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Changeset 11799 for NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/NEMO/subfiles/chap_DIA.tex – NEMO

Ignore:
Timestamp:
2019-10-25T16:27:34+02:00 (5 years ago)
Author:
mocavero
Message:

Update the branch to v4.0.1 of the trunk

Location:
NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc
Files:
5 edited

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  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/NEMO/subfiles/chap_DIA.tex

    r11435 r11799  
    22 
    33\begin{document} 
    4 % ================================================================ 
    5 % Chapter I/O & Diagnostics 
    6 % ================================================================ 
     4 
    75\chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)} 
    86\label{chap:DIA} 
    97 
     8%    {\em 4.0} & {\em Mirek Andrejczuk, Massimiliano Drudi} & {\em }  \\ 
     9%    {\em }      & {\em Dorotea Iovino, Nicolas Martin} & {\em }  \\ 
     10%    {\em 3.6} & {\em Gurvan Madec, Sebastien Masson } & {\em }  \\ 
     11%    {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em }  \\ 
     12%    {\em }      & {\em Christian Ethe, Sebastien Masson } & {\em }  \\ 
     13 
     14\thispagestyle{plain} 
     15 
    1016\chaptertoc 
    1117 
    12 \vfill 
    13 \begin{figure}[b] 
    14 \subsubsection*{Changes record} 
    15 \begin{tabular}{l||l|m{0.65\linewidth}} 
    16     Release   & Author        & Modifications \\ 
    17     {\em 4.0} & {\em Mirek Andrejczuk, Massimiliano Drudi} & {\em }  \\ 
    18     {\em }      & {\em Dorotea Iovino, Nicolas Martin} & {\em }  \\ 
    19     {\em 3.6} & {\em Gurvan Madec, Sebastien Masson } & {\em }  \\ 
    20     {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em }  \\ 
    21     {\em }      & {\em Christian Ethe, Sebastien Masson } & {\em }  \\ 
    22 \end{tabular} 
    23 \end{figure} 
    24  
    25 \newpage 
    26  
    27 % ================================================================ 
    28 %       Old Model Output 
    29 % ================================================================ 
     18\paragraph{Changes record} ~\\ 
     19 
     20{\footnotesize 
     21  \begin{tabularx}{\textwidth}{l||X|X} 
     22    Release & Author(s) & Modifications \\ 
     23    \hline 
     24    {\em   4.0} & {\em ...} & {\em ...} \\ 
     25    {\em   3.6} & {\em ...} & {\em ...} \\ 
     26    {\em   3.4} & {\em ...} & {\em ...} \\ 
     27    {\em <=3.4} & {\em ...} & {\em ...} 
     28  \end{tabularx} 
     29} 
     30 
     31\clearpage 
     32 
     33%% ================================================================================================= 
    3034\section{Model output} 
    3135\label{sec:DIA_io_old} 
    … …  
    5357%\gmcomment{                    % start of gmcomment 
    5458 
    55 % ================================================================ 
    56 % Diagnostics 
    57 % ================================================================ 
     59%% ================================================================================================= 
    5860\section{Standard model output (IOM)} 
    5961\label{sec:DIA_iom} 
    … …  
    6466 
    6567\begin{enumerate} 
    66 \item 
    67   The complete and flexible control of the output files through external XML files adapted by 
     68\item The complete and flexible control of the output files through external XML files adapted by 
    6869  the user from standard templates. 
    69 \item 
    70   To achieve high performance and scalable output through the optional distribution of 
     70\item To achieve high performance and scalable output through the optional distribution of 
    7171  all diagnostic output related tasks to dedicated processes. 
    7272\end{enumerate} 
    … …  
    7676 
    7777\begin{itemize} 
    78 \item 
    79   The choice of output frequencies that can be different for each file (including real months and years). 
    80 \item 
    81   The choice of file contents; includes complete flexibility over which data are written in which files 
     78\item The choice of output frequencies that can be different for each file (including real months and years). 
     79\item The choice of file contents; includes complete flexibility over which data are written in which files 
    8280  (the same data can be written in different files). 
    83 \item 
    84   The possibility to split output files at a chosen frequency. 
    85 \item 
    86   The possibility to extract a vertical or an horizontal subdomain. 
    87 \item 
    88   The choice of the temporal operation to perform, \eg: average, accumulate, instantaneous, min, max and once. 
    89 \item 
    90   Control over metadata via a large XML "database" of possible output fields. 
     81\item The possibility to split output files at a chosen frequency. 
     82\item The possibility to extract a vertical or an horizontal subdomain. 
     83\item The choice of the temporal operation to perform, \eg: average, accumulate, instantaneous, min, max and once. 
     84\item Control over metadata via a large XML "database" of possible output fields. 
    9185\end{itemize} 
    9286 
    … …  
    122116even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server. 
    123117 
     118%% ================================================================================================= 
    124119\subsection{XIOS: Reading and writing restart file} 
    125120 
    126121XIOS may be used to read single file restart produced by \NEMO. Currently only the variables written to 
    127 file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np{ln\_xios\_read}\forcode{ = .true. } 
     122file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np[=.true. ]{ln_xios_read}{ln\_xios\_read} 
    128123in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default \NEMO 
    129124functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read 
    … …  
    140135dimension \forcode{z} defined in restart file must be renamed to \forcode{nav_lev}.\\ 
    141136 
    142 XIOS can also be used to write \NEMO\ restart. A namelist parameter \np{nn\_wxios} is used to determine the 
     137XIOS can also be used to write \NEMO\ restart. A namelist parameter \np{nn_wxios}{nn\_wxios} is used to determine the 
    143138type of restart \NEMO\ will write. If it is set to 0, default \NEMO\ functionality will be used - each 
    144139processor writes its own restart file; if it is set to 1 XIOS will write restart into a single file; 
    145 for \np{nn\_wxios}\forcode{ = 2} the restart will be written by XIOS into multiple files, one for each XIOS server. 
    146 Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np{nn\_wxios}\forcode{ = 2}}. The restart will 
     140for \np[=2]{nn_wxios}{nn\_wxios} the restart will be written by XIOS into multiple files, one for each XIOS server. 
     141Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np[=2]{nn_wxios}{nn\_wxios}}. The restart will 
    147142have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by \NEMO\ only, 
    148143and may be useful when there is a need to change number of processors used to run simulation. 
    149144 
    150145If an additional variable must be written to a restart file, the following steps are needed: 
    151 \begin{description} 
    152    \item[step 1:] add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and 
     146\begin{enumerate} 
     147\item Add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and 
    153148define correct grid for the variable (\forcode{grid_N_3D} - 3D variable, \forcode{grid_N} - 2D variable, \forcode{grid_vector} - 
    1541491D variable, \forcode{grid_scalar} - scalar), 
    155    \item[step 2:] add variable to the list of fields written by restart.  This can be done either in subroutine 
     150\item Add variable to the list of fields written by restart.  This can be done either in subroutine 
    156151\rou{iom\_set\_rstw\_core} (\mdl{iom}) or by calling  \rou{iom\_set\_rstw\_active} (\mdl{iom}) with the name of a variable 
    157152as an argument. This convention follows approach for writing restart using iom, where variables are 
    158153written either by \rou{rst\_write} or by calling \rou{iom\_rstput} from individual routines. 
