgcm Numerical Solution Procedure \ref{chap:discretization}, the time
 evolution of potential temperature, $\theta$, equation is solved prognostically.
-The total pressure, $p$, is diagnosed by summing pressure due to surface 
+The total pressure, $p$, is diagnosed by summing pressure due to surface
 elevation $\eta$ and the hydrostatic pressure.
 \\
 
 \subsubsection{Numerical Stability Criteria}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 The Laplacian dissipation coefficient, $A_{h}$, is set to $5 \times 10^5 m s^{-1}$.
-This value is chosen to yield a Munk layer width \cite{adcroft:95},
+This value is chosen to yield a Munk layer width \citep{adcroft:95},
 \begin{eqnarray}
-\label{EQ:eg-global-munk_layer}
+\label{eq:eg-global-munk_layer}
 && M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
 \end{eqnarray}
 
 \noindent  of $\approx 600$km. This is greater than the model
-resolution in low-latitudes, $\Delta x \approx 400{\rm km}$, ensuring that the frictional 
+resolution in low-latitudes, $\Delta x \approx 400{\rm km}$, ensuring that the frictional
 boundary layer is adequately resolved.
 \\
 
-\noindent The model is stepped forward with a 
-time step $\delta t_{\theta}=30~{\rm hours}$ for thermodynamic variables and
-$\delta t_{v}=40~{\rm minutes}$ for momentum terms. With this time step, the stability 
-parameter to the horizontal Laplacian friction \cite{adcroft:95}
+\noindent The model is stepped forward with a time step $\Delta
+t_{\theta}=24~{\rm hours}$ for thermodynamic variables and $\Delta
+t_{v}=30~{\rm minutes}$ for momentum terms. With this time step,
+the stability parameter to the horizontal Laplacian friction
+\citep{adcroft:95}
 \begin{eqnarray}
-\label{EQ:eg-global-laplacian_stability}
-&& S_{l} = 4 \frac{A_{h} \delta t_{v}}{{\Delta x}^2}
+\label{eq:eg-global-laplacian_stability}
+&& S_{l} = 4 \frac{A_{h} \Delta t_{v}}{{\Delta x}^2}
 \end{eqnarray}
 
-\noindent evaluates to 0.16 at a latitude of $\phi=80^{\circ}$, which is below the 
-0.3 upper limit for stability. The zonal grid spacing $\Delta x$ is smallest at
-$\phi=80^{\circ}$ where $\Delta x=r\cos(\phi)\Delta \phi\approx 77{\rm km}$.
-\\
+\noindent evaluates to 0.6 at a latitude of $\phi=80^{\circ}$, which
+is above the 0.3 upper limit for stability, but the zonal grid spacing
+$\Delta x$ is smallest at $\phi=80^{\circ}$ where $\Delta
+x=r\cos(\phi)\Delta \phi\approx 77{\rm km}$ and the stability
+criterion is already met 1 grid cell equatorwards (at $\phi=76^{\circ}$).
+
 
-\noindent The vertical dissipation coefficient, $A_{z}$, is set to 
+\noindent The vertical dissipation coefficient, $A_{z}$, is set to
 $1\times10^{-3} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
 \begin{eqnarray}
-\label{EQ:eg-global-laplacian_stability_z}
-S_{l} = 4 \frac{A_{z} \delta t_{v}}{{\Delta z}^2}
+\label{eq:eg-global-laplacian_stability_z}
+&& S_{l} = 4 \frac{A_{z} \Delta t_{v}}{{\Delta z}^2}
 \end{eqnarray}
 
-\noindent evaluates to $0.015$ for the smallest model
-level spacing ($\Delta z_{1}=50{\rm m}$) which is again well below
+\noindent evaluates to $0.0029$ for the smallest model
+level spacing ($\Delta z_{1}=50{\rm m}$) which is well below
 the upper stability limit.
 \\
 
