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1% ================================================================
2% Chapter I/O & Diagnostics
3% ================================================================
4\chapter{Ouput and Diagnostics (IOM, DIA, TRD, FLO)}
5\label{DIA}
6\minitoc
7
8\newpage
9$\ $\newline    % force a new ligne
10
11% ================================================================
12%       Old Model Output
13% ================================================================
14\section{Old Model Output (default or \key{dimgout})}
15\label{DIA_io_old}
16
17The model outputs are of three types: the restart file, the output listing,
18and the diagnostic output file(s). The restart file is used internally by the code when
19the user wants to start the model with initial conditions defined by a
20previous simulation. It contains all the information that is necessary in
21order for there to be no changes in the model results (even at the computer
22precision) between a run performed with several restarts and the same run
23performed in one step. It should be noted that this requires that the restart file
24contain two consecutive time steps for all the prognostic variables, and
25that it is saved in the same binary format as the one used by the computer
26that is to read it (in particular, 32 bits binary IEEE format must not be used for
27this file).
28
29The output listing and file(s) are predefined but should be checked
30and eventually adapted to the user's needs. The output listing is stored in
31the $ocean.output$ file. The information is printed from within the code on the
32logical unit $numout$. To locate these prints, use the UNIX command
33"\textit{grep -i numout}" in the source code directory.
34
35By default, diagnostic output files are written in NetCDF format but an IEEE binary output format, called DIMG, can be choosen by defining \key{dimgout}.
36
37Since version 3.2, when defining \key{iomput}, an I/O server has been added which provides more flexibility in the choice of the fields to be written as well as how the writing work is distributed over the processors in massively parallel computing. The complete description of the use of this I/O server is presented in the next section.
38
39By default, if neither \key{iomput} nor \key{dimgout} are defined, NEMO produces NetCDF with the old IOIPSL library which has been kept for compatibility and its easy installation. However, the IOIPSL library is quite inefficient on parallel machines and, since version 3.2, many diagnostic options have been added presuming the use of \key{iomput}. The usefulness of the default IOIPSL-based option is expected to reduce with each new release. If \key{iomput} is not defined, output files and content are defined in the \mdl{diawri} module and contain mean (or instantaneous if \key{diainstant} is defined) values over a regular period of nn\_write time-steps (namelist parameter).
40
41%\gmcomment{                    % start of gmcomment
42
43% ================================================================
44% Diagnostics
45% ================================================================
46\section{Standard model Output (IOM)}
47\label{DIA_iom}
48
49
50Since version 3.2, iomput is the NEMO output interface of choice. It has been designed to be simple to use, flexible and efficient. The two main purposes of iomput are:
51\begin{enumerate}
52\item The complete and flexible control of the output files through external XML files adapted by the user from standard templates.
53\item To achieve high performance and scalable output through the optional distribution of all diagnostic output related tasks to dedicated processes.
54\end{enumerate}
55The first functionality allows the user to specify, without code changes or recompilation, aspects of the diagnostic output stream, such as:
56\begin{itemize}
57\item The choice of output frequencies that can be different for each file (including real months and years).
58\item The choice of file contents; includes complete flexibility over which data are written in which files (the same data can be written in different files).
59\item The possibility to split output files at a choosen frequency.
60\item The possibility to extract a vertical or an horizontal subdomain.
61\item The choice of the temporal operation to perform, e.g.: average, accumulate, instantaneous, min, max and once.
62\item Control over metadata via a large XML "database" of possible output fields.
63\end{itemize}
64In addition, iomput allows the user to add the output of any new variable (scalar, 2D or 3D) in the code in a very easy way. All details of iomput functionalities are listed in the following subsections. Examples of the XML files that control the outputs can be found in:
65\begin{alltt}
66\begin{verbatim}
67  NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml
68  NEMOGCM/CONFIG/SHARED/field_def.xml
69  and
70  NEMOGCM/CONFIG/SHARED/domain_def.xml.
71\end{verbatim}
72\end{alltt}
73
74The second functionality targets output performance when running in parallel (\key{mpp\_mpi}). Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO 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.
75
76Since version 3.5, the iom\_put interface depends on an external code called \href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}. This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to create a single output file and therefore to bypass the rebuilding phase. Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to an HDF5 library that has been correctly compiled (i.e. with the configure option $--$enable-parallel). Note that the files created by iomput through XIOS are incompatible with NetCDF3. All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3.
77
78Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers, where N is typically much less than the number of NEMO processors, will reduce the number of output files created. This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors. Note that for smaller configurations, the rebuilding phase can be avoided, even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server.
79
80\subsection{XIOS: the IO\_SERVER}
81
82\subsubsection{Attached or detached mode?}
83
84Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS}, the io\_server developed by Yann Meurdesoif from IPSL. The behaviour of the io subsystem is controlled by settings in the external XML files listed above. Key settings in the iodef.xml file are {\tt using\_server} and the {\tt type} tag associated with each defined file. The {\tt using\_server} setting determines whether or not the server will be used in ''attached mode'' (as a library) [{\tt false}] or in ''detached mode'' (as an external executable on N additional, dedicated cpus) [{\tt true}]. The ''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''.
85
86In attached mode and if the type of file is ''multiple\_file'', then each NEMO process will also act as an IO server and produce its own set of output files. Superficially, this emulates the standard behaviour in previous versions, However, the subdomain written out by each process does not correspond to the {\tt jpi x jpj x jpk} domain actually computed by the process (although it may if {\tt jpni=1}). Instead each process will have collected and written out a number of complete longitudinal strips. If the ''one\_file'' option is chosen then all processes will collect their longitudinal strips and write (in parallel) to a single output file.
87
88In detached mode and if the type of file is ''multiple\_file'', then each stand-alone XIOS process will collect data for a range of complete longitudinal strips and write to its own set of output files. If the ''one\_file'' option is chosen then all XIOS processes will collect their longitudinal strips and write (in parallel) to a single output file. Note running in detached mode requires launching a Multiple Process Multiple Data (MPMD) parallel job. The following subsection provides a typical example but the syntax will vary in different MPP environments.
89
90\subsubsection{Number of cpu used by XIOS in detached mode}
91
92The number of cores used by the XIOS is specified when launching the model. The number of cores dedicated to XIOS should be from ~1/10 to ~1/50 of the number or cores dedicated to NEMO. Some manufacturers suggest using O($\sqrt{N}$) dedicated IO processors for N processors but this is a general recommendation and not specific to NEMO. It is difficult to provide precise recommendations because the optimal choice will depend on the particular hardware properties of the target system (parallel filesystem performance, available memory, memory bandwidth etc.) and the volume and frequency of data to be created. Here is an example of 2 cpus for the io\_server and 62 cpu for nemo using mpirun:
93
94\texttt{ mpirun -np 62 ./nemo.exe : -np 2 ./xios\_server.exe }
95
96\subsubsection{Control of XIOS: the XIOS context in iodef.xml}
97
98As well as the {\tt using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml. See the XML basics section below for more details on XML syntax and rules.
99
100\begin{tabular}{|p{4cm}|p{6.0cm}|p{2.0cm}|}
101   \hline
102   variable name & 
103   description & 
104   example \\ 
105   \hline   
106   \hline
107   buffer\_size & 
108   buffer size used by XIOS to send data from NEMO to XIOS. Larger is more efficient. Note that needed/used buffer sizes are summarized at the end of the job & 
109   25000000 \\ 
110   \hline   
111   buffer\_server\_factor\_size & 
112   ratio between NEMO and XIOS buffer size. Should be 2. & 
113   2 \\ 
114   \hline
115   info\_level & 
116   verbosity level (0 to 100) & 
117   0 \\ 
118   \hline
119   using\_server & 
120   activate attached(false) or detached(true) mode & 
121   true \\ 
122   \hline
123   using\_oasis & 
124   XIOS is used with OASIS(true) or not (false) & 
125   false \\ 
126   \hline
127   oasis\_codes\_id & 
128   when using oasis, define the identifier of NEMO in the namcouple. Note that the identifier of XIOS is xios.x & 
129   oceanx \\ 
130   \hline   
131\end{tabular}
132
133
134\subsection{Practical issues}
135
136\subsubsection{Installation}
137
138As mentioned, XIOS is supported separately and must be downloaded and compiled before it can be used with NEMO. See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance. NEMO will need to link to the compiled XIOS library. The
139\href{http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/XIOS-IO-server-installation-and-use}{XIOS with NEMO} guide provides an example illustration of how this can be achieved.