    159 \end{description} 
    160  
     154\end{enumerate} 
    161155 
    162156An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451. 
    163157 
    164  
     158%% ================================================================================================= 
    165159\subsection{XIOS: XML Inputs-Outputs Server} 
    166160 
     161%% ================================================================================================= 
    167162\subsubsection{Attached or detached mode?} 
    168163 
    … …  
    174169\xmlline|<variable id="using_server" type="bool"></variable>| 
    175170 
    176 The {\ttfamily using\_server} setting determines whether or not the server will be used in \textit{attached mode} 
    177 (as a library) [{\ttfamily> false <}] or in \textit{detached mode} 
    178 (as an external executable on N additional, dedicated cpus) [{\ttfamily > true <}]. 
    179 The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications. 
     171The \texttt{using\_server} setting determines whether or not the server will be used in 
     172\textit{attached mode} 
     173(as a library) [\texttt{> false <}] or in \textit{detached mode} 
     174(as an external executable on N additional, dedicated cpus) [\texttt{ > true <}]. 
     175The \textit{attached mode} is simpler to use but much less efficient for 
     176massively parallel applications. 
    180177The type of each file can be either ''multiple\_file'' or ''one\_file''. 
    181178 
    … …  
    197194The following subsection provides a typical example but the syntax will vary in different MPP environments. 
    198195 
     196%% ================================================================================================= 
    199197\subsubsection{Number of cpu used by XIOS in detached mode} 
    200198 
    … …  
    211209\cmd|mpirun -np 62 ./nemo.exe : -np 2 ./xios_server.exe| 
    212210 
     211%% ================================================================================================= 
    213212\subsubsection{Control of XIOS: the context in iodef.xml} 
    214213 
    … …  
    218217 
    219218\begin{table} 
    220   \scriptsize 
    221219  \begin{tabularx}{\textwidth}{|lXl|} 
    222220    \hline 
    … …  
    257255\end{table} 
    258256 
     257%% ================================================================================================= 
    259258\subsection{Practical issues} 
    260259 
     260%% ================================================================================================= 
    261261\subsubsection{Installation} 
    262262 
    … …  
    267267{Extract and install XIOS} guide provides an example illustration of how this can be achieved. 
    268268 
     269%% ================================================================================================= 
    269270\subsubsection{Add your own outputs} 
    270271 
    … …  
    275276 
    276277\begin{enumerate} 
    277 \item[1.] 
    278   in \NEMO\ code, add a \forcode{CALL iom_put( 'identifier', array )} where you want to output a 2D or 3D array. 
    279 \item[2.] 
    280   If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in 
     278\item in \NEMO\ code, add a \forcode{CALL iom_put( 'identifier', array )} where you want to output a 2D or 3D array. 
     279\item If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in 
    281280  the upper part of your module. 
    282 \item[3.] 
    283   in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code 
     281\item in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code 
    284282  (see subsequent sections for a details of the XML syntax and rules). 
    285283  For example: 
    286  
    287284\begin{xmllines} 
    288285<field_definition> 
    … …  
    293290</field_definition> 
    294291\end{xmllines} 
    295  
    296292Note your definition must be added to the field\_group whose reference grid is consistent with the size of 
    297293the array passed to iomput. 
    … …  
    300296(iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file. 
    301297\eg: 
    302  
    303298\begin{xmllines} 
    304299<grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> 
    305300\end{xmllines} 
    306  
    307 Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step, 
     301Note, if your array is computed within the surface module each \np{nn_fsbc}{nn\_fsbc} time\_step, 
    308302add the field definition within the field\_group defined with the id "SBC": 
    309303\xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations 
    310304(iom\_set\_field\_attr in \mdl{iom}) 
    311 \item[4.] 
    312   add your field in one of the output files defined in iodef.xml 
     305\item add your field in one of the output files defined in iodef.xml 
    313306  (again see subsequent sections for syntax and rules) 
    314  
    315307\begin{xmllines} 
    316308<file id="file1" .../> 
    … …  
    320312</file> 
    321313\end{xmllines} 
    322  
    323314\end{enumerate} 
    324315 
     316%% ================================================================================================= 
    325317\subsection{XML fundamentals} 
    326318 
     319%% ================================================================================================= 
    327320\subsubsection{ XML basic rules} 
    328321 
    … …  
    334327See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details. 
    335328 
     329%% ================================================================================================= 
    336330\subsubsection{Structure of the XML file used in \NEMO} 
    337331 
    … …  
    341335 
    342336\begin{table} 
    343   \scriptsize 
    344337  \begin{tabular*}{\textwidth}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 
    345338    \hline 
    … …  
    373366 
    374367\begin{table} 
    375   \scriptsize 
    376368  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 
    377369    \hline 
    … …  
    398390 
    399391\begin{table} 
    400   \scriptsize 
    401392  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 
    402393    \hline 
    … …  
    418409 
    419410\begin{table} 
    420   \scriptsize 
    421411  \begin{tabular}{|p{0.15\textwidth}p{0.4\textwidth}p{0.35\textwidth}|} 
    422412    \hline 
    … …  
    443433\end{table} 
    444434 
     435%% ================================================================================================= 
    445436\subsubsection{Nesting XML files} 
    446437 
    … …  
    459450\end{xmllines} 
    460451 
     452%% ================================================================================================= 
    461453\subsubsection{Use of inheritance} 
    462454 
    … …  
    499491Inherit (and overwrite, if needed) the attributes of a tag you are refering to. 
    500492 
     493%% ================================================================================================= 
    501494\subsubsection{Use of groups} 
    502495 
    … …  
    540533\end{xmllines} 
    541534 
     535%% ================================================================================================= 
    542536\subsection{Detailed functionalities} 
    543537 
    … …  
    545539the new functionalities offered by the XML interface of XIOS. 
    546540 
     541%% ================================================================================================= 
    547542\subsubsection{Define horizontal subdomains} 
    548543 
    … …  
    586581We are therefore advising to use the ''one\_file'' type in this case. 
