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1\documentclass[../main/NEMO_manual]{subfiles}
2
3\begin{document}
4% ================================================================
5% Chapter I/O & Diagnostics
6% ================================================================
7\chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)}
8\label{chap:DIA}
9
10\minitoc
11
12\newpage
13
14% ================================================================
15%       Old Model Output
16% ================================================================
17\section{Old model output (default)}
18\label{sec:DIA_io_old}
19
20The model outputs are of three types: the restart file, the output listing, and the diagnostic output file(s).
21The restart file is used internally by the code when the user wants to start the model with
22initial conditions defined by a previous simulation.
23It contains all the information that is necessary in order for there to be no changes in the model results
24(even at the computer precision) between a run performed with several restarts and
25the same run performed in one step.
26It should be noted that this requires that the restart file contains two consecutive time steps for
27all the prognostic variables, and that it is saved in the same binary format as the one used by the computer that
28is to read it (in particular, 32 bits binary IEEE format must not be used for this file).
29
30The output listing and file(s) are predefined but should be checked and eventually adapted to the user's needs.
31The output listing is stored in the $ocean.output$ file.
32The information is printed from within the code on the logical unit $numout$.
33To locate these prints, use the UNIX command "\textit{grep -i numout}" in the source code directory.
34
35By default, diagnostic output files are written in NetCDF format.
36Since version 3.2, when defining \key{iomput}, an I/O server has been added which
37provides more flexibility in the choice of the fields to be written as well as how
38the writing work is distributed over the processors in massively parallel computing.
39A complete description of the use of this I/O server is presented in the next section.
40
41By default, \key{iomput} is not defined,
42NEMO produces NetCDF with the old IOIPSL library which has been kept for compatibility and its easy installation.
43However, the IOIPSL library is quite inefficient on parallel machines and, since version 3.2,
44many diagnostic options have been added presuming the use of \key{iomput}.
45The usefulness of the default IOIPSL-based option is expected to reduce with each new release.
46If \key{iomput} is not defined, output files and content are defined in the \mdl{diawri} module and
47contain mean (or instantaneous if \key{diainstant} is defined) values over a regular period of
48nn\_write time-steps (namelist parameter).
49
50%\gmcomment{                    % start of gmcomment
51
52% ================================================================
53% Diagnostics
54% ================================================================
55\section{Standard model output (IOM)}
56\label{sec:DIA_iom}
57
58Since version 3.2, iomput is the NEMO output interface of choice.
59It has been designed to be simple to use, flexible and efficient.
60The two main purposes of iomput are:
61
62\begin{enumerate}
63\item
64  The complete and flexible control of the output files through external XML files adapted by
65  the user from standard templates.
66\item
67  To achieve high performance and scalable output through the optional distribution of
68  all diagnostic output related tasks to dedicated processes.
69\end{enumerate}
70
71The first functionality allows the user to specify, without code changes or recompilation,
72aspects of the diagnostic output stream, such as:
73
74\begin{itemize}
75\item
76  The choice of output frequencies that can be different for each file (including real months and years).
77\item
78  The choice of file contents; includes complete flexibility over which data are written in which files
79  (the same data can be written in different files).
80\item
81  The possibility to split output files at a chosen frequency.
82\item
83  The possibility to extract a vertical or an horizontal subdomain.
84\item
85  The choice of the temporal operation to perform, \eg: average, accumulate, instantaneous, min, max and once.
86\item
87  Control over metadata via a large XML "database" of possible output fields.
88\end{itemize}
89
90In addition, iomput allows the user to add in the code the output of any new variable (scalar, 2D or 3D)
91in a very easy way.
92All details of iomput functionalities are listed in the following subsections.
93Examples of the XML files that control the outputs can be found in: \path{NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml},
94\path{NEMOGCM/CONFIG/SHARED/field_def.xml} and \path{NEMOGCM/CONFIG/SHARED/domain_def.xml}. \\
95
96The second functionality targets output performance when running in parallel (\key{mpp\_mpi}).
97Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO processes)
98to collect and write the outputs.
99With an appropriate choice of N by the user, the bottleneck associated with the writing of
100the output files can be greatly reduced.
101
102In version 3.6, the iom\_put interface depends on
103an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/branchs/xios-1.0}{XIOS-1.0} 
104(use of revision 618 or higher is required).
105This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to
106create a single output file and therefore to bypass the rebuilding phase.
107Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to
108an HDF5 library that has been correctly compiled (\ie with the configure option $--$enable-parallel).
109Note that the files created by iomput through XIOS are incompatible with NetCDF3.
110All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3.
111
112Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers,
113where N is typically much less than the number of NEMO processors, will reduce the number of output files created.
114This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors.
115Note that for smaller configurations, the rebuilding phase can be avoided,
116even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server.
117
118\subsection{XIOS: Reading and writing restart file}
119
120XIOS may be used to read single file restart produced by NEMO. Currently only the variables written to
121file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np{ln\_xios\_read}\forcode{ = .true. }
122in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default NEMO
123functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read
124restart, all definitions are done within the NEMO code. For high resolution configuration, however,
125there may be a need to add the following line in iodef.xml (xios context):
126
127\begin{xmllines}
128<variable id="recv_field_timeout"        type="double">1800</variable>
129\end{xmllines}
130
131This variable sets timeout for reading.
132
133If XIOS is to be used to read restart from file generated with an earlier NEMO version (3.6 for instance),
134dimension \forcode{z} defined in restart file must be renamed to \forcode{nav_lev}.\\
135
136XIOS can also be used to write NEMO restart. A namelist parameter \np{nn\_wxios} is used to determine the
137type of restart NEMO will write. If it is set to 0, default NEMO functionality will be used - each
138processor writes its own restart file; if it is set to 1 XIOS will write restart into a single file;
139for \np{nn\_wxios = 2} the restart will be written by XIOS into multiple files, one for each XIOS server.
140Note, however, that \textbf{NEMO will not read restart generated by XIOS when \np{nn\_wxios = 2}}. The restart will
141have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by NEMO only,
142and may be useful when there is a need to change number of processors used to run simulation.
143
144If an additional variable must be written to a restart file, the following steps are needed:
145\begin{description}
146   \item[step 1:] add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and
147define correct grid for the variable (\forcode{grid_N_3D} - 3D variable, \forcode{grid_N} - 2D variable, \forcode{grid_vector} -
1481D variable, \forcode{grid_scalar} - scalar),
149   \item[step 2:] add variable to the list of fields written by restart.  This can be done either in subroutine
150\rou{iom\_set\_rstw\_core} (\mdl{iom}) or by calling  \rou{iom\_set\_rstw\_active} (\mdl{iom}) with the name of a variable
151as an argument. This convention follows approach for writing restart using iom, where variables are
152written either by \rou{rst\_write} or by calling \rou{iom\_rstput} from individual routines.
153\end{description}
154
155
156An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451.
157
158
159\subsection{XIOS: XML Inputs-Outputs Server}
160
161\subsubsection{Attached or detached mode?}
162
163Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS},
164the io\_server developed by Yann Meurdesoif from IPSL.
165The behaviour of the I/O subsystem is controlled by settings in the external XML files listed above.
166Key settings in the iodef.xml file are the tags associated with each defined file.