140
141\subsubsection{Add your own outputs}
142
143It is very easy to add your own outputs with iomput. Many standard fields and diagnostics are already prepared (i.e., steps 1 to 3 below have been done) and simply need to be activated by including the required output in a file definition in iodef.xml (step 4). To add new output variables, all 4 of the following steps must be taken.
144\begin{description}
145\item[1.] in NEMO code, add a \\
146\texttt{      CALL iom\_put( 'identifier', array ) } \\
147where you want to output a 2D or 3D array.
148
149\item[2.] If necessary, add \\
150\texttt{   USE iom\ \ \ \ \ \ \ \ \ \ \ \ ! I/O manager library }  \\
151to the list of used modules in the upper part of your module.
152
153\item[3.] in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code (see subsequent sections for a details of the XML syntax and rules). For example:
154\vspace{-20pt}
155\begin{alltt}  {{\scriptsize
156\begin{verbatim}
157   <field_definition>
158      <!-- T grid -->
159
160     <field_group id="grid_T" grid_ref="grid_T_3D">
161      ...
162      <field id="identifier" long_name="blabla" ... />   
163      ...
164   </field_definition>
165\end{verbatim}
166}}\end{alltt} 
167Note your definition must be added to the field\_group whose reference grid is consistent with the size of the array passed to iomput. The grid\_ref attribute refers to definitions set in iodef.xml which, in turn, reference grids and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in iom.F90) or defined in the domain\_def.xml file. E.g.:
168\vspace{-20pt}
169\begin{alltt}  {{\scriptsize
170\begin{verbatim}
171     <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/>
172\end{verbatim}
173}}\end{alltt} 
174Note, if your array is computed within the surface module each nn\_fsbc time\_step,
175add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$ which has been defined with the correct frequency of operations (iom\_set\_field\_attr in iom.F90)
176
177\item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules)   \\
178\vspace{-20pt}
179\begin{alltt}  {{\scriptsize
180\begin{verbatim}
181   <file id="file1" .../>   
182      ...
183      <field field_ref="identifier" />   
184      ...
185   </file>   
186\end{verbatim}
187}}\end{alltt} 
188
189\end{description}
190\subsection{XML fundamentals}
191
192\subsubsection{ XML basic rules}
193
194XML tags begin with the less-than character ("$<$") and end with the greater-than character (''$>$'').
195You use tags to mark the start and end of elements, which are the logical units of information
196in an XML document. In addition to marking the beginning of an element, XML start tags also
197provide a place to specify attributes. An attribute specifies a single property for an element,
198using a name/value pair, for example: $<$a b="x" c="y" b="z"$>$ ... $<$/a$>$.
199See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details.
200
201\subsubsection{Structure of the xml file used in NEMO}
202
203The XML file used in XIOS is structured by 7 families of tags: context, axis, domain, grid, field, file and variable. Each tag family has hierarchy of three flavors (except for context):
204\\
205\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|}
206   \hline
207   flavor &
208   description &
209   example \\
210   \hline
211   \hline
212   root &
213   declaration of the root element that can contain element groups or elements &
214   {\scriptsize \verb? < file_definition ... >?} \\
215   \hline
216   group &
217   declaration of a group element that can contain element groups or elements &
218   {\scriptsize \verb? < file_group ... >?} \\
219   \hline
220   element &
221   declaration of an element that can contain elements &
222   {\scriptsize \verb? < file ... >?} \\
223   \hline
224\end{tabular}
225\\
226
227Each element may have several attributes. Some attributes are mandatory, other are optional but have a default value and other are are completely optional. Id is a special attribute used to identify an element or a group of elements. It must be unique for a kind of element. It is optional, but no reference to the corresponding element can be done if it is not defined.
228
229The XML file is split into context tags that are used to isolate IO definition from different codes or different parts of a code. No interference is possible between 2 different contexts. Each context has its own calendar and an associated timestep. In NEMO, we used the following contexts (that can be defined in any order):\\
230\\
231\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|}
232   \hline
233   context &
234   description &
235   example \\
236   \hline
237   \hline
238   context xios &
239   context containing information for XIOS &
240   {\scriptsize \verb? <context id="xios" ...  ?} \\
241   \hline
242   context nemo &
243   context containing IO information for NEMO (mother grid when using AGRIF) &
244   {\scriptsize \verb? <context id="nemo" ... ?} \\
245   \hline
246   context 1\_nemo &
247   context containing IO information for NEMO child grid 1 (when using AGRIF) &
248   {\scriptsize \verb? <context id="1_nemo" ...  ?} \\
249   \hline
250   context n\_nemo &
251   context containing IO information for NEMO child grid n (when using AGRIF) &
252   {\scriptsize \verb? <context id="n_nemo" ...  ?} \\
253   \hline
254\end{tabular}
255\\
256
257\noindent The xios context contains only 1 tag:
258\\
259\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|}
260   \hline
261   context tag &
262   description &
263   example \\
264   \hline
265   \hline
266   variable\_definition &
267   define variables needed by XIOS. This can be seen as a kind of namelist for XIOS. &
268   {\scriptsize \verb? <variable_definition ... ?} \\
269   \hline
270\end{tabular}
271\\
272
273\noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts (that can be defined in any order):\\
274\\
275\begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|}
276   \hline
277   context tag &
278   description &
279   example \\
280   \hline
281   \hline
282   field\_definition &
283   define all variables that can potentially be outputted &
284   {\scriptsize \verb? <field_definition ... ?} \\
285   \hline
286   file\_definition &
287   define the netcdf files to be created and the variables they will contain &
288   {\scriptsize \verb? <file_definition ... ?} \\
289   \hline
290   axis\_definition &
291   define vertical axis &
292   {\scriptsize \verb? <axis_definition ... ?} \\
293   \hline
294   domain\_definition &
295   define the horizontal grids &
296   {\scriptsize \verb? <domain_definition ... ?} \\
297   \hline
298   grid\_definition &
299   define the 2D and 3D grids (association of an axis and a domain) &
300   {\scriptsize \verb? <grid_definition ... ?} \\
301   \hline
302\end{tabular}
303\\
304
305\subsubsection{Nesting XML files}
306
307The XML file can be split in different parts to improve its readability and facilitate its use. The inclusion of XML files into the main XML file can be done through the attribute src: \\
308{\scriptsize \verb? <context src="./nemo_def.xml" /> ?}\\
309 
310\noindent In NEMO, by default, the field and domain definition is done in 2 separate files:
311{\scriptsize \tt
312\begin{verbatim}
313NEMOGCM/CONFIG/SHARED/field_def.xml
314and
315NEMOGCM/CONFIG/SHARED/domain_def.xml
316\end{verbatim}
317}
318\noindent that are included in the main iodef.xml file through the following commands: \\
319{\scriptsize \verb? <field_definition src="./field_def.xml" /> ? \\
320\verb? <domain_definition src="./domain_def.xml" /> ? }
321
322
323\subsubsection{Use of inheritance}
324
325XML extensively uses the concept of inheritance. XML has a tree based structure with a parent-child oriented relation: all children inherit attributes from parent, but an attribute defined in a child replace the inherited attribute value. Note that the special attribute ''id'' is never inherited.  \\
326\\
327example 1: Direct inheritance.
328\vspace{-20pt}
329\begin{alltt}  {{\scriptsize   
330\begin{verbatim}
331   <field_definition operation="average" >
332     <field id="sst"                    />   <!-- averaged      sst -->
333     <field id="sss" operation="instant"/>   <!-- instantaneous sss -->
334   </field_definition>
335\end{verbatim}
336}}\end{alltt} 
337
338The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average''
339of the attribute ''operation'' from its parent. Note that a child can overwrite
340the attribute definition inherited from its parents. In the example above, the field ''sss'' will
341for example output instantaneous values instead of average values. \\
342\\
343example 2: Inheritance by reference.
344\vspace{-20pt}
345\begin{alltt}  {{\scriptsize
346\begin{verbatim}
347   <field_definition>
348     <field id="sst" long_name="sea surface temperature" />   
349     <field id="sss" long_name="sea surface salinity"    /> 
350   </field_definition>     
351
352   <file_definition>
353     <file id="myfile" output_freq="1d" />   
354       <field field_ref="sst"                            />  <!-- default def -->
355       <field field_ref="sss" long_name="my description" />  <!-- overwrite   -->
356     </file>   
357   </file_definition>
358\end{verbatim}
359}}\end{alltt} 
360Inherit (and overwrite, if needed) the attributes of a tag you are refering to.
361
362\subsubsection{Use of Groups}
363
364Groups can be used for 2 purposes. Firstly, the group can be used to define common attributes to be shared by the elements of the group through inheritance. In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''. Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''.