-The values of the horizontal ($K_{h}$) and vertical ($K_{z}$) diffusion coefficients 
-for both temperature and salinity are set to $1 \times 10^{3}~{\rm m}^{2}{\rm s}^{-1}$ 
-and $3 \times 10^{-5}~{\rm m}^{2}{\rm s}^{-1}$ respectively. The stability limit 
-related to $K_{h}$ will be at $\phi=80^{\circ}$ where $\Delta x \approx 77 {\rm km}$. 
-Here the stability parameter 
-\begin{eqnarray} 
-\label{EQ:eg-global-laplacian_stability_xtheta}
-S_{l} = \frac{4 K_{h} \delta t_{\theta}}{{\Delta x}^2} 
-\end{eqnarray}
-evaluates to $0.07$, well below the stability limit of $S_{l} \approx 0.5$. The 
-stability parameter related to $K_{z}$
-\begin{eqnarray} 
-\label{EQ:eg-global-laplacian_stability_ztheta}
-S_{l} = \frac{4 K_{z} \delta t_{\theta}}{{\Delta z}^2} 
-\end{eqnarray}
-evaluates to $0.005$ for $\min(\Delta z)=50{\rm m}$, well below the stability limit 
-of $S_{l} \approx 0.5$.
-\\
+% The values of the horizontal ($K_{h}$) and vertical ($K_{z}$) diffusion coefficients
+% for both temperature and salinity are set to $1 \times 10^{3}~{\rm m}^{2}{\rm s}^{-1}$
+% and $3 \times 10^{-5}~{\rm m}^{2}{\rm s}^{-1}$ respectively. The stability limit
+% related to $K_{h}$ will be at $\phi=80^{\circ}$ where $\Delta x \approx 77 {\rm km}$.
+% Here the stability parameter
+% \begin{eqnarray}
+% \label{eq:eg-global-laplacian_stability_xtheta}
+% S_{l} = \frac{4 K_{h} \Delta t_{\theta}}{{\Delta x}^2}
+% \end{eqnarray}
+% evaluates to $0.07$, well below the stability limit of $S_{l} \approx 0.5$. The
+% stability parameter related to $K_{z}$
+% \begin{eqnarray}
+% \label{eq:eg-global-laplacian_stability_ztheta}
+% S_{l} = \frac{4 K_{z} \Delta t_{\theta}}{{\Delta z}^2}
+% \end{eqnarray}
+% evaluates to $0.005$ for $\min(\Delta z)=50{\rm m}$, well below the stability limit
+% of $S_{l} \approx 0.5$.
+% \\
 
 \noindent The numerical stability for inertial oscillations
-\cite{adcroft:95} 
+\citep{adcroft:95}
 
 \begin{eqnarray}
-\label{EQ:eg-global-inertial_stability}
-S_{i} = f^{2} {\delta t_v}^2
+\label{eq:eg-global-inertial_stability}
+&& S_{i} = f^{2} {\Delta t_v}^2
 \end{eqnarray}
 
-\noindent evaluates to $0.24$ for $f=2\omega\sin(80^{\circ})=1.43\times10^{-4}~{\rm s}^{-1}$, which is close to 
-the $S_{i} < 1$ upper limit for stability.
+\noindent evaluates to $0.07$ for
+$f=2\omega\sin(80^{\circ})=1.43\times10^{-4}~{\rm s}^{-1}$, which is
+below the $S_{i} < 1$ upper limit for stability.
 \\
 
-\noindent The advective CFL \cite{adcroft:95} for a extreme maximum 
+\noindent The advective CFL \citep{adcroft:95} for a extreme maximum
 horizontal flow
 speed of $ | \vec{u} | = 2 ms^{-1}$
 
 \begin{eqnarray}
-\label{EQ:eg-global-cfl_stability}
-S_{a} = \frac{| \vec{u} | \delta t_{v}}{ \Delta x}
+\label{eq:eg-global-cfl_stability}
+&& S_{a} = \frac{| \vec{u} | \Delta t_{v}}{ \Delta x}
 \end{eqnarray}
 