167
168\xmlline|<variable id="using_server" type="bool"></variable>|
169
170The {\tt using\_server} setting determines whether or not the server will be used in \textit{attached mode}
171(as a library) [{\tt> false <}] or in \textit{detached mode}
172(as an external executable on N additional, dedicated cpus) [{\tt > true <}].
173The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications.
174The type of each file can be either ''multiple\_file'' or ''one\_file''.
175
176In \textit{attached mode} and if the type of file is ''multiple\_file'',
177then each NEMO process will also act as an IO server and produce its own set of output files.
178Superficially, this emulates the standard behaviour in previous versions.
179However, the subdomain written out by each process does not correspond to
180the \forcode{jpi x jpj x jpk} domain actually computed by the process (although it may if \forcode{jpni=1}).
181Instead each process will have collected and written out a number of complete longitudinal strips.
182If the ''one\_file'' option is chosen then all processes will collect their longitudinal strips and
183write (in parallel) to a single output file.
184
185In \textit{detached mode} and if the type of file is ''multiple\_file'',
186then each stand-alone XIOS process will collect data for a range of complete longitudinal strips and
187write to its own set of output files.
188If the ''one\_file'' option is chosen then all XIOS processes will collect their longitudinal strips and
189write (in parallel) to a single output file.
190Note running in detached mode requires launching a Multiple Process Multiple Data (MPMD) parallel job.
191The following subsection provides a typical example but the syntax will vary in different MPP environments.
192
193\subsubsection{Number of cpu used by XIOS in detached mode}
194
195The number of cores used by the XIOS is specified when launching the model.
196The number of cores dedicated to XIOS should be from \texttildelow1/10 to \texttildelow1/50 of the number of
197cores dedicated to NEMO.
198Some manufacturers suggest using O($\sqrt{N}$) dedicated IO processors for N processors but
199this is a general recommendation and not specific to NEMO.
200It is difficult to provide precise recommendations because the optimal choice will depend on
201the particular hardware properties of the target system
202(parallel filesystem performance, available memory, memory bandwidth etc.)
203and the volume and frequency of data to be created.
204Here is an example of 2 cpus for the io\_server and 62 cpu for nemo using mpirun:
205\cmd|mpirun -np 62 ./nemo.exe : -np 2 ./xios_server.exe|
206
207\subsubsection{Control of XIOS: the context in iodef.xml}
208
209As well as the {\tt using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml.
210See the XML basics section below for more details on XML syntax and rules.
211
212\begin{table}
213  \scriptsize
214  \begin{tabularx}{\textwidth}{|lXl|}
215    \hline
216    variable name                                                           &
217    description                                                             &
218    example  \\
219    \hline
220    \hline
221    buffer\_size                                                            &
222    buffer size used by XIOS to send data from NEMO to XIOS.
223    Larger is more efficient.
224    Note that needed/used buffer sizes are summarized at the end of the job &
225    25000000 \\
226    \hline
227    buffer\_server\_factor\_size                                            &
228    ratio between NEMO and XIOS buffer size.
229    Should be 2.                                                            &
230    2        \\
231    \hline
232    info\_level                                                             &
233    verbosity level (0 to 100)                                              &
234    0        \\
235    \hline
236    using\_server                                                           &
237    activate attached(false) or detached(true) mode                         &
238    true     \\
239    \hline
240    using\_oasis                                                            &
241    XIOS is used with OASIS(true) or not (false)                            &
242    false    \\
243    \hline
244    oasis\_codes\_id                                                        &
245    when using oasis, define the identifier of NEMO in the namcouple.
246    Note that the identifier of XIOS is xios.x                              &
247    oceanx   \\
248    \hline
249  \end{tabularx}
250\end{table}
251
252\subsection{Practical issues}
253
254\subsubsection{Installation}
255
256As mentioned, XIOS is supported separately and must be downloaded and compiled before it can be used with NEMO.
257See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance.
258NEMO will need to link to the compiled XIOS library.
259The \href{https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ModelInterfacing/InputsOutputs#Inputs-OutputsusingXIOS}
260{XIOS with NEMO} guide provides an example illustration of how this can be achieved.
261
262\subsubsection{Add your own outputs}
263
264It is very easy to add your own outputs with iomput.
265Many standard fields and diagnostics are already prepared (\ie, steps 1 to 3 below have been done) and
266simply need to be activated by including the required output in a file definition in iodef.xml (step 4).
267To add new output variables, all 4 of the following steps must be taken.
268
269\begin{enumerate}
270\item[1.]
271  in NEMO code, add a \forcode{CALL iom\_put( 'identifier', array )} where you want to output a 2D or 3D array.
272\item[2.]
273  If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in
274  the upper part of your module.
275\item[3.]
276  in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code
277  (see subsequent sections for a details of the XML syntax and rules).
278  For example:
279
280\begin{xmllines}
281<field_definition>
282   <field_group id="grid_T" grid_ref="grid_T_3D"> <!-- T grid -->
283   ...
284      <field id="identifier" long_name="blabla" ... />   
285      ...
286</field_definition>
287\end{xmllines}
288
289Note your definition must be added to the field\_group whose reference grid is consistent with the size of
290the array passed to iomput.
291The grid\_ref attribute refers to definitions set in iodef.xml which, in turn,
292reference grids and axes either defined in the code
293(iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file.
294\eg:
295
296\begin{xmllines}
297<grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/>
298\end{xmllines}
299
300Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step,
301add the field definition within the field\_group defined with the id "SBC":
302\xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations
303(iom\_set\_field\_attr in \mdl{iom})
304\item[4.]
305  add your field in one of the output files defined in iodef.xml
306  (again see subsequent sections for syntax and rules)
307
308\begin{xmllines}
309<file id="file1" .../>  
310...
311   <field field_ref="identifier" />   
312   ...
313</file>   
314\end{xmllines}
315
316\end{enumerate}
317
318\subsection{XML fundamentals}
319
320\subsubsection{ XML basic rules}
321
322XML tags begin with the less-than character ("$<$") and end with the greater-than character ("$>$").
323You use tags to mark the start and end of elements, which are the logical units of information in an XML document.
324In addition to marking the beginning of an element, XML start tags also provide a place to specify attributes.
325An attribute specifies a single property for an element, using a name/value pair, for example:
326\xmlcode{<a b="x" c="y" d="z"> ... </a>}.
327See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details.
328
329\subsubsection{Structure of the XML file used in NEMO}
330
331The XML file used in XIOS is structured by 7 families of tags:
332context, axis, domain, grid, field, file and variable.
333Each tag family has hierarchy of three flavors (except for context):
334
335\begin{table}
336  \scriptsize
337  \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
338    \hline
339    flavor  & description                                                                 &
340                                                                                            example                          \\
341    \hline
342    \hline
343    root    & declaration of the root element that can contain element groups or elements &
344                                                                                            \xmlcode{<file_definition ... >} \\
345    \hline
346    group   & declaration of a group element that can contain element groups or elements  &
347                                                                                            \xmlcode{<file_group      ... >} \\
348    \hline
349    element & declaration of an element that can contain elements                         &
350                                                                                            \xmlcode{<file            ... >} \\
351    \hline
352  \end{tabular*}
353\end{table}
354
355Each element may have several attributes.