    587582 
     583%% ================================================================================================= 
    588584\subsubsection{Define vertical zooms} 
    589585 
    … …  
    609605\end{xmllines} 
    610606 
     607%% ================================================================================================= 
    611608\subsubsection{Control of the output file names} 
    612609 
    … …  
    634631 
    635632\begin{table} 
    636   \scriptsize 
    637633  \begin{tabularx}{\textwidth}{|lX|} 
    638634    \hline 
    … …  
    682678\noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d} 
    683679 
     680%% ================================================================================================= 
    684681\subsubsection{Other controls of the XML attributes from \NEMO} 
    685682 
    … …  
    695692 
    696693\begin{table} 
    697   \scriptsize 
    698   \begin{tabularx}{\textwidth}{|X|c|c|c|} 
     694  \begin{tabular}{|l|c|c|} 
    699695    \hline 
    700696    tag ids affected by automatic definition of some of their attributes & 
    701697    name attribute                                                       & 
    702     attribute value                      \\ 
     698    attribute value                                                      \\ 
    703699    \hline 
    704700    \hline 
    705701    field\_definition                                                    & 
    706702    freq\_op                                                             & 
    707     \np{rn\_rdt}                         \\ 
     703    \np{rn_rdt}{rn\_rdt}                                                         \\ 
    708704    \hline 
    709705    SBC                                                                  & 
    710706    freq\_op                                                             & 
    711     \np{rn\_rdt} $\times$ \np{nn\_fsbc}  \\ 
     707    \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_fsbc}{nn\_fsbc}                                  \\ 
    712708    \hline 
    713709    ptrc\_T                                                              & 
    714710    freq\_op                                                             & 
    715     \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ 
     711    \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_dttrc}{nn\_dttrc}                                \\ 
    716712    \hline 
    717713    diad\_T                                                              & 
    718714    freq\_op                                                             & 
    719     \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ 
     715    \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_dttrc}{nn\_dttrc}                                \\ 
    720716    \hline 
    721717    EqT, EqU, EqW                                                        & 
    722718    jbegin, ni,                                                          & 
    723     according to the grid                \\ 
    724     & 
     719    according to the grid                                                \\ 
     720                                                                         & 
    725721    name\_suffix                                                         & 
    726     \\ 
     722                                                                         \\ 
    727723    \hline 
    728724    TAO, RAMA and PIRATA moorings                                        & 
    729725    zoom\_ibegin, zoom\_jbegin,                                          & 
    730     according to the grid                \\ 
    731     & 
     726    according to the grid                                                \\ 
     727                                                                         & 
    732728    name\_suffix                                                         & 
    733     \\ 
    734     \hline 
    735   \end{tabularx} 
     729                                                                         \\ 
     730    \hline 
     731  \end{tabular} 
    736732\end{table} 
    737733 
     734%% ================================================================================================= 
    738735\subsubsection{Advanced use of XIOS functionalities} 
    739736 
     737%% ================================================================================================= 
    740738\subsection{XML reference tables} 
    741 \label{subsec:IOM_xmlref} 
     739\label{subsec:DIA_IOM_xmlref} 
    742740 
    743741\begin{enumerate} 
    744 \item 
    745   Simple computation: directly define the computation when refering to the variable in the file definition. 
     742\item Simple computation: directly define the computation when refering to the variable in the file definition. 
    746743 
    747744\begin{xmllines} 
    … …  
    751748\end{xmllines} 
    752749 
    753 \item 
    754   Simple computation: define a new variable and use it in the file definition. 
     750\item Simple computation: define a new variable and use it in the file definition. 
    755751 
    756752in field\_definition: 
    … …  
    769765sst2 won't be evaluated. 
    770766 
    771 \item 
    772   Change of variable precision: 
     767\item Change of variable precision: 
    773768 
    774769\begin{xmllines} 
    … …  
    783778Forcing double precision outputs with prec="8" (for example in the field\_definition) will avoid this problem. 
    784779 
    785 \item 
    786   add user defined attributes: 
     780\item add user defined attributes: 
    787781 
    788782\begin{xmllines} 
    … …  
    799793\end{xmllines} 
    800794 
    801 \item 
    802   use of the ``@'' function: example 1, weighted temporal average 
     795\item use of the ``@'' function: example 1, weighted temporal average 
    803796 
    804797 - define a new variable in field\_definition 
    … …  
    828821Note that in this case, freq\_op must be equal to the file output\_freq. 
    829822 
    830 \item 
    831   use of the ``@'' function: example 2, monthly SSH standard deviation 
     823\item use of the ``@'' function: example 2, monthly SSH standard deviation 
    832824 
    833825 - define a new variable in field\_definition 
    … …  
    859851Note that in this case, freq\_op must be equal to the file output\_freq. 
    860852 
    861 \item 
    862   use of the ``@'' function: example 3, monthly average of SST diurnal cycle 
     853\item use of the ``@'' function: example 3, monthly average of SST diurnal cycle 
    863854 
    864855 - define 2 new variables in field\_definition 
    … …  
    891882field\_ref="sst" means that attributes not explicitely defined, are inherited from sst field. 
    892883 
     884%% ================================================================================================= 
    893885\subsubsection{Tag list per family} 
    894886 
    895887\begin{table} 
    896   \scriptsize 
    897888  \begin{tabularx}{\textwidth}{|l|X|X|l|X|} 
    898889    \hline 
    … …  
    917908    \hline 
    918909  \end{tabularx} 
    919   \caption{Context tags} 
     910  \caption{XIOS: context tags} 
    920911\end{table} 
    921912 
    922913\begin{table} 
    923   \scriptsize 
    924914  \begin{tabularx}{\textwidth}{|l|X|X|X|l|} 
    925915    \hline 
    … …  
    952942    \hline 
    953943  \end{tabularx} 
    954   \caption{Field tags ("\ttfamily{field\_*}")} 
     944  \caption{XIOS: field tags ("\texttt{field\_*}")} 
    955945\end{table} 
    956946 
    957947\begin{table} 
    958   \scriptsize 
    959948  \begin{tabularx}{\textwidth}{|l|X|X|X|l|} 
    960949    \hline 
    … …  
    988977    \hline 
    989978  \end{tabularx} 
    990   \caption{File tags ("\ttfamily{file\_*}")} 
     979  \caption{XIOS: file tags ("\texttt{file\_*}")} 
    991980\end{table} 
    992981 
    993982\begin{table} 
    994   \scriptsize 