-\noindent evaluates to $6 \times 10^{-2}$. This is well below the stability 
+\noindent evaluates to $5 \times 10^{-2}$. This is well below the stability
 limit of 0.5.
 \\
 
 \noindent The stability parameter for internal gravity waves propagating
-with a maximum speed of $c_{g}=10~{\rm ms}^{-1}$
-\cite{adcroft:95}
+ with a maximum speed of $c_{g}=10~{\rm ms}^{-1}$
+\citep{adcroft:95}
 
 \begin{eqnarray}
-\label{EQ:eg-global-gfl_stability}
-S_{c} = \frac{c_{g} \delta t_{v}}{ \Delta x}
+\label{eq:eg-global-gfl_stability}
+&& S_{c} = \frac{c_{g} \Delta t_{v}}{ \Delta x}
 \end{eqnarray}
 
-\noindent evaluates to $3 \times 10^{-1}$. This is close to the linear
+\noindent evaluates to $2.3 \times 10^{-1}$. This is close to the linear
 stability limit of 0.5.
-  
+
 \subsection{Experiment Configuration}
-\label{www:tutorials}
-\label{SEC:eg-global-clim_ocn_examp_exp_config}
+%\label{www:tutorials}
+\label{sec:eg-global-clim_ocn_examp_exp_config}
 
-The model configuration for this experiment resides under the 
-directory {\it tutorial\_examples/global\_ocean\_circulation/}.  
-The experiment files 
+The model configuration for this experiment resides under the
+directory {\it tutorial\_global\_oce\_latlon/}. The experiment files
 
 \begin{itemize}
 \item {\it input/data}
 \item {\it input/data.pkg}
 \item {\it input/eedata},
-\item {\it input/windx.bin},
-\item {\it input/windy.bin},
-\item {\it input/salt.bin},
-\item {\it input/theta.bin},
-\item {\it input/SSS.bin},
-\item {\it input/SST.bin},
-\item {\it input/topog.bin},
-\item {\it code/CPP\_EEOPTIONS.h}
-\item {\it code/CPP\_OPTIONS.h},
-\item {\it code/SIZE.h}. 
+\item {\it input/trenberth\_taux.bin},
+\item {\it input/trenberth\_tauy.bin},
+\item {\it input/lev\_s.bin},
+\item {\it input/lev\_t.bin},
+\item {\it input/lev\_sss.bin},
+\item {\it input/lev\_sst.bin},
+\item {\it input/bathymetry.bin},
+%\item {\it code/CPP\_EEOPTIONS.h}
+%\item {\it code/CPP\_OPTIONS.h},
+\item {\it code/SIZE.h}.
 \end{itemize}
 contain the code customizations and parameter settings for these
 experiments. Below we describe the customizations
 to these files associated with this experiment.
 