365\vspace{-20pt}
366\begin{alltt}  {{\scriptsize
367\begin{verbatim}
368   <field_group id="grid_T" grid_ref="grid_T_2D">
369    <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/>
370    <field id="sst"  long_name="sea surface temperature" unit="degC"                     />
371    <field id="sss"  long_name="sea surface salinity"    unit="psu"                      />
372    <field id="ssh"  long_name="sea surface height"      unit="m"                        />
373         ...
374\end{verbatim}
375}}\end{alltt} 
376
377Secondly, the group can be used to replace a list of elements. Several examples of groups of fields are proposed at the end of the file {\tt CONFIG/SHARED/field\_def.xml}. For example, a short list of the usual variables related to the U grid:
378\vspace{-20pt}
379\begin{alltt}  {{\scriptsize
380\begin{verbatim}
381   <field_group id="groupU" >
382    <field field_ref="uoce"  />
383    <field field_ref="suoce" />
384    <field field_ref="utau"  />
385   </field_group>
386\end{verbatim}
387}}\end{alltt} 
388that can be directly included in a file through the following syntax:
389\vspace{-20pt}
390\begin{alltt}  {{\scriptsize
391\begin{verbatim}
392   <file id="myfile_U" output_freq="1d" />   
393    <field_group group_ref="groupU"/> 
394    <field field_ref="uocetr_eff"  />  <!-- add another field -->
395   </file>   
396\end{verbatim}
397}}\end{alltt} 
398
399\subsection{Detailed functionalities }
400
401The file {\tt NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml} provides several examples of the use of the new functionalities offered by the XML interface of XIOS.
402
403\subsubsection{Define horizontal subdomains}
404Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of the tag family domain. It must therefore be done in the domain part of the XML file. For example, in {\tt CONFIG/SHARED/domain\_def.xml}, we provide the following example of a definition of a 5 by 5 box with the bottom left corner at point (10,10).
405\vspace{-20pt}
406\begin{alltt}  {{\scriptsize
407\begin{verbatim}
408   <domain_group id="grid_T">
409    <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" />
410\end{verbatim}
411}}\end{alltt} 
412The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. For example:
413\vspace{-20pt}
414\begin{alltt}  {{\scriptsize
415\begin{verbatim}
416   <file id="myfile_vzoom" output_freq="1d" >
417      <field field_ref="toce" domain_ref="myzoom"/>
418   </file>
419\end{verbatim}
420}}\end{alltt} 
421Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain. The Equatorial section, the TAO, RAMA and PIRATA moorings are alredy registered in the code and can therefore be outputted without taking care of their (i,j) position in the grid. These predefined domains can be activated by the use of specific domain\_ref: ''EqT'', ''EqU'' or ''EqW'' for the equatorial sections and the mooring position for TAO, RAMA and PIRATA followed by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...)
422\vspace{-20pt}
423\begin{alltt}  {{\scriptsize
424\begin{verbatim}
425   <file id="myfile_vzoom" output_freq="1d" >
426      <field field_ref="toce" domain_ref="0n180wT"/>
427   </file>
428\end{verbatim}
429}}\end{alltt} 
430Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if you use the ''multiple\_file'' type for your output files, you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat, \href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}). We are therefore advising to use the ''one\_file'' type in this case.
431
432\subsubsection{Define vertical zooms}
433Vertical zooms are defined through the attributs zoom\_begin and zoom\_end of the tag family axis. It must therefore be done in the axis part of the XML file. For example, in NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml, we provide the following example:
434\vspace{-20pt}
435\begin{alltt}  {{\scriptsize
436\begin{verbatim}
437   <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" >
438      <axis id="deptht" />
439      <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" />
440\end{verbatim}
441}}\end{alltt} 
442The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. For example:
443\vspace{-20pt}
444\begin{alltt}  {{\scriptsize
445\begin{verbatim}
446   <file id="myfile_hzoom" output_freq="1d" >
447      <field field_ref="toce" axis_ref="deptht_myzoom"/>
448   </file>
449\end{verbatim}
450}}\end{alltt} 
451
452\subsubsection{Control of the output file names}
453
454The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. for example:
455\vspace{-20pt}
456\begin{alltt}  {{\scriptsize
457\begin{verbatim}
458   <file_group id="1d" output_freq="1d" name="myfile_1d" >
459      <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA"  -->
460         ...
461      </file>
462      <file id="myfileB" name_suffix="_BBB" > <!-- will create file "myfile_1d_BBB" -->
463         ...
464      </file>
465   </file_group>
466\end{verbatim}
467}}\end{alltt} 
468However it is often very convienent to define the file name with the name of the experiment, the output file frequency and the date of the beginning and the end of the simulation (which are informations stored either in the namelist or in the XML file). To do so, we added the following rule: if the id of the tag file is ''fileN''(where N = 1 to 999 on 1 to 3 digits) or one of the predefined sections or moorings (see next subsection), the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by:\\
469\\
470\begin{tabular}{|p{4cm}|p{8cm}|}
471   \hline
472   \centering placeholder string & automatically  replaced by \\
473   \hline
474   \hline
475   \centering @expname@ &
476   the experiment name (from cn\_exp in the namelist) \\
477   \hline
478   \centering @freq@ &
479   output frequency (from attribute output\_freq) \\
480   \hline
481   \centering @startdate@  &
482   starting date of the simulation (from nn\_date0 in the restart or the namelist). \verb?yyyymmdd? format \\
483   \hline
484   \centering @startdatefull@  & 
485   starting date of the simulation (from nn\_date0 in the restart or the namelist). \verb?yyyymmdd_hh:mm:ss? format \\
486   \hline
487   \centering @enddate@  &
488   ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \verb?yyyymmdd? format \\
489   \hline
490   \centering @enddatefull@  & 
491   ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \verb?yyyymmdd_hh:mm:ss? format \\
492   \hline
493\end{tabular}\\
494\\
495
496\noindent For example,
497{{\scriptsize
498\begin{verbatim}
499   <file id="myfile_hzoom" name="myfile_@expname@_@startdate@_freq@freq@" output_freq="1d" >
500\end{verbatim}
501}}
502\noindent with the namelist:
503{{\scriptsize
504\begin{verbatim}
505   cn_exp      =  "ORCA2"
506   nn_date0    =  19891231
507   ln_rstart   = .false.
508\end{verbatim}
509}}
510\noindent will give the following file name radical:
511{{\scriptsize
512\begin{verbatim}
513   myfile_ORCA2_19891231_freq1d
514\end{verbatim}
515}}
516
517\subsubsection{Other controls of the xml attributes from NEMO}
518
519The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in iom.F90). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary).
