--- manual/s_phys_pkgs/text/exch2.tex	2004/03/15 20:11:56	1.10
+++ manual/s_phys_pkgs/text/exch2.tex	2004/03/15 22:39:28	1.11
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.10 2004/03/15 20:11:56 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.11 2004/03/15 22:39:28 afe Exp $
 % $Name:  $
 
 %%  * Introduction
@@ -31,57 +31,59 @@
 \filelink{pkg/exch2/W2\_EXCH2\_TOPOLOGY.h}{pkg-exch2-W2_EXCH2_TOPOLOGY.h}
 and assigned in
 \filelink{pkg/exch2/w2\_e2setup.F}{pkg-exch2-w2_e2setup.F}. The
-validity of the cube topology depends on the \texttt{SIZE.h} file as
+validity of the cube topology depends on the \file{SIZE.h} file as
 detailed below.  Both files are generated by Matlab scripts in
-\texttt{utils/exch2/matlab-topology-generator}; see Section
-\ref{sec:topogen} for details on creating alternate topologies.  The
-default files provided in the release configure a cubed sphere
-topology of six tiles, one per subdomain, each with 32$\times$32 grid
-points, all running on a single processor.  Pregenerated examples of
-these files with alternate topologies are provided under
-\texttt{utils/exch2/code-mods} along with the appropriate
-\texttt{SIZE.h} file for single-processor execution.
+\file{utils/exch2/matlab-topology-generator}; see Section
+\ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2}
+for details on creating alternate topologies.  The default files
+provided in the release configure a cubed sphere topology of six
+tiles, one per subdomain, each with 32$\times$32 grid points, all
+running on a single processor.  Pregenerated examples of these files
+with alternate topologies are provided under
+\file{utils/exch2/code-mods} along with the appropriate \file{SIZE.h}
+file for single-processor execution.
 
 \subsection{Invoking exch2}
 
 To use exch2 with the cubed sphere, the following conditions must be
 met: \\
 
-$\bullet$ The exch2 package is included when \texttt{genmake2} is run.  The
-  easiest way to do this is to add the line \texttt{exch2} to the
-  \texttt{profile.conf} file -- see Section \ref{sect:buildingCode}
-  for general details. \\
-
-$\bullet$ An example of \texttt{W2\_EXCH2\_TOPOLOGY.h} and
-  \texttt{w2\_e2setup.F} must reside in a directory containing code
-  linked when \texttt{genmake2} runs.  The safest place to put these
-  is the directory indicated in the \texttt{-mods=DIR} command line
-  modifier (typically \texttt{../code}), or the build directory.  The
-  default versions of these files reside in \texttt{pkg/exch2} and are
+$\bullet$ The exch2 package is included when \file{genmake2} is run.
+  The easiest way to do this is to add the line \code{exch2} to the
+  \file{profile.conf} file -- see Section
+  \ref{sect:buildingCode}\sectiontitle{Building the code} for general
+  details. \\
+
+$\bullet$ An example of \file{W2\_EXCH2\_TOPOLOGY.h} and
+  \file{w2\_e2setup.F} must reside in a directory containing code
+  linked when \file{genmake2} runs.  The safest place to put these
+  is the directory indicated in the \code{-mods=DIR} command line
+  modifier (typically \file{../code}), or the build directory.  The
+  default versions of these files reside in \file{pkg/exch2} and are
   linked automatically if no other versions exist elsewhere in the
   link path, but they should be left untouched to avoid breaking
   configurations other than the one you intend to modify.\\
 
 $\bullet$ Files containing grid parameters, named
-  \texttt{tile}???\texttt{.mitgrid} where ??? is \texttt{001} through
-  \texttt{006} (one per subdomain), must be in the working directory
+  \file{tile???.mitgrid} where \file{???} is \file{001} through
+  \file{006} (one per subdomain), must be in the working directory
   when the MITgcm executable is run.  These files are provided in the
   example experiments for cubed sphere configurations with
   32$\times$32 cube sides and are non-trivial to generate -- please
   contact MITgcm support if you want to generate files for other
   configurations. \\
 
