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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{Model output}
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.
28
29The output listing and file(s) are predefined but should be checked and eventually adapted to the user's needs.
30The output listing is stored in the $ocean.output$ file.
31The information is printed from within the code on the logical unit $numout$.
32To locate these prints, use the UNIX command "\textit{grep -i numout}" in the source code directory.
33
34By default, diagnostic output files are written in NetCDF format.
35Since version 3.2, when defining \key{iomput}, an I/O server has been added which
36provides more flexibility in the choice of the fields to be written as well as how
37the writing work is distributed over the processors in massively parallel computing.
38A complete description of the use of this I/O server is presented in the next section.
39
40%\gmcomment{                    % start of gmcomment
41
42% ================================================================
43% Diagnostics
44% ================================================================
45\section{Standard model output (IOM)}
46\label{sec:DIA_iom}
47
48Since version 3.2, iomput is the NEMO output interface of choice.
49It has been designed to be simple to use, flexible and efficient.
50The two main purposes of iomput are:
51
52\begin{enumerate}
53\item
54  The complete and flexible control of the output files through external XML files adapted by
55  the user from standard templates.
56\item
57  To achieve high performance and scalable output through the optional distribution of
58  all diagnostic output related tasks to dedicated processes.
59\end{enumerate}
60
61The first functionality allows the user to specify, without code changes or recompilation,
62aspects of the diagnostic output stream, such as:
63
64\begin{itemize}
65\item
66  The choice of output frequencies that can be different for each file (including real months and years).
67\item
68  The choice of file contents; includes complete flexibility over which data are written in which files
69  (the same data can be written in different files).
70\item
71  The possibility to split output files at a chosen frequency.
72\item
73  The possibility to extract a vertical or an horizontal subdomain.
74\item
75  The choice of the temporal operation to perform, \eg: average, accumulate, instantaneous, min, max and once.
76\item
77  Control over metadata via a large XML "database" of possible output fields.
78\end{itemize}
79
80In addition, iomput allows the user to add in the code the output of any new variable (scalar, 2D or 3D)
81in a very easy way.
82All details of iomput functionalities are listed in the following subsections.
83Examples of the XML files that control the outputs can be found in:
84\path{cfgs/ORCA2_ICE_PISCES/EXPREF/iodef.xml},
85\path{cfgs/SHARED/field_def_nemo-oce.xml},
86\path{cfgs/SHARED/field_def_nemo-pisces.xml},
87\path{cfgs/SHARED/field_def_nemo-ice.xml} and \path{cfgs/SHARED/domain_def_nemo.xml}. \\
88
89The second functionality targets output performance when running in parallel (\key{mpp\_mpi}).
90Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO processes)
91to collect and write the outputs.
92With an appropriate choice of N by the user, the bottleneck associated with the writing of
93the output files can be greatly reduced.
94
95In version 3.6, the iom\_put interface depends on
96an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/branchs/xios-2.5}{XIOS-2.5} 
97(use of revision 618 or higher is required).
98This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to
99create a single output file and therefore to bypass the rebuilding phase.
100Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to
101an HDF5 library that has been correctly compiled (\ie with the configure option $--$enable-parallel).
102Note that the files created by iomput through XIOS are incompatible with NetCDF3.
103All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3.
104
105Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers,
106where N is typically much less than the number of NEMO processors, will reduce the number of output files created.
107This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors.
108Note that for smaller configurations, the rebuilding phase can be avoided,
109even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server.
110
111\subsection{XIOS: Reading and writing restart file}
112
113XIOS may be used to read single file restart produced by NEMO. Currently only the variables written to
114file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np{ln\_xios\_read}\forcode{ = .true. }
115in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default NEMO
116functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read
117restart, all definitions are done within the NEMO code. For high resolution configuration, however,
118there may be a need to add the following line in iodef.xml (xios context):
119
120\begin{xmllines}
121<variable id="recv_field_timeout"        type="double">1800</variable>
122\end{xmllines}
123
124This variable sets timeout for reading.
125
126If XIOS is to be used to read restart from file generated with an earlier NEMO version (3.6 for instance),
127dimension \forcode{z} defined in restart file must be renamed to \forcode{nav_lev}.\\
128
129XIOS can also be used to write NEMO restart. A namelist parameter \np{nn\_wxios} is used to determine the
130type of restart NEMO will write. If it is set to 0, default NEMO functionality will be used - each
131processor writes its own restart file; if it is set to 1 XIOS will write restart into a single file;
132for \np{nn\_wxios = 2} the restart will be written by XIOS into multiple files, one for each XIOS server.
133Note, however, that \textbf{NEMO will not read restart generated by XIOS when \np{nn\_wxios = 2}}. The restart will
134have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by NEMO only,
135and may be useful when there is a need to change number of processors used to run simulation.
136
137If an additional variable must be written to a restart file, the following steps are needed:
138\begin{description}
139   \item[step 1:] add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and
140define correct grid for the variable (\forcode{grid_N_3D} - 3D variable, \forcode{grid_N} - 2D variable, \forcode{grid_vector} -
1411D variable, \forcode{grid_scalar} - scalar),
142   \item[step 2:] add variable to the list of fields written by restart.  This can be done either in subroutine
143\rou{iom\_set\_rstw\_core} (\mdl{iom}) or by calling  \rou{iom\_set\_rstw\_active} (\mdl{iom}) with the name of a variable
144as an argument. This convention follows approach for writing restart using iom, where variables are
145written either by \rou{rst\_write} or by calling \rou{iom\_rstput} from individual routines.
146\end{description}
147
148
149An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451.
150
151
152\subsection{XIOS: XML Inputs-Outputs Server}
153
154\subsubsection{Attached or detached mode?}
155
156Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS},
157the io\_server developed by Yann Meurdesoif from IPSL.
158The behaviour of the I/O subsystem is controlled by settings in the external XML files listed above.
159Key settings in the iodef.xml file are the tags associated with each defined file.
160
161\xmlline|<variable id="using_server" type="bool"></variable>|
162
163The {\ttfamily using\_server} setting determines whether or not the server will be used in \textit{attached mode}
164(as a library) [{\ttfamily> false <}] or in \textit{detached mode}
165(as an external executable on N additional, dedicated cpus) [{\ttfamily > true <}].
166The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications.
167The type of each file can be either ''multiple\_file'' or ''one\_file''.
168
169In \textit{attached mode} and if the type of file is ''multiple\_file'',
170then each NEMO process will also act as an IO server and produce its own set of output files.
171Superficially, this emulates the standard behaviour in previous versions.
172However, the subdomain written out by each process does not correspond to
173the \forcode{jpi x jpj x jpk} domain actually computed by the process (although it may if \forcode{jpni=1}).
174Instead each process will have collected and written out a number of complete longitudinal strips.
175If the ''one\_file'' option is chosen then all processes will collect their longitudinal strips and
176write (in parallel) to a single output file.
177
178In \textit{detached mode} and if the type of file is ''multiple\_file'',
179then each stand-alone XIOS process will collect data for a range of complete longitudinal strips and
180write to its own set of output files.
181If the ''one\_file'' option is chosen then all XIOS processes will collect their longitudinal strips and
182write (in parallel) to a single output file.
183Note running in detached mode requires launching a Multiple Process Multiple Data (MPMD) parallel job.
184The following subsection provides a typical example but the syntax will vary in different MPP environments.
185
186\subsubsection{Number of cpu used by XIOS in detached mode}
187
188The number of cores used by the XIOS is specified when launching the model.
189The number of cores dedicated to XIOS should be from \texttildelow1/10 to \texttildelow1/50 of the number of
190cores dedicated to NEMO.
191Some manufacturers suggest using O($\sqrt{N}$) dedicated IO processors for N processors but
192this is a general recommendation and not specific to NEMO.
193It is difficult to provide precise recommendations because the optimal choice will depend on
194the particular hardware properties of the target system
195(parallel filesystem performance, available memory, memory bandwidth etc.)
196and the volume and frequency of data to be created.
197Here is an example of 2 cpus for the io\_server and 62 cpu for nemo using mpirun:
198\cmd|mpirun -np 62 ./nemo.exe : -np 2 ./xios_server.exe|
199
200\subsubsection{Control of XIOS: the context in iodef.xml}
201
202As well as the {\ttfamily using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml.
203See the XML basics section below for more details on XML syntax and rules.
204
205\begin{table}
206  \scriptsize
207  \begin{tabularx}{\textwidth}{|lXl|}
208    \hline
209    variable name                                                           &
210    description                                                             &
211    example  \\
212    \hline
213    \hline
214    buffer\_size                                                            &
215    buffer size used by XIOS to send data from NEMO to XIOS.
216    Larger is more efficient.
217    Note that needed/used buffer sizes are summarized at the end of the job &
218    25000000 \\
219    \hline
220    buffer\_server\_factor\_size                                            &
221    ratio between NEMO and XIOS buffer size.
222    Should be 2.                                                            &
223    2        \\
224    \hline
225    info\_level                                                             &
226    verbosity level (0 to 100)                                              &
227    0        \\
228    \hline
229    using\_server                                                           &
230    activate attached(false) or detached(true) mode                         &
231    true     \\
232    \hline
233    using\_oasis                                                            &
234    XIOS is used with OASIS(true) or not (false)                            &
235    false    \\
236    \hline
237    oasis\_codes\_id                                                        &
238    when using oasis, define the identifier of NEMO in the namcouple.
239    Note that the identifier of XIOS is xios.x                              &
240    oceanx   \\
241    \hline
242  \end{tabularx}
243\end{table}
244
245\subsection{Practical issues}
246
247\subsubsection{Installation}
248
249As mentioned, XIOS is supported separately and must be downloaded and compiled before it can be used with NEMO.
250See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance.
251NEMO will need to link to the compiled XIOS library.
252The \href{https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/guide/html/install.html#extract-and-install-xios}
253{Extract and install XIOS} guide provides an example illustration of how this can be achieved.
254
255\subsubsection{Add your own outputs}
256
257It is very easy to add your own outputs with iomput.
258Many standard fields and diagnostics are already prepared (\ie, steps 1 to 3 below have been done) and
259simply need to be activated by including the required output in a file definition in iodef.xml (step 4).
260To add new output variables, all 4 of the following steps must be taken.
261
262\begin{enumerate}
263\item[1.]
264  in NEMO code, add a \forcode{CALL iom_put( 'identifier', array )} where you want to output a 2D or 3D array.