520
521Here is the list of these attributes:\\
522\\
523\begin{tabular}{|l|c|c|c|}
524   \hline
525 \multicolumn{2}{|c|}{tag ids affected by automatic           }  & name      & attribute value \\
526  \multicolumn{2}{|c|}{definition of some of their attributes }  & attribute  &        \\
527   \hline
528   \hline
529    \multicolumn{2}{|c|}{field\_definition} & freq\_op & \np{rn\_rdt} \\
530   \hline
531    \multicolumn{2}{|c|}{SBC}               & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_fsbc}  \\
532   \hline
533    \multicolumn{2}{|c|}{ptrc\_T}           & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\
534   \hline
535    \multicolumn{2}{|c|}{diad\_T}           & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\
536   \hline
537    \multicolumn{2}{|c|}{EqT, EqU, EqW} & jbegin, ni,      & according to the grid    \\
538    \multicolumn{2}{|c|}{                         } & name\_suffix &                                      \\
539   \hline
540   \multicolumn{2}{|c|}{TAO, RAMA and PIRATA moorings} & zoom\_ibegin, zoom\_jbegin, & according to the grid    \\
541    \multicolumn{2}{|c|}{                                                       } & name\_suffix &                                      \\
542   \hline
543\end{tabular}
544
545
546\subsection{XML reference tables}
547
548\subsubsection{Tag list}
549
550\begin{longtable}{|p{2.2cm}|p{2.5cm}|p{3.5cm}|p{2.2cm}|p{1.6cm}|}
551   \hline
552   tag name & 
553   description & 
554   accepted attribute & 
555   child of &
556   parent of \endhead
557   \hline   
558   simulation & 
559   this tag is the root tag which encapsulates all the content of the xml file &
560   none &
561   none &
562   context \\
563   \hline   
564   context &
565   encapsulates parts of the xml file dedicated to different codes or different parts of a code &
566   id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin &
567   simulation &
568   all root tags: ... \_definition \\
569   \hline   
570   \hline   
571   field\_definition &
572   encapsulates the definition of all the fields that can potentially be outputted &
573   axis\_ref, default\_value, domain\_ref, enabled, grid\_ref, level, operation, prec, src &
574   context &
575   field or field\_group \\
576   \hline   
577   field\_group &
578   encapsulates a group of fields &
579   axis\_ref, default\_value, domain\_ref, enabled, group\_ref, grid\_ref, id, level, operation, prec, src &
580   field\_definition, field\_group, file &
581   field or field\_group \\
582   \hline   
583   field &
584   define a specific field &
585   axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref, id, level, long\_name, name, operation, prec, standard\_name, unit &
586   field\_definition, field\_group, file &
587   none \\
588   \hline   
589   \hline   
590   file\_definition & 
591   encapsulates the definition of all the files that will be outputted &
592   enabled, min\_digits, name, name\_suffix, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src &
593   context & 
594   file or file\_group \\
595   \hline   
596   file\_group & 
597   encapsulates a group of files that will be outputted &
598   enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src &
599   file\_definition, file\_group & 
600   file or file\_group \\
601   \hline   
602   file & 
603   define the contents of a file to be outputted &
604   enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src &
605   file\_definition, file\_group & 
606   field \\
607   \hline   
608   axis\_definition & 
609   define all the vertical axis potentially used by the variables &
610   src &
611   context & 
612   axis\_group, axis \\
613   \hline   
614   axis\_group & 
615   encapsulates a group of vertical axis &
616   id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
617   axis\_definition, axis\_group & 
618   axis\_group, axis \\
619   \hline   
620   axis & 
621   define a vertical axis &
622   id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
623   axis\_definition, axis\_group  & 
624   none \\
625   \hline   
626   \hline   
627   domain\_\-definition & 
628   define all the horizontal domains potentially used by the variables &
629   src &
630   context & 
631   domain\_\-group, domain \\
632   \hline   
633   domain\_group & 
634   encapsulates a group of horizontal domains &
635   id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj &
636   domain\_\-definition, domain\_group & 
637   domain\_\-group, domain \\
638   \hline   
639   domain & 
640   define an horizontal domain &
641   id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj &
642   domain\_\-definition, domain\_group & 
643   none \\
644   \hline   
645   \hline   
646   grid\_definition & 
647   define all the grid (association of a domain and/or an axis) potentially used by the variables &
648   src &
649   context & 
650   grid\_group, grid \\
651   \hline   
652   grid\_group & 
653   encapsulates a group of grids &
654   id, domain\_ref, axis\_ref &
655   grid\_definition, grid\_group & 
656   grid\_group, grid \\
657   \hline   
658   grid & 
659   define a grid &
660   id, domain\_ref, axis\_ref &
661   grid\_definition, grid\_group & 
662   none \\
663   \hline   
664\end{longtable}
665
666
667\subsubsection{Attributes list}
668
669\begin{longtable}{|p{2.2cm}|p{4cm}|p{3.8cm}|p{2cm}|}
670   \hline
671   attribute name & 
672   description & 
673   example & 
674   accepted by \endhead
675   \hline   
676   axis\_ref & 
677   refers to the id of a vertical axis & 
678   axis\_ref="deptht" & 
679   field, grid families \\ 
680   \hline   
681   enabled & 
682   switch on/off the output of a field or a file & 
683   enabled=".TRUE." & 
684   field, file families \\ 
685   \hline   
686   default\_value & 
687   missing\_value definition & 
688   default\_value="1.e20" & 
689   field family \\ 
690   \hline   
691   description & 
692   just for information, not used & 
693   description="ocean T grid variables" & 
694   all tags \\ 
695   \hline   
696   domain\_ref & 
697   refers to the id of a domain & 
698   domain\_ref="grid\_T" & 
699   field or grid families \\ 
700   \hline   
701   field\_ref & 
702   id of the field we want to add in a file & 
703   field\_ref="toce" & 
704   field \\ 
705   \hline   
706   grid\_ref & 
707   refers to the id of a grid & 
708   grid\_ref="grid\_T\_2D" & 
709   field family \\ 
710   \hline   
711   group\_ref & 
712   refer to a group of variables & 
713   group\_ref="mooring" & 
714   field\_group \\ 
715   \hline   
716   id & 
717   allow to identify a tag & 
718   id="nemo" &
719   accepted by all tags except simulation \\ 
720   \hline   
721   level & 
722   output priority of a field: 0 (high) to 10 (low)& 
723   level="1" & 
724   field family \\ 
725   \hline   
726   long\_name & 
727   define the long\_name attribute in the NetCDF file & 
728   long\_name="Vertical T levels" & 
729   field \\ 
730   \hline   
731   min\_digits & 
732   specify the minimum of digits used in the core number in the name of the NetCDF file & 
733   min\_digits="4" & 
734   file family \\ 
735   \hline   
736   name & 
737   name of a variable or a file. If the name of a file is undefined, its id is used as a name & 
738   name="tos" & 
739   field or file families \\ 
740   \hline   
741   name\_suffix & 
742   suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file & 
743   name\_suffix="\_myzoom" & 
744   file family \\ 
745   \hline   
746   attribute name & 
747   description & 
748   example & 
749   accepted by \\ 
750   \hline   
751   \hline   
752   operation & 
753   type of temporal operation: average, accumulate, instantaneous, min, max and once & 
754   operation="average" & 
755   field family \\ 
756   \hline   
757   output\_freq & 
758   operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. & 
759   output\_freq="1d12h" & 
760   field family \\ 
761   \hline   
762   output\_level & 
763   output priority of variables in a file: 0 (high) to 10 (low). All variables listed in the file with a level smaller or equal to output\_level will be output. Other variables won't be output even if they are listed in the file. & 
764   output\_level="10"& 
765   file family \\ 
766   \hline   
767   positive & 
768   convention used for the orientation of vertival axis (positive downward in \NEMO). & 
769   positive="down" & 
770   axis family \\ 
771   \hline   
772   prec & 
773   output precision: real 4 or real 8 & 
774   prec="4" & 
775   field family \\ 
776   \hline   
777   split\_freq & 
778   frequency at which to temporally split output files. Units can be ts (timestep), y, mo, d, h, mi, s. Useful for long runs to prevent over-sized output files.& 
779   split\_freq="1mo" & 
780   file family \\ 
781   \hline   
782   split\_freq\-\_format & 
783   date format used in the name of temporally split output files. Can be specified
784   using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s & 
785   split\_freq\_format= "\%y\%mo\%d" & 
786   file family \\ 
787   \hline   
788   src & 
789   allow to include a file & 
790   src="./field\_def.xml" & 
791   accepted by all tags except simulation \\ 
792   \hline   
793   standard\_name & 
794   define the standard\_name attribute in the NetCDF file & 
795   standard\_name= "Eastward\_Sea\_Ice\_Transport" & 
796   field \\ 
797   \hline   
798   sync\_freq & 
799   NetCDF file synchronization frequency (update of the time\_counter). units can be ts (timestep), y, mo, d, h, mi, s. & 
800   sync\_freq="10d" & 
801   file family \\ 
802   \hline   
803   attribute name & 
804   description & 
805   example & 
806   accepted by \\ 
807   \hline   
808   \hline   
809   time\_origin & 
810   specify the origin of the time counter & 
811   time\_origin="1900-01-01 00:00:00"& 
812   context \\ 
813   \hline   
814   type (1)& 
815   specify if the output files are to be split spatially (multiple\_file) or not (one\_file) & 
816   type="multiple\_file" & 
817   file familly \\ 
818   \hline   
819   type (2)& 
820   define the type of a variable tag & 
821   type="boolean" & 
822   variable \\ 
823   \hline   
824   unit & 
825   unit of a variable or the vertical axis & 
826   unit="m" & 
827   field and axis families \\ 
828   \hline   
829   zoom\_ibegin & 
830   starting point along x direction of the zoom. Automatically defined for TAO/RAMA/PIRATA moorings & 
831   zoom\_ibegin="1" & 
832   domain family \\ 
833   \hline   
834   zoom\_jbegin & 
835   starting point along y direction of the zoom. Automatically defined for TAO/RAMA/PIRATA moorings & 
836   zoom\_jbegin="1" & 
837   domain family \\ 
838   \hline   
839   zoom\_ni & 
840   zoom extent along x direction & 
841   zoom\_ni="1" & 
842   domain family \\ 
843   \hline   
844   zoom\_nj & 
845   zoom extent along y direction & 
846   zoom\_nj="1" & 
847   domain family \\ 
848   \hline   
849\end{longtable}
850
851
852
853% ================================================================
854%       NetCDF4 support
855% ================================================================
856\section{NetCDF4 Support (\key{netcdf4})}
857\label{DIA_iom}
858
859Since version 3.3, support for NetCDF4 chunking and (loss-less) compression has
860been included.  These options build on the standard NetCDF output and allow
861the user control over the size of the chunks via namelist settings. Chunking
862and compression can lead to significant reductions in file sizes for a small
863runtime overhead. For a fuller discussion on chunking and other performance
864issues the reader is referred to the NetCDF4 documentation found
865\href{http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.html#Chunking}{here}.
