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1\documentclass[../main/NEMO_manual]{subfiles}
2
3\begin{document}
4% ================================================================
5% Chapter I/O & Diagnostics
6% ================================================================
7\chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)}
8\label{chap:DIA}
9
10\minitoc
11
12\newpage
13
14% ================================================================
15%       Old Model Output
16% ================================================================
17\section{Old model output (default)}
18\label{sec:DIA_io_old}
19
20The model outputs are of three types: the restart file, the output listing, and the diagnostic output file(s).
21The restart file is used internally by the code when the user wants to start the model with
22initial conditions defined by a previous simulation.
23It contains all the information that is necessary in order for there to be no changes in the model results
24(even at the computer precision) between a run performed with several restarts and
25the same run performed in one step.
26It should be noted that this requires that the restart file contains two consecutive time steps for
27all the prognostic variables, and that it is saved in the same binary format as the one used by the computer that
28is to read it (in particular, 32 bits binary IEEE format must not be used for this file).
29
30The output listing and file(s) are predefined but should be checked and eventually adapted to the user's needs.
31The output listing is stored in the $ocean.output$ file.
32The information is printed from within the code on the logical unit $numout$.
33To locate these prints, use the UNIX command "\textit{grep -i numout}" in the source code directory.
34
35By default, diagnostic output files are written in NetCDF format.
36Since version 3.2, when defining \key{iomput}, an I/O server has been added which
37provides more flexibility in the choice of the fields to be written as well as how
38the writing work is distributed over the processors in massively parallel computing.
39A complete description of the use of this I/O server is presented in the next section.
40
41By default, \key{iomput} is not defined,
42NEMO produces NetCDF with the old IOIPSL library which has been kept for compatibility and its easy installation.
43However, the IOIPSL library is quite inefficient on parallel machines and, since version 3.2,
44many diagnostic options have been added presuming the use of \key{iomput}.
45The usefulness of the default IOIPSL-based option is expected to reduce with each new release.
46If \key{iomput} is not defined, output files and content are defined in the \mdl{diawri} module and
47contain mean (or instantaneous if \key{diainstant} is defined) values over a regular period of
48nn\_write time-steps (namelist parameter).
49
50%\gmcomment{                    % start of gmcomment
51
52% ================================================================
53% Diagnostics
54% ================================================================
55\section{Standard model output (IOM)}
56\label{sec:DIA_iom}
57
58Since version 3.2, iomput is the NEMO output interface of choice.
59It has been designed to be simple to use, flexible and efficient.
60The two main purposes of iomput are:
61
62\begin{enumerate}
63\item
64  The complete and flexible control of the output files through external XML files adapted by
65  the user from standard templates.
66\item
67  To achieve high performance and scalable output through the optional distribution of
68  all diagnostic output related tasks to dedicated processes.
69\end{enumerate}
70
71The first functionality allows the user to specify, without code changes or recompilation,
72aspects of the diagnostic output stream, such as:
73
74\begin{itemize}
75\item
76  The choice of output frequencies that can be different for each file (including real months and years).
77\item
78  The choice of file contents; includes complete flexibility over which data are written in which files
79  (the same data can be written in different files).
80\item
81  The possibility to split output files at a chosen frequency.
82\item
83  The possibility to extract a vertical or an horizontal subdomain.
84\item
85  The choice of the temporal operation to perform, $e.g.$: average, accumulate, instantaneous, min, max and once.
86\item
87  Control over metadata via a large XML "database" of possible output fields.
88\end{itemize}
89
90In addition, iomput allows the user to add in the code the output of any new variable (scalar, 2D or 3D)
91in a very easy way.
92All details of iomput functionalities are listed in the following subsections.
93Examples of the XML files that control the outputs can be found in: \path{NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml},
94\path{NEMOGCM/CONFIG/SHARED/field_def.xml} and \path{NEMOGCM/CONFIG/SHARED/domain_def.xml}. \\
95
96The second functionality targets output performance when running in parallel (\key{mpp\_mpi}).
97Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO processes)
98to collect and write the outputs.
99With an appropriate choice of N by the user, the bottleneck associated with the writing of
100the output files can be greatly reduced.
101
102In version 3.6, the iom\_put interface depends on
103an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/branchs/xios-1.0}{XIOS-1.0} 
104(use of revision 618 or higher is required).
105This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to
106create a single output file and therefore to bypass the rebuilding phase.
107Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to
108an HDF5 library that has been correctly compiled ($i.e.$ with the configure option $--$enable-parallel).
109Note that the files created by iomput through XIOS are incompatible with NetCDF3.
110All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3.
111
112Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers,
113where N is typically much less than the number of NEMO processors, will reduce the number of output files created.
114This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors.
115Note that for smaller configurations, the rebuilding phase can be avoided,
116even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server.
117
118\subsection{XIOS: XML Inputs-Outputs Server}
119
120\subsubsection{Attached or detached mode?}
121
122Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS},
123the io\_server developed by Yann Meurdesoif from IPSL.
124The behaviour of the I/O subsystem is controlled by settings in the external XML files listed above.
125Key settings in the iodef.xml file are the tags associated with each defined file.
126
127\xmlline|<variable id="using_server" type="bool"></variable>|
128
129The {\tt using\_server} setting determines whether or not the server will be used in \textit{attached mode}
130(as a library) [{\tt> false <}] or in \textit{detached mode}
131(as an external executable on N additional, dedicated cpus) [{\tt > true <}].
132The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications.
133The type of each file can be either ''multiple\_file'' or ''one\_file''.
134
135In \textit{attached mode} and if the type of file is ''multiple\_file'',
136then each NEMO process will also act as an IO server and produce its own set of output files.
137Superficially, this emulates the standard behaviour in previous versions.
138However, the subdomain written out by each process does not correspond to
139the \forcode{jpi x jpj x jpk} domain actually computed by the process (although it may if \forcode{jpni=1}).
140Instead each process will have collected and written out a number of complete longitudinal strips.
141If the ''one\_file'' option is chosen then all processes will collect their longitudinal strips and
142write (in parallel) to a single output file.
143
144In \textit{detached mode} and if the type of file is ''multiple\_file'',
145then each stand-alone XIOS process will collect data for a range of complete longitudinal strips and
146write to its own set of output files.
147If the ''one\_file'' option is chosen then all XIOS processes will collect their longitudinal strips and
148write (in parallel) to a single output file.
149Note running in detached mode requires launching a Multiple Process Multiple Data (MPMD) parallel job.
150The following subsection provides a typical example but the syntax will vary in different MPP environments.
151
152\subsubsection{Number of cpu used by XIOS in detached mode}
153
154The number of cores used by the XIOS is specified when launching the model.
155The number of cores dedicated to XIOS should be from \texttildelow1/10 to \texttildelow1/50 of the number of
156cores dedicated to NEMO.
157Some manufacturers suggest using O($\sqrt{N}$) dedicated IO processors for N processors but
158this is a general recommendation and not specific to NEMO.
159It is difficult to provide precise recommendations because the optimal choice will depend on
160the particular hardware properties of the target system
161(parallel filesystem performance, available memory, memory bandwidth etc.)
162and the volume and frequency of data to be created.
163Here is an example of 2 cpus for the io\_server and 62 cpu for nemo using mpirun:
164\cmd|mpirun -np 62 ./nemo.exe : -np 2 ./xios_server.exe|
165
166\subsubsection{Control of XIOS: the context in iodef.xml}
167
168As well as the {\tt using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml.
169See the XML basics section below for more details on XML syntax and rules.
170
171\begin{table}
172  \scriptsize
173  \begin{tabularx}{\textwidth}{|lXl|}
174    \hline
175    variable name                                                           &
176    description                                                             &
177    example  \\
178    \hline
179    \hline
180    buffer\_size                                                            &
181    buffer size used by XIOS to send data from NEMO to XIOS.
182    Larger is more efficient.
183    Note that needed/used buffer sizes are summarized at the end of the job &
184    25000000 \\
185    \hline
186    buffer\_server\_factor\_size                                            &
187    ratio between NEMO and XIOS buffer size.
188    Should be 2.                                                            &
189    2        \\
190    \hline
191    info\_level                                                             &
192    verbosity level (0 to 100)                                              &
193    0        \\
194    \hline
195    using\_server                                                           &
196    activate attached(false) or detached(true) mode                         &
197    true     \\
198    \hline
199    using\_oasis                                                            &
200    XIOS is used with OASIS(true) or not (false)                            &
201    false    \\
202    \hline
203    oasis\_codes\_id                                                        &
204    when using oasis, define the identifier of NEMO in the namcouple.
205    Note that the identifier of XIOS is xios.x                              &
206    oceanx   \\
207    \hline
208  \end{tabularx}
209\end{table}
210
211\subsection{Practical issues}
212
213\subsubsection{Installation}
214
215As mentioned, XIOS is supported separately and must be downloaded and compiled before it can be used with NEMO.
216See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance.
217NEMO will need to link to the compiled XIOS library.
218The \href{https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ModelInterfacing/InputsOutputs#Inputs-OutputsusingXIOS}
219{XIOS with NEMO} guide provides an example illustration of how this can be achieved.
220
221\subsubsection{Add your own outputs}
222
223It is very easy to add your own outputs with iomput.
224Many standard fields and diagnostics are already prepared ($i.e.$, steps 1 to 3 below have been done) and
225simply need to be activated by including the required output in a file definition in iodef.xml (step 4).
226To add new output variables, all 4 of the following steps must be taken.
227
228\begin{enumerate}
229\item[1.]
230  in NEMO code, add a \forcode{CALL iom\_put( 'identifier', array )} where you want to output a 2D or 3D array.
231\item[2.]
232  If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in
233  the upper part of your module.
234\item[3.]
235  in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code
236  (see subsequent sections for a details of the XML syntax and rules).
237  For example:
238
239\begin{xmllines}
240<field_definition>
241   <field_group id="grid_T" grid_ref="grid_T_3D"> <!-- T grid -->
242   ...
243      <field id="identifier" long_name="blabla" ... />   
244      ...
245</field_definition>
246\end{xmllines}
247
248Note your definition must be added to the field\_group whose reference grid is consistent with the size of
249the array passed to iomput.
