revise general intro on XIOS and include key_xios3

latex/NEMO/subfiles/chap_DIA.tex

@@ -32,8 +32,26 @@
 \section{Model output}
 \label{sec:DIA_io_old}
 
-The model outputs are of three types: the restart file; the output log/progress listings;
-and the diagnostic output file(s).  
+The model outputs are of three types: the output log/progress listings; 
+the diagnostic output file(s); and the restart file(s)
+
+
+The output listing and file(s) are predefined but should be checked and eventually adapted
+to the user's needs. The output listing is stored in the \textit{ocean.output} file. The
+information is printed from within the code on the logical unit \texttt{numout}. To
+locate these prints, use the UNIX command "\textit{grep -i numout}" in the source code
+directory. The \textit{ocean.output} file is the first place to check if something appears
+to have gone wrong with the model since any detectable errors will be reported here.
+Additional progress information can be requested using the options explained in
+\autoref{subsec:MISC_statusinfo}.
+
+Diagnostic output files are written in NetCDF format and the structure of legacy output files is predefined.
+The legacy output files contain by default the time averaged fields, but by activating the macro \key{diainstant} 
+it is possible to switch the full output to the instantaneous time value. 
+When compiled with \key{xios}, \NEMO\ can employ the full capability of an I/O server (XIOS)
+which provides flexibility in the choice of the fields to be written as well as how the writing tasks are distributed
+over the processors in a massively parallel computing environment. A complete description
+of the use of this I/O server is presented in the next section.
 
 The restart file is used by the code when the user wants to start the model with initial
 conditions defined by a previous simulation.  Restart files are NetCDF files containing
@@ -49,22 +67,6 @@ must first be combined into a whole domain restart file. This can be done using
 4.2 to write restarts via XIOS (see \autoref{subsec:XIOS_restarts}) with which it is possible to
 write a whole domain restart file from a running model.
 
-The output listing and file(s) are predefined but should be checked and eventually adapted
-to the user's needs.  The output listing is stored in the \textit{ocean.output} file.  The
-information is printed from within the code on the logical unit \texttt{numout}.  To
-locate these prints, use the UNIX command "\textit{grep -i numout}" in the source code
-directory. The \textit{ocean.output} file is the first place to check if something appears
-to have gone wrong with the model since any detectable errors will be reported here.
-Additional progress information can be requested using the options explained in
-\autoref{subsec:MISC_statusinfo}.
-
-Diagnostic output files are written in NetCDF format.  When compiled with \key{xios},
-\NEMO\ can employ the full capability of an I/O server (XIOS)  which provides flexibility
-in the choice of the fields to be written as well as how the writing tasks are distributed
-over the processors in a massively parallel computing environment.  A complete description
-of the use of this I/O server is presented in the next section.
-
-
 %% =================================================================================================
 \section{Standard model output (\texttt{iom\_put})}
 \label{sec:DIA_iom}
@@ -104,13 +106,13 @@ provides the possibility to specify N dedicated I/O processes (in addition to th
 processes) to collect and write the outputs.  With an appropriate choice of N by the user,
 the bottleneck associated with the writing of the output files can be greatly reduced.
 
-In version 4.2, the \rou{iom\_put} interface depends on
-an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/trunk}{XIOS}
+Since version 3.6, the \rou{iom\_put} interface depends on an external code called \XIOS, 
 which is developed independently and has its own repository and support pages. Further details
-are available in the \href{https://sites.nemo-ocean.io/user-guide/}{NEMO User guide}. Note that
-version 4.2. requires the trunk version of XIOS; this is a change from earlier versions which
-recommended the tagged XIOS2.5 release.
-%(use of revision 618 or higher is required).
+are available in the \href{https://sites.nemo-ocean.io/user-guide/}{NEMO User guide}. 
+Note that by default the model is interfaced with the trunk version of 
+\href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS2/trunk}{XIOS2}, but it is possible to use also 
+the more recent version \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS3/trunk}{XIOS3} 
+by adding the macro \key{xios3} in the configuration cpp file.\\
 
 The IO server can also take advantage of the parallel I/O functionality of NetCDF4 to
 create a single output file and therefore to bypass any rebuilding phase. This facility is ideal for
@@ -139,7 +141,7 @@ NetCDF4 library, simply by employing only one dedicated I/O server.
 \label{subsec:XIOS_restarts}
 
 
-New from 4.2, XIOS may be used to read from a single file restart produced by \NEMO. 
+New from version 4.2, XIOS may be used to read from a single file restart produced by \NEMO. 
 This does not add a new functionality (since NEMO has long had the capability for all
 processes to read their patch from a single, combined restart file) but it may be advantageous 
 on systems which struggle with too many simultaneous accesses to one file.  The