866
867The new features are only available when the code has been linked with a
868NetCDF4 library (version 4.1 onwards, recommended) which has been built
869with HDF5 support (version 1.8.4 onwards, recommended). Datasets created
870with chunking and compression are not backwards compatible with NetCDF3
871"classic" format but most analysis codes can be relinked simply with the
872new libraries and will then read both NetCDF3 and NetCDF4 files. NEMO
873executables linked with NetCDF4 libraries can be made to produce NetCDF3
874files by setting the \np{ln\_nc4zip} logical to false in the \textit{namnc4} 
875namelist:
876
877%------------------------------------------namnc4----------------------------------------------------
878\namdisplay{namnc4}
879%-------------------------------------------------------------------------------------------------------------
880
881If \key{netcdf4} has not been defined, these namelist parameters are not read.
882In this case, \np{ln\_nc4zip} is set false and dummy routines for a few
883NetCDF4-specific functions are defined. These functions will not be used but
884need to be included so that compilation is possible with NetCDF3 libraries.
885
886When using NetCDF4 libraries, \key{netcdf4} should be defined even if the
887intention is to create only NetCDF3-compatible files. This is necessary to
888avoid duplication between the dummy routines and the actual routines present
889in the library. Most compilers will fail at compile time when faced with
890such duplication. Thus when linking with NetCDF4 libraries the user must
891define \key{netcdf4} and control the type of NetCDF file produced via the
892namelist parameter.
893
894Chunking and compression is applied only to 4D fields and there is no
895advantage in chunking across more than one time dimension since previously
896written chunks would have to be read back and decompressed before being
897added to. Therefore, user control over chunk sizes is provided only for the
898three space dimensions. The user sets an approximate number of chunks along
899each spatial axis. The actual size of the chunks will depend on global domain
900size for mono-processors or, more likely, the local processor domain size for
901distributed processing. The derived values are subject to practical minimum
902values (to avoid wastefully small chunk sizes) and cannot be greater than the
903domain size in any dimension. The algorithm used is:
904
905\vspace{-20pt}
906\begin{alltt}  {{\scriptsize 
907\begin{verbatim}
908     ichunksz(1) = MIN( idomain_size,MAX( (idomain_size-1)/nn_nchunks_i + 1 ,16 ) )
909     ichunksz(2) = MIN( jdomain_size,MAX( (jdomain_size-1)/nn_nchunks_j + 1 ,16 ) )
910     ichunksz(3) = MIN( kdomain_size,MAX( (kdomain_size-1)/nn_nchunks_k + 1 , 1 ) )
911     ichunksz(4) = 1
912\end{verbatim}
913}}\end{alltt} 
914
915\noindent As an example, setting:
916\vspace{-20pt}
917\begin{alltt}  {{\scriptsize
918\begin{verbatim}
919     nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31
920\end{verbatim}
921}}\end{alltt} \vspace{-10pt}
922
923\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1}
924respectively in the mono-processor case (i.e. global domain of {\small\tt 182x149x31}).
925An illustration of the potential space savings that NetCDF4 chunking and compression
926provides is given in table \ref{Tab_NC4} which compares the results of two short
927runs of the ORCA2\_LIM reference configuration with a 4x2 mpi partitioning. Note
928the variation in the compression ratio achieved which reflects chiefly the dry to wet
929volume ratio of each processing region.
930
931%------------------------------------------TABLE----------------------------------------------------
932\begin{table}  \begin{tabular}{lrrr}
933Filename & NetCDF3 & NetCDF4 & Reduction\\
934         &filesize & filesize & \% \\
935         &(KB)     & (KB)     & \\
936ORCA2\_restart\_0000.nc & 16420 & 8860 & 47\%\\
937ORCA2\_restart\_0001.nc & 16064 & 11456 & 29\%\\
938ORCA2\_restart\_0002.nc & 16064 & 9744 & 40\%\\
939ORCA2\_restart\_0003.nc & 16420 & 9404 & 43\%\\
940ORCA2\_restart\_0004.nc & 16200 & 5844 & 64\%\\
941ORCA2\_restart\_0005.nc & 15848 & 8172 & 49\%\\
942ORCA2\_restart\_0006.nc & 15848 & 8012 & 50\%\\
943ORCA2\_restart\_0007.nc & 16200 & 5148 & 69\%\\
944ORCA2\_2d\_grid\_T\_0000.nc & 2200 & 1504 & 32\%\\
945ORCA2\_2d\_grid\_T\_0001.nc & 2200 & 1748 & 21\%\\
946ORCA2\_2d\_grid\_T\_0002.nc & 2200 & 1592 & 28\%\\
947ORCA2\_2d\_grid\_T\_0003.nc & 2200 & 1540 & 30\%\\
948ORCA2\_2d\_grid\_T\_0004.nc & 2200 & 1204 & 46\%\\
949ORCA2\_2d\_grid\_T\_0005.nc & 2200 & 1444 & 35\%\\
950ORCA2\_2d\_grid\_T\_0006.nc & 2200 & 1428 & 36\%\\
951ORCA2\_2d\_grid\_T\_0007.nc & 2200 & 1148 & 48\%\\
952             ...            &  ... &  ... & ..  \\
953ORCA2\_2d\_grid\_W\_0000.nc & 4416 & 2240 & 50\%\\
954ORCA2\_2d\_grid\_W\_0001.nc & 4416 & 2924 & 34\%\\
955ORCA2\_2d\_grid\_W\_0002.nc & 4416 & 2512 & 44\%\\
956ORCA2\_2d\_grid\_W\_0003.nc & 4416 & 2368 & 47\%\\
957ORCA2\_2d\_grid\_W\_0004.nc & 4416 & 1432 & 68\%\\
958ORCA2\_2d\_grid\_W\_0005.nc & 4416 & 1972 & 56\%\\
959ORCA2\_2d\_grid\_W\_0006.nc & 4416 & 2028 & 55\%\\
960ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\%\\
961\end{tabular}
962\caption{   \label{Tab_NC4} 
963Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression}
964\end{table}
965%----------------------------------------------------------------------------------------------------
966
967When \key{iomput} is activated with \key{netcdf4} chunking and
968compression parameters for fields produced via \np{iom\_put} calls are
969set via an equivalent and identically named namelist to \textit{namnc4} 
970in \np{xmlio\_server.def}. Typically this namelist serves the mean files
971whilst the \ngn{ namnc4} in the main namelist file continues to serve the
972restart files. This duplication is unfortunate but appropriate since, if
973using io\_servers, the domain sizes of the individual files produced by the
974io\_server processes may be different to those produced by the invidual
975processing regions and different chunking choices may be desired.
976 
977
978% -------------------------------------------------------------------------------------------------------------
979%       Tracer/Dynamics Trends
980% -------------------------------------------------------------------------------------------------------------
981\section[Tracer/Dynamics Trends (TRD)]
982                  {Tracer/Dynamics Trends  (\key{trdtra}, \key{trddyn},    \\ 
983                                                             \key{trddvor}, \key{trdmld})}
984\label{DIA_trd}
985
986%------------------------------------------namtrd----------------------------------------------------
987\namdisplay{namtrd} 
988%-------------------------------------------------------------------------------------------------------------
989
990When \key{trddyn} and/or \key{trddyn} CPP variables are defined, each
991trend of the dynamics and/or temperature and salinity time evolution equations
992is stored in three-dimensional arrays just after their computation ($i.e.$ at the end
993of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines). Options are defined by
994\ngn{namtrd} namelist variables. These trends are then
995used in \mdl{trdmod} (see TRD directory) every \textit{nn\_trd } time-steps.