-$\bullet$ As always when compiling MITgcm, the file \texttt{SIZE.h}
-  must be placed where \texttt{genmake2} will find it.  In particular
-  for the exch2, the domain decompositin specified in \texttt{SIZE.h}
+$\bullet$ As always when compiling MITgcm, the file \file{SIZE.h}
+  must be placed where \file{genmake2} will find it.  In particular
+  for the exch2, the domain decomposition specified in \file{SIZE.h}
   must correspond with the particular configuration's topology
-  specified in \texttt{W2\_EXCH2\_TOPOLOGY.h} and
-  \texttt{w2\_e2setup.F}.  Domain decomposition issues particular to
-  exch2 are addressed in Section \ref{sec:topogen}: ``Generating
-  Topology Files for exch2''; a more general background on the subject
+  specified in \file{W2\_EXCH2\_TOPOLOGY.h} and
+  \file{w2\_e2setup.F}.  Domain decomposition issues particular to
+  exch2 are addressed in Section \ref{sec:topogen} \sectiontitle{Generating
+  Topology Files for exch2}; a more general background on the subject
   relvant to MITgcm is presented in Section
-  \ref{sect:specifying_a_decomposition}: ``Specifying a
-  decomposition''.\\
+  \ref{sect:specifying_a_decomposition}\sectiontitle{Specifying a
+  decomposition}.\\
 
 As of the time of writing the following examples use exch2 and may be
 used for guidance:
@@ -101,17 +103,17 @@
 \label{sec:topogen}
 
 Alternate cubed sphere topologies may be created using the Matlab
-scripts in \texttt{utils/exch2/matlab-topology-generator}. Running the
-m-file \texttt{driver} from the Matlab prompt (without passing any
-function parameters) generates exch2 topology files
-\texttt{W2\_EXCH2\_TOPOLOGY.h} and \texttt{w2\_e2setup.F} in the
-working directory and displays via Matlab a figure of the topology.
-The other m-files in the directory are subroutines of \texttt{driver}
-and should not be run except for development purposes. \\
+scripts in \file{utils/exch2/matlab-topology-generator}. Running the
+m-file \file{driver.m} from the Matlab prompt (there are no parameters
+to pass) generates exch2 topology files \file{W2\_EXCH2\_TOPOLOGY.h}
+and \file{w2\_e2setup.F} in the working directory and displays a
+figure of the topology via Matlab.  The other m-files in the directory
+are subroutines of \file{driver.m} and should not be run except for
+development purposes. \\
 
 The parameters that determine the dimensions and topology of the
-generated configuration are nr, nb, ng, tnx and tny, and all are
-assigned early in the script.
+generated configuration are \code{nr}, \code{nb}, \code{ng},
+\code{tnx} and \code{tny}, and all are assigned early in the script.
 
 The first three determine the size of the subdomains (cube faces) and
 hence the size of the overall domain.  Each one determines the number
@@ -122,12 +124,12 @@
 resolutions around the axes to allow (for example) greater resolution
 around the equator.\\
 
-The parameters tnx and tny determine the dimensions of the tiles into
-which the subdomains are decomposed, and must evenly divide the
-integer assigned to nr, nb and ng.  The result is a rectangular tiling
-of the subdomain.  Figure \ref{fig:24tile} shows one possible topology
-for a twenty-four tile cube, and figure \ref{fig:12tile} shows one for
-twelve tiles. \\
+The parameters \code{tnx} and \code{tny} determine the dimensions of
+the tiles into which the subdomains are decomposed, and must evenly
+divide the integer assigned to \code{nr}, \code{nb} and \code{ng}.
+The result is a rectangular tiling of the subdomain.  Figure
+\ref{fig:24tile} shows one possible topology for a twenty-four tile
+cube, and figure \ref{fig:12tile} shows one for twelve tiles. \\
 
 \begin{figure}
 \begin{center}
@@ -136,7 +138,7 @@
  }
 \end{center} 
 \caption{Plot of cubed sphere topology with a 32$\times$32 grid and
-twenty-four tiles (tnx=16, tny=16)
+twenty-four tiles (\code{tnx=16, tny=16})
 } \label{fig:24tile}
 \end{figure}
 
@@ -147,14 +149,14 @@
  }
 \end{center} 
 \caption{Plot of cubed sphere topology with a 32$\times$32 grid and
-twelve tiles (tnx=16, tny=32)
+twelve tiles (\code{tnx=16, tny=32})
 } \label{fig:12tile}
 \end{figure}
 
 Tiles can be selected from the topology to be omitted from being
-allocated memory and processors.  This kind of tuning is useful in
+allocated memory and processors.  This kind otuning is useful in
 ocean modeling for omitting tiles that fall entirely on land.  The
-tiles omitted are specified in the file \texttt{blanklist.txt} by
+tiles omitted are specified in the file \file{blanklist.txt} by
 their tile number in the topology, separated by a newline. \\
 
 