265\item[2.]
266  If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in
267  the upper part of your module.
268\item[3.]
269  in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code
270  (see subsequent sections for a details of the XML syntax and rules).
271  For example:
272
273\begin{xmllines}
274<field_definition>
275   <field_group id="grid_T" grid_ref="grid_T_3D"> <!-- T grid -->
276   ...
277      <field id="identifier" long_name="blabla" ... />   
278      ...
279</field_definition>
280\end{xmllines}
281
282Note your definition must be added to the field\_group whose reference grid is consistent with the size of
283the array passed to iomput.
284The grid\_ref attribute refers to definitions set in iodef.xml which, in turn,
285reference grids and axes either defined in the code
286(iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file.
287\eg:
288
289\begin{xmllines}
290<grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/>
291\end{xmllines}
292
293Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step,
294add the field definition within the field\_group defined with the id "SBC":
295\xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations
296(iom\_set\_field\_attr in \mdl{iom})
297\item[4.]
298  add your field in one of the output files defined in iodef.xml
299  (again see subsequent sections for syntax and rules)
300
301\begin{xmllines}
302<file id="file1" .../>  
303...
304   <field field_ref="identifier" />   
305   ...
306</file>   
307\end{xmllines}
308
309\end{enumerate}
310
311\subsection{XML fundamentals}
312
313\subsubsection{ XML basic rules}
314
315XML tags begin with the less-than character ("$<$") and end with the greater-than character ("$>$").
316You use tags to mark the start and end of elements, which are the logical units of information in an XML document.
317In addition to marking the beginning of an element, XML start tags also provide a place to specify attributes.
318An attribute specifies a single property for an element, using a name/value pair, for example:
319\xmlcode{<a b="x" c="y" d="z"> ... </a>}.
320See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details.
321
322\subsubsection{Structure of the XML file used in NEMO}
323
324The XML file used in XIOS is structured by 7 families of tags:
325context, axis, domain, grid, field, file and variable.
326Each tag family has hierarchy of three flavors (except for context):
327
328\begin{table}
329  \scriptsize
330  \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
331    \hline
332    flavor  & description                                                                 &
333                                                                                            example                          \\
334    \hline
335    \hline
336    root    & declaration of the root element that can contain element groups or elements &
337                                                                                            \xmlcode{<file_definition ... >} \\
338    \hline
339    group   & declaration of a group element that can contain element groups or elements  &
340                                                                                            \xmlcode{<file_group      ... >} \\
341    \hline
342    element & declaration of an element that can contain elements                         &
343                                                                                            \xmlcode{<file            ... >} \\
344    \hline
345  \end{tabular*}
346\end{table}
347
348Each element may have several attributes.
349Some attributes are mandatory, other are optional but have a default value and other are completely optional.
350Id is a special attribute used to identify an element or a group of elements.
351It must be unique for a kind of element.
352It is optional, but no reference to the corresponding element can be done if it is not defined.
353
354The XML file is split into context tags that are used to isolate IO definition from
355different codes or different parts of a code.
356No interference is possible between 2 different contexts.
357Each context has its own calendar and an associated timestep.
358In \NEMO, we used the following contexts (that can be defined in any order):
359
360\begin{table}
361  \scriptsize
362  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
363    \hline
364    context         &   description                                                                &
365                                                                                                     example                              \\
366    \hline
367    \hline
368    context xios    &   context containing information for XIOS                                    &
369                                                                                                     \xmlcode{<context id="xios" ... >}   \\
370    \hline
371    context nemo    &   context containing IO information for NEMO (mother grid when using AGRIF)  & 
372                                                                                                     \xmlcode{<context id="nemo" ... >}   \\
373    \hline
374    context 1\_nemo &   context containing IO information for NEMO child grid 1 (when using AGRIF) & 
375                                                                                                     \xmlcode{<context id="1_nemo" ... >} \\
376    \hline
377    context n\_nemo &   context containing IO information for NEMO child grid n (when using AGRIF) & 
378                                                                                                     \xmlcode{<context id="n_nemo" ... >} \\
379    \hline
380  \end{tabular}
381\end{table}
382
383\noindent The xios context contains only 1 tag:
384
385\begin{table}
386  \scriptsize
387  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
388    \hline
389    context tag                                      &
390                                                       description                                      &
391                                                                                                          example                              \\
392    \hline
393    \hline
394    variable\_definition                             &
395                                                       define variables needed by XIOS.
396                                                       This can be seen as a kind of namelist for XIOS. &
397                                                                                                          \xmlcode{<variable_definition ... >} \\
398    \hline
399   \end{tabular}
400\end{table}
401
402\noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts
403(that can be defined in any order):
404
405\begin{table}
406  \scriptsize
407  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
408    \hline
409    context tag        &   description                                                               &
410                                                                                                       example                            \\
411    \hline
412    \hline
413    field\_definition  &   define all variables that can potentially be outputted                    &
414                                                                                                       \xmlcode{<field_definition ... >}  \\
415    \hline
416    file\_definition   &   define the netcdf files to be created and the variables they will contain &
417                                                                                                       \xmlcode{<file_definition ... >}   \\
418    \hline
419    axis\_definition   &   define vertical axis                                                      &
420                                                                                                       \xmlcode{<axis_definition ... >}   \\
421    \hline
422    domain\_definition &   define the horizontal grids                                               &
423                                                                                                       \xmlcode{<domain_definition ... >} \\
424    \hline
425    grid\_definition   &   define the 2D and 3D grids (association of an axis and a domain)          &
426                                                                                                       \xmlcode{<grid_definition ... >}   \\
427    \hline
428  \end{tabular}
429\end{table}
430
431\subsubsection{Nesting XML files}
432
433The XML file can be split in different parts to improve its readability and facilitate its use.
434The inclusion of XML files into the main XML file can be done through the attribute src:
435\xmlline|<context src="./nemo_def.xml" />|
436 
437\noindent In NEMO, by default, the field definition is done in 3 separate files (
438\path{cfgs/SHARED/field_def_nemo-oce.xml},
439\path{cfgs/SHARED/field_def_nemo-pisces.xml} and
440\path{cfgs/SHARED/field_def_nemo-ice.xml} ) and the  domain definition is done in another file ( \path{cfgs/SHARED/domain_def_nemo.xml} )
441that
442are included in the main iodef.xml file through the following commands:
443\begin{xmllines}
444<context id="nemo" src="./context_nemo.xml"/>
445\end{xmllines}
446
447\subsubsection{Use of inheritance}
448
449XML extensively uses the concept of inheritance.
450XML has a tree based structure with a parent-child oriented relation: all children inherit attributes from parent,
451but an attribute defined in a child replace the inherited attribute value.
452Note that the special attribute ''id'' is never inherited.
453\\
454\\
455example 1: Direct inheritance.
456
457\begin{xmllines}
458<field_definition operation="average" >
459   <field id="sst"                    />   <!-- averaged      sst -->
460   <field id="sss" operation="instant"/>   <!-- instantaneous sss -->
461</field_definition>
462\end{xmllines}
463
464The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average'' of
465the attribute ''operation'' from its parent.
466Note that a child can overwrite the attribute definition inherited from its parents.
467In the example above, the field ''sss'' will for example output instantaneous values instead of average values.
468\\
469\\
470example 2: Inheritance by reference.
471
472\begin{xmllines}
473<field_definition>
474   <field id="sst" long_name="sea surface temperature" />
475   <field id="sss" long_name="sea surface salinity"    />
476</field_definition>
477<file_definition>
478   <file id="myfile" output_freq="1d" />   
479      <field field_ref="sst"                            />  <!-- default def -->
480      <field field_ref="sss" long_name="my description" />  <!-- overwrite   -->
481   </file>
482</file_definition>
483\end{xmllines}
484
485Inherit (and overwrite, if needed) the attributes of a tag you are refering to.
486
487\subsubsection{Use of groups}
488
489Groups can be used for 2 purposes.
490Firstly, the group can be used to define common attributes to be shared by the elements of
491the group through inheritance.
492In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''.
493Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''.
494
495\begin{xmllines}
496<field_group id="grid_T" grid_ref="grid_T_2D">
497   <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/>
498   <field id="sst"  long_name="sea surface temperature" unit="degC"                     />
499   <field id="sss"  long_name="sea surface salinity"    unit="psu"                      />
500   <field id="ssh"  long_name="sea surface height"      unit="m"                        />
501   ...
502\end{xmllines}
503
504Secondly, the group can be used to replace a list of elements.
505Several examples of groups of fields are proposed at the end of the XML field files (
506\path{cfgs/SHARED/field_def_nemo-oce.xml},
507\path{cfgs/SHARED/field_def_nemo-pisces.xml} and
508\path{cfgs/SHARED/field_def_nemo-ice.xml} ) .
509For example, a short list of the usual variables related to the U grid:
510
511\begin{xmllines}
512<field_group id="groupU" >
513   <field field_ref="uoce"  />
514   <field field_ref="ssu" />
515   <field field_ref="utau"  />
516</field_group>
517\end{xmllines}
518
519that can be directly included in a file through the following syntax:
520
521\begin{xmllines}
522<file id="myfile_U" output_freq="1d" />
523   <field_group group_ref="groupU" />
524   <field field_ref="uocetr_eff"   />  <!-- add another field -->
525</file>   
526\end{xmllines}
527
528\subsection{Detailed functionalities}
529
530The file \path{NEMOGCM/CONFIG/ORCA2_LIM/iodef_demo.xml} provides several examples of the use of
531the new functionalities offered by the XML interface of XIOS.
532
533\subsubsection{Define horizontal subdomains}
534
535Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of
536the tag family domain.
537It must therefore be done in the domain part of the XML file.
538For example, in \path{cfgs/SHARED/domain_def.xml}, we provide the following example of a definition of
539a 5 by 5 box with the bottom left corner at point (10,10).
540
541\begin{xmllines}
542<domain id="myzoomT" domain_ref="grid_T">
543   <zoom_domain ibegin="10" jbegin="10" ni="5" nj="5" />
544\end{xmllines}
545
546The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field.
547For example:
548
549\begin{xmllines}
550<file id="myfile_vzoom" output_freq="1d" >
551   <field field_ref="toce" domain_ref="myzoomT"/>
552</file>
553\end{xmllines}
554
555Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain.
556The Equatorial section, the TAO, RAMA and PIRATA moorings are already registered in the code and
557can therefore be outputted without taking care of their (i,j) position in the grid.