356Some attributes are mandatory, other are optional but have a default value and other are completely optional.
357Id is a special attribute used to identify an element or a group of elements.
358It must be unique for a kind of element.
359It is optional, but no reference to the corresponding element can be done if it is not defined.
360
361The XML file is split into context tags that are used to isolate IO definition from
362different codes or different parts of a code.
363No interference is possible between 2 different contexts.
364Each context has its own calendar and an associated timestep.
365In \NEMO, we used the following contexts (that can be defined in any order):
366
367\begin{table}
368  \scriptsize
369  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
370    \hline
371    context         &   description                                                                &
372                                                                                                     example                              \\
373    \hline
374    \hline
375    context xios    &   context containing information for XIOS                                    &
376                                                                                                     \xmlcode{<context id="xios" ... >}   \\
377    \hline
378    context nemo    &   context containing IO information for NEMO (mother grid when using AGRIF)  & 
379                                                                                                     \xmlcode{<context id="nemo" ... >}   \\
380    \hline
381    context 1\_nemo &   context containing IO information for NEMO child grid 1 (when using AGRIF) & 
382                                                                                                     \xmlcode{<context id="1_nemo" ... >} \\
383    \hline
384    context n\_nemo &   context containing IO information for NEMO child grid n (when using AGRIF) & 
385                                                                                                     \xmlcode{<context id="n_nemo" ... >} \\
386    \hline
387  \end{tabular}
388\end{table}
389
390\noindent The xios context contains only 1 tag:
391
392\begin{table}
393  \scriptsize
394  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
395    \hline
396    context tag                                      &
397                                                       description                                      &
398                                                                                                          example                              \\
399    \hline
400    \hline
401    variable\_definition                             &
402                                                       define variables needed by XIOS.
403                                                       This can be seen as a kind of namelist for XIOS. &
404                                                                                                          \xmlcode{<variable_definition ... >} \\
405    \hline
406   \end{tabular}
407\end{table}
408
409\noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts
410(that can be defined in any order):
411
412\begin{table}
413  \scriptsize
414  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|}
415    \hline
416    context tag        &   description                                                               &
417                                                                                                       example                            \\
418    \hline
419    \hline
420    field\_definition  &   define all variables that can potentially be outputted                    &
421                                                                                                       \xmlcode{<field_definition ... >}  \\
422    \hline
423    file\_definition   &   define the netcdf files to be created and the variables they will contain &
424                                                                                                       \xmlcode{<file_definition ... >}   \\
425    \hline
426    axis\_definition   &   define vertical axis                                                      &
427                                                                                                       \xmlcode{<axis_definition ... >}   \\
428    \hline
429    domain\_definition &   define the horizontal grids                                               &
430                                                                                                       \xmlcode{<domain_definition ... >} \\
431    \hline
432    grid\_definition   &   define the 2D and 3D grids (association of an axis and a domain)          &
433                                                                                                       \xmlcode{<grid_definition ... >}   \\
434    \hline
435  \end{tabular}
436\end{table}
437
438\subsubsection{Nesting XML files}
439
440The XML file can be split in different parts to improve its readability and facilitate its use.
441The inclusion of XML files into the main XML file can be done through the attribute src:
442\xmlline|<context src="./nemo_def.xml" />|
443 
444\noindent In NEMO, by default, the field and domain definition is done in 2 separate files:
445\path{NEMOGCM/CONFIG/SHARED/field_def.xml} and \path{NEMOGCM/CONFIG/SHARED/domain_def.xml} that
446are included in the main iodef.xml file through the following commands:
447\begin{xmllines}
448<field_definition src="./field_def.xml" />
449<domain_definition src="./domain_def.xml" />
450\end{xmllines}
451
452\subsubsection{Use of inheritance}
453
454XML extensively uses the concept of inheritance.
455XML has a tree based structure with a parent-child oriented relation: all children inherit attributes from parent,
456but an attribute defined in a child replace the inherited attribute value.
457Note that the special attribute ''id'' is never inherited.
458\\
459\\
460example 1: Direct inheritance.
461
462\begin{xmllines}
463<field_definition operation="average" >
464   <field id="sst"                    />   <!-- averaged      sst -->
465   <field id="sss" operation="instant"/>   <!-- instantaneous sss -->
466</field_definition>
467\end{xmllines}
468
469The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average'' of
470the attribute ''operation'' from its parent.
471Note that a child can overwrite the attribute definition inherited from its parents.
472In the example above, the field ''sss'' will for example output instantaneous values instead of average values.
473\\
474\\
475example 2: Inheritance by reference.
476
477\begin{xmllines}
478<field_definition>
479   <field id="sst" long_name="sea surface temperature" />
480   <field id="sss" long_name="sea surface salinity"    />
481</field_definition>
482<file_definition>
483   <file id="myfile" output_freq="1d" />   
484      <field field_ref="sst"                            />  <!-- default def -->
485      <field field_ref="sss" long_name="my description" />  <!-- overwrite   -->
486   </file>
487</file_definition>
488\end{xmllines}
489
490Inherit (and overwrite, if needed) the attributes of a tag you are refering to.
491
492\subsubsection{Use of groups}
493
494Groups can be used for 2 purposes.
495Firstly, the group can be used to define common attributes to be shared by the elements of
496the group through inheritance.
497In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''.
498Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''.
499
500\begin{xmllines}
501<field_group id="grid_T" grid_ref="grid_T_2D">
502   <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/>
503   <field id="sst"  long_name="sea surface temperature" unit="degC"                     />
504   <field id="sss"  long_name="sea surface salinity"    unit="psu"                      />
505   <field id="ssh"  long_name="sea surface height"      unit="m"                        />
506   ...
507\end{xmllines}
508
509Secondly, the group can be used to replace a list of elements.
510Several examples of groups of fields are proposed at the end of the file \path{CONFIG/SHARED/field_def.xml}.
511For example, a short list of the usual variables related to the U grid:
512
513\begin{xmllines}
514<field_group id="groupU" >
515   <field field_ref="uoce"  />
516   <field field_ref="suoce" />
517   <field field_ref="utau"  />
518</field_group>
519\end{xmllines}
520
521that can be directly included in a file through the following syntax:
522
523\begin{xmllines}
524<file id="myfile_U" output_freq="1d" />
525   <field_group group_ref="groupU" />
526   <field field_ref="uocetr_eff"   />  <!-- add another field -->
527</file>   
528\end{xmllines}
529
530\subsection{Detailed functionalities}
531
532The file \path{NEMOGCM/CONFIG/ORCA2_LIM/iodef_demo.xml} provides several examples of the use of
533the new functionalities offered by the XML interface of XIOS.
534
535\subsubsection{Define horizontal subdomains}
536
537Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of
538the tag family domain.
539It must therefore be done in the domain part of the XML file.
540For example, in \path{CONFIG/SHARED/domain_def.xml}, we provide the following example of a definition of
541a 5 by 5 box with the bottom left corner at point (10,10).
542
543\begin{xmllines}
544<domain_group id="grid_T">
545   <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" />
546\end{xmllines}
547
548The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field.