    995983  \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 
    996984    \hline 
    … …  
    10211009    \hline 
    10221010  \end{tabularx} 
    1023   \caption{Axis tags ("\ttfamily{axis\_*}")} 
     1011  \caption{XIOS: axis tags ("\texttt{axis\_*}")} 
    10241012\end{table} 
    10251013 
    10261014\begin{table} 
    1027   \scriptsize 
    10281015  \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 
    10291016    \hline 
    … …  
    10541041    \hline 
    10551042  \end{tabularx} 
    1056   \caption{Domain tags ("\ttfamily{domain\_*)}"} 
     1043  \caption{XIOS: domain tags ("\texttt{domain\_*)}"} 
    10571044\end{table} 
    10581045 
    10591046\begin{table} 
    1060   \scriptsize 
    10611047  \begin{tabularx}{\textwidth}{|l|X|X|X|X|} 
    10621048    \hline 
    … …  
    10871073    \hline 
    10881074  \end{tabularx} 
    1089   \caption{Grid tags ("\ttfamily{grid\_*}")} 
     1075  \caption{XIOS: grid tags ("\texttt{grid\_*}")} 
    10901076\end{table} 
    10911077 
     1078%% ================================================================================================= 
    10921079\subsubsection{Attributes list per family} 
    10931080 
    10941081\begin{table} 
    1095   \scriptsize 
    10961082  \begin{tabularx}{\textwidth}{|l|X|l|l|} 
    10971083    \hline 
    … …  
    11281114    \hline 
    11291115  \end{tabularx} 
    1130   \caption{Reference attributes ("\ttfamily{*\_ref}")} 
     1116  \caption{XIOS: reference attributes ("\texttt{*\_ref}")} 
    11311117\end{table} 
    11321118 
    11331119\begin{table} 
    1134   \scriptsize 
    11351120  \begin{tabularx}{\textwidth}{|l|X|l|l|} 
    11361121    \hline 
    … …  
    11641149    \hline 
    11651150  \end{tabularx} 
    1166   \caption{Domain attributes ("\ttfamily{zoom\_*}")} 
     1151  \caption{XIOS: domain attributes ("\texttt{zoom\_*}")} 
    11671152\end{table} 
    11681153 
    11691154\begin{table} 
    1170   \scriptsize 
    11711155  \begin{tabularx}{\textwidth}{|l|X|l|l|} 
    11721156    \hline 
    … …  
    12191203    \hline 
    12201204  \end{tabularx} 
    1221   \caption{File attributes} 
     1205  \caption{XIOS: file attributes} 
    12221206\end{table} 
    12231207 
    12241208\begin{table} 
    1225   \scriptsize 
    12261209  \begin{tabularx}{\textwidth}{|l|X|l|l|} 
    12271210    \hline 
    … …  
    12681251    \hline 
    12691252  \end{tabularx} 
    1270   \caption{Field attributes} 
     1253  \caption{XIOS: field attributes} 
    12711254\end{table} 
    12721255 
    12731256\begin{table} 
    1274   \scriptsize 
    12751257  \begin{tabularx}{\textwidth}{|l|X|X|X|} 
    12761258    \hline 
    … …  
    13271309    \hline 
    13281310  \end{tabularx} 
    1329   \caption{Miscellaneous attributes} 
     1311  \caption{XIOS: miscellaneous attributes} 
    13301312\end{table} 
    13311313 
     1314%% ================================================================================================= 
    13321315\subsection{CF metadata standard compliance} 
    13331316 
    … …  
    13361319the CF metadata standard. 
    13371320Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of 
    1338 section \autoref{subsec:IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard. 
     1321section \autoref{subsec:DIA_IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard. 
    13391322 
    13401323Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by 
    1341 the namelist parameter \np{ln\_cfmeta} in the \nam{run} namelist. 
     1324the namelist parameter \np{ln_cfmeta}{ln\_cfmeta} in the \nam{run}{run} namelist. 
    13421325This must be set to true if these metadata are to be included in the output files. 
    13431326 
    1344  
    1345 % ================================================================ 
    1346 %       NetCDF4 support 
    1347 % ================================================================ 
    1348 \section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})] 
    1349 {NetCDF4 support (\protect\key{netcdf4})} 
     1327%% ================================================================================================= 
     1328\section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})]{NetCDF4 support (\protect\key{netcdf4})} 
    13501329\label{sec:DIA_nc4} 
    13511330 
    … …  
    13621341most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files. 
    13631342\NEMO\ executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by 
    1364 setting the \np{ln\_nc4zip} logical to false in the \nam{nc4} namelist: 
    1365  
    1366 %------------------------------------------namnc4---------------------------------------------------- 
    1367  
    1368 \nlst{namnc4} 
    1369 %------------------------------------------------------------------------------------------------------------- 
     1343setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4}{nc4} namelist: 
     1344 
     1345\begin{listing} 
     1346  \nlst{namnc4} 
     1347  \caption{\forcode{&namnc4}} 
     1348  \label{lst:namnc4} 
     1349\end{listing} 
    13701350 
    13711351If \key{netcdf4} has not been defined, these namelist parameters are not read. 
    1372 In this case, \np{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined. 
     1352In this case, \np{ln_nc4zip}{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined. 
    13731353These functions will not be used but need to be included so that compilation is possible with NetCDF3 libraries. 
    13741354 
    … …  
    14041384\end{forlines} 
    14051385 
    1406 \noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\ttfamily 46x38x1} respectively in 
    1407 the mono-processor case (\ie\ global domain of {\small\ttfamily 182x149x31}). 
     1386\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\texttt 46x38x1} respectively in 
     1387the mono-processor case (\ie\ global domain of {\small\texttt 182x149x31}). 
    14081388An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in 
    1409 table \autoref{tab:NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with 
     1389table \autoref{tab:DIA_NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with 
    14101390a 4x2 mpi partitioning. 
    14111391Note the variation in the compression ratio achieved which reflects chiefly the dry to wet volume ratio of 
    14121392each processing region. 
    14131393 
    1414 %------------------------------------------TABLE---------------------------------------------------- 
    14151394\begin{table} 
    1416   \scriptsize 
    14171395  \centering 
    14181396  \begin{tabular}{lrrr} 
    … …  
    14461424    ORCA2\_2d\_grid\_W\_0007.nc & 4416    & 1368     & 70\%      \\ 
    14471425  \end{tabular} 
    1448   \caption{ 
    1449     \protect\label{tab:NC4} 
    1450     Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression 
    1451   } 
     1426  \caption{Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression} 
     1427  \label{tab:DIA_NC4} 
    14521428\end{table} 
    1453 %---------------------------------------------------------------------------------------------------- 
    14541429 
    14551430When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via 
    1456 \rou{iom\_put} calls are set via an equivalent and identically named namelist to \nam{nc4} in 
     1431\rou{iom\_put} calls are set via an equivalent and identically named namelist to \nam{nc4}{nc4} in 
    14571432\textit{xmlio\_server.def}. 
    1458 Typically this namelist serves the mean files whilst the \nam{nc4} in the main namelist file continues to 
     1433Typically this namelist serves the mean files whilst the \nam{nc4}{nc4} in the main namelist file continues to 
    14591434serve the restart files. 
    14601435This duplication is unfortunate but appropriate since, if using io\_servers, the domain sizes of 
    … …  
    14621437the invidual processing regions and different chunking choices may be desired. 