558These predefined domains can be activated by the use of specific domain\_ref:
559''EqT'', ''EqU'' or ''EqW'' for the equatorial sections and
560the mooring position for TAO, RAMA and PIRATA followed by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...)
561
562\begin{xmllines}
563<file id="myfile_vzoom" output_freq="1d" >
564   <field field_ref="toce" domain_ref="0n180wT"/>
565</file>
566\end{xmllines}
567
568Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if
569you use the ''multiple\_file'' type for your output files,
570you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat,
571\href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}).
572We are therefore advising to use the ''one\_file'' type in this case.
573
574\subsubsection{Define vertical zooms}
575
576Vertical zooms are defined through the attributs zoom\_begin and zoom\_n of the tag family axis.
577It must therefore be done in the axis part of the XML file.
578For example, in \path{cfgs/ORCA2_ICE_PISCES/EXPREF/iodef_demo.xml}, we provide the following example:
579
580\begin{xmllines}
581<axis_definition>
582   <axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" />
583   <axis id="deptht_zoom" azix_ref="deptht" >
584      <zoom_axis zoom_begin="1" zoom_n="10" />
585   </axis>
586\end{xmllines}
587
588The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field.
589For example:
590
591\begin{xmllines}
592<file id="myfile_hzoom" output_freq="1d" >
593   <field field_ref="toce" axis_ref="deptht_myzoom"/>
594</file>
595\end{xmllines}
596
597\subsubsection{Control of the output file names}
598
599The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file.
600For example:
601
602\begin{xmllines}
603<file_group id="1d" output_freq="1d" name="myfile_1d" >
604   <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA"  -->
605      ...
606   </file>
607   <file id="myfileB" name_suffix="_BBB" > <!-- will create file "myfile_1d_BBB" -->
608      ...
609   </file>
610</file_group>
611\end{xmllines}
612
613However it is often very convienent to define the file name with the name of the experiment,
614the output file frequency and the date of the beginning and the end of the simulation
615(which are informations stored either in the namelist or in the XML file).
616To do so, we added the following rule:
617if the id of the tag file is ''fileN'' (where N = 1 to 999 on 1 to 3 digits) or
618one of the predefined sections or moorings (see next subsection),
619the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by:
620
621\begin{table}
622  \scriptsize
623  \begin{tabularx}{\textwidth}{|lX|}
624    \hline
625    \centering placeholder string &
626    automatically replaced by                          \\
627    \hline
628    \hline
629    \centering @expname@          &
630    the experiment name (from cn\_exp in the namelist) \\
631    \hline
632    \centering @freq@             &
633    output frequency (from attribute output\_freq)     \\
634    \hline
635    \centering @startdate@        &
636    starting date of the simulation (from nn\_date0 in the restart or the namelist).
637    \newline
638    \verb?yyyymmdd?          format                   \\
639    \hline
640    \centering @startdatefull@    &
641    starting date of the simulation (from nn\_date0 in the restart or the namelist).
642    \newline
643    \verb?yyyymmdd_hh:mm:ss? format                    \\
644    \hline
645    \centering @enddate@          &
646    ending date of the simulation   (from nn\_date0 and nn\_itend  in the namelist).
647    \newline
648    \verb?yyyymmdd?          format                    \\
649    \hline
650    \centering @enddatefull@      &
651    ending date of the simulation   (from nn\_date0 and nn\_itend  in the namelist).
652    \newline
653    \verb?yyyymmdd_hh:mm:ss? format                    \\
654    \hline
655  \end{tabularx}
656\end{table}
657
658\noindent For example,
659\xmlline|<file id="myfile_hzoom" name="myfile_@expname@_@startdate@_freq@freq@" output_freq="1d" >|
660
661\noindent with the namelist:
662\begin{forlines}
663cn_exp    = "ORCA2"
664nn_date0  = 19891231
665ln_rstart = .false.
666\end{forlines}
667
668\noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d}
669
670\subsubsection{Other controls of the XML attributes from NEMO}
671
672The values of some attributes are defined by subroutine calls within NEMO
673(calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in \mdl{iom}).
674Any definition given in the XML file will be overwritten.
675By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the XML file
676(but this is not necessary).
677\\
678
679Here is the list of these attributes:
680\\
681
682\begin{table}
683  \scriptsize
684  \begin{tabularx}{\textwidth}{|X|c|c|c|}
685    \hline
686    tag ids affected by automatic definition of some of their attributes &
687    name attribute                                                       &
688    attribute value                      \\
689    \hline
690    \hline
691    field\_definition                                                    &
692    freq\_op                                                             &
693    \np{rn\_rdt}                         \\
694    \hline
695    SBC                                                                  &
696    freq\_op                                                             &
697    \np{rn\_rdt} $\times$ \np{nn\_fsbc}  \\
698    \hline
699    ptrc\_T                                                              &
700    freq\_op                                                             &
701    \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\
702    \hline
703    diad\_T                                                              &
704    freq\_op                                                             &
705    \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\
706    \hline
707    EqT, EqU, EqW                                                        &
708    jbegin, ni,                                                          &
709    according to the grid                \\
710    &
711    name\_suffix                                                         &
712    \\
713    \hline
714    TAO, RAMA and PIRATA moorings                                        &
715    zoom\_ibegin, zoom\_jbegin,                                          &
716    according to the grid                \\
717    &
718    name\_suffix                                                         &
719    \\
720    \hline
721  \end{tabularx}
722\end{table}
723
724\subsubsection{Advanced use of XIOS functionalities}
725
726\subsection{XML reference tables}
727\label{subsec:IOM_xmlref}
728
729\begin{enumerate}
730\item
731  Simple computation: directly define the computation when refering to the variable in the file definition.
732
733\begin{xmllines}
734<field field_ref="sst"  name="tosK"  unit="degK" > sst + 273.15 </field>
735<field field_ref="taum" name="taum2" unit="N2/m4" long_name="square of wind stress module" > taum * taum </field>
736<field field_ref="qt"   name="stupid_check" > qt - qsr - qns </field>
737\end{xmllines}
738
739\item
740  Simple computation: define a new variable and use it in the file definition.
741
742in field\_definition:
743
744\begin{xmllines}
745<field id="sst2" long_name="square of sea surface temperature" unit="degC2" >  sst * sst </field >
746\end{xmllines}
747
748in file\_definition:
749
750\begin{xmllines}
751<field field_ref="sst2" > sst2 </field>
752\end{xmllines}
753
754Note that in this case, the following syntaxe \xmlcode{<field field_ref="sst2" />} is not working as
755sst2 won't be evaluated.
756
757\item
758  Change of variable precision:
759
760\begin{xmllines}
761<!-- force to keep real 8 -->
762<field field_ref="sst" name="tos_r8" prec="8" />
763<!-- integer 2  with add_offset and scale_factor attributes -->
764<field field_ref="sss" name="sos_i2" prec="2" add_offset="20." scale_factor="1.e-3" />
765\end{xmllines}
766
767Note that, then the code is crashing, writting real4 variables forces a numerical conversion from
768real8 to real4 which will create an internal error in NetCDF and will avoid the creation of the output files.
769Forcing double precision outputs with prec="8" (for example in the field\_definition) will avoid this problem.
770
771\item
772  add user defined attributes:
773
774\begin{xmllines}
775<file_group id="1d" output_freq="1d" output_level="10" enabled=".true."> <!-- 1d files -->
776   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
777      <field field_ref="sst" name="tos" >
778         <variable id="my_attribute1" type="string"  > blabla </variable>
779         <variable id="my_attribute2" type="integer" > 3      </variable>
780         <variable id="my_attribute3" type="float"   > 5.0    </variable>
781      </field>
782      <variable id="my_global_attribute" type="string" > blabla_global </variable>
783   </file>
784</file_group>
785\end{xmllines}
786
787\item
788  use of the ``@'' function: example 1, weighted temporal average
789
790 - define a new variable in field\_definition
791
792\begin{xmllines}
793<field id="toce_e3t" long_name="temperature * e3t" unit="degC*m" grid_ref="grid_T_3D" >toce * e3t</field>
794\end{xmllines}
795
796 - use it when defining your file.
797
798\begin{xmllines}
799<file_group id="5d" output_freq="5d"  output_level="10" enabled=".true." >  <!-- 5d files --> 
800   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
801      <field field_ref="toce" operation="instant" freq_op="5d" > @toce_e3t / @e3t </field>
802   </file>
803</file_group>
804\end{xmllines}
805
806The freq\_op="5d" attribute is used to define the operation frequency of the ``@'' function: here 5 day.
807The temporal operation done by the ``@'' is the one defined in the field definition:
808here we use the default, average.
809So, in the above case, @toce\_e3t will do the 5-day mean of toce*e3t.
810Operation="instant" refers to the temporal operation to be performed on the field''@toce\_e3t / @e3t'':
811here the temporal average is alreday done by the ``@'' function so we just use instant to do the ratio of
812the 2 mean values.
813field\_ref="toce" means that attributes not explicitely defined, are inherited from toce field.
814Note that in this case, freq\_op must be equal to the file output\_freq.
815
816\item
817  use of the ``@'' function: example 2, monthly SSH standard deviation
818
819 - define a new variable in field\_definition
820
821\begin{xmllines}
822<field id="ssh2" long_name="square of sea surface temperature" unit="degC2" > ssh * ssh </field >
823\end{xmllines}
824
825 - use it when defining your file.
826
827\begin{xmllines}
828<file_group id="1m" output_freq="1m"  output_level="10" enabled=".true." >  <!-- 1m files --> 
829   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
830      <field field_ref="ssh" name="sshstd" long_name="sea_surface_temperature_standard_deviation"
831      operation="instant" freq_op="1m" >
832         sqrt( @ssh2 - @ssh * @ssh )
833      </field>
834   </file>
835</file_group>
836\end{xmllines}
837
838The freq\_op="1m" attribute is used to define the operation frequency of the ``@'' function: here 1 month.
839The temporal operation done by the ``@'' is the one defined in the field definition:
840here we use the default, average.
841So, in the above case, @ssh2 will do the monthly mean of ssh*ssh.
842Operation="instant" refers to the temporal operation to be performed on the field ''sqrt( @ssh2 - @ssh * @ssh )'':
843here the temporal average is alreday done by the ``@'' function so we just use instant.
844field\_ref="ssh" means that attributes not explicitely defined, are inherited from ssh field.
