--- manual/s_getstarted/text/customization.tex	2004/10/14 14:24:28	1.1
+++ manual/s_getstarted/text/customization.tex	2009/08/06 19:12:47	1.9
@@ -1,4 +1,8 @@
-\section[Customizing MITgcm]{Doing it yourself: customizing the code}
+\section[Customizing MITgcm]{Doing it yourself: customizing the model configuration}
+\label{sect:customize}
+\begin{rawhtml}
+<!-- CMIREDIR:customizing_mitgcm: -->
+\end{rawhtml}
 
 When you are ready to run the model in the configuration you want, the
 easiest thing is to use and adapt the setup of the case studies
@@ -9,8 +13,6 @@
 part is covered in the parallel implementation section) and on the
 variables and parameters that you are likely to change.
 
-\subsection{Configuration and setup}
-
 The CPP keys relative to the ``numerical model'' part of the code are
 all defined and set in the file \textit{CPP\_OPTIONS.h }in the
 directory \textit{ model/inc }or in one of the \textit{code
@@ -22,13 +24,18 @@
 to be located in the directory where you will run the model. The
 parameters are initialized in the routine
 \textit{model/src/ini\_parms.F}.  Look at this routine to see in what
-part of the namelist the parameters are located.
+part of the namelist the parameters are located. Here is a complete list 
+of the model parameters related to the main model (namelist parameters
+for the packages are located in the package descriptions), their meaning, 
+and their default values:
+
+\input{./part3/main-parms.tex}
 
 In what follows the parameters are grouped into categories related to
 the computational domain, the equations solved in the model, and the
 simulation controls.
 
-\subsection{Computational domain, geometry and time-discretization}
+\subsection{Parameters: Computational domain, geometry and time-discretization}
 
 \begin{description}
 \item[dimensions] \ 
@@ -47,7 +54,7 @@
   through the logical variables \textbf{usingCartesianGrid},
   \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.
   In the case of spherical and curvilinear grids, the southern
-  boundary is defined through the variable \textbf{phiMin} which
+  boundary is defined through the variable \textbf{ygOrigin} which
   corresponds to the latitude of the southern most cell face (in
   degrees). The resolution along the x and y directions is controlled
   by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the
@@ -121,7 +128,7 @@
 \end{description}
 
 
-\subsection{Equation of state}
+\subsection{Parameters: Equation of state}
 
 First, because the model equations are written in terms of
 perturbations, a reference thermodynamic state needs to be specified.
@@ -176,7 +183,7 @@
 For none of these options an reference profile of temperature or
 salinity is required.
 
-\subsection{Momentum equations}
+\subsection{Parameters: Momentum equations}
 
 In this section, we only focus for now on the parameters that you are
 likely to change, i.e. the ones relative to forcing and dissipation
@@ -195,9 +202,19 @@
 \begin{description}
 \item[initialization] \ 
   
-  The velocity components are initialized to 0 unless the simulation
-  is starting from a pickup file (see section on simulation control
-  parameters).
+  The initial horizontal velocity components can be specified from 
+  binary files \textbf{uVelInitFile} and \textbf{vVelInitFile}.
+  These files should contain 3D data ordered in an (x,y,r) fashion with 
+  k=1 as the first vertical level (surface level). 
+  If no file names are provided, the velocity is initialised to zero.
+  The initial vertical velocity is always derived from the horizontal velocity
+  using the continuity equation, even in the case of non-hydrostatic simulation 
+  (see, e.g.: {\it tutorial\_deep\_convection/input/data}).
+
+  In the case of a restart (from the end of a previous simulation), 
+  the velocity field is read from a pickup file
+  (see section on simulation control parameters) 
+  and the initial velocity files are ignored.
 
 \item[forcing] \ 
   
@@ -246,9 +263,8 @@
   set to \texttt{'.FALSE.'}, free-slip boundary conditions are
   applied. If no-slip boundary conditions are applied at the bottom, a
   bottom drag can be applied as well. Two forms are available: linear
-  (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and
-  quadratic (set the variable \textbf{bottomDragQuadratic} in
-  m$^{-1}$).
+  (set the variable \textbf{bottomDragLinear} in m/s) and
+  quadratic (set the variable \textbf{bottomDragQuadratic}, dimensionless).
 
   The Fourier and Shapiro filters are described elsewhere.
 
@@ -282,7 +298,7 @@
 
 \end{description} 
 
-\subsection{Tracer equations}
+\subsection{Parameters: Tracer equations}
 
 This section covers the tracer equations i.e. the potential
 temperature equation and the salinity (for the ocean) or specific
@@ -374,7 +390,7 @@
 
 \end{description}
 
-\subsection{Simulation controls}
+\subsection{Parameters: Simulation controls}
 
 The model ''clock'' is defined by the variable \textbf{deltaTClock}
 (in s) which determines the IO frequencies and is used in tagging