    14631438 
    1464 % ------------------------------------------------------------------------------------------------------------- 
    1465 %       Tracer/Dynamics Trends 
    1466 % ------------------------------------------------------------------------------------------------------------- 
    1467 \section[Tracer/Dynamics trends (\texttt{namtrd})] 
    1468 {Tracer/Dynamics trends (\protect\nam{trd})} 
     1439%% ================================================================================================= 
     1440\section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd}{trd})} 
    14691441\label{sec:DIA_trd} 
    14701442 
    1471 %------------------------------------------namtrd---------------------------------------------------- 
    1472  
    1473 \nlst{namtrd} 
    1474 %------------------------------------------------------------------------------------------------------------- 
     1443\begin{listing} 
     1444  \nlst{namtrd} 
     1445  \caption{\forcode{&namtrd}} 
     1446  \label{lst:namtrd} 
     1447\end{listing} 
    14751448 
    14761449Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to 
    14771450\mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation 
    14781451(\ie\ at the end of each \textit{dyn....F90} and/or \textit{tra....F90} routines). 
    1479 This capability is controlled by options offered in \nam{trd} namelist. 
     1452This capability is controlled by options offered in \nam{trd}{trd} namelist. 
    14801453Note that the output are done with XIOS, and therefore the \key{iomput} is required. 
    14811454 
    1482 What is done depends on the \nam{trd} logical set to \forcode{.true.}: 
     1455What is done depends on the \nam{trd}{trd} logical set to \forcode{.true.}: 
    14831456 
    14841457\begin{description} 
    1485 \item[\np{ln\_glo\_trd}]: 
    1486   at each \np{nn\_trd} time-step a check of the basin averaged properties of 
     1458\item [{\np{ln_glo_trd}{ln\_glo\_trd}}]: at each \np{nn_trd}{nn\_trd} time-step a check of the basin averaged properties of 
    14871459  the momentum and tracer equations is performed. 
    14881460  This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$, 
    14891461  and potential energy time evolution equations properties; 
    1490 \item[\np{ln\_dyn\_trd}]: 
    1491   each 3D trend of the evolution of the two momentum components is output; 
    1492 \item[\np{ln\_dyn\_mxl}]: 
    1493   each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output; 
    1494 \item[\np{ln\_vor\_trd}]: 
    1495   a vertical summation of the moment tendencies is performed, 
     1462\item [{\np{ln_dyn_trd}{ln\_dyn\_trd}}]: each 3D trend of the evolution of the two momentum components is output; 
     1463\item [{\np{ln_dyn_mxl}{ln\_dyn\_mxl}}]: each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output; 
     1464\item [{\np{ln_vor_trd}{ln\_vor\_trd}}]: a vertical summation of the moment tendencies is performed, 
    14961465  then the curl is computed to obtain the barotropic vorticity tendencies which are output; 
    1497 \item[\np{ln\_KE\_trd}] : 
    1498   each 3D trend of the Kinetic Energy equation is output; 
    1499 \item[\np{ln\_tra\_trd}]: 
    1500   each 3D trend of the evolution of temperature and salinity is output; 
    1501 \item[\np{ln\_tra\_mxl}]: 
    1502   each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output; 
     1466\item [{\np{ln_KE_trd}{ln\_KE\_trd}}]  : each 3D trend of the Kinetic Energy equation is output; 
     1467\item [{\np{ln_tra_trd}{ln\_tra\_trd}}]: each 3D trend of the evolution of temperature and salinity is output; 
     1468\item [{\np{ln_tra_mxl}{ln\_tra\_mxl}}]: each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output; 
    15031469\end{description} 
    15041470 
    … …  
    15071473 
    15081474\textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested. 
    1509 In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} are not working, 
    1510 and none of the options have been tested with variable volume (\ie\ \np{ln\_linssh}\forcode{ = .true.}). 
    1511  
    1512 % ------------------------------------------------------------------------------------------------------------- 
    1513 %       On-line Floats trajectories 
    1514 % ------------------------------------------------------------------------------------------------------------- 
    1515 \section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})] 
    1516 {FLO: On-Line Floats trajectories (\protect\key{floats})} 
    1517 \label{sec:FLO} 
    1518 %--------------------------------------------namflo------------------------------------------------------- 
    1519  
    1520 \nlst{namflo} 
    1521 %-------------------------------------------------------------------------------------------------------------- 
     1475In particular, options associated with \np{ln_dyn_mxl}{ln\_dyn\_mxl}, \np{ln_vor_trd}{ln\_vor\_trd}, and \np{ln_tra_mxl}{ln\_tra\_mxl} are not working, 
     1476and none of the options have been tested with variable volume (\ie\ \np[=.true.]{ln_linssh}{ln\_linssh}). 
     1477 
     1478%% ================================================================================================= 
     1479\section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})]{FLO: On-Line Floats trajectories (\protect\key{floats})} 
     1480\label{sec:DIA_FLO} 
     1481 
     1482\begin{listing} 
     1483  \nlst{namflo} 
     1484  \caption{\forcode{&namflo}} 
     1485  \label{lst:namflo} 
     1486\end{listing} 
    15221487 
    15231488The on-line computation of floats advected either by the three dimensional velocity field or constraint to 
    15241489remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project. 
    1525 Options are defined by \nam{flo} namelist variables. 
     1490Options are defined by \nam{flo}{flo} namelist variables. 
    15261491The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option), 
    1527 or on a $4^th$ Runge-Hutta algorithm (\np{ln\_flork4}\forcode{ = .true.}). 
     1492or on a $4^th$ Runge-Hutta algorithm (\np[=.true.]{ln_flork4}{ln\_flork4}). 
    15281493Note that the \cite{blanke.raynaud_JPO97} algorithm have the advantage of providing trajectories which 
    15291494are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry. 
    15301495 
     1496%% ================================================================================================= 
    15311497\subsubsection{Input data: initial coordinates} 
    15321498 
    15331499Initial coordinates can be given with Ariane Tools convention 
    1534 (IJK coordinates, (\np{ln\_ariane}\forcode{ = .true.}) ) or with longitude and latitude. 
     1500(IJK coordinates, (\np[=.true.]{ln_ariane}{ln\_ariane}) ) or with longitude and latitude. 
    15351501 
    15361502In case of Ariane convention, input filename is \textit{init\_float\_ariane}. 
    15371503Its format is: \\ 
    1538 {\scriptsize \texttt{I J K nisobfl itrash}} 
     1504{ \texttt{I J K nisobfl itrash}} 
    15391505 
    15401506\noindent with: 
    … …  
    15481514\noindent Example: \\ 
    15491515\noindent 
    1550 {\scriptsize 
     1516{ 
    15511517  \texttt{ 
    15521518    100.00000  90.00000  -1.50000 1.00000   0.00000   \\ 
    … …  
    15591525In the other case (longitude and latitude), input filename is init\_float. 