250The grid\_ref attribute refers to definitions set in iodef.xml which, in turn,
251reference grids and axes either defined in the code
252(iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file.
253$e.g.$:
254
255\begin{xmllines}
256<grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/>
257\end{xmllines}
258
259Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step,
260add the field definition within the field\_group defined with the id "SBC":
261\xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations
262(iom\_set\_field\_attr in \mdl{iom})
263\item[4.]
264  add your field in one of the output files defined in iodef.xml
265  (again see subsequent sections for syntax and rules)
266
267\begin{xmllines}
268<file id="file1" .../>  
269...
270   <field field_ref="identifier" />   
271   ...
272</file>   
273\end{xmllines}
274
275\end{enumerate}
276
277\subsection{XML fundamentals}
278
279\subsubsection{ XML basic rules}
280
281XML tags begin with the less-than character ("$<$") and end with the greater-than character ("$>$").
282You use tags to mark the start and end of elements, which are the logical units of information in an XML document.
283In addition to marking the beginning of an element, XML start tags also provide a place to specify attributes.
284An attribute specifies a single property for an element, using a name/value pair, for example:
285\xmlcode{<a b="x" c="y" d="z"> ... </a>}.
286See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details.
287
288\subsubsection{Structure of the XML file used in NEMO}
289
290The XML file used in XIOS is structured by 7 families of tags:
291context, axis, domain, grid, field, file and variable.
292Each tag family has hierarchy of three flavors (except for context):
293
294\begin{table}
295  \scriptsize
296  \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
297    \hline
298    flavor  & description                                                                 &
299                                                                                            example                          \\
300    \hline
301    \hline
302    root    & declaration of the root element that can contain element groups or elements &
303                                                                                            \xmlcode{<file_definition ... >} \\
304    \hline
305    group   & declaration of a group element that can contain element groups or elements  &
306                                                                                            \xmlcode{<file_group      ... >} \\
307    \hline
308    element & declaration of an element that can contain elements                         &
309                                                                                            \xmlcode{<file            ... >} \\
310    \hline
311  \end{tabular*}
312\end{table}
313
314Each element may have several attributes.
315Some attributes are mandatory, other are optional but have a default value and other are completely optional.
316Id is a special attribute used to identify an element or a group of elements.
317It must be unique for a kind of element.
318It is optional, but no reference to the corresponding element can be done if it is not defined.
319
320The XML file is split into context tags that are used to isolate IO definition from
321different codes or different parts of a code.
322No interference is possible between 2 different contexts.
323Each context has its own calendar and an associated timestep.
324In \NEMO, we used the following contexts (that can be defined in any order):
325
326\begin{table}
327  \scriptsize
328  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
329    \hline
330    context         &   description                                                                &
331                                                                                                     example                              \\
332    \hline
333    \hline
334    context xios    &   context containing information for XIOS                                    &
335                                                                                                     \xmlcode{<context id="xios" ... >}   \\
336    \hline
337    context nemo    &   context containing IO information for NEMO (mother grid when using AGRIF)  & 
338                                                                                                     \xmlcode{<context id="nemo" ... >}   \\
339    \hline
340    context 1\_nemo &   context containing IO information for NEMO child grid 1 (when using AGRIF) & 
341                                                                                                     \xmlcode{<context id="1_nemo" ... >} \\
342    \hline
343    context n\_nemo &   context containing IO information for NEMO child grid n (when using AGRIF) & 
344                                                                                                     \xmlcode{<context id="n_nemo" ... >} \\
345    \hline
346  \end{tabular}
347\end{table}
348
349\noindent The xios context contains only 1 tag:
350
351\begin{table}
352  \scriptsize
353  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
354    \hline
355    context tag                                      &
356                                                       description                                      &
357                                                                                                          example                              \\
358    \hline
359    \hline
360    variable\_definition                             &
361                                                       define variables needed by XIOS.
362                                                       This can be seen as a kind of namelist for XIOS. &
363                                                                                                          \xmlcode{<variable_definition ... >} \\
364    \hline
365   \end{tabular}
366\end{table}
367
368\noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts
369(that can be defined in any order):
370
371\begin{table}
372  \scriptsize
373  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
374    \hline
375    context tag        &   description                                                               &
376                                                                                                       example                            \\
377    \hline
378    \hline
379    field\_definition  &   define all variables that can potentially be outputted                    &
380                                                                                                       \xmlcode{<field_definition ... >}  \\
381    \hline
382    file\_definition   &   define the netcdf files to be created and the variables they will contain &
383                                                                                                       \xmlcode{<file_definition ... >}   \\
384    \hline
385    axis\_definition   &   define vertical axis                                                      &
386                                                                                                       \xmlcode{<axis_definition ... >}   \\
387    \hline
388    domain\_definition &   define the horizontal grids                                               &
389                                                                                                       \xmlcode{<domain_definition ... >} \\
390    \hline
391    grid\_definition   &   define the 2D and 3D grids (association of an axis and a domain)          &
392                                                                                                       \xmlcode{<grid_definition ... >}   \\
393    \hline
394  \end{tabular}
395\end{table}
396
397\subsubsection{Nesting XML files}
398
399The XML file can be split in different parts to improve its readability and facilitate its use.
400The inclusion of XML files into the main XML file can be done through the attribute src:
401\xmlline|<context src="./nemo_def.xml" />|
402 
403\noindent In NEMO, by default, the field and domain definition is done in 2 separate files:
404\path{NEMOGCM/CONFIG/SHARED/field_def.xml} and \path{NEMOGCM/CONFIG/SHARED/domain_def.xml} that
405are included in the main iodef.xml file through the following commands:
406\begin{xmllines}
407<field_definition src="./field_def.xml" />
408<domain_definition src="./domain_def.xml" />
409\end{xmllines}
410
411\subsubsection{Use of inheritance}
412
413XML extensively uses the concept of inheritance.
414XML has a tree based structure with a parent-child oriented relation: all children inherit attributes from parent,
415but an attribute defined in a child replace the inherited attribute value.
416Note that the special attribute ''id'' is never inherited.
417\\
418\\
419example 1: Direct inheritance.
420
421\begin{xmllines}
422<field_definition operation="average" >
423   <field id="sst"                    />   <!-- averaged      sst -->
424   <field id="sss" operation="instant"/>   <!-- instantaneous sss -->
425</field_definition>
426\end{xmllines}
427
428The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average'' of
429the attribute ''operation'' from its parent.
430Note that a child can overwrite the attribute definition inherited from its parents.
431In the example above, the field ''sss'' will for example output instantaneous values instead of average values.
432\\
433\\
434example 2: Inheritance by reference.
435
436\begin{xmllines}
437<field_definition>
438   <field id="sst" long_name="sea surface temperature" />
439   <field id="sss" long_name="sea surface salinity"    />
440</field_definition>
441<file_definition>
442   <file id="myfile" output_freq="1d" />   
443      <field field_ref="sst"                            />  <!-- default def -->
444      <field field_ref="sss" long_name="my description" />  <!-- overwrite   -->
445   </file>
446</file_definition>
447\end{xmllines}
448
449Inherit (and overwrite, if needed) the attributes of a tag you are refering to.
450
451\subsubsection{Use of groups}
452
453Groups can be used for 2 purposes.
454Firstly, the group can be used to define common attributes to be shared by the elements of
455the group through inheritance.
456In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''.
457Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''.
458
459\begin{xmllines}
460<field_group id="grid_T" grid_ref="grid_T_2D">
461   <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/>
462   <field id="sst"  long_name="sea surface temperature" unit="degC"                     />
463   <field id="sss"  long_name="sea surface salinity"    unit="psu"                      />
464   <field id="ssh"  long_name="sea surface height"      unit="m"                        />
465   ...
466\end{xmllines}
467
468Secondly, the group can be used to replace a list of elements.
469Several examples of groups of fields are proposed at the end of the file \path{CONFIG/SHARED/field_def.xml}.
470For example, a short list of the usual variables related to the U grid:
471
472\begin{xmllines}
473<field_group id="groupU" >
474   <field field_ref="uoce"  />
475   <field field_ref="suoce" />
476   <field field_ref="utau"  />
477</field_group>
478\end{xmllines}
479
480that can be directly included in a file through the following syntax:
481
482\begin{xmllines}
483<file id="myfile_U" output_freq="1d" />
484   <field_group group_ref="groupU" />
485   <field field_ref="uocetr_eff"   />  <!-- add another field -->
486</file>   
487\end{xmllines}
488
489\subsection{Detailed functionalities}
490
491The file \path{NEMOGCM/CONFIG/ORCA2_LIM/iodef_demo.xml} provides several examples of the use of
492the new functionalities offered by the XML interface of XIOS.
493
494\subsubsection{Define horizontal subdomains}
495
496Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of
497the tag family domain.
498It must therefore be done in the domain part of the XML file.
499For example, in \path{CONFIG/SHARED/domain_def.xml}, we provide the following example of a definition of
500a 5 by 5 box with the bottom left corner at point (10,10).
501
502\begin{xmllines}
503<domain_group id="grid_T">
504   <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" />
505\end{xmllines}
506
507The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field.
508For example:
509
510\begin{xmllines}
511<file id="myfile_vzoom" output_freq="1d" >
512   <field field_ref="toce" domain_ref="myzoom"/>
513</file>
514\end{xmllines}
515
516Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain.
517The Equatorial section, the TAO, RAMA and PIRATA moorings are already registered in the code and
518can therefore be outputted without taking care of their (i,j) position in the grid.
519These predefined domains can be activated by the use of specific domain\_ref:
520''EqT'', ''EqU'' or ''EqW'' for the equatorial sections and
521the mooring position for TAO, RAMA and PIRATA followed by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...)
522
523\begin{xmllines}
524<file id="myfile_vzoom" output_freq="1d" >
525   <field field_ref="toce" domain_ref="0n180wT"/>
526</file>
527\end{xmllines}
528
529Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if
530you use the ''multiple\_file'' type for your output files,
531you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat,
532\href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}).
533We are therefore advising to use the ''one\_file'' type in this case.
534
535\subsubsection{Define vertical zooms}
536
537Vertical zooms are defined through the attributs zoom\_begin and zoom\_end of the tag family axis.