996
997What is done depends on the CPP keys defined:
998\begin{description}
999\item[\key{trddyn}, \key{trdtra}] : a check of the basin averaged properties of the momentum
1000and/or tracer equations is performed ;
1001\item[\key{trdvor}] : a vertical summation of the moment tendencies is performed,
1002then the curl is computed to obtain the barotropic vorticity tendencies which are output ;
1003\item[\key{trdmld}] : output of the tracer tendencies averaged vertically 
1004either over the mixed layer (\np{nn\_ctls}=0),
1005or       over a fixed number of model levels (\np{nn\_ctls}$>$1 provides the number of level),
1006or       over a spatially varying but temporally fixed number of levels (typically the base
1007of the winter mixed layer) read in \ifile{ctlsurf\_idx} (\np{nn\_ctls}=1) ;
1008\end{description}
1009
1010The units in the output file can be changed using the \np{nn\_ucf} namelist parameter.
1011For example, in case of salinity tendency the units are given by PSU/s/\np{nn\_ucf}.
1012Setting \np{nn\_ucf}=86400 ($i.e.$ the number of second in a day) provides the tendencies in PSU/d.
1013
1014When \key{trdmld} is defined, two time averaging procedure are proposed.
1015Setting \np{ln\_trdmld\_instant} to \textit{true}, a simple time averaging is performed,
1016so that the resulting tendency is the contribution to the change of a quantity between
1017the two instantaneous values taken at the extremities of the time averaging period.
1018Setting \np{ln\_trdmld\_instant} to \textit{false}, a double time averaging is performed,
1019so that the resulting tendency is the contribution to the change of a quantity between
1020two \textit{time mean} values. The later option requires the use of an extra file, \ifile{restart\_mld} 
1021(\np{ln\_trdmld\_restart}=true), to restart a run.
1022
1023
1024Note that the mixed layer tendency diagnostic can also be used on biogeochemical models
1025via the \key{trdtrc} and \key{trdmld\_trc} CPP keys.
1026
1027% -------------------------------------------------------------------------------------------------------------
1028%       On-line Floats trajectories
1029% -------------------------------------------------------------------------------------------------------------
1030\section{On-line Floats trajectories (FLO) (\key{floats})}
1031\label{FLO}
1032%--------------------------------------------namflo-------------------------------------------------------
1033\namdisplay{namflo} 
1034%--------------------------------------------------------------------------------------------------------------
1035
1036The on-line computation of floats advected either by the three dimensional velocity
1037field or constraint to remain at a given depth ($w = 0$ in the computation) have been
1038introduced in the system during the CLIPPER project. Options are defined by \ngn{namflo}
1039namelis variables. The algorithm used is based
1040either on the work of \cite{Blanke_Raynaud_JPO97} (default option), or on a $4^th$
1041Runge-Hutta algorithm (\np{ln\_flork4}=true). Note that the \cite{Blanke_Raynaud_JPO97} 
1042algorithm have the advantage of providing trajectories which are consistent with the
1043numeric of the code, so that the trajectories never intercept the bathymetry.
1044
1045\subsubsection{ Input data: initial coordinates }
1046
1047Initial coordinates can be given with Ariane Tools convention ( IJK coordinates ,(\np{ln\_ariane}=true) )
1048or with longitude and latitude.
1049
1050
1051In case of Ariane convention, input filename is \np{init\_float\_ariane}. Its format is:
1052
1053\texttt{ I J K nisobfl itrash itrash }
1054
1055\noindent with:
1056
1057 - I,J,K  : indexes of initial position
1058
1059 - nisobfl: 0 for an isobar float, 1 for a float following the w velocity 
1060
1061 - itrash : set to zero; it is a dummy variable to respect Ariane Tools convention
1062
1063 - itrash :set to zero; it is a dummy variable to respect Ariane Tools convention
1064
1065\noindent Example:\\
1066\noindent \texttt{ 100.00000  90.00000  -1.50000 1.00000   0.00000}\\
1067\texttt{ 102.00000  90.00000  -1.50000 1.00000   0.00000}\\
1068\texttt{ 104.00000  90.00000  -1.50000 1.00000   0.00000}\\
1069\texttt{ 106.00000  90.00000  -1.50000 1.00000   0.00000}\\
1070\texttt{ 108.00000  90.00000  -1.50000 1.00000   0.00000}\\
1071
1072
1073In the other case ( longitude and latitude ), input filename is init\_float. Its format is:
1074
1075\texttt{ Long Lat depth nisobfl ngrpfl itrash}
1076
1077\noindent with:
1078
1079 - Long, Lat, depth  : Longitude, latitude, depth
1080
1081 - nisobfl: 0 for an isobar float, 1 for a float following the w velocity
1082
1083 - ngrpfl : number to identify searcher group
1084
1085 - itrash :set to 1; it is a dummy variable.
1086
1087\noindent Example:
1088
1089\noindent\texttt{  20.0 0.0 0.0 0 1 1 }\\
1090\texttt{ -21.0 0.0 0.0 0 1 1 }\\
1091\texttt{ -22.0 0.0 0.0 0 1 1 }\\
1092\texttt{ -23.0 0.0 0.0 0 1 1 }\\
1093\texttt{ -24.0 0.0 0.0 0 1 1 }\\
1094
1095\np{jpnfl} is the total number of floats during the run.
1096When initial positions are read in a restart file ( \np{ln\_rstflo}= .TRUE. ),  \np{jpnflnewflo}
1097can be added in the initialization file.
1098
1099\subsubsection{ Output data }
1100
1101\np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} 
1102is the frequency of creation of the float restart file.
1103
1104Output data can be written in ascii files (\np{ln\_flo\_ascii} = .TRUE. ). In that case,
1105output filename is trajec\_float.
1106
1107Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii} = .FALSE. ). There are 2 possibilities:
1108
1109 - if (\key{iomput}) is used, outputs are selected in  iodef.xml. Here it is an example of specification
1110   to put in files description section:
1111
1112\vspace{-30pt}
1113\begin{alltt}  {{\scriptsize
1114\begin{verbatim}
1115
1116     <group id="1d\_grid\_T" name="auto" description="ocean T grid variables" >   }
1117       <file id="floats"  description="floats variables"> }\\
1118           <field ref="traj\_lon"   name="floats\_longitude"   freq\_op="86400" />}
1119           <field ref="traj\_lat"   name="floats\_latitude"    freq\_op="86400" />}
1120           <field ref="traj\_dep"   name="floats\_depth"       freq\_op="86400" />}
1121           <field ref="traj\_temp"  name="floats\_temperature" freq\_op="86400" />}
1122           <field ref="traj\_salt"  name="floats\_salinity"    freq\_op="86400" />}
1123           <field ref="traj\_dens"  name="floats\_density"     freq\_op="86400" />}
1124           <field ref="traj\_group" name="floats\_group"       freq\_op="86400" />}
1125       </file>}
1126  </group>}
1127
1128\end{verbatim}
1129}}\end{alltt}
1130
1131
1132 -  if (\key{iomput}) is not used, a file called trajec\_float.nc will be created by IOIPSL library.
1133
1134
1135
1136See also \href{http://stockage.univ-brest.fr/~grima/Ariane/}{here} the web site describing
1137the off-line use of this marvellous diagnostic tool.
1138
1139
1140% -------------------------------------------------------------------------------------------------------------
1141%       Harmonic analysis of tidal constituents
1142% -------------------------------------------------------------------------------------------------------------
1143\section{Harmonic analysis of tidal constituents (\key{diaharm}) }
1144\label{DIA_diag_harm}
1145
1146A module is available to compute the amplitude and phase for tidal waves.
1147This diagnostic is actived with \key{diaharm}.
1148
1149%------------------------------------------namdia_harm----------------------------------------------------
1150\namdisplay{namdia_harm}
1151%----------------------------------------------------------------------------------------------------------
1152
1153Concerning the on-line Harmonic analysis, some parameters are available in namelist
1154\ngn{namdia\_harm} :
1155
1156- \texttt{nit000\_han} is the first time step used for harmonic analysis
1157
1158- \texttt{nitend\_han} is the last time step used for harmonic analysis
1159
1160- \texttt{nstep\_han} is the time step frequency for harmonic analysis
1161
1162- \texttt{nb\_ana} is the number of harmonics to analyse
1163
1164- \texttt{tname} is an array with names of tidal constituents to analyse
1165
1166\texttt{nit000\_han} and \texttt{nitend\_han} must be between \texttt{nit000} and \texttt{nitend} of the simulation.
1167The restart capability is not implemented.
1168
1169The Harmonic analysis solve this equation:
1170\begin{equation}
1171h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i}
1172\end{equation}
1173
1174With $A_{j}$,$\nu_{j}$,$\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error.
1175$h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\
1176We can rewrite this equation:
1177\begin{equation}
1178h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i}
1179\end{equation}
1180with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ et $\phi_{j}=arctan(S_{j}/C_{j})$.
1181
1182We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave.