549For example:
550
551\begin{xmllines}
552<file id="myfile_vzoom" output_freq="1d" >
553   <field field_ref="toce" domain_ref="myzoom"/>
554</file>
555\end{xmllines}
556
557Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain.
558The Equatorial section, the TAO, RAMA and PIRATA moorings are already registered in the code and
559can therefore be outputted without taking care of their (i,j) position in the grid.
560These predefined domains can be activated by the use of specific domain\_ref:
561''EqT'', ''EqU'' or ''EqW'' for the equatorial sections and
562the mooring position for TAO, RAMA and PIRATA followed by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...)
563
564\begin{xmllines}
565<file id="myfile_vzoom" output_freq="1d" >
566   <field field_ref="toce" domain_ref="0n180wT"/>
567</file>
568\end{xmllines}
569
570Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if
571you use the ''multiple\_file'' type for your output files,
572you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat,
573\href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}).
574We are therefore advising to use the ''one\_file'' type in this case.
575
576\subsubsection{Define vertical zooms}
577
578Vertical zooms are defined through the attributs zoom\_begin and zoom\_end of the tag family axis.
579It must therefore be done in the axis part of the XML file.
580For example, in \path{NEMOGCM/CONFIG/ORCA2_LIM/iodef_demo.xml}, we provide the following example:
581
582\begin{xmllines}
583<axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" >
584   <axis id="deptht" />
585   <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" />
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 convection 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 ("\tt{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 ("\tt{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 ("\tt{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 ("\tt{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 ("\tt{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 ("\tt{*\_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 ("\tt{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-1.0 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 (\protect\key{netcdf4})}
1335\label{sec:DIA_nc4}
1336
1337Since version 3.3, support for NetCDF4 chunking and (loss-less) compression has been included.
1338These options build on the standard NetCDF output and allow the user control over the size of the chunks via
1339namelist settings.
1340Chunking and compression can lead to significant reductions in file sizes for a small runtime overhead.
1341For a fuller discussion on chunking and other performance issues the reader is referred to
1342the NetCDF4 documentation found \href{http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.html#Chunking}{here}.
1343
1344The new features are only available when the code has been linked with a NetCDF4 library
1345(version 4.1 onwards, recommended) which has been built with HDF5 support (version 1.8.4 onwards, recommended).
1346Datasets created with chunking and compression are not backwards compatible with NetCDF3 "classic" format but
1347most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files.
1348NEMO executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by
1349setting the \np{ln\_nc4zip} logical to false in the \textit{namnc4} namelist:
1350
1351%------------------------------------------namnc4----------------------------------------------------
1352
1353\nlst{namnc4}
1354%-------------------------------------------------------------------------------------------------------------
1355
1356If \key{netcdf4} has not been defined, these namelist parameters are not read.
1357In this case, \np{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined.
1358These functions will not be used but need to be included so that compilation is possible with NetCDF3 libraries.
1359
1360When using NetCDF4 libraries, \key{netcdf4} should be defined even if the intention is to
1361create only NetCDF3-compatible files.
1362This is necessary to avoid duplication between the dummy routines and the actual routines present in the library.
1363Most compilers will fail at compile time when faced with such duplication.
1364Thus when linking with NetCDF4 libraries the user must define \key{netcdf4} and
1365control the type of NetCDF file produced via the namelist parameter.
1366
1367Chunking and compression is applied only to 4D fields and
1368there is no advantage in chunking across more than one time dimension since
1369previously written chunks would have to be read back and decompressed before being added to.
1370Therefore, user control over chunk sizes is provided only for the three space dimensions.
1371The user sets an approximate number of chunks along each spatial axis.
1372The actual size of the chunks will depend on global domain size for mono-processors or, more likely,
1373the local processor domain size for distributed processing.
1374The derived values are subject to practical minimum values (to avoid wastefully small chunk sizes) and
1375cannot be greater than the domain size in any dimension.
1376The algorithm used is:
1377
1378\begin{forlines}
1379ichunksz(1) = MIN(idomain_size, MAX((idomain_size-1) / nn_nchunks_i + 1 ,16 ))
1380ichunksz(2) = MIN(jdomain_size, MAX((jdomain_size-1) / nn_nchunks_j + 1 ,16 ))
1381ichunksz(3) = MIN(kdomain_size, MAX((kdomain_size-1) / nn_nchunks_k + 1 , 1 ))
1382ichunksz(4) = 1
1383\end{forlines}
1384
1385\noindent As an example, setting:
1386
1387\begin{forlines}
1388nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31
1389\end{forlines}
1390
1391\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1} respectively in
1392the mono-processor case (\ie global domain of {\small\tt 182x149x31}).
1393An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in
1394table \autoref{tab:NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with
1395a 4x2 mpi partitioning.
1396Note the variation in the compression ratio achieved which reflects chiefly the dry to wet volume ratio of
1397each processing region.
1398
1399%------------------------------------------TABLE----------------------------------------------------
1400\begin{table}
1401  \scriptsize
1402  \centering
1403  \begin{tabular}{lrrr}
1404    Filename                    & NetCDF3 & NetCDF4  & Reduction \\
1405                                & filesize   & filesize & \%        \\
1406                                & (KB)    & (KB)     &           \\
1407    ORCA2\_restart\_0000.nc     & 16420   & 8860     & 47\%      \\
1408    ORCA2\_restart\_0001.nc     & 16064   & 11456    & 29\%      \\
1409    ORCA2\_restart\_0002.nc     & 16064      & 9744     & 40\%      \\
1410    ORCA2\_restart\_0003.nc     & 16420      & 9404     & 43\%      \\
1411    ORCA2\_restart\_0004.nc     & 16200   & 5844     & 64\%      \\
1412    ORCA2\_restart\_0005.nc     & 15848   & 8172     & 49\%      \\
1413    ORCA2\_restart\_0006.nc     & 15848   & 8012     & 50\%      \\
1414    ORCA2\_restart\_0007.nc     & 16200   & 5148     & 69\%      \\
1415    ORCA2\_2d\_grid\_T\_0000.nc & 2200       & 1504     & 32\%      \\
1416    ORCA2\_2d\_grid\_T\_0001.nc & 2200       & 1748     & 21\%      \\
1417    ORCA2\_2d\_grid\_T\_0002.nc & 2200       & 1592     & 28\%      \\
1418    ORCA2\_2d\_grid\_T\_0003.nc & 2200       & 1540     & 30\%      \\
1419    ORCA2\_2d\_grid\_T\_0004.nc & 2200       & 1204     & 46\%      \\
1420    ORCA2\_2d\_grid\_T\_0005.nc & 2200       & 1444     & 35\%      \\
1421    ORCA2\_2d\_grid\_T\_0006.nc & 2200       & 1428     & 36\%      \\
1422    ORCA2\_2d\_grid\_T\_0007.nc & 2200    & 1148     & 48\%      \\
1423    ...                         & ...     & ...      & ...       \\
1424    ORCA2\_2d\_grid\_W\_0000.nc & 4416    & 2240     & 50\%      \\
1425    ORCA2\_2d\_grid\_W\_0001.nc & 4416    & 2924     & 34\%      \\
1426    ORCA2\_2d\_grid\_W\_0002.nc & 4416    & 2512     & 44\%      \\
1427    ORCA2\_2d\_grid\_W\_0003.nc & 4416    & 2368     & 47\%      \\
1428    ORCA2\_2d\_grid\_W\_0004.nc & 4416    & 1432     & 68\%      \\
1429    ORCA2\_2d\_grid\_W\_0005.nc & 4416    & 1972     & 56\%      \\
1430    ORCA2\_2d\_grid\_W\_0006.nc & 4416    & 2028     & 55\%      \\
1431    ORCA2\_2d\_grid\_W\_0007.nc & 4416    & 1368     & 70\%      \\
1432  \end{tabular}
1433  \caption{
1434    \protect\label{tab:NC4}
1435    Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression
1436  }
1437\end{table}
1438%----------------------------------------------------------------------------------------------------
1439
1440When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via
1441\np{iom\_put} calls are set via an equivalent and identically named namelist to \textit{namnc4} in
1442\np{xmlio\_server.def}.