    15601526Its format is: \\ 
    1561 {\scriptsize \texttt{Long Lat depth nisobfl ngrpfl itrash}} 
     1527{ \texttt{Long Lat depth nisobfl ngrpfl itrash}} 
    15621528 
    15631529\noindent with: 
    … …  
    15731539\noindent Example: \\ 
    15741540\noindent 
    1575 {\scriptsize 
     1541{ 
    15761542  \texttt{ 
    15771543    20.0 0.0 0.0 0 1 1    \\ 
    … …  
    15821548} \\ 
    15831549 
    1584 \np{jpnfl} is the total number of floats during the run. 
    1585 When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{ = .true.} ), 
    1586 \np{jpnflnewflo} can be added in the initialization file. 
    1587  
     1550\np{jpnfl}{jpnfl} is the total number of floats during the run. 
     1551When initial positions are read in a restart file (\np[=.true.]{ln_rstflo}{ln\_rstflo} ), 
     1552\np{jpnflnewflo}{jpnflnewflo} can be added in the initialization file. 
     1553 
     1554%% ================================================================================================= 
    15881555\subsubsection{Output data} 
    15891556 
    1590 \np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} is the frequency of 
     1557\np{nn_writefl}{nn\_writefl} is the frequency of writing in float output file and \np{nn_stockfl}{nn\_stockfl} is the frequency of 
    15911558creation of the float restart file. 
    15921559 
    1593 Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{ = .true.}). 
     1560Output data can be written in ascii files (\np[=.true.]{ln_flo_ascii}{ln\_flo\_ascii}). 
    15941561In that case, output filename is trajec\_float. 
    15951562 
    1596 Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{ = .false.}) with 
     1563Another possiblity of writing format is Netcdf (\np[=.false.]{ln_flo_ascii}{ln\_flo\_ascii}) with 
    15971564\key{iomput} and outputs selected in iodef.xml. 
    15981565Here it is an example of specification to put in files description section: 
    … …  
    16121579\end{xmllines} 
    16131580 
    1614  
    1615 % ------------------------------------------------------------------------------------------------------------- 
    1616 %       Harmonic analysis of tidal constituents 
    1617 % ------------------------------------------------------------------------------------------------------------- 
    1618 \section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})] 
    1619 {Harmonic analysis of tidal constituents (\protect\key{diaharm})} 
     1581%% ================================================================================================= 
     1582\section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})]{Harmonic analysis of tidal constituents (\protect\key{diaharm})} 
    16201583\label{sec:DIA_diag_harm} 
    16211584 
    1622 %------------------------------------------nam_diaharm---------------------------------------------------- 
    1623 % 
    1624 \nlst{nam_diaharm} 
    1625 %---------------------------------------------------------------------------------------------------------- 
     1585\begin{listing} 
     1586  \nlst{nam_diaharm} 
     1587  \caption{\forcode{&nam_diaharm}} 
     1588  \label{lst:nam_diaharm} 
     1589\end{listing} 
    16261590 
    16271591A module is available to compute the amplitude and phase of tidal waves. 
    16281592This on-line Harmonic analysis is actived with \key{diaharm}. 
    16291593 
    1630 Some parameters are available in namelist \nam{\_diaharm}: 
    1631  
    1632  - \np{nit000\_han} is the first time step used for harmonic analysis 
    1633  
    1634  - \np{nitend\_han} is the  last time step used for harmonic analysis 
    1635  
    1636  - \np{nstep\_han}  is the  time step frequency for harmonic analysis 
    1637  
    1638 % - \np{nb\_ana}     is the number of harmonics to analyse 
    1639  
    1640  - \np{tname}       is an array with names of tidal constituents to analyse 
    1641  
    1642  \np{nit000\_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation. 
     1594Some parameters are available in namelist \nam{_diaharm}{\_diaharm}: 
     1595 
     1596 - \np{nit000_han}{nit000\_han} is the first time step used for harmonic analysis 
     1597 
     1598 - \np{nitend_han}{nitend\_han} is the  last time step used for harmonic analysis 
     1599 
     1600 - \np{nstep_han}{nstep\_han}  is the  time step frequency for harmonic analysis 
     1601 
     1602% - \np{nb_ana}{nb\_ana}     is the number of harmonics to analyse 
     1603 
     1604 - \np{tname}{tname}       is an array with names of tidal constituents to analyse 
     1605 
     1606 \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000}{nit000} and \np{nitend}{nitend} of the simulation. 
    16431607 The restart capability is not implemented. 
    16441608 
    … …  
    16611625We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave. 
    16621626 
    1663 % ------------------------------------------------------------------------------------------------------------- 
    1664 %       Sections transports 
    1665 % ------------------------------------------------------------------------------------------------------------- 
    1666 \section[Transports across sections (\texttt{\textbf{key\_diadct}})] 
    1667 {Transports across sections (\protect\key{diadct})} 
     1627%% ================================================================================================= 
     1628\section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})} 
    16681629\label{sec:DIA_diag_dct} 
    16691630 
    1670 %------------------------------------------namdct---------------------------------------------------- 
    1671  
    1672 \nlst{namdct} 
    1673 %------------------------------------------------------------------------------------------------------------- 
     1631\begin{listing} 
     1632  \nlst{nam_diadct} 
     1633  \caption{\forcode{&nam_diadct}} 
     1634  \label{lst:nam_diadct} 
     1635\end{listing} 
    16741636 
    16751637A module is available to compute the transport of volume, heat and salt through sections. 