 \subsubsection{Driving Datasets}
-\label{www:tutorials}
+%\label{www:tutorials}
 
-Figures (\ref{FIG:sim_config_tclim}-\ref{FIG:sim_config_empmr}) show the
-relaxation temperature ($\theta^{\ast}$) and salinity ($S^{\ast}$) fields,
-the wind stress components ($\tau_x$ and $\tau_y$), the heat flux ($Q$)
+%% New figures are included before
+%% Relaxation temperature
+%\begin{figure}
+%\centering
+%\includegraphics[]{relax_temperature.eps}
+%\caption{Relaxation temperature for January}
+%\label{fig:relax_temperature}
+%\end{figure}
+
+%% Relaxation salinity
+%\begin{figure}
+%\centering
+%\includegraphics[]{relax_salinity.eps}
+%\caption{Relaxation salinity for January}
+%\label{fig:relax_salinity}
+%\end{figure}
+
+%% tau_x
+%\begin{figure}
+%\centering
+%\includegraphics[]{tau_x.eps}
+%\caption{zonal wind stress for January}
+%\label{fig:tau_x}
+%\end{figure}
+
+%% tau_y
+%\begin{figure}
+%\centering
+%\includegraphics[]{tau_y.eps}
+%\caption{meridional wind stress for January}
+%\label{fig:tau_y}
+%\end{figure}
+
+%% Qnet
+%\begin{figure}
+%\centering
+%\includegraphics[]{qnet.eps}
+%\caption{Heat flux for January}
+%\label{fig:qnet}
+%\end{figure}
+
+%% EmPmR
+%\begin{figure}
+%\centering
+%\includegraphics[]{empmr.eps}
+%\caption{Fresh water flux for January}
+%\label{fig:empmr}
+%\end{figure}
+
+%% Bathymetry
+%\begin{figure}
+%\centering
+%\includegraphics[]{bathymetry.eps}
+%\caption{Bathymetry}
+%\label{fig:bathymetry}
+%\end{figure}
+
+
+Figures (\ref{fig:sim_config_tclim_pcoord}-\ref{fig:sim_config_empmr_pcoord})
+%(\ref{fig:sim_config_tclim}-\ref{fig:sim_config_empmr})
+show the relaxation temperature ($\theta^{\ast}$) and salinity ($S^{\ast}$)
+fields, the wind stress components ($\tau_x$ and $\tau_y$), the heat flux ($Q$)
 and the net fresh water flux (${\cal E} - {\cal P} - {\cal R}$) used
-in equations \ref{EQ:global_forcing_fu}-\ref{EQ:global_forcing_fs}. The figures
-also indicate the lateral extent and coastline used in the experiment.
-Figure ({\ref{FIG:model_bathymetry}) shows the depth contours of the model
-domain.
-
+in equations
+(\ref{eq:eg-global-global_forcing_fu}-\ref{eq:eg-global-global_forcing_fs}).
+The figures also indicate the lateral extent and coastline used in the
+experiment. Figure ({\it --- missing figure --- }) %ref{fig:model_bathymetry})
+shows the depth contours of the model domain.
 