845Note that in this case, freq\_op must be equal to the file output\_freq.
846
847\item
848  use of the ``@'' function: example 3, monthly average of SST diurnal cycle
849
850 - define 2 new variables in field\_definition
851
852\begin{xmllines}
853<field id="sstmax" field_ref="sst" long_name="max of sea surface temperature" operation="maximum" />
854<field id="sstmin" field_ref="sst" long_name="min of sea surface temperature" operation="minimum" />
855\end{xmllines}
856
857 - use these 2 new variables when defining your file.
858
859\begin{xmllines}
860<file_group id="1m" output_freq="1m"  output_level="10" enabled=".true." >  <!-- 1m files --> 
861   <file id="file1" name_suffix="_grid_T" description="ocean T grid variables" >
862      <field field_ref="sst" name="sstdcy" long_name="amplitude of sst diurnal cycle" operation="average" freq_op="1d" >
863         @sstmax - @sstmin
864      </field>
865   </file>
866</file_group>
867\end{xmllines}
868
869\end{enumerate}
870
871The freq\_op="1d" attribute is used to define the operation frequency of the ``@'' function: here 1 day.
872The temporal operation done by the ``@'' is the one defined in the field definition:
873here maximum for sstmax and minimum for sstmin.
874So, in the above case, @sstmax will do the daily max and @sstmin the daily min.
875Operation="average" refers to the temporal operation to be performed on the field ``@sstmax - @sstmin'':
876here monthly mean (of daily max - daily min of the sst).
877field\_ref="sst" means that attributes not explicitely defined, are inherited from sst field.
878
879\subsubsection{Tag list per family}
880
881\begin{table}
882  \scriptsize
883  \begin{tabularx}{\textwidth}{|l|X|X|l|X|}
884    \hline
885    tag name                                                                                     &
886    description                                                                                  &
887    accepted attribute                                                                           &
888    child of                                                                                     &
889    parent of                       \\
890    \hline
891    \hline
892    simulation                                                                                   &
893    this tag is the root tag which encapsulates all the content of the XML file                  &
894    none                                                                                         &
895    none                                                                                         &
896    context                         \\
897    \hline
898    context                                                                                      &
899    encapsulates parts of the XML file dedicated to different codes or different parts of a code &
900    id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin             &
901    simulation                                                                                   &
902    all root tags: ... \_definition \\
903    \hline
904  \end{tabularx}
905  \caption{Context tags}
906\end{table}
907
908\begin{table}
909  \scriptsize
910  \begin{tabularx}{\textwidth}{|l|X|X|X|l|}
911    \hline
912    tag name                                                                                &
913    description                                                                             &
914    accepted attribute                                                                      &
915    child of                                                                                &
916    parent of             \\
917    \hline
918    \hline
919    field\_definition                                                                       &
920    encapsulates the definition of all the fields that can potentially be outputted         &
921    axis\_ref, default\_value, domain\_ref, enabled, grid\_ref, level, operation, prec, src &
922    context                                                                                 &
923    field or field\_group \\
924    \hline
925    field\_group                                                                            &
926    encapsulates a group of fields                                                          &
927    axis\_ref, default\_value, domain\_ref, enabled, group\_ref, grid\_ref,
928    id, level, operation, prec, src                                                         &
929    field\_definition, field\_group, file                                                   &
930    field or field\_group \\
931    \hline
932    field                                                                                   &
933    define a specific field                                                                 &
934    axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref,
935    id, level, long\_name, name, operation, prec, standard\_name, unit                      &
936    field\_definition, field\_group, file                                                   &
937    none                  \\
938    \hline
939  \end{tabularx}
940  \caption{Field tags ("\ttfamily{field\_*}")}
941\end{table}
942
943\begin{table}
944  \scriptsize
945  \begin{tabularx}{\textwidth}{|l|X|X|X|l|}
946    \hline
947    tag name                                                            &
948    description                                                         &
949    accepted attribute                                                  &
950    child of                                                            &
951    parent of           \\
952    \hline
953    \hline
954    file\_definition                                                    &
955    encapsulates the definition of all the files that will be outputted &
956    enabled, min\_digits, name, name\_suffix, output\_level,
957    split\_freq\_format, split\_freq, sync\_freq, type, src             &
958    context                                                             &
959    file or file\_group \\
960    \hline
961    file\_group                                                         &
962    encapsulates a group of files that will be outputted                &
963    enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level,
964    split\_freq\_format, split\_freq, sync\_freq, type, src             &
965    file\_definition, file\_group                                       &
966    file or file\_group \\
967    \hline
968    file                                                                &
969    define the contents of a file to be outputted                       &
970    enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level,
971    split\_freq\_format, split\_freq, sync\_freq, type, src             &
972    file\_definition, file\_group                                       &
973    field               \\
974    \hline
975  \end{tabularx}
976  \caption{File tags ("\ttfamily{file\_*}")}
977\end{table}
978
979\begin{table}
980  \scriptsize
981  \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
982    \hline
983    tag name                                                                               &
984    description                                                                            &
985    accepted attribute                                                                     &
986    child of                                                                               &
987    parent of         \\
988    \hline
989    \hline
990    axis\_definition                                                                       &
991    define all the vertical axis potentially used by the variables                         &
992    src                                                                                    &
993    context                                                                                &
994    axis\_group, axis \\
995    \hline
996    axis\_group                                                                            &
997    encapsulates a group of vertical axis                                                  &
998    id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
999    axis\_definition, axis\_group                                                          &
1000    axis\_group, axis \\
1001    \hline
1002    axis                                                                                   &
1003    define a vertical axis                                                                 &
1004    id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size &
1005    axis\_definition, axis\_group                                                          &
1006    none             \\
1007    \hline
1008  \end{tabularx}
1009  \caption{Axis tags ("\ttfamily{axis\_*}")}
1010\end{table}
1011
1012\begin{table}
1013  \scriptsize
1014  \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
1015    \hline
1016    tag name                                                            &
1017    description                                                         &
1018    accepted attribute                                                  &
1019    child of                                                            &
1020    parent of               \\
1021    \hline
1022    \hline
1023    domain\_\-definition                                                &
1024    define all the horizontal domains potentially used by the variables &
1025    src                                                                 &
1026    context                                                             &
1027    domain\_\-group, domain \\
1028    \hline
1029    domain\_group                                                       &
1030    encapsulates a group of horizontal domains                          &
1031    id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj  &
1032    domain\_\-definition, domain\_group                                 &
1033    domain\_\-group, domain \\
1034    \hline
1035    domain                                                              &
1036    define an horizontal domain                                         &
1037    id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj  &
1038    domain\_\-definition, domain\_group                                 &
1039    none                    \\
1040    \hline
1041  \end{tabularx}
1042  \caption{Domain tags ("\ttfamily{domain\_*)}"}
1043\end{table}
1044
1045\begin{table}
1046  \scriptsize
1047  \begin{tabularx}{\textwidth}{|l|X|X|X|X|}
1048    \hline
1049    tag name                                                                                     &
1050    description                                                                                  &
1051    accepted attribute                                                                           &
1052    child of                                                                                     &
1053    parent of                       \\
1054    \hline
1055    \hline
1056    grid\_definition                                                                               &
1057    define all the grid (association of a domain and/or an axis) potentially used by the variables &
1058    src                                                                                            &
1059    context                                                                                        &
1060    grid\_group, grid   \\
1061    \hline
1062    grid\_group                                                                                    &
1063    encapsulates a group of grids                                                                  &
1064    id, domain\_ref,axis\_ref                                                                      &
1065    grid\_definition, grid\_group                                                                  &
1066    grid\_group, grid   \\
1067    \hline
1068    grid                                                                                           &
1069    define a grid                                                                                  &
1070    id, domain\_ref,axis\_ref                                                                      &
1071    grid\_definition, grid\_group                                                                  &
1072    none                \\
1073    \hline
1074  \end{tabularx}
1075  \caption{Grid tags ("\ttfamily{grid\_*}")}
1076\end{table}
1077
1078\subsubsection{Attributes list per family}
1079
1080\begin{table}
1081  \scriptsize
1082  \begin{tabularx}{\textwidth}{|l|X|l|l|}
1083    \hline
1084    attribute name                           &
1085    description                              &
1086    example                                  &
1087    accepted by            \\
1088    \hline
1089    \hline
1090    axis\_ref                                &
1091    refers to the id of a vertical axis      &
1092    axis\_ref="deptht"                       &
1093    field, grid families   \\
1094    \hline
1095    domain\_ref                              &
1096    refers to the id of a domain             &
1097    domain\_ref="grid\_T"                    &
1098    field or grid families \\
1099    \hline
1100    field\_ref                               &
1101    id of the field we want to add in a file &
1102    field\_ref="toce"                        &
1103    field                  \\
1104    \hline
1105    grid\_ref                                &
1106    refers to the id of a grid               &
1107    grid\_ref="grid\_T\_2D"                  &
1108    field family           \\
1109    \hline
1110    group\_ref                               &
1111    refer to a group of variables            &
1112    group\_ref="mooring"                     &
1113    field\_group           \\
1114    \hline
1115  \end{tabularx}
1116  \caption{Reference attributes ("\ttfamily{*\_ref}")}
1117\end{table}
1118
1119\begin{table}
1120  \scriptsize
1121  \begin{tabularx}{\textwidth}{|l|X|l|l|}
1122    \hline
1123    attribute name                                     &
1124    description                                        &
1125    example                                            &
1126    accepted by   \\
1127    \hline
1128    \hline
1129    zoom\_ibegin                                       &
1130    starting point along x direction of the zoom.
1131    Automatically defined for TAO/RAMA/PIRATA moorings &
1132    zoom\_ibegin="1"                                   &
1133    domain family \\
1134    \hline
1135    zoom\_jbegin                                       &
1136    starting point along y direction of the zoom.