    … …  
    16891651- \texttt{salt\_transport}   for   salt transports (unit: $10^{9}Kg s^{-1}$) \\ 
    16901652 
    1691 Namelist variables in \nam{dct} control how frequently the flows are summed and the time scales over which 
     1653Namelist variables in \nam{_diadct}{\_diadct} control how frequently the flows are summed and the time scales over which 
    16921654they are averaged, as well as the level of output for debugging: 
    1693 \np{nn\_dct}   : frequency of instantaneous transports computing 
    1694 \np{nn\_dctwri}: frequency of writing ( mean of instantaneous transports ) 
    1695 \np{nn\_debug} : debugging of the section 
    1696  
     1655\np{nn_dct}{nn\_dct}   : frequency of instantaneous transports computing 
     1656\np{nn_dctwri}{nn\_dctwri}: frequency of writing ( mean of instantaneous transports ) 
     1657\np{nn_debug}{nn\_debug} : debugging of the section 
     1658 
     1659%% ================================================================================================= 
    16971660\subsubsection{Creating a binary file containing the pathway of each section} 
    16981661 
    … …  
    17041667 
    17051668Each section is defined by: \\ 
    1706 \noindent {\scriptsize \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\ 
     1669\noindent { \texttt{long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name}} \\ 
    17071670with: 
    17081671 
    … …  
    17211684 
    17221685\noindent If nclass $\neq$ 0, the next lines contain the class type and the nclass bounds: \\ 
    1723 {\scriptsize 
     1686{ 
    17241687  \texttt{ 
    17251688    long1 lat1 long2 lat2 nclass (ok/no)strpond (no)ice section\_name \\ 
    … …  
    17541717 and the ATL\_Cuba\_Florida with 4 temperature clases (5 class bounds), are shown: \\ 
    17551718 \noindent 
    1756  {\scriptsize 
     1719 { 
    17571720   \texttt{ 
    17581721     -68.    -54.5   -60.    -64.7  00 okstrpond noice ACC\_Drake\_Passage \\ 
    … …  
    17661729 } 
    17671730 
     1731%% ================================================================================================= 
    17681732\subsubsection{To read the output files} 
    17691733 
    17701734The output format is: \\ 
    1771 {\scriptsize 
     1735{ 
    17721736  \texttt{ 
    17731737    date, time-step number, section number,                \\ 
    … …  
    17911755 
    17921756\begin{table} 
    1793   \scriptsize 
    17941757  \begin{tabular}{|l|l|l|l|l|} 
    17951758    \hline 
    … …  
    18051768\end{table} 
    18061769 
    1807 % ================================================================ 
    1808 % Steric effect in sea surface height 
    1809 % ================================================================ 
     1770%% ================================================================================================= 
    18101771\section{Diagnosing the steric effect in sea surface height} 
    18111772\label{sec:DIA_steric} 
    1812  
    18131773 
    18141774Changes in steric sea level are caused when changes in the density of the water column imply an expansion or 
    … …  
    18471807    \mathcal{V} &=  \mathcal{A}  \;\bar{\eta} 
    18481808  \end{split} 
    1849   \label{eq:MV_nBq} 
     1809  \label{eq:DIA_MV_nBq} 
    18501810\end{equation} 
    18511811 
    … …  
    18551815  \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} ) 
    18561816  = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface} 
    1857   \label{eq:Co_nBq} 
     1817  \label{eq:DIA_Co_nBq} 
    18581818\end{equation} 
    18591819 
    … …  
    18641824\begin{equation} 
    18651825  \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}} 
    1866   \label{eq:Mass_nBq} 
     1826  \label{eq:DIA_Mass_nBq} 
    18671827\end{equation} 
    18681828 
    18691829where $\overline{\textit{emp}} = \int_S \textit{emp}\,ds$ is the net mass flux through the ocean surface. 
    1870 Bringing \autoref{eq:Mass_nBq} and the time derivative of \autoref{eq:MV_nBq} together leads to 
     1830Bringing \autoref{eq:DIA_Mass_nBq} and the time derivative of \autoref{eq:DIA_MV_nBq} together leads to 
    18711831the evolution equation of the mean sea level 
    18721832 
    … …  
    18741834  \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}} 
    18751835  - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}} 
    1876   \label{eq:ssh_nBq} 
     1836  \label{eq:DIA_ssh_nBq} 
    18771837\end{equation} 
    18781838 
    1879 The first term in equation \autoref{eq:ssh_nBq} alters sea level by adding or subtracting mass from the ocean. 
     1839The first term in equation \autoref{eq:DIA_ssh_nBq} alters sea level by adding or subtracting mass from the ocean. 
    18801840The second term arises from temporal changes in the global mean density; \ie\ from steric effects. 
    18811841 
    18821842In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ appears multiplied by 
    18831843the gravity (\ie\ in the hydrostatic balance of the primitive Equations). 
    1884 In particular, the mass conservation equation, \autoref{eq:Co_nBq}, degenerates into the incompressibility equation: 
     1844In particular, the mass conservation equation, \autoref{eq:DIA_Co_nBq}, degenerates into the incompressibility equation: 
    18851845 
    18861846\[ 
    18871847  \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface} 
    1888   % \label{eq:Co_Bq} 
     1848  % \label{eq:DIA_Co_Bq} 
    18891849\] 
    18901850 
    … …  
    18931853\[ 
    18941854  \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o} 
    1895   % \label{eq:V_Bq} 
     1855  % \label{eq:DIA_V_Bq} 
    18961856\] 
    18971857 
    … …  
    19121872\begin{equation} 
    19131873  \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A} 
    1914   \label{eq:M_Bq} 
     1874  \label{eq:DIA_M_Bq} 
    19151875\end{equation} 
    19161876 
    … …  
    19191879Introducing the total density anomaly, $\mathcal{D}= \int_D d_a \,dv$, 
    19201880where $d_a = (\rho -\rho_o ) / \rho_o$ is the density anomaly used in \NEMO\ (cf. \autoref{subsec:TRA_eos}) 
    1921 in \autoref{eq:M_Bq} leads to a very simple form for the steric height: 
     1881in \autoref{eq:DIA_M_Bq} leads to a very simple form for the steric height: 
    19221882 
    19231883\begin{equation} 
    19241884  \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D} 
    1925   \label{eq:steric_Bq} 
     1885  \label{eq:DIA_steric_Bq} 
    19261886\end{equation} 
    19271887 
    … …  
    19431903(wetting and drying of grid point is not allowed). 
    19441904 
    1945 Third, the discretisation of \autoref{eq:steric_Bq} depends on the type of free surface which is considered. 
    1946 In the non linear free surface case, \ie\ \np{ln\_linssh}\forcode{ = .true.}, it is given by 
     1905Third, the discretisation of \autoref{eq:DIA_steric_Bq} depends on the type of free surface which is considered. 
     1906In the non linear free surface case, \ie\ \np[=.true.]{ln_linssh}{ln\_linssh}, it is given by 
    19471907 
    19481908\[ 
    19491909  \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} }{ \sum_{i,\,j,\,k}       e_{1t} e_{2t} e_{3t} } 
    1950   % \label{eq:discrete_steric_Bq_nfs} 
     1910  % \label{eq:DIA_discrete_steric_Bq_nfs} 
    19511911\] 
    19521912 
    … …  
    19581918  \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 } 
    19591919                  { \sum_{i,\,j,\,k}       e_{1t}e_{2t}e_{3t} + \sum_{i,\,j}       e_{1t}e_{2t} \eta } 
    1960   % \label{eq:discrete_steric_Bq_fs} 
     1920  % \label{eq:DIA_discrete_steric_Bq_fs} 
    19611921\] 
    19621922 
    … …  
    19781938\[ 
    19791939  \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv 
    1980   % \label{eq:thermosteric_Bq} 
     1940  % \label{eq:DIA_thermosteric_Bq} 
    19811941\] 
    19821942 
    … …  
    19851945Both steric and thermosteric sea level are computed in \mdl{diaar5}. 
    19861946 
    1987 % ------------------------------------------------------------------------------------------------------------- 
    1988 %       Other Diagnostics 
    1989 % ------------------------------------------------------------------------------------------------------------- 
    1990 \section[Other diagnostics] 
    1991 {Other diagnostics} 
     1947%% ================================================================================================= 
     1948\section{Other diagnostics} 
    19921949\label{sec:DIA_diag_others} 
    19931950 
    … …  
    19951952The available ready-to-add diagnostics modules can be found in directory DIA. 