538It must therefore be done in the axis part of the XML file.
539For example, in \path{NEMOGCM/CONFIG/ORCA2_LIM/iodef_demo.xml}, we provide the following example:
540
541\begin{xmllines}
542<axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" >
543   <axis id="deptht" />
544   <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" />
545\end{xmllines}
546
547The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field.
548For example:
549
550\begin{xmllines}
551<file id="myfile_hzoom" output_freq="1d" >
552   <field field_ref="toce" axis_ref="deptht_myzoom"/>
553</file>
554\end{xmllines}
555
556\subsubsection{Control of the output file names}
557
558The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file.
559For example:
560
561\begin{xmllines}
562<file_group id="1d" output_freq="1d" name="myfile_1d" >
563   <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA"  -->
564      ...
565   </file>
566   <file id="myfileB" name_suffix="_BBB" > <!-- will create file "myfile_1d_BBB" -->
567      ...
568   </file>
569</file_group>
570\end{xmllines}
571
572However it is often very convienent to define the file name with the name of the experiment,
573the output file frequency and the date of the beginning and the end of the simulation
574(which are informations stored either in the namelist or in the XML file).
575To do so, we added the following rule:
576if the id of the tag file is ''fileN'' (where N = 1 to 999 on 1 to 3 digits) or
577one of the predefined sections or moorings (see next subsection),
578the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by:
579
580\begin{table}
581  \scriptsize
582  \begin{tabularx}{\textwidth}{|lX|}
583    \hline
584    \centering placeholder string &
585    automatically replaced by                          \\
586    \hline
587    \hline
588    \centering @expname@          &
589    the experiment name (from cn\_exp in the namelist) \\
590    \hline
591    \centering @freq@             &
592    output frequency (from attribute output\_freq)     \\
593    \hline
594    \centering @startdate@        &
595    starting date of the simulation (from nn\_date0 in the restart or the namelist).
596    \newline
597    \verb?yyyymmdd?          format                   \\
598    \hline
599    \centering @startdatefull@    &
600    starting date of the simulation (from nn\_date0 in the restart or the namelist).
601    \newline
602    \verb?yyyymmdd_hh:mm:ss? format                    \\
603    \hline
604    \centering @enddate@          &
605    ending date of the simulation   (from nn\_date0 and nn\_itend  in the namelist).
606    \newline
607    \verb?yyyymmdd?          format                    \\
608    \hline
609    \centering @enddatefull@      &
610    ending date of the simulation   (from nn\_date0 and nn\_itend  in the namelist).
611    \newline
612    \verb?yyyymmdd_hh:mm:ss? format                    \\
613    \hline
614  \end{tabularx}
615\end{table}
616
617\noindent For example,
618\xmlline|<file id="myfile_hzoom" name="myfile_@expname@_@startdate@_freq@freq@" output_freq="1d" >|
619
620\noindent with the namelist:
621\begin{forlines}
622cn_exp    = "ORCA2"
623nn_date0  = 19891231
624ln_rstart = .false.
625\end{forlines}
626
627\noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d}
628
629\subsubsection{Other controls of the XML attributes from NEMO}
630
631The values of some attributes are defined by subroutine calls within NEMO
632(calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in \mdl{iom}).
633Any definition given in the XML file will be overwritten.
634By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the XML file
635(but this is not necessary).
636\\
637
638Here is the list of these attributes:
639\\
640
641\begin{table}
642  \scriptsize
643  \begin{tabularx}{\textwidth}{|X|c|c|c|}
644    \hline
645    tag ids affected by automatic definition of some of their attributes &
646    name attribute                                                       &
647    attribute value                      \\
648    \hline
649    \hline
650    field\_definition                                                    &
651    freq\_op                                                             &
652    \np{rn\_rdt}                         \\
653    \hline
654    SBC                                                                  &
655    freq\_op                                                             &
656    \np{rn\_rdt} $\times$ \np{nn\_fsbc}  \\
657    \hline
658    ptrc\_T                                                              &
659    freq\_op                                                             &
660    \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\
661    \hline
662    diad\_T                                                              &
663    freq\_op                                                             &
664    \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\
665    \hline
666    EqT, EqU, EqW                                                        &
667    jbegin, ni,                                                          &
668    according to the grid                \\
669    &
670    name\_suffix                                                         &
671    \\
672    \hline
673    TAO, RAMA and PIRATA moorings                                        &
674    zoom\_ibegin, zoom\_jbegin,                                          &
675    according to the grid                \\
676    &
677    name\_suffix                                                         &
678    \\
679    \hline
680  \end{tabularx}
681\end{table}
682
683\subsubsection{Advanced use of XIOS functionalities}
684
685\subsection{XML reference tables}
686\label{subsec:IOM_xmlref}
687
688\begin{enumerate}
689\item
690  Simple computation: directly define the computation when refering to the variable in the file definition.
691
692\begin{xmllines}
693<field field_ref="sst"  name="tosK"  unit="degK" > sst + 273.15 </field>
694<field field_ref="taum" name="taum2" unit="N2/m4" long_name="square of wind stress module" > taum * taum </field>
695<field field_ref="qt"   name="stupid_check" > qt - qsr - qns </field>
696\end{xmllines}
697
698\item
699  Simple computation: define a new variable and use it in the file definition.
700
701in field\_definition:
702
703\begin{xmllines}
704<field id="sst2" long_name="square of sea surface temperature" unit="degC2" >  sst * sst </field >
705\end{xmllines}
706
707in file\_definition:
708
709\begin{xmllines}
710<field field_ref="sst2" > sst2 </field>
711\end{xmllines}
712
713Note that in this case, the following syntaxe \xmlcode{<field field_ref="sst2" />} is not working as
714sst2 won't be evaluated.
715
716\item
717  Change of variable precision:
718
719\begin{xmllines}
720<!-- force to keep real 8 -->
721<field field_ref="sst" name="tos_r8" prec="8" />
722<!-- integer 2  with add_offset and scale_factor attributes -->
723<field field_ref="sss" name="sos_i2" prec="2" add_offset="20." scale_factor="1.e-3" />
724\end{xmllines}
725
726Note that, then the code is crashing, writting real4 variables forces a numerical convection from
727real8 to real4 which will create an internal error in NetCDF and will avoid the creation of the output files.
728Forcing double precision outputs with prec="8" (for example in the field\_definition) will avoid this problem.
729
730\item
731  add user defined attributes:
732
733\begin{xmllines}
734<file_group id="1d" output_freq="1d" output_level="10" enabled=".true."> <!-- 1d files -->
735   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
736      <field field_ref="sst" name="tos" >
737         <variable id="my_attribute1" type="string"  > blabla </variable>
738         <variable id="my_attribute2" type="integer" > 3      </variable>
739         <variable id="my_attribute3" type="float"   > 5.0    </variable>
740      </field>
741      <variable id="my_global_attribute" type="string" > blabla_global </variable>
742   </file>
743</file_group>
744\end{xmllines}
745
746\item
747  use of the ``@'' function: example 1, weighted temporal average
748
749 - define a new variable in field\_definition
750
751\begin{xmllines}
752<field id="toce_e3t" long_name="temperature * e3t" unit="degC*m" grid_ref="grid_T_3D" >toce * e3t</field>
753\end{xmllines}
754
755 - use it when defining your file.
756
757\begin{xmllines}
758<file_group id="5d" output_freq="5d"  output_level="10" enabled=".true." >  <!-- 5d files --> 
759   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
760      <field field_ref="toce" operation="instant" freq_op="5d" > @toce_e3t / @e3t </field>
761   </file>
762</file_group>
763\end{xmllines}
764
765The freq\_op="5d" attribute is used to define the operation frequency of the ``@'' function: here 5 day.
766The temporal operation done by the ``@'' is the one defined in the field definition:
767here we use the default, average.
768So, in the above case, @toce\_e3t will do the 5-day mean of toce*e3t.
769Operation="instant" refers to the temporal operation to be performed on the field''@toce\_e3t / @e3t'':
770here the temporal average is alreday done by the ``@'' function so we just use instant to do the ratio of
771the 2 mean values.
772field\_ref="toce" means that attributes not explicitely defined, are inherited from toce field.
773Note that in this case, freq\_op must be equal to the file output\_freq.
774
775\item
776  use of the ``@'' function: example 2, monthly SSH standard deviation
777
778 - define a new variable in field\_definition
779
780\begin{xmllines}
781<field id="ssh2" long_name="square of sea surface temperature" unit="degC2" > ssh * ssh </field >
782\end{xmllines}
783
784 - use it when defining your file.
785
786\begin{xmllines}
787<file_group id="1m" output_freq="1m"  output_level="10" enabled=".true." >  <!-- 1m files --> 
788   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
789      <field field_ref="ssh" name="sshstd" long_name="sea_surface_temperature_standard_deviation"
790      operation="instant" freq_op="1m" >
791         sqrt( @ssh2 - @ssh * @ssh )
792      </field>
793   </file>
794</file_group>
795\end{xmllines}
796
797The freq\_op="1m" attribute is used to define the operation frequency of the ``@'' function: here 1 month.
798The temporal operation done by the ``@'' is the one defined in the field definition:
799here we use the default, average.
800So, in the above case, @ssh2 will do the monthly mean of ssh*ssh.
801Operation="instant" refers to the temporal operation to be performed on the field ''sqrt( @ssh2 - @ssh * @ssh )'':
802here the temporal average is alreday done by the ``@'' function so we just use instant.
803field\_ref="ssh" means that attributes not explicitely defined, are inherited from ssh field.
804Note that in this case, freq\_op must be equal to the file output\_freq.
805
806\item
807  use of the ``@'' function: example 3, monthly average of SST diurnal cycle
808
809 - define 2 new variables in field\_definition
810
811\begin{xmllines}
812<field id="sstmax" field_ref="sst" long_name="max of sea surface temperature" operation="maximum" />
813<field id="sstmin" field_ref="sst" long_name="min of sea surface temperature" operation="minimum" />
814\end{xmllines}
815
816 - use these 2 new variables when defining your file.