1137    Automatically defined for TAO/RAMA/PIRATA moorings &
1138    zoom\_jbegin="1"                                   &
1139    domain family \\
1140    \hline
1141    zoom\_ni                                           &
1142    zoom extent along x direction                      &
1143    zoom\_ni="1"                                       &
1144    domain family \\
1145    \hline
1146    zoom\_nj                                           &
1147    zoom extent along y direction                      &
1148    zoom\_nj="1"                                       &
1149    domain family \\
1150    \hline
1151  \end{tabularx}
1152  \caption{Domain attributes ("\ttfamily{zoom\_*}")}
1153\end{table}
1154
1155\begin{table}
1156  \scriptsize
1157  \begin{tabularx}{\textwidth}{|l|X|l|l|}
1158    \hline
1159    attribute name                                                                                       &
1160    description                                                                                          &
1161    example                                                                                              &
1162    accepted by                            \\
1163    \hline
1164    \hline
1165    min\_digits                                                                                          &
1166    specify the minimum of digits used in the core number in the name of the NetCDF file                 &
1167    min\_digits="4"                                                                                      &
1168    file family                            \\
1169    \hline
1170    name\_suffix                                                                                         &
1171    suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file &
1172    name\_suffix="\_myzoom"                                                                              &
1173    file family                            \\
1174    \hline
1175    output\_level                                                                                        &
1176    output priority of variables in a file: 0 (high) to 10 (low).
1177    All variables listed in the file with a level smaller or equal to output\_level will be output.
1178    Other variables won't be output even if they are listed in the file.                                 &
1179    output\_level="10"                                                                                   &
1180    file family                            \\
1181    \hline
1182    split\_freq                                                                                          &
1183    frequency at which to temporally split output files.
1184    Units can be ts (timestep), y, mo, d, h, mi, s.
1185    Useful for long runs to prevent over-sized output files.                                             &
1186    split\_freq="1mo"                                                                                    &
1187    file family                            \\
1188    \hline
1189    split\_freq\-\_format                                                                                &
1190    date format used in the name of temporally split output files.
1191    Can be specified using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s                      &
1192    split\_freq\_format= "\%y\%mo\%d"                                                                    &
1193    file family                            \\
1194    \hline
1195    sync\_freq                                                                                           &
1196    NetCDF file synchronization frequency (update of the time\_counter).
1197    Units can be ts (timestep), y, mo, d, h, mi, s.                                                      &
1198    sync\_freq="10d"                                                                                     &
1199    file family                            \\
1200    \hline
1201    type (1)                                                                                             &
1202    specify if the output files are to be split spatially (multiple\_file) or not (one\_file)            &
1203    type="multiple\_file"                                                                                &
1204    file familly                           \\
1205    \hline
1206  \end{tabularx}
1207  \caption{File attributes}
1208\end{table}
1209
1210\begin{table}
1211  \scriptsize
1212  \begin{tabularx}{\textwidth}{|l|X|l|l|}
1213    \hline
1214    attribute name                                                                                       &
1215    description                                                                                          &
1216    example                                                                                              &
1217    accepted by                            \\
1218    \hline
1219    \hline
1220    default\_value                                                                                       &
1221    missing\_value definition                                                                            &
1222    default\_value="1.e20"                                                                               &
1223    field family                           \\
1224    \hline
1225    level                                                                                                &
1226    output priority of a field: 0 (high) to 10 (low)                                                     &
1227    level="1"                                                                                            &
1228    field family                           \\
1229    \hline
1230    operation                                                                                            &
1231    type of temporal operation: average, accumulate, instantaneous, min, max and once                    &
1232    operation="average"                                                                                  &
1233    field family                           \\
1234    \hline
1235    output\_freq                                                                                         &
1236    operation frequency. units can be ts (timestep), y, mo, d, h, mi, s.                                 &
1237    output\_freq="1d12h"                                                                                 &
1238    field family                           \\
1239    \hline
1240    prec                                                                                                 &
1241    output precision: real 4 or real 8                                                                   &
1242    prec="4"                                                                                             &
1243    field family                           \\
1244    \hline
1245    long\_name                                                                                           &
1246    define the long\_name attribute in the NetCDF file                                                   &
1247    long\_name="Vertical T levels"                                                                       &
1248    field                                  \\
1249    \hline
1250    standard\_name                                                                                       &
1251    define the standard\_name attribute in the NetCDF file                                               &
1252    standard\_name= "Eastward\_Sea\_Ice\_Transport"                                                      &
1253    field                                  \\
1254    \hline
1255  \end{tabularx}
1256  \caption{Field attributes}
1257\end{table}
1258
1259\begin{table}
1260  \scriptsize
1261  \begin{tabularx}{\textwidth}{|l|X|X|X|}
1262    \hline
1263    attribute name                                                                                       &
1264    description                                                                                          &
1265    example                                                                                              &
1266    accepted by                            \\
1267    \hline
1268    \hline
1269    enabled                                                                                              &
1270    switch on/off the output of a field or a file                                                        &
1271    enabled=".true."                                                                                     &
1272    field, file families                   \\
1273    \hline
1274    description                                                                                          &
1275    just for information, not used                                                                       &
1276    description="ocean T grid variables"                                                                 &
1277    all tags                               \\
1278    \hline
1279    id                                                                                                   &
1280    allow to identify a tag                                                                              &
1281    id="nemo"                                                                                            &
1282    accepted by all tags except simulation \\
1283    \hline
1284    name                                                                                                 &
1285    name of a variable or a file. If the name of a file is undefined, its id is used as a name           &
1286    name="tos"                                                                                           &
1287    field or file families                 \\
1288    \hline
1289    positive                                                                                             &
1290    convention used for the orientation of vertival axis (positive downward in \NEMO).                   &
1291    positive="down"                                                                                      &
1292    axis family                            \\
1293    \hline
1294    src                                                                                                  &
1295    allow to include a file                                                                              &
1296    src="./field\_def.xml"                                                                               &
1297    accepted by all tags except simulation \\
1298    \hline
1299    time\_origin                                                                                         &
1300    specify the origin of the time counter                                                               &
1301    time\_origin="1900-01-01 00:00:00"                                                                   &
1302    context                                \\
1303    \hline
1304    type (2)                                                                                             &
1305    define the type of a variable tag                                                                    &
1306    type="boolean"                                                                                       &
1307    variable                               \\
1308    \hline
1309    unit                                                                                                 &
1310    unit of a variable or the vertical axis                                                              &
1311    unit="m"                                                                                             &
1312    field and axis families                \\
1313    \hline
1314  \end{tabularx}
1315  \caption{Miscellaneous attributes}
1316\end{table}
1317
1318\subsection{CF metadata standard compliance}
1319
1320Output from the XIOS IO server is compliant with
1321\href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of
1322the CF metadata standard.
1323Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of
1324section \autoref{subsec:IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard.
1325
1326Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by
1327the namelist parameter \np{ln\_cfmeta} in the \ngn{namrun} namelist.
1328This must be set to true if these metadata are to be included in the output files.
1329
1330
1331% ================================================================
1332%       NetCDF4 support
1333% ================================================================
1334\section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})]
1335{NetCDF4 support (\protect\key{netcdf4})}
1336\label{sec:DIA_nc4}
1337
1338Since version 3.3, support for NetCDF4 chunking and (loss-less) compression has been included.
1339These options build on the standard NetCDF output and allow the user control over the size of the chunks via
1340namelist settings.
1341Chunking and compression can lead to significant reductions in file sizes for a small runtime overhead.
1342For a fuller discussion on chunking and other performance issues the reader is referred to
1343the NetCDF4 documentation found \href{https://www.unidata.ucar.edu/software/netcdf/docs/netcdf_perf_chunking.html}{here}.
1344
1345The new features are only available when the code has been linked with a NetCDF4 library
1346(version 4.1 onwards, recommended) which has been built with HDF5 support (version 1.8.4 onwards, recommended).
1347Datasets created with chunking and compression are not backwards compatible with NetCDF3 "classic" format but
1348most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files.
1349NEMO executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by
1350setting the \np{ln\_nc4zip} logical to false in the \textit{namnc4} namelist:
1351
1352%------------------------------------------namnc4----------------------------------------------------
1353
1354\nlst{namnc4}
1355%-------------------------------------------------------------------------------------------------------------
1356
1357If \key{netcdf4} has not been defined, these namelist parameters are not read.
1358In this case, \np{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined.
1359These functions will not be used but need to be included so that compilation is possible with NetCDF3 libraries.
1360
1361When using NetCDF4 libraries, \key{netcdf4} should be defined even if the intention is to
1362create only NetCDF3-compatible files.
1363This is necessary to avoid duplication between the dummy routines and the actual routines present in the library.
1364Most compilers will fail at compile time when faced with such duplication.
1365Thus when linking with NetCDF4 libraries the user must define \key{netcdf4} and
1366control the type of NetCDF file produced via the namelist parameter.
1367
1368Chunking and compression is applied only to 4D fields and
1369there is no advantage in chunking across more than one time dimension since
1370previously written chunks would have to be read back and decompressed before being added to.
1371Therefore, user control over chunk sizes is provided only for the three space dimensions.
1372The user sets an approximate number of chunks along each spatial axis.
1373The actual size of the chunks will depend on global domain size for mono-processors or, more likely,
1374the local processor domain size for distributed processing.
1375The derived values are subject to practical minimum values (to avoid wastefully small chunk sizes) and
1376cannot be greater than the domain size in any dimension.
1377The algorithm used is:
1378
1379\begin{forlines}
1380ichunksz(1) = MIN(idomain_size, MAX((idomain_size-1) / nn_nchunks_i + 1 ,16 ))
1381ichunksz(2) = MIN(jdomain_size, MAX((jdomain_size-1) / nn_nchunks_j + 1 ,16 ))
1382ichunksz(3) = MIN(kdomain_size, MAX((kdomain_size-1) / nn_nchunks_k + 1 , 1 ))
1383ichunksz(4) = 1
1384\end{forlines}
1385
1386\noindent As an example, setting:
1387
1388\begin{forlines}
1389nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31
1390\end{forlines}
1391
1392\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\ttfamily 46x38x1} respectively in
1393the mono-processor case (\ie global domain of {\small\ttfamily 182x149x31}).
1394An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in
1395table \autoref{tab:NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with
1396a 4x2 mpi partitioning.
1397Note the variation in the compression ratio achieved which reflects chiefly the dry to wet volume ratio of
1398each processing region.