    19961953 
    1997 \subsection[Depth of various quantities (\textit{diahth.F90})] 
    1998 {Depth of various quantities (\protect\mdl{diahth})} 
     1954%% ================================================================================================= 
     1955\subsection[Depth of various quantities (\textit{diahth.F90})]{Depth of various quantities (\protect\mdl{diahth})} 
    19991956 
    20001957Among the available diagnostics the following ones are obtained when defining the \key{diahth} CPP key: 
    … …  
    20081965- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) 
    20091966 
    2010  
    2011 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    20121967\begin{figure}[!t] 
    2013   \begin{center} 
    2014     \includegraphics[width=\textwidth]{Fig_mask_subasins} 
    2015     \caption{ 
    2016       \protect\label{fig:mask_subasins} 
    2017       Decomposition of the World Ocean (here ORCA2) into sub-basin used in to 
    2018       compute the heat and salt transports as well as the meridional stream-function: 
    2019       Atlantic basin (red), Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green). 
    2020       Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay are removed from the sub-basins. 
    2021       Note also that the Arctic Ocean has been split into Atlantic and Pacific basins along the North fold line. 
    2022     } 
    2023   \end{center} 
     1968  \centering 
     1969  \includegraphics[width=0.66\textwidth]{Fig_mask_subasins} 
     1970  \caption[Decomposition of the World Ocean to compute transports as well as 
     1971  the meridional stream-function]{ 
     1972    Decomposition of the World Ocean (here ORCA2) into sub-basin used in to 
     1973    compute the heat and salt transports as well as the meridional stream-function: 
     1974    Atlantic basin (red), Pacific basin (green), 
     1975    Indian basin (blue), Indo-Pacific basin (blue+green). 
     1976    Note that semi-enclosed seas (Red, Med and Baltic seas) as well as 
     1977    Hudson Bay are removed from the sub-basins. 
     1978    Note also that the Arctic Ocean has been split into Atlantic and 
     1979    Pacific basins along the North fold line. 
     1980  } 
     1981  \label{fig:DIA_mask_subasins} 
    20241982\end{figure} 
    2025 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    2026  
    2027 % ----------------------------------------------------------- 
    2028 %       CMIP specific diagnostics 
    2029 % ----------------------------------------------------------- 
    2030 \subsection[CMIP specific diagnostics (\textit{diaar5.F90}, \textit{diaptr.F90})] 
    2031 {CMIP specific diagnostics (\protect\mdl{diaar5})} 
     1983 
     1984%% ================================================================================================= 
     1985\subsection[CMIP specific diagnostics (\textit{diaar5.F90}, \textit{diaptr.F90})]{CMIP specific diagnostics (\protect\mdl{diaar5})} 
    20321986 
    20331987A series of diagnostics has been added in the \mdl{diaar5} and \mdl{diaptr}. 
    … …  
    20391993sea water pressure at sea floor (botpres), dynamic sea surface height (sshdyn). 
    20401994 
    2041 In \mdl{diaptr} when \np{ln\_diaptr}\forcode{ = .true.} 
    2042 (see the \nam{ptr} namelist below) can be computed on-line the poleward heat and salt transports, 
     1995In \mdl{diaptr} when \np[=.true.]{ln_diaptr}{ln\_diaptr} 
     1996(see the \nam{ptr}{ptr} namelist below) can be computed on-line the poleward heat and salt transports, 
    20431997their advective and diffusive component, and the meriodional stream function . 
    2044 When \np{ln\_subbas}\forcode{ = .true.}, transports and stream function are computed for the Atlantic, Indian, 
     1998When \np[=.true.]{ln_subbas}{ln\_subbas}, transports and stream function are computed for the Atlantic, Indian, 
    20451999Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean. 
    20462000The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays, 
    2047 the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:mask_subasins}). 
    2048  
    2049 %------------------------------------------namptr----------------------------------------- 
    2050  
    2051 \nlst{namptr} 
    2052 %----------------------------------------------------------------------------------------- 
    2053  
    2054 % ----------------------------------------------------------- 
    2055 %       25 hour mean and hourly Surface, Mid and Bed 
    2056 % ----------------------------------------------------------- 
     2001the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:DIA_mask_subasins}). 
     2002 
     2003\begin{listing} 
     2004  \nlst{namptr} 
     2005  \caption{\forcode{&namptr}} 
     2006  \label{lst:namptr} 
     2007\end{listing} 
     2008 
     2009%% ================================================================================================= 
    20572010\subsection{25 hour mean output for tidal models} 
    20582011 
    2059 %------------------------------------------nam_dia25h------------------------------------- 
    2060  
    2061 \nlst{nam_dia25h} 
    2062 %----------------------------------------------------------------------------------------- 
     2012\begin{listing} 
     2013  \nlst{nam_dia25h} 
     2014  \caption{\forcode{&nam_dia25h}} 
     2015  \label{lst:nam_dia25h} 
     2016\end{listing} 
    20632017 
    20642018A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean. 
    … …  
    20672021This diagnostic is actived with the logical $ln\_dia25h$. 
    20682022 
    2069 % ----------------------------------------------------------- 
    2070 %     Top Middle and Bed hourly output 
    2071 % ----------------------------------------------------------- 
     2023%% ================================================================================================= 
    20722024\subsection{Top middle and bed hourly output} 
    20732025 
    2074 %------------------------------------------nam_diatmb----------------------------------------------------- 
    2075  
    2076 \nlst{nam_diatmb} 
    2077 %---------------------------------------------------------------------------------------------------------- 
     2026\begin{listing} 
     2027  \nlst{nam_diatmb} 
     2028  \caption{\forcode{&nam_diatmb}} 
     2029  \label{lst:nam_diatmb} 
     2030\end{listing} 
    20782031 
    20792032A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables. 
    … …  
    20832036This diagnostic is actived with the logical $ln\_diatmb$. 
    20842037 
    2085 % ----------------------------------------------------------- 
    2086 %     Courant numbers 
    2087 % ----------------------------------------------------------- 
     2038%% ================================================================================================= 
    20882039\subsection{Courant numbers} 
    20892040 
    … …  
    20932044\[ 
    20942045  C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}} 
    2095   % \label{eq:CFL} 
     2046  % \label{eq:DIA_CFL} 
    20962047\] 
    20972048 
    … …  
    21022053Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step. 
    21032054 
    2104 The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \nam{ctl} namelist. 
     2055The variables can be activated by setting the \np{nn_diacfl}{nn\_diacfl} namelist parameter to 1 in the \nam{ctl}{ctl} namelist. 
    21052056The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. 
    21062057In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of 
    … …  
    21102061The maximum values from the run are also copied to the ocean.output file. 
    21112062 
    2112 % ================================================================ 
    2113  
    2114 \biblio 
    2115  
    2116 \pindex 
     2063\onlyinsubfile{\input{../../global/epilogue}} 
    21172064 
    21182065\end{document} 
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