1443Typically this namelist serves the mean files whilst the \ngn{ namnc4} in the main namelist file continues to
1444serve the restart files.
1445This duplication is unfortunate but appropriate since, if using io\_servers, the domain sizes of
1446the individual files produced by the io\_server processes may be different to those produced by
1447the invidual processing regions and different chunking choices may be desired.
1448 
1449% -------------------------------------------------------------------------------------------------------------
1450%       Tracer/Dynamics Trends
1451% -------------------------------------------------------------------------------------------------------------
1452\section{Tracer/Dynamics trends  (\protect\ngn{namtrd})}
1453\label{sec:DIA_trd}
1454
1455%------------------------------------------namtrd----------------------------------------------------
1456
1457\nlst{namtrd} 
1458%-------------------------------------------------------------------------------------------------------------
1459
1460Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to
1461\mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation
1462(\ie at the end of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines).
1463This capability is controlled by options offered in \ngn{namtrd} namelist.
1464Note that the output are done with xIOS, and therefore the \key{IOM} is required.
1465
1466What is done depends on the \ngn{namtrd} logical set to \forcode{.true.}:
1467
1468\begin{description}
1469\item[\np{ln\_glo\_trd}]:
1470  at each \np{nn\_trd} time-step a check of the basin averaged properties of
1471  the momentum and tracer equations is performed.
1472  This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$,
1473  and potential energy time evolution equations properties;
1474\item[\np{ln\_dyn\_trd}]:
1475  each 3D trend of the evolution of the two momentum components is output;
1476\item[\np{ln\_dyn\_mxl}]:
1477  each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output;
1478\item[\np{ln\_vor\_trd}]:
1479  a vertical summation of the moment tendencies is performed,
1480  then the curl is computed to obtain the barotropic vorticity tendencies which are output;
1481\item[\np{ln\_KE\_trd}] :
1482  each 3D trend of the Kinetic Energy equation is output;
1483\item[\np{ln\_tra\_trd}]:
1484  each 3D trend of the evolution of temperature and salinity is output;
1485\item[\np{ln\_tra\_mxl}]:
1486  each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output;
1487\end{description}
1488
1489Note that the mixed layer tendency diagnostic can also be used on biogeochemical models via
1490the \key{trdtrc} and \key{trdmld\_trc} CPP keys.
1491
1492\textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested.
1493In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} are not working,
1494and none of the options have been tested with variable volume (\ie \key{vvl} defined).
1495
1496% -------------------------------------------------------------------------------------------------------------
1497%       On-line Floats trajectories
1498% -------------------------------------------------------------------------------------------------------------
1499\section{FLO: On-Line Floats trajectories (\protect\key{floats})}
1500\label{sec:FLO}
1501%--------------------------------------------namflo-------------------------------------------------------
1502
1503\nlst{namflo} 
1504%--------------------------------------------------------------------------------------------------------------
1505
1506The on-line computation of floats advected either by the three dimensional velocity field or constraint to
1507remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project.
1508Options are defined by \ngn{namflo} namelis variables.
1509The algorithm used is based either on the work of \cite{Blanke_Raynaud_JPO97} (default option),
1510or on a $4^th$ Runge-Hutta algorithm (\np{ln\_flork4}\forcode{ = .true.}).
1511Note that the \cite{Blanke_Raynaud_JPO97} algorithm have the advantage of providing trajectories which
1512are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry.
1513
1514\subsubsection{Input data: initial coordinates}
1515
1516Initial coordinates can be given with Ariane Tools convention
1517(IJK coordinates, (\np{ln\_ariane}\forcode{ = .true.}) ) or with longitude and latitude.
1518
1519In case of Ariane convention, input filename is \np{init\_float\_ariane}.
1520Its format is: \\
1521{\scriptsize \texttt{I J K nisobfl itrash itrash}}
1522
1523\noindent with:
1524
1525 - I,J,K  : indexes of initial position
1526
1527 - nisobfl: 0 for an isobar float, 1 for a float following the w velocity 
1528
1529 - itrash : set to zero; it is a dummy variable to respect Ariane Tools convention
1530
1531\noindent Example: \\
1532\noindent
1533{\scriptsize
1534  \texttt{
1535    100.00000  90.00000  -1.50000 1.00000   0.00000   \\
1536    102.00000  90.00000  -1.50000 1.00000   0.00000   \\
1537    104.00000  90.00000  -1.50000 1.00000   0.00000   \\
1538    106.00000  90.00000  -1.50000 1.00000   0.00000   \\
1539    108.00000  90.00000  -1.50000 1.00000   0.00000}
1540} \\
1541
1542In the other case (longitude and latitude), input filename is init\_float.
1543Its format is: \\
1544{\scriptsize \texttt{Long Lat depth nisobfl ngrpfl itrash}}
1545
1546\noindent with:
1547
1548 - Long, Lat, depth  : Longitude, latitude, depth
1549
1550 - nisobfl: 0 for an isobar float, 1 for a float following the w velocity
1551
1552 - ngrpfl : number to identify searcher group
1553
1554 - itrash :set to 1; it is a dummy variable.
1555
1556\noindent Example: \\
1557\noindent
1558{\scriptsize
1559  \texttt{
1560    20.0 0.0 0.0 0 1 1    \\
1561    -21.0 0.0 0.0 0 1 1    \\
1562    -22.0 0.0 0.0 0 1 1    \\
1563    -23.0 0.0 0.0 0 1 1    \\
1564    -24.0 0.0 0.0 0 1 1 }
1565} \\
1566
1567\np{jpnfl} is the total number of floats during the run.
1568When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{ = .true.} ),
1569\np{jpnflnewflo} can be added in the initialization file.
1570
1571\subsubsection{Output data}
1572
1573\np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} is the frequency of
1574creation of the float restart file.
1575
1576Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{ = .true.}).
1577In that case, output filename is trajec\_float.
1578
1579Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{ = .false.}).
1580There are 2 possibilities:
1581
1582- if (\key{iomput}) is used, outputs are selected in  iodef.xml.