1183
1184% -------------------------------------------------------------------------------------------------------------
1185%       Sections transports
1186% -------------------------------------------------------------------------------------------------------------
1187\section{Transports across sections (\key{diadct}) }
1188\label{DIA_diag_dct}
1189
1190A module is available to compute the transport of volume, heat and salt through sections. This diagnostic
1191is actived with \key{diadct}.
1192
1193Each section is defined by the coordinates of its 2 extremities. The pathways between them are contructed
1194using tools which can be found in  \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT} and are written in a binary file
1195 \texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is later read in by NEMO to compute on-line transports.
1196
1197The on-line transports module creates three output ascii files:
1198
1199- \texttt{volume\_transport} for volume transports (  unit: $10^{6} m^{3} s^{-1}$ )
1200
1201- \texttt{heat\_transport}   for heat transports   (  unit: $10^{15} W $ )
1202
1203- \texttt{salt\_transport}   for salt transports   (  unit: $10^{9}Kg s^{-1}$ )\\
1204
1205
1206Namelist variables in \ngn{namdct} control how frequently the flows are summed
1207and the time scales over which they are averaged, as well as the level of output for debugging:
1208
1209%------------------------------------------namdct----------------------------------------------------
1210\namdisplay{namdct}
1211%-------------------------------------------------------------------------------------------------------------
1212
1213\texttt{nn\_dct}: frequency of instantaneous transports computing
1214
1215\texttt{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
1216
1217\texttt{nn\_debug}: debugging of the section
1218
1219\subsubsection{ To create a binary file containing the pathway of each section }
1220
1221In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run}, the file \texttt{ {list\_sections.ascii\_global}}
1222contains a list of all the sections that are to be computed (this list of sections is based on MERSEA project metrics).
1223
1224Another file is available for the GYRE configuration (\texttt{ {list\_sections.ascii\_GYRE}}).
1225
1226Each section is defined by:
1227
1228\noindent \texttt{ long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name }\\
1229with:
1230
1231- \texttt{long1 lat1} , coordinates of the first extremity of the section;
1232
1233- \texttt{long2 lat2} , coordinates of the second extremity of the section;
1234
1235- \texttt{nclass} the number of bounds of your classes (e.g. 3 bounds for 2 classes);
1236
1237- \texttt{okstrpond} to compute heat and salt transport, \texttt{nostrpond} if no;
1238
1239- \texttt{ice}  to compute surface and volume ice transports, \texttt{noice} if no. \\
1240
1241
1242\noindent The results of the computing of transports, and the directions of positive
1243 and negative flow do not depend on the order of the 2 extremities in this file.\\ 
1244
1245
1246\noindent If nclass =/ 0,the next lines contain the class type and the nclass bounds:
1247
1248\texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}
1249
1250\texttt{classtype}
1251
1252\texttt{zbound1}
1253
1254\texttt{zbound2}
1255
1256\texttt{.}
1257
1258\texttt{.}
1259
1260\texttt{nclass-1}
1261
1262\texttt{nclass}
1263
1264\noindent where \texttt{classtype} can be:
1265
1266- \texttt{zsal} for salinity classes
1267
1268- \texttt{ztem} for temperature classes
1269
1270- \texttt{zlay} for depth classes
1271
1272- \texttt{zsigi} for insitu density classes
1273
1274- \texttt{zsigp} for potential density classes \\
1275
1276 
1277The script \texttt{job.ksh} computes the pathway for each section and creates a binary file
1278\texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is read by NEMO. \\
1279
1280It is possible to use this tools for new configuations: \texttt{job.ksh} has to be updated
1281with the coordinates file name and path. \\
1282
1283
1284Examples of two sections, the ACC\_Drake\_Passage with no classes, and the
1285 ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown:
1286
1287\noindent \texttt{ -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage}
1288
1289\noindent \texttt{ -80.5    22.5   -80.5    25.5  05 nostrpond noice ATL\_Cuba\_Florida}
1290
1291\noindent \texttt{ztem}
1292
1293\noindent \texttt{-2.0}
1294
1295\noindent \texttt{ 4.5}
1296
1297\noindent \texttt{ 7.0}
1298
1299\noindent \texttt{12.0}
1300
1301\noindent \texttt{40.0}
1302
1303
1304\subsubsection{ To read the output files }
1305
1306The output format is :
1307 
1308{\small\texttt{date, time-step number, section number, section name, section slope coefficient, class number,
1309class name, class bound 1 , classe bound2, transport\_direction1 ,  transport\_direction2, transport\_total}}\\
1310
1311
1312For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class
1313and the last line corresponds to the total transport summed over all classes. For sections with no classes, class number
1314\texttt{ 1 } corresponds to \texttt{ total class } and this class is called  \texttt{N}, meaning \texttt{none}.\\
1315
1316
1317\noindent \texttt{ transport\_direction1 } is the positive part of the transport ( \texttt{ > = 0 } ).
1318
1319\noindent \texttt{ transport\_direction2 } is the negative part of the transport ( \texttt{ < = 0 } ).\\
1320
1321
1322\noindent The \texttt{section slope coefficient} gives information about the significance of transports signs and direction:\\
1323
1324
1325
1326\begin{tabular}{|c|c|c|c|p{4cm}|}
1327\hline
1328section slope coefficient & section type & direction 1 & direction 2 & total transport \\ \hline
13290.    &  horizontal & northward & southward & postive: northward  \\ \hline
13301000. &  vertical   & eastward  & westward  & postive: eastward  \\ \hline               
1331\texttt{=/0, =/ 1000.}   &  diagonal   & eastward  & westward  & postive: eastward  \\ \hline               
1332\end{tabular}
1333
1334
1335
1336% -------------------------------------------------------------------------------------------------------------
1337%       Other Diagnostics
1338% -------------------------------------------------------------------------------------------------------------
1339\section{Other Diagnostics (\key{diahth}, \key{diaar5})}
1340\label{DIA_diag_others}
1341
1342
1343Aside from the standard model variables, other diagnostics can be computed
1344on-line. The available ready-to-add diagnostics routines can be found in directory DIA.
1345Among the available diagnostics the following ones are obtained when defining
1346the \key{diahth} CPP key:
1347
1348- the mixed layer depth (based on a density criterion, \citet{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth})
1349
1350- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth})
1351
1352- the depth of the 20\deg C isotherm (\mdl{diahth})
1353
1354- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth})
1355
1356The poleward heat and salt transports, their advective and diffusive component, and
1357the meriodional stream function can be computed on-line in \mdl{diaptr} 
1358\np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below). 
1359When \np{ln\_subbas}~=~true, transports and stream function are computed
1360for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S)
1361as well as for the World Ocean. The sub-basin decomposition requires an input file
1362(\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask
1363been deduced from the sum of the Indian and Pacific mask (Fig~\ref{Fig_mask_subasins}).
1364
1365%------------------------------------------namptr----------------------------------------------------
1366\namdisplay{namptr} 
1367%-------------------------------------------------------------------------------------------------------------
1368%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1369\begin{figure}[!t]     \begin{center}
1370\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf}
1371\caption{   \label{Fig_mask_subasins}
1372Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute
1373the heat and salt transports as well as the meridional stream-function: Atlantic basin (red),
1374Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).
1375Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay
1376are removed from the sub-basins. Note also that the Arctic Ocean has been split
1377into Atlantic and Pacific basins along the North fold line.  }
1378\end{center}   \end{figure} 
1379%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1380
1381In addition, a series of diagnostics has been added in the \mdl{diaar5}.
1382They corresponds to outputs that are required for AR5 simulations
1383(see Section \ref{DIA_steric} below for one of them).
1384Activating those outputs requires to define the \key{diaar5} CPP key.
1385\\
1386\\
1387
1388
1389
1390% ================================================================
1391% Steric effect in sea surface height
1392% ================================================================
1393\section{Diagnosing the Steric effect in sea surface height}
1394\label{DIA_steric}
1395
1396
1397Changes in steric sea level are caused when changes in the density of the water
1398column imply an expansion or contraction of the column. It is essentially produced
1399through surface heating/cooling and to a lesser extent through non-linear effects of
1400the equation of state (cabbeling, thermobaricity...).
1401Non-Boussinesq models contain all ocean effects within the ocean acting
1402on the sea level. In particular, they include the steric effect. In contrast,
1403Boussinesq models, such as \NEMO, conserve volume, rather than mass,
1404and so do not properly represent expansion or contraction. The steric effect is
1405therefore not explicitely represented.