1399
1400%------------------------------------------TABLE----------------------------------------------------
1401\begin{table}
1402  \scriptsize
1403  \centering
1404  \begin{tabular}{lrrr}
1405    Filename                    & NetCDF3 & NetCDF4  & Reduction \\
1406                                & filesize   & filesize & \%        \\
1407                                & (KB)    & (KB)     &           \\
1408    ORCA2\_restart\_0000.nc     & 16420   & 8860     & 47\%      \\
1409    ORCA2\_restart\_0001.nc     & 16064   & 11456    & 29\%      \\
1410    ORCA2\_restart\_0002.nc     & 16064      & 9744     & 40\%      \\
1411    ORCA2\_restart\_0003.nc     & 16420      & 9404     & 43\%      \\
1412    ORCA2\_restart\_0004.nc     & 16200   & 5844     & 64\%      \\
1413    ORCA2\_restart\_0005.nc     & 15848   & 8172     & 49\%      \\
1414    ORCA2\_restart\_0006.nc     & 15848   & 8012     & 50\%      \\
1415    ORCA2\_restart\_0007.nc     & 16200   & 5148     & 69\%      \\
1416    ORCA2\_2d\_grid\_T\_0000.nc & 2200       & 1504     & 32\%      \\
1417    ORCA2\_2d\_grid\_T\_0001.nc & 2200       & 1748     & 21\%      \\
1418    ORCA2\_2d\_grid\_T\_0002.nc & 2200       & 1592     & 28\%      \\
1419    ORCA2\_2d\_grid\_T\_0003.nc & 2200       & 1540     & 30\%      \\
1420    ORCA2\_2d\_grid\_T\_0004.nc & 2200       & 1204     & 46\%      \\
1421    ORCA2\_2d\_grid\_T\_0005.nc & 2200       & 1444     & 35\%      \\
1422    ORCA2\_2d\_grid\_T\_0006.nc & 2200       & 1428     & 36\%      \\
1423    ORCA2\_2d\_grid\_T\_0007.nc & 2200    & 1148     & 48\%      \\
1424    ...                         & ...     & ...      & ...       \\
1425    ORCA2\_2d\_grid\_W\_0000.nc & 4416    & 2240     & 50\%      \\
1426    ORCA2\_2d\_grid\_W\_0001.nc & 4416    & 2924     & 34\%      \\
1427    ORCA2\_2d\_grid\_W\_0002.nc & 4416    & 2512     & 44\%      \\
1428    ORCA2\_2d\_grid\_W\_0003.nc & 4416    & 2368     & 47\%      \\
1429    ORCA2\_2d\_grid\_W\_0004.nc & 4416    & 1432     & 68\%      \\
1430    ORCA2\_2d\_grid\_W\_0005.nc & 4416    & 1972     & 56\%      \\
1431    ORCA2\_2d\_grid\_W\_0006.nc & 4416    & 2028     & 55\%      \\
1432    ORCA2\_2d\_grid\_W\_0007.nc & 4416    & 1368     & 70\%      \\
1433  \end{tabular}
1434  \caption{
1435    \protect\label{tab:NC4}
1436    Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression
1437  }
1438\end{table}
1439%----------------------------------------------------------------------------------------------------
1440
1441When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via
1442\np{iom\_put} calls are set via an equivalent and identically named namelist to \textit{namnc4} in
1443\np{xmlio\_server.def}.
1444Typically this namelist serves the mean files whilst the \ngn{ namnc4} in the main namelist file continues to
1445serve the restart files.
1446This duplication is unfortunate but appropriate since, if using io\_servers, the domain sizes of
1447the individual files produced by the io\_server processes may be different to those produced by
1448the invidual processing regions and different chunking choices may be desired.
1449 
1450% -------------------------------------------------------------------------------------------------------------
1451%       Tracer/Dynamics Trends
1452% -------------------------------------------------------------------------------------------------------------
1453\section[Tracer/Dynamics trends (\texttt{namtrd})]
1454{Tracer/Dynamics trends (\protect\ngn{namtrd})}
1455\label{sec:DIA_trd}
1456
1457%------------------------------------------namtrd----------------------------------------------------
1458
1459\nlst{namtrd} 
1460%-------------------------------------------------------------------------------------------------------------
1461
1462Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to
1463\mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation
1464(\ie at the end of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines).
1465This capability is controlled by options offered in \ngn{namtrd} namelist.
1466Note that the output are done with XIOS, and therefore the \key{iomput} is required.
1467
1468What is done depends on the \ngn{namtrd} logical set to \forcode{.true.}:
1469
1470\begin{description}
1471\item[\np{ln\_glo\_trd}]:
1472  at each \np{nn\_trd} time-step a check of the basin averaged properties of
1473  the momentum and tracer equations is performed.
1474  This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$,
1475  and potential energy time evolution equations properties;
1476\item[\np{ln\_dyn\_trd}]:
1477  each 3D trend of the evolution of the two momentum components is output;
1478\item[\np{ln\_dyn\_mxl}]:
1479  each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output;
1480\item[\np{ln\_vor\_trd}]:
1481  a vertical summation of the moment tendencies is performed,
1482  then the curl is computed to obtain the barotropic vorticity tendencies which are output;
1483\item[\np{ln\_KE\_trd}] :
1484  each 3D trend of the Kinetic Energy equation is output;
1485\item[\np{ln\_tra\_trd}]:
1486  each 3D trend of the evolution of temperature and salinity is output;
1487\item[\np{ln\_tra\_mxl}]:
1488  each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output;
1489\end{description}
1490
1491Note that the mixed layer tendency diagnostic can also be used on biogeochemical models via
1492the \key{trdtrc} and \key{trdmxl\_trc} CPP keys.
1493
1494\textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested.
1495In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} are not working,
1496and none of the options have been tested with variable volume (\ie \np{ln\_linssh}\forcode{ = .true.}).
1497
1498% -------------------------------------------------------------------------------------------------------------
1499%       On-line Floats trajectories
1500% -------------------------------------------------------------------------------------------------------------
1501\section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})]
1502{FLO: On-Line Floats trajectories (\protect\key{floats})}
1503\label{sec:FLO}
1504%--------------------------------------------namflo-------------------------------------------------------
1505
1506\nlst{namflo} 
1507%--------------------------------------------------------------------------------------------------------------
1508
1509The on-line computation of floats advected either by the three dimensional velocity field or constraint to
1510remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project.
1511Options are defined by \ngn{namflo} namelist variables.
1512The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option),
1513or on a $4^th$ Runge-Hutta algorithm (\np{ln\_flork4}\forcode{ = .true.}).
1514Note that the \cite{blanke.raynaud_JPO97} algorithm have the advantage of providing trajectories which
1515are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry.
1516
1517\subsubsection{Input data: initial coordinates}
1518
1519Initial coordinates can be given with Ariane Tools convention
1520(IJK coordinates, (\np{ln\_ariane}\forcode{ = .true.}) ) or with longitude and latitude.
1521
1522In case of Ariane convention, input filename is \np{init\_float\_ariane}.
1523Its format is: \\
1524{\scriptsize \texttt{I J K nisobfl itrash}}
1525
1526\noindent with:
1527
1528 - I,J,K  : indexes of initial position
1529
1530 - nisobfl: 0 for an isobar float, 1 for a float following the w velocity 
1531
1532 - itrash : set to zero; it is a dummy variable to respect Ariane Tools convention
1533
1534\noindent Example: \\
1535\noindent
1536{\scriptsize
1537  \texttt{
1538    100.00000  90.00000  -1.50000 1.00000   0.00000   \\
1539    102.00000  90.00000  -1.50000 1.00000   0.00000   \\
1540    104.00000  90.00000  -1.50000 1.00000   0.00000   \\
1541    106.00000  90.00000  -1.50000 1.00000   0.00000   \\
1542    108.00000  90.00000  -1.50000 1.00000   0.00000}
1543} \\
1544
1545In the other case (longitude and latitude), input filename is init\_float.
1546Its format is: \\
1547{\scriptsize \texttt{Long Lat depth nisobfl ngrpfl itrash}}
1548
1549\noindent with:
1550
1551 - Long, Lat, depth  : Longitude, latitude, depth
1552
1553 - nisobfl: 0 for an isobar float, 1 for a float following the w velocity
1554
1555 - ngrpfl : number to identify searcher group
1556
1557 - itrash :set to 1; it is a dummy variable.
1558
1559\noindent Example: \\
1560\noindent
1561{\scriptsize
1562  \texttt{
1563    20.0 0.0 0.0 0 1 1    \\
1564    -21.0 0.0 0.0 0 1 1    \\
1565    -22.0 0.0 0.0 0 1 1    \\
1566    -23.0 0.0 0.0 0 1 1    \\
1567    -24.0 0.0 0.0 0 1 1 }
1568} \\
1569
1570\np{jpnfl} is the total number of floats during the run.
1571When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{ = .true.} ),
1572\np{jpnflnewflo} can be added in the initialization file.
1573
1574\subsubsection{Output data}
1575
1576\np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} is the frequency of
1577creation of the float restart file.
1578
1579Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{ = .true.}).
1580In that case, output filename is trajec\_float.
1581
1582Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{ = .false.}) with
1583\key{iomput} and outputs selected in iodef.xml.
1584Here it is an example of specification to put in files description section:
1585
1586\begin{xmllines}
1587<group id="1d_grid_T" name="auto" description="ocean T grid variables" >   }
1588   <file id="floats"  description="floats variables"> }
1589      <field ref="traj_lon"   name="floats_longitude"   freq_op="86400" />}
1590      <field ref="traj_lat"   name="floats_latitude"    freq_op="86400" />}
1591      <field ref="traj_dep"   name="floats_depth"       freq_op="86400" />}
1592      <field ref="traj_temp"  name="floats_temperature" freq_op="86400" />}
1593      <field ref="traj_salt"  name="floats_salinity"    freq_op="86400" />}
1594      <field ref="traj_dens"  name="floats_density"     freq_op="86400" />}
1595      <field ref="traj_group" name="floats_group"       freq_op="86400" />}
1596   </file>}
1597</group>}
1598\end{xmllines}
1599
1600
1601% -------------------------------------------------------------------------------------------------------------
1602%       Harmonic analysis of tidal constituents
1603% -------------------------------------------------------------------------------------------------------------
1604\section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})]
1605{Harmonic analysis of tidal constituents (\protect\key{diaharm})}
1606\label{sec:DIA_diag_harm}
1607
1608%------------------------------------------nam_diaharm----------------------------------------------------
1609%
1610\nlst{nam_diaharm}
1611%----------------------------------------------------------------------------------------------------------
1612
1613A module is available to compute the amplitude and phase of tidal waves.
1614This on-line Harmonic analysis is actived with \key{diaharm}.