1583Here it is an example of specification to put in files description section:
1584
1585\begin{xmllines}
1586<group id="1d_grid_T" name="auto" description="ocean T grid variables" >   }
1587   <file id="floats"  description="floats variables"> }
1588      <field ref="traj_lon"   name="floats_longitude"   freq_op="86400" />}
1589      <field ref="traj_lat"   name="floats_latitude"    freq_op="86400" />}
1590      <field ref="traj_dep"   name="floats_depth"       freq_op="86400" />}
1591      <field ref="traj_temp"  name="floats_temperature" freq_op="86400" />}
1592      <field ref="traj_salt"  name="floats_salinity"    freq_op="86400" />}
1593      <field ref="traj_dens"  name="floats_density"     freq_op="86400" />}
1594      <field ref="traj_group" name="floats_group"       freq_op="86400" />}
1595   </file>}
1596</group>}
1597\end{xmllines}
1598
1599 -  if (\key{iomput}) is not used, a file called \ifile{trajec\_float} will be created by IOIPSL library.
1600
1601 See also \href{http://stockage.univ-brest.fr/~grima/Ariane/}{here} the web site describing the off-line use of
1602 this marvellous diagnostic tool.
1603
1604% -------------------------------------------------------------------------------------------------------------
1605%       Harmonic analysis of tidal constituents
1606% -------------------------------------------------------------------------------------------------------------
1607\section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) }
1608\label{sec:DIA_diag_harm}
1609
1610%------------------------------------------namdia_harm----------------------------------------------------
1611%
1612\nlst{nam_diaharm}
1613%----------------------------------------------------------------------------------------------------------
1614
1615A module is available to compute the amplitude and phase of tidal waves.
1616This on-line Harmonic analysis is actived with \key{diaharm}.
1617
1618Some parameters are available in namelist \ngn{namdia\_harm}:
1619
1620 - \np{nit000\_han} is the first time step used for harmonic analysis
1621
1622 - \np{nitend\_han} is the  last time step used for harmonic analysis
1623
1624 - \np{nstep\_han}  is the  time step frequency for harmonic analysis
1625
1626 - \np{nb\_ana}     is the number of harmonics to analyse
1627
1628 - \np{tname}       is an array with names of tidal constituents to analyse
1629
1630 \np{nit000\_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation.
1631 The restart capability is not implemented.
1632
1633 The Harmonic analysis solve the following equation:
1634
1635 \[
1636   h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i}
1637 \]
1638
1639With $A_{j}$, $\nu_{j}$, $\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error.
1640$h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\
1641We can rewrite this equation:
1642
1643\[
1644  h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i}
1645\]
1646
1647with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ and $\phi_{j}=arctan(S_{j}/C_{j})$.
1648
1649We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave.
1650
1651% -------------------------------------------------------------------------------------------------------------
1652%       Sections transports
1653% -------------------------------------------------------------------------------------------------------------
1654\section{Transports across sections (\protect\key{diadct}) }
1655\label{sec:DIA_diag_dct}
1656
1657%------------------------------------------namdct----------------------------------------------------
1658
1659\nlst{namdct}
1660%-------------------------------------------------------------------------------------------------------------
1661
1662A module is available to compute the transport of volume, heat and salt through sections.
1663This diagnostic is actived with \key{diadct}.
1664
1665Each section is defined by the coordinates of its 2 extremities.
1666The pathways between them are contructed using tools which can be found in \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT}
1667and are written in a binary file \texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is later read in by
1668NEMO to compute on-line transports.
1669
1670The on-line transports module creates three output ascii files:
1671
1672- \texttt{volume\_transport} for volume transports (unit: $10^{6} m^{3} s^{-1}$)
1673
1674- \texttt{heat\_transport}   for   heat transports (unit: $10^{15} W$)
1675
1676- \texttt{salt\_transport}   for   salt transports (unit: $10^{9}Kg s^{-1}$) \\
1677
1678Namelist variables in \ngn{namdct} control how frequently the flows are summed and the time scales over which
1679they are averaged, as well as the level of output for debugging:
1680\np{nn\_dct}   : frequency of instantaneous transports computing
1681\np{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
1682\np{nn\_debug} : debugging of the section
1683
1684\subsubsection{Creating a binary file containing the pathway of each section}
1685
1686In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run},
1687the file \textit{ {list\_sections.ascii\_global}} contains a list of all the sections that are to be computed
1688(this list of sections is based on MERSEA project metrics).
1689
1690Another file is available for the GYRE configuration (\texttt{ {list\_sections.ascii\_GYRE}}).
1691
1692Each section is defined by: \\
1693\noindent {\scriptsize \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\
1694with:
1695
1696 - \texttt{long1 lat1}, coordinates of the  first extremity of the section;
1697
1698 - \texttt{long2 lat2}, coordinates of the second extremity of the section;
1699
1700 - \texttt{nclass}    the number of bounds of your classes (\eg bounds for 2 classes);
1701
1702 - \texttt{okstrpond} to compute    heat and       salt transports, \texttt{nostrpond} if no;
1703
1704 - \texttt{ice}       to compute surface and volume ice transports, \texttt{noice}     if no. \\
1705
1706 \noindent The results of the computing of transports, and the directions of positive and
1707 negative flow do not depend on the order of the 2 extremities in this file. \\
1708
1709\noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\
1710{\scriptsize
1711  \texttt{
1712    long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\
1713    classtype                                                         \\
1714    zbound1                                                           \\
1715    zbound2                                                           \\
1716    .                                                                 \\
1717    .                                                                 \\
1718    nclass-1                                                          \\
1719    nclass}
1720}
1721
1722\noindent where \texttt{classtype} can be:
1723
1724 - \texttt{zsal}  for          salinity classes
1725
1726 - \texttt{ztem}  for       temperature classes
1727
1728 - \texttt{zlay}  for             depth classes
1729
1730 - \texttt{zsigi} for    insitu density classes
1731
1732 - \texttt{zsigp} for potential density classes \\
1733 
1734 The script \texttt{job.ksh} computes the pathway for each section and creates a binary file
1735 \texttt{section\_ijglobal.diadct\_ORCA2\_LIM} which is read by NEMO. \\
1736
1737 It is possible to use this tools for new configuations: \texttt{job.ksh} has to be updated with
1738 the coordinates file name and path. \\
1739
1740 Examples of two sections, the ACC\_Drake\_Passage with no classes,
1741 and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\
1742 \noindent
1743 {\scriptsize
1744   \texttt{
1745     -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage \\
1746     -80.5    22.5   -80.5    25.5  05 nostrpond noice ATL\_Cuba\_Florida  \\
1747     ztem                                                                  \\
1748     -2.0                                                                  \\
1749     4.5                                                                  \\
1750     7.0                                                                  \\
1751     12.0                                                                  \\
1752     40.0}
1753 }
1754
1755\subsubsection{To read the output files}
1756
1757The output format is: \\
1758{\scriptsize
1759  \texttt{
1760    date, time-step number, section number,                \\
1761    section name, section slope coefficient, class number, \\
1762    class name, class bound 1 , classe bound2,             \\
1763    transport\_direction1, transport\_direction2,          \\
1764    transport\_total}
1765}                                     \\
1766
1767For sections with classes, the first \texttt{nclass-1} lines correspond to the transport for each class and
1768the last line corresponds to the total transport summed over all classes.
1769For sections with no classes, class number \texttt{1} corresponds to \texttt{total class} and
1770this class is called \texttt{N}, meaning \texttt{none}.