817
818\begin{xmllines}
819<file_group id="1m" output_freq="1m"  output_level="10" enabled=".true." >  <!-- 1m files --> 
820   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
821      <field field_ref="sst" name="sstdcy" long_name="amplitude of sst diurnal cycle" operation="average" freq_op="1d" >
822         @sstmax - @sstmin
823      </field>
824   </file>
825</file_group>
826\end{xmllines}
827
828\end{enumerate}
829
830The freq\_op="1d" attribute is used to define the operation frequency of the ``@'' function: here 1 day.
831The temporal operation done by the ``@'' is the one defined in the field definition:
832here maximum for sstmax and minimum for sstmin.
833So, in the above case, @sstmax will do the daily max and @sstmin the daily min.
834Operation="average" refers to the temporal operation to be performed on the field ``@sstmax - @sstmin'':
835here monthly mean (of daily max - daily min of the sst).
836field\_ref="sst" means that attributes not explicitely defined, are inherited from sst field.
837
838\subsubsection{Tag list per family}
839
840\begin{table}
841  \scriptsize
842  \begin{tabularx}{\textwidth}{|l|X|X|l|X|}
843    \hline
844    tag name                                                                                     &
845    description                                                                                  &
846    accepted attribute                                                                           &
847    child of                                                                                     &
848    parent of                       \\
849    \hline
850    \hline
851    simulation                                                                                   &
852    this tag is the root tag which encapsulates all the content of the XML file                  &
853    none                                                                                         &
854    none                                                                                         &
855    context                         \\
856    \hline
857    context                                                                                      &
858    encapsulates parts of the XML file dedicated to different codes or different parts of a code &
859    id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin             &
860    simulation                                                                                   &
861    all root tags: ... \_definition \\
862    \hline
863  \end{tabularx}
864  \caption{Context tags}
865\end{table}
866
867\begin{table}
868  \scriptsize
869  \begin{tabularx}{\textwidth}{|l|X|X|X|l|}
870    \hline
871    tag name                                                                                &
872    description                                                                             &
873    accepted attribute                                                                      &
874    child of                                                                                &
875    parent of             \\
876    \hline
877    \hline
878    field\_definition                                                                       &
879    encapsulates the definition of all the fields that can potentially be outputted         &
880    axis\_ref, default\_value, domain\_ref, enabled, grid\_ref, level, operation, prec, src &
881    context                                                                                 &
882    field or field\_group \\
883    \hline
884    field\_group                                                                            &
885    encapsulates a group of fields                                                          &
886    axis\_ref, default\_value, domain\_ref, enabled, group\_ref, grid\_ref,
887    id, level, operation, prec, src                                                         &
888    field\_definition, field\_group, file                                                   &
889    field or field\_group \\
890    \hline
891    field                                                                                   &
892    define a specific field                                                                 &
893    axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref,
894    id, level, long\_name, name, operation, prec, standard\_name, unit                      &
895    field\_definition, field\_group, file                                                   &
896    none                  \\
897    \hline
898  \end{tabularx}
899  \caption{Field tags ("\tt{field\_*}")}
900\end{table}
901
902\begin{table}
903  \scriptsize
904  \begin{tabularx}{\textwidth}{|l|X|X|X|l|}
905    \hline
906    tag name                                                            &
907    description                                                         &
908    accepted attribute                                                  &
909    child of                                                            &
910    parent of           \\
911    \hline
912    \hline
913    file\_definition                                                    &
914    encapsulates the definition of all the files that will be outputted &
915    enabled, min\_digits, name, name\_suffix, output\_level,
916    split\_freq\_format, split\_freq, sync\_freq, type, src             &
917    context                                                             &
918    file or file\_group \\
919    \hline
920    file\_group                                                         &
921    encapsulates a group of files that will be outputted                &
922    enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level,
923    split\_freq\_format, split\_freq, sync\_freq, type, src             &
924    file\_definition, file\_group                                       &
925    file or file\_group \\
926    \hline
927    file                                                                &
928    define the contents of a file to be outputted                       &
929    enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level,
930    split\_freq\_format, split\_freq, sync\_freq, type, src             &
931    file\_definition, file\_group                                       &
932    field               \\
933    \hline
934  \end{tabularx}
935  \caption{File tags ("\tt{file\_*}")}
936\end{table}
937
938\begin{table}
939  \scriptsize
940  \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
941    \hline
942    tag name                                                                               &
943    description                                                                            &
944    accepted attribute                                                                     &
945    child of                                                                               &
946    parent of         \\
947    \hline
948    \hline
949    axis\_definition                                                                       &
950    define all the vertical axis potentially used by the variables                         &
951    src                                                                                    &
952    context                                                                                &
953    axis\_group, axis \\
954    \hline
955    axis\_group                                                                            &
956    encapsulates a group of vertical axis                                                  &
957    id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
958    axis\_definition, axis\_group                                                          &
959    axis\_group, axis \\
960    \hline
961    axis                                                                                   &
962    define a vertical axis                                                                 &
963    id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
964    axis\_definition, axis\_group                                                          &
965    none             \\
966    \hline
967  \end{tabularx}
968  \caption{Axis tags ("\tt{axis\_*}")}
969\end{table}
970
971\begin{table}
972  \scriptsize
973  \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
974    \hline
975    tag name                                                            &
976    description                                                         &
977    accepted attribute                                                  &
978    child of                                                            &
979    parent of               \\
980    \hline
981    \hline
982    domain\_\-definition                                                &
983    define all the horizontal domains potentially used by the variables &
984    src                                                                 &
985    context                                                             &
986    domain\_\-group, domain \\
987    \hline
988    domain\_group                                                       &
989    encapsulates a group of horizontal domains                          &
990    id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj  &
991    domain\_\-definition, domain\_group                                 &
992    domain\_\-group, domain \\
993    \hline
994    domain                                                              &
995    define an horizontal domain                                         &
996    id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj  &
997    domain\_\-definition, domain\_group                                 &
998    none                    \\
999    \hline
1000  \end{tabularx}
1001  \caption{Domain tags ("\tt{domain\_*)}"}
1002\end{table}
1003
1004\begin{table}
1005  \scriptsize
1006  \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
1007    \hline
1008    tag name                                                                                     &
1009    description                                                                                  &
1010    accepted attribute                                                                           &
1011    child of                                                                                     &
1012    parent of                       \\
1013    \hline
1014    \hline
1015    grid\_definition                                                                               &
1016    define all the grid (association of a domain and/or an axis) potentially used by the variables &
1017    src                                                                                            &
1018    context                                                                                        &
1019    grid\_group, grid   \\
1020    \hline
1021    grid\_group                                                                                    &
1022    encapsulates a group of grids                                                                  &
1023    id, domain\_ref,axis\_ref                                                                      &
1024    grid\_definition, grid\_group                                                                  &
1025    grid\_group, grid   \\
1026    \hline
1027    grid                                                                                           &
1028    define a grid                                                                                  &
1029    id, domain\_ref,axis\_ref                                                                      &
1030    grid\_definition, grid\_group                                                                  &
1031    none                \\
1032    \hline
1033  \end{tabularx}
1034  \caption{Grid tags ("\tt{grid\_*}")}
1035\end{table}
1036
1037\subsubsection{Attributes list per family}
1038
1039\begin{table}
1040  \scriptsize
1041  \begin{tabularx}{\textwidth}{|l|X|l|l|}
1042    \hline
1043    attribute name                           &
1044    description                              &
1045    example                                  &
1046    accepted by            \\
1047    \hline
1048    \hline
1049    axis\_ref                                &
1050    refers to the id of a vertical axis      &
1051    axis\_ref="deptht"                       &
1052    field, grid families   \\
1053    \hline
1054    domain\_ref                              &
1055    refers to the id of a domain             &
1056    domain\_ref="grid\_T"                    &
1057    field or grid families \\
1058    \hline
1059    field\_ref                               &
1060    id of the field we want to add in a file &
1061    field\_ref="toce"                        &
1062    field                  \\
1063    \hline
1064    grid\_ref                                &
1065    refers to the id of a grid               &
1066    grid\_ref="grid\_T\_2D"                  &
1067    field family           \\
1068    \hline
1069    group\_ref                               &
1070    refer to a group of variables            &
1071    group\_ref="mooring"                     &
1072    field\_group           \\
1073    \hline
1074  \end{tabularx}
1075  \caption{Reference attributes ("\tt{*\_ref}")}
1076\end{table}
1077
1078\begin{table}
1079  \scriptsize
1080  \begin{tabularx}{\textwidth}{|l|X|l|l|}
1081    \hline
1082    attribute name                                     &
1083    description                                        &
1084    example                                            &
1085    accepted by   \\
1086    \hline
1087    \hline
1088    zoom\_ibegin                                       &
1089    starting point along x direction of the zoom.
1090    Automatically defined for TAO/RAMA/PIRATA moorings &
1091    zoom\_ibegin="1"                                   &
1092    domain family \\
1093    \hline
1094    zoom\_jbegin                                       &
1095    starting point along y direction of the zoom.
1096    Automatically defined for TAO/RAMA/PIRATA moorings &
1097    zoom\_jbegin="1"                                   &
1098    domain family \\
1099    \hline
1100    zoom\_ni                                           &
1101    zoom extent along x direction                      &
1102    zoom\_ni="1"                                       &
1103    domain family \\
1104    \hline
1105    zoom\_nj                                           &
1106    zoom extent along y direction                      &
1107    zoom\_nj="1"                                       &
1108    domain family \\
1109    \hline
1110  \end{tabularx}
1111  \caption{Domain attributes ("\tt{zoom\_*}")}
1112\end{table}
1113
1114\begin{table}
1115  \scriptsize
1116  \begin{tabularx}{\textwidth}{|l|X|l|l|}
1117    \hline
1118    attribute name                                                                                       &
1119    description                                                                                          &
1120    example                                                                                              &
1121    accepted by                            \\
1122    \hline
1123    \hline
1124    min\_digits                                                                                          &
1125    specify the minimum of digits used in the core number in the name of the NetCDF file                 &
1126    min\_digits="4"                                                                                      &
1127    file family                            \\
1128    \hline
1129    name\_suffix                                                                                         &
1130    suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file &
1131    name\_suffix="\_myzoom"                                                                              &
1132    file family                            \\
1133    \hline
1134    output\_level                                                                                        &
1135    output priority of variables in a file: 0 (high) to 10 (low).