1615
1616Some parameters are available in namelist \ngn{nam\_diaharm}:
1617
1618 - \np{nit000\_han} is the first time step used for harmonic analysis
1619
1620 - \np{nitend\_han} is the  last time step used for harmonic analysis
1621
1622 - \np{nstep\_han}  is the  time step frequency for harmonic analysis
1623
1624 - \np{nb\_ana}     is the number of harmonics to analyse
1625
1626 - \np{tname}       is an array with names of tidal constituents to analyse
1627
1628 \np{nit000\_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation.
1629 The restart capability is not implemented.
1630
1631 The Harmonic analysis solve the following equation:
1632
1633 \[
1634   h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i}
1635 \]
1636
1637With $A_{j}$, $\nu_{j}$, $\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error.
1638$h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\
1639We can rewrite this equation:
1640
1641\[
1642  h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i}
1643\]
1644
1645with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ and $\phi_{j}=arctan(S_{j}/C_{j})$.
1646
1647We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave.
1648
1649% -------------------------------------------------------------------------------------------------------------
1650%       Sections transports
1651% -------------------------------------------------------------------------------------------------------------
1652\section[Transports across sections (\texttt{\textbf{key\_diadct}})]
1653{Transports across sections (\protect\key{diadct})}
1654\label{sec:DIA_diag_dct}
1655
1656%------------------------------------------namdct----------------------------------------------------
1657
1658\nlst{namdct}
1659%-------------------------------------------------------------------------------------------------------------
1660
1661A module is available to compute the transport of volume, heat and salt through sections.
1662This diagnostic is actived with \key{diadct}.
1663
1664Each section is defined by the coordinates of its 2 extremities.
1665The pathways between them are contructed using tools which can be found in \texttt{tools/SECTIONS\_DIADCT}
1666and are written in a binary file \texttt{section\_ijglobal.diadct} which is later read in by
1667NEMO to compute on-line transports.
1668
1669The on-line transports module creates three output ascii files:
1670
1671- \texttt{volume\_transport} for volume transports (unit: $10^{6} m^{3} s^{-1}$)
1672
1673- \texttt{heat\_transport}   for   heat transports (unit: $10^{15} W$)
1674
1675- \texttt{salt\_transport}   for   salt transports (unit: $10^{9}Kg s^{-1}$) \\
1676
1677Namelist variables in \ngn{namdct} control how frequently the flows are summed and the time scales over which
1678they are averaged, as well as the level of output for debugging:
1679\np{nn\_dct}   : frequency of instantaneous transports computing
1680\np{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
1681\np{nn\_debug} : debugging of the section
1682
1683\subsubsection{Creating a binary file containing the pathway of each section}
1684
1685In \texttt{tools/SECTIONS\_DIADCT/run},
1686the file \textit{ {list\_sections.ascii\_global}} contains a list of all the sections that are to be computed
1687(this list of sections is based on MERSEA project metrics).
1688
1689Another file is available for the GYRE configuration (\texttt{ {list\_sections.ascii\_GYRE}}).
1690
1691Each section is defined by: \\
1692\noindent {\scriptsize \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\
1693with:
1694
1695 - \texttt{long1 lat1}, coordinates of the  first extremity of the section;
1696
1697 - \texttt{long2 lat2}, coordinates of the second extremity of the section;
1698
1699 - \texttt{nclass}    the number of bounds of your classes (\eg bounds for 2 classes);
1700
1701 - \texttt{okstrpond} to compute    heat and       salt transports, \texttt{nostrpond} if no;
1702
1703 - \texttt{ice}       to compute surface and volume ice transports, \texttt{noice}     if no. \\
1704
1705 \noindent The results of the computing of transports, and the directions of positive and
1706 negative flow do not depend on the order of the 2 extremities in this file. \\
1707
1708\noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\
1709{\scriptsize
1710  \texttt{
1711    long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\
1712    classtype                                                         \\
1713    zbound1                                                           \\
1714    zbound2                                                           \\
1715    .                                                                 \\
1716    .                                                                 \\
1717    nclass-1                                                          \\
1718    nclass}
1719}
1720
1721\noindent where \texttt{classtype} can be:
1722
1723 - \texttt{zsal}  for          salinity classes
1724
1725 - \texttt{ztem}  for       temperature classes
1726
1727 - \texttt{zlay}  for             depth classes
1728
1729 - \texttt{zsigi} for    insitu density classes
1730
1731 - \texttt{zsigp} for potential density classes \\
1732 
1733 The script \texttt{job.ksh} computes the pathway for each section and creates a binary file
1734 \texttt{section\_ijglobal.diadct} which is read by NEMO. \\
1735
1736 It is possible to use this tools for new configuations: \texttt{job.ksh} has to be updated with
1737 the coordinates file name and path. \\
1738
1739 Examples of two sections, the ACC\_Drake\_Passage with no classes,
1740 and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\
1741 \noindent
1742 {\scriptsize
1743   \texttt{
1744     -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage \\
1745     -80.5    22.5   -80.5    25.5  05 nostrpond noice ATL\_Cuba\_Florida  \\
1746     ztem                                                                  \\
1747     -2.0                                                                  \\
1748     4.5                                                                  \\
1749     7.0                                                                  \\
1750     12.0                                                                  \\
1751     40.0}
1752 }
1753
1754\subsubsection{To read the output files}
1755
1756The output format is: \\
1757{\scriptsize
1758  \texttt{
1759    date, time-step number, section number,                \\
1760    section name, section slope coefficient, class number, \\
1761    class name, class bound 1 , classe bound2,             \\
1762    transport\_direction1, transport\_direction2,          \\
1763    transport\_total}
1764}                                     \\
1765
1766For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class and
1767the last line corresponds to the total transport summed over all classes.
1768For sections with no classes, class number \texttt{1} corresponds to \texttt{total class} and
1769this class is called \texttt{N}, meaning \texttt{none}.
1770
1771- \texttt{transport\_direction1} is the positive part of the transport ($\geq$ 0).
1772
1773- \texttt{transport\_direction2} is the negative part of the transport ($\leq$ 0). \\
1774
1775\noindent The \texttt{section slope coefficient} gives information about the significance of transports signs and
1776direction: \\
1777
1778\begin{table}
1779  \scriptsize
1780  \begin{tabular}{|l|l|l|l|l|}
1781    \hline
1782    section slope coefficient      & section type & direction 1 & direction 2 & total transport    \\
1783    \hline
1784    0.                             & horizontal  & northward   & southward   & postive: northward    \\
1785    \hline
1786    1000.                          & vertical     & eastward    & westward    & postive: eastward     \\
1787    \hline
1788    \texttt{$\neq$ 0, $\neq$ 1000.} & diagonal     & eastward    & westward     & postive: eastward      \\
1789    \hline
1790  \end{tabular}
1791\end{table}
1792
1793% ================================================================
1794% Steric effect in sea surface height
1795% ================================================================
1796\section{Diagnosing the steric effect in sea surface height}
1797\label{sec:DIA_steric}
1798
1799
1800Changes in steric sea level are caused when changes in the density of the water column imply an expansion or
1801contraction of the column.
1802It is essentially produced through surface heating/cooling and to a lesser extent through non-linear effects of
1803the equation of state (cabbeling, thermobaricity...).
1804Non-Boussinesq models contain all ocean effects within the ocean acting on the sea level.
1805In particular, they include the steric effect.
1806In contrast, Boussinesq models, such as \NEMO, conserve volume, rather than mass,
1807and so do not properly represent expansion or contraction.
1808The steric effect is therefore not explicitely represented.
1809This approximation does not represent a serious error with respect to the flow field calculated by the model
1810\citep{greatbatch_JGR94}, but extra attention is required when investigating sea level,
1811as steric changes are an important contribution to local changes in sea level on seasonal and climatic time scales.
1812This is especially true for investigation into sea level rise due to global warming.
1813
1814Fortunately, the steric contribution to the sea level consists of a spatially uniform component that
1815can be diagnosed by considering the mass budget of the world ocean \citep{greatbatch_JGR94}.
1816In order to better understand how global mean sea level evolves and thus how the steric sea level can be diagnosed,
1817we compare, in the following, the non-Boussinesq and Boussinesq cases.
1818
1819Let denote
1820$\mathcal{M}$ the total mass    of liquid seawater ($\mathcal{M} = \int_D \rho dv$),
1821$\mathcal{V}$ the total volume  of        seawater      ($\mathcal{V} = \int_D dv$),
1822$\mathcal{A}$ the total surface of       the ocean      ($\mathcal{A} = \int_S ds$),
1823$\bar{\rho}$ the global mean  seawater (\textit{in situ}) density
1824($\bar{\rho} = 1/\mathcal{V} \int_D \rho \,dv$), and
1825$\bar{\eta}$ the global mean sea level
1826($\bar{\eta} = 1/\mathcal{A} \int_S \eta \,ds$).
1827
1828A non-Boussinesq fluid conserves mass. It satisfies the following relations:
1829
1830\begin{equation}
1831  \begin{split}
1832    \mathcal{M} &\mathcal{V}  \;\bar{\rho} \\
1833    \mathcal{V} &\mathcal{A}  \;\bar{\eta}
1834  \end{split}
1835  \label{eq:MV_nBq}
1836\end{equation}
1837
1838Temporal changes in total mass is obtained from the density conservation equation:
1839
1840\begin{equation}
1841  \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} )
1842  = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface}
1843  \label{eq:Co_nBq}
1844\end{equation}
1845
1846where $\rho$ is the \textit{in situ} density, and \textit{emp} the surface mass exchanges with the other media of
1847the Earth system (atmosphere, sea-ice, land).
1848Its global averaged leads to the total mass change
1849
1850\begin{equation}
1851  \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}}
1852  \label{eq:Mass_nBq}
1853\end{equation}
1854
1855where $\overline{\textit{emp}} = \int_S \textit{emp}\,ds$ is the net mass flux through the ocean surface.
1856Bringing \autoref{eq:Mass_nBq} and the time derivative of \autoref{eq:MV_nBq} together leads to
1857the evolution equation of the mean sea level
1858
1859\begin{equation}
1860  \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}}
1861  - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}}
1862  \label{eq:ssh_nBq}
1863\end{equation}
1864
1865The first term in equation \autoref{eq:ssh_nBq} alters sea level by adding or subtracting mass from the ocean.
1866The second term arises from temporal changes in the global mean density; \ie from steric effects.
1867
1868In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ appears multiplied by
1869the gravity (\ie in the hydrostatic balance of the primitive Equations).