 \subsubsection{File {\it input/data}}
-\label{www:tutorials}
-
-This file, reproduced completely below, specifies the main parameters 
-for the experiment. The parameters that are significant for this configuration
-are
-
-\begin{itemize}
-
-\item Lines 7-10 and 11-14 
-\begin{verbatim} tRef= 16.0 , 15.2 , 14.5 , 13.9 , 13.3 ,  \end{verbatim} 
-$\cdots$ \\
-set reference values for potential
-temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and
-${\rm ppt}$. The entries are ordered from surface to depth.
-Density is calculated from anomalies at each level evaluated
-with respect to the reference values set here.\\
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_THETA}({\it ini\_theta.F})
-\end{minipage}
-}
-
-
-\item Line 15, 
-\begin{verbatim} viscAz=1.E-3, \end{verbatim}
-this line sets the vertical Laplacian dissipation coefficient to
-$1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions
-for this operator are specified later. This variable is copied into
-model general vertical coordinate variable {\bf viscAr}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
-\end{minipage}
-}
-
-\item Line 16, 
-\begin{verbatim}
-viscAh=5.E5,
-\end{verbatim} 
-this line sets the horizontal Laplacian frictional dissipation coefficient to
-$5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions
-for this operator are specified later.
-
-\item Lines 17,
-\begin{verbatim}
-no_slip_sides=.FALSE.
-\end{verbatim}
-this line selects a free-slip lateral boundary condition for
-the horizontal Laplacian friction operator 
-e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and
-$\frac{\partial v}{\partial x}$=0 along boundaries in $x$.
-
-\item Lines 9,
-\begin{verbatim}
-no_slip_bottom=.TRUE.
-\end{verbatim}
-this line selects a no-slip boundary condition for bottom
-boundary condition in the vertical Laplacian friction operator 
-e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.
-
-\item Line 19,
-\begin{verbatim}
-diffKhT=1.E3,
-\end{verbatim}
-this line sets the horizontal diffusion coefficient for temperature
-to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
-operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
-all boundaries.
-
-\item Line 20,
-\begin{verbatim}
-diffKzT=3.E-5,
-\end{verbatim}
-this line sets the vertical diffusion coefficient for temperature
-to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary 
-condition on this operator is $\frac{\partial}{\partial z}=0$ at both
-the upper and lower boundaries.
-
-\item Line 21,
-\begin{verbatim}
-diffKhS=1.E3,
-\end{verbatim}
-this line sets the horizontal diffusion coefficient for salinity
-to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
-operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
-all boundaries.
-
-\item Line 22,
-\begin{verbatim}
-diffKzS=3.E-5,
-\end{verbatim}
-this line sets the vertical diffusion coefficient for salinity
-to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary 
-condition on this operator is $\frac{\partial}{\partial z}=0$ at both
-the upper and lower boundaries.
-
-\item Lines 23-26
-\begin{verbatim}
-beta=1.E-11,
-\end{verbatim}
-\vspace{-5mm}$\cdots$\\
-These settings do not apply for this experiment.
-
-\item Line 27,
-\begin{verbatim}
-gravity=9.81,
-\end{verbatim}
-Sets the gravitational acceleration coefficient to $9.81{\rm m}{\rm s}^{-1}$.\\
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\
-{\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\
-{\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\
-{\it S/R INI\_PARMS}~({\it ini\_parms.F})\\
-{\it S/R SOLVE\_FOR\_PRESSURE}~({\it solve\_for\_pressure.F})
-\end{minipage}
-}
-
-
-\item Line 28-29,
-\begin{verbatim}
-rigidLid=.FALSE., 
-implicitFreeSurface=.TRUE., 
-\end{verbatim}
-Selects the barotropic pressure equation to be the implicit free surface
-formulation.
-
-\item Line 30,
-\begin{verbatim}
-eosType='POLY3',
-\end{verbatim}
-Selects the third order polynomial form of the equation of state.\\
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R FIND\_RHO}~({\it find\_rho.F})\\
-{\it S/R FIND\_ALPHA}~({\it find\_alpha.F})
-\end{minipage}
-}
-
-\item Line 31,