1771
1772- \texttt{transport\_direction1} is the positive part of the transport ($\geq$ 0).
1773
1774- \texttt{transport\_direction2} is the negative part of the transport ($\leq$ 0). \\
1775
1776\noindent The \texttt{section slope coefficient} gives information about the significance of transports signs and
1777direction: \\
1778
1779\begin{table}
1780  \scriptsize
1781  \begin{tabular}{|l|l|l|l|l|}
1782    \hline
1783    section slope coefficient      & section type & direction 1 & direction 2 & total transport    \\
1784    \hline
1785    0.                             & horizontal  & northward   & southward   & postive: northward    \\
1786    \hline
1787    1000.                          & vertical     & eastward    & westward    & postive: eastward     \\
1788    \hline
1789    \texttt{$\neq$ 0, $\neq$ 1000.} & diagonal     & eastward    & westward     & postive: eastward      \\
1790    \hline
1791  \end{tabular}
1792\end{table}
1793
1794% ================================================================
1795% Steric effect in sea surface height
1796% ================================================================
1797\section{Diagnosing the steric effect in sea surface height}
1798\label{sec:DIA_steric}
1799
1800
1801Changes in steric sea level are caused when changes in the density of the water column imply an expansion or
1802contraction of the column.
1803It is essentially produced through surface heating/cooling and to a lesser extent through non-linear effects of
1804the equation of state (cabbeling, thermobaricity...).
1805Non-Boussinesq models contain all ocean effects within the ocean acting on the sea level.
1806In particular, they include the steric effect.
1807In contrast, Boussinesq models, such as \NEMO, conserve volume, rather than mass,
1808and so do not properly represent expansion or contraction.
1809The steric effect is therefore not explicitely represented.
1810This approximation does not represent a serious error with respect to the flow field calculated by the model
1811\citep{Greatbatch_JGR94}, but extra attention is required when investigating sea level,
1812as steric changes are an important contribution to local changes in sea level on seasonal and climatic time scales.
1813This is especially true for investigation into sea level rise due to global warming.
1814
1815Fortunately, the steric contribution to the sea level consists of a spatially uniform component that
1816can be diagnosed by considering the mass budget of the world ocean \citep{Greatbatch_JGR94}.
1817In order to better understand how global mean sea level evolves and thus how the steric sea level can be diagnosed,
1818we compare, in the following, the non-Boussinesq and Boussinesq cases.
1819
1820Let denote
1821$\mathcal{M}$ the total mass    of liquid seawater ($\mathcal{M} = \int_D \rho dv$),
1822$\mathcal{V}$ the total volume  of        seawater      ($\mathcal{V} = \int_D dv$),
1823$\mathcal{A}$ the total surface of       the ocean      ($\mathcal{A} = \int_S ds$),
1824$\bar{\rho}$ the global mean  seawater (\textit{in situ}) density
1825($\bar{\rho} = 1/\mathcal{V} \int_D \rho \,dv$), and
1826$\bar{\eta}$ the global mean sea level
1827($\bar{\eta} = 1/\mathcal{A} \int_S \eta \,ds$).
1828
1829A non-Boussinesq fluid conserves mass. It satisfies the following relations:
1830
1831\begin{equation}
1832  \begin{split}
1833    \mathcal{M} &\mathcal{V}  \;\bar{\rho} \\
1834    \mathcal{V} &\mathcal{A}  \;\bar{\eta}
1835  \end{split}
1836  \label{eq:MV_nBq}
1837\end{equation}
1838
1839Temporal changes in total mass is obtained from the density conservation equation:
1840
1841\begin{equation}
1842  \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} )
1843  = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface}
1844  \label{eq:Co_nBq}
1845\end{equation}
1846
1847where $\rho$ is the \textit{in situ} density, and \textit{emp} the surface mass exchanges with the other media of
1848the Earth system (atmosphere, sea-ice, land).
1849Its global averaged leads to the total mass change
1850
1851\begin{equation}
1852  \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}}
1853  \label{eq:Mass_nBq}
1854\end{equation}
1855
1856where $\overline{\textit{emp}} = \int_S \textit{emp}\,ds$ is the net mass flux through the ocean surface.
1857Bringing \autoref{eq:Mass_nBq} and the time derivative of \autoref{eq:MV_nBq} together leads to
1858the evolution equation of the mean sea level
1859
1860\begin{equation}
1861  \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}}
1862  - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}}
1863  \label{eq:ssh_nBq}
1864\end{equation}
1865
1866The first term in equation \autoref{eq:ssh_nBq} alters sea level by adding or subtracting mass from the ocean.
1867The second term arises from temporal changes in the global mean density; \ie from steric effects.
1868
1869In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ appears multiplied by
1870the gravity (\ie in the hydrostatic balance of the primitive Equations).
1871In particular, the mass conservation equation, \autoref{eq:Co_nBq}, degenerates into the incompressibility equation:
1872
1873\[
1874  \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface}
1875  % \label{eq:Co_Bq}
1876\]
1877
1878and the global average of this equation now gives the temporal change of the total volume,
1879
1880\[
1881  \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o}
1882  % \label{eq:V_Bq}
1883\]
1884
1885Only the volume is conserved, not mass, or, more precisely, the mass which is conserved is the Boussinesq mass,
1886$\mathcal{M}_o = \rho_o \mathcal{V}$.
1887The total volume (or equivalently the global mean sea level) is altered only by net volume fluxes across
1888the ocean surface, not by changes in mean mass of the ocean: the steric effect is missing in a Boussinesq fluid.
1889
1890Nevertheless, following \citep{Greatbatch_JGR94}, the steric effect on the volume can be diagnosed by
1891considering the mass budget of the ocean.
1892The apparent changes in $\mathcal{M}$, mass of the ocean, which are not induced by surface mass flux
1893must be compensated by a spatially uniform change in the mean sea level due to expansion/contraction of the ocean
1894\citep{Greatbatch_JGR94}.
1895In others words, the Boussinesq mass, $\mathcal{M}_o$, can be related to $\mathcal{M}$,
1896the total mass of the ocean seen by the Boussinesq model, via the steric contribution to the sea level,
1897$\eta_s$, a spatially uniform variable, as follows:
1898
1899\begin{equation}
1900  \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A}
1901  \label{eq:M_Bq}
1902\end{equation}
1903
1904Any change in $\mathcal{M}$ which cannot be explained by the net mass flux through the ocean surface
1905is converted into a mean change in sea level.
1906Introducing the total density anomaly, $\mathcal{D}= \int_D d_a \,dv$,
1907where $d_a = (\rho -\rho_o ) / \rho_o$ is the density anomaly used in \NEMO (cf. \autoref{subsec:TRA_eos})
1908in \autoref{eq:M_Bq} leads to a very simple form for the steric height:
1909
1910\begin{equation}
1911  \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D}
1912  \label{eq:steric_Bq}
1913\end{equation}
1914
1915The above formulation of the steric height of a Boussinesq ocean requires four remarks.
1916First, one can be tempted to define $\rho_o$ as the initial value of $\mathcal{M}/\mathcal{V}$,
1917\ie set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero.
1918We do not recommend that.