1870In particular, the mass conservation equation, \autoref{eq:Co_nBq}, degenerates into the incompressibility equation:
1871
1872\[
1873  \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface}
1874  % \label{eq:Co_Bq}
1875\]
1876
1877and the global average of this equation now gives the temporal change of the total volume,
1878
1879\[
1880  \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o}
1881  % \label{eq:V_Bq}
1882\]
1883
1884Only the volume is conserved, not mass, or, more precisely, the mass which is conserved is the Boussinesq mass,
1885$\mathcal{M}_o = \rho_o \mathcal{V}$.
1886The total volume (or equivalently the global mean sea level) is altered only by net volume fluxes across
1887the ocean surface, not by changes in mean mass of the ocean: the steric effect is missing in a Boussinesq fluid.
1888
1889Nevertheless, following \citep{greatbatch_JGR94}, the steric effect on the volume can be diagnosed by
1890considering the mass budget of the ocean.
1891The apparent changes in $\mathcal{M}$, mass of the ocean, which are not induced by surface mass flux
1892must be compensated by a spatially uniform change in the mean sea level due to expansion/contraction of the ocean
1893\citep{greatbatch_JGR94}.
1894In others words, the Boussinesq mass, $\mathcal{M}_o$, can be related to $\mathcal{M}$,
1895the total mass of the ocean seen by the Boussinesq model, via the steric contribution to the sea level,
1896$\eta_s$, a spatially uniform variable, as follows:
1897
1898\begin{equation}
1899  \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A}
1900  \label{eq:M_Bq}
1901\end{equation}
1902
1903Any change in $\mathcal{M}$ which cannot be explained by the net mass flux through the ocean surface
1904is converted into a mean change in sea level.
1905Introducing the total density anomaly, $\mathcal{D}= \int_D d_a \,dv$,
1906where $d_a = (\rho -\rho_o ) / \rho_o$ is the density anomaly used in \NEMO (cf. \autoref{subsec:TRA_eos})
1907in \autoref{eq:M_Bq} leads to a very simple form for the steric height:
1908
1909\begin{equation}
1910  \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D}
1911  \label{eq:steric_Bq}
1912\end{equation}
1913
1914The above formulation of the steric height of a Boussinesq ocean requires four remarks.
1915First, one can be tempted to define $\rho_o$ as the initial value of $\mathcal{M}/\mathcal{V}$,
1916\ie set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero.
1917We do not recommend that.
1918Indeed, in this case $\rho_o$ depends on the initial state of the ocean.
1919Since $\rho_o$ has a direct effect on the dynamics of the ocean
1920(it appears in the pressure gradient term of the momentum equation)
1921it is definitively not a good idea when inter-comparing experiments.
1922We better recommend to fixe once for all $\rho_o$ to $1035\;Kg\,m^{-3}$.
1923This value is a sensible choice for the reference density used in a Boussinesq ocean climate model since,
1924with the exception of only a small percentage of the ocean, density in the World Ocean varies by no more than
19252$\%$ from this value (\cite{gill_bk82}, page 47).
1926
1927Second, we have assumed here that the total ocean surface, $\mathcal{A}$,
1928does not change when the sea level is changing as it is the case in all global ocean GCMs
1929(wetting and drying of grid point is not allowed).
1930 
1931Third, the discretisation of \autoref{eq:steric_Bq} depends on the type of free surface which is considered.
1932In the non linear free surface case, \ie \np{ln\_linssh}\forcode{ = .true.}, it is given by
1933
1934\[
1935  \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} }{ \sum_{i,\,j,\,k}       e_{1t} e_{2t} e_{3t} }
1936  % \label{eq:discrete_steric_Bq_nfs}
1937\]
1938
1939whereas in the linear free surface,
1940the volume above the \textit{z=0} surface must be explicitly taken into account to
1941better approximate the total ocean mass and thus the steric sea level:
1942
1943\[
1944  \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta }
1945                  { \sum_{i,\,j,\,k}       e_{1t}e_{2t}e_{3t} + \sum_{i,\,j}       e_{1t}e_{2t} \eta }
1946  % \label{eq:discrete_steric_Bq_fs}
1947\]
1948
1949The fourth and last remark concerns the effective sea level and the presence of sea-ice.
1950In the real ocean, sea ice (and snow above it)  depresses the liquid seawater through its mass loading.
1951This depression is a result of the mass of sea ice/snow system acting on the liquid ocean.
1952There is, however, no dynamical effect associated with these depressions in the liquid ocean sea level,
1953so that there are no associated ocean currents.
1954Hence, the dynamically relevant sea level is the effective sea level,
1955\ie the sea level as if sea ice (and snow) were converted to liquid seawater \citep{campin.marshall.ea_OM08}.
1956However, in the current version of \NEMO the sea-ice is levitating above the ocean without mass exchanges between
1957ice and ocean.
1958Therefore the model effective sea level is always given by $\eta + \eta_s$, whether or not there is sea ice present.
1959
1960In AR5 outputs, the thermosteric sea level is demanded.
1961It is steric sea level due to changes in ocean density arising just from changes in temperature.
1962It is given by:
1963
1964\[
1965  \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv
1966  % \label{eq:thermosteric_Bq}
1967\]
1968
1969where $S_o$ and $p_o$ are the initial salinity and pressure, respectively.
1970
1971Both steric and thermosteric sea level are computed in \mdl{diaar5}.
1972
1973% -------------------------------------------------------------------------------------------------------------
1974%       Other Diagnostics
1975% -------------------------------------------------------------------------------------------------------------
1976\section[Other diagnostics]
1977{Other diagnostics}
1978\label{sec:DIA_diag_others}
1979
1980Aside from the standard model variables, other diagnostics can be computed on-line.
1981The available ready-to-add diagnostics modules can be found in directory DIA.
1982
1983\subsection[Depth of various quantities (\textit{diahth.F90})]
1984{Depth of various quantities (\protect\mdl{diahth})}
1985
1986Among the available diagnostics the following ones are obtained when defining the \key{diahth} CPP key:
1987
1988- the mixed layer depth (based on a density criterion \citep{de-boyer-montegut.madec.ea_JGR04}) (\mdl{diahth})
1989
1990- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth})
1991
1992- the depth of the 20\deg{C} isotherm (\mdl{diahth})
1993
1994- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth})
1995
1996
1997%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1998\begin{figure}[!t]
1999  \begin{center}
2000    \includegraphics[width=\textwidth]{Fig_mask_subasins}
2001    \caption{
2002      \protect\label{fig:mask_subasins}
2003      Decomposition of the World Ocean (here ORCA2) into sub-basin used in to
2004      compute the heat and salt transports as well as the meridional stream-function:
2005      Atlantic basin (red), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).
2006      Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay are removed from the sub-basins.
2007      Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line.
2008    }
2009  \end{center}
2010\end{figure} 
2011%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2012
2013% -----------------------------------------------------------
2014%       CMIP specific diagnostics
2015% -----------------------------------------------------------
2016\subsection[CMIP specific diagnostics (\textit{diaar5.F90}, \textit{diaptr.F90})]
2017{CMIP specific diagnostics (\protect\mdl{diaar5})}
2018
2019A series of diagnostics has been added in the \mdl{diaar5} and \mdl{diaptr}.
2020In \mdl{diaar5} they correspond to outputs that are required for AR5 simulations (CMIP5)
2021(see also \autoref{sec:DIA_steric} for one of them).
2022The module \mdl{diaar5} is active when one of the following outputs is required : global total volume (voltot), global mean ssh (sshtot), global total mass (masstot), global mean temperature (temptot), global mean ssh steric (sshsteric), global mean ssh thermosteric (sshthster), global mean salinity (saltot), sea water pressure at sea floor (botpres), dynamic sea surface height (sshdyn).
2023
2024In \mdl{diaptr} when \np{ln\_diaptr}\forcode{ = .true.} 
2025(see the \textit{\ngn{namptr} } namelist below) can be computed on-line the poleward heat and salt transports, their advective and diffusive component, and the meriodional stream function .
2026When \np{ln\_subbas}\forcode{ = .true.}, transports and stream function are computed for the Atlantic, Indian,
2027Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean.
2028The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays,
2029the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:mask_subasins}).
2030
2031%------------------------------------------namptr-----------------------------------------
2032
2033\nlst{namptr} 
2034%-----------------------------------------------------------------------------------------
2035
2036% -----------------------------------------------------------
2037%       25 hour mean and hourly Surface, Mid and Bed
2038% -----------------------------------------------------------
2039\subsection{25 hour mean output for tidal models}
2040
2041%------------------------------------------nam_dia25h-------------------------------------
2042
2043\nlst{nam_dia25h}
2044%-----------------------------------------------------------------------------------------
2045
2046A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean.
2047The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from
2048midnight at the start of the day to midight at the day end.
2049This diagnostic is actived with the logical $ln\_dia25h$.
2050
2051% -----------------------------------------------------------
2052%     Top Middle and Bed hourly output
2053% -----------------------------------------------------------
2054\subsection{Top middle and bed hourly output}
2055
2056%------------------------------------------nam_diatmb-----------------------------------------------------
2057
2058\nlst{nam_diatmb}
2059%----------------------------------------------------------------------------------------------------------
2060
2061A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables.
2062This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs.
2063The tidal signal is retained but the overall data usage is cut to just three vertical levels.
2064Also the bottom level is calculated for each cell.
2065This diagnostic is actived with the logical $ln\_diatmb$.
2066
2067% -----------------------------------------------------------
2068%     Courant numbers
2069% -----------------------------------------------------------
2070\subsection{Courant numbers}
2071
2072Courant numbers provide a theoretical indication of the model's numerical stability.
2073The advective Courant numbers can be calculated according to
2074
2075\[
2076  C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}}
2077  % \label{eq:CFL}
2078\]
2079
2080in the zonal, meridional and vertical directions respectively.
2081The vertical component is included although it is not strictly valid as the vertical velocity is calculated from
2082the continuity equation rather than as a prognostic variable.
2083Physically this represents the rate at which information is propogated across a grid cell.
2084Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step.
2085
2086The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist.
2087The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii.
2088In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of
2089where the maximum value occurs.
2090At 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
2091with the coordinates of each.
2092The maximum values from the run are also copied to the ocean.output file.
2093
2094% ================================================================
2095
2096\biblio
2097
2098\pindex
2099
2100\end{document}
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