Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex
===================================================================
--- NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex	(revision 11543)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex	(revision 11558)
@@ -174,8 +174,10 @@
 \xmlline|<variable id="using_server" type="bool"></variable>|
 
-The {\ttfamily using\_server} setting determines whether or not the server will be used in \textit{attached mode}
-(as a library) [{\ttfamily> false <}] or in \textit{detached mode}
-(as an external executable on N additional, dedicated cpus) [{\ttfamily > true <}].
-The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications.
+The \texttt{using\_server} setting determines whether or not the server will be used in
+\textit{attached mode}
+(as a library) [\texttt{> false <}] or in \textit{detached mode}
+(as an external executable on N additional, dedicated cpus) [\texttt{ > true <}].
+The \textit{attached mode} is simpler to use but much less efficient for
+massively parallel applications.
 The type of each file can be either ''multiple\_file'' or ''one\_file''.
 
@@ -218,5 +220,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|lXl|}
     \hline
@@ -341,5 +342,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
     \hline
@@ -373,5 +373,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
     \hline
@@ -398,5 +397,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
     \hline
@@ -418,5 +416,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
     \hline
@@ -634,5 +631,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|lX|}
     \hline
@@ -695,5 +691,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|l|c|c|}
     \hline
@@ -894,5 +889,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|l|X|}
     \hline
@@ -917,9 +911,8 @@
     \hline
   \end{tabularx}
-  \caption{Context tags}
+  \caption{XIOS: context tags}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|l|}
     \hline
@@ -952,9 +945,8 @@
     \hline
   \end{tabularx}
-  \caption{Field tags ("\ttfamily{field\_*}")}
+  \caption{XIOS: field tags ("\texttt{field\_*}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|l|}
     \hline
@@ -988,9 +980,8 @@
     \hline
   \end{tabularx}
-  \caption{File tags ("\ttfamily{file\_*}")}
+  \caption{XIOS: file tags ("\texttt{file\_*}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
     \hline
@@ -1021,9 +1012,8 @@
     \hline
   \end{tabularx}
-  \caption{Axis tags ("\ttfamily{axis\_*}")}
+  \caption{XIOS: axis tags ("\texttt{axis\_*}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
     \hline
@@ -1054,9 +1044,8 @@
     \hline
   \end{tabularx}
-  \caption{Domain tags ("\ttfamily{domain\_*)}"}
+  \caption{XIOS: domain tags ("\texttt{domain\_*)}"}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
     \hline
@@ -1087,5 +1076,5 @@
     \hline
   \end{tabularx}
-  \caption{Grid tags ("\ttfamily{grid\_*}")}
+  \caption{XIOS: grid tags ("\texttt{grid\_*}")}
 \end{table}
 
@@ -1093,5 +1082,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|l|l|}
     \hline
@@ -1128,9 +1116,8 @@
     \hline
   \end{tabularx}
-  \caption{Reference attributes ("\ttfamily{*\_ref}")}
+  \caption{XIOS: reference attributes ("\texttt{*\_ref}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|l|l|}
     \hline
@@ -1164,9 +1151,8 @@
     \hline
   \end{tabularx}
-  \caption{Domain attributes ("\ttfamily{zoom\_*}")}
+  \caption{XIOS: domain attributes ("\texttt{zoom\_*}")}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|l|l|}
     \hline
@@ -1219,9 +1205,8 @@
     \hline
   \end{tabularx}
-  \caption{File attributes}
+  \caption{XIOS: file attributes}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|l|l|}
     \hline
@@ -1268,9 +1253,8 @@
     \hline
   \end{tabularx}
-  \caption{Field attributes}
+  \caption{XIOS: field attributes}
 \end{table}
 
 \begin{table}
-  \scriptsize
   \begin{tabularx}{\textwidth}{|l|X|X|X|}
     \hline
@@ -1327,5 +1311,5 @@
     \hline
   \end{tabularx}
-  \caption{Miscellaneous attributes}
+  \caption{XIOS: miscellaneous attributes}
 \end{table}
 
@@ -1366,5 +1350,9 @@
 %------------------------------------------namnc4----------------------------------------------------
 
-\nlst{namnc4}
+\begin{listing}
+  \nlst{namnc4}
+  \caption{\texttt{namnc4}}
+  \label{lst:namnc4}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1404,6 +1392,6 @@
 \end{forlines}
 
-\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\ttfamily 46x38x1} respectively in
-the mono-processor case (\ie\ global domain of {\small\ttfamily 182x149x31}).
+\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\texttt 46x38x1} respectively in
+the mono-processor case (\ie\ global domain of {\small\texttt 182x149x31}).
 An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in
 table \autoref{tab:DIA_NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with
@@ -1414,5 +1402,4 @@
 %------------------------------------------TABLE----------------------------------------------------
 \begin{table}
-  \scriptsize
   \centering
   \begin{tabular}{lrrr}
@@ -1446,8 +1433,6 @@
     ORCA2\_2d\_grid\_W\_0007.nc & 4416		& 1368	  & 70\%      \\
   \end{tabular}
-  \caption{
-    \protect\label{tab:DIA_NC4}
-    Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression
-  }
+  \caption{Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression}
+  \label{tab:DIA_NC4}
 \end{table}
 %----------------------------------------------------------------------------------------------------
@@ -1471,5 +1456,9 @@
 %------------------------------------------namtrd----------------------------------------------------
 