1136    All variables listed in the file with a level smaller or equal to output\_level will be output.
1137    Other variables won't be output even if they are listed in the file.                                 &
1138    output\_level="10"                                                                                   &
1139    file family                            \\
1140    \hline
1141    split\_freq                                                                                          &
1142    frequency at which to temporally split output files.
1143    Units can be ts (timestep), y, mo, d, h, mi, s.
1144    Useful for long runs to prevent over-sized output files.                                             &
1145    split\_freq="1mo"                                                                                    &
1146    file family                            \\
1147    \hline
1148    split\_freq\-\_format                                                                                &
1149    date format used in the name of temporally split output files.
1150    Can be specified using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s                      &
1151    split\_freq\_format= "\%y\%mo\%d"                                                                    &
1152    file family                            \\
1153    \hline
1154    sync\_freq                                                                                           &
1155    NetCDF file synchronization frequency (update of the time\_counter).
1156    Units can be ts (timestep), y, mo, d, h, mi, s.                                                      &
1157    sync\_freq="10d"                                                                                     &
1158    file family                            \\
1159    \hline
1160    type (1)                                                                                             &
1161    specify if the output files are to be split spatially (multiple\_file) or not (one\_file)            &
1162    type="multiple\_file"                                                                                &
1163    file familly                           \\
1164    \hline
1165  \end{tabularx}
1166  \caption{File attributes}
1167\end{table}
1168
1169\begin{table}
1170  \scriptsize
1171  \begin{tabularx}{\textwidth}{|l|X|l|l|}
1172    \hline
1173    attribute name                                                                                       &
1174    description                                                                                          &
1175    example                                                                                              &
1176    accepted by                            \\
1177    \hline
1178    \hline
1179    default\_value                                                                                       &
1180    missing\_value definition                                                                            &
1181    default\_value="1.e20"                                                                               &
1182    field family                           \\
1183    \hline
1184    level                                                                                                &
1185    output priority of a field: 0 (high) to 10 (low)                                                     &
1186    level="1"                                                                                            &
1187    field family                           \\
1188    \hline
1189    operation                                                                                            &
1190    type of temporal operation: average, accumulate, instantaneous, min, max and once                    &
1191    operation="average"                                                                                  &
1192    field family                           \\
1193    \hline
1194    output\_freq                                                                                         &
1195    operation frequency. units can be ts (timestep), y, mo, d, h, mi, s.                                 &
1196    output\_freq="1d12h"                                                                                 &
1197    field family                           \\
1198    \hline
1199    prec                                                                                                 &
1200    output precision: real 4 or real 8                                                                   &
1201    prec="4"                                                                                             &
1202    field family                           \\
1203    \hline
1204    long\_name                                                                                           &
1205    define the long\_name attribute in the NetCDF file                                                   &
1206    long\_name="Vertical T levels"                                                                       &
1207    field                                  \\
1208    \hline
1209    standard\_name                                                                                       &
1210    define the standard\_name attribute in the NetCDF file                                               &
1211    standard\_name= "Eastward\_Sea\_Ice\_Transport"                                                      &
1212    field                                  \\
1213    \hline
1214  \end{tabularx}
1215  \caption{Field attributes}
1216\end{table}
1217
1218\begin{table}
1219  \scriptsize
1220  \begin{tabularx}{\textwidth}{|l|X|X|X|}
1221    \hline
1222    attribute name                                                                                       &
1223    description                                                                                          &
1224    example                                                                                              &
1225    accepted by                            \\
1226    \hline
1227    \hline
1228    enabled                                                                                              &
1229    switch on/off the output of a field or a file                                                        &
1230    enabled=".true."                                                                                     &
1231    field, file families                   \\
1232    \hline
1233    description                                                                                          &
1234    just for information, not used                                                                       &
1235    description="ocean T grid variables"                                                                 &
1236    all tags                               \\
1237    \hline
1238    id                                                                                                   &
1239    allow to identify a tag                                                                              &
1240    id="nemo"                                                                                            &
1241    accepted by all tags except simulation \\
1242    \hline
1243    name                                                                                                 &
1244    name of a variable or a file. If the name of a file is undefined, its id is used as a name           &
1245    name="tos"                                                                                           &
1246    field or file families                 \\
1247    \hline
1248    positive                                                                                             &
1249    convention used for the orientation of vertival axis (positive downward in \NEMO).                   &
1250    positive="down"                                                                                      &
1251    axis family                            \\
1252    \hline
1253    src                                                                                                  &
1254    allow to include a file                                                                              &
1255    src="./field\_def.xml"                                                                               &
1256    accepted by all tags except simulation \\
1257    \hline
1258    time\_origin                                                                                         &
1259    specify the origin of the time counter                                                               &
1260    time\_origin="1900-01-01 00:00:00"                                                                   &
1261    context                                \\
1262    \hline
1263    type (2)                                                                                             &
1264    define the type of a variable tag                                                                    &
1265    type="boolean"                                                                                       &
1266    variable                               \\
1267    \hline
1268    unit                                                                                                 &
1269    unit of a variable or the vertical axis                                                              &
1270    unit="m"                                                                                             &
1271    field and axis families                \\
1272    \hline
1273  \end{tabularx}
1274  \caption{Miscellaneous attributes}
1275\end{table}
1276
1277\subsection{CF metadata standard compliance}
1278
1279Output from the XIOS-1.0 IO server is compliant with
1280\href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of
1281the CF metadata standard.
1282Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of
1283section \autoref{subsec:IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard.
1284
1285Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by
1286the namelist parameter \np{ln\_cfmeta} in the \ngn{namrun} namelist.
1287This must be set to true if these metadata are to be included in the output files.
1288
1289
1290% ================================================================
1291%       NetCDF4 support
1292% ================================================================
1293\section{NetCDF4 support (\protect\key{netcdf4})}
1294\label{sec:DIA_nc4}
1295
1296Since version 3.3, support for NetCDF4 chunking and (loss-less) compression has been included.
1297These options build on the standard NetCDF output and allow the user control over the size of the chunks via
1298namelist settings.
1299Chunking and compression can lead to significant reductions in file sizes for a small runtime overhead.
1300For a fuller discussion on chunking and other performance issues the reader is referred to
1301the NetCDF4 documentation found \href{http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.html#Chunking}{here}.
1302
1303The new features are only available when the code has been linked with a NetCDF4 library
1304(version 4.1 onwards, recommended) which has been built with HDF5 support (version 1.8.4 onwards, recommended).
1305Datasets created with chunking and compression are not backwards compatible with NetCDF3 "classic" format but
1306most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files.
1307NEMO executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by
1308setting the \np{ln\_nc4zip} logical to false in the \textit{namnc4} namelist:
1309
1310%------------------------------------------namnc4----------------------------------------------------
1311
1312\nlst{namnc4}
1313%-------------------------------------------------------------------------------------------------------------
1314
1315If \key{netcdf4} has not been defined, these namelist parameters are not read.
1316In this case, \np{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined.
1317These functions will not be used but need to be included so that compilation is possible with NetCDF3 libraries.
1318
1319When using NetCDF4 libraries, \key{netcdf4} should be defined even if the intention is to
1320create only NetCDF3-compatible files.
1321This is necessary to avoid duplication between the dummy routines and the actual routines present in the library.
1322Most compilers will fail at compile time when faced with such duplication.
1323Thus when linking with NetCDF4 libraries the user must define \key{netcdf4} and
1324control the type of NetCDF file produced via the namelist parameter.
1325
1326Chunking and compression is applied only to 4D fields and
1327there is no advantage in chunking across more than one time dimension since
1328previously written chunks would have to be read back and decompressed before being added to.
1329Therefore, user control over chunk sizes is provided only for the three space dimensions.
1330The user sets an approximate number of chunks along each spatial axis.
1331The actual size of the chunks will depend on global domain size for mono-processors or, more likely,
1332the local processor domain size for distributed processing.
1333The derived values are subject to practical minimum values (to avoid wastefully small chunk sizes) and
1334cannot be greater than the domain size in any dimension.
1335The algorithm used is:
1336
1337\begin{forlines}
1338ichunksz(1) = MIN(idomain_size, MAX((idomain_size-1) / nn_nchunks_i + 1 ,16 ))
1339ichunksz(2) = MIN(jdomain_size, MAX((jdomain_size-1) / nn_nchunks_j + 1 ,16 ))
1340ichunksz(3) = MIN(kdomain_size, MAX((kdomain_size-1) / nn_nchunks_k + 1 , 1 ))
1341ichunksz(4) = 1
1342\end{forlines}
1343
1344\noindent As an example, setting:
1345
1346\begin{forlines}
1347nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31
1348\end{forlines}
1349
1350\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1} respectively in
1351the mono-processor case (i.e. global domain of {\small\tt 182x149x31}).
1352An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in
1353table \autoref{tab:NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with
1354a 4x2 mpi partitioning.
1355Note the variation in the compression ratio achieved which reflects chiefly the dry to wet volume ratio of
1356each processing region.