-\begin{verbatim}
-readBinaryPrec=32,
-\end{verbatim}
-Sets format for reading binary input datasets holding model fields to
-use 32-bit representation for floating-point numbers.\\
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R READ\_WRITE\_FLD}~({\it read\_write\_fld.F})\\
-{\it S/R READ\_WRITE\_REC}~({\it read\_write\_rec.F})
-\end{minipage}
-}
-
-\item Line 36,
-\begin{verbatim}
-cg2dMaxIters=1000,
-\end{verbatim}
-Sets maximum number of iterations the two-dimensional, conjugate
-gradient solver will use, {\bf irrespective of convergence 
-criteria being met}.\\
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R CG2D}~({\it cg2d.F})
-\end{minipage}
-}
-
-\item Line 37,
-\begin{verbatim}
-cg2dTargetResidual=1.E-13,
-\end{verbatim}
-Sets the tolerance which the two-dimensional, conjugate
-gradient solver will use to test for convergence in equation 
-\ref{EQ:congrad_2d_resid} to $1 \times 10^{-13}$.
-Solver will iterate until 
-tolerance falls below this value or until the maximum number of
-solver iterations is reached.\\
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R CG2D}~({\it cg2d.F})
-\end{minipage}
-}
-
-\item Line 42,
-\begin{verbatim}
-startTime=0,
-\end{verbatim}
-Sets the starting time for the model internal time counter.
-When set to non-zero this option implicitly requests a 
-checkpoint file be read for initial state.
-By default the checkpoint file is named according to
-the integer number of time steps in the {\bf startTime} value.
-The internal time counter works in seconds.
-
-\item Line 43,
-\begin{verbatim}
-endTime=2808000.,
-\end{verbatim}
-Sets the time (in seconds) at which this simulation will terminate.
-At the end of a simulation a checkpoint file is automatically
-written so that a numerical experiment can consist of multiple
-stages.
-
-\item Line 44,
-\begin{verbatim}
-#endTime=62208000000,
-\end{verbatim}
-A commented out setting for endTime for a 2000 year simulation.
-
-\item Line 45,
-\begin{verbatim}
-deltaTmom=2400.0,
-\end{verbatim}
-Sets the timestep $\delta t_{v}$ used in the momentum equations to
-$20~{\rm mins}$.
-See section \ref{SEC:mom_time_stepping}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R TIMESTEP}({\it timestep.F})
-\end{minipage}
-}
-
-\item Line 46,
-\begin{verbatim}
-tauCD=321428.,
-\end{verbatim}
-Sets the D-grid to C-grid coupling time scale $\tau_{CD}$ used in the momentum equations.
-See section \ref{SEC:cd_scheme}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R INI\_PARMS}({\it ini\_parms.F})\\
-{\it S/R MOM\_FLUXFORM}({\it mom\_fluxform.F})
-\end{minipage}
-}
-
-\item Line 47,
-\begin{verbatim}
-deltaTtracer=108000.,
-\end{verbatim}
-Sets the default timestep, $\delta t_{\theta}$, for tracer equations to
-$30~{\rm hours}$.
-See section \ref{SEC:tracer_time_stepping}.
-
-\fbox{
-\begin{minipage}{5.0in}
-{\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F})
-\end{minipage}
-}
-
-\item Line 47,
-\begin{verbatim}
-bathyFile='topog.box'
-\end{verbatim}
-This line specifies the name of the file from which the domain
-bathymetry is read. This file is a two-dimensional ($x,y$) map of
-depths. This file is assumed to contain 64-bit binary numbers 
-giving the depth of the model at each grid cell, ordered with the x 
-coordinate varying fastest. The points are ordered from low coordinate
-to high coordinate for both axes. The units and orientation of the
-depths in this file are the same as used in the MITgcm code. In this
-experiment, a depth of $0m$ indicates a solid wall and a depth
-of $-2000m$ indicates open ocean. The matlab program
-{\it input/gendata.m} shows an example of how to generate a
-bathymetry file.
-
-
-\item Line 50,
-\begin{verbatim}
-zonalWindFile='windx.sin_y'
-\end{verbatim}
-This line specifies the name of the file from which the x-direction
-surface wind stress is read. This file is also a two-dimensional
-($x,y$) map and is enumerated and formatted in the same manner as the 
-bathymetry file. The matlab program {\it input/gendata.m} includes example 
-code to generate a valid 
-{\bf zonalWindFile} 
-file.  
-
-\end{itemize}
+%\label{www:tutorials}
 