-\nlst{namtrd}
+\begin{listing}
+  \nlst{namtrd}
+  \caption{\texttt{namtrd}}
+  \label{lst:namtrd}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1518,5 +1507,9 @@
 %--------------------------------------------namflo-------------------------------------------------------
 
-\nlst{namflo}
+\begin{listing}
+  \nlst{namflo}
+  \caption{\texttt{namflo}}
+  \label{lst:namflo}
+\end{listing}
 %--------------------------------------------------------------------------------------------------------------
 
@@ -1536,5 +1529,5 @@
 In case of Ariane convention, input filename is \textit{init\_float\_ariane}.
 Its format is: \\
-{\scriptsize \texttt{I J K nisobfl itrash}}
+{ \texttt{I J K nisobfl itrash}}
 
 \noindent with:
@@ -1548,5 +1541,5 @@
 \noindent Example: \\
 \noindent
-{\scriptsize
+{
   \texttt{
     100.00000  90.00000  -1.50000 1.00000   0.00000   \\
@@ -1559,5 +1552,5 @@
 In the other case (longitude and latitude), input filename is init\_float.
 Its format is: \\
-{\scriptsize \texttt{Long Lat depth nisobfl ngrpfl itrash}}
+{ \texttt{Long Lat depth nisobfl ngrpfl itrash}}
 
 \noindent with:
@@ -1573,5 +1566,5 @@
 \noindent Example: \\
 \noindent
-{\scriptsize
+{
   \texttt{
     20.0 0.0 0.0 0 1 1    \\
@@ -1622,5 +1615,9 @@
 %------------------------------------------nam_diaharm----------------------------------------------------
 %
-\nlst{nam_diaharm}
+\begin{listing}
+  \nlst{nam_diaharm}
+  \caption{\texttt{nam\_diaharm}}
+  \label{lst:nam_diaharm}
+\end{listing}
 %----------------------------------------------------------------------------------------------------------
 
@@ -1670,5 +1667,9 @@
 %------------------------------------------nam_diadct----------------------------------------------------
 
-\nlst{nam_diadct}
+\begin{listing}
+  \nlst{nam_diadct}
+  \caption{\texttt{nam\_diadct}}
+  \label{lst:nam_diadct}
+\end{listing}
 %-------------------------------------------------------------------------------------------------------------
 
@@ -1704,5 +1705,5 @@
 
 Each section is defined by: \\
-\noindent {\scriptsize \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\
+\noindent { \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\
 with:
 
@@ -1721,5 +1722,5 @@
 
 \noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\
-{\scriptsize
+{
   \texttt{
     long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\
@@ -1754,5 +1755,5 @@
  and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\
  \noindent
- {\scriptsize
+ {
    \texttt{
      -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage \\
@@ -1769,5 +1770,5 @@
 
 The output format is: \\
-{\scriptsize
+{
   \texttt{
     date, time-step number, section number,                \\
@@ -1791,5 +1792,4 @@
 
 \begin{table}
-  \scriptsize
   \begin{tabular}{|l|l|l|l|l|}
     \hline
@@ -2011,15 +2011,18 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_mask_subasins}
-    \caption{
-      \protect\label{fig:DIA_mask_subasins}
-		Decomposition of the World Ocean (here ORCA2) into sub-basin used in to
-      compute the heat and salt transports as well as the meridional stream-function:
-      Atlantic basin (red), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).
-		Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay are removed from the sub-basins.
-      Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=\textwidth]{Fig_mask_subasins}
+  \caption[Decomposition of the World Ocean to compute transports as well as
+  the meridional stream-function]{
+    Decomposition of the World Ocean (here ORCA2) into sub-basin used in to
+    compute the heat and salt transports as well as the meridional stream-function:
+    Atlantic basin (red), Pacific basin (green),
+    Indian basin (blue), Indo-Pacific basin (blue+green).
+    Note that semi-enclosed seas (Red, Med and Baltic seas) as well as
+    Hudson Bay are removed from the sub-basins.
+    Note also that the Arctic Ocean has been split into Atlantic and
+    Pacific basins along the North fold line.
+  }
+  \label{fig:DIA_mask_subasins}
 \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -2049,5 +2052,9 @@
 %------------------------------------------namptr-----------------------------------------
 
-\nlst{namptr}
+\begin{listing}
+  \nlst{namptr}
+  \caption{\texttt{namptr}}
+  \label{lst:namptr}
+\end{listing}
 %-----------------------------------------------------------------------------------------
 
@@ -2059,5 +2066,9 @@
 %------------------------------------------nam_dia25h-------------------------------------
 
-\nlst{nam_dia25h}
+\begin{listing}
+  \nlst{nam_dia25h}
+  \caption{\texttt{nam\_dia25h}}
+  \label{lst:nam_dia25h}
+\end{listing}
 %-----------------------------------------------------------------------------------------
 
@@ -2074,5 +2085,9 @@
 %------------------------------------------nam_diatmb-----------------------------------------------------
 
-\nlst{nam_diatmb}
+\begin{listing}
+  \nlst{nam_diatmb}
+  \caption{\texttt{nam\_diatmb}}
+  \label{lst:nam_diatmb}
+\end{listing}
 %----------------------------------------------------------------------------------------------------------
 