1357
1358%------------------------------------------TABLE----------------------------------------------------
1359\begin{table}
1360  \scriptsize
1361  \centering
1362  \begin{tabular}{lrrr}
1363    Filename                    & NetCDF3 & NetCDF4  & Reduction \\
1364                                & filesize   & filesize & \%        \\
1365                                & (KB)    & (KB)     &           \\
1366    ORCA2\_restart\_0000.nc     & 16420   & 8860     & 47\%      \\
1367    ORCA2\_restart\_0001.nc     & 16064   & 11456    & 29\%      \\
1368    ORCA2\_restart\_0002.nc     & 16064      & 9744     & 40\%      \\
1369    ORCA2\_restart\_0003.nc     & 16420      & 9404     & 43\%      \\
1370    ORCA2\_restart\_0004.nc     & 16200   & 5844     & 64\%      \\
1371    ORCA2\_restart\_0005.nc     & 15848   & 8172     & 49\%      \\
1372    ORCA2\_restart\_0006.nc     & 15848   & 8012     & 50\%      \\
1373    ORCA2\_restart\_0007.nc     & 16200   & 5148     & 69\%      \\
1374    ORCA2\_2d\_grid\_T\_0000.nc & 2200       & 1504     & 32\%      \\
1375    ORCA2\_2d\_grid\_T\_0001.nc & 2200       & 1748     & 21\%      \\
1376    ORCA2\_2d\_grid\_T\_0002.nc & 2200       & 1592     & 28\%      \\
1377    ORCA2\_2d\_grid\_T\_0003.nc & 2200       & 1540     & 30\%      \\
1378    ORCA2\_2d\_grid\_T\_0004.nc & 2200       & 1204     & 46\%      \\
1379    ORCA2\_2d\_grid\_T\_0005.nc & 2200       & 1444     & 35\%      \\
1380    ORCA2\_2d\_grid\_T\_0006.nc & 2200       & 1428     & 36\%      \\
1381    ORCA2\_2d\_grid\_T\_0007.nc & 2200    & 1148     & 48\%      \\
1382    ...                         & ...     & ...      & ...       \\
1383    ORCA2\_2d\_grid\_W\_0000.nc & 4416    & 2240     & 50\%      \\
1384    ORCA2\_2d\_grid\_W\_0001.nc & 4416    & 2924     & 34\%      \\
1385    ORCA2\_2d\_grid\_W\_0002.nc & 4416    & 2512     & 44\%      \\
1386    ORCA2\_2d\_grid\_W\_0003.nc & 4416    & 2368     & 47\%      \\
1387    ORCA2\_2d\_grid\_W\_0004.nc & 4416    & 1432     & 68\%      \\
1388    ORCA2\_2d\_grid\_W\_0005.nc & 4416    & 1972     & 56\%      \\
1389    ORCA2\_2d\_grid\_W\_0006.nc & 4416    & 2028     & 55\%      \\
1390    ORCA2\_2d\_grid\_W\_0007.nc & 4416    & 1368     & 70\%      \\
1391  \end{tabular}
1392  \caption{
1393    \protect\label{tab:NC4}
1394    Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression
1395  }
1396\end{table}
1397%----------------------------------------------------------------------------------------------------
1398
1399When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via
1400\np{iom\_put} calls are set via an equivalent and identically named namelist to \textit{namnc4} in
1401\np{xmlio\_server.def}.
1402Typically this namelist serves the mean files whilst the \ngn{ namnc4} in the main namelist file continues to
1403serve the restart files.
1404This duplication is unfortunate but appropriate since, if using io\_servers, the domain sizes of
1405the individual files produced by the io\_server processes may be different to those produced by
1406the invidual processing regions and different chunking choices may be desired.
1407 
1408% -------------------------------------------------------------------------------------------------------------
1409%       Tracer/Dynamics Trends
1410% -------------------------------------------------------------------------------------------------------------
1411\section{Tracer/Dynamics trends  (\protect\ngn{namtrd})}
1412\label{sec:DIA_trd}
1413
1414%------------------------------------------namtrd----------------------------------------------------
1415
1416\nlst{namtrd} 
1417%-------------------------------------------------------------------------------------------------------------
1418
1419Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to
1420\mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation
1421($i.e.$ at the end of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines).
1422This capability is controlled by options offered in \ngn{namtrd} namelist.
1423Note that the output are done with xIOS, and therefore the \key{IOM} is required.
1424
1425What is done depends on the \ngn{namtrd} logical set to \forcode{.true.}:
1426
1427\begin{description}
1428\item[\np{ln\_glo\_trd}]:
1429  at each \np{nn\_trd} time-step a check of the basin averaged properties of
1430  the momentum and tracer equations is performed.
1431  This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$,
1432  and potential energy time evolution equations properties;
1433\item[\np{ln\_dyn\_trd}]:
1434  each 3D trend of the evolution of the two momentum components is output;
1435\item[\np{ln\_dyn\_mxl}]:
1436  each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output;
1437\item[\np{ln\_vor\_trd}]:
1438  a vertical summation of the moment tendencies is performed,
1439  then the curl is computed to obtain the barotropic vorticity tendencies which are output;
1440\item[\np{ln\_KE\_trd}] :
1441  each 3D trend of the Kinetic Energy equation is output;
1442\item[\np{ln\_tra\_trd}]:
1443  each 3D trend of the evolution of temperature and salinity is output;
1444\item[\np{ln\_tra\_mxl}]:
1445  each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output;
1446\end{description}
1447
1448Note that the mixed layer tendency diagnostic can also be used on biogeochemical models via
1449the \key{trdtrc} and \key{trdmld\_trc} CPP keys.
1450
1451\textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested.
1452In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} are not working,
1453and none of the options have been tested with variable volume ($i.e.$ \key{vvl} defined).
1454
1455% -------------------------------------------------------------------------------------------------------------
1456%       On-line Floats trajectories
1457% -------------------------------------------------------------------------------------------------------------
1458\section{FLO: On-Line Floats trajectories (\protect\key{floats})}
1459\label{sec:FLO}
1460%--------------------------------------------namflo-------------------------------------------------------
1461
1462\nlst{namflo} 
1463%--------------------------------------------------------------------------------------------------------------
1464
1465The on-line computation of floats advected either by the three dimensional velocity field or constraint to
1466remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project.
1467Options are defined by \ngn{namflo} namelis variables.
1468The algorithm used is based either on the work of \cite{Blanke_Raynaud_JPO97} (default option),
1469or on a $4^th$ Runge-Hutta algorithm (\np{ln\_flork4}\forcode{ = .true.}).
1470Note that the \cite{Blanke_Raynaud_JPO97} algorithm have the advantage of providing trajectories which
1471are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry.
1472
1473\subsubsection{Input data: initial coordinates}
1474
1475Initial coordinates can be given with Ariane Tools convention
1476(IJK coordinates, (\np{ln\_ariane}\forcode{ = .true.}) ) or with longitude and latitude.
1477
1478In case of Ariane convention, input filename is \np{init\_float\_ariane}.
1479Its format is: \\
1480{\scriptsize \texttt{I J K nisobfl itrash itrash}}
1481
1482\noindent with:
1483
1484 - I,J,K  : indexes of initial position
1485
1486 - nisobfl: 0 for an isobar float, 1 for a float following the w velocity 
1487
1488 - itrash : set to zero; it is a dummy variable to respect Ariane Tools convention
1489
1490\noindent Example: \\
1491\noindent
1492{\scriptsize
1493  \texttt{
1494    100.00000  90.00000  -1.50000 1.00000   0.00000   \\
1495    102.00000  90.00000  -1.50000 1.00000   0.00000   \\
1496    104.00000  90.00000  -1.50000 1.00000   0.00000   \\
1497    106.00000  90.00000  -1.50000 1.00000   0.00000   \\
1498    108.00000  90.00000  -1.50000 1.00000   0.00000}
1499} \\
1500
1501In the other case (longitude and latitude), input filename is init\_float.
1502Its format is: \\
1503{\scriptsize \texttt{Long Lat depth nisobfl ngrpfl itrash}}
1504
1505\noindent with:
1506
1507 - Long, Lat, depth  : Longitude, latitude, depth
1508
1509 - nisobfl: 0 for an isobar float, 1 for a float following the w velocity
1510
1511 - ngrpfl : number to identify searcher group
1512
1513 - itrash :set to 1; it is a dummy variable.
1514
1515\noindent Example: \\
1516\noindent
1517{\scriptsize
1518  \texttt{
1519    20.0 0.0 0.0 0 1 1    \\
1520    -21.0 0.0 0.0 0 1 1    \\
1521    -22.0 0.0 0.0 0 1 1    \\
1522    -23.0 0.0 0.0 0 1 1    \\
1523    -24.0 0.0 0.0 0 1 1 }
1524} \\
1525
1526\np{jpnfl} is the total number of floats during the run.
1527When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{ = .true.} ),
1528\np{jpnflnewflo} can be added in the initialization file.
1529
1530\subsubsection{Output data}
1531
1532\np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} is the frequency of
1533creation of the float restart file.
1534
1535Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{ = .true.}).
1536In that case, output filename is trajec\_float.
1537
1538Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{ = .false.}).
1539There are 2 possibilities:
1540
1541- if (\key{iomput}) is used, outputs are selected in  iodef.xml.
1542Here it is an example of specification to put in files description section:
1543
1544\begin{xmllines}
1545<group id="1d_grid_T" name="auto" description="ocean T grid variables" >   }
1546   <file id="floats"  description="floats variables"> }
1547      <field ref="traj_lon"   name="floats_longitude"   freq_op="86400" />}
1548      <field ref="traj_lat"   name="floats_latitude"    freq_op="86400" />}
1549      <field ref="traj_dep"   name="floats_depth"       freq_op="86400" />}
1550      <field ref="traj_temp"  name="floats_temperature" freq_op="86400" />}
1551      <field ref="traj_salt"  name="floats_salinity"    freq_op="86400" />}
1552      <field ref="traj_dens"  name="floats_density"     freq_op="86400" />}
1553      <field ref="traj_group" name="floats_group"       freq_op="86400" />}
1554   </file>}
1555</group>}
1556\end{xmllines}
1557
1558 -  if (\key{iomput}) is not used, a file called \ifile{trajec\_float} will be created by IOIPSL library.
1559
1560 See also \href{http://stockage.univ-brest.fr/~grima/Ariane/}{here} the web site describing the off-line use of
1561 this marvellous diagnostic tool.
1562
1563% -------------------------------------------------------------------------------------------------------------
1564%       Harmonic analysis of tidal constituents
1565% -------------------------------------------------------------------------------------------------------------
1566\section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) }
1567\label{sec:DIA_diag_harm}
1568
1569%------------------------------------------namdia_harm----------------------------------------------------
1570%
1571\nlst{nam_diaharm}
1572%----------------------------------------------------------------------------------------------------------
1573
1574A module is available to compute the amplitude and phase of tidal waves.
1575This on-line Harmonic analysis is actived with \key{diaharm}.