1406This approximation does not represent a serious error with respect to the flow field
1407calculated by the model \citep{Greatbatch_JGR94}, but extra attention is required
1408when investigating sea level, as steric changes are an important
1409contribution to local changes in sea level on seasonal and climatic time scales.
1410This is especially true for investigation into sea level rise due to global warming.
1411
1412Fortunately, the steric contribution to the sea level consists of a spatially uniform
1413component that can be diagnosed by considering the mass budget of the world
1414ocean \citep{Greatbatch_JGR94}.
1415In order to better understand how global mean sea level evolves and thus how
1416the steric sea level can be diagnosed, we compare, in the following, the
1417non-Boussinesq and Boussinesq cases.
1418
1419Let denote
1420$\mathcal{M}$ the total mass of liquid seawater ($\mathcal{M}=\int_D \rho dv$),
1421$\mathcal{V}$ the total volume of seawater ($\mathcal{V}=\int_D dv$),
1422$\mathcal{A}$ the total surface of the ocean ($\mathcal{A}=\int_S ds$),
1423$\bar{\rho}$ the global mean seawater (\textit{in situ}) density ($\bar{\rho}= 1/\mathcal{V} \int_D \rho \,dv$), and
1424$\bar{\eta}$ the global mean sea level ($\bar{\eta}=1/\mathcal{A}\int_S \eta \,ds$).
1425
1426A non-Boussinesq fluid conserves mass. It satisfies the following relations:
1427\begin{equation} \label{Eq_MV_nBq} 
1428\begin{split} 
1429\mathcal{M} &\mathcal{V}  \;\bar{\rho}       \\
1430\mathcal{V} &\mathcal{A}  \;\bar{\eta} 
1431\end{split}
1432\end{equation}
1433Temporal changes in total mass is obtained from the density conservation equation :
1434\begin{equation}  \label{Eq_Co_nBq}
1435\frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} ) = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface}
1436\end{equation}
1437where $\rho$ is the \textit{in situ} density, and \textit{emp} the surface mass
1438exchanges with the other media of the Earth system (atmosphere, sea-ice, land).
1439Its global averaged leads to the total mass change
1440\begin{equation}  \label{Eq_Mass_nBq}
1441\partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}}
1442\end{equation}
1443where $\overline{\textit{emp}}=\int_S \textit{emp}\,ds$ is the net mass flux
1444through the ocean surface.
1445Bringing \eqref{Eq_Mass_nBq} and the time derivative of \eqref{Eq_MV_nBq} 
1446together leads to the evolution equation of the mean sea level
1447\begin{equation} \label{Eq_ssh_nBq}
1448  \partial_t \bar{\eta} =  \frac{\overline{\textit{emp}}}{ \bar{\rho}} 
1449               - \frac{\mathcal{V}}{\mathcal{A}}  \;\frac{\partial_t \bar{\rho} }{\bar{\rho}}
1450\end{equation}
1451The first term in equation \eqref{Eq_ssh_nBq} alters sea level by adding or
1452subtracting mass from the ocean.
1453The second term arises from temporal changes in the global mean
1454density; $i.e.$ from steric effects.
1455
1456In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ 
1457appears multiplied by the gravity ($i.e.$ in the hydrostatic balance of the primitive Equations).
1458In particular, the mass conservation equation, \eqref{Eq_Co_nBq}, degenerates into
1459the incompressibility equation:
1460\begin{equation}  \label{Eq_Co_Bq}
1461\frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) =  \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface}
1462\end{equation}
1463and the global average of this equation now gives the temporal change of the total volume,
1464\begin{equation}  \label{Eq_V_Bq}
1465  \partial_t \mathcal{V} =   \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o} 
1466\end{equation}
1467Only the volume is conserved, not mass, or, more precisely, the mass which is conserved is the
1468Boussinesq mass, $\mathcal{M}_o = \rho_o \mathcal{V}$. The total volume (or equivalently 
1469the global mean sea level) is altered only by net volume fluxes across the ocean surface, 
1470not by changes in mean mass of the ocean: the steric effect is missing in a Boussinesq fluid.
1471 
1472Nevertheless, following \citep{Greatbatch_JGR94}, the steric effect on the volume can be
1473diagnosed by considering the mass budget of the ocean.
1474The apparent changes in $\mathcal{M}$, mass of the ocean, which are not induced by surface
1475mass flux must be compensated by a spatially uniform change in the mean sea level due to
1476expansion/contraction of the ocean \citep{Greatbatch_JGR94}. In others words, the Boussinesq
1477mass, $\mathcal{M}_o$, can be related to $\mathcal{M}$, the  total mass of the ocean seen
1478by the Boussinesq model, via the steric contribution to the sea level, $\eta_s$, a spatially
1479uniform variable, as follows:
1480\begin{equation}  \label{Eq_M_Bq}
1481   \mathcal{M}_o  =  \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A} 
1482\end{equation}
1483Any change in $\mathcal{M}$ which cannot be explained by the net mass flux through
1484the ocean surface is converted into a mean change in sea level. Introducing the total density
1485anomaly, $\mathcal{D}= \int_D d_a \,dv$, where $d_a= (\rho -\rho_o ) / \rho_o$ 
1486is the density anomaly used in \NEMO (cf. \S\ref{TRA_eos}) in \eqref{Eq_M_Bq}
1487leads to a very simple form for the steric height:
1488\begin{equation}  \label{Eq_steric_Bq}
1489   \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D} 
1490\end{equation}
1491
1492The above formulation of the steric height of a Boussinesq ocean requires four remarks.
1493First, one can be tempted to define $\rho_o$ as the initial value of $\mathcal{M}/\mathcal{V}$,
1494$i.e.$ set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero. We do not
1495recommend that. Indeed, in this case $\rho_o$ depends on the initial state of the ocean.
1496Since $\rho_o$ has a direct effect on the dynamics of the ocean (it appears in the pressure
1497gradient term of the momentum equation) it is definitively not a good idea when
1498inter-comparing experiments.
1499We better recommend to fixe once for all $\rho_o$ to $1035\;Kg\,m^{-3}$. This value is a
1500sensible choice for the reference density used in a Boussinesq ocean climate model since,
1501with the exception of only a small percentage of the ocean, density in the World Ocean
1502varies by no more than 2$\%$ from this value (\cite{Gill1982}, page 47).
1503
1504Second, we have assumed here that the total ocean surface, $\mathcal{A}$, does not
1505change when the sea level is changing as it is the case in all global ocean GCMs
1506(wetting and drying of grid point is not allowed).
1507 
1508Third, the discretisation of \eqref{Eq_steric_Bq} depends on the type of free surface
1509which is considered. In the non linear free surface case, $i.e.$ \key{vvl} defined, it is
1510given by
1511\begin{equation}  \label{Eq_discrete_steric_Bq}
1512   \eta_s =  - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} }
1513                  { \sum_{i,\,j,\,k}         e_{1t} e_{2t} e_{3t} } 
1514\end{equation}
1515whereas in the linear free surface, the volume above the \textit{z=0} surface must be explicitly taken
1516into account to better approximate the total ocean mass and thus the steric sea level:
1517\begin{equation}  \label{Eq_discrete_steric_Bq}
1518   \eta_s =  - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta }
1519                     {\sum_{i,\,j,\,k} e_{1t}e_{2t}e_{3t} + \sum_{i,\,j}           e_{1t}e_{2t} \eta } 
1520\end{equation}
1521
1522The fourth and last remark concerns the effective sea level and the presence of sea-ice.
1523In the real ocean, sea ice (and snow above it)  depresses the liquid seawater through
1524its mass loading. This depression is a result of the mass of sea ice/snow system acting
1525on the liquid ocean. There is, however, no dynamical effect associated with these depressions
1526in the liquid ocean sea level, so that there are no associated ocean currents. Hence, the
1527dynamically relevant sea level is the effective sea level, $i.e.$ the sea level as if sea ice
1528(and snow) were converted to liquid seawater \citep{Campin_al_OM08}. However,
1529in the current version of \NEMO the sea-ice is levitating above the ocean without
1530mass exchanges between ice and ocean. Therefore the model effective sea level
1531is always given by $\eta + \eta_s$, whether or not there is sea ice present.
1532
1533In AR5 outputs, the thermosteric sea level is demanded. It is steric sea level due to
1534changes in ocean density arising just from changes in temperature. It is given by:
1535\begin{equation}  \label{Eq_thermosteric_Bq}
1536   \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv
1537\end{equation}
1538where $S_o$ and $p_o$ are the initial salinity and pressure, respectively.
1539
1540Both steric and thermosteric sea level are computed in \mdl{diaar5} which needs
1541the \key{diaar5} defined to be called.
1542
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