-\noindent other lines in the file {\it input/data} are standard values
-that are described in the MITgcm Getting Started and MITgcm Parameters
-notes.
-
-\begin{small}
-\input{part3/case_studies/climatalogical_ogcm/input/data}
-\end{small}
+\input{s_examples/global_oce_latlon/inp_data}
 
 \subsubsection{File {\it input/data.pkg}}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
 \subsubsection{File {\it input/eedata}}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 This file uses standard default values and does not contain
 customisations for this experiment.
 
-\subsubsection{File {\it input/windx.sin\_y}}
-\label{www:tutorials}
-
-The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$) 
-map of wind stress ,$\tau_{x}$, values. The units used are $Nm^{-2}$.
-Although $\tau_{x}$ is only a function of $y$n in this experiment
-this file must still define a complete two-dimensional map in order
-to be compatible with the standard code for loading forcing fields 
-in MITgcm. The included matlab program {\it input/gendata.m} gives a complete
-code for creating the {\it input/windx.sin\_y} file.
-
-\subsubsection{File {\it input/topog.box}}
-\label{www:tutorials}
-
-
-The {\it input/topog.box} file specifies a two-dimensional ($x,y$) 
-map of depth values. For this experiment values are either
-$0m$ or $-2000\,{\rm m}$, corresponding respectively to a wall or to deep
-ocean. The file contains a raw binary stream of data that is enumerated
-in the same way as standard MITgcm two-dimensional, horizontal arrays.
-The included matlab program {\it input/gendata.m} gives a complete
-code for creating the {\it input/topog.box} file.
+\subsubsection{Files{\it input/trenberth\_taux.bin} and {\it
+  input/trenberth\_tauy.bin}}
+%\label{www:tutorials}
+
+The {\it input/trenberth\_taux.bin} and {\it
+  input/trenberth\_tauy.bin} files specify a three-dimensional
+($x,y,time$) map of wind stress, $(\tau_{x},\tau_{y})$, values
+\citep{trenberth90}. The units used are $Nm^{-2}$.
+
+\subsubsection{File {\it input/bathymetry.bin}}
+%\label{www:tutorials}
+
+The {\it input/bathymetry.bin} file specifies a two-dimensional
+($x,y$) map of depth values. For this experiment values range
+between~$0$ and $-5200\,{\rm m}$, and have been derived from
+ETOPO5. The file contains a raw binary stream of data that is
+enumerated in the same way as standard MITgcm two-dimensional,
+horizontal arrays.
 
 \subsubsection{File {\it code/SIZE.h}}
-\label{www:tutorials}
-
-Two lines are customized in this file for the current experiment
-
-\begin{itemize}
-
-\item Line 39, 
-\begin{verbatim} sNx=60, \end{verbatim} this line sets
-the lateral domain extent in grid points for the
-axis aligned with the x-coordinate.
-
-\item Line 40, 
-\begin{verbatim} sNy=60, \end{verbatim} this line sets
-the lateral domain extent in grid points for the
-axis aligned with the y-coordinate.
-
-\item Line 49, 
-\begin{verbatim} Nr=4,   \end{verbatim} this line sets
-the vertical domain extent in grid points.
-
-\end{itemize}
+%\label{www:tutorials}
 
-\begin{small}
-\input{part3/case_studies/climatalogical_ogcm/code/SIZE.h}
-\end{small}
+\input{s_examples/global_oce_latlon/cod_SIZE.h}
 
-\subsubsection{File {\it code/CPP\_OPTIONS.h}}
-\label{www:tutorials}
+%\subsubsection{File {\it code/CPP\_OPTIONS.h}}
+%\label{www:tutorials}
 
-This file uses standard default values and does not contain
-customisations for this experiment.
+%This file uses standard default values and does not contain
+%customisations for this experiment.
 
 
-\subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
-\label{www:tutorials}
+%\subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
+%\label{www:tutorials}
 
-This file uses standard default values and does not contain
-customisations for this experiment.
+%This file uses standard default values and does not contain
+%customisations for this experiment.
 
 \subsubsection{Other Files }
-\label{www:tutorials}
+%\label{www:tutorials}
 
-Other files relevant to this experiment are
-\begin{itemize}
-\item {\it model/src/ini\_cori.F}. This file initializes the model
-coriolis variables {\bf fCorU}.
-\item {\it model/src/ini\_spherical\_polar\_grid.F}
-\item {\it model/src/ini\_parms.F},
-\item {\it input/windx.sin\_y},
-\end{itemize}
-contain the code customisations and parameter settings for this 
-experiments. Below we describe the customisations
-to these files associated with this experiment.
+% Other files relevant to this experiment are
+% \begin{itemize}
+% \item {\it model/src/ini\_cori.F}. This file initializes the model
+% coriolis variables {\bf fCorU}.
+% \item {\it model/src/ini\_spherical\_polar\_grid.F}
+% \item {\it model/src/ini\_parms.F},
+% \item {\it input/windx.sin\_y},
+% \end{itemize}
+% contain the code customisations and parameter settings for this
+% experiments. Below we describe the customisations
+% to these files associated with this experiment.