1576
1577Some parameters are available in namelist \ngn{namdia\_harm}:
1578
1579 - \np{nit000\_han} is the first time step used for harmonic analysis
1580
1581 - \np{nitend\_han} is the  last time step used for harmonic analysis
1582
1583 - \np{nstep\_han}  is the  time step frequency for harmonic analysis
1584
1585 - \np{nb\_ana}     is the number of harmonics to analyse
1586
1587 - \np{tname}       is an array with names of tidal constituents to analyse
1588
1589 \np{nit000\_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation.
1590 The restart capability is not implemented.
1591
1592 The Harmonic analysis solve the following equation:
1593
1594 \[
1595   h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i}
1596 \]
1597
1598With $A_{j}$, $\nu_{j}$, $\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error.
1599$h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\
1600We can rewrite this equation:
1601
1602\[
1603  h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i}
1604\]
1605
1606with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ and $\phi_{j}=arctan(S_{j}/C_{j})$.
1607
1608We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave.
1609
1610% -------------------------------------------------------------------------------------------------------------
1611%       Sections transports
1612% -------------------------------------------------------------------------------------------------------------
1613\section{Transports across sections (\protect\key{diadct}) }
1614\label{sec:DIA_diag_dct}
1615
1616%------------------------------------------namdct----------------------------------------------------
1617
1618\nlst{namdct}
1619%-------------------------------------------------------------------------------------------------------------
1620
1621A module is available to compute the transport of volume, heat and salt through sections.
1622This diagnostic is actived with \key{diadct}.
1623
1624Each section is defined by the coordinates of its 2 extremities.
1625The pathways between them are contructed using tools which can be found in \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT}
1626and are written in a binary file \texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is later read in by
1627NEMO to compute on-line transports.
1628
1629The on-line transports module creates three output ascii files:
1630
1631- \texttt{volume\_transport} for volume transports (unit: $10^{6} m^{3} s^{-1}$)
1632
1633- \texttt{heat\_transport}   for   heat transports (unit: $10^{15} W$)
1634
1635- \texttt{salt\_transport}   for   salt transports (unit: $10^{9}Kg s^{-1}$) \\
1636
1637Namelist variables in \ngn{namdct} control how frequently the flows are summed and the time scales over which
1638they are averaged, as well as the level of output for debugging:
1639\np{nn\_dct}   : frequency of instantaneous transports computing
1640\np{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
1641\np{nn\_debug} : debugging of the section
1642
1643\subsubsection{Creating a binary file containing the pathway of each section}
1644
1645In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run},
1646the file \textit{ {list\_sections.ascii\_global}} contains a list of all the sections that are to be computed
1647(this list of sections is based on MERSEA project metrics).
1648
1649Another file is available for the GYRE configuration (\texttt{ {list\_sections.ascii\_GYRE}}).
1650
1651Each section is defined by: \\
1652\noindent {\scriptsize \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\
1653with:
1654
1655 - \texttt{long1 lat1}, coordinates of the  first extremity of the section;
1656
1657 - \texttt{long2 lat2}, coordinates of the second extremity of the section;
1658
1659 - \texttt{nclass}    the number of bounds of your classes (e.g. 3 bounds for 2 classes);
1660
1661 - \texttt{okstrpond} to compute    heat and       salt transports, \texttt{nostrpond} if no;
1662
1663 - \texttt{ice}       to compute surface and volume ice transports, \texttt{noice}     if no. \\
1664
1665 \noindent The results of the computing of transports, and the directions of positive and
1666 negative flow do not depend on the order of the 2 extremities in this file. \\
1667
1668\noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\
1669{\scriptsize
1670  \texttt{
1671    long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\
1672    classtype                                                         \\
1673    zbound1                                                           \\
1674    zbound2                                                           \\
1675    .                                                                 \\
1676    .                                                                 \\
1677    nclass-1                                                          \\
1678    nclass}
1679}
1680
1681\noindent where \texttt{classtype} can be:
1682
1683 - \texttt{zsal}  for          salinity classes
1684
1685 - \texttt{ztem}  for       temperature classes
1686
1687 - \texttt{zlay}  for             depth classes
1688
1689 - \texttt{zsigi} for    insitu density classes
1690
1691 - \texttt{zsigp} for potential density classes \\
1692 
1693 The script \texttt{job.ksh} computes the pathway for each section and creates a binary file
1694 \texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is read by NEMO. \\
1695
1696 It is possible to use this tools for new configuations: \texttt{job.ksh} has to be updated with
1697 the coordinates file name and path. \\
1698
1699 Examples of two sections, the ACC\_Drake\_Passage with no classes,
1700 and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\
1701 \noindent
1702 {\scriptsize
1703   \texttt{
1704     -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage \\
1705     -80.5    22.5   -80.5    25.5  05 nostrpond noice ATL\_Cuba\_Florida  \\
1706     ztem                                                                  \\
1707     -2.0                                                                  \\
1708     4.5                                                                  \\
1709     7.0                                                                  \\
1710     12.0                                                                  \\
1711     40.0}
1712 }
1713
1714\subsubsection{To read the output files}
1715
1716The output format is: \\
1717{\scriptsize
1718  \texttt{
1719    date, time-step number, section number,                \\
1720    section name, section slope coefficient, class number, \\
1721    class name, class bound 1 , classe bound2,             \\
1722    transport\_direction1, transport\_direction2,          \\
1723    transport\_total}
1724}                                     \\
1725
1726For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class and
1727the last line corresponds to the total transport summed over all classes.
1728For sections with no classes, class number \texttt{1} corresponds to \texttt{total class} and
1729this class is called \texttt{N}, meaning \texttt{none}.
1730
1731- \texttt{transport\_direction1} is the positive part of the transport ($\geq$ 0).
1732
1733- \texttt{transport\_direction2} is the negative part of the transport ($\leq$ 0). \\
1734
1735\noindent The \texttt{section slope coefficient} gives information about the significance of transports signs and
1736direction: \\
1737
1738\begin{table}
1739  \scriptsize
1740  \begin{tabular}{|l|l|l|l|l|}
1741    \hline
1742    section slope coefficient      & section type & direction 1 & direction 2 & total transport    \\
1743    \hline
1744    0.                             & horizontal  & northward   & southward   & postive: northward    \\
1745    \hline
1746    1000.                          & vertical     & eastward    & westward    & postive: eastward     \\
1747    \hline
1748    \texttt{$\neq$ 0, $\neq$ 1000.} & diagonal     & eastward    & westward     & postive: eastward      \\
1749    \hline
1750  \end{tabular}
1751\end{table}
1752
1753% ================================================================
1754% Steric effect in sea surface height
1755% ================================================================
1756\section{Diagnosing the steric effect in sea surface height}
1757\label{sec:DIA_steric}
1758
1759
1760Changes in steric sea level are caused when changes in the density of the water column imply an expansion or
1761contraction of the column.
1762It is essentially produced through surface heating/cooling and to a lesser extent through non-linear effects of
1763the equation of state (cabbeling, thermobaricity...).
1764Non-Boussinesq models contain all ocean effects within the ocean acting on the sea level.
1765In particular, they include the steric effect.
1766In contrast, Boussinesq models, such as \NEMO, conserve volume, rather than mass,
1767and so do not properly represent expansion or contraction.
1768The steric effect is therefore not explicitely represented.
1769This approximation does not represent a serious error with respect to the flow field calculated by the model
1770\citep{Greatbatch_JGR94}, but extra attention is required when investigating sea level,
1771as steric changes are an important contribution to local changes in sea level on seasonal and climatic time scales.
1772This is especially true for investigation into sea level rise due to global warming.
1773
1774Fortunately, the steric contribution to the sea level consists of a spatially uniform component that
1775can be diagnosed by considering the mass budget of the world ocean \citep{Greatbatch_JGR94}.
1776In order to better understand how global mean sea level evolves and thus how the steric sea level can be diagnosed,
1777we compare, in the following, the non-Boussinesq and Boussinesq cases.
1778
1779Let denote
1780$\mathcal{M}$ the total mass    of liquid seawater ($\mathcal{M} = \int_D \rho dv$),
1781$\mathcal{V}$ the total volume  of        seawater      ($\mathcal{V} = \int_D dv$),
1782$\mathcal{A}$ the total surface of       the ocean      ($\mathcal{A} = \int_S ds$),
1783$\bar{\rho}$ the global mean  seawater (\textit{in situ}) density
1784($\bar{\rho} = 1/\mathcal{V} \int_D \rho \,dv$), and
1785$\bar{\eta}$ the global mean sea level
1786($\bar{\eta} = 1/\mathcal{A} \int_S \eta \,ds$).
1787
1788A non-Boussinesq fluid conserves mass. It satisfies the following relations:
1789
1790\begin{equation}
1791  \begin{split}
1792    \mathcal{M} &\mathcal{V}  \;\bar{\rho} \\
1793    \mathcal{V} &\mathcal{A}  \;\bar{\eta}
1794  \end{split}
1795  \label{eq:MV_nBq}
1796\end{equation}
1797
1798Temporal changes in total mass is obtained from the density conservation equation:
1799
1800\begin{equation}
1801  \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} )
1802  = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface}
1803  \label{eq:Co_nBq}
1804\end{equation}
1805
1806where $\rho$ is the \textit{in situ} density, and \textit{emp} the surface mass exchanges with the other media of
1807the Earth system (atmosphere, sea-ice, land).
1808Its global averaged leads to the total mass change
1809
1810\begin{equation}
1811  \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}}
1812  \label{eq:Mass_nBq}
1813\end{equation}
1814
1815where $\overline{\textit{emp}} = \int_S \textit{emp}\,ds$ is the net mass flux through the ocean surface.
1816Bringing \autoref{eq:Mass_nBq} and the time derivative of \autoref{eq:MV_nBq} together leads to
1817the evolution equation of the mean sea level
1818
1819\begin{equation}
1820  \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}}
1821  - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}}
1822  \label{eq:ssh_nBq}
1823\end{equation}
1824
1825The first term in equation \autoref{eq:ssh_nBq} alters sea level by adding or subtracting mass from the ocean.
1826The second term arises from temporal changes in the global mean density; $i.e.$ from steric effects.
1827
1828In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ appears multiplied by
1829the gravity ($i.e.$ in the hydrostatic balance of the primitive Equations).