1919Indeed, in this case $\rho_o$ depends on the initial state of the ocean.
1920Since $\rho_o$ has a direct effect on the dynamics of the ocean
1921(it appears in the pressure gradient term of the momentum equation)
1922it is definitively not a good idea when inter-comparing experiments.
1923We better recommend to fixe once for all $\rho_o$ to $1035\;Kg\,m^{-3}$.
1924This value is a sensible choice for the reference density used in a Boussinesq ocean climate model since,
1925with the exception of only a small percentage of the ocean, density in the World Ocean varies by no more than
19262$\%$ from this value (\cite{Gill1982}, page 47).
1927
1928Second, we have assumed here that the total ocean surface, $\mathcal{A}$,
1929does not change when the sea level is changing as it is the case in all global ocean GCMs
1930(wetting and drying of grid point is not allowed).
1931 
1932Third, the discretisation of \autoref{eq:steric_Bq} depends on the type of free surface which is considered.
1933In the non linear free surface case, \ie \key{vvl} defined, it is given by
1934
1935\[
1936  \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} }{ \sum_{i,\,j,\,k}       e_{1t} e_{2t} e_{3t} }
1937  % \label{eq:discrete_steric_Bq_nfs}
1938\]
1939
1940whereas in the linear free surface,
1941the volume above the \textit{z=0} surface must be explicitly taken into account to
1942better approximate the total ocean mass and thus the steric sea level:
1943
1944\[
1945  \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta }
1946                  { \sum_{i,\,j,\,k}       e_{1t}e_{2t}e_{3t} + \sum_{i,\,j}       e_{1t}e_{2t} \eta }
1947  % \label{eq:discrete_steric_Bq_fs}
1948\]
1949
1950The fourth and last remark concerns the effective sea level and the presence of sea-ice.
1951In the real ocean, sea ice (and snow above it)  depresses the liquid seawater through its mass loading.
1952This depression is a result of the mass of sea ice/snow system acting on the liquid ocean.
1953There is, however, no dynamical effect associated with these depressions in the liquid ocean sea level,
1954so that there are no associated ocean currents.
1955Hence, the dynamically relevant sea level is the effective sea level,
1956\ie the sea level as if sea ice (and snow) were converted to liquid seawater \citep{Campin_al_OM08}.
1957However, in the current version of \NEMO the sea-ice is levitating above the ocean without mass exchanges between
1958ice and ocean.
1959Therefore the model effective sea level is always given by $\eta + \eta_s$, whether or not there is sea ice present.
1960
1961In AR5 outputs, the thermosteric sea level is demanded.
1962It is steric sea level due to changes in ocean density arising just from changes in temperature.
1963It is given by:
1964
1965\[
1966  \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv
1967  % \label{eq:thermosteric_Bq}
1968\]
1969
1970where $S_o$ and $p_o$ are the initial salinity and pressure, respectively.
1971
1972Both steric and thermosteric sea level are computed in \mdl{diaar5} which needs the \key{diaar5} defined to
1973be called.
1974
1975% -------------------------------------------------------------------------------------------------------------
1976%       Other Diagnostics
1977% -------------------------------------------------------------------------------------------------------------
1978\section{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})}
1979\label{sec:DIA_diag_others}
1980
1981Aside from the standard model variables, other diagnostics can be computed on-line.
1982The available ready-to-add diagnostics modules can be found in directory DIA.
1983
1984\subsection{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_al_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%     Poleward heat and salt transports
1998% -----------------------------------------------------------
1999
2000\subsection{Poleward heat and salt transports (\protect\mdl{diaptr})}
2001
2002%------------------------------------------namptr-----------------------------------------
2003
2004\nlst{namptr} 
2005%-----------------------------------------------------------------------------------------
2006
2007The poleward heat and salt transports, their advective and diffusive component,
2008and the meriodional stream function can be computed on-line in \mdl{diaptr} \np{ln\_diaptr} to true
2009(see the \textit{\ngn{namptr} } namelist below).
2010When \np{ln\_subbas}\forcode{ = .true.}, transports and stream function are computed for the Atlantic, Indian,
2011Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean.
2012The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays,
2013the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:mask_subasins}).
2014
2015%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2016\begin{figure}[!t]
2017  \begin{center}
2018    \includegraphics[width=1.0\textwidth]{Fig_mask_subasins}
2019    \caption{
2020      \protect\label{fig:mask_subasins}
2021      Decomposition of the World Ocean (here ORCA2) into sub-basin used in to
2022      compute the heat and salt transports as well as the meridional stream-function:
2023      Atlantic basin (red), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).
2024      Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay are removed from the sub-basins.
2025      Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line.
2026    }
2027  \end{center}
2028\end{figure} 
2029%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2030
2031% -----------------------------------------------------------
2032%       CMIP specific diagnostics
2033% -----------------------------------------------------------
2034\subsection{CMIP specific diagnostics (\protect\mdl{diaar5})}
2035
2036A series of diagnostics has been added in the \mdl{diaar5}.
2037They corresponds to outputs that are required for AR5 simulations (CMIP5)
2038(see also \autoref{sec:DIA_steric} for one of them).
2039Activating those outputs requires to define the \key{diaar5} CPP key.
2040
2041% -----------------------------------------------------------
2042%       25 hour mean and hourly Surface, Mid and Bed
2043% -----------------------------------------------------------
2044\subsection{25 hour mean output for tidal models}
2045
2046%------------------------------------------nam_dia25h-------------------------------------
2047
2048\nlst{nam_dia25h}
2049%-----------------------------------------------------------------------------------------
2050
2051A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean.
2052The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from
2053midnight at the start of the day to midight at the day end.
2054This diagnostic is actived with the logical $ln\_dia25h$.
2055
2056% -----------------------------------------------------------
2057%     Top Middle and Bed hourly output
2058% -----------------------------------------------------------
2059\subsection{Top middle and bed hourly output}
2060
2061%------------------------------------------nam_diatmb-----------------------------------------------------
2062
2063\nlst{nam_diatmb}
2064%----------------------------------------------------------------------------------------------------------
2065
2066A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables.
2067This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs.
2068The tidal signal is retained but the overall data usage is cut to just three vertical levels.
2069Also the bottom level is calculated for each cell.
2070This diagnostic is actived with the logical $ln\_diatmb$.
2071
2072% -----------------------------------------------------------
2073%     Courant numbers
2074% -----------------------------------------------------------
2075\subsection{Courant numbers}
2076
2077Courant numbers provide a theoretical indication of the model's numerical stability.
2078The advective Courant numbers can be calculated according to
2079
2080\[
2081  C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}}
2082  % \label{eq:CFL}
2083\]
2084
2085in the zonal, meridional and vertical directions respectively.
2086The vertical component is included although it is not strictly valid as the vertical velocity is calculated from
2087the continuity equation rather than as a prognostic variable.
2088Physically this represents the rate at which information is propogated across a grid cell.
2089Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step.
2090
2091The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist.
2092The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii.
2093In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of
2094where the maximum value occurs.
2095At 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
2096with the coordinates of each.
2097The maximum values from the run are also copied to the ocean.output file.
2098
2099% ================================================================
2100
2101\biblio
2102
2103\pindex
2104
2105\end{document}
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