1830In particular, the mass conservation equation, \autoref{eq:Co_nBq}, degenerates into the incompressibility equation:
1831
1832\[
1833  \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface}
1834  % \label{eq:Co_Bq}
1835\]
1836
1837and the global average of this equation now gives the temporal change of the total volume,
1838
1839\[
1840  \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o}
1841  % \label{eq:V_Bq}
1842\]
1843
1844Only the volume is conserved, not mass, or, more precisely, the mass which is conserved is the Boussinesq mass,
1845$\mathcal{M}_o = \rho_o \mathcal{V}$.
1846The total volume (or equivalently the global mean sea level) is altered only by net volume fluxes across
1847the ocean surface, not by changes in mean mass of the ocean: the steric effect is missing in a Boussinesq fluid.
1848
1849Nevertheless, following \citep{Greatbatch_JGR94}, the steric effect on the volume can be diagnosed by
1850considering the mass budget of the ocean.
1851The apparent changes in $\mathcal{M}$, mass of the ocean, which are not induced by surface mass flux
1852must be compensated by a spatially uniform change in the mean sea level due to expansion/contraction of the ocean
1853\citep{Greatbatch_JGR94}.
1854In others words, the Boussinesq mass, $\mathcal{M}_o$, can be related to $\mathcal{M}$,
1855the total mass of the ocean seen by the Boussinesq model, via the steric contribution to the sea level,
1856$\eta_s$, a spatially uniform variable, as follows:
1857
1858\begin{equation}
1859  \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A}
1860  \label{eq:M_Bq}
1861\end{equation}
1862
1863Any change in $\mathcal{M}$ which cannot be explained by the net mass flux through the ocean surface
1864is converted into a mean change in sea level.
1865Introducing the total density anomaly, $\mathcal{D}= \int_D d_a \,dv$,
1866where $d_a = (\rho -\rho_o ) / \rho_o$ is the density anomaly used in \NEMO (cf. \autoref{subsec:TRA_eos})
1867in \autoref{eq:M_Bq} leads to a very simple form for the steric height:
1868
1869\begin{equation}
1870  \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D}
1871  \label{eq:steric_Bq}
1872\end{equation}
1873
1874The above formulation of the steric height of a Boussinesq ocean requires four remarks.
1875First, one can be tempted to define $\rho_o$ as the initial value of $\mathcal{M}/\mathcal{V}$,
1876$i.e.$ set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero.
1877We do not recommend that.
1878Indeed, in this case $\rho_o$ depends on the initial state of the ocean.
1879Since $\rho_o$ has a direct effect on the dynamics of the ocean
1880(it appears in the pressure gradient term of the momentum equation)
1881it is definitively not a good idea when inter-comparing experiments.
1882We better recommend to fixe once for all $\rho_o$ to $1035\;Kg\,m^{-3}$.
1883This value is a sensible choice for the reference density used in a Boussinesq ocean climate model since,
1884with the exception of only a small percentage of the ocean, density in the World Ocean varies by no more than
18852$\%$ from this value (\cite{Gill1982}, page 47).
1886
1887Second, we have assumed here that the total ocean surface, $\mathcal{A}$,
1888does not change when the sea level is changing as it is the case in all global ocean GCMs
1889(wetting and drying of grid point is not allowed).
1890 
1891Third, the discretisation of \autoref{eq:steric_Bq} depends on the type of free surface which is considered.
1892In the non linear free surface case, $i.e.$ \key{vvl} defined, it is given by
1893
1894\[
1895  \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} }{ \sum_{i,\,j,\,k}       e_{1t} e_{2t} e_{3t} }
1896  % \label{eq:discrete_steric_Bq_nfs}
1897\]
1898
1899whereas in the linear free surface,
1900the volume above the \textit{z=0} surface must be explicitly taken into account to
1901better approximate the total ocean mass and thus the steric sea level:
1902
1903\[
1904  \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta }
1905                  { \sum_{i,\,j,\,k}       e_{1t}e_{2t}e_{3t} + \sum_{i,\,j}       e_{1t}e_{2t} \eta }
1906  % \label{eq:discrete_steric_Bq_fs}
1907\]
1908
1909The fourth and last remark concerns the effective sea level and the presence of sea-ice.
1910In the real ocean, sea ice (and snow above it)  depresses the liquid seawater through its mass loading.
1911This depression is a result of the mass of sea ice/snow system acting on the liquid ocean.
1912There is, however, no dynamical effect associated with these depressions in the liquid ocean sea level,
1913so that there are no associated ocean currents.
1914Hence, the dynamically relevant sea level is the effective sea level,
1915$i.e.$ the sea level as if sea ice (and snow) were converted to liquid seawater \citep{Campin_al_OM08}.
1916However, in the current version of \NEMO the sea-ice is levitating above the ocean without mass exchanges between
1917ice and ocean.
1918Therefore the model effective sea level is always given by $\eta + \eta_s$, whether or not there is sea ice present.
1919
1920In AR5 outputs, the thermosteric sea level is demanded.
1921It is steric sea level due to changes in ocean density arising just from changes in temperature.
1922It is given by:
1923
1924\[
1925  \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv
1926  % \label{eq:thermosteric_Bq}
1927\]
1928
1929where $S_o$ and $p_o$ are the initial salinity and pressure, respectively.
1930
1931Both steric and thermosteric sea level are computed in \mdl{diaar5} which needs the \key{diaar5} defined to
1932be called.
1933
1934% -------------------------------------------------------------------------------------------------------------
1935%       Other Diagnostics
1936% -------------------------------------------------------------------------------------------------------------
1937\section{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})}
1938\label{sec:DIA_diag_others}
1939
1940Aside from the standard model variables, other diagnostics can be computed on-line.
1941The available ready-to-add diagnostics modules can be found in directory DIA.
1942
1943\subsection{Depth of various quantities (\protect\mdl{diahth})}
1944
1945Among the available diagnostics the following ones are obtained when defining the \key{diahth} CPP key:
1946
1947- the mixed layer depth (based on a density criterion \citep{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth})
1948
1949- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth})
1950
1951- the depth of the 20\deg C isotherm (\mdl{diahth})
1952
1953- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth})
1954
1955% -----------------------------------------------------------
1956%     Poleward heat and salt transports
1957% -----------------------------------------------------------
1958
1959\subsection{Poleward heat and salt transports (\protect\mdl{diaptr})}
1960
1961%------------------------------------------namptr-----------------------------------------
1962
1963\nlst{namptr} 
1964%-----------------------------------------------------------------------------------------
1965
1966The poleward heat and salt transports, their advective and diffusive component,
1967and the meriodional stream function can be computed on-line in \mdl{diaptr} \np{ln\_diaptr} to true
1968(see the \textit{\ngn{namptr} } namelist below).
1969When \np{ln\_subbas}\forcode{ = .true.}, transports and stream function are computed for the Atlantic, Indian,
1970Pacific and Indo-Pacific Oceans (defined north of 30\deg S) as well as for the World Ocean.
1971The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays,
1972the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:mask_subasins}).
1973
1974%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1975\begin{figure}[!t]
1976  \begin{center}
1977    \includegraphics[width=1.0\textwidth]{Fig_mask_subasins}
1978    \caption{
1979      \protect\label{fig:mask_subasins}
1980      Decomposition of the World Ocean (here ORCA2) into sub-basin used in to
1981      compute the heat and salt transports as well as the meridional stream-function:
1982      Atlantic basin (red), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).
1983      Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay are removed from the sub-basins.
1984      Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line.
1985    }
1986  \end{center}
1987\end{figure} 
1988%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1989
1990% -----------------------------------------------------------
1991%       CMIP specific diagnostics
1992% -----------------------------------------------------------
1993\subsection{CMIP specific diagnostics (\protect\mdl{diaar5})}
1994
1995A series of diagnostics has been added in the \mdl{diaar5}.
1996They corresponds to outputs that are required for AR5 simulations (CMIP5)
1997(see also \autoref{sec:DIA_steric} for one of them).
1998Activating those outputs requires to define the \key{diaar5} CPP key.
1999
2000% -----------------------------------------------------------
2001%       25 hour mean and hourly Surface, Mid and Bed
2002% -----------------------------------------------------------
2003\subsection{25 hour mean output for tidal models}
2004
2005%------------------------------------------nam_dia25h-------------------------------------
2006
2007\nlst{nam_dia25h}
2008%-----------------------------------------------------------------------------------------
2009
2010A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean.
2011The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from
2012midnight at the start of the day to midight at the day end.
2013This diagnostic is actived with the logical $ln\_dia25h$.
2014
2015% -----------------------------------------------------------
2016%     Top Middle and Bed hourly output
2017% -----------------------------------------------------------
2018\subsection{Top middle and bed hourly output}
2019
2020%------------------------------------------nam_diatmb-----------------------------------------------------
2021
2022\nlst{nam_diatmb}
2023%----------------------------------------------------------------------------------------------------------
2024
2025A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables.
2026This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs.
2027The tidal signal is retained but the overall data usage is cut to just three vertical levels.
2028Also the bottom level is calculated for each cell.
2029This diagnostic is actived with the logical $ln\_diatmb$.
2030
2031% -----------------------------------------------------------
2032%     Courant numbers
2033% -----------------------------------------------------------
2034\subsection{Courant numbers}
2035
2036Courant numbers provide a theoretical indication of the model's numerical stability.
2037The advective Courant numbers can be calculated according to
2038
2039\[
2040  C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}}
2041  % \label{eq:CFL}
2042\]
2043
2044in the zonal, meridional and vertical directions respectively.
2045The vertical component is included although it is not strictly valid as the vertical velocity is calculated from
2046the continuity equation rather than as a prognostic variable.
2047Physically this represents the rate at which information is propogated across a grid cell.
2048Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step.
2049
2050The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist.
2051The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii.
2052In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of
2053where the maximum value occurs.
2054At the end of the model run the maximum value of $C_u$, $C_v$, and $C_w$ for the whole model run is printed along
2055with the coordinates of each.
2056The maximum values from the run are also copied to the ocean.output file.
2057
2058% ================================================================
2059
2060\biblio
2061
2062\end